diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 28fc51cd45..5323724a9a 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -129,9 +129,9 @@ For the basic code styling complex uses `clang-format`, the formatting file is i
- Be sure to include the following at the bottom of all documentation files
```markdown
-## DREAM3DNX Help ##
+## DREAM3D-NX Help ##
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
```
## Community
diff --git a/PortingFilters.md b/PortingFilters.md
index b078c05604..7f2a2b267b 100644
--- a/PortingFilters.md
+++ b/PortingFilters.md
@@ -1,4 +1,4 @@
-# Porting a Filter #
+# Porting a Filter
Depending on where the ported filter is coming from determines what you need to
do. The sections are as follows:
@@ -13,17 +13,17 @@ do. The sections are as follows:
-## SECTION 1 : Porting From ***SIMPL*** to ***Filters Folder*** ##
+## SECTION 1 : Porting From ***SIMPL*** to ***Filters Folder***
This will be the most common type of Filter porting. The steps for this are as
follows:
-### Go to FreeNas and pull the custom build of DREAM3D ###
+### Go to FreeNas and pull the custom build of DREAM3D
This custom build has **ALL** ***SIMPL*** plugins compiled so you don't need
to worry about what filters will be available
-### Load up ***SIMPL*** DREAM3D and navigate to ***ComplexFilterGen*** ###
+### Load up ***SIMPL*** DREAM3D and navigate to ***ComplexFilterGen***
Here you will need to set the command arguments using the following syntax:
@@ -40,14 +40,14 @@ Some nuances to note for this are as follows:
You will need to update the various CMake files inside the target complex plugin in order to start compiling the new filter code inside of a complex build.
-## SECTION 2 : Porting stubs from existing folder to ***Filters Folder*** ##
+## SECTION 2 : Porting stubs from existing folder to ***Filters Folder***
Some plugins have existing stubs in folders other than the primary ***Filters***
folder.
-### Move the Filter and Algorithm files to the active ***Filters Folder*** ###
+### Move the Filter and Algorithm files to the active ***Filters Folder***
-### Update the Legacy UUID Maps ###
+### Update the Legacy UUID Maps
- Open the LegacyUUIDMapping header file for this Plugin
- Find and uncomment the include statement for the filter being moved
@@ -63,12 +63,12 @@ folder.
> ***@@__MAP__UPDATE__TOKEN__DO__NOT__DELETE__@@***
- ### Update the CMakeLists.txt files to reflect the changes ###
+ ### Update the CMakeLists.txt files to reflect the changes
This includes the ones for the unit tests and the one at the plugin level
-## SECTION 3 : Developing a Test File ##
+## SECTION 3 : Developing a Test File
Firstly, it is important to ensure that each unit test does not just instantiate filter. Current standards require the following:
@@ -79,7 +79,7 @@ Firstly, it is important to ensure that each unit test does not just instantiate
Test Files should **NOT** output strings to the terminal. Output should be in the form of catch2 errors.
-### Adding a new data file to ***DREAM3D Data Repo*** ###
+### Adding a new data file to ***DREAM3D Data Repo***
For adding the data file to the DREAM3D repo one should follow the following steps:
@@ -100,7 +100,7 @@ GitHub Repo : REQUIRE(nullptr != filter);
-## SECTION 4 : Multithreading ##
+## SECTION 4 : Multithreading
At the current time, the only filters that should be made parallel are those that could be considered "embarrassingly parallel". It is important to remember that the cost of creating a thread is hefty so it should only be done when there is a sizeable amount of work available for each thread. Complex has two types: ParallelTaskAlgorithm and ParallelDataAlgorithm. Task Runner is for parsing multiple objects and Data Runner is for parsing a single object.
-### Syntax for Complex ###
+### Syntax for Complex
This is an examplar use case and doesn't truly encompass all possible use cases for the functions, but instead serves to show how it should be structured in most cases.
@@ -163,11 +163,11 @@ In the exectuting function:
> dataAlg.execute(::FilterNameImpl(object, argument));
-## SECTION 5 : Progress Updating ##
+## SECTION 5 : Progress Updating
With out of core functionality on the way, it is now a requirement for each and every filter to have progress updates and checks for cancel. This section shows threadsafe progress updating and message structuring.
-### ThreadSafe Progress Messaging ###
+### ThreadSafe Progress Messaging
This is an example that aims to reduce the number of times a mutex lock is called.
@@ -189,7 +189,7 @@ This is an example that aims to reduce the number of times a mutex lock is calle
This function should avoid being called too many times in a thread as it would significantly slow it down.
-### Message Structuring ###
+### Message Structuring
For error messaging the following syntax should be used:
@@ -198,11 +198,11 @@ For error messaging the following syntax should be used:
The number at the start is an arbitrary value save for the fact it must be negative.
-## SECTION 6 : Utilizing API's to the fullest ##
+## SECTION 6 : Utilizing API's to the fullest
This section aims to tackle ***complex*** convenience functions from major API's:
-### Utilizing the ExecuteDataFunction ###
+### Utilizing the ExecuteDataFunction
These templated varg functions aim to eliminate the need for type switches, this is done using functors. Below is example syntax:
@@ -224,7 +224,7 @@ In the executing function:
> ExecuteDataFunction(FilterNameFunctor{}, selectedArrayRef.getDataType(), selectedArrayRef, argumentBool);
-## SECTION 7 : Useful Tips and Tricks ##
+## SECTION 7 : Useful Tips and Tricks
This section is just for basic genralized tips to help make our code better:
diff --git a/README.md b/README.md
index e251932bab..cebaa47525 100644
--- a/README.md
+++ b/README.md
@@ -21,7 +21,7 @@ The vision for the DREAM.3D project is to produce accessible software tools that
## Public Release Notice
-This software library is directly supported by USAF Contract _FA8650-22-C-5290_ and has been cleared as publicly releasable under the following:
+This software library is directly supported by USAF Contract *FA8650-22-C-5290* and has been cleared as publicly releasable under the following:
```text
AFRL has completed the review process for your case on 14 Sep 2022:
diff --git a/docs/Code_Style_Guide.md b/docs/Code_Style_Guide.md
index 4f5245d15a..75a75ea82d 100644
--- a/docs/Code_Style_Guide.md
+++ b/docs/Code_Style_Guide.md
@@ -1,16 +1,16 @@
-# Code Style Guide #
+# Code Style Guide
This is the style guide for the COMPLEX library. When contributing sources to the complex repository we ask that all contributions follow this style guide. These general rules have been developed over the years in an effort to allow efficient coding practices.
-## Source Code Line Endings ##
+## Source Code Line Endings
All source code line endings should be in "Unix" style "\n". Every text editor understands these line endings on every platform **except** the "Notepad" application on Windows.
-## Use of Tabs ##
+## Use of Tabs
Spaces should be used instead of hard tabs. This helps file portability across different editors. DREAM.3D uses a standard whereby all indents use two spaces.
-## Always Use an Include Guard ##
+## Always Use an Include Guard
Always use
@@ -18,7 +18,7 @@ Always use
at the top of *EVERY* header file.
-## Special Constants ##
+## Special Constants
nullptr should be used in conjunction with only raw pointers and 0 (zero) should be used in conjunction with numeric values:
@@ -28,14 +28,14 @@ nullptr should be used in conjunction with only raw pointers and 0 (zero) should
int i = 0; // Good
int i = NULL; // Bad
-## Array Initialization ##
+## Array Initialization
Prefer the use of C++11 std::array instead of "C" style arrays.
int32_t foo[3]; // BAD.. No initialization of the internal data
std::array foo = {0,0,0};
-## The Dereference operator `*` and the Address-Of Operator `&` Should Be Directly Connected with the Type-Specifier ##
+## The Dereference operator `*` and the Address-Of Operator `&` Should Be Directly Connected with the Type-Specifier
int32* p; // Correct
int32 *p; // Incorrect
@@ -43,7 +43,7 @@ Prefer the use of C++11 std::array instead of "C" style arrays.
The `int32* p;` form emphasizes type over syntax while the `int32 *p;` form emphasizes syntax over type. Although both forms are equally valid C++, the heavy emphasis on types in C++ suggests that `int32* p;` is the preferable form.
-## Always Implement the "Big Five" in C++ Classes ##
+## Always Implement the "Big Five" in C++ Classes
When writing C++ classes the programmer will always define the "Big Three" which are defined as:
@@ -70,7 +70,7 @@ should be marked as deleted or default'ed or manually implemented.
Note that with C++11, programmers now have the ability to inform the compiler which of these operations can be constructed by default and which can be ignored using the `default` and `delete` keywords.
-## Naming conventions ##
+## Naming conventions
There is an include clang-tidy file that most IDE's can use to assist with some of the major areas. One area is the naming conventions that COMPLEX uses. Here are the basic rules:
@@ -84,7 +84,7 @@ There is an include clang-tidy file that most IDE's can use to assist with some
- Free Functions are `UpperCamelCase`
- Macros are `ALL_UPPER_SNAKE_CASE`
-## String Constants ##
+## String Constants
String constants in C++ should be declared as:
@@ -103,6 +103,6 @@ When using ANSI C one should use a char* for constant strings:
Using this type of approach allows for quicker code updates when constant values need to be changed.
-## Clang Formatting ##
+## Clang Formatting
`clang-format` is a tool to automatically format C++ code. You should run 'clang-format' on your code before opening a Pull Request to make sure it passes the *clang-format pr* check. You can install `clang-format` and `git-clang-format` with `npm install -g clang-format`. To automatically format a file according to a project's C++ code style, run `clang-format -i path/to/complex/file`, which is supported on macOS/Linux/Windows. If you want to run `clang-format` on all the changed code on your latest git commit (HEAD), you can run `git-clang-format HEAD~1`. Run `git-clang-format -h` for extra help.
diff --git a/docs/Porting_Filters.md b/docs/Porting_Filters.md
index 72e000f9a7..9de3892ab2 100644
--- a/docs/Porting_Filters.md
+++ b/docs/Porting_Filters.md
@@ -1,6 +1,6 @@
-# Porting Filter Notes #
+# Porting Filter Notes
-## Porting Checklist ##
+## Porting Checklist
- [ ] Parameters should be generally broken down into "Input Parameters", "Required Data Objects", "Created Data Objects". There can be exceptions to this.
- [ ] ChoicesParameter selections should be an enumeration defined in the filer header
@@ -16,7 +16,7 @@ static inline constexpr StringLiteral k_AlignmentType_Key = "alignment_type";
- [ ] Filters should have both the Filter class and Algorithm class for anything beyond trivial needs
-## Converting Types ##
+## Converting Types
- `QString => std::string`
- `QVector<> => std::vector<>`
@@ -39,7 +39,7 @@ COMPLEX
then you can optionally return the `result` variable if needed
-## QString operations ##
+## QString operations
There are some substitutions for the QString operations.
See [https://en.cppreference.com/w/cpp/string/basic_string](https://en.cppreference.com/w/cpp/string/basic_string) for
@@ -47,7 +47,7 @@ more information about std::string
There is a file `complex/Utilities/StringUtilities.hpp` that has some QString functionality that is needed.
-## Getting a Geometry from the DataStructure ##
+## Getting a Geometry from the DataStructure
If you know the path to the Geometry:
@@ -56,11 +56,11 @@ If you know the path to the Geometry:
TriangleGeom& triangleGeom = dataStructure.getDataRefAs(triangleGeometryDataPath);
```
-## Resizing Attribute Matrix ##
+## Resizing Attribute Matrix
If your codes specifically resize the AttributeMatrix, this is not needed anymore.
-## QString Formatting ##
+## QString Formatting
Use the `format` library
@@ -72,7 +72,7 @@ QString msg = QString("Error reading Triangle '%1'. Object Count was %2 and shou
std::string msg = fmt::format("Error reading Triangle '{}}'. Object Count was {} and should have been {}", t, objsRead, k_StlElementCount);
```
-## Get An Array from the DataStructure ##
+## Get An Array from the DataStructure
Example of getting an array and summing the values using range based for loop.
@@ -86,13 +86,13 @@ Example of getting an array and summing the values using range based for loop.
}
```
-## Chaining Together DataPath + String to form new DataPath ##
+## Chaining Together DataPath + String to form new DataPath
```c++
DataPath triangleAreasDataPath = geometryPath.createChildPath(triangleFaceDataGroupName).createChildPath("Triangle Areas");
```
-## Print out the preflight errors during a Unit Test ##
+## Print out the preflight errors during a Unit Test
```c++
auto preflightResult = filter.preflight(dataGraph, args);
@@ -105,7 +105,7 @@ Example of getting an array and summing the values using range based for loop.
}
```
-## Moving from Pointer based array navigation ##
+## Moving from Pointer based array navigation
Previously inside of SIMPL one would have done the following to get the raw pointer
to the data stored in a DataArray:
@@ -126,7 +126,7 @@ Note the use of a *Reference Variable* instead of the pointer. The developer can
code such as `vertex[index]` to get/set a value but the code `vertex = i` to move a pointer
**will not work**.
-## Selecting Geometry from a Parameter ##
+## Selecting Geometry from a Parameter
If you need to have the user select a Geometry then you should use a `DataPathSelectionParameter`.
@@ -134,14 +134,14 @@ If you need to have the user select a Geometry then you should use a `DataPathSe
params.insert(std::make_unique(k_TriangleGeometry_Key, "Triangle Geometry to Sample", "", DataPath{}));
```
-## Transferring Data from one Geometry to Another ##
+## Transferring Data from one Geometry to Another
There are several filters (those that create a new geometry from an existing one) where
the user is allowed to "transfer" data from the source geometry onto the newly created
geometry. QuickSurfaceMeshFilter and PointSampleTriangleGeometryFilter both are examples
of how to perform this transfer of data.
-## Parallel Algorithms ##
+## Parallel Algorithms
There are several classes that can be used to help the developer write parallel algorithms.
@@ -150,7 +150,7 @@ on the situation. `AlignSections.cpp` and `CropImageGeoemtry.cpp` both use a tas
parallelism. `RotateSampleRefFrameFilter.cpp` shows an example
of using ParallelData3DAlgorithm.
-## Constants for Pi and Others ##
+## Constants for Pi and Others
```cpp
#include "complex/Common/Numbers.hpp"
@@ -162,7 +162,7 @@ and use it this way:
double foo = complex::numbers::k_180OverPi * 232.0;
```
-## MessageHandler ##
+## MessageHandler
All filters give you access to the MessageHandler class that sends status, progress, error and warning messages back to
the user.
@@ -181,7 +181,7 @@ and
m_MessageHandler(IFilter::Message::Type::Progress, progressMessage, static_cast(progressInt));
```
-## Creating Array within an Attribute Matrix ##
+## Creating Array within an Attribute Matrix
If you have a filter that needs to create an array in something like a cell attribute matrix or
a feature attribute matrix then the following filters have examples.
@@ -220,7 +220,7 @@ then you replace the macro with the following template function:
The first 2 arguments to the above function are used by the function, any additional arguments are passed directly to
your functor implementation.
-## Porting SIMPL Filter ##
+## Porting SIMPL Filter
- Create Filter class in "PLUGIN_NAME/src/PLUGIN_NAME/Filters/xxxxFilter[.hpp|.cpp]"
- Update Plugin's top level CMakeLists.txt to include the filter
@@ -228,7 +228,7 @@ your functor implementation.
- Update Plugin's top level CMakeLists.txt to include the algorithm
- Ensure the UUID is the proper UUID from the know mappings file.
-### Parameters ###
+### Parameters#
Use proper grouping in the parameters to help the User Interface.
@@ -248,6 +248,6 @@ There are potentially 3 sections of parameters:
these should be used as needed by the filter.
-## Processing a Geometry In Place ##
+## Processing a Geometry In Place
Sometimes a filter needs allow the user to process it's geometry "in place" in order to ease the number of filters that are needed to remove temporary DataObjecsts. If your filter needs this kind of capability, then take a look at the "CropImageGeometry" or "RotateSampleRefFrame" filters.
diff --git a/docs/index.rst b/docs/index.rst
deleted file mode 100644
index c955ec6402..0000000000
--- a/docs/index.rst
+++ /dev/null
@@ -1,21 +0,0 @@
-.. complex documentation master file, created by
- sphinx-quickstart on Sun Jun 20 22:11:48 2021.
- You can adapt this file completely to your liking, but it should at least
- contain the root `toctree` directive.
-
-Welcome to complex's documentation!
-===================================
-
-.. toctree::
- :maxdepth: 2
- :caption: Contents:
-
-.. doxygenclass:: complex::IFilter
- :members:
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
diff --git a/src/Plugins/ComplexCore/docs/AbaqusHexahedronWriterFilter.md b/src/Plugins/ComplexCore/docs/AbaqusHexahedronWriterFilter.md
index 76132f405d..5165aa8521 100644
--- a/src/Plugins/ComplexCore/docs/AbaqusHexahedronWriterFilter.md
+++ b/src/Plugins/ComplexCore/docs/AbaqusHexahedronWriterFilter.md
@@ -12,6 +12,7 @@ This **Filter** produces the basic five Abaqus .inp files for input into the Aba
The master file:
+```text
*Heading
Job 101
** Job name : Job 101
@@ -27,9 +28,11 @@ The master file:
**
** ----------------------------------------------------------------
**
+```
The _nodes.inp file:
+```text
** Generated by : DREAM3DLib Version 5.1.566.e1e7b7f
** ----------------------------------------------------------------
**
@@ -39,10 +42,11 @@ The _nodes.inp file:
3, 1.000000, 0.000000, 0.000000
4, 1.500000, 0.000000, 0.000000
..
-
+```
The _elset.inp file:
+```text
** Generated by : DREAM3DLib Version 5.1.566.e1e7b7f
** ----------------------------------------------------------------
**
@@ -77,10 +81,11 @@ The _elset.inp file:
32448
*Elset, elset=Grain2_set
..
-
+```
The _elems.inp file:
+```text
** Generated by : DREAM3DLib Version 5.1.566.e1e7b7f
** ----------------------------------------------------------------
**
@@ -92,10 +97,11 @@ The _elems.inp file:
5, 1095, 6, 5, 1094, 1128, 39, 38, 1127
6, 1096, 7, 6, 1095, 1129, 40, 39, 1128
..
-
+```
The _sects.inp file:
+```text
** Generated by : DREAM3DLib Version 5.1.566.e1e7b7f
** ----------------------------------------------------------------
**
@@ -109,37 +115,14 @@ The _sects.inp file:
*Solid Section, elset=Grain2_set, material=Grain_Mat2
..
-
-
-## Parameters
-
-| Name | Type | Description |
-|------------------|------|------------------------|
-| Hour Glass Stiffness | int32_t | Only recommended if using C3D8R elements |
-| Job Name | String | Job Name, if desired |
-| Output Path | File Path | The output path for the .inp files |
-| Output File Prefix | String | Prefix for the name of the 5 files |
-
-## Required Geometry
+```
-Image
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Cell** belongs |
-
-## Created Objects
-
-None
+% Auto generated parameter table will be inserted here
## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/AddBadDataFilter.md b/src/Plugins/ComplexCore/docs/AddBadDataFilter.md
index f54ad62c3f..b09ddd6fb5 100644
--- a/src/Plugins/ComplexCore/docs/AddBadDataFilter.md
+++ b/src/Plugins/ComplexCore/docs/AddBadDataFilter.md
@@ -12,37 +12,12 @@ All **Attribute Arrays** that belong to the same **Attribute Matrix** as the sel
For more information on synthetic building, visit the tutorial.
-## Parameters
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Use Seed | bool | Whether a seed shouold be used for random generation |
-| Seed | uint64 | This is the value fed into the random generator |
-| Add Random Noise | bool | Whether to add random Poisson noise to the whole volume |
-| Volume Fraction Random Noise | float | Fraction of noise to add over the whole volume |
-| Add Boundary Noise | bool | Whether to add noise to the boundary **Cells** |
-| Volume Fraction Boundary Noise | float | Fraction of noise to add to the boundary **Cells** |
-
-## Required Geometry
-
-Image
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | GBEuclideanDistances | int32 | (1) | Manhattan distances of each **Cell** to the closest **Feature** boundary |
-
-## Created Objects
-
-None
+% Auto generated parameter table will be inserted here
## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/AlignGeometries.md b/src/Plugins/ComplexCore/docs/AlignGeometries.md
index 1277b431b0..9bfd71bc07 100644
--- a/src/Plugins/ComplexCore/docs/AlignGeometries.md
+++ b/src/Plugins/ComplexCore/docs/AlignGeometries.md
@@ -1,10 +1,10 @@
# Align Geometries
-## Group (Subgroup) ##
+## Group (Subgroup)
DREAM3DReview (DREAM3DReview)
-## Description ##
+## Description
This **Filter** will align 2 Geometry objects using 1 of several alignment methods:
@@ -19,33 +19,12 @@ This **Filter** will align 2 Geometry objects using 1 of several alignment metho
The input geometries can be of any type. The *Moving* geometry is moved in space to the *Target* geometry.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------|------|------|
-| Method | Integer | 0=Centroid, 1=Origin, 2-7 for the various planes |
-
-## Required Geometry ##
-
-Required Geometry Type -or- Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|-----|
-| **Data Container** | Moving Geometry | Must have a geometry | N/A | The Geometry that is going to be moved |
-| **Data Container** | Target Geometry |Must have a geometry | N/A | The Target Geometry that the moving is going to be aligned to. |
-
-## Created Objects ##
-
-None. The operation is done in place
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/AlignSectionsFeatureCentroidFilter.md b/src/Plugins/ComplexCore/docs/AlignSectionsFeatureCentroidFilter.md
index a09cda2d2f..4b0978a78d 100644
--- a/src/Plugins/ComplexCore/docs/AlignSectionsFeatureCentroidFilter.md
+++ b/src/Plugins/ComplexCore/docs/AlignSectionsFeatureCentroidFilter.md
@@ -1,15 +1,14 @@
-# Align Sections (Feature Centroid)
+# Align Sections (Feature Centroid)
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Reconstruction (Alignment)
-## Description ##
+## Description
This **Filter** attempts to align 'sections' of the sample perpendicular to the Z-direction by determining the position that closest aligns the centroid(s) of previously defined "regions". The "regions" are defined by a boolean array where the **Cells** have been flagged by another **Filter**. Typically, during reading/processing of the data, each **Cell** is subject to a "quality metric" (or threshold) that defines if the **Cell** is *good*. This threshold can be used to define areas of each slice that are bad, either due to actual features in the microstructure or external references inserted by the user/experimentalist. If these "regions" of *bad* **Cells** are believed to be consistent through sections, then this **Filter** will preserve that by aligning those "regions" on top of one another on consecutive sections. The algorithm of this **Filter** is as follows:
-1. Determine the centroid of all **Cells** that are flagged with a boolean value equal to *true* for each section
+1. Determine the centroid of all **Cells** that are flagged with a boolean value equal to *true* for each section
2. Determine the shifts that place centroids of consecutive sections on top of one another
3. Round the shifts determined in step 2 to the nearest multiple of the **Cell** resolution. (This forces the sections to be shifted by full **Cell** increments)
@@ -21,41 +20,17 @@ The user can choose to write the determined shift to an output file by enabling
The user can also decide to remove a *background shift* present in the sample. The process for this is to fit a line to the X and Y shifts along the Z-direction of the sample. The individual shifts are then modified to make the slope of the fit line be 0. Effectively, this process is trying to keep the top and bottom section of the sample fixed. Some combinations of sample geometry and internal features can result in this algorithm introducing a 'shear' in the sample and the *Linear Background Subtraction* will attempt to correct for this.
-## Parameters ##
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Write Alignment Shift File | bool | Whether to write the shifts applied to each section to a file |
-| Alignment File | File Path | The output file path where the user would like the shifts applied to the section to be written. Only needed if *Write Alignment Shifts File* is checked |
-| Linear Background Subtraction | bool | Whether to remove a *background shift* present in the alignment |
-| Use Refernece Slice | bool | Whether the centroids of each section should be compared to a reference slice instead of their neighboring section |
-| Reference Slice | int32_t | Slice number to use as reference. Only needed if *Use Reference Slice* is checked |
-
-## Required Geometry ##
-
-Image
-
-## Required Objects ##
+% Auto generated parameter table will be inserted here
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | Mask | bool | (1) | Specifies if the **Cell** is to be counted as part of the *sample* or not |
-
-## Created Objects ##
-
-None
-
-## Example Pipelines ##
+## Example Pipelines
+ (10) SmallIN100 Full Reconstruction
+ (03) SmallIN100 Alignment
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/AlignSectionsListFilter.md b/src/Plugins/ComplexCore/docs/AlignSectionsListFilter.md
index c225ae7dfb..4e80d58bdf 100644
--- a/src/Plugins/ComplexCore/docs/AlignSectionsListFilter.md
+++ b/src/Plugins/ComplexCore/docs/AlignSectionsListFilter.md
@@ -1,11 +1,10 @@
# Align Sections (List)
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Reconstruction (Alignment)
-## Description ##
+## Description
This **Filter** will apply the cell shifts from a user specified txt file to each section of an Image Geometry. It accepts an alignment .txt file that has full **Cells** shifts that have already been calculated in it.
@@ -14,7 +13,6 @@ If the alignment file was generated by another DREAM.3D alignment filter then th
slice_n slice_n+1 newxshift newyshift xshifts yshifts
etc...
-
Otherwise, the format of the file is as follows:
slice_number xshift yshift
@@ -24,35 +22,14 @@ Otherwise, the format of the file is as follows:
The slices must be ordered from the bottom of the sample to the top of the sample (i.e., the first line of shifts should be the second slice relative to the first, then the next line is the third slice relative to the second, and so on). Also, the file must be either space or tab delimited.
-## Parameters ##
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Input File | File Path | The input .txt file path containing the shifts to apply to the sections |
-| DREAM.3D Alignment File | Bool | Turn this ON if the alignment file was generated by another DREAM.3D Alignment filter |
-
-## Required Geometry ##
-
-Image
-
-## Required Objects ##
-
-None
+% Auto generated parameter table will be inserted here
-## Created Objects ##
+## Example Pipelines
-None
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/AppendImageGeometryZSliceFilter.md b/src/Plugins/ComplexCore/docs/AppendImageGeometryZSliceFilter.md
index 9e0667046a..116549b4ec 100644
--- a/src/Plugins/ComplexCore/docs/AppendImageGeometryZSliceFilter.md
+++ b/src/Plugins/ComplexCore/docs/AppendImageGeometryZSliceFilter.md
@@ -1,54 +1,27 @@
-# Append Z-Slice
-
+# Append Z-Slice
## Group (Subgroup)
Sampling (Memory/Management)
-
## Description
-This filter allows the user to append an Image Geometry onto the "end" of another Image Geometry. The input and
-destination **ImageGeometry** objects must have the same X&Y dimensions. Optional Checks for equal **Resolution** values
+This filter allows the user to append an Image Geometry onto the "end" of another Image Geometry. The input and
+destination **ImageGeometry** objects must have the same X&Y dimensions. Optional Checks for equal **Resolution** values
can also be performed.
-For example, if the user has an already existing **Image Geometry** that is 100 voxels in the *X* direction by 200 pixels in the
+For example, if the user has an already existing **Image Geometry** that is 100 voxels in the *X* direction by 200 pixels in the
*Y* direction and composed of 5 *Z* slices then appending another data set that is the same dimensions in X & Y but contains
10 *Z* slices then the resulting **Image Geometry** will have a total of 15 *Z* slices.
-
-## Parameters
-
-| Name | Type | Description |
-|------------------|------| ------------|
-| Check Resolution | Boolean | Checks to make sure the spacing for the input geometry and destination geometry match |
-| Save as new geometry | Boolean | Instead of overwritting the existing destination geometry when appending the input data, save the results to a new geometry |
-| New Image Geometry | DataPath | The full path to the new image geometry where the appended results are stored when the save as new geometry is on |
-
-## Required Geometry
-
-Image
-
-## Required Arrays
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Attribute Matrix** | Input Cell Data | Cell | N/A | The incoming cell data that is to be appended. |
-| **Attribute Matrix** | Destination Cell Data | Cell | N/A | The destination cell data that is the final location for the appended data. |
-
-
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
-
## License & Copyright
Please see the description file distributed with this **Plugin**
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/ApplyTransformationToGeometryFilter.md b/src/Plugins/ComplexCore/docs/ApplyTransformationToGeometryFilter.md
index a377fdc0b2..abb84908ae 100644
--- a/src/Plugins/ComplexCore/docs/ApplyTransformationToGeometryFilter.md
+++ b/src/Plugins/ComplexCore/docs/ApplyTransformationToGeometryFilter.md
@@ -43,54 +43,14 @@ The user may select from a variety of options for the type of transformation to
| Enum Value | Transformation Type | Representation |
|------------|------------------------------------|--------------------------------------------------------------------------------------|
-| 0 | No Transformation | Identity transformation |
+| 0 | No Transformation | Identity transformation |
| 1 | Pre-Computed Transformation Matrix | A 4x4 transformation matrix, supplied by an **Attribute Array** in *row major* order |
-| 2 | Manual Transformation Matrix | Manually entered 4x4 transformation matrix |
-| 3 | Rotation | Rotation about the supplied axis-angle (Angle in Degrees). |
+| 2 | Manual Transformation Matrix | Manually entered 4x4 transformation matrix |
+| 3 | Rotation | Rotation about the supplied axis-angle (Angle in Degrees). |
| 4 | Translation | Translation by the supplied (x, y, z) values |
| 5 | Scale | Scaling by the supplied (x, y, z) values |
-## Parameters
-
-| Name | Type | Description |
-|-----------------------------------------------------------|-------------|---------------------------------------------------------------------------------------------------------------------------------------------|
-| Transformation Type | Enumeration | Type of transformation to be used. (0-5) |
-| Transformation Matrix | float (4x4) | Entries of the 4x4 transformation matrix, if *Manual* is chosen for the *Transformation Type* |
-| Rotation Axis-Angle (ijk) | float (4x) | axis-angle (Angle in Degrees) |
-| Translation | float (3x) | (x, y, z) translation values, if *Translation* is chosen for the *Transformation Type* |
-| Scale | float (3x) | (x, y, z) scale values, if *Scale* is chosen for the *Transformation Type* |
-| Translate Geometry To Global Origin Before Transformation | boolean | If enabled, translates the geometry to (0, 0, 0), applies the transformation, and then translates the geometry back to its original origin. |
-| Precomputed Transformation Matrix Data Path | DataPath | |
-| Geometry to be transformed. | DataPath | |
-
-### Image Geometry Transformation Options
-
-| Enum Value | Interpolation Type |
-|------------|-------------------------------------------|
-| 0 | No Interpolation |
-| 1 | Nearest Neighbor |
-| 2 | Linear/Bi linear/Tri linear Interpolation |
-
-| Name | Type | Description |
-|-----------------------|-------------|--------------------------------------------------------|
-| Interpolation Type | Enumeration | Type of Interpolation to be used. (0-2) |
-| Cell Attribute Matrix | DataPath | The path to the Image Geometry's Cell Attribute Matrix |
-
-## Required Geometry
-
-Any **Unstructured Geometry** or **Image Geometry**
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|---------------|----------------------|-------|----------------------|------------------------------------------------------------------------------------------------------------|
-| **Geometry** | None | N/A | N/A | The unstructured **Geometry** or Image Geometry to transform |
-| **DataArray** | TransformationMatrix | float | 4x4 | The pre-computed transformation matrix to apply, if _Pre-Computed_ is chosen for the *Transformation Type* |
-
-## Created Objects
-
-+ Unstructured Geometry: None
-+ Image Geometry: New Image Geometry (The input geometry is discarded)
+% Auto generated parameter table will be inserted here
## Example Pipelines
@@ -102,8 +62,6 @@ Any **Unstructured Geometry** or **Image Geometry**
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/ApproximatePointCloudHull.md b/src/Plugins/ComplexCore/docs/ApproximatePointCloudHull.md
index 7f87580e6f..d4539448ab 100644
--- a/src/Plugins/ComplexCore/docs/ApproximatePointCloudHull.md
+++ b/src/Plugins/ComplexCore/docs/ApproximatePointCloudHull.md
@@ -1,11 +1,11 @@
Approximate Point Cloud Hull
=============
-## Group (Subgroup) ##
+## Group (Subgroup)
Point Cloud (Geometry)
-## Description ##
+## Description
This **Filter** determines a set of points that approximates the surface (or *hull*) or a 3D point cloud represented by a **Vertex Geometry**. The hull is approximate in that the surface points are not guaranteed to hve belonged to the original point cloud; instead, the determined set of points is meant to represent a sampling of where the 3D point cloud surface occurs. To following steps are used to approximate the hull:
@@ -20,33 +20,12 @@ The above algorithm is significantly faster that other geometric approaches for
Note that the resulting hull geometry does not inherit any **Attribute Arrays** from the original point cloud.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------|------|------|
-| Grid Resolution | float 3x | The resolution of the sampling grid |
-| Minimum Number of Empty Neighbors | int | The minimum number of voxel neighbors that must contain 0 points for a voxel to be considered on the surface |
-
-## Required Geometry ##
-
-Vertex
-
-## Required Objects ##
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|-----|
-| **Data Container** | None | N/A | N/A | **Data Container** holding the input **Vertex Geometry** |
-
-## Created Objects ##
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|-----|
-| **Data Container** | HullDataContainer | N/A | N/A | **Data Container** holding the approximated surface **Vertex Geometry** |
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/ArrayCalculatorFilter.md b/src/Plugins/ComplexCore/docs/ArrayCalculatorFilter.md
index 29c0c1c5b9..ec92b234b3 100644
--- a/src/Plugins/ComplexCore/docs/ArrayCalculatorFilter.md
+++ b/src/Plugins/ComplexCore/docs/ArrayCalculatorFilter.md
@@ -1,29 +1,28 @@
# Attribute Array Calculator
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Core (Generation)
-## Description ##
+## Description
This **Filter** performs calculations on **Attribute Arrays** using the mathematical expression entered by the user, referred to as the *infix expression*. Calculations follow standard mathematical order of operations rules. Parentheses may be used to influence priority. The output of the entered equation is stored as a new **Attribute Array** of type double in an **Attribute Matrix** chosen by the user.
-
-## Usage & Syntax ##
+
+## Usage & Syntax
The user may enter any valid mathematical expression that uses numbers, operators and/or available **Attribute Arrays**. This expression may be typed into the **Filter** or entered using the available calculator interface. The **Filter** automatically determines how many tuples and component dimensions the output array requires. Should the entered expression use arrays, computations performed by the **Filter** are performed per tuple, i.e. each tuple has the same expression performed. Therefore, any **Attribute Arrays** used in the entered expression must have the same number of tuples. To help prevent most cases of tuple incompatibilities, the user must select an **Attribute Matrix** to serve as the source for arrays to be used in the expression. Additionally, the output array will have the same number of tuples as the arrays used in the infix expression, and must be placed in an **Attribute Matrix** that has the same number of tuples as the source **Attribute Matrix**.
All items in the entered infix expression, including values within arrays, will be cast to doubles for computation, and the resulting output will be stored as doubles. If the output array needs to be a different type for use as input to another **Filter**, consider using the Convert Attribute Data Type **Filter**.
-### Expressions Without Arrays ###
+### Expressions Without Arrays
-It is possible to enter an infix expression that does not contain any **Attribute Array**, similar to a standard calculator. In this case, the output array is simply a single numeric value that is stored in a single component, one tuple array. Because the output array will only have one tuple, it must be placed in an **Attribute Matrix** that has exactly one tuple. If such an **Attribute Matrix** is not available in the data structure, it can be created using the Create Attribute Matrix **Filter**.
+It is possible to enter an infix expression that does not contain any **Attribute Array**, similar to a standard calculator. In this case, the output array is simply a single numeric value that is stored in a single component, one tuple array. Because the output array will only have one tuple, it must be placed in an **Attribute Matrix** that has exactly one tuple. If such an **Attribute Matrix** is not available in the data structure, it can be created using the Create Attribute Matrix **Filter**.
-### Operators ###
+### Operators
There are several mathematical operators available for usage in an infix expression. Operators may either be *binary* (requiring two items to operate) or *unary* (requiring only one item to operate). Some unary operators may also require more than one argument. The tables below list the available mathematical operators.
-#### Binary Operators ####
+#### Binary Operators
| Symbol | Name | Operation |
|-----------|----------|---------------|
@@ -31,42 +30,42 @@ There are several mathematical operators available for usage in an infix express
| `-` | subtraction | Subtracts two items |
| `*` | multiplication | Multiplies two items |
| `/` | division | Divides two items |
-| **x^y** | exponentiation | Raises the base *x* to the *y* power |
+| x^y | exponentiation | Raises the base *x* to the *y* power |
-#### Unary Operators ####
+#### Unary Operators
| Symbol | Name | Number of Arguments | Operation |
|-----------|----------|-------------------------------|---------------|
-| **e^y** | exponential function | 1 | Raises *e* to the *y* power |
-| **sin(x)** | sine function | 1 | Computes the sine of *x* |
-| **cos(x)** | cosine function | 1 | Computes the cosine of *x* |
-| **tan(x)** | tangent function | 1 | Computes the tangent of *x* |
-| **asin(x)** | arcsine function | 1 | Computes the arcsine of *x* |
-| **acos(x)** | arccosine function | 1 | Computes the arccosine of *x* |
-| **atan(x)** | arctangent function | 1 | Computes the arctangent of *x* |
-| **abs(x)** | absolute value | 1 | Returns the absolute value of *x* |
-| **ceil(x)** | ceiling function | 1 | Returns the smallest integral value not less than *x* |
-| **floor(x)** | floor function | 1 | Returns the largest integral value not greater than *x* |
-| **log10(x)** | base 10 logarithm | 1 | Computes the base 10 logarithm of *x* |
-| **ln(x)** | natural logarithm | 1 | Computes the natural logarithm of *x* |
-| **sqrt(x)** | square root | 1 | Computes the square root of *x* |
-| **log(b, x)** | base *b* logarithm | 2 | Computes the base *b* logarithm of *x* |
-| **root(r, ind)** | *indth* root | 2 | Computes the *indth* root of the radicand*r* |
-
-#### Trigonometric Operators and Degrees/Radians ####
+| e^y | exponential function | 1 | Raises *e* to the *y* power |
+| sin(x) | sine function | 1 | Computes the sine of *x* |
+| cos(x) | cosine function | 1 | Computes the cosine of *x* |
+| tan(x) | tangent function | 1 | Computes the tangent of *x* |
+| asin(x) | arcsine function | 1 | Computes the arcsine of *x* |
+| acos(x) | arccosine function | 1 | Computes the arccosine of *x* |
+| atan(x) | arctangent function | 1 | Computes the arctangent of *x* |
+| abs(x) | absolute value | 1 | Returns the absolute value of *x* |
+| ceil(x) | ceiling function | 1 | Returns the smallest integral value not less than *x* |
+| floor(x) | floor function | 1 | Returns the largest integral value not greater than *x* |
+| log10(x) | base 10 logarithm | 1 | Computes the base 10 logarithm of *x* |
+| ln(x) | natural logarithm | 1 | Computes the natural logarithm of *x* |
+| sqrt(x) | square root | 1 | Computes the square root of *x* |
+| log(b, x) | base *b* logarithm | 2 | Computes the base *b* logarithm of *x* |
+| root(r, ind) | *indth* root | 2 | Computes the *indth* root of the radicand*r* |
+
+#### Trigonometric Operators and Degrees/Radians
The direct trigonometric operators (**sin**, **cos** and **tan**) can operate on either radians or degrees, which can be selected by the user from the **Filter** interface. Similarly, the inverse trigonometric operators (**asin**, **acos** and **atan**) will return either radians or degrees depending on the selection in the **Filter** interface. Note that by default, DREAM.3D **Filters** generally assume angle values are in radians. The Convert Angles to Degrees or Radians can be used to convert arrays from radians to degrees and vice versa.
-#### Undefined Operations and Operators Out-Of-Range ####
+#### Undefined Operations and Operators Out-Of-Range
-This **Filter** allows for undefined operations to occur. The return values for these operations will be the same return value obtained from the utilized C/C++ function. For example, the divide by zero operation in C/C++ is undefined behavior, so the result is not guaranteed (however, most platforms will follow the IEEE floating point standard and a value of +infinity will be returned). Similarly, a domain error may occur if an operator function is used with arguments out of range. For example, entering `arcsin(-2)`, `ln(-7.34)` or `sqrt(-14.89)` results in a domain error. The return value here is again not guaranteed, but would most likely be NaN.
+This **Filter** allows for undefined operations to occur. The return values for these operations will be the same return value obtained from the utilized C/C++ function. For example, the divide by zero operation in C/C++ is undefined behavior, so the result is not guaranteed (however, most platforms will follow the IEEE floating point standard and a value of +infinity will be returned). Similarly, a domain error may occur if an operator function is used with arguments out of range. For example, entering `arcsin(-2)`, `ln(-7.34)` or `sqrt(-14.89)` results in a domain error. The return value here is again not guaranteed, but would most likely be NaN.
-### Using Arrays in Expressions ###
+### Using Arrays in Expressions
Any **Attribute Array** available in the selected **Attribute Matrix** is eligible to be used in the infix expression and multiple arrays may be used in the same expression, but all arrays in any given expression must have the same number of components. Arrays may be entered into the infix expression by typing their exact name, or by using the dropdown menus in the interface labeled *Scalars* (for single component arrays) or *Vectors* (for multi-component arrays). Operations on arrays are computed tuple-by-tuple. For example, consider a single component **Attribute Array** named *Foo* that has five tuples, with the values stored being the first 5 prime numbers. The array *Foo* then looks as follows:
-
+
[2, 3, 5, 7, 11]
-
+
If the user enters the infix expression `Foo + 3`, the result of the **Filter** is a new array with exactly five tuples that contains the values:
[5, 6, 8, 10, 14]
@@ -74,10 +73,10 @@ If the user enters the infix expression `Foo + 3`, the result of the **Filter**
Now consider another single component array named *Bar* that has the value 4.25 at all tuples. If the infix expression `(Foo + Bar) * 4` is entered, then the output values are as follows:
[25, 29, 37, 45, 61]
-
-If there is a third available array named *Baz* that has three components, it cannot be used in infix expressions with *Foo* or *Bar*. For example, the infix expression `Foo + Baz` is not valid, and a parsing error will be presented.
-#### Using Multi-Component Arrays ####
+If there is a third available array named *Baz* that has three components, it cannot be used in infix expressions with *Foo* or *Bar*. For example, the infix expression `Foo + Baz` is not valid, and a parsing error will be presented.
+
+#### Using Multi-Component Arrays
There are two ways to enter multi-component arrays into the infix expression. Arrays may be entered without an index for a component. In this case, operations are performed both tuple-by-tuple *and* component-by-component, and the output array will have the same number of components as the input arrays. For example, consider two arrays *Foo* and *Bar* that are each 3-component arrays with two tuples whose values are as follows:
@@ -98,7 +97,7 @@ The infix expression `Foo[0] * Bar[2]` multiplies the first component of *Foo* w
[-3, -24]
-#### Explicit Array Names ####
+#### Explicit Array Names
It is possible to force the **Filter** to treat a term in the infix expression as the literal name of an **Attribute Array**. To force an item to be considered an array name literal, surround it in double quotes. Forcing literal names in this fashion allows for arrays to take the same name as mathematical operators. Consider the following examples:
@@ -110,7 +109,7 @@ It is possible to force the **Filter** to treat a term in the infix expression a
In most cases, attempting to write equations like these without putting the double quotes around the desired array name will cause an error due to ambiguity.
-## Examples ##
+## Examples
Confidence Index + 3 / ln(4*Fit)
@@ -136,36 +135,14 @@ This equation takes the cube root of *8* and stores the result in an array with
This equation raises *3* to the power of the value stored in every component of every tuple in *Array1*. The resulting array has the same tuple and component size of *Array1*.
-## Parameters ##
-
-None
-
-## Required Geometry ##
-
-Not Applicable
+% Auto generated parameter table will be inserted here
-## Required Objects ##
+## Example Pipelines
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|----------------|
-| Any **Attribute Matrix** | None | Any | N/A | Source **Attribute Matrix** for arrays available to the mathematical expression |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|----------------|
-| Any **Attribute Array** | Output | double | varies | Output of mathematical expression |
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/AvizoRectilinearCoordinateWriterFilter.md b/src/Plugins/ComplexCore/docs/AvizoRectilinearCoordinateWriterFilter.md
index cae0ac4e73..ee86ac4567 100644
--- a/src/Plugins/ComplexCore/docs/AvizoRectilinearCoordinateWriterFilter.md
+++ b/src/Plugins/ComplexCore/docs/AvizoRectilinearCoordinateWriterFilter.md
@@ -1,16 +1,14 @@
# Avizo Rectilinear Coordinate Writer
-
-## Group (Subgroup)
+## Group (Subgroup)
IO (Output)
-## Description
+## Description
This filter writes out a native Avizo Rectilinear Coordinate data file. Values should be present from segmentation of experimental data or synthetic generation and cannot be determined by this filter. Not having these values will result in the filter to fail/not execute.
-### Example Output
-
+### Example Output
# AmiraMesh BINARY-LITTLE-ENDIAN 2.1
# Dimensions in x-, y-, and z-direction
@@ -32,38 +30,14 @@ This filter writes out a native Avizo Rectilinear Coordinate data file. Values s
# Data section follows
..
-## Parameters
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Output File | File Path | Amira Mesh .am file created|
-| Write Binary File | Boolean | Binary file created, if checked |
-
-## Required Geometry
-
-Image
-
-## Required Objects
-
-| Type | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|-----|
-| Cell | FeatureIds | Ids (Int) that specify to which **Feature** each **Cell** belongs. | (1) | Filters Known to Create Data: Segment Features (Misorientation, C-Axis Misorientation, Scalar) (Reconstruction), Read Dx File (IO), Read Ph File (IO), Pack Primary Phases (SyntheticBuilding), Insert Precipitate Phases (SyntheticBuilding), Establish Matrix Phase (SyntheticBuilding)
+% Auto generated parameter table will be inserted here
+## Example Pipelines
-## Created Objects
-
-None
-
-## Example Pipelines
-
-
-
-## License & Copyright
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/AvizoUniformCoordinateWriterFilter.md b/src/Plugins/ComplexCore/docs/AvizoUniformCoordinateWriterFilter.md
index ca6c9b6649..3fca61a2a1 100644
--- a/src/Plugins/ComplexCore/docs/AvizoUniformCoordinateWriterFilter.md
+++ b/src/Plugins/ComplexCore/docs/AvizoUniformCoordinateWriterFilter.md
@@ -1,16 +1,14 @@
# Avizo Uniform Coordinate Writer
-
-## Group (Subgroup)
+## Group (Subgroup)
IO (Output)
-## Description
+## Description
This filter writes out a native Avizo Uniform Coordinate data file. Values should be present from segmentation of experimental data or synthetic generation and cannot be determined by this filter. Not having these values will result in the filter to fail/not execute.
-### Example Output
-
+### Example Output
# AmiraMesh BINARY-LITTLE-ENDIAN 2.1
# Dimensions in x-, y-, and z-direction
@@ -33,42 +31,14 @@ This filter writes out a native Avizo Uniform Coordinate data file. Values shoul
# Data section follows
..
-## Parameters
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Output File | File Path | Amira Mesh .am file created|
-| Write Binary File | Boolean | Binary file created, if checked |
-
-
-## Required Geometry
-
-Image
-
-
-## Required Objects
-
-| Type | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|-----|
-| Cell | FeatureIds | Ids (Int) that specify to which **Feature** each **Cell** belongs. | (1) | Filters Known to Create Data: Segment Features (Misorientation, C-Axis Misorientation, Scalar) (Reconstruction), Read Dx File (IO), Read Ph File (IO), Pack Primary Phases (SyntheticBuilding), Insert Precipitate Phases (SyntheticBuilding), Establish Matrix Phase (SyntheticBuilding)
+% Auto generated parameter table will be inserted here
+## Example Pipelines
-## Created Objects
-
-None
-
-
-
-## Example Pipelines
-
-
-
-## License & Copyright
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/CalculateArrayHistogramFilter.md b/src/Plugins/ComplexCore/docs/CalculateArrayHistogramFilter.md
index c76d82fc78..45e87c208c 100644
--- a/src/Plugins/ComplexCore/docs/CalculateArrayHistogramFilter.md
+++ b/src/Plugins/ComplexCore/docs/CalculateArrayHistogramFilter.md
@@ -43,36 +43,7 @@ The range on the data is [1.6, 5.1]. Using 8 bins starting from 1.5 with a bin w
Also see Histogram Quick Reference at [https://plot.ly/histogram/](https://plot.ly/histogram/).
-## Parameters
-
-| Name | Type | Decision |
-|------|------|------|
-| Number of Bins | int32 | This determines how many bins the data is sorted into for histogram |
-| Use Custom Min & Max Range | bool | Toggles on custom range values for the histogram |
-| Min Value | float64 | Sets the lower limit for histogram range. Only needed if *Use Custom Min & Max Range* is checked |
-| Max Value | float64 | Sets the higher limit for histogram range. Only needed if *Use Custom Min & Max Range* is checked |
-| Create new DataGroup for Histograms | bool | If checked new **DataGroup** will be created to store the histogram(s) |
-| Output DataGroup Path | DataPath | The **DataPath** to existing **DataGroup** to insert histogram(s) into |
-| New DataGroup Path | DataPath | The **DataPath** to the new **DataGroup** that will store histogram(s). Replaces
-*Output DataGroup Path* if *Create New DataGroup for Histograms* is checked |
-
-## Required Geometry
-
-None
-
-## Required Objects
-
-| Kind | Default Name | Type | Description |
-|------|--------------|------|-------------|
-| **DataArray** | DataArray(s) to Histogram | DataArray | Specifies to which **DataArray(s)** to create a histogram from |
-
-## Created Objects
-
-| Kind | Default Name | Type | Description |
-|------|--------------|------|-------------|
-| **DataArray** | **DataArray** name + "Histogram" | DataArray | A new **DataArray** stored in specified **DataGroup** in which
-the histogram will be generated based on **DataArray** specified in *DataArray(s) to Histogram* (One per **DataArray** in
-*DataArray(s) to Histogram*) |
+% Auto generated parameter table will be inserted here
## Example Pipelines
@@ -83,11 +54,9 @@ the histogram will be generated based on **DataArray** specified in *DataArray(s
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
### Example Data (Raw)
diff --git a/src/Plugins/ComplexCore/docs/CalculateFeatureSizesFilter.md b/src/Plugins/ComplexCore/docs/CalculateFeatureSizesFilter.md
index 4c3c8a4752..60f7af27ec 100644
--- a/src/Plugins/ComplexCore/docs/CalculateFeatureSizesFilter.md
+++ b/src/Plugins/ComplexCore/docs/CalculateFeatureSizesFilter.md
@@ -1,42 +1,18 @@
-# Find Feature Sizes
+# Find Feature Sizes
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Statistics (Morphological)
-## Description ##
+## Description
This **Filter** calculates the sizes of all **Features**. The **Filter** simply iterates through all **Elements** querying for the **Feature** that owns them and keeping a tally for each **Feature**. The tally is then stored as *NumElements* and the *Volume* and *EquivalentDiameter* are also calculated (and stored) by knowing the volume of each **Element**.
During the computation of the **Feature** sizes, the size of each individual **Element** is computed and stored in the corresponding **Geometry**. By default, these sizes are deleted after executing the **Filter** to save memory. If you wish to store the **Element** sizes, select the *Generate Missing Element Sizes* option. The sizes will be stored within the **Geometry** definition itself, not as a separate **Attribute Array**.
-## Parameters ##
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Generate Missing Element Sizes | bool | If checked this will generate and store the element sizes ONLY if the geometry does not already contain them |
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
+% Auto generated parameter table will be inserted here
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Element Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Element** belongs |
-| **Attribute Matrix** | FeatureData | Feature | N/A | **Feature Attribute Matrix** of the selected *Feature Ids* |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | EquivalentDiameters | float | (1) | Diameter of a sphere with the same volume as the **Feature** |
-| **Feature Attribute Array** | NumElements | int32_t | (1) | Number of **Elements** that are owned by the **Feature**. This value does not place any distinction between **Elements** that may be of a different size |
-| **Feature Attribute Array** | Volumes | float | (1) | Volume of the **Feature**. This value may be "redundant" from the NumElements value if all **Elements** are the same size and is calculable from the EquivalentDiameters value |
-
-## Example Pipelines ##
+## Example Pipelines
+ (01) SmallIN100 Morphological Statistics
+ (10) SmallIN100 Full Reconstruction
@@ -45,12 +21,10 @@ Not Applicable
+ (06) SmallIN100 Synthetic
+ (09) Image Segmentation
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/CalculateTriangleAreasFilter.md b/src/Plugins/ComplexCore/docs/CalculateTriangleAreasFilter.md
index 9a6aac7d45..86180454b8 100644
--- a/src/Plugins/ComplexCore/docs/CalculateTriangleAreasFilter.md
+++ b/src/Plugins/ComplexCore/docs/CalculateTriangleAreasFilter.md
@@ -1,48 +1,28 @@
# Generate Triangle Areas
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Surface Meshing (Misc)
-## Description ##
+## Description
+
+This **Filter** computes the area of each **Triangle** in a **Triangle Geometry** by calculating the following:
-This **Filter** computes the area of each **Triangle** in a **Triangle Geometry** by calculating the following:
-
1/2*|AB||AC|sin(O)
where *O* is the angle between |AB| and |AC|.
-## Parameters ##
-
-None
-
-## Required Geometry ##
-
-Triangle
-
-## Required Objects ##
+% Auto generated parameter table will be inserted here
-None
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Face Attribute Array** | FaceAreas | double | (1) | Specifies the area of each **Face** |
-
-
-## Example Pipelines ##
+## Example Pipelines
+ (03) SmallIN100 Mesh Statistics
+ Triangle_Face_Data_Demo.d3dpipeline
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/ChangeAngleRepresentation.md b/src/Plugins/ComplexCore/docs/ChangeAngleRepresentation.md
index 68c3b4bda8..71f0f18e09 100644
--- a/src/Plugins/ComplexCore/docs/ChangeAngleRepresentation.md
+++ b/src/Plugins/ComplexCore/docs/ChangeAngleRepresentation.md
@@ -1,53 +1,32 @@
-# Convert Angles to Degrees or Radians
+# Convert Angles to Degrees or Radians
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Orientation Analysis (Conversion)
-## Description ##
+## Description
-This **Filter** will multiply the values of every **Element** by a factor to convert *degrees to radians* or *radians to degrees*. The user needs to know the units of their data in order to use this **Filter** properly.
+This **Filter** will multiply the values of every **Element** by a factor to convert *degrees to radians* or *radians to degrees*. The user needs to know the units of their data in order to use this **Filter** properly.
-### Example Usage ###
+### Example Usage
2D data files that are in *HKL*'s .ctf format use degrees. 3D data files in *HKL*'s .ctf format use radians. All files in *TSL*'s .ang format use radians. If other file types are used, determine the units before running this **Filter**.
-
-Generally, all **Filters** within DREAM.3D use radians as a default unit, but **Filters** may be added that require the Euler angles to be in degrees and this **Filter** will allow the user to move back-and-forth between the units.
-
-If the wrong conversion is selected (e.g., the user chooses *degrees to radians*, but their data is already in radians), the **Filter** will apply the conversion anyway and will result in erroneous data being used for the rest of the pipeline. If unsure about the units, check with the software supplier.
-
-## Parameters ##
-
-| Name | Type | Description |
-|------|------|-------------|
-| Conversion Type | Enumeration | Tells the **Filter** which conversion is being made |
-
-## Required Geometry ##
-Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Element Attribute Array** | None | float | (n) | Values that represent angles in degrees or radians |
+Generally, all **Filters** within DREAM.3D use radians as a default unit, but **Filters** may be added that require the Euler angles to be in degrees and this **Filter** will allow the user to move back-and-forth between the units.
-## Created Objects ##
+If the wrong conversion is selected (e.g., the user chooses *degrees to radians*, but their data is already in radians), the **Filter** will apply the conversion anyway and will result in erroneous data being used for the rest of the pipeline. If unsure about the units, check with the software supplier.
-None
+% Auto generated parameter table will be inserted here
-## Example Pipelines ##
+## Example Pipelines
+ TxCopper_Exposed
+ TxCopper_Unexposed
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/CombineAttributeArraysFilter.md b/src/Plugins/ComplexCore/docs/CombineAttributeArraysFilter.md
index 6d4360bdf2..f06f0939db 100644
--- a/src/Plugins/ComplexCore/docs/CombineAttributeArraysFilter.md
+++ b/src/Plugins/ComplexCore/docs/CombineAttributeArraysFilter.md
@@ -1,78 +1,43 @@
-# Combine Attribute Arrays
+# Combine Attribute Arrays
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Core (Memory/Management)
-## Description ##
+## Description
This **Filter** will "stack" any number of user-chosen **Attribute Arrays** into a single attribute array and allows the option to remove the original **Attribute Arrays** once this operation is completed. The arrays must all share the same primitive type and number of tuples, but may have differing component dimensions. The resulting combined array will have a total number of components equal to the sum of the number of components for each stacked array. The order in which the components are placed in the combined array is the same as the ordering chosen by the user when selecting the arrays. For example, consider two arrays, one that is a 3-vector and one that is a scalar. The values in memory appear as follows:
_Vector_: tuple 1 - { v1 v2 v3 } ; tuple 2 - { v1 v2 v3 } ; tuple 3 - { v1 v2 v3 } ...
-_Scalar_: tuple 1 - { s1 } ; tuple 2 - { s1 } ; tuple 3 - { s1 } ...
-
-To have the components of the combined array contain the scalar values first, use the box and arrows to the right of the array selection to move the scalar array above the vector array:
+_Scalar_: tuple 1 - { s1 } ; tuple 2 - { s1 } ; tuple 3 - { s1 } ...
------
+To have the components of the combined array contain the scalar values first, use the box and arrows to the right of the array selection to move the scalar array above the vector array:
![Combine Attribute Arrays: Scalar First](Images/CombineAttributeArraysGUI_1.png)
------
-
After executing the **Filter**, the combined array will have component dimensions of 1 x 4, and will have values in memory as follows:
_Combined (scalar first)_: tuple 1 - { s1 v1 v2 v3 } ; tuple 2 - { s1 v1 v2 v3 } ; tuple 3 - { s1 v1 v2 v3 } ...
To have the components of the combined array contain the vector values first, simply move the vector array above the scalar array:
------
-
![Combine Attribute Arrays: Vector First](Images/CombineAttributeArraysGUI_2.png)
------
-
After executing the **Filter**, the combined array will still have component dimensions of 1 x 4, and but now the values in memory are as follows:
_Combined (vector first)_: tuple 1 - { v1 v2 v3 s1 } ; tuple 2 - { v1 v2 v3 s1 } ; tuple 3 - { v1 v2 v3 s1 } ...
The user may also select to normalize the resulting combined array. The normalization procedure will enforce a range of [0, 1] for all values in the combined array. This may be useful for combining two arrays that have different order of magnitude data. Note that this option will fundamentally change the underlying data in the combined array from the original incoming arrays.
+% Auto generated parameter table will be inserted here
-## Parameters ##
-
-| Name | Type | Description |
-|------------------|------|-------------|
-| Standardize Data | bool | Whether to standardize the combine data on the interval [0, 1] |
-| Move Data | bool | Whether to remove the original arrays after combining the data |
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
+## Example Pipelines
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|----------------|
-| Any **Attribute Array** | None | Any | Any | **Attribute Arrays** to combine |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|----------------|
-| Any **Attribute Array** | CombinedData | Any | Any | Combined **Attribute Array** name |
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/CombineStlFilesFilter.md b/src/Plugins/ComplexCore/docs/CombineStlFilesFilter.md
index adf1265f24..44b6710279 100644
--- a/src/Plugins/ComplexCore/docs/CombineStlFilesFilter.md
+++ b/src/Plugins/ComplexCore/docs/CombineStlFilesFilter.md
@@ -1,39 +1,23 @@
-# Combine STL Files
+# Combine STL Files
-## Group (Subgroup)
+## Group (Subgroup)
AMProcessMonitoring (AMProcessMonitoring)
-## Description
+## Description
This **Filter** combines all of the STL files from a given directory into a single triangle geometry. This filter will make use of the **Import STL File Filter** to read in each stl file in the given directory and then will proceed to combine each of the imported files into a single triangle geometry.
-## Parameters
-| Name | Type | Description |
-|------|------|------|
-| Path to STL Files | Directory Path | The path to the folder containing all the STL files to be combined |
-
-## Required Geometry
-Not Applicable
-
-## Created Objects
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|-----|
-| **Geometry** | TriangleGeometry | N/A | N/A | The path to the triangle geometry to be created from the combined STL files |
-| **Face Attribute Matrix** | FaceData | Face | N/A | Created **Face Attribute Matrix** name for the combined geometry |
-| **Face Attribute Array** | FaceNormals | double | (3) | Specifies the normal of each **Face** in the combined geometry |
-| **Vertex Attribute Matrix** | VertexData | Vertex | N/A | Created **Vertex Attribute Matrix** name for the combined geometry |
+% Auto generated parameter table will be inserted here
## Example Pipelines
CombineStlFiles
-## License & Copyright
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/ComputeFeatureRectFilter.md b/src/Plugins/ComplexCore/docs/ComputeFeatureRectFilter.md
index 21a281b501..58c98fb586 100644
--- a/src/Plugins/ComplexCore/docs/ComputeFeatureRectFilter.md
+++ b/src/Plugins/ComplexCore/docs/ComputeFeatureRectFilter.md
@@ -1,22 +1,20 @@
-# Compute Feature Rect #
+# Compute Feature Rect
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Reconstruction (Reconstruction)
-## Description ##
+## Description
This **Filter** computes the XYZ minimum and maximum coordinates for each **Feature** in a segmentation. This data can be important for finding the smallest encompassing volume. This values are given in **Pixel** coordinates.
| | 0 | 1 | 2 | 3 | 4 |
|-------|---|---|---|---|---|
-| **0** | 0 | 0 | 1 | 0 | 0 |
-| **1** | 0 | 0 | 1 | 1 | 0 |
-| **2** | 0 | 1 | 1 | 1 | 1 |
-| **3** | 0 | 0 | 1 | 1 | 0 |
-| **4** | 0 | 0 | 0 | 0 | 0 |
-
+| 0 | 0 | 0 | 1 | 0 | 0 |
+| 1 | 0 | 0 | 1 | 1 | 0 |
+| 2 | 0 | 1 | 1 | 1 | 1 |
+| 3 | 0 | 0 | 1 | 1 | 0 |
+| 4 | 0 | 0 | 0 | 0 | 0 |
If the example matrix above which represents a single feature where the feature ID = 1, the output of the filter would be:
@@ -28,38 +26,14 @@ If the example matrix above which represents a single feature where the feature
Y Max = 3
Z Max = 0
+% Auto generated parameter table will be inserted here
-## Parameters ##
-
-N/A
-
-## Required Geometry ##
-
-N/A
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|-----|
-| **FeatureIds** | FeatureIdsArrayName | int32_t | (1) | |
-| **Feature Attribute Matrix** | N/A | Feature AttributeMatrix | N/A | The path to the cell feature **Attribute Matrix** |
+## Example Pipelines
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|-----|
-| **Feature Attribute Array** | FeatureRect | uint32 | (6) | Xmin, Ymin, Zmin, Xmax, Ymax, Zmax |
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/ComputeMomentInvariants2DFilter.md b/src/Plugins/ComplexCore/docs/ComputeMomentInvariants2DFilter.md
index bbdee2d746..c36f245479 100644
--- a/src/Plugins/ComplexCore/docs/ComputeMomentInvariants2DFilter.md
+++ b/src/Plugins/ComplexCore/docs/ComputeMomentInvariants2DFilter.md
@@ -1,55 +1,20 @@
-# Compute MomentInvariants (2D)
+# Compute MomentInvariants (2D)
-
-## Group (Subgroup)
+## Group (Subgroup)
Statistics (Statistics)
-## Description
+## Description
This **Filter** computes the 2D Omega-1 and Omega 2 values from the *Central Moments* matrix and optionally will normalize the values to a unit circle and also optionally save the *Central Moments* matrix as a DataArray to the *Cell Feature Attribute Matrix*. Based off the paper by MacSleyne et. al [1], the algorithm will calculate the 2D central moments for each feature starting at *feature id = 1*. Because *feature id 0* is of special significance and typically is a matrix or background it is ignored in this filter. If any feature id has a Z Delta of > 1, the feature will be skipped. This algorithm works strictly in the XY plane and is meant to be applied to a 2D image. Using the research from the cited paper certain shapes can be detected using the Omega-1 and Omega-2 values. An example usage is finding elliptical shapes in an image:
-
See below figure from [1] that can help the user classify objects.
![Example appllication of filter to identify elliptical particales (red) which are differentiated from non-elliptical particals (purple)](Images/ComputeMomentInvariants_Fig1.png)
-
![Example appllication of filter to identify elliptical particales (red) which are differentiated from non-elliptical particals (purple)](Images/ComputeMomentInvariants2D.png)
-
-
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| Normalize MomentInvariants | Bool | Should the algorithm normalize the results to unit circle. |
-| Save Central Moments | Bool | Write the Central Moments to a new Data Array |
-
-
-## Required Geometry
-
-ImageGeom
-
-
- CentralMomentsArrayPath 2
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| Cell **Attribute Array** | FeatureIds | int32_t | (1) | The Feature Ids array to analyze for ellipsoids |
-| Cell **Attribute Array** | FeatureRectArray | uint32_t | (6) | Array holding the min xy and max xy pixel coordinates of each feature id |
-
-
-
-## Created Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| Cell **Attribute Array** | Omega1 | float | (1) | Omega1 value |
-| Cell **Attribute Array** | Omega2 | float | (1) | Omega2 value |
-| Cell **Attribute Array** | CentralMoments | float | (3)(3) | Central Moments value |
+% Auto generated parameter table will be inserted here
# Citations
@@ -59,17 +24,12 @@ ImageGeom
# Acknowledgements
The authors would like to thank Dr. Marc De Graef from Carnegie Mellon University for enlightening discussions and a concrete implementation from which to start this filter.
+## Example Pipelines
-## Example Pipelines
-
-
-
-## License & Copyright
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/ConditionalSetValue.md b/src/Plugins/ComplexCore/docs/ConditionalSetValue.md
index 7c6094d179..9294585937 100644
--- a/src/Plugins/ComplexCore/docs/ConditionalSetValue.md
+++ b/src/Plugins/ComplexCore/docs/ConditionalSetValue.md
@@ -1,14 +1,14 @@
# Replace Value in Array (Conditional)
-## Group (Subgroup) ##
+## Group (Subgroup)
Core (Misc)
-## Description ##
+## Description
This **Filter** replaces values in a user specified **Attribute Array** with a user specified value a second boolean **Attribute Array** specifies, but only when **Use Conditional Mask** is *true*. For example, if the user entered a *Replace Value* of *5.5*, then for every occurence of *true* in the conditional boolean array, the selected **Attribute Array** would be changed to 5.5. If **Use Conditional Mask** is *false*, then **Value to Replace** will be searched for in the provided **Attribute Array** and all instances will be replaced. Below are the ranges for the values that can be entered for the different primitive types of arrays (for user reference). The selected **Attribute Array** must be a scalar array.
-
-### Primitive Data Types ##
+
+### Primitive Data Types
| Type | Size | Range |
|------------------|------|--------------------|
@@ -24,40 +24,12 @@ This **Filter** replaces values in a user specified **Attribute Array** with a u
| Double | 64 bit | -1.7e+308 to -2.2e-308, 0.0, 2.2e-308 to 1.7e+308 (15 digits)|
| Boolean | 8 bit |0 = false and any other value will be forced to 1 = true|
-## Parameters ##
-
-| Name | Type | Description |
-|------------------|------|-------------|
-| New Value | std::string | Value to replace the removed values in the array [will be typecasted to appropriate value later] |
-
-## Optional Data Mask ##
-| Name | Type | Description |
-|------------------|------|-------------|
-| Use Conditional Mask | bool | Whether to use a boolean mask array to replace values marked true |
-| Invert Mask | bool | If checked values marked FALSE will be replaced instead |
-| Any **Attribute Array** | None | Bool | (1) | The complete path to the conditional array that will determine which values/entries will be replaced if index is true|
-| Value to Replace | std::string | The numerical value that will be replaced in the array [will be typecasted to appropriate value later] |
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
+% Auto generated parameter table will be inserted here
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|----------------|
-| Any **Attribute Array** | None | Any | (1) | Path to **Attribute Array** that will have values replaced |
-
-## Created Objects ##
-
-None
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/ConvertColorToGrayScaleFilter.md b/src/Plugins/ComplexCore/docs/ConvertColorToGrayScaleFilter.md
index f478a3a98b..3057199d7f 100644
--- a/src/Plugins/ComplexCore/docs/ConvertColorToGrayScaleFilter.md
+++ b/src/Plugins/ComplexCore/docs/ConvertColorToGrayScaleFilter.md
@@ -1,11 +1,10 @@
-# Color to GrayScale
+# Color to GrayScale
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Processing (Image)
-## Description ##
+## Description
This **Filter** allows the user to select a *flattening* method for turning an array of RGB or RGBa values into grayscale values.
@@ -16,51 +15,21 @@ This **Filter** allows the user to select a *flattening* method for turning an a
The user can select 1 or more image data arrays which are assumed to be multi-component arrays of unsigned 8 bit values. The user can create a new AttributeMatrix if they want to store all the newly created arrays in a separate AttributeMatrix.
-### Additional GrayScale Conversions ###
+### Additional GrayScale Conversions
The following are some additional accepted grayscale conversions
+ RMY Greyscale: Red: 0.5 Green: 0.419 Blue: 0.081
+ (YIQ/NTSC): Red: 0.299 Green: 0.587 Blue: 0.114
+% Auto generated parameter table will be inserted here
-## Parameters ##
-
-| Name | Type | Description |
-|------|------|------|
-| Flattening Method | Enumeration | Which method to use when flattening the RGB array |
-| Luminosity Triplet | 3xFloats | Only used if Luminosity is selected as conversion method |
-| Color Channel | 1 Int | Only needed if the Color Channel conversion method is selected |
-| Output Array Prefix | String | This prefix will be added to each array name that is selected for conversion to form the new array name |
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Element Attribute Array(s)** | ImageData | uint8_t | (3) or (4) | RGB or RGBA values |
-
-## Created Objects ##
+## Example Pipelines
-| Kind | Default Name | Type | Component Dimensions (dimension, size) | Description |
-|------|--------------|-------------|---------|-----|
-| **Element Attribute Array** | GrayScale Data | uint8_t | (1) | Grayscale values |
-| AttributeMatrix (Optional) | | | | |
-
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/ConvertDataFilter.md b/src/Plugins/ComplexCore/docs/ConvertDataFilter.md
index a99c9bc309..a6251c6db8 100644
--- a/src/Plugins/ComplexCore/docs/ConvertDataFilter.md
+++ b/src/Plugins/ComplexCore/docs/ConvertDataFilter.md
@@ -1,18 +1,16 @@
-# Convert Attribute Data Type
+# Convert Attribute Data Type
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Core (Misc)
-
-## Description ##
+## Description
This **Filter** converts attribute data from one primitive type to another by using the built in translation of the compiler. This **Filter** can be used if the user needs to convert an array into a type that is accepted by another **Filter**. For example, a **Filter** may need an input array to be of type _int32_t_ but the array that the user would like to use is _uint16_t_. The user may use this **Filter** to create a new array that has the proper target type (_int32_t_).
**This Filter is here for convenience and should be used with great care and understanding of the input and output data. This Filter should rarely be required, and if the user thinks that they require this Filter then a detailed examination of all the data involved should be undertaken to avoid possible undefined behaviors.**
-### Important Notes ###
+### Important Notes
**Up Casting**
@@ -26,38 +24,14 @@ Down casting can have undefined behavior depending on the primitive types involv
When converting data from signed values to unsigned values or vice-versa, there can also be undefined behavior. For example, if the user were to convert a signed 4 byte integer array to an unsigned 4 byte integer array and the input array has negative values, then the conversion rules are undefined and may differ from operating system to operating system.
-## Parameters ##
-
-| Name | Type | Description |
-|------------------|------|--------------|
-| Scalar Type | Enumeration | Convert to this data type |
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| Any **Attribute Array** | None | Any | Any | Array to convert |
+% Auto generated parameter table will be inserted here
-## Created Objects ##
+## Example Pipelines
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| Any **Attribute Array** | None | Any | Any | The converted array |
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/CopyDataObjectFilter.md b/src/Plugins/ComplexCore/docs/CopyDataObjectFilter.md
index 1a7f443161..d214802e28 100644
--- a/src/Plugins/ComplexCore/docs/CopyDataObjectFilter.md
+++ b/src/Plugins/ComplexCore/docs/CopyDataObjectFilter.md
@@ -1,17 +1,17 @@
# Copy Data Object
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Core (Generation)
-## Description ##
+## Description
This **Filter** deep copies one or more DataObjects.
-**In the case of copying _DataObject_s that inherit from _BaseGroup_**, such as *DataGroup* or _AttributeMatrix_, **it will copy all of the child objects recursively**, that is to say all of an object's children and childrens' children and so on will be copied if applicable.
+**In the case of copying _DataObject_s that inherit from _BaseGroup_**, such as _DataGroup_ or _AttributeMatrix_, **it will copy all of the child objects recursively**, that is to say all of an object's children and childrens' children and so on will be copied if applicable.
+
+Commonly used _BaseGroup_ children:
-Commonly used *BaseGroup* children:
- **_ALL_** Geometries
- _DataGroup_
- _AttributeMatrix_
@@ -19,39 +19,16 @@ Commonly used *BaseGroup* children:
See the DataStructure section of the reference manual for a complete hierarchy.
-When the *Copy to New Parent* is toggled true a new parameter will appear. This parameter, _Copied Parent Group_, allows for the selected arrays to all be copied into whatever data container you place here.
-
-## Parameters ##
-
-None
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
+When the _Copy to New Parent_ is toggled true a new parameter will appear. This parameter, _Copied Parent Group_, allows for the selected arrays to all be copied into whatever data container you place here.
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|----------------|
-| DataObject | N/A | N/A | N/A | The list of DataObjects to copy. |
-| bool | false | N/A | N/A | Whether to copy the DataObjects to a new parent or not. |
-| DataGroup | N/A | N/A | N/A | The group to be used as the parent for all the DataObject copies if the Copy to New Parent option is selected |
-| string | _COPY | N/A | N/A | The suffix string to be appended to each copy's name |
+% Auto generated parameter table will be inserted here
-## Created Objects ##
+## Example Pipelines
-A deep copy of the DataObjects selected in the input.
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/CopyFeatureArrayToElementArray.md b/src/Plugins/ComplexCore/docs/CopyFeatureArrayToElementArray.md
index 376af82813..191633ec44 100644
--- a/src/Plugins/ComplexCore/docs/CopyFeatureArrayToElementArray.md
+++ b/src/Plugins/ComplexCore/docs/CopyFeatureArrayToElementArray.md
@@ -1,47 +1,21 @@
-# Create Element Array from Feature Array
+# Create Element Array from Feature Array
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Core (Memory/Management)
-## Description ##
+## Description
This **Filter** copies the values associated with a **Feature** to all the **Elements** that belong to that **Feature**. Xmdf visualization files write only the **Element** attributes, so if the user wants to display a spatial map of a **Feature** level attribute, this **Filter** will transfer that information down to the **Element** level.
-## Parameters ##
-
-None
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| Feature **Attribute Array** | None | Any | Any | **Feature** data to copy to **Element** data |
-| Element **Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Element** belongs |
-
+% Auto generated parameter table will be inserted here
-## Created Objects ##
+## Example Pipelines
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| Element **Attribute Array** | None | Any | Any | Copied **Attribute Array** |
-
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/CreateAttributeMatrixFilter.md b/src/Plugins/ComplexCore/docs/CreateAttributeMatrixFilter.md
index d3a017f3d7..a4a3ac885f 100644
--- a/src/Plugins/ComplexCore/docs/CreateAttributeMatrixFilter.md
+++ b/src/Plugins/ComplexCore/docs/CreateAttributeMatrixFilter.md
@@ -1,50 +1,21 @@
-# Create Attribute Matrix #
+# Create Attribute Matrix
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Core (Generation)
-
-## Description ##
+## Description
This **Filter** creates a new **Attribute Matrix**.
-### Example Usage ###
+### Example Usage
If you wanted to create an **Attribute Matrix** to represent a 3D volume where the dimensions of the 3 orthogonal axesare X=3, y=4 and Z=5, then the *Tuple Dimensions* would have a value of (3, 4, 5).
-## Parameters ##
-
-| Name | Type | Description |
-|------|------|-------------|
-| DataObject Path | DataPath | Where **Attribute Matrix** will be created |
-| Attribute Matrix Dimensions | Any | An array that contains the size of each tuple dimension |
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Data Container** | None | N/A | N/A | **Data Container** for the created **Attribute Matrix** |
-
-## Created Objects ##
+% Auto generated parameter table will be inserted here
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Attribute Matrix** | None | Any | N/A | Created **Attribute Matrix** name |
+## Example Pipelines
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-
-
-
-
diff --git a/src/Plugins/ComplexCore/docs/CreateDataArray.md b/src/Plugins/ComplexCore/docs/CreateDataArray.md
index 617216f1e5..58289efdc7 100644
--- a/src/Plugins/ComplexCore/docs/CreateDataArray.md
+++ b/src/Plugins/ComplexCore/docs/CreateDataArray.md
@@ -1,10 +1,10 @@
# Create Data Array
-## Group (Subgroup) ##
+## Group (Subgroup)
Core (Generation)
-## Description ##
+## Description
This **Filter** creates an **Data Array** of any primitive type with any number of components along a *single component dimension*. For example, a scalar as (1) or a 3-vector as (3), but *not* a matrix as (3, 3). The array is initialized to a user define value or with random values within a specified range.
@@ -18,11 +18,11 @@ Another example is if you want to create a floating point array where each tuple
2.5
-When creating a Data Array within an Attribute matrix, the tuple dimensions will **always** be taken direct from the Attribute Matrix. This means that the *Set Tuple Dimensions* parameter can be unchecked to hide the tuple dimensions entry table.
+When creating a Data Array within an Attribute matrix, the tuple dimensions will **always** be taken direct from the Attribute Matrix. This means that the *Set Tuple Dimensions* parameter can be unchecked to hide the tuple dimensions entry table.
If the parent is **NOT an Attribute Matrix**, then the user ***MUST*** set the tuple dimensions themselves.
-### Scalar Type Values ###
+### Scalar Type Values
static const int Int8 = 0;
static const int UInt8 = 1;
@@ -36,7 +36,7 @@ If the parent is **NOT an Attribute Matrix**, then the user ***MUST*** set the t
static const int Double = 9;
static const int Bool = 10;
-### Primitive Data Type Valid Ranges ##
+### Primitive Data Type Valid Ranges
| Type | Size | Range |
|------------------|------|--------------------|
@@ -55,38 +55,14 @@ If the parent is **NOT an Attribute Matrix**, then the user ***MUST*** set the t
The number of components should be at least 1. Examples of *Number of Components* would be 3 for an RGB Image, 1 for a gray scale image, 1 for a scalar array, 4 for a quaternions array, etc. All values of the array will be initialized to the user set value. The initialization value text box
must have a user entry or the default value *0* will be used.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------------------|------|-------------|
-| Set Tuple Dimensions | bool | This allows the user to set the tuple dimensions directly rather than just inheriting them. This option is NOT required if you are creating the Data Array in an Attribute Matrix |
-| Numeric Type | Enumeration | Primitive data type for created array |
-| Number of Components | int32_t | The number of components that each tuple contains. Matrix are row major form within SIMPL|
-| Initialization Value | String | Initialization value for array |
-| Data Format | String | This value will specify which data format is used by the array's data store. An empty string results in in-memory data store. |
+## Example Pipelines
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-None
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|----------------|
-| Any **Attribute Array** | None | Any | Any | Created **Attribute Array** location and name |
-
-## Example Pipelines ##
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/CreateDataGroup.md b/src/Plugins/ComplexCore/docs/CreateDataGroup.md
index 4f026839e0..d689600b43 100644
--- a/src/Plugins/ComplexCore/docs/CreateDataGroup.md
+++ b/src/Plugins/ComplexCore/docs/CreateDataGroup.md
@@ -1,45 +1,23 @@
-# Create Data Group
+# Create Data Group
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Core (Generation)
-## Description ##
+## Description
This **Filter** creates a new **DataGroup**.
-Unlike _AttributeMatrix_, _DataGroup_s are capable of holding any *DataObject* of any size.
-
-## Parameters ##
-
-None
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-Not Applicable
+Unlike _AttributeMatrix_, _DataGroup_s are capable of holding any _DataObject_ of any size.
-## Created Objects ##
+% Auto generated parameter table will be inserted here
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|----------------|
-| **Data Container** | DataContainer | N/A | N/A | Created **Data Container** name |
+## Example Pipelines
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/CreateFeatureArrayFromElementArray.md b/src/Plugins/ComplexCore/docs/CreateFeatureArrayFromElementArray.md
index 13ff92496c..0b9e9eb6cc 100644
--- a/src/Plugins/ComplexCore/docs/CreateFeatureArrayFromElementArray.md
+++ b/src/Plugins/ComplexCore/docs/CreateFeatureArrayFromElementArray.md
@@ -1,48 +1,21 @@
-# Create Feature Array From Element Array
+# Create Feature Array From Element Array
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Core (Memory/Management)
-## Description ##
-
-This **Filter** copies all the associated **Element** data of a selected **Element Array** to the **Feature** to which the **Elements** belong. The value stored for each **Feature** will be the value of the *last element copied*.
-
-## Parameters ##
-
-None
-
-## Required Geometry ##
-
-Not Applicable
-
+## Description
-## Required Objects ##
+This **Filter** copies all the associated **Element** data of a selected **Element Array** to the **Feature** to which the **Elements** belong. The value stored for each **Feature** will be the value of the *last element copied*.
-| Kind | Type | Component Dimensions | Description |
-|------|------|----------------------|-------------|
-| Element Array DataPath | Any | Any | **Element** data to copy to **Feature** data |
-| Element Array DataPath | int32_t | (1) | Specifies to which **Feature** each **Element** belongs |
-| Cell Feature **Attribute Matrix** | Cell Feauture | N/A | The path to the cell feature **Attribute Matrix** |
+% Auto generated parameter table will be inserted here
+## Example Pipelines
-## Created Objects ##
-
-| Kind | Type | Component Dimensions | Description |
-|------|------|----------------------|-------------|
-| Feature Array DataPath | Any | Any | The copied array containing **Feature** data |
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/CreateGeometryFilter.md b/src/Plugins/ComplexCore/docs/CreateGeometryFilter.md
index 8bba3b7c1a..af4e1b30ae 100644
--- a/src/Plugins/ComplexCore/docs/CreateGeometryFilter.md
+++ b/src/Plugins/ComplexCore/docs/CreateGeometryFilter.md
@@ -1,17 +1,16 @@
-# Create Geometry
+# Create Geometry
-
-## Group (Subgroup) ##
+## Group (Subgroup)
DREAM3D Review (Geometry)
-## Description ##
+## Description
This **Filter** creates a **Geometry** object and the necessary **Element Attribute Matrices** on which to store **Attribute Arrays** and **Element Attribute Arrays** which define the geometry. The type of **Attribute Matrices** and **Attribute Arrays** created depends on the kind of **Geometry** being created:
| Type | Attribute Matrices | Attribute Arrays |
|------------------|--------------------|-------------|
-| Image | Cell |
+| Image | Cell |
| Rectilinear Grid | Cell | x, y, & z Bounds |
| Vertex | Vertex | Vertices |
| Edge | Vertex + Edge | Vertices + Edges |
@@ -20,47 +19,47 @@ This **Filter** creates a **Geometry** object and the necessary **Element Attrib
| Tetrahedral | Vertex + Cell | Vertices + Cells |
| Hexahedral | Vertex + Cell | Vertices + Cells |
-### Understanding Geometries ###
+### Understanding Geometries
This **Filter** requires the user to enter information that defines the topological information for the chosen **Geometry**. Choosing valid information for a given **Geometry** necessitates an understanding of how **DREAM.3D** stores and interprets this information. A general overview of the data model used in **DREAM.3D** may be found here. More specific information for **Geometry** objects is provided below.
-#### Grid Geometries ####
+#### Grid Geometries
-##### Image #####
+##### Image
-An **Image Geometry** is a _grid-like_ **Geometry**, and is the simplest and most widely used of the basic **Geometry** types. An **Image Geometry** is a _regular, rectilinear grid_; if the *dimenionality* of the image is _d_, then only _3*d_ numbers are needed to completely define the **Geometry**: three _d_-vectors for the _dimensions_, _origin_, and _resolution_. Dimensions define the extents of the grid, the resolution defines the spacing between grid planes for each orthogonal direction (constant along a given direction), and the origin defines the physical location of the *bottom left* grid point in _d_-dimensional space. The dimensions are stored as _unsigned 64-bit integers_, while the origin and resolution are stored as _32-bit floats_.
+An **Image Geometry** is a _grid-like_ **Geometry**, and is the simplest and most widely used of the basic **Geometry** types. An **Image Geometry** is a _regular, rectilinear grid_; if the _dimenionality_ of the image is _d_, then only _3*d_ numbers are needed to completely define the **Geometry**: three _d_-vectors for the _dimensions_, _origin_, and _resolution_. Dimensions define the extents of the grid, the resolution defines the spacing between grid planes for each orthogonal direction (constant along a given direction), and the origin defines the physical location of the _bottom left_ grid point in _d_-dimensional space. The dimensions are stored as _unsigned 64-bit integers_, while the origin and resolution are stored as _32-bit floats_.
-All **Image Geometries** in **DREAM.3D** are defined using 3-vectors (3D images). A 2D image is assumed when one of the dimension values is exactly 1; the 2D image is then considered a plane. Most **DREAM.3D** **Filters** will properly take account for the **Image** dimension if it matters (for example, the Find Feature Shapes **Filter** accounts for whether the **Image** is 2D or 3D when computing values such as *aspect ratios* or _axis Euler angles_). No dimension may be negative or equal to 0. The resolution and origin have no value restrictions. This **Filter** requires the user to enter the nine values for the dimenions, origin, and resolution.
+All **Image Geometries** in **DREAM.3D** are defined using 3-vectors (3D images). A 2D image is assumed when one of the dimension values is exactly 1; the 2D image is then considered a plane. Most **DREAM.3D** **Filters** will properly take account for the **Image** dimension if it matters (for example, the Find Feature Shapes **Filter** accounts for whether the **Image** is 2D or 3D when computing values such as _aspect ratios_ or _axis Euler angles_). No dimension may be negative or equal to 0. The resolution and origin have no value restrictions. This **Filter** requires the user to enter the nine values for the dimenions, origin, and resolution.
Since all **Image Geometries** are implicitly 3D (even when plane-like), the fundamental building-block of an image is a _voxel_, which is a 3D object; therefore, the basic **Element** type for an **Image Geometry** is **Cell**. **Attribute Arrays** associated with **Image Cells** are assumed to raster _x-y-z_, fastest to slowest.
-##### Rectilinear Grid #####
+##### Rectilinear Grid
-A **Rectilinear Grid Geometry** is a _grid-like_ **Geometry**. Similar to an **Image Geometry**, a **Rectilinear Grid Geometry** has grid extents (dimensions), but is allowed to have variable *resolution* along each orthogonal direction. The **Geometry** then requires a total of (xdim + 1) + (ydim + 1) + (zdim + 1) numbers to define the topology. The values are stored in three separate arrays termed the _x bounds_, _y bounds_, and _z bounds_. These bounds arrays store the spatial location of all the planes along a given orthogonal direction. The spacing for a given plane (equivalent to the resolution for an **Image Geometry**) is then the difference between two of these contiguous array values. An origin does not need to be defined for a **Rectilinear Grid Geometry**, since the grid's location in space is explicitly encoded in its bounds arrays. This **Filter** requires the user to select **Attribute Arrays** that define the three bounds arrays. These arrays must be _single component, 32-bit float_ arrays. Additionally, the values for each of the bounds arrays must be _strictly increasing_, which guarantees that computing the spacing for a given plane yields a postive value.
+A **Rectilinear Grid Geometry** is a _grid-like_ **Geometry**. Similar to an **Image Geometry**, a **Rectilinear Grid Geometry** has grid extents (dimensions), but is allowed to have variable _resolution_ along each orthogonal direction. The **Geometry** then requires a total of (xdim + 1) + (ydim + 1) + (zdim + 1) numbers to define the topology. The values are stored in three separate arrays termed the _x bounds_, _y bounds_, and _z bounds_. These bounds arrays store the spatial location of all the planes along a given orthogonal direction. The spacing for a given plane (equivalent to the resolution for an **Image Geometry**) is then the difference between two of these contiguous array values. An origin does not need to be defined for a **Rectilinear Grid Geometry**, since the grid's location in space is explicitly encoded in its bounds arrays. This **Filter** requires the user to select **Attribute Arrays** that define the three bounds arrays. These arrays must be _single component, 32-bit float_ arrays. Additionally, the values for each of the bounds arrays must be _strictly increasing_, which guarantees that computing the spacing for a given plane yields a postive value.
A **Rectilinear Grid Geometry** may be defined as 2D; the associated bounds array for the plane dimension is then exactly two. No bounds arrays may have less than two values. Since all **Rectilinear Grid Geometries** are implicitly 3D (even when plane-like), the fundamental building-block of an image is a _voxel_, which is a 3D object; therefore, the basic **Element** type for an **Image Geometry** is **Cell**. **Attribute Arrays** associated with **Rectilinear Grid Cells** are assumed to raster _x-y-z_, fastest to slowest.
-#### Unstructured and Mesh-Like Geometries ####
+#### Unstructured and Mesh-Like Geometries
-##### Vertex #####
+##### Vertex
-A **Vertex Geometry** is an *unstructured* **Geometry**. An unstructured **Geometry** requires explicit definition of point coordinates. Sometimes referred to as a _point cloud_, a **Vertex Geometry** is simply a collection of points. Defining this topology requires a total number of values equal to *d* times the total number of points, where *d* is the dimensionality of the point cloud; within **DREAM.3D**, *d* is always taken to be three. The point coordinates are stored as _32-bit floats_; no other range restrictions are enforced. This **Filter** requires the user to select an **Attribute Array** that defines these point coordinates. The array must have *three components* and consist of _32-bit floats_. The number of *tuples* in the array defines the number of vertices in the resulting **Vertex Geometry**.
+A **Vertex Geometry** is an _unstructured_ **Geometry**. An unstructured **Geometry** requires explicit definition of point coordinates. Sometimes referred to as a _point cloud_, a **Vertex Geometry** is simply a collection of points. Defining this topology requires a total number of values equal to _d_ times the total number of points, where _d_ is the dimensionality of the point cloud; within **DREAM.3D**, _d_ is always taken to be three. The point coordinates are stored as _32-bit floats_; no other range restrictions are enforced. This **Filter** requires the user to select an **Attribute Array** that defines these point coordinates. The array must have _three components_ and consist of _32-bit floats_. The number of _tuples_ in the array defines the number of vertices in the resulting **Vertex Geometry**.
The fundamental **Element** type of a **Vertex Geometry** is _vertices_. Data stored in a **Vertex Attribute Matrix** is ordered according to **Vertex** _Ids_. Therefore, the nth tuple in the supplied **Vertex** list corresponds to the data stored in the nth column of the **Vertex Attribute Matrix**. By convetion, **Vertex** Ids are _zero indexed_.
-##### Mesh-Like Geometries #####
+##### Mesh-Like Geometries
The following **Geometries** are considered _mesh-like_, and all share similar features concerning their storage and interpretation. A mesh-like **Geometry** is an unstructured **Geometry** that additionally requires explicit definition of the connectivity of its **Elements** and its **Vertices**. The **Element** type defines the kind of **Geometry** and the number of **Vertices** needed to define that **Element**:
| Name | Element Type | Number of Vertices Per Element |
|------------------|--------------------|--------------------|
-| Edge | line | 2 |
+| Edge | line | 2 |
| Triangle | triangle | 3 |
| Quadrilateral | quadrilateral | 4 |
| Tetrahedral | tetrahedron | 4 |
| Hexahedral | hexahedron | 8 |
-The storage scheme adopted by **DREAM.3D** requires at least two arrays to define mesh-like **Geometries**: a list of **Vertices** (i.e., the vertex coordinates) and the **Element** connectivities (i.e., which vertices belong to a given **Element**). To maintain simplicity, flexibility, and small memory overhead, **DREAM.3D** uses the concept of _shared vertex lists_. In this paradigm, the vertex coordinates are stored only once per *unique* vertex. Consider a **Quadrilateral Geometry** that consists of just two squares that share one side. In this example, there are exactly *six* unique vertices. The **Attribute Array** that defines the coordinates of these **Vertices** would then have six _tuples_, with three values at each tuple (the x, y, and z positions of that **Vertex**). Writing each tuple on one line, the array could look like this:
+The storage scheme adopted by **DREAM.3D** requires at least two arrays to define mesh-like **Geometries**: a list of **Vertices** (i.e., the vertex coordinates) and the **Element** connectivities (i.e., which vertices belong to a given **Element**). To maintain simplicity, flexibility, and small memory overhead, **DREAM.3D** uses the concept of _shared vertex lists_. In this paradigm, the vertex coordinates are stored only once per _unique_ vertex. Consider a **Quadrilateral Geometry** that consists of just two squares that share one side. In this example, there are exactly _six_ unique vertices. The **Attribute Array** that defines the coordinates of these **Vertices** would then have six _tuples_, with three values at each tuple (the x, y, and z positions of that **Vertex**). Writing each tuple on one line, the array could look like this:
0.0 0.0 0.0 // Vertex Id 0
1.0 0.0 0.0 // Vertex Id 1
@@ -69,42 +68,42 @@ The storage scheme adopted by **DREAM.3D** requires at least two arrays to defin
2.0 0.0 0.0 // Vertex Id 4
2.0 1.0 0.0 // Vertex Id 5
-**Element** connectivities are stored in **Attribute Arrays** that have a number of tuples equal to the total number of **Elements**, with a number of components at each tuple equal to the number of vertices per element. In this example, a quadrilateral list would have two tuples, with four values stored at each tuple (the four vertex Ids that define that quadrilateral). When defining **Elements**, the order in which the **Vertex** Ids are listed, called the _winding_, is important, since this ordering defines the direction of the normal. By convention, the *right hand rule* used. Thus, given the above vertex positions, the following list of **Vertex** Ids defines two quadrilaterals whose normals point along the positive z direction:
+**Element** connectivities are stored in **Attribute Arrays** that have a number of tuples equal to the total number of **Elements**, with a number of components at each tuple equal to the number of vertices per element. In this example, a quadrilateral list would have two tuples, with four values stored at each tuple (the four vertex Ids that define that quadrilateral). When defining **Elements**, the order in which the **Vertex** Ids are listed, called the _winding_, is important, since this ordering defines the direction of the normal. By convention, the _right hand rule_ used. Thus, given the above vertex positions, the following list of **Vertex** Ids defines two quadrilaterals whose normals point along the positive z direction:
0 1 3 2 // Quad Id 0
1 4 5 3 // Quad Id 1
-
+
Creating any mesh-like **Geometry** requires the user to supply two arrays: one that defines the vertex coordinates (the _shared vertex list_), which is a three component array of floats; and one that defines the **Element** connectivities, which is a n-component array (where n is the number of vertices per element) of _signed 64-bit integers_. Note that any **Element** Id values (**Vertex** or otherwise) are _zero indexed_.
-The shared list schema for mesh storage has the benefit of being space efficient, time efficient when iterating in sequence over vertices or elements, and capable of storing *nonmanifold* meshes. An example of a nonmanifold mesh is a **Triangle Geometry** that has more than two triangles sharing the same edge. This specific example of nonmanifold meshes occurs frequently in **DREAM.3D** surface meshes of polycrystals, where many nonmanifold entities may exist (i.e., triple lines and quad points). A significant downside of shared lists is that computing adjacency information, such as the neighbors of a given element or the elements that share a vertex, requires iterating over the entire **Geometry**; other mesh data structures avoid this limitation. Additionally, since the lists are stored as **Attribute Arrays**, which hold information contiguously in memory, adding or removing vertices or elements is tedious and potentially slow.
+The shared list schema for mesh storage has the benefit of being space efficient, time efficient when iterating in sequence over vertices or elements, and capable of storing _nonmanifold_ meshes. An example of a nonmanifold mesh is a **Triangle Geometry** that has more than two triangles sharing the same edge. This specific example of nonmanifold meshes occurs frequently in **DREAM.3D** surface meshes of polycrystals, where many nonmanifold entities may exist (i.e., triple lines and quad points). A significant downside of shared lists is that computing adjacency information, such as the neighbors of a given element or the elements that share a vertex, requires iterating over the entire **Geometry**; other mesh data structures avoid this limitation. Additionally, since the lists are stored as **Attribute Arrays**, which hold information contiguously in memory, adding or removing vertices or elements is tedious and potentially slow.
Note that although the default interpretation of lists that define mesh-like **Geometries** is shared, no undefined behavior should be observed if the information is not stored shared (i.e., if the same **Vertex** is stored more than once with a different Id). Additionally, not all **Vertices** are required to be associated with an **Element**. The primary requirement is that the largest **Vertex** Ids listed in the **Element** list must not be larger than the total number of **Vertices**.
-
-##### Edge #####
+
+##### Edge
An **Edge Geometry** is the simplest _mesh-like_ **Geometry**, consisting of a collection of edges connecting two vertices. Creating an **Edge Geometry** requires supplying a shared **Vertex** list and an **Edge** list.
-##### Triangle #####
+##### Triangle
A **Triangle Geometry** is a _mesh-like_ **Geometry**, consisting of a collection of triangles connecting three vertices; it is a type of _surface mesh_. Creating a **Triangle Geometry** requires supplying a shared **Vertex** list and a **Triangle** list.
-##### Quadrilateral #####
+##### Quadrilateral
A **Quadrilateral Geometry** is a _mesh-like_ **Geometry**, consisting of a collection of quadrilaterals connecting four vertices; it is a type of _surface mesh_. Creating a **Quadrilateral Geometry** requires supplying a shared **Vertex** list and a **Quadrilateral** list.
-##### Tetrahedral #####
+##### Tetrahedral
A **Tetrahedral Geometry** is a _mesh-like_ **Geometry**, consisting of a collection of tetrahedra connecting four vertices; it is a type of _volume mesh_. Creating a **Tetrahedral Geometry** requires supplying a shared **Vertex** list and a **Tetrahedral** list. The winding that define tetrahedra require one additional convention to complement the right hand rule. By convention, the first three vertices define the tetrahedra _base_; the winding of these vertices by the right hand rule defines a normal that points _towards the fourth vertex_. This convention is useful since applying it consistently allows for the volume of the tetrahedra to be _signed_, which is important for determining if a tetrahedron is "inverted".
-##### Hexahedral #####
+##### Hexahedral
A **Hexahedral Geometry** is a _mesh-like_ **Geometry**, consisting of a collection of hexahedra connecting eight vertices; it is a type of _volume mesh_. Creating a **Hexahedral Geometry** requires supplying a shared **Vertex** list and a **Hexahedral** list.
-### Defining Geometries with Attribute Arrays ###
+### Defining Geometries with Attribute Arrays
- For **Geometries** that require the selection of **Attribute Arrays** (all **Geometries** except **Image**), the arrays will be *copied* to create the new **Geometry**. Therefore, any operations on the original array will not affect the topology of the **Geometry**, and any geometric operations will not affect the original array. This behavior can be adjusted in the filter by using the *Array Handling* boolean. ###
+ For **Geometries** that require the selection of **Attribute Arrays** (all **Geometries** except **Image**), the arrays will be _copied_ to create the new **Geometry**. Therefore, any operations on the original array will not affect the topology of the **Geometry**, and any geometric operations will not affect the original array. This behavior can be adjusted in the filter by using the _Array Handling_ boolean.
-This **Filter** will validate that the arrays selected to define a **Geometry** "make sense", given the above information for how **Geometries** are stored in **DREAM.3D** (for example, no dimension for an **Image** may be less than or equal to zero, no bounds arrays for a **Rectilinear Grid** may have less than two values, and no **Vertex** Ids stored in a shared **Element** list may be larger than the total number of **Vertices** in the shared **Vertex** list). The checks that require accessing the actual array values (as opposed to just descriptive information) will be performed at run time. By default, these checks will only produce warnings, allowing the **Pipeline** to continue; the user may opt to change these warnings to errors by selecting the *Treat Geometry Warnings as Errors* option.
+This **Filter** will validate that the arrays selected to define a **Geometry** "make sense", given the above information for how **Geometries** are stored in **DREAM.3D** (for example, no dimension for an **Image** may be less than or equal to zero, no bounds arrays for a **Rectilinear Grid** may have less than two values, and no **Vertex** Ids stored in a shared **Element** list may be larger than the total number of **Vertices** in the shared **Vertex** list). The checks that require accessing the actual array values (as opposed to just descriptive information) will be performed at run time. By default, these checks will only produce warnings, allowing the **Pipeline** to continue; the user may opt to change these warnings to errors by selecting the _Treat Geometry Warnings as Errors_ option.
Generally, arrays used by this **Filter** to create **Geometries** must be supplied by the user. One method to import geometric information into **DREAM.3D** is to read the information in from a text file using the Import ASCII Data **Filter**. For example, imagine having an external simulation code that creates a tetrahedral volume mesh with two associated field values, one stored on the mesh vertices and one stored on the mesh tetrahedra. It is possible to import this mesh and corresponding information into **DREAM.3D** for further analysis. The user must supply at least two files: one that contains the vertex information and one that contains the tetrahedra information. The vertex file would contain, on each line, the three coordinates of the vertex and the value of the field array on that vertex. It may, for example, look like this:
@@ -115,7 +114,7 @@ Generally, arrays used by this **Filter** to create **Geometries** must be suppl
-12.3 3.456 2.323 567.4
3.450 9.782 6.567 120.2
.....
-
+
In this above example, the vertex information begins on line 4; thus, line 4 defines **Vertex** Id 0, line 5 defines **Vertex** Id 1, etc. Similarly, a file containing information about tetrahedra is needed:
# Some header information
@@ -126,51 +125,15 @@ In this above example, the vertex information begins on line 4; thus, line 4 def
6 9 7 8 16.78
.....
- Again, the real information begins on line 4, which defines the connectivity for **Tetrahedra** Id 0. These Id values refer to the **Vertex** Ids from the first file (for example, a **Vertex** Id of 0 corresponds to the information on line 4 of the first file). Remember to consider the *right hand rule* when dealing with mesh-like **Geometries**, as this will affect the **Vertex** ordering!
-
+ Again, the real information begins on line 4, which defines the connectivity for **Tetrahedra** Id 0. These Id values refer to the **Vertex** Ids from the first file (for example, a **Vertex** Id of 0 corresponds to the information on line 4 of the first file). Remember to consider the _right hand rule_ when dealing with mesh-like **Geometries**, as this will affect the **Vertex** ordering!
+
Assuming it is possible to get the mesh into files similar to the above ones, it is straightforward to import the information into **DREAM.3D**. First, create an emtpy Data Container. Then, run the Import ASCII Data **Filter** for the vertex file. In the above example, line 3 could be used as headers to define the array names (remember that **Vertex** positions must be of type _float_!). Allow the reader wizard to create an **Attribute Matrix** in which to store the arrays. Repeat the process with another Import ASCII Data **Filter** to read the tetrahedra information (remember in this case that Id values must be of type _int64\_t_!). At this point, there will be two **Attribute Matrices** in the **Data Container**, one with 4 arrays (the **Vertex** information) and one with 5 arrays (the **Tetrahedra** information). The Create Geometry **Filter** wants the **Vertex** list as a three component array and the **Tetrahedra** list as a four component array. To combine the individual arrays into ones of the proper component dimension, run the Combine Attribute Arrays **Filter**. At this point, the Create Geometry **Filter** may be used to create a **Tetrahedral Geometry** using the combined arrays. After this **Filter**, the Move Data **Filter** may be used to move the arrays that represent the values stored on the **Vertices** and **Tetrahedra** into the created **Vertex** and **Cell Attribute Matrices**.
-
- When creating **Geometries**, remember to consider all the various rules for how a **Geometry** is stored and interpreted. In particular, remeber that **Element** Ids are always zero indexed, mesh-like **Geometries** obey the *right hand rule* for windings and normal directions, and **Element** lists are by default considered _shared_. Note that although the storage scheme used by **DREAM.3D** (shared lists) is highly generic, some **Filters** may assume that the **Geometry** is reasonably _well formed_.
-
-## Parameters ##
-| Geometry Type | Value |
-| --|--|
-| ImageGeometry | 0 |
-| RectGridGeometry | 1 |
-| VertexGeometry | 2 |
-| EdgeGeometry | 3 |
-| TriangleGeometry | 4 |
-| QuadGeometry | 5 |
-| TetGeometry | 6 |
-| HexGeometry | 7 |
-
-| Name | Type | Description |
-|------|------|-------------|
-| Geometry Type | Enumeration | The type of **Geometry** to create |
-| Treat Geometry Warnings as Errors | bool | Whether run time warnings for **Geometries** should be treated as errors |
-| Array Handling | bool | Determines if the arrays that make up the geometry primitives should be **Moved** or **Copied** to the created Geometry object. |
-| Dimensions | size_t (3x) | The number of cells in each of the X, Y, Z directions, if *Image* is chosen |
-| Origin | float (3x) | The origin of each of the axes in X, Y, Z order, if *Image* is chosen |
-| Resolution | float (3x) | The length scale of each voxel/pixel, if *Image* is chosen |
-
-## Required Geometry ###
-
-None
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Geometry Path** | None | N/A | N/A | **Data Path** in which to place the created **Geometry** |
-| Various **Attribute Arrays** | None | float/int64_t | 1/2/3/4 | Various **Attribute Arrays** used to define the **Geometry** topology; see the above documentation for a detailed discussion of what kinds of information are needed for each **Geometry** |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| Various **Attribute Matrices** | None | Vertex/Edge/Face/Cell | N/A | Various **Attribute Matrices** used to store information for the new **Geometry**; see the above documentation for a detailed discussion of what kinds of **Attribute Matrices** are created for each **Geometry** |
-
-## Example Pipelines ##
+
+ When creating **Geometries**, remember to consider all the various rules for how a **Geometry** is stored and interpreted. In particular, remeber that **Element** Ids are always zero indexed, mesh-like **Geometries** obey the _right hand rule_ for windings and normal directions, and **Element** lists are by default considered _shared_. Note that although the storage scheme used by **DREAM.3D** (shared lists) is highly generic, some **Filters** may assume that the **Geometry** is reasonably _well formed_.
+
+% Auto generated parameter table will be inserted here
+
+## Example Pipelines
+ CreateVertexGeometry
+ CreateTriangleGeometry
@@ -178,12 +141,10 @@ None
+ CreateQuadGeometry
+ CreateRectilinearGrid
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/CreateImageGeometry.md b/src/Plugins/ComplexCore/docs/CreateImageGeometry.md
index 59912fee62..d591fe8594 100644
--- a/src/Plugins/ComplexCore/docs/CreateImageGeometry.md
+++ b/src/Plugins/ComplexCore/docs/CreateImageGeometry.md
@@ -1,54 +1,27 @@
# Create Geometry (Image)
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Core (Generation)
-
-## Description ##
+## Description
This **Filter** creates an **Image Geometry** specifically for the representation of a 3D rectilinear grid of voxels (3D) or pixels
(2D). Each axis can have its starting point (origin), resolution, and length defined for the **Geometry**. The **Data Container** in which to place the **Image Geometry** must be specified.
-### Example Usage ###
+### Example Usage
If you are reading in raw binary data that represents data on a rectilinear grid, the user will need to run this
filter first to create a description of the **Geometry**.
-## Parameters ##
-
-| Name | Type | Description |
-|------------------|------|-------------|
-| Dimensions | size_t (3x) | The number of cells in each of the X, Y, Z directions |
-| Origin | float (3x) | The origin of each of the axes in X, Y, Z order |
-| Resolution | float (3x) | The length scale of each voxel/pixel |
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Data Container** | None | N/A | N/A | **Data Container** in which to place the created **Image Geometry** |
+% Auto generated parameter table will be inserted here
+## Example Pipelines
-## Created Objects ##
-
-Not Applicable
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/CropImageGeometry.md b/src/Plugins/ComplexCore/docs/CropImageGeometry.md
index 3001f307dc..160cee98a9 100644
--- a/src/Plugins/ComplexCore/docs/CropImageGeometry.md
+++ b/src/Plugins/ComplexCore/docs/CropImageGeometry.md
@@ -1,6 +1,6 @@
# Crop Geometry (Image)
-## Description ##
+## Description
This **Filter** allows the user to crop an **Image Geometry** of interest. The input parameters are in units of **Cells**. For example, if a **Image Geometry** was 100x100x100 **Cells** and each **Cell** was 0.25 x 0.25 x 0.25 units of resolution, then if the user wanted to crop the last 5 microns in the X direction, then the user would enter the following:
@@ -19,32 +19,14 @@ The user has the option to save the cropped volume as a new **Data Container** o
Normally this **Filter** will leave the origin of the volume set at (0, 0, 0), which means output files like the Xdmf file will have the same (0, 0, 0) origin. When viewing both the original larger volume and the new cropped volume simultaneously the cropped volume and the original volume will have the same origin which makes the cropped volume look like it was shifted in space. In order to keep the cropped volume at the same absolute position in space the user should turn **ON** the *Update Origin* check box.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------|------|-------------|
-| Image Geom | DataPath | DataPath to the target ImageGeom |
-| New Image Geom | DataPath | Created ImageGeom |
-| Min Voxels | std::vector | Lower bounds of the volume to crop out |
-| Max Voxels | std::vector | Upper bounds of the volume to crop out |
-| Renumber Features | bool | Whether the **Features** should be renumbered |
-| Features IDs | DataPath | DataPath to the target Feature IDs array |
-| Voxel Arrays | std::vector | DataArrays to crop |
-| New Cell Features Group Name | std::string | Specifies the name of the DataGroup containing cropped DataArrays |
-| Remove Original Geometry | bool | Whether the current **Geometry** should be removed after cropping |
+## Example Pipelines
-## Required Geometry ##
-
-Image
-
-## Example Pipelines ##
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/CropVertexGeometry.md b/src/Plugins/ComplexCore/docs/CropVertexGeometry.md
index 002c454dc5..a614f7c4d2 100644
--- a/src/Plugins/ComplexCore/docs/CropVertexGeometry.md
+++ b/src/Plugins/ComplexCore/docs/CropVertexGeometry.md
@@ -1,48 +1,19 @@
# Crop Geometry (Vertex)
-
-## Group (Subgroup) ##
+## Group (Subgroup)
DREAM3D Review (Cropping/Cutting)
-## Description ##
+## Description
This **Filter** crops a **Vertex Geometry** by the given bounding box. Unlike the cropping of an Image, it is unknown until run time how the **Geometry** will be changed by the cropping operation. Therefore, this **Filter** requires that a new **Data Container** be created to contain the cropped **Vertex Geometry**. This new **Data Container** will contain copies of any **Feature** or **Ensemble** **Attribute Matrices** from the original **Data Container**. Additionally, all **Vertex** data will be copied, with tuples *removed* for any **Vertices** outside the bounding box. The user must supply a name for the cropped **Data Container**, but all other copied objects (**Attribute Matrices** and **Data Arrays**) will retain the same names as the original source.
-_Note:_ Since it cannot be known before run time how many **Vertices** will be removed during cropping, the new **Vertex Geometry** and all associated **Vertex** data to be copied will be initialized to have size 0. Any **Feature** or **Ensemble** information will retain the same dimensions and size.
-
-## Parameters ##
-
-| Name | Type | Description |
-|------|------|-------------|
-| Cropped Vertex Geometry | DataPath | Created VertexGeom Path |
-| Vertex Data Name | String | Name of Vertex DataObject |
-| Minimum Vertex Position | vec3 | the minimum x,y,z position |
-| Maximum Vertex Position | vec3 | the maximum x,y,z position |
-| Vertex Data Arrays to Crop | DataPath(s) | The path to all vertex data arrays to crop |
-
-## Required Geometry ###
-
-Vertex
-
-## Required Objects ##
-
-None
+*Note:* Since it cannot be known before run time how many **Vertices** will be removed during cropping, the new **Vertex Geometry** and all associated **Vertex** data to be copied will be initialized to have size 0. Any **Feature** or **Ensemble** information will retain the same dimensions and size.
-## Created Objects ##
+% Auto generated parameter table will be inserted here
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| Cropped **Data Group** | CroppedDataContainer | N/A | N/A | **Data Container** holding the cropped **Vertex Geometry** and any copied **Attribute Matrices** and **Attribute Arrays** |
+## Example Pipelines
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-
-
-
-
diff --git a/src/Plugins/ComplexCore/docs/DeleteData.md b/src/Plugins/ComplexCore/docs/DeleteData.md
index 0452440c5d..a1044ccbed 100644
--- a/src/Plugins/ComplexCore/docs/DeleteData.md
+++ b/src/Plugins/ComplexCore/docs/DeleteData.md
@@ -1,42 +1,21 @@
-# Delete Data
+# Delete Data
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Core (Memory/Management)
-## Description ##
+## Description
This **Filter** allows the user to remove specified objects from the existing structure. This can be helpful if the user has operations that need as much memory as possible and there are extra objects that are not needed residing in memory. Alternatively, this **Filter** allows the user to remove objects that may share a name with another object further in the **Pipeline** that another **Filter** tries to create, since DREAM.3D generally does not allows objects at the same hierarchy to share the same name.
-## Parameters ##
-
-None
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| Any | None | Any | Any | Objects to delete |
+% Auto generated parameter table will be inserted here
-## Created Objects ##
+## Example Pipelines
-None
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/ErodeDilateBadDataFilter.md b/src/Plugins/ComplexCore/docs/ErodeDilateBadDataFilter.md
index 6c68ced0a0..4e84a98109 100644
--- a/src/Plugins/ComplexCore/docs/ErodeDilateBadDataFilter.md
+++ b/src/Plugins/ComplexCore/docs/ErodeDilateBadDataFilter.md
@@ -11,23 +11,23 @@ been marked as a *bad* **Cell**.
### Dilation
-If the **bad** data is _dilated_, the Filter grows the *bad* data by one **Cell** in
+If the **bad** data is *dilated*, the Filter grows the *bad* data by one **Cell** in
an iterative sequence for a user defined number of iterations. During the *dilate* process the *Feature Id* of any
Cell neighboring a *bad* **Cell** will be changed to *0*.
-| Before Dilation | After Dilation |
+| Before Dilation | After Dilation |
|--------------------------------------|--------------------------------------|
| ![](Images/ErodeDilateBadData_1.png) | ![](Images/ErodeDilateBadData_2.png) |
### Erosion
-If the *bad* data is _eroded_, the Filter shrinks the
+If the *bad* data is *eroded*, the Filter shrinks the
bad data by one **Cell** in an iterative sequence for a user defined number of iterations. During the *erode* process
the *Feature Id* of the *bad* **Cell** is changed from *0* to the *Feature Id* of the majority of its neighbors. If
-there is a tie between two _Feature Ids_, then one of the *Feature Ids*, chosen randomly, will be assigned to the *bad*
+there is a tie between two *Feature Ids*, then one of the *Feature Ids*, chosen randomly, will be assigned to the *bad*
**Cell**.
-| Before Erosion | After Erosion |
+| Before Erosion | After Erosion |
|--------------------------------------|--------------------------------------|
| ![](Images/ErodeDilateBadData_1.png) | ![](Images/ErodeDilateBadData_3.png) |
@@ -41,49 +41,24 @@ Goals a user might be trying to accomplish with this Filter include:
up as *bad* data) are generally smaller in the scans than in the specimen, because the beam, when it is just inside
the pore, still can pick up signal from the material just beneath the pore.
-Running the _erode-dilate_ operations in pairs can often change the size of some objects without affecting others. For
+Running the *erode-dilate* operations in pairs can often change the size of some objects without affecting others. For
example, if there were a number of big pores and a number of single *bad* **Cells**, running a single *erode* operation
-would remove the single **Cells** and reduce the pores by one **Cell**. If this is followed immediately by a _dilate_
+would remove the single **Cells** and reduce the pores by one **Cell**. If this is followed immediately by a *dilate*
operation, then the pores would grow by one **Cell** and return to near their original size, while the single **Cells**
would remain removed and not "grow back".
-## Parameters
-
-| Name | Type | Description |
-|----------------------|-------------|------------------------------------------------------|
-| Operation | Enumeration | Whether to erode (0) or dilate (1) |
-| Number of Iterations | int32_t | The number of iterations to use for erosion/dilation |
-| X Direction | bool | Whether to erode/dilate in the X direction |
-| Y Direction | bool | Whether to erode/dilate in the Y direction |
-| Z Direction | bool | Whether to erode/dilate in the Z direction |
-
-## Required Geometry
-
-Image
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|--------------------------|----------------|----------|----------------------|------------------------------------------------------------------|
-| **Image Geometry** | Image Geometry | DataPath | N/A | The path to the Image Geometry where the feature Ids are stored. |
-| **Cell Attribute Array** | FeatureIds | int32 | (1) | Specifies to which **Feature** each **Cell** belongs |
-
-## Created Objects
-
-None
+% Auto generated parameter table will be inserted here
## Example Pipelines
-+ (08) SmallIN100 Full Reconstruction
-+ (07) SmallIN100 Final Processing
-+ 04_Steiner Compact
+- (08) SmallIN100 Full Reconstruction
+- (07) SmallIN100 Final Processing
+- 04_Steiner Compact
## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/ErodeDilateCoordinationNumberFilter.md b/src/Plugins/ComplexCore/docs/ErodeDilateCoordinationNumberFilter.md
index 39adbbdedd..ccdbe033b9 100644
--- a/src/Plugins/ComplexCore/docs/ErodeDilateCoordinationNumberFilter.md
+++ b/src/Plugins/ComplexCore/docs/ErodeDilateCoordinationNumberFilter.md
@@ -16,35 +16,14 @@ are *coarsened* to fill the removed **Cells**.
By default, the **Filter** will only perform a single iteration and will not concern itself with the possibility that
after one iteration, **Cells** that were acceptable may become unacceptable by the original *coordination number*
-criteria due to the small changes to the structure during the *coarsening*. The user can opt to enable the _Loop Until
-Gone_ parameter, which will continue to run until no **Cells** fail the original criteria.
+criteria due to the small changes to the structure during the *coarsening*. The user can opt to enable the *Loop Until
+Gone* parameter, which will continue to run until no **Cells** fail the original criteria.
-
-| Before Filter | After Filter |
+| Before Filter | After Filter |
|--------------------------------------|--------------------------------------|
| ![](Images/ErodeDilateCoordinationNumber_Before.png) | ![](Images/ErodeDilateCoordinationNumber_After.png) |
-## Parameters
-
-| Name | Type | Description |
-|---------------------|---------|------------------------------------------------------------------------------------------------------------------------------------|
-| Coordination Number | int32_t | Number of neighboring **Cells** that can be of opposite classification before a **Cell** will be removed |
-| Loop Until Gone | bool | Whether to run a single iteration or iterate until no *bad* **Cells** have more than the above number of *good* neighbor **Cells** |
-
-## Required Geometry
-
-Image
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|--------------------------|----------------|----------|----------------------|------------------------------------------------------------------|
-| **Image Geometry** | Image Geometry | DataPath | N/A | The path to the Image Geometry where the feature Ids are stored. |
-| **Cell Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Cell** belongs |
-
-## Created Objects
-
-None
+% Auto generated parameter table will be inserted here
## Example Pipelines
@@ -52,8 +31,6 @@ None
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/ErodeDilateMaskFilter.md b/src/Plugins/ComplexCore/docs/ErodeDilateMaskFilter.md
index 06378541db..aa6b31aeb8 100644
--- a/src/Plugins/ComplexCore/docs/ErodeDilateMaskFilter.md
+++ b/src/Plugins/ComplexCore/docs/ErodeDilateMaskFilter.md
@@ -6,50 +6,26 @@ Processing (Cleanup)
## Description
-If the mask is _dilated_, the **Filter** grows the *true* regions by one **Cell** in an iterative sequence for a user
-defined number of iterations. During the *dilate* process, the classification of any **Cell** neighboring a *false* *
-*Cell** will be changed to *true*. If the mask is _eroded_, the **Filter** shrinks the *true* regions by one **Cell** in
-an iterative sequence for a user defined number of iterations. During the *erode* process, the classification of the
-*false* **Cells** is changed to *true* if one of its neighbors is *true*. The **Filter** also offers the option(s) to
+If the mask is _dilated_, the **Filter** grows the _true_ regions by one **Cell** in an iterative sequence for a user
+defined number of iterations. During the _dilate_ process, the classification of any **Cell** neighboring a _false_ *
+*Cell** will be changed to _true_. If the mask is _eroded_, the **Filter** shrinks the _true_ regions by one **Cell** in
+an iterative sequence for a user defined number of iterations. During the _erode_ process, the classification of the
+*false* **Cells** is changed to _true_ if one of its neighbors is _true_. The **Filter** also offers the option(s) to
turn on/off the erosion or dilation in specific directions (X, Y or Z).
-This filter will ONLY change the *Mask* data array and not any of the other data arrays in the same attribute matrix.
-
+This filter will ONLY change the _Mask_ data array and not any of the other data arrays in the same attribute matrix.
The example images below were generated **AFTER** the execution of the filter and essentially any black pixel is where the **Mask** was false and any other color is where the **Mask** is true. (The colors are the typical IPF Colors using a <001> reference direction)
-| Before Dilatation | After Dilation |
+| Before Dilatation | After Dilation |
|--------------------------------------|--------------------------------------|
| ![](Images/ErodeDilateMask_Before.png) | ![](Images/ErodeDilateMask_Dilate.png) |
-
-| Before Erosion | After Erosion |
+| Before Erosion | After Erosion |
|--------------------------------------|--------------------------------------|
| ![](Images/ErodeDilateMask_Before.png) | ![](Images/ErodeDilateMask_Erode.png) |
-## Parameters
-
-| Name | Type | Description |
-|----------------------|-------------|------------------------------------------------------|
-| Operation | Enumeration | Whether to dilate or erode |
-| Number of Iterations | int32_t | The number of iterations to use for erosion/dilation |
-| X Direction | bool | Whether to erode/dilate in the X direction |
-| Y Direction | bool | Whether to erode/dilate in the Y direction |
-| Z Direction | bool | Whether to erode/dilate in the Z direction |
-
-## Required Geometry
-
-Image
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensionss | Description |
-|--------------------------|--------------|------|-----------------------|-----------------------------------------------------------|
-| **Cell Attribute Array** | Mask | bool | (1) | Used to define whether the **Cells** are part of the mask |
-
-## Created Objects
-
-None
+% Auto generated parameter table will be inserted here
## Example Pipelines
@@ -57,8 +33,6 @@ None
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/ExecuteProcessFilter.md b/src/Plugins/ComplexCore/docs/ExecuteProcessFilter.md
index 3a059b9b69..e8018b0952 100644
--- a/src/Plugins/ComplexCore/docs/ExecuteProcessFilter.md
+++ b/src/Plugins/ComplexCore/docs/ExecuteProcessFilter.md
@@ -1,11 +1,10 @@
# Execute Process
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Core (Misc)
-## Description ##
+## Description
This filter allows the user to execute any application, program, shell script or any other executable program on the computer system. Any output can be found in the user specified log file.
@@ -19,44 +18,20 @@ Simple command with arguments (for Windows users)
> C:/Applications/DREAM3D-6.6.332/nxrunner.exe C:/Applications/DREAM3D/DREAM3D-6.6.332/Data/MyPipeline.json
-For a command with spaces in the path
+For a command with spaces in the path
> "C:/Program Files/DREAM3D-6.6.332/nxrunner.exe" "C:/Program Files/DREAM3D-6.6.332/PrebuiltPipelines/Workshop/EBSD Reconstruction/(01) SmallIN100 Archive.json"
-## Parameters ##
-
-| Name | Type | Description |
-|------------------|------|-------------|
-| Command Line | String| The complete command to execute. |
-| Should Block | Bool | Whether to block the pipeline process while the command executes or not. |
-| Timeout | Int32 | The amount of time (in ms) to wait for the command to start/finish when blocking is selected. |
-| Output Log File | File Path | The log file where the output from the process will be stored. |
-
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-None
+% Auto generated parameter table will be inserted here
-## Created Objects ##
-
-None
-
-
-## Example Pipelines ##
+## Example Pipelines
ExecuteProcess
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/ExportDREAM3DFilter.md b/src/Plugins/ComplexCore/docs/ExportDREAM3DFilter.md
index 040f2c2347..7df7886ab3 100644
--- a/src/Plugins/ComplexCore/docs/ExportDREAM3DFilter.md
+++ b/src/Plugins/ComplexCore/docs/ExportDREAM3DFilter.md
@@ -1,39 +1,19 @@
# ExportDREAM3DFilter
-## Description ##
+## Description
This **Filter** dumps the data structure to an hdf5 file with the .dream3d extension.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------|------|-------------|
-| Export File Path | Filesystem Path | The file path the DataStructure should be written to as an HDF5 file. |
-| Write Xdmf File | bool | Whether or not to write the data out an xdmf file |
-
-
-## Required Geometry ###
-
-None
-
-## Required Objects ##
-
-None
-
-## Created Objects ##
-
-None
-
-## Example Pipelines ##
+## Example Pipelines
ALL
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/ExtractComponentAsArrayFilter.md b/src/Plugins/ComplexCore/docs/ExtractComponentAsArrayFilter.md
index b7e2192da3..ef4932af77 100644
--- a/src/Plugins/ComplexCore/docs/ExtractComponentAsArrayFilter.md
+++ b/src/Plugins/ComplexCore/docs/ExtractComponentAsArrayFilter.md
@@ -1,53 +1,25 @@
# Extract Component as Attribute Array
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Core (Memory/Management)
-## Description ##
+## Description
This **Filter** will do one of the following to one component of a multicomponent **Attribute Array**:
+
- Remove 1 component from multicomponent **Attribute Array** completely [This is done implicitly so long as **Move Extracted Components To New Array** is false]
- Extract 1 component from multicomponent **Attribute Array** and store it in a new **DataArray** without removing from original
- Extract 1 component from multicomponent **Attribute Array** and store it in a new **DataArray** and remove that component from the original
-## Parameters ##
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Move Extracted Components To New Array | bool | The bool that determines if extracted components will be stored in new array |
-| Remove Extracted Components from Old Array | bool | The bool that determines if extracted components will be deleted from original array |
-| Component Number to Extract | int32_t | The index of which component to extract |
-
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| Any **Attribute Array** | None | Any | >1 | Multicomponent **Attribute Array** to use as input |
+% Auto generated parameter table will be inserted here
+## Example Pipelines
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| Any **Attribute Array** | None | Any | (1) | Scalar **Attribute Array** name |
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/ExtractInternalSurfacesFromTriangleGeometry.md b/src/Plugins/ComplexCore/docs/ExtractInternalSurfacesFromTriangleGeometry.md
index 150daad296..f8a5d08a19 100644
--- a/src/Plugins/ComplexCore/docs/ExtractInternalSurfacesFromTriangleGeometry.md
+++ b/src/Plugins/ComplexCore/docs/ExtractInternalSurfacesFromTriangleGeometry.md
@@ -1,55 +1,30 @@
# Extract Internal Surfaces from Triangle Geometry
-## Group (Subgroup) ##
+## Group (Subgroup)
Geometry
-## Description ##
+## Description
This **Filter** extracts any **Triangles** from the supplied **Triangle Geometry** that contain any *internal nodes*, then uses these extracted **Triangles** to create a new **Data Container** with the reduced **Triangle Geometry**. This operation is the same as removing all **Triangles** that only lie of the outer surface of the supplied **Triangle Geometry**. The user must supply a **Vertex Attribute Array** that defines the type for each node of the **Triangle Geometry**. Node types may take the following values:
| Id Value | Node Type |
|----------|-----------|
-| 2 | Normal **Vertex** |
+| 2 | Normal **Vertex |
| 3 | Triple Line |
| 4 | Quadruple Point |
| 12 | Normal **Vertex** on the outer surface |
| 13 | Triple Line on the outer surface |
| 14 | Quadruple Point on the outer surface |
-This **Filter** has the effect of removing any **Triangles** that only contain **Vertices** whose node Id values are 12, 13, or 14. In general, this *node type* array is created when the original surface mesh is created.
+This **Filter** has the effect of removing any **Triangles** that only contain **Vertices** whose node Id values are 12, 13, or 14. In general, this *node type* array is created when the original surface mesh is created.
It is unknown until runtime how the **Geometry** will be changed by removing certain **Vertices** and **Triangles**.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-None
+## Example Pipelines
-## Required Geometry ###
-
-Triangle
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Vertex Data Array** | NodeTypes | int8 | (1) | Specifies the type of node in the **Geometry** |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| Geometry | None | Triangle | N/A | The new Triangle Geometry |
-| Attribute Matrix | Vertex Data | N/A | N/A | Created vertex data AttributeMatrix name |
-| Attribute Matrix | Face Data | N/A | N/A | Created face data AttributeMatrix name |
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-
-
-
diff --git a/src/Plugins/ComplexCore/docs/ExtractVertexGeometryFilter.md b/src/Plugins/ComplexCore/docs/ExtractVertexGeometryFilter.md
index 89b9330c24..8976d3062a 100644
--- a/src/Plugins/ComplexCore/docs/ExtractVertexGeometryFilter.md
+++ b/src/Plugins/ComplexCore/docs/ExtractVertexGeometryFilter.md
@@ -1,42 +1,25 @@
# Extract Vertex Geometry
-## Group (Subgroup) ##
+## Group (Subgroup)
Core Filters (Conversion)
-## Description ##
+## Description
This filter will extract all the voxel centers of an Image Geometry or a RectilinearGrid geometry
-into a new VertexGeometry. The user is given the option to copy or move cell arrays over to the
+into a new VertexGeometry. The user is given the option to copy or move cell arrays over to the
newly created VertexGeometry.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------|------|-------------|
-| Array Handling | int | 0=Move Arrays, 1=Copy Arrays |
-| Use Mask | Bool | Use a mask array to determine which vertices are extracted |
-| Mask | DataPath | The path to the mask array |
-| Input Geometry | DataPath | The path to the input geometry that will be extracted into a vertex geometry |
-| Included Attribute Arrays | std::vector | List of DataPaths to either copy or move |
-| Output Vertex Geometry | DataPath | The path to the vertex geometry that will be output by this filter |
-| Output Vertex Attribute Matrix Name | string | The name of the vertex attribute matrix that will be created as a child of the output vertex geometry |
-| Output Shared Vertex List Name | string | The name of the shared vertex list name that will be output with the vertex geometry |
-
-## Required Geometry ##
-
-Required Geometry Type: **ImageGeom** or **RectGridGeom**
-
-## Example Pipelines ##
+## Example Pipelines
PrebuiltPipelines/Examples/Extract Vertex Geometry.json
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/FeatureDataCSVWriterFilter.md b/src/Plugins/ComplexCore/docs/FeatureDataCSVWriterFilter.md
index 1a7a22d378..af879ddbb2 100644
--- a/src/Plugins/ComplexCore/docs/FeatureDataCSVWriterFilter.md
+++ b/src/Plugins/ComplexCore/docs/FeatureDataCSVWriterFilter.md
@@ -1,18 +1,17 @@
# Write Feature Data as CSV File
-## Group (Subgroup) ##
+## Group (Subgroup)
IO (Output)
-## Description ##
+## Description
This **Filter** writes the data associated with each **Feature** to a file name specified by the user in *CSV* format. Every array in the **Feature** map is written as a column of data in the *CSV* file. The user can choose to also write the neighbor data. Neighbor data are data arrays that are associated with the neighbors of a **Feature**, such as: list of neighbors, list of misorientations, list of shared surface areas, etc. These blocks of info are written after the scalar data arrays. Since the number of neighbors is variable for each **Feature**, the data is written as follows (for each **Feature**): Id, number of neighbors, value1, value2,...valueN.
+### Example Output
-### Example Output ###
+The *CSV* file:
-The *CSV* file:
-
5414
Feature_ID,Active,AvgEuler_0,AvgEuler_1,AvgEuler_2,AvgQuats_0,AvgQuats_1,AvgQuats_2,AvgQuats_3,NumNeighbors2,Phases
1,1,4.7367158,0.40832964,1.1398145,-0.045759138,0.19751814,0.19773535,0.95905864,6,1
@@ -40,40 +39,16 @@ The *CSV* file with Write Neighbor Data checked:
4,1,886
5,26,61,224,278,454,786,923,1119,1137,1478,1517,1525,1651,1812,1814,2227,2233,2731,2750,2907,2930,3175,3548,3619,4492,4791,5010
+% Auto generated parameter table will be inserted here
-## Parameters ##
-
-| Name | Type |Description |
-|------|------|------|
-| Output File | File Path | The output .csv file path |
-| Write Neighbor Data | bool | Whether to write the **Feature** neighbor data |
-| Write Number of Features Line | bool | Write the total number of features as the first line. Writing this line may interfere with standard CSV parsers. Default=ON |
-| Delimiter | choice | The delimiter character used to parse the file (Takes _COMMA_, _SEMICOLON_, _COLON_, _TAB_, or _SPACE_) |
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **AttributeMatrix** | None | Feature | N/A | **AttributeMatrix** that holds the data to write |
-
-## Created Objects ##
+## Example Pipelines
None
-## Example Pipelines ##
-
-None
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/FeatureFaceCurvatureFilter.md b/src/Plugins/ComplexCore/docs/FeatureFaceCurvatureFilter.md
index dbda87d2e2..7a9b054680 100644
--- a/src/Plugins/ComplexCore/docs/FeatureFaceCurvatureFilter.md
+++ b/src/Plugins/ComplexCore/docs/FeatureFaceCurvatureFilter.md
@@ -1,10 +1,10 @@
-# Find Feature Face Curvature #
+# Find Feature Face Curvature
-## Group (Subgroup) ##
+## Group (Subgroup)
Surface Meshing (Curvature)
-## Description ##
+## Description
This **Filter** calculates *principal direction vectors* and the *principal curvatures*, and optionally the *mean* and *Gaussian* curvature, for each **Triangle** in a **Triangle Geometry** using the technique in [1]. The groups of **Triangles** over which to compute the curvatures is determines by the **Features** they are associated, denoted by their **Face Labels**. The curvature information will be stored in a **Face Attribute Matrix**.
@@ -13,61 +13,21 @@ Principal Curvatures 1 and 2 are the κ 1 and κ 2
*Note*: Computing the Weingarten matrix values is an experimental feature, and there is no guarantee at this time that the values are correct.
------
-
![Curvature Coloring of a Feature](Images/FeatureFaceCurvatureFilter.png)
@image latex FeatureFaceCurvatureFilter.png "Curvature Coloring of a Feature" width = 6in
------
-
-## Parameters ##
-
-| Name | Type | Description |
-| ------ | ------ | ---------- - |
-| Neighborhood Ring Count | int32_t | The size of the neighborhood to use to calculate the curvature values |
-| Compute Principal Direction Vectors | bool | Whether to compute the principal direction vectors |
-| Compute Gaussian Curvature | bool | Whether to compute the Gaussian curvature values |
-| Compute Mean Curvature | bool | Whether to compute the mean curvature values |
-| Compute Weingarten Matrix | bool | Whether to compute the weingarten matrix values |
-| Use Face Normals for Curve Fitting | bool | Whether to use the **Face** normals to improve the least squares fit |
-
-## Required Geometry ##
-
-Triangle
+% Auto generated parameter table will be inserted here
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-| ------ | -------------- | ------------ - | -------- - | ---- - |
-|**Attribute Matrix**| FaceData | Face | N / A | Specifies which **Attribute Matrix** to store the results |
-|**Face Attribute Array**| FaceLabels | int32_t | (2) | Specifies which **Features** are on either side of each **Face** |
-|**Face Attribute Array**| FeatureFaceIds | int32_t | (1) | Specifies to which **Feature** boundary each **Face** belongs |
-|**Face Attribute Array**| FaceNormals | double | (3) | Specifies the normal of each **Face** |
-|**Face Attribute Array**| FaceCentroids | double | (3) | Specifies the centroid of each **Face** |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-| ------ | -------------- | ------------ - | -------- - | ---- - |
-|**Face Attribute Array**| PrincipalCurvature1 | double | (1) | First set eigenvalues of the Wiengarten matrix (κ1). Only created if *Compute Principal Direction Vectors*is checked |
-|**Face Attribute Array**| PrincipalCurvature2 | double | (1) | Second set eigenvalues of the Wiengarten matrix (κ2). Only created if *Compute Principal Direction Vectors*is checked |
-|**Face Attribute Array**| PrincipalDirection1 | double | (3) | First set of eigenvectors. Only created if *Compute Principal Direction Vectors*is checked |
-|**Face Attribute Array**| PrincipalDirection2 | double | (3) | Second set of eigenvectors. Only created if *Compute Principal Direction Vectors*is checked |
-|**Face Attribute Array**| MeanCurvatures | double | (1) | Mean curvature values. Only created if *Compute Mean Curvature*is checked |
-|**Face Attribute Array**| GaussianCurvatures | double | (1) | Gaussian curvature values. Only created if *Compute Gaussian Curvature*is checked |
-|**Face Attribute Array**| WeingartenMatrix | double | (4) | Weingarten matrix values. Only created if *Compute Weingarten Matrix*is checked |
-
-## References ##
+## References
[1] J. Goldfeather, V. Interrante, "A Novel Cubic-Order Algorithm for Approximating Principal Direction Vectors", ACM Transactions on Graphics 2004, 23(1), pp. 45 - 63.
-## Example Pipelines ##
+## Example Pipelines
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this**Plugin**
-## DREAM.3D Mailing Lists ##
+## DREAM.3D Mailing Lists
If you need more help with a**Filter**, please consider asking your question on the [DREAM.3D Users Google group!](https://groups.google.com/forum/?hl=en#!forum/dream3d-users)
-
diff --git a/src/Plugins/ComplexCore/docs/FillBadDataFilter.md b/src/Plugins/ComplexCore/docs/FillBadDataFilter.md
index 25efb11010..5f98612b74 100644
--- a/src/Plugins/ComplexCore/docs/FillBadDataFilter.md
+++ b/src/Plugins/ComplexCore/docs/FillBadDataFilter.md
@@ -1,5 +1,4 @@
-# Fill Bad Data
-
+# Fill Bad Data
## Group (Subgroup)
@@ -7,7 +6,7 @@ Processing (Cleanup)
## Description
-This **Filter** removes small *noise* in the data, but keeps larger regions that are possibly **Features**, e.g., pores or defects. This **Filter** collects the *bad* **Cells** (*Feature Id = 0*) and *erodes* them until none remain. However, contiguous groups of *bad* **Cells** that have at least as many **Cells** as the minimum allowed defect size entered by the user will not be _eroded_.
+This **Filter** removes small *noise* in the data, but keeps larger regions that are possibly **Features**, e.g., pores or defects. This **Filter** collects the *bad* **Cells** (*Feature Id = 0*) and *erodes* them until none remain. However, contiguous groups of *bad* **Cells** that have at least as many **Cells** as the minimum allowed defect size entered by the user will not be *eroded*.
| Small IN100 Before | Small IN100 After |
|--|--|
@@ -15,28 +14,7 @@ This **Filter** removes small *noise* in the data, but keeps larger regions that
The above images show the before and after results of running this filter with a minimum defect size of 1000 voxels. Note that because the minimum defect size was set to 1000 voxels that the over scan area was not modified (the area in all black around the sample).
-## Parameters
-
-| Name | Type | Decision |
-|------|------|------|
-| Minimum Allowed Defect Size | int32_t | The size at which a group of *bad* **Cells** are left unfilled as a "defect" |
-| Replace Bad Data | bool | Whether to replace all data or just *Feature Ids* |
-| Store Defects as New Phase | bool | Will update voxels that are part of larger defects to have a new phase value |
-
-## Required Geometry
-
-Image
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Cell** belongs |
-| **Cell Attribute Array** | Phases | int32_t | (1) | Specifies to which **Ensemble** each **Cell** belongs. Only required if *Store Defects as New Phase* is checked |
-
-## Created Objects
-
-None
+% Auto generated parameter table will be inserted here
## Example Pipelines
@@ -46,8 +24,6 @@ None
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/FindArrayStatisticsFilter.md b/src/Plugins/ComplexCore/docs/FindArrayStatisticsFilter.md
index 6277196a12..c207afb58f 100644
--- a/src/Plugins/ComplexCore/docs/FindArrayStatisticsFilter.md
+++ b/src/Plugins/ComplexCore/docs/FindArrayStatisticsFilter.md
@@ -1,10 +1,10 @@
-# Find Attribute Array Statistics #
+# Find Attribute Array Statistics
-## Group (Subgroup) ##
+## Group (Subgroup)
DREAM3D Review (Statistics)
-## Description ##
+## Description
This **Filter** computes a variety of statistics for a given scalar array. The currently available statistics are array length, minimum, maximum, (arithmetic) mean, median, mode, standard deviation, and summation; any combination of these statistics may be computed by this **Filter**. Any scalar array, of any primitive type, may be used as input. The type of the output arrays depends on the kind of statistic computed:
@@ -32,68 +32,14 @@ Special operations occur for certain statistics if the supplied array is of type
**Note**: If *Find Histogram* is on AND *Compute Statistics Per Feature/Ensemble* is on, then any features that have the exact same value throughout the entire feature will have its first histogram bin set to the total count of feature values. All other bins will be 0.
-## Parameters ##
-
-| Name | Type | Description |
-|-----------------------------------------|------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| Find Histogram | bool | Whether to compute the histogram of the input array |
-| Histogram Min Value | double | Min cutoff value for histogram |
-| Histogram Max Value | double | Max cutoff value for histogram |
-| Number of Bins | int32_t | Number of bins in histogram |
-| Use Full Range For Histogram | bool | If true, ignore min and max and use min and max from array upon which histogram is computed |
-| Find Length | bool | Whether to compute the length of the input array |
-| Find Minimum | bool | Whether to compute the minimum of the input array |
-| Find Maximum | bool | Whether to compute the maximum of the input array |
-| Find Mean | bool | Whether to compute the arithmetic mean of the input array |
-| Find Median | bool | Whether to compute the median of the input array |
-| Find Mode | bool | Whether to compute the mode of the input array. The input array may have multiple modes, so the modes are stored in a NeighborList. |
-| Find Standard Deviation | bool | Whether to compute the standard deviation of the input array |
-| Find Summation | bool | Whether to compute the summation of the input array |
-| Find Number of Unique Values | bool | Whether to compute the number of unique values in the input array |
-| Use Mask | bool | Whether to use a boolean mask array to ignore certain points flagged as *false* from the statistics |
-| Compute Statistics Per Feature/Ensemble | bool | Whether the statistics should be computed on a **Feature/Ensemble** basis |
-| Standardize Data | bool | Whether the input array should be standardized to have mean of 0 and unit variance; *Find Mean* and *Find Standard Deviation* must be selected to use this option |
-
-## Required Geometry ##
-
-None
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|-----|
-| Any **Attribute Array** | None | Any | (1) | Input **Attribute Array** for which to compute statistics |
-| **Attribute Array** | None | int32_t | (1) | Specifies to which **Feature/Ensemble** each point in the input **Attribute Array** belongs, if *Compute Statistics Per Feature/Ensemble* is checked |
-| **Attribute Array** | Mask | bool | (1) | Specifies if the point is to be counted in the statistics, if *Use Mask* is checked |
-| Destination **Attribute Matrix** | None | Any | N/A | **Attribute Matrix** in which to store the computed statistics |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|---------------------|----------------------------|---------------------------------|----------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| **Attribute Array** | Feature-Has-Data | bool | (1) | Indicates, for each feature, whether or not the feature actually contains any data (only usable when *Compute Statistics Per Feature/Ensemble* is turned on). This array is especially useful to help determine whether or not the outputted statistics are actually valid or not for a given feature. |
-| **Attribute Array** | Histogram | uint64 | (Number of Bins) | Histogram of the input array, if _Find Histogram_ is checked |
-| **Attribute Array** | Most Populated Bin | uint64 | (2) | Most populated bin from the histogram of the input array, if _Find Histogram_ is checked. First component is the bin index (0-based), second component is the number of values in the bin. |
-| **Neighbor List** | Modal Histogram Bin Ranges | float | (1) | Ranges, in physical units, of histogram bin(s) that contain mode value(s). _Find Histogram_, _Find Modal Histogram Bin Ranges_, and _Find Mode_ must all be checked. The min/max values are stored in the neighbor list arrays from bin 0 - bin N (Example: [bin0min, bin0max, bin1min, bin1max, ... binNmin, binNmax]) |
-| **Attribute Array** | Length | int64_t | (1) | Length of the input array, if _Find Length_ is checked |
-| **Attribute Array** | Minimum | same as input **Attribute Array** | (1) | Minimum of the input array, if _Find Minimum_ is checked |
-| **Attribute Array** | Maximum | same as input **Attribute Array** | (1) | Maximum of the input array, if _Find Maximum_ is checked |
-| **Attribute Array** | Mean | double | (1) | Arithmetic mean of the input array, if _Find Mean_ is checked |
-| **Attribute Array** | Median | double | (1) | Median of the input array, if _Find Median_ is checked |
-| **Neighbor List** | Mode | same as input **Attribute Array** | (1) | Modes of the input array, if _Find Mode_ is checked |
-| **Attribute Array** | Standard Deviation | double | (1) | Standard deviation of the input array, if _Find Standard Deviation_ is checked |
-| **Attribute Array** | Summation | double | (1) | Summation of the input array, if _Find Summation_ is checked |
-| **Attribute Array** | Standardized | double | (1) | Standardized version of the input array, if _Standardize Data_ is checked |
-| **Attribute Array** | Number of Unique Values | int32_t | (1) | The number of unique values in the input array, if _Find Number of Unique Values_ is checked |
-
-## Example Pipelines ##
-
-## License & Copyright ##
+% Auto generated parameter table will be inserted here
-Please see the description file distributed with this plugin.
+## Example Pipelines
-## DREAM3DNX Help ##
+## License & Copyright
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
+Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/FindBiasedFeaturesFilter.md b/src/Plugins/ComplexCore/docs/FindBiasedFeaturesFilter.md
index 17eb7c5c5c..788a7ee75a 100644
--- a/src/Plugins/ComplexCore/docs/FindBiasedFeaturesFilter.md
+++ b/src/Plugins/ComplexCore/docs/FindBiasedFeaturesFilter.md
@@ -1,51 +1,28 @@
# Find Biased Features (Bounding Box)
-
## Group (Subgroup)
Generic (Spatial)
## Description
-This **Filter** determines which **Features** are *biased* by the outer surfaces of the sample. Larger **Features** are more likely to intersect the outer surfaces and thus it is not sufficient to only note which **Features** touch the outer surfaces of the sample. Denoting which **Features** are biased is important so that they may be excluded from any statistical analyses. The algorithm for determining whether a **Feature** is *biased* is as follows:
+This **Filter** determines which **Features** are *biased* by the outer surfaces of the sample. Larger **Features** are more likely to intersect the outer surfaces and thus it is not sufficient to only note which **Features** touch the outer surfaces of the sample. Denoting which **Features** are biased is important so that they may be excluded from any statistical analyses. The algorithm for determining whether a **Feature** is *biased* is as follows:
1. The *centroids* of all **Features** are calculated
2. All **Features** are tested to determine if they touch an outer surface of the sample
3. The largest box is found that does not include any of the *centroids* of **Features** that intersect an outer surface of the sample
4. Each **Feature**'s *centroid* is checked to see whether it lies within the box.
-*If a **Feature**'s *centroid* lies within the box, then the **Feature** is said to be _unbiased_, and if it lies outside the box, then the **Feature** is said to be _biased_.*
+*If a **Feature**'s *centroid* lies within the box, then the **Feature** is said to be *unbiased*, and if it lies outside the box, then the **Feature** is said to be *biased*.*
-By definition of the box, no **Feature** that intersects an outer surface of the sample can be considered _unbiased_, but it should be noted that **Features** that do not intersect the outer surfaces may still be considered _biased_. This algorithm works to determine the biased **Features** because all **Features** have one (and only one) centroid, no matter their size. Generally, this method will deem more small **Features** biased than the set of **Features** that just intersect the outer surfaces - and this corrects for the increased likelihood that larger **Features** will touch an outer surface.
+By definition of the box, no **Feature** that intersects an outer surface of the sample can be considered *unbiased*, but it should be noted that **Features** that do not intersect the outer surfaces may still be considered *biased*. This algorithm works to determine the biased **Features** because all **Features** have one (and only one) centroid, no matter their size. Generally, this method will deem more small **Features** biased than the set of **Features** that just intersect the outer surfaces - and this corrects for the increased likelihood that larger **Features** will touch an outer surface.
*Note:* This **Filter** is a modification of an algorithm from Dave Rowenhorst (Naval Research Laboratory).
The images below show the feature ids before and after running this filter. The image on the right shows the biased features colored in red, the unbiased features colored by their feature id, the bounding box (described in step 3 of the algorithm above), and the feature centroids (white for unbiased and purple for biased).
![2D Before and After Biased Features](Images/FindBiasedFeaturesBeforeAndAfter.png)
-## Parameters
-
-| Name | Type | Description |
-|------------------|------|-------------|
-| Apply Phase by Phase | bool | Whether to apply the biased **Features** algorithm per **Ensemble** |
-
-## Required Geometry
-
-Image
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | Centroids | float | (3) | X, Y, Z coordinates of **Feature** center of mass |
-| **Feature Attribute Array** | SurfaceFeatures | bool | (1) | Flag of 1 if **Feature** touches an outer surface or of 0 if it does not |
-| **Feature Attribute Array** | Phases | int32_t | (1) | Specifies to which **Ensemble** each **Feature** belongs. Only required if *Apply Phase by Phase* is checked |
-
-## Created Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | BiasedFeatures | bool | (1) | Flag of 1 if **Feature** is biased or of 0 if it is not |
+% Auto generated parameter table will be inserted here
## Example Pipelines
@@ -55,8 +32,6 @@ Image
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/FindBoundaryCellsFilter.md b/src/Plugins/ComplexCore/docs/FindBoundaryCellsFilter.md
index 6c2e563896..fd62731913 100644
--- a/src/Plugins/ComplexCore/docs/FindBoundaryCellsFilter.md
+++ b/src/Plugins/ComplexCore/docs/FindBoundaryCellsFilter.md
@@ -1,48 +1,25 @@
# Find Boundary Cells (Image)
-
## Group (Subgroup)
Generic (Spatial)
## Description
-This **Filter** determines, for each **Cell**, the number of neighboring **Cells** that are owned by a different **Feature**. The algorithm for determining this is as follows:
+This **Filter** determines, for each **Cell**, the number of neighboring **Cells** that are owned by a different **Feature**. The algorithm for determining this is as follows:
1. Identify the **Feature** to which a **Cell** belongs
2. Identify the **Features** to which each of the current **Cell**'s six (6) face-face neighboring **Cells** (front, back, left, right, up, down) belong
-3. Determine the number of those neighboring **Cells** belonging to a different **Feature** than the current **Cell**.
+3. Determine the number of those neighboring **Cells** belonging to a different **Feature** than the current **Cell**.
4. Repeat 1-3 for all **Cells**
-
| Small IN100 Feature Ids Input | Small IN100 Boundary Cells Output |
|--|--|
| ![Feature Ids](Images/FindBoundaryCellsInput.png) | ![Boundary Cells](Images/FindBoundaryCellsOutput.png) |
-## Parameters
-
-| Name | Type | Description |
-|------------------|------|-------------|
-| Ignore Feature 0 | bool | Do not use feature 0 |
-| Include Volume Boundary | bool | Include the Cell boundaries |
-
-## Required Geometry
-
-Image
-
-## Required Objects
+% Auto generated parameter table will be inserted here
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Cell** belongs. |
-
-## Created Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | BoundaryCells | int8_t | (1) | The number of neighboring **Cells** of a given **Cell** that belong to a different **Feature** than itself. Values will range from *0* to *6* |
-
-## Example Pipelines
+## Example Pipelines
+ FindBoundaryCells.d3dpipeline
@@ -50,8 +27,6 @@ Image
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/FindBoundaryElementFractionsFilter.md b/src/Plugins/ComplexCore/docs/FindBoundaryElementFractionsFilter.md
index cf5ddf88cf..be767b02d5 100644
--- a/src/Plugins/ComplexCore/docs/FindBoundaryElementFractionsFilter.md
+++ b/src/Plugins/ComplexCore/docs/FindBoundaryElementFractionsFilter.md
@@ -1,6 +1,5 @@
# Find Feature Boundary Element Fractions
-
## Group (Subgroup)
Statistics (Morphological)
@@ -9,37 +8,14 @@ Statistics (Morphological)
This **Filter** calculates the fraction of **Elements** of each **Feature** that are on the "surface" of that **Feature**. The **Filter** simply iterates through all **Elements** asking for the **Feature** that owns them and if the **Element** is a "surface" **Element**. Each **Feature** counts the total number of **Elements** it owns and the number of those **Elements** that are "surface" **Elements**. The fraction is then stored for each **Feature**.
-## Parameters
-
-None
-
-## Required Geometry
-
-Not Applicable
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Element Attribute Array** | Feature Ids | int32 | (1) | Specifies to which **Feature** each **Element** belongs |
-| **Element Attribute Array** | Surface Elements | int32 | (1) | The number of neighboring **Elements** of a given **Element** that belong to a different **Feature** than itself |
-| **Attribute Matrix** | Feature Data | AttributeMatrix | N/A | Parent Attribute Matrix for the *Surface Element Fractions* Array to be created in |
-
-## Created Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | Surface Element Fractions | float32 | (1) | Fraction of **Elements** belonging to the **Feature** that are "surface" **Elements** |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/FindDifferencesMap.md b/src/Plugins/ComplexCore/docs/FindDifferencesMap.md
index d8e4779e4b..fc629d7460 100644
--- a/src/Plugins/ComplexCore/docs/FindDifferencesMap.md
+++ b/src/Plugins/ComplexCore/docs/FindDifferencesMap.md
@@ -1,11 +1,10 @@
-# Find Difference Map
+# Find Difference Map
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Statistics (Misc)
-## Description ##
+## Description
This **Filter** calculates the difference between two **Attribute Arrays**. The arrays must have the same *primitive type* (e.g., float), *component dimensions* and *number of tuples*. The **Filter** uses the following pseudocode to calculate the difference map:
@@ -15,41 +14,18 @@ This **Filter** calculates the difference between two **Attribute Arrays**. The
end loop over number of components
end loop over all tuples
-Note that in the above algorithm, the difference is taken as the *first selected* **Attribute Array** minus the *second selected* **Attribute Array**. The differences are also taken _component by component_. Therefore, two selected scalar arrays will result in a scalar difference map, whereas two selected 3 component vector arrays would result in a 3 component vector difference map, where component values are the scalar differences between the components of the input arrays.
-
-**WARNING: The resulting difference values *may be negative* if the values of the first array are smaller than those in the second array. Therefore, if the two arrays are _unsigned integers_, it may be possible to underflow the resulting difference map values if the first array is sufficiently smaller than the second array. "Underflow" means that what should be a negative value will end up being a potentially very large value!**
-
-## Parameters ##
-
-None
-
-## Required Geometry ##
-
-Not Applicable
+Note that in the above algorithm, the difference is taken as the *first selected* **Attribute Array** minus the *second selected* **Attribute Array**. The differences are also taken *component by component*. Therefore, two selected scalar arrays will result in a scalar difference map, whereas two selected 3 component vector arrays would result in a 3 component vector difference map, where component values are the scalar differences between the components of the input arrays.
-## Required Objects ##
+**WARNING: The resulting difference values *may be negative* if the values of the first array are smaller than those in the second array. Therefore, if the two arrays are *unsigned integers*, it may be possible to underflow the resulting difference map values if the first array is sufficiently smaller than the second array. "Underflow" means that what should be a negative value will end up being a potentially very large value!**
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| Any **Attribute Array** | None | Any | Any | The first selected **Attribute Array**. This array's values will be the first argument for the subtraction operation |
-| Any **Attribute Array** | None | Any | Any | The second selected **Attribute Array**. This array's values will be subtracted from the first selected **Attribute Array** values |
+% Auto generated parameter table will be inserted here
-## Created Objects ##
+## Example Pipelines
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| Any **Attribute Array** | DifferenceMap | Same as input arrays | Same as input arrays | The difference map **Attribute Array** |
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/FindEuclideanDistMapFilter.md b/src/Plugins/ComplexCore/docs/FindEuclideanDistMapFilter.md
index 8c01d97428..a1b755bd61 100644
--- a/src/Plugins/ComplexCore/docs/FindEuclideanDistMapFilter.md
+++ b/src/Plugins/ComplexCore/docs/FindEuclideanDistMapFilter.md
@@ -1,11 +1,10 @@
-# Find Euclidean Distance Map
+# Find Euclidean Distance Map
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Statistics (Morphological)
-## Description ##
+## Description
This **Filter** calculates the distance of each **Cell** from the nearest **Feature** boundary, **triple line** and/or **quadruple point**. The following algorithm explains the process:
@@ -13,56 +12,24 @@ This **Filter** calculates the distance of each **Cell** from the nearest **Feat
2. For all **Cells** that have *at least 2* different neighbors, set their *GBEuclideanDistance* to *0*. For all **Cells** that have *at least 3* different neighbors, set their *TJEuclideanDistance* to *0*. For all **Cells** that have *at least 4* different neighbors, set their *QPEuclideanDistance* to *0*
3. For each of the three *EuclideanDistace* maps, iteratively "grow" out from the **Cells** identified to have a distance of *0* by the following sub-steps:
- - Determine the **Cells** that neighbor a **Cell** of distance *0* in the current map.
- - Assign a distance of *1* to those **Cells** and list the *0* **Cell** neighbor as their *nearest neighbor*
- - Repeat previous two sub-steps, increasing the distances by *1* each iteration, until no **Cells** remain without a distance and *nearest neighbor* assigned.
+- Determine the **Cells** that neighbor a **Cell** of distance *0* in the current map.
+- Assign a distance of *1* to those **Cells** and list the *0* **Cell** neighbor as their *nearest neighbor*
+- Repeat previous two sub-steps, increasing the distances by *1* each iteration, until no **Cells** remain without a distance and *nearest neighbor* assigned.
*Note:* the distances calculated at this point are "city-block" distances and not "shortest distance" distances.
4. If the option *Calculate Manhattan Distance* is *false*, then the "city-block" distances are overwritten with the *Euclidean Distance* from the **Cell** to its *nearest neighbor* **Cell** and stored in a *float* array instead of an *integer* array.
+% Auto generated parameter table will be inserted here
-## Parameters ##
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Calculate Manhattan Distance | bool | Whether the distance to boundaries, triple lines and quadruple points is stored as "city block" or "Euclidean" distances |
-| Calculate Distance to Boundaries | bool | Whetherthe distance of each **Cell** to a **Feature** boundary is calculated |
-| Calculate Distance to Triple Lines | bool | Whetherthe distance of each **Cell** to a triple line between **Features** is calculated |
-| Calculate Distance to Quadruple Points | bool | Whetherthe distance of each **Cell** to a quadruple point between **Features** is calculated |
-| Store the Nearest Boundary Cells | bool | Whether to store the *nearest neighbors* of **Cell**
-
-
-## Required Geometry ##
-
-Image
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Cell** belongs |
+## Example Pipelines
-## Created Objects ##
+- (01) SmallIN100 Morphological Statistics
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | GBEuclideanDistances | float | (1) | Distance the **Cells** are from the *boundary* of the **Feature** they belong to. Only created if *Calculate Distance to Boundaries* is checked |
-| **Cell Attribute Array** | TJEuclideanDistances | float | (1) | Distance the **Cells** are from a *triple junction* of **Features**. Only created if *Calculate Distance to Triple Lines* is checked |
-| **Cell Attribute Array** | QPEuclideanDistances | float | (1) | Distance the **Cells** are from a *quadruple point* of **Features**. Only created if *Calculate Distance to Quadruple Points* is checked |
-| **Cell Attribute Array** | NearestNeighbors | int32_t | (3) | Indices of the closest **Cell** that touches a boundary, triple and quadruple point for each **Cell**. Only created if *Store the Nearest Boundary Cells* is checked |
-
-
-## Example Pipelines ##
-
-+ (01) SmallIN100 Morphological Statistics
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/FindFeatureCentroidsFilter.md b/src/Plugins/ComplexCore/docs/FindFeatureCentroidsFilter.md
index 5784592cd8..dbfad0da92 100644
--- a/src/Plugins/ComplexCore/docs/FindFeatureCentroidsFilter.md
+++ b/src/Plugins/ComplexCore/docs/FindFeatureCentroidsFilter.md
@@ -1,46 +1,25 @@
-# Find Feature Centroids
+# Find Feature Centroids
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Generic (Misc)
-## Description ##
+## Description
This **Filter** calculates the *centroid* of each **Feature** by determining the average X, Y, and Z position of all the **Cells** belonging to the **Feature**. Note that **Features** that intersect the outer surfaces of the sample will still have *centroids* calculated, but they will be *centroids* of the truncated part of the **Feature** that lies inside the sample.
-## Parameters ##
-
-None
-
-## Required Geometry ##
-
-Image
-
-## Required Objects ##
+% Auto generated parameter table will be inserted here
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Cell** belongs |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | Centroids | float | (3) | X, Y, Z coordinates of **Feature** center of mass |
-
-## Example Pipelines ##
+## Example Pipelines
+ (01) SmallIN100 Morphological Statistics
+ InsertTransformationPhase
+ (06) SmallIN100 Synthetic
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/FindFeatureClusteringFilter.md b/src/Plugins/ComplexCore/docs/FindFeatureClusteringFilter.md
index d241fd3cdc..a62992b78c 100644
--- a/src/Plugins/ComplexCore/docs/FindFeatureClusteringFilter.md
+++ b/src/Plugins/ComplexCore/docs/FindFeatureClusteringFilter.md
@@ -1,6 +1,5 @@
# Find Feature Clustering
-
## Group (Subgroup)
Statistics (Morphological)
@@ -12,41 +11,12 @@ This Filter determines the radial distribution function (RDF), as a histogram, o
1. Find the Euclidean distance from the current **Feature** centroid to all other **Feature** centroids of the same specified phase
2. Put all caclulated distances in a clustering list
3. Repeat 1-2 for all **Features**
-4. Sort the data into the specified number of bins, all equally sized in distance from the minimum distance to the maximum distance between **Features**. For example, if the user chooses 10 bins, and the minimum distance between **Features** is 10 units and the maximum distance is 80 units, each bin will be 8 units
-5. Normalize the RDF by the probability of finding the **Features** if distributed randomly in the given box
-
-*Note:* Because the algorithm iterates over all the **Features**, each distance will be double counted. For example, the distance from **Feature** 1 to **Feature** 2 will be counted along with the distance from **Feature** 2 to **Feature** 1, which will be identical.
-
-## Parameters
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Number of Bins for RDF | int32_t | Number of bins to split the RDF |
-| Phase Index | int32_t | **Ensemble** number for which to calculate the RDF and clustering list |
-| Remove Biased Features | bool | Default=OFF |
-| Set Random Seed | bool | When checked, allows the user to set the seed value used to randomly generate the points in the RDF (Default=ON) |
-| Seed Value | uint64_t | The seed value used to generate the points in the RDF when the Set Random Seed option is ON |
-
-## Required Geometry
+4. Sort the data into the specified number of bins, all equally sized in distance from the minimum distance to the maximum distance between **Features**. For example, if the user chooses 10 bins, and the minimum distance between **Features** is 10 units and the maximum distance is 80 units, each bin will be 8 units
+5. Normalize the RDF by the probability of finding the **Features** if distributed randomly in the given box
-Image
+*Note:* Because the algorithm iterates over all the **Features**, each distance will be double counted. For example, the distance from **Feature** 1 to **Feature** 2 will be counted along with the distance from **Feature** 2 to **Feature** 1, which will be identical.
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | EquivalentDiameters | float | (1) | Diameter of a sphere with the same volume as the **Feature** |
-| **Feature Attribute Array** | Phases | int32_t | (1) | Specifies to which **Ensemble** each **Feature** belongs |
-| **Feature Attribute Array** | Centroids | float | (3) | X, Y, Z coordinates of **Feature** center of mass |
-| **Feature Attribute Array** | BiasedFeatures | bool | (1) | Specifies which features are biased and therefor should be removed if the Remove Biased Features option is on |
-
-## Created Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | ClusteringList | float | (1) | Distance of each **Features**'s centroid to ever other **Features**'s centroid |
-| **Ensemble Attribute Array** | RDF | float | (Number of Bins) | A histogram of the normalized frequency at each bin |
-| **Ensemble Attribute Array** | RDFMaxMinDistances | float | (2) | The max and min distance found between **Features** |
+% Auto generated parameter table will be inserted here
## Example Pipelines
@@ -56,8 +26,6 @@ Image
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/FindFeaturePhasesBinaryFilter.md b/src/Plugins/ComplexCore/docs/FindFeaturePhasesBinaryFilter.md
index 4a24d92acc..6cb7a90b86 100644
--- a/src/Plugins/ComplexCore/docs/FindFeaturePhasesBinaryFilter.md
+++ b/src/Plugins/ComplexCore/docs/FindFeaturePhasesBinaryFilter.md
@@ -8,27 +8,7 @@ Generic (Misc)
This **Filter** assigns an **Ensemble** Id number to binary data. The *true* **Cells** will be **Ensemble** 1, and *false* **Cells** will be **Ensemble** 0. This **Filter** is generally useful when the **Cell Ensembles** were not known ahead of time. For example, if an image is segmented into precipitates and non-precipitates, this **Filter** will assign the precipitates to **Ensemble** 1, and the non-precipitates to **Ensemble** 0.
-## Parameters
-
-None
-
-## Required Geometry
-
-Image
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Cell** belongs |
-| **Cell Attribute Array** | Mask | bool | (1) | Specifies if the **Cell** is to be counted in the algorithm |
-| **Attribute Matrix** | Cell Data Attribute Matrix | Attribute Matrix | N/A | The *Cell Data* **Attribute Matrix** of the **Image Geometry** where the *Binary Phases Array* will be created |
-
-## Created Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | Binary Feature Phases Array Name | int32_t | (1) | Specifies to which **Ensemble** each **Feature** belongs |
+% Auto generated parameter table will be inserted here
## Example Pipelines
@@ -36,8 +16,6 @@ Image
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/FindFeaturePhasesFilter.md b/src/Plugins/ComplexCore/docs/FindFeaturePhasesFilter.md
index 44183eb42c..e92cc94f0f 100644
--- a/src/Plugins/ComplexCore/docs/FindFeaturePhasesFilter.md
+++ b/src/Plugins/ComplexCore/docs/FindFeaturePhasesFilter.md
@@ -1,48 +1,25 @@
-# Find Feature Phases
+# Find Feature Phases
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Generic (Misc)
-## Description ##
+## Description
This **Filter** determines the **Ensemble** of each **Feature** by querying the **Ensemble** of the **Elements** that belong to the **Feature**. Note that it is assumed that all **Elements** belonging to a **Feature** are of the same **Feature**, and thus any **Element** can be used to determine the **Ensemble** of the **Feature** that owns that **Element**.
-## Parameters ##
-
-None
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Element Attribute Array** | Phases | int32_t | (1) | Specifies to which **Ensemble** each **Element** belongs |
-| **Element Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Element** belongs |
+% Auto generated parameter table will be inserted here
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | Phases | int32_t | (1) | Specifies to which **Ensemble** each **Feature** belongs |
-
-
-## Example Pipelines ##
+## Example Pipelines
+ (10) SmallIN100 Full Reconstruction
+ INL Export
+ (06) SmallIN100 Postsegmentation Processing
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/FindLargestCrossSectionsFilter.md b/src/Plugins/ComplexCore/docs/FindLargestCrossSectionsFilter.md
index 086f12130b..fc61a4369c 100644
--- a/src/Plugins/ComplexCore/docs/FindLargestCrossSectionsFilter.md
+++ b/src/Plugins/ComplexCore/docs/FindLargestCrossSectionsFilter.md
@@ -1,6 +1,5 @@
# Find Feature Largest Cross-Section Areas
-
## Group (Subgroup)
Statistics (Morphological)
@@ -9,39 +8,14 @@ Statistics (Morphological)
This **Filter** calculates the largest cross-sectional area on a user-defined plane for all **Features**. The **Filter** simply iterates through all **Cells** (on each section) asking for **Feature** that owns them. On each section, the count of **Cells** for each **Feature** is then converted to an area and stored as the *LargestCrossSection* if the area for the current section is larger than the existing *LargestCrossSection* for that **Feature**.
-## Parameters
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Plane of Interest | Enumeration | Specifies which plane to consider when determining the maximum cross-section for each **Feature** |
-
-## Required Geometry
-
-Image
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Cell** belongs |
-
-## Created Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | LargestCrossSection | flaot | (1) | Area of largest cross-section for **Feature** perpendicular to the user specified direction |
-
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
-
## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/FindNeighborListStatistics.md b/src/Plugins/ComplexCore/docs/FindNeighborListStatistics.md
index ceac4eba86..771edc386d 100644
--- a/src/Plugins/ComplexCore/docs/FindNeighborListStatistics.md
+++ b/src/Plugins/ComplexCore/docs/FindNeighborListStatistics.md
@@ -1,10 +1,10 @@
# Find NeighborList Statistics
-## Group (Subgroup) ##
+## Group (Subgroup)
Statistics (Misc Filters)
-## Description ##
+## Description
This **Filter** finds the selected statistics for each list contained in a NeighborList container. Each of those statistics are reported back as new Attribute Arrays. The user selectable statistics are:
@@ -16,56 +16,12 @@ This **Filter** finds the selected statistics for each list contained in a Neigh
+ Standard Deviation of each list
+ Summation of each list
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------|------|-------------|
-| Find Length | Bool | Find the Length of each List |
-| Find Minimum | Bool | Find the Minimum of each List |
-| Find Maximum | Bool | Find the Maximum of each List |
-| Find Mean | Bool | Find the Mean of each List |
-| Find Median | Bool | Find the Median of each List |
-| Find Standard Deviation | Bool | Find the Standard Deviation of each List |
-| Find Summation | Bool | Find the Summation of each List |
-| Input Neighbor List | NeighborList\ | The input NeighborList |
-| Output AttributeMatrix | DataArrayPath | The Output NeighborList |
-| Length Array Name | String | The name of the Output Length Attribute Array |
-| Minimum Array Name | String | The name of the Output Minimum Attribute Array |
-| Maximum Array Name | String | The name of the Output Maximum Attribute Array |
-| Mean Array Name | String | The name of the Output Mean Attribute Array |
-| Median Array Name | String | The name of the Output Median Attribute Array |
-| Standard Deviation Array Name | String | The name of the Output Standard Deviation Attribute Array |
-| Summation Array Name | String | The name of the Output Summation Attribute Array |
-
-## Required Geometry ###
-
-Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Attribute Matrix** | Attribute Matrix Name | N/A | N/A | Output Attribute Matrix |
-| **Input NeighborList** | NeighborList Name | int32_t/float/etc. | (1) | The input NeighborList. Boolean Not allowed. |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Length Attribute Array** | Length | float | (1) | Output Length Array |
-| **Minimum Attribute Array** | Minimum | float | (1) | Output Minimum Array |
-| **Maximum Attribute Array** | Maximum | float | (1) | Output Maximum Array |
-| **Mean Attribute Array** | Mean | float | (1) | Output Mean Array |
-| **Median Attribute Array** | Median | float | (1) | Output Median Array |
-| **Standard Deviation Attribute Array** | Standard Deviation | float | (1) | Output Standard Deviation Array |
-| **Summation Attribute Array** | Summation | float | (1) | Output Summation Array |
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/FindNeighborhoodsFilter.md b/src/Plugins/ComplexCore/docs/FindNeighborhoodsFilter.md
index 5540a3ea0f..e05d865fc4 100644
--- a/src/Plugins/ComplexCore/docs/FindNeighborhoodsFilter.md
+++ b/src/Plugins/ComplexCore/docs/FindNeighborhoodsFilter.md
@@ -1,11 +1,10 @@
-# Find Feature Neighborhoods
+# Find Feature Neighborhoods
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Statistics (Morphological)
-## Description ##
+## Description
This **Filter** determines the number of **Features**, for each **Feature**, whose *centroids* lie within a distance equal to a user defined multiple of the average *Equivalent Sphere Diameter* (*average of all **Features**). The algorithm for determining the number of **Features** is given below:
@@ -13,43 +12,18 @@ This **Filter** determines the number of **Features**, for each **Feature**, who
2. Check every other **Feature**'s *centroid* to see if it lies within the sphere and keep count and list of those that satisfy
3. Repeat 1. & 2. for all **Features**
-## Parameters ##
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Multiples of Average Diameter | float | Defines the search radius to use when looking for "neighboring" **Features** |
-
-## Required Geometry ##
-
-Image
-
-## Required Objects ##
+% Auto generated parameter table will be inserted here
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | EquivalentDiameters | float | (1) | Diameter of a sphere with the same volume as the **Feature** |
-| **Feature Attribute Array** | Phases | int32_t | (1) | Specifies to which **Ensemble** each **Feature** belongs |
-| **Feature Attribute Array** | Centroids | float | (3) | X, Y, Z coordinates of **Feature** center of mass |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | Neighborhoods | int32_t | (1) | Number of **Features** that have their centroid within the user specified multiple of equivalent sphere diameters from each **Feature** |
-| **Feature Attribute Array** | NeighborhoodLists | List of int32_t | (1) | List of the **Features** whose centroids are within the user specified multiple of equivalent sphere diameter from each **Feature** |
-
-## Example Pipelines ##
+## Example Pipelines
+ (01) SmallIN100 Morphological Statistics
+ InsertTransformationPhase
+ (06) SmallIN100 Synthetic
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/FindNeighbors.md b/src/Plugins/ComplexCore/docs/FindNeighbors.md
index b78df7374f..790bef4077 100644
--- a/src/Plugins/ComplexCore/docs/FindNeighbors.md
+++ b/src/Plugins/ComplexCore/docs/FindNeighbors.md
@@ -1,11 +1,10 @@
-# Find Feature Neighbors
+# Find Feature Neighbors
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Statistics (Morphological)
-## Description ##
+## Description
This **Filter** determines, for each **Feature**, the number of other **Features** that are in contact with it. The algorithm for determining the number of "contiguous" neighbors of each **Feature** is as follows:
@@ -16,35 +15,9 @@ This **Filter** determines, for each **Feature**, the number of other **Features
While performing the above steps, the number of neighboring **Cells** with a different **Feature** owner than a given **Cell** is stored, which identifies whether a **Cell** lies on the surface/edge/corner of a **Feature** (i.e. the **Feature** boundary). Additionally, the surface area shared between each set of contiguous **Features** is calculated by tracking the number of times two neighboring **Cells** correspond to a contiguous **Feature** pair. The **Filter** also notes which **Features** touch the outer surface of the sample (this is obtained for "free" while performing the above algorithm). The **Filter** gives the user the option whether or not they want to store this additional information.
-## Parameters ##
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Store Boundary Cells Array | bool | Whether to store the boundary **Cells** array |
-| Store Surface Features Array | bool | Whether to store the surface **Features** array |
-
-## Required Geometry ##
-
-Image
-
-## Required Objects ##
+% Auto generated parameter table will be inserted here
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Cell** belongs |
-| **Feature Attribute Matrix** | CellFeatureData | Cell Feature | N/A | **Feature Attribute Matrix** of the selected *Feature Ids* |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | BoundaryCells | int8_t | (1) | The number of neighboring **Cells** of a given **Cell** that belong to a different **Feature** than itself. Values will range from *0* to *6*. Only created if *Store Boundary Cells Array* is checked|
-| **Feature Attribute Array** | NumNeighbors | int32_t | (1) | Number of contiguous neighboring **Features** for a given **Feature** |
-| **Feature Attribute Array** | NeighborList | List of int32_t | (1) | List of the contiguous neighboring **Features** for a given **Feature** |
-| **Feature Attribute Array** | SharedSurfaceAreaLists | List of float | (1) | List of the shared surface area for each of the contiguous neighboring **Features** for a given **Feature** |
-| **Feature Attribute Array** | SurfaceFeatures | bool | (1) | Flag equal to 1 if the **Feature** touches an outer surface of the sample and equal to 0 if it does not. Only created if *Store Surface Features Array* is checked |
-
-## Example Pipelines ##
+## Example Pipelines
+ (01) SmallIN100 Morphological Statistics
+ (10) SmallIN100 Full Reconstruction
@@ -56,12 +29,10 @@ Image
+ (04) Two Phase Cubic Hexagonal Particles Equiaxed
+ (06) SmallIN100 Synthetic
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/FindNumFeaturesFilter.md b/src/Plugins/ComplexCore/docs/FindNumFeaturesFilter.md
index 3cbcf60735..16c242a516 100644
--- a/src/Plugins/ComplexCore/docs/FindNumFeaturesFilter.md
+++ b/src/Plugins/ComplexCore/docs/FindNumFeaturesFilter.md
@@ -1,45 +1,23 @@
# Find Number of Features
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Statistics (Morphological)
-## Description ##
+## Description
This **Filter** determines the number of **Features** in each **Ensemble** by summing the total number of rows in the feature attribute matrix belonging to each phase.
-## Parameters ##
-
-None
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
+% Auto generated parameter table will be inserted here
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | Phases | int32 | (1) | Specifies to which **Ensemble** each **Feature** belongs |
-| **Attribute Matrix** | EnsembleData | Ensemble AttributeMatrix | N/A | The path to the ensemble **Attribute Matrix** |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Ensemble Attribute Array** | NumFeatures | int32 | (1) | Number of **Features** that belong each **Ensemble** |
-
-## Example Pipelines ##
+## Example Pipelines
+ INL Export
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/FindSurfaceAreaToVolumeFilter.md b/src/Plugins/ComplexCore/docs/FindSurfaceAreaToVolumeFilter.md
index 73980efab8..f4b3ad37fa 100644
--- a/src/Plugins/ComplexCore/docs/FindSurfaceAreaToVolumeFilter.md
+++ b/src/Plugins/ComplexCore/docs/FindSurfaceAreaToVolumeFilter.md
@@ -14,29 +14,7 @@ This filter also optionally calculate the [Sphericity](https://en.wikipedia.org/
![Equation for Sphericity used in the filter](Images/Sphericity_Equation.png)
-## Parameters
-
-| Name | Type |
-|------|------|
-| Calculate Sphericity | Boolean |
-
-## Required Geometry
-
-Image
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Cell** belongs |
-| **Feature Attribute Array** | NumCells | int32_t | (1) | Number of **Cells** that are owned by the **Feature**. This value does not place any distinction between **Cells** that may be of a different size |
-
-## Created Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | SurfaceAreaVolumeRatio | float | (1) | Ratio of surface area to volume for each **Feature**. The units are inverse length |
-| **Feature Attribute Array** | Sphericity | float | (1) | The sphericity of each feature |
+% Auto generated parameter table will be inserted here
## Example Pipelines
@@ -46,8 +24,6 @@ Image
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/FindSurfaceFeatures.md b/src/Plugins/ComplexCore/docs/FindSurfaceFeatures.md
index b46689e174..1447f1eca0 100644
--- a/src/Plugins/ComplexCore/docs/FindSurfaceFeatures.md
+++ b/src/Plugins/ComplexCore/docs/FindSurfaceFeatures.md
@@ -15,9 +15,9 @@ This **Filter** determines whether a **Feature** touches an outer *Surface* of t
The output of this filter is a **Feature** level array of booleans where 0=Interior/Not touching and 1=Surface/Touching.
-_Note_: If there are voxels within the volume that have **Feature ID=0** then any feature touching those voxels will be considered a *Surface* feature.
+*Note*: If there are voxels within the volume that have **Feature ID=0** then any feature touching those voxels will be considered a *Surface* feature.
-_Note_: The version of this filter in legacy DREAM.3D had two bugs: one that indexed into neighboring features incorrectly (DREAM3D repo issue #988), and another that incorrectly labeled feature 0 as a surface feature when feature 0 exists in the feature ids array (DREAM3D repo issue #989). Both of these bugs have been fixed in this new version.
+*Note*: The version of this filter in legacy DREAM.3D had two bugs: one that indexed into neighboring features incorrectly (DREAM3D repo issue #988), and another that incorrectly labeled feature 0 as a surface feature when feature 0 exists in the feature ids array (DREAM3D repo issue #989). Both of these bugs have been fixed in this new version.
### 2D Image Geometry
@@ -30,26 +30,7 @@ If the structure/data is actually 2D, then the dimension that is planar is not c
| ![FindSurfaceFeatures_Cylinder](Images/FindSurfaceFeatures_Cylinder.png) | ![FindSurfaceFeatures_Square](Images/FindSurfaceFeatures_Square.png) |
| Example showing features touching Feature ID=0 (Black voxels) | Example showing features touching the outer surface of the bounding box |
-## Parameters
-
-None
-
-## Required Geometry
-
-Image
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Cell** belongs |
-| Cell Feature **Attribute Matrix** | Cell Feauture | N/A | The path to the cell feature **Attribute Matrix** |
-
-## Created Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | SurfaceFeatures | bool | (1) | Flag of 1 if **Feature** touches an outer surface or of 0 if it does not |
+% Auto generated parameter table will be inserted here
## Example Pipelines
@@ -59,8 +40,6 @@ Image
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/FindTriangleGeomCentroidsFilter.md b/src/Plugins/ComplexCore/docs/FindTriangleGeomCentroidsFilter.md
index defb9616e5..29ccd01c0d 100644
--- a/src/Plugins/ComplexCore/docs/FindTriangleGeomCentroidsFilter.md
+++ b/src/Plugins/ComplexCore/docs/FindTriangleGeomCentroidsFilter.md
@@ -14,26 +14,7 @@ using the following algorithm:
node to be entered once for a given owner*)
3. For each **Feature**, find the average (x,y,z) coordinate from the set of nodes that bound it
-## Parameters
-
-None
-
-## Required Geometry
-
-Triangle
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|--------------------------|-----------------|--------------|----------------------|------------------------------------------------------------------|
-| **Face Attribute Array** | FaceLabels | int32_t | (2) | Specifies which **Features** are on either side of each **Face** |
-| **Attribute Matrix** | FaceFeatureData | Face Feature | N/A | **Feature Attribute Matrix** of the selected *Face Labels* |
-
-## Created Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|-----------------------------|--------------|-------|----------------------|--------------------------------------------------------------------|
-| **Feature Attribute Array** | Centroids | float | (3) | Coordinates of the center of mass for a given enclosed **Feature** |
+% Auto generated parameter table will be inserted here
## Example Pipelines
@@ -41,8 +22,6 @@ Triangle
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/FindTriangleGeomSizesFilter.md b/src/Plugins/ComplexCore/docs/FindTriangleGeomSizesFilter.md
index 8de7b7ecd4..2da2dc9091 100644
--- a/src/Plugins/ComplexCore/docs/FindTriangleGeomSizesFilter.md
+++ b/src/Plugins/ComplexCore/docs/FindTriangleGeomSizesFilter.md
@@ -18,31 +18,12 @@ Labels_ array. The volume of any generic polyhedron can be computed using the fo
4. Compute the signed volume of each tetrahedron
5. Sum the signed tetrahedra volumes to obtain the volume of the enclosing polyhedron
-This computation is *not* the same as the Find Feature Sizes for **Triangle Geometries**, which computes the sum of the
+This computation is _not_ the same as the Find Feature Sizes for **Triangle Geometries**, which computes the sum of the
unit element sizes for a set of **Features** (thus, the Find Feature Sizes would compute the _area_
of **Features** in a **Triangle Geometry**, whereas this **Filter** is specialized to compute the enclosed volumes of **
Features** in a surface mesh).
-## Parameters
-
-None
-
-## Required Geometry
-
-Triangle
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|--------------------------|--------------|---------|----------------------|------------------------------------------------------------------|
-| **Face Attribute Array** | FaceLabels | int32_t | (2) | Specifies which **Features** are on either side of each **Face** |
-
-## Created Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|-----------------------------|-----------------|--------------|----------------------|-------------------------------------------|
-| **Attribute Matrix** | FaceFeatureData | Face Feature | N/A | Created **Feature Attribute Matrix** name |
-| **Feature Attribute Array** | Volumes | float | (1) | Volume of the enclosed **Feature** |
+% Auto generated parameter table will be inserted here
## Example Pipelines
@@ -50,8 +31,6 @@ Triangle
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/FindVertexToTriangleDistancesFilter.md b/src/Plugins/ComplexCore/docs/FindVertexToTriangleDistancesFilter.md
index 280aa700a3..cc47fc32fc 100644
--- a/src/Plugins/ComplexCore/docs/FindVertexToTriangleDistancesFilter.md
+++ b/src/Plugins/ComplexCore/docs/FindVertexToTriangleDistancesFilter.md
@@ -1,38 +1,20 @@
-Find Vertex to Triangle Distances
+Find Vertex to Triangle Distances
=============
-## Group (Subgroup) ##
-Sampling (Spatial)
-
-## Description ##
-This **Filter** computes distances between points in a **Vertex Geoemtry** and triangles in a **Triangle Geoemtry**. Specifically, for each point in the **Vertex Geometry**, the Euclidean distance to the closest triangle in the **Triangle Geoemtry** is stored. This distance is *signed*: if the point lies on the side of the triangle to which the triangle normal points, then the distance is positive; otherwise, the distance is negative. Additionally, the ID the closest triangle is stored for each point.
-
-## Parameters ##
+## Group (Subgroup)
-None
+Sampling (Spatial)
-## Required Geometry ##
-Vertex and Triangle
+## Description
-## Required Objects ##
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|-----|
-| **Data Container** | None | N/A | N/A | **Data Container** holding the source **Vertex Geometry** |
-| **Data Container** | None | N/A | N/A | **Data Container** holding the target **Triangle Geometry** |
-| **Face Attribute Array** | None | float | (3)) | Normals for the target **Triangle Geometry** |
+This **Filter** computes distances between points in a **Vertex Geoemtry** and triangles in a **Triangle Geoemtry**. Specifically, for each point in the **Vertex Geometry**, the Euclidean distance to the closest triangle in the **Triangle Geoemtry** is stored. This distance is *signed*: if the point lies on the side of the triangle to which the triangle normal points, then the distance is positive; otherwise, the distance is negative. Additionally, the ID the closest triangle is stored for each point.
-## Created Objects ##
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|-----|
-| **Vertex Attribute Array** | Distances | float | (1) | Euclidean distance to the closest triangle for each point |
-| **Vertex Attribute Array** | ClosestTriangleId | int32_t | (1) | Id of the closest triangle for each point |
+% Auto generated parameter table will be inserted here
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/FindVolFractionsFilter.md b/src/Plugins/ComplexCore/docs/FindVolFractionsFilter.md
index aed0a39293..69cf4e2f8f 100644
--- a/src/Plugins/ComplexCore/docs/FindVolFractionsFilter.md
+++ b/src/Plugins/ComplexCore/docs/FindVolFractionsFilter.md
@@ -1,44 +1,21 @@
# Find Volume Fractions of Ensembles
-## Group (Subgroup) ##
+## Group (Subgroup)
Statistics (Morphological)
-## Description ##
+## Description
This **Filter** determines the volume fraction of each **Ensemble**. The **Filter** counts the number of **Cells** belonging to each **Ensemble** and stores the number fraction.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-None
+## Example Pipelines
-## Required Geometry ##
-
-None
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | Phases | int32 | (1) | Specifies to which **Ensemble** each **Cell** belongs |
-| **Attribute Matrix** | CellEnsembleData | Ensemble AttributeMatrix | N/A | The path to the cell ensemble **Attribute Matrix** |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Ensemble Attribute Array** | VolFractions | float | (1) | Fraction of volume that belongs to each **Ensemble** |
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/GenerateColorTableFilter.md b/src/Plugins/ComplexCore/docs/GenerateColorTableFilter.md
index 65001894c9..b1278c60a1 100644
--- a/src/Plugins/ComplexCore/docs/GenerateColorTableFilter.md
+++ b/src/Plugins/ComplexCore/docs/GenerateColorTableFilter.md
@@ -1,42 +1,18 @@
# Generate Color Table
-## Description ##
+## Description
This **Filter** generates a color table array for a given 1-component input array. Each element of the input array
is normalized and converted to a color based on where the value falls in the spectrum of the selected color preset.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|-----------------|------|-------------------------------------------------------------------|
-| Selected Preset | JSON | The selected color preset, used to generate the color table array |
+## Example Pipelines
-## Required Geometry ###
-
-None
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-----|----------------------|----------------------------------------------------------------|
-| **Attribute Array** | N/A | Any | (1) | 1-component input array used to generate the color table array |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------|----------------------|---------------------------------------------------------|
-| **Attribute Array** | N/A | uint8 | (3) | RGB output color table array |
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/GenerateVectorColorsFilter.md b/src/Plugins/ComplexCore/docs/GenerateVectorColorsFilter.md
index f69047763c..98d13fc42f 100644
--- a/src/Plugins/ComplexCore/docs/GenerateVectorColorsFilter.md
+++ b/src/Plugins/ComplexCore/docs/GenerateVectorColorsFilter.md
@@ -1,47 +1,23 @@
-# Generate Vector Colors #
+# Generate Vector Colors
-## Group (Subgroup) ##
+## Group (Subgroup)
Generic (Coloring)
-## Description ##
+## Description
This **Filter** generates a color for each **Element** based on the vector assigned to that **Element** in the input vector data. The color scheme assigns a unique color to all points on the unit hemisphere using a HSV-like scheme. The color space is approximately represented by the following legend.
![Images/VectorColors](Images/VectorColors.png)
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------------------|------|-------------|
-| Apply to Good Voxels Only (Bad Voxels Will Be Black) | bool | Whether or not to assign colors to *bad* voxels or leave them black |
+## Example Pipelines
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Element Attribute Array** | VectorData | float32 | (3) | Vectors the colors will represent |
-| **Element Attribute Array** | Mask | bool | (1) | Used to define **Elements** as *good* or *bad* |
-
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Element Attribute Array** | Colors | uint8 | (3) | RGB colors |
-
-## Example Pipelines ##
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/IdentifySample.md b/src/Plugins/ComplexCore/docs/IdentifySample.md
index c3d307a280..68d3ae33f4 100644
--- a/src/Plugins/ComplexCore/docs/IdentifySample.md
+++ b/src/Plugins/ComplexCore/docs/IdentifySample.md
@@ -20,27 +20,9 @@ If *Fill Holes* is set to *true*:
| Name | Description |
|------|-------------|
|![Small IN100 IPF Map](Images/Small_IN100.png) | Good dataset to use this filter |
-|![APTR IPF Colors](Images/aptr12_001_0.png) | **NOT** a good data set to use because there is **no** overscan of the sample. |
+|![APTR IPF Colors](Images/aptr12_001_0.png) | NOT** a good data set to use because there is **no** overscan of the sample. |
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| Fill Holes in Largest Feature | bool | Whether to fill holes within sample after it is identified |
-
-## Required Geometry
-
-Image
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | Mask | bool | (1) | *Mask* array defining what is sample and what is not |
-
-## Created Objects
-
-None
+% Auto generated parameter table will be inserted here
## Example Pipelines
@@ -52,8 +34,6 @@ None
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/ImageContouringFilter.md b/src/Plugins/ComplexCore/docs/ImageContouringFilter.md
index d4283d5759..348ee5bce0 100644
--- a/src/Plugins/ComplexCore/docs/ImageContouringFilter.md
+++ b/src/Plugins/ComplexCore/docs/ImageContouringFilter.md
@@ -12,27 +12,7 @@ Here's what the results look like:
![3D-Contouring](Images/3D-contouring.png)
-## Parameters
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Contour value | float64 | This is the thresholding value that will be used to create the *Contouring Geometry* |
-
-## Required Geometry
-
-Image
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Data Array** | Data Array to Contour | Any | (1) | This is the array that will be parsed in order to create the contouring geometry, this is what the *Contour Value* will be compared against |
-
-## Created Objects
-
-| Kind | Default Name | Type | Description |
-|------|--------------|------|-------------|
-| Geometry | Contouring Geometry | TriangleGeom | This stores the 3D contouring line and the normals for the vertices |
+% Auto generated parameter table will be inserted here
## License & Copyright
@@ -41,6 +21,3 @@ Please see the description file distributed with this **Plugin**
## DREAM.3D Interaction
If you need more help with a **Filter**, please consider asking your question on the [DREAM.3D Help Forum!](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues)
-
-
-
diff --git a/src/Plugins/ComplexCore/docs/Images/ComputeMomentInvariants2D.png b/src/Plugins/ComplexCore/docs/Images/ComputeMomentInvariants2D.png
new file mode 100644
index 0000000000..4d1e9a9539
Binary files /dev/null and b/src/Plugins/ComplexCore/docs/Images/ComputeMomentInvariants2D.png differ
diff --git a/src/Plugins/ComplexCore/docs/Images/ComputeMomentInvariants_Fig1.png b/src/Plugins/ComplexCore/docs/Images/ComputeMomentInvariants_Fig1.png
new file mode 100644
index 0000000000..a25a4acfd8
Binary files /dev/null and b/src/Plugins/ComplexCore/docs/Images/ComputeMomentInvariants_Fig1.png differ
diff --git a/src/Plugins/ComplexCore/docs/ImportBinaryCTNorthstarFilter.md b/src/Plugins/ComplexCore/docs/ImportBinaryCTNorthstarFilter.md
index c6e18dc549..786f151e5d 100644
--- a/src/Plugins/ComplexCore/docs/ImportBinaryCTNorthstarFilter.md
+++ b/src/Plugins/ComplexCore/docs/ImportBinaryCTNorthstarFilter.md
@@ -1,10 +1,10 @@
-# Import North Star Imaging CT File (Binary) #
+# Import North Star Imaging CT File (Binary)
-## Group (Subgroup) ##
+## Group (Subgroup)
IOFilters (Input)
-## Description ##
+## Description
This **Filter** will import a NorthStar Imaging data set consisting of a single .nsihdr and one or more .nsidat files. The data is read into an Image Geometry. The user can import a subvolume instead of reading the entire data set into memory.
@@ -12,38 +12,12 @@ The user should note that when using the subvolume feature that the ending voxel
The .nsihdr file will be read during preflight and the .nsidat file(s) will be extracted from there. The expectation is that the .nsidat files are in the same directory as the .nsihdr files.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------|------|-------------|
-| Input Header File | String | Path to the .nsihdr file |
-| Length Unit | integer | Enumeration value into the units table. Default is mm |
-| Import Subvolume | Boolean | Import a subvolume instead of the entire volume |
-| Starting Voxel | 3xInteger | The voxel indices to start the subvolume import at. |
-| Ending Voxel | 3xInteger | The voxel indices to end the subvolume import at (Inclusive). |
-
-## Required Geometry ###
-
-Not Applicable
-
-## Required Objects ##
-
-Not Applicable
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Image Geometry** | CT Image Geometry | ImageGeom | N/A | |
-| **Attribute Matrix** | CT Scan Data | Attribute Matrix | N/A | |
-| **Data Array** | Density | float | (1) | Density Data |
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/ImportDREAM3DFilter.md b/src/Plugins/ComplexCore/docs/ImportDREAM3DFilter.md
index 52b9d92551..4f5d29f9e6 100644
--- a/src/Plugins/ComplexCore/docs/ImportDREAM3DFilter.md
+++ b/src/Plugins/ComplexCore/docs/ImportDREAM3DFilter.md
@@ -1,34 +1,15 @@
# ImportDREAM3DFilter
-## Description ##
+## Description
This **Filter** reads the data structure to an hdf5 file with the .dream3d extension.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------|------|-------------|
-| Import File Path | Filesystem Path | The file path the DataStructure should be read from as an HDF5 file. |
-
-## Required Geometry ###
-
-None
-
-## Required Objects ##
-
-None
-
-## Created Objects ##
-
-None
-
-## Example Pipelines ##
+## Example Pipelines
ALL
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-
-
-
diff --git a/src/Plugins/ComplexCore/docs/ImportDeformKeyFileV12Filter.md b/src/Plugins/ComplexCore/docs/ImportDeformKeyFileV12Filter.md
index 4a0558a751..3b04ddd21b 100644
--- a/src/Plugins/ComplexCore/docs/ImportDeformKeyFileV12Filter.md
+++ b/src/Plugins/ComplexCore/docs/ImportDeformKeyFileV12Filter.md
@@ -10,32 +10,12 @@ This **Filter** reads DEFORM v12 key files and saves the data in a newly created
It reads the quadrilateral mesh data (nodal coordinates and connectivity), and the value of variables such as stress, strain, ndtmp, etc at cells and nodes.
-## Parameters
-
-| Name | Type | Description |
-|------|------|------|
-| Input File | Path | Name and address of the input DEFORM v12 key file |
-
-## Required Geometry
-
-Not Applicable
-
-## Required Objects
-
-## Created Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|-----|
-| **QuadGeom** | Quad Geometry | QuadGeom | N/A | Created **QuadGeom** path and name |
-| **Attribute Matrix** | Vertex Data | Vertex | N/A | Created **Vertex Attribute Matrix** name |
-| **Attribute Matrix** | Cell Data | Cell | N/A | Created **Cell Attribute Matrix** name |
+% Auto generated parameter table will be inserted here
## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/ImportHDF5Dataset.md b/src/Plugins/ComplexCore/docs/ImportHDF5Dataset.md
index 0056ad35e4..b5a6a341fa 100644
--- a/src/Plugins/ComplexCore/docs/ImportHDF5Dataset.md
+++ b/src/Plugins/ComplexCore/docs/ImportHDF5Dataset.md
@@ -1,10 +1,10 @@
# Import HDF5 Dataset
-## Group (Subgroup) ##
+## Group (Subgroup)
Core (IO/Read)
-## Description ##
+## Description
This **Filter** allows the user to import datasets from an HDF5 file and store them as attribute arrays in DREAM.3D. This filter supports importing datasets with any number of dimensions, as long as the created attribute array's total number of components and the tuple count of the destination attribute matrix multiply together to match the HDF5 dataset's total number of elements.
@@ -14,7 +14,7 @@ The component dimensions are input as a comma-delimited list of dimensional valu
2. 5, 2, 1 = 5x2x1
3. 6 = 6
-### Examples ###
+### Examples
1. Suppose we have a 1D dataset in an HDF5 file with dimension **12,000**.
We can input component dimensions of **5, 2, 2** and set the destination attribute matrix tuple dimensions to **35 x 5 x 2 x 2**
@@ -37,38 +37,14 @@ We can input component dimensions of **2** and set our destination attribute mat
![Example Image](Images/ImportHDF5Dataset_ui.png)
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------|------| ----------- |
-| HDF5 File | String | The path to the HDF5 file |
-| Checked Datasets | N/A | The checked datasets in the file tree to import |
-| Component Dimensions | String | The component dimensions that the imported dataset will have. This is a comma-delimited list of dimensional values |
+## Example Pipelines
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Attribute Matrix** | None | DataArrayPath | N/A | **Attribute Matrix** used to store imported data |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Data Array(s)** | Name of dataset(s) from HDF5 file | Type from HDF5 file | Input as a filter parameter | The created Attribute Array(s) |
-
-## Example Pipelines ##
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/ImportVolumeGraphicsFileFilter.md b/src/Plugins/ComplexCore/docs/ImportVolumeGraphicsFileFilter.md
index 4d5b50b8fa..82939e51c6 100644
--- a/src/Plugins/ComplexCore/docs/ImportVolumeGraphicsFileFilter.md
+++ b/src/Plugins/ComplexCore/docs/ImportVolumeGraphicsFileFilter.md
@@ -1,44 +1,19 @@
-# Import Volume Graphics Files (.vgi, .vol) #
+# Import Volume Graphics Files (.vgi, .vol)
-## Group (Subgroup) ##
+## Group (Subgroup)
Import/Export
-## Description ##
+## Description
This **Filter** will import Volume Graphics data files in the form of .vgi/.vol pairs. Both files must exist and be in the same directory for the filter to work. The .vgi file is read to find out the dimensions, spacing and units of the data. The name of the .vol file is also contained in the .vgi file.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------|------|-------------|
-| VolumeGraphics .vgi File | std::filesystem::path | Path to the .vgi file on disk |
-| Image Geometry | DataPath | Name of the created Image Geometry |
-| Cell Attribute Matrix | std::string | Name of the created AttributeMatrix |
-| Density | std::string | Name of the created Cell Data |
-
-## Required Geometry ###
-
-Not Applicable
-
-## Required Objects ##
-
-Not Applicable
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Image Geometry** | VolumeGraphics | Image Geometry | N/A | |
-| **Attribute Matrix** | CT Data | Cell Attribute Matrix | N/A | |
-| **Element Attribute Array** | Density | float | (1) | raw data |
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/InitializeData.md b/src/Plugins/ComplexCore/docs/InitializeData.md
index 57d8a101df..9329e4c126 100644
--- a/src/Plugins/ComplexCore/docs/InitializeData.md
+++ b/src/Plugins/ComplexCore/docs/InitializeData.md
@@ -1,49 +1,21 @@
-# Initialize Data
+# Initialize Data
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Processing (Cleanup)
-## Description ##
+## Description
This **Filter** allows the user to define a subvolume of the data set in which the **Filter** will reset all data by writing *zeros (0)* into every array for every **Cell** within the subvolume.
-## Parameters ##
-
-| Name | Type | Description |
-|------|------|-------------|
-| X Min | int32_t | Minimum X bound in **Cells** |
-| Y Min | int32_t | Minimum Y bound in **Cells** |
-| Z Min | int32_t | Minimum Z bound in **Cells** |
-| X Max | int32_t | Maximum X bound in **Cells** |
-| Y Max | int32_t | Maximum Y bound in **Cells** |
-| Z Max | int32_t | Maximum Z bound in **Cells** |
-
-## Required Geometry ##
-
-Image
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Attribute Matrix** | CellData | Cell | N/A | **Cell** data in which to initialize a subvolume to zeros |
+% Auto generated parameter table will be inserted here
-## Created Objects ##
+## Example Pipelines
-None
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/InterpolatePointCloudToRegularGridFilter.md b/src/Plugins/ComplexCore/docs/InterpolatePointCloudToRegularGridFilter.md
index 8ba867b4df..fc6e291ab8 100644
--- a/src/Plugins/ComplexCore/docs/InterpolatePointCloudToRegularGridFilter.md
+++ b/src/Plugins/ComplexCore/docs/InterpolatePointCloudToRegularGridFilter.md
@@ -1,11 +1,11 @@
Interpolate Point Cloud to Regular Grid
=============
-## Group (Subgroup) ##
+## Group (Subgroup)
Sampling (Interpolation)
-## Description ##
+## Description
This **Filter** interpolates the values of arrays stored in a **Vertex Geometry** onto a user-selected **Image Geometry**. The user defines the (x,y,z) radii of a kernel in *real space units*. This kernel can be intialized to either *uniform* or *Gaussian*. The interpolation algorithm proceeds as follows:
@@ -17,41 +17,12 @@ The result of the above approach is a list of data at each voxel in the **Image
A mask may be supplied to the filter. Points that are not within the mask are ignored during interpolation. Additionally, the distances between each voxel and the source point for the intersecting kernel may be stored; this significantly increases the required memory. Arrays may be passed through to the image geometry without applying any interpolation. This operation is equivalent to used a uniform kernel.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------|------|-------------|
-| Use Mask | bool | Whether to use a mask when interpolating the vertex arrays |
-| Store Kernel Distances | bool | Whether to store the kernel distances for each vertex |
-| Interpolation Technique | Enumeration | The type of kernel to use, either *Uniform* or *Gaussian* |
-| Kernel Size | float 3x | The size of the interpolation kernel, in real space units |
-
-## Required Geometry ###
-
-Vertex and Image
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Data Container** | None | N/A | N/A | **Data Container** holding the **Vertex Geometry** to interpolate |
-| **Data Container** | None | N/A | N/A | **Data Container** holding the **Image Geometry** that serves as the target grid for interpolation |
-| **Vertex Attribute Array** | VoxelIndices | size_t | (1) | The indices that indicate in which voxel in the supplied **Image Geometry** each vertex lies |
-| Various **Attribute Array** | None | Varies | (1) | The **Vertex Attribute Arrays** to interpolate |
-| Various **Attribute Array** | None | Varies | (1) | The **Vertex Attribute Arrays** to copy |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Attribute Matrix** | InterpolatedAttributeMatrix | Cell | N/A | **Attribute Matrix** that stores the interpolated **Attribute Arrays** |
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/IterativeClosestPointFilter.md b/src/Plugins/ComplexCore/docs/IterativeClosestPointFilter.md
index 82ddea3d2e..49ac7b63a8 100644
--- a/src/Plugins/ComplexCore/docs/IterativeClosestPointFilter.md
+++ b/src/Plugins/ComplexCore/docs/IterativeClosestPointFilter.md
@@ -1,10 +1,10 @@
# IterativeClosestPoint
-## Group (Subgroup) ##
+## Group (Subgroup)
Reconstruction (Alignment)
-## Description ##
+## Description
This **Filter** estimates the rigid body transformation (i.e., rotation and translation) between two sets of points represted by **Vertex Geometries** using the *iterative closest point* (ICP) algorithm. The two **Vertex Geometries** are not required to have the same number of points. The **Filter** first initializes temporary storage for each set of points and a global transformation. Then, the alignment algorithm iterates through the following steps:
@@ -17,42 +17,14 @@ Iterations proceed for a fixed number of user-defined steps. The final rigid bo
ICP has a number of advantages, such as robustness to noise and no requirement that the two sets of points to be the same size. However, peformance may suffer if the two sets of points are of siginficantly different size.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------|------|------|
-| Number of Iterations | int | Number if iterations for the ICP algorithm |
-| Apply Transform to Moving Geometry | bool | Whether to apply the computed transform to the moving **Vertex Geometry** |
+## Example Pipelines
-## Required Geometry ##
-
-Vertex
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|-----|
-| **Data Container** | None | N/A | N/A | **Data Container** holding the moving **Vertex Geometry** |
-| **Data Container** | None | N/A | N/A | **Data Container** holding the target **Vertex Geometry** |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|-----|
-| **Attribute Matrix** | TransformAttributeMatrix | Generic | N/A | **Attribute Matrix** that stores the computed transformation |
-| **Attribute Array** | Transform | float | (4, 4) | Computed transformation matrix |
-
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/KMeansFilter.md b/src/Plugins/ComplexCore/docs/KMeansFilter.md
index b72f6b18c9..3028265096 100644
--- a/src/Plugins/ComplexCore/docs/KMeansFilter.md
+++ b/src/Plugins/ComplexCore/docs/KMeansFilter.md
@@ -1,16 +1,16 @@
-# K Means #
+# K Means
-## Group (Subgroup) ##
+## Group (Subgroup)
DREAM3D Review (Clustering)
-## Description ##
+## Description
***Warning:* The randomnes in this filter is not currently consistent between operating systems even if the same seed is used. Specifically between Unix and Windows. This does not affect the results, but the IDs will not correspond. For example if the Cluster Identifier at index one on Linux is 1 it could be 2 on Windows, the overarching clusters will be the same, but their IDs will be different.**
-This **Filter** applies the k means algorithm to an **Attribute Array**. K means is a *clustering algorithm* that assigns to each point of the **Attribute Array** a _cluster Id_. The user must specify the number of clusters in which to partition the array. Specifically, a k means partitioning is a _Voronoi tesselation_; an optimal solution to the k means problem is such that each point in the data set is associated with the cluster that has the closest mean. This partitioning is the one that minimizes the within cluster variance (i.e., minimizes the within cluster sum of squares differences). Thus, the "metric" used for k means is the 2-norm (the _Euclidean norm_; the squared Euclidean norm may also be used since this maintains the triangle inequality).
+This **Filter** applies the k means algorithm to an **Attribute Array**. K means is a *clustering algorithm* that assigns to each point of the **Attribute Array** a *cluster Id*. The user must specify the number of clusters in which to partition the array. Specifically, a k means partitioning is a *Voronoi tesselation*; an optimal solution to the k means problem is such that each point in the data set is associated with the cluster that has the closest mean. This partitioning is the one that minimizes the within cluster variance (i.e., minimizes the within cluster sum of squares differences). Thus, the "metric" used for k means is the 2-norm (the *Euclidean norm*; the squared Euclidean norm may also be used since this maintains the triangle inequality).
-Optimal solutions to the k means partitioning problem are computationally difficult; this **Filter** used _Lloyd's algorithm_ to approximate the solution. Lloyd's algorithm is an iterative algorithm that proceeds as follows:
+Optimal solutions to the k means partitioning problem are computationally difficult; this **Filter** used *Lloyd's algorithm* to approximate the solution. Lloyd's algorithm is an iterative algorithm that proceeds as follows:
1. Choose k points at random to serve as the initial cluster "means"
2. Until convergence, repeat the following steps:
@@ -18,9 +18,9 @@ Optimal solutions to the k means partitioning problem are computationally diffic
- Associate each point with the closest mean, where "closest" is the smallest 2-norm distance
- Recompute the means based on the new tesselation
-Convergence is defined as when the computed means change very little (precisely, when the differences are within machine epsilon). Since Lloyd's algorithm is iterative, it only serves as an approximation, and may result in different classifications on each execution with the same input data. The user may opt to use a mask to ignore certain points; where the mask is _false_, the points will be placed in cluster 0.
+Convergence is defined as when the computed means change very little (precisely, when the differences are within machine epsilon). Since Lloyd's algorithm is iterative, it only serves as an approximation, and may result in different classifications on each execution with the same input data. The user may opt to use a mask to ignore certain points; where the mask is *false*, the points will be placed in cluster 0.
-A clustering algorithm can be considered a kind of segmentation; this implementation of k means does not rely on the **Geometry** on which the data lie, only the *topology* of the space that the array itself forms. Therefore, this **Filter** has the effect of creating either **Features** or **Ensembles** depending on the kind of array passed to it for clustering. If an **Element** array (e.g., voxel-level **Cell** data) is passed to the **Filter**, then **Features** are created (in the previous example, a **Cell Feature Attribute Matrix** will be created). If a **Feature** array is passed to the **Filter**, then an **Ensemble Attribute Matrix** is created. The following table shows what type of **Attribute Matrix** is created based on what sort of array is used for clustering:
+A clustering algorithm can be considered a kind of segmentation; this implementation of k means does not rely on the **Geometry** on which the data lie, only the *topology* of the space that the array itself forms. Therefore, this **Filter** has the effect of creating either **Features** or **Ensembles** depending on the kind of array passed to it for clustering. If an **Element** array (e.g., voxel-level **Cell** data) is passed to the **Filter**, then **Features** are created (in the previous example, a **Cell Feature Attribute Matrix** will be created). If a **Feature** array is passed to the **Filter**, then an Ensemble Attribute Matrix** is created. The following table shows what type of **Attribute Matrix** is created based on what sort of array is used for clustering:
| Attribute Matrix Source | Attribute Matrix Created |
|------------------|--------------------|
@@ -40,45 +40,18 @@ A clustering algorithm can be considered a kind of segmentation; this implementa
This **Filter** will store the means for the final clusters within the created **Attribute Matrix**.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------|------|-------------|
-| Number of Clusters | int32_t | The number of clusters in which to partition the array |
-| Distance Metric | Enumeration | The metric used to determine the distances between points; only 2-norm metrics (i.e., Euclidean or squared Euclidean) may be chosen |
-| Use Mask | bool | Whether to use a boolean mask array to ignore certain points flagged as *false* from the algorithm |
-
-## Required Geometry ###
-
-None
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| Any **Attribute Array** | None | Any| Any | The **Attribute Array** to cluster |
-| **Attrubute Array** | Mask | bool | (1) | Specifies if the point is to be counted in the algorithm, if *Use Mask* is checked |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Attribute Matrix** | ClusterData | Feature/Ensemble | N/A | The **Attribute Matrix** in which to store information associated with the created clusters |
-| **Attribute Array** | ClusterIds | int32_t | (1) | Specifies to which cluster each point belongs |
-| **Attribute Array** | ClusterMeans | double | (1) | The means of the final clusters |
-
-## References ##
+## References
[1] Least squares quantization in PCM, S.P. Lloyd, IEEE Transactions on Information Theory, vol. 28 (2), pp. 129-137, 1982.
-## Example Pipelines ##
+## Example Pipelines
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/KMedoidsFilter.md b/src/Plugins/ComplexCore/docs/KMedoidsFilter.md
index 63ef5120e1..aa188bdf91 100644
--- a/src/Plugins/ComplexCore/docs/KMedoidsFilter.md
+++ b/src/Plugins/ComplexCore/docs/KMedoidsFilter.md
@@ -1,14 +1,14 @@
-# K Medoids #
+# K Medoids
-## Group (Subgroup) ##
+## Group (Subgroup)
DREAM3D Review (Clustering)
-## Description ##
+## Description
***Warning:* The randomnes in this filter is not currently consistent between operating systems even if the same seed is used. Specifically between Unix and Windows. This does not affect the results, but the IDs will not correspond. For example if the Cluster Identifier at index one on Linux is 1 it could be 2 on Windows, the overarching clusters will be the same, but their IDs will be different.**
-This **Filter** applies the k medoids algorithm to an **Attribute Array**. K medoids is a *clustering algorithm* that assigns to each point of the **Attribute Array** a _cluster Id_. The user must specify the number of clusters in which to partition the array. Specifically, a k medoids partitioning is such that each point in the data set is associated with the cluster that minimizes the sum of the pair-wise distances between the data points and their associated cluster centers (medoids). This approach is analogous to k means, but uses actual data points (the medoids) as the cluster exemplars instead of the means. Medoids in this context refer to the data point in each cluster that is most like all other data points, i.e., that data point whose average distance to all other data points in the cluster is smallest. Unlike k means, since pair-wise distances are minimized instead of variance, any arbirtary concept of "distance" may be used; this **Filter** allows for the selection of a variety of distance metrics.
+This **Filter** applies the k medoids algorithm to an **Attribute Array**. K medoids is a *clustering algorithm* that assigns to each point of the **Attribute Array** a *cluster Id*. The user must specify the number of clusters in which to partition the array. Specifically, a k medoids partitioning is such that each point in the data set is associated with the cluster that minimizes the sum of the pair-wise distances between the data points and their associated cluster centers (medoids). This approach is analogous to k means, but uses actual data points (the medoids) as the cluster exemplars instead of the means. Medoids in this context refer to the data point in each cluster that is most like all other data points, i.e., that data point whose average distance to all other data points in the cluster is smallest. Unlike k means, since pair-wise distances are minimized instead of variance, any arbirtary concept of "distance" may be used; this **Filter** allows for the selection of a variety of distance metrics.
This **Filter** uses the *Voronoi iteration* algorithm to produce the clustering. The algorithm is iterative and proceeds as follows:
@@ -19,9 +19,9 @@ This **Filter** uses the *Voronoi iteration* algorithm to produce the clustering
- For each cluster, change the medoid to the point in that cluster that minimizes the sum of distances between that point and all other points in the cluster
- Reassign each point to the closest medoid
-Convergence is defined as when the medoids no longer change position. Since the algorithm is iterative, it only serves as an approximation, and may result in different classifications on each execution with the same input data. The user may opt to use a mask to ignore certain points; where the mask is _false_, the points will be placed in cluster 0.
+Convergence is defined as when the medoids no longer change position. Since the algorithm is iterative, it only serves as an approximation, and may result in different classifications on each execution with the same input data. The user may opt to use a mask to ignore certain points; where the mask is *false*, the points will be placed in cluster 0.
-A clustering algorithm can be considered a kind of segmentation; this implementation of k medoids does not rely on the **Geometry** on which the data lie, only the *topology* of the space that the array itself forms. Therefore, this **Filter** has the effect of creating either **Features** or **Ensembles** depending on the kind of array passed to it for clustering. If an **Element** array (e.g., voxel-level **Cell** data) is passed to the **Filter**, then **Features** are created (in the previous example, a **Cell Feature Attribute Matrix** will be created). If a **Feature** array is passed to the **Filter**, then an **Ensemble Attribute Matrix** is created. The following table shows what type of **Attribute Matrix** is created based on what sort of array is used for clustering:
+A clustering algorithm can be considered a kind of segmentation; this implementation of k medoids does not rely on the **Geometry** on which the data lie, only the *topology* of the space that the array itself forms. Therefore, this **Filter** has the effect of creating either **Features** or **Ensembles** depending on the kind of array passed to it for clustering. If an **Element** array (e.g., voxel-level **Cell** data) is passed to the **Filter**, then **Features** are created (in the previous example, a **Cell Feature Attribute Matrix** will be created). If a **Feature** array is passed to the **Filter**, then an Ensemble Attribute Matrix** is created. The following table shows what type of **Attribute Matrix** is created based on what sort of array is used for clustering:
| Attribute Matrix Source | Attribute Matrix Created |
|------------------|--------------------|
@@ -41,45 +41,18 @@ A clustering algorithm can be considered a kind of segmentation; this implementa
This **Filter** will store the medoids for the final clusters within the created **Attribute Matrix**.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------|------|-------------|
-| Number of Clusters | int32_t | The number of clusters in which to partition the array |
-| Distance Metric | Enumeration | The metric used to determine the distances between points |
-| Use Mask | bool | Whether to use a boolean mask array to ignore certain points flagged as *false* from the algorithm |
-
-## Required Geometry ###
-
-None
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| Any **Attribute Array** | None | Any| Any | The **Attribute Array** to cluster |
-| **Attrubute Array** | Mask | bool | (1) | Specifies if the point is to be counted in the algorithm, if *Use Mask* is checked |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Attribute Matrix** | ClusterData | Feature/Ensemble | N/A | The **Attribute Matrix** in which to store information associated with the created clusters |
-| **Attribute Array** | ClusterIds | int32_t | (1) | Specifies to which cluster each point belongs |
-| **Attribute Array** | ClusterMeans | double | (1) | The means of the final clusters |
-
-## References ##
+## References
[1] A simple and fast algorithm for K-medoids clustering, H.S. Park and C.H. Jun, Expert Systems with Applications, vol. 28 (2), pp. 3336-3341, 2009.
-## Example Pipelines ##
+## Example Pipelines
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/LaplacianSmoothingFilter.md b/src/Plugins/ComplexCore/docs/LaplacianSmoothingFilter.md
index 8f12538ce7..c56440a8b3 100644
--- a/src/Plugins/ComplexCore/docs/LaplacianSmoothingFilter.md
+++ b/src/Plugins/ComplexCore/docs/LaplacianSmoothingFilter.md
@@ -1,11 +1,10 @@
# Laplacian Smoothing
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Surface Meshing (Smoothing)
-## Description ##
+## Description
This **Filter** applies Laplacian smoothing to a **Triangle Geometry** that represents a surface mesh. A. Belyaev [2] has a concise explanation of the Laplacian Smoothing as follows:
@@ -28,23 +27,21 @@ where n is the number of neighbors. The local update rule
![](Images/Laplacian_Eq2.png)
-
applied to every point of the triangulated surface is called Laplacian smoothing of the surface. Typically the factor λ is a small positive number, and the process (2) is executed repeatedly. The Laplacian smoothing algorithm reduces the high frequency surface information and tends to flatten the surface. See Fig. 2 where Laplacian smoothing is applied to a triangulated model of a Noh mask.
-If λ is too small, one needs more iterations for smoothing and the smoothing process becomes time-consuming. If λ is not small enough, the smoothing process becomes unstable.
+If λ is too small, one needs more iterations for smoothing and the smoothing process becomes time-consuming. If λ is not small enough, the smoothing process becomes unstable.
---------------------------
In the Laplacian algorithm the λ term has a range of 0 ≤ λ ≤ 1 and defines a relative distance that a node can move relative to the positions of the nodes neighbors. A λ = 0 value will effectively stop those node types from any movement during the algorithm thus by allowing the user to set this value for specific types of nodes the user can arrest the shrinkage of the surface mesh during the smoothing process.
-
-### Taubin's Lambda-Mu Smoothing Algorithm ##
+### Taubin's Lambda-Mu Smoothing Algorithm
One of the options for the filter allows the user to apply Taubin's Lambda-Mu variation on Laplacian smoothing. This variation removes the shrinkage typically found with Laplacian smoothing by adding an additional step within each iteration where the negative of the (Lambda value \* Mu Factor) which effectively moves the points in the **opposite** direction from the initial movement. Because of this negative movement the number of iterations to achieve the same level of smoothing is greatly increased, on the order of 10x to 20x.
-### Algorithm Usage and Memory Requirements ###
+### Algorithm Usage and Memory Requirements
-Currently, if you lock the *Default Lambda* value to zero (0), the triple lines and quadruple points will not be able to move because none of their neighbors can move. The user may want to consider allowing a small value of λ for the default nodes which will allow some movement of the triple lines and/or quadruple Points.
+Currently, if you lock the *Default Lambda* value to zero (0), the triple lines and quadruple points will not be able to move because none of their neighbors can move. The user may want to consider allowing a small value of λ for the default nodes which will allow some movement of the triple lines and/or quadruple Points.
This **Filter** will create additional internal arrays in order to facilitate the calculations. These arrays are
@@ -54,7 +51,7 @@ This **Filter** will create additional internal arrays in order to facilitate th
- Integer for number of connections for each node (same size as nodes array)
- 64 bit float for delta values (3x size of nodes array)
-Due to these array allocations this **Filter** can consume large amounts of memory if the starting mesh has a large number of nodes.
+Due to these array allocations this **Filter** can consume large amounts of memory if the starting mesh has a large number of nodes.
The values for the *Node Type* array can take one of the following values.
namespace SurfaceMesh {
@@ -71,53 +68,22 @@ The values for the *Node Type* array can take one of the following values.
For more information on surface meshing, visit the tutorial.
+% Auto generated parameter table will be inserted here
-## Parameters ##
-
-| Name | Type | Description |
-|------|------|-------------|
-| Iteration Steps | int32_t | Number of iteration steps to perform. More steps causes more smoothing but will also cause the volume to shrink more. _Inreasing this number too high may cause collapse of points!_ |
-| Default Lambda | float | Value of λ to apply to general internal nodes that are not triple lines, quadruple points or on the surface of the volume |
-| Use Taubin Smoothing | boolean | Use Taubin's Lambda-Mu algorithm. |
-| Mu Factor | float | A value that is multipied by Lambda the result of which is the *mu* in Taubin's paper. The value should be a negative value. |
-| Triple Line Lambda | float | Value of λ to apply to nodes designated as triple line nodes. |
-| Quadruple Points Lambda | float | Value of λ to apply to nodes designated as quadruple points. |
-| Outer Points Lambda | float | The value of λ to apply to nodes that lie on the outer surface of the volume |
-| Outer Triple Line Lambda | float | Value of λ for triple lines that lie on the outer surface of the volume |
-| Outer Quadruple Points Lambda | float | Value of λ for the quadruple Points that lie on the outer surface of the volume. |
-
-## Required Geometry ##
-
-Triangle
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Vertex Attribute Array** | NodeTypes | int8_t | (1) | Specifies the type of node in the **Geometry** |
-| **Face Attribute Array** | FaceLabels | int32_t | (2) | Specifies which **Features** are on either side of each **Face** |
-
-## Created Objects ##
-
-None
-
-## References ##
+## References
[1] D. A. Feature, (1988) Laplacian smoothing and Delaunay triangulations. Commun. appl. numer. methods, 4: 709 712. doi: 10.1002/cnm.1630040603
-[2] A. Belyaev, Mesh smoothing and enhancing curvature estimation, [http://www.mpi-inf.mpg.de/ ag4-gm/handouts/06gm_surf3.pdf](http://www.mpi-inf.mpg.de/ ag4-gm/handouts/06gm_surf3.pdf).
+[2] A. Belyaev, Mesh smoothing and enhancing curvature estimation, [http://www.mpi-inf.mpg.de/ ag4-gm/handouts/06gm_surf3.pdf]( ag4-gm/handouts/06gm_surf3.pdf).
+## Example Pipelines
-## Example Pipelines ##
+- (02) SmallIN100 Smooth Mesh
-+ (02) SmallIN100 Smooth Mesh
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/LosAlamosFFTWriterFilter.md b/src/Plugins/ComplexCore/docs/LosAlamosFFTWriterFilter.md
index faeff45346..1a0fffaee0 100644
--- a/src/Plugins/ComplexCore/docs/LosAlamosFFTWriterFilter.md
+++ b/src/Plugins/ComplexCore/docs/LosAlamosFFTWriterFilter.md
@@ -18,7 +18,7 @@ The Euler angles are in degrees. X, Y, Z are integer indices into the **Image**
### Example Output
-The output file:
+The output file:
90.000 0.000 0.000 1 1 1 0 1
90.000 0.000 0.000 2 1 1 0 1
@@ -41,27 +41,7 @@ The output file:
90.000 0.000 0.000 19 1 1 0 1
..
-## Parameters
-
-| Name | Type | Description |
-|------------------|------|-------------|
-| Output File | File Path | The output .txt file path |
-
-## Required Geometry
-
-Image
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | FeaturesIds | int32_t | (1) | Specifies to which **Feature** each **Cell** belongs |
-| **Cell Attribute Array** | EulerAngles | float | (3) | Three angles defining the orientation of the **Cell** in Bunge convention (Z-X-Z) |
-| **Cell Attribute Array** | Phases | int32_t | (1) | Specifies to which **Ensemble** each **Cell** belongs |
-
-## Created Objects
-
-None
+% Auto generated parameter table will be inserted here
## References
@@ -73,8 +53,6 @@ None
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/MapPointCloudToRegularGridFilter.md b/src/Plugins/ComplexCore/docs/MapPointCloudToRegularGridFilter.md
index 88095556a4..7f8603d7d9 100644
--- a/src/Plugins/ComplexCore/docs/MapPointCloudToRegularGridFilter.md
+++ b/src/Plugins/ComplexCore/docs/MapPointCloudToRegularGridFilter.md
@@ -1,48 +1,22 @@
Map Point Cloud to Regular Grid
=============
-## Group (Subgroup)
+## Group (Subgroup)
Sampling (Mapping)
-## Description
+## Description
This **Filter** determines, for a user-defined grid, in which voxel each point in a **Vertex Geometry** lies. The user can either construct a sampling grid by specifying the dimensions, or select a pre-existing **Image Geometry** to use as the sampling grid. The voxel indices that each point lies in are stored on the vertices.
Additionally, the user may opt to use a mask; points for which the mask are false are ignored when computing voxel indices (instead, they are initialized to voxel 0).
-## Parameters
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------|------|-------------|
-| Sampling Grid Type | Enumeration | The method used to create the sampling grid, either *Manual* or *Use Existing Image Geometry* |
-| Grid Dimensions | int 3x | Dimensions of the sampling grid, if *Manual* is selected |
-| Use Mask | bool | Whether to use a mask for the input **Vertex Geometry** |
-
-## Required Geometry
-
-Vertex
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Data Container** | None | N/A | N/A | **Data Container** holding the input **Vertex Geometry** |
-| **Data Container** | None | N/A | N/A | **Data Container** holding the sampling **Image Geometry**, if *Use Existing Image Geometry* is selected |
-| **Vertex Attribute Array** | None | bool | (1) | Vertex mask, if *Use Mask* is selected |
-
-## Created Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Vertex Attribute Array** | VoxelIndices | size_t | (1) | Indices of the voxels in which each point lies |
-
-## License & Copyright
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/MinNeighbors.md b/src/Plugins/ComplexCore/docs/MinNeighbors.md
index a63ae5178a..208a0b667a 100644
--- a/src/Plugins/ComplexCore/docs/MinNeighbors.md
+++ b/src/Plugins/ComplexCore/docs/MinNeighbors.md
@@ -1,55 +1,30 @@
# Minimum Number of Neighbors
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Processing (Cleanup)
-## Description ##
+## Description
This **Filter** sets the minimum number of contiguous neighboring **Features** a **Feature** must have to remain in the structure. Entering zero results in nothing changing. Entering a number larger than the maximum number of neighbors of any **Feature** generates an *error* (since all **Features** would be removed). The user needs to proceed conservatively here when choosing the value for the minimum to avoid accidentally exceeding the maximum. After **Features** are removed for not having enough neighbors, the remaining **Features** are *coarsened* iteratively, one **Cell** per iteration, until the gaps left by the removed **Features** are filled. Effectively, this is an isotropic **Feature** growth in the regions around removed **Features**.
The **Filter** can be run in a mode where the minimum number of neighbors is applied to a single **Ensemble**. The user can select to apply the minimum to one specific **Ensemble**.
-## Notes ##
+## Notes
If any features are removed **and** the Cell Feature AttributeMatrix contains any *NeighborList* data arrays those arrays will be **REMOVED** because those lists are now invalid. Re-run the *Find Neighbors* filter to re-create the lists.
-## Parameters ##
-
-| Name | Type | Description |
-|------|------|-------------|
-| Minimum Number Neighbors | int32_t | Number of neighbors a **Feature** must have to remain as a **Feature** |
-| Apply to Single Phase | bool | Whether to apply minimum to single ensemble or all ensembles |
-| Phase Index | int32_t | Which **Ensemble** to apply minimum to. Only needed if *Apply to Single Phase Only* is checked |
-
-## Required Geometry ##
-
-Image
-
-## Required Objects ##
+% Auto generated parameter table will be inserted here
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Cell** belongs |
-| **Feature Attribute Array** | Phases | int32_t | (1) | Specifies to which **Ensemble** each **Feature** belongs. Only required if *Apply to Single Phase Only* is checked |
-| **Feature Attribute Array** | NumNeighbors | int32_t | (1) | Number of contiguous neighboring **Features** for each **Feature** |
-
-## Created Objects ##
-
-None
-
-## Example Pipelines ##
+## Example Pipelines
+ (10) SmallIN100 Full Reconstruction
+ (06) SmallIN100 Postsegmentation Processing
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/MoveData.md b/src/Plugins/ComplexCore/docs/MoveData.md
index 7ef5c18184..05231ee927 100644
--- a/src/Plugins/ComplexCore/docs/MoveData.md
+++ b/src/Plugins/ComplexCore/docs/MoveData.md
@@ -1,46 +1,21 @@
# Move Data
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Core (Memory/Management)
-## Description ##
-
-This **Filter** allows the user to move an **Attribute Array** from one **Attribute Matrix** to another compatible **Attribute Matrix** or to move an **Attribute Matrix** from one **Data Container** to another **Data Container**. **Attribute Matrices** are compatible if the *number of tuples* are equal, **not** the actual *tuple dimensions*.
-
-## Parameters ##
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Data to Move | DataPath | The complete path to the data object to be moved |
-| New Parent | DataPath | The complete path to the parent data object to which the data will be moved |
-
-## Required Geometry ##
-
-Not Applicable
+## Description
-## Required Objects ##
+This **Filter** allows the user to move an **Attribute Array** from one **Attribute Matrix** to another compatible **Attribute Matrix** or to move an **Attribute Matrix** from one **Data Container** to another **Data Container**. **Attribute Matrices** are compatible if the *number of tuples* are equal, **not** the actual *tuple dimensions*.
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Data Object** | None | Any | N/A | **Data Object** to move |
-| **Base Group** Child | None | Any | Any | **Base Group** to be moved into |
+% Auto generated parameter table will be inserted here
-## Created Objects ##
+## Example Pipelines
-None
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/MultiThresholdObjects.md b/src/Plugins/ComplexCore/docs/MultiThresholdObjects.md
index 0bdb51d5bf..b6705b4980 100644
--- a/src/Plugins/ComplexCore/docs/MultiThresholdObjects.md
+++ b/src/Plugins/ComplexCore/docs/MultiThresholdObjects.md
@@ -1,11 +1,10 @@
-# Threshold Objects 2
+# Threshold Objects 2
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Processing (Threshold)
-## Description ##
+## Description
This **Filter** allows the user to input single or multiple criteria for thresholding **Attribute Arrays** in an **Attribute Matrix**. Internally, the algorithm creates the output boolean arrays for each comparison that the user creates. Comparisons can be either a value and boolean operator (*Less Than*, *Greater Than*, *Equal To*, *Not Equal To*) or a collective set of comparisons. Then all the output arrays are compared with their given comparison operator ( *And* / *Or* ) with the value of a set being the result of its own comparisons calculated from top to bottom.
@@ -17,43 +16,14 @@ It is possible to set custom values for both the TRUE and FALSE values that will
**NOTE**: If custom TRUE/FALSE values are chosen, then using the resulting mask array in any other filters that require a mask array will break those other filters. This is because most other filters that require a mask array make the assumption that the true/false values are 1/0.
-## Parameters ##
-
-| Name | Type | Description |
-|--------------------------|-----------------|----------------------------------------------------------------------------------------------------------------|
-| Data Arrays to Threshold | Comparison List | This is the set of criteria applied to the objects the selected arrays correspond to when doing the thresholding |
-| Use Custom TRUE Value | bool | Specifies whether to output a custom TRUE value |
-| Custom TRUE Value | float64 | The custom TRUE value (the default value is 1) |
-| Use Custom FALSE Value | bool | Specifies whether to output a custom FALSE value |
-| Custom FALSE Value | float64 | The custom FALSE value (the default value is 0) |
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| Any **Attribute Array** | None | Any | (1) | Array(s) selected in criteria set |
-
-## Created Objects ##
+% Auto generated parameter table will be inserted here
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| Any **Attribute Array** | Mask | bool | (1) | Specifies whether the objects passed the set of criteria applied during thresholding |
+## Example Pipelines
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/NearestPointFuseRegularGridsFilter.md b/src/Plugins/ComplexCore/docs/NearestPointFuseRegularGridsFilter.md
index 00e536d20d..d34e8619a8 100644
--- a/src/Plugins/ComplexCore/docs/NearestPointFuseRegularGridsFilter.md
+++ b/src/Plugins/ComplexCore/docs/NearestPointFuseRegularGridsFilter.md
@@ -10,31 +10,12 @@ This **Filter** fuses two **Image Geometry** data sets together. The grid of **C
*Note:* The *Sampling* **Data Container** remains identical after this **Filter**, but the *Reference* **Data Container**, while "geometrically identical", gains all the attribute arrays from the *Sampling* **Data Container**.
-## Parameters
-
-None
-
-## Required Geometry
-
-Image
-
-## Required Objects
-
-None
-
-## Created Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Attribute Matrix** | CellData | Cell | N/A | *Reference* **Cell** data to use for fusion |
-| **Attribute Matrix** | CellData | Cell | N/A | *Sampling* **Cell** data to use for fusion |
+% Auto generated parameter table will be inserted here
## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/PartitionGeometryFilter.md b/src/Plugins/ComplexCore/docs/PartitionGeometryFilter.md
index 824dbdd0b8..825ce4dda1 100644
--- a/src/Plugins/ComplexCore/docs/PartitionGeometryFilter.md
+++ b/src/Plugins/ComplexCore/docs/PartitionGeometryFilter.md
@@ -1,19 +1,20 @@
# Partition Geometry
-## Group (Subgroup) ##
+## Group (Subgroup)
Reconstruction (Reconstruction)
-## Description ##
+## Description
This **Filter** generates a partition grid and assigns partition IDs for every voxel/node of a given geometry.
If the **Filter** determines that any voxel/node of the original geometry is out-of-bounds compared to the generated partition grid, the **Out-Of-Bounds Cell ID** will be used as the partition ID in the output partition IDs array.
-## Partitioning Modes ##
+## Partitioning Modes
+
There are four available partitioning modes to choose from: **1. Basic**, **2. Advanced**, **3. Bounding Box**, and **4. Existing Partition Grid**
-### Basic ###
+### Basic
This partitioning mode is commonly used to create a partition grid that is exactly the same size as the input geometry and divided up into a specific number of cells in the X, Y, & Z dimensions. This mode requires the **Starting Feature ID**, **Number of Cells Per Axis**, and (optionally) the **Use Vertex Mask** input parameters.
@@ -35,7 +36,7 @@ In **Figure 1** above, the PartitionGeometry filter is using the SmallIN100 imag
In **Figure 1A** above, feature ID 111 is shown highlighted in the newly created partition grid. In **Figure 1B** above, the same 111 feature ID is shown as the assigned partition ID for the currently highlighted voxel.
-### **Advanced** ###
+### **Advanced**
This partitioning mode is commonly used to create a custom sized partition grid that the input geometry may or may not fit within. This mode requires the **Starting Feature ID**, **Out-of-Bounds Feature ID**, **Number of Cells Per Axis**, **Partition Grid Origin**, **Cell Length**, and (optionally) the **Use Vertex Mask** input parameters.
@@ -75,7 +76,7 @@ In **Figure 3A** above, the newly created partition grid is shown intersecting t
In **Figure 3B** above, the SmallIN100 dataset is sliced open to show the partition IDs that have been set with the corresponding feature IDs from the partition grid.
-### **Bounding Box** ###
+### **Bounding Box**
This partitioning mode is commonly used to create a custom sized partition grid using a minimum and maximum grid coordinate. The input geometry may or may not fit within this partition grid. This mode is very similar to the **Advanced** partitioning mode; it requires the **Starting Feature ID**, **Out-of-Bounds Feature ID**, **Number of Cells Per Axis**, **Minimum Grid Coordinate**, **Maximum Grid Coordinate**, and (optionally) the **Use Vertex Mask** input parameters. Basically, instead of specifying a partition grid origin and cell length to determine the location and physical size of the partition grid, the minimum and maximum grid coordinates are used.
@@ -91,11 +92,11 @@ In **Figure 4** above, the PartitionGeometry filter is using the SmallIN100 imag
In **Figure 4A** above, the SmallIN100 dataset is shown. In **Figure 4B** above, the dataset is sliced to show the newly created partition grid contained within. The partition grid is about 5 units smaller on all sides compared to the SmallIN100 input geometry.
-### **Existing Partition Grid** ###
+### **Existing Partition Grid**
This partitioning mode is chosen when the user already has a partition grid from a previous run of the Partition Geometry filter. Just select an existing **Partition Grid Geometry** and pick the **Out-of-Bounds Feature ID**, and then partition IDs will be assigned to the input dataset when the filter is executed.
-## Using A Vertex Mask ##
+## Using A Vertex Mask
On all partitioning modes, a vertex mask can be used with a vertex-based input geometry to determine which vertices should be assigned a valid partition ID. Any vertices with a mask value of 0 or False will have its Partition ID set to the Out-of-Bounds Feature ID.
@@ -103,39 +104,16 @@ On all partitioning modes, a vertex mask can be used with a vertex-based input g
|:---:|:---:|
| ![](Images/PartitionGeometry/UseVertexMask_1a.png) | ![](Images/PartitionGeometry/UseVertexMask_1b.png) |
-## Parameters ##
-
-| Name | Type | Description |
-|------|------|------|
-| Input Geometry to Partition | DataPath | The path to the geometry object that the filter will partition. |
-| Input Geometry Cell Attribute Matrix | DataPath | The path to the attribute matrix where the partition ids array will be stored. |
-| Partitioning Mode | int | The mode used to partition the geometry. The choices are Basic, Advanced, Bounding Box, and Existing Partition Grid. |
-| Starting Feature ID | int | The starting ID to use when creating the partition grid. |
-| Out-Of-Bounds Feature ID | int | The default ID used when the voxel or node in the input geometry is out-of-bounds compared to the partition grid. Available in all modes except for Basic mode (not needed since all voxels are in-bounds). |
-| Number of Cells Per Axis (X,Y,Z) | IntVec3 | The number of cells that will be created in each partition grid axis. |
-| Partition Grid Origin (X,Y,Z) | FloatVec3 | The origin of the partition grid. Only available in Advanced mode. |
-| Cell Length (X,Y,Z) | FloatVec3 | The length of each cell in each partition grid axis. Only available in Advanced mode. |
-| Minimum Grid Coordinate (X,Y,Z) | FloatVec3 | The minimum coordinate for the bounding box of the partition grid. Only available in Bounding Box mode. |
-| Maximum Grid Coordinate (X,Y,Z) | FloatVec3 | The maximum coordinate for the bounding box of the partition grid. Only available in Bounding Box mode. |
-| Existing Partition Grid | DataPath | The path to an image geometry that contains an existing partition grid. Only available in Existing Partition Grid mode. |
-| Use Vertex Mask | bool | Determines whether or not to use a vertex mask when partitioning the input geometry. |
-| Vertex Mask | DataPath | The path to the vertex mask array. |
-| Feature Attribute Matrix | string | The name of the feature attribute matrix that will be created. |
-| Partition Ids | string | The name of the partition ids array that will be created. |
-| Partition Grid Geometry | DataPath | The path to the partition grid geometry that will be created. |
-| Cell Attribute Matrix | string | The name of the attribute matrix that will be created as a child of the partition grid geometry. |
-| Feature Ids | string | The name of the feature ids array that will be created as a child of Cell Attribute Matrix. |
-
-## Example Pipelines ##
+% Auto generated parameter table will be inserted here
+
+## Example Pipelines
None
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/PointSampleTriangleGeometryFilter.md b/src/Plugins/ComplexCore/docs/PointSampleTriangleGeometryFilter.md
index f804a394ca..907f172ba6 100644
--- a/src/Plugins/ComplexCore/docs/PointSampleTriangleGeometryFilter.md
+++ b/src/Plugins/ComplexCore/docs/PointSampleTriangleGeometryFilter.md
@@ -1,10 +1,10 @@
# Point Sample Triangle Geometry
-## Group (Subgroup) ##
+## Group (Subgroup)
DREAM3D Review (Geometry)
-## Description ##
+## Description
This **Filter** randomly samples point locations on **Triangles** in a **Triangle Geometry**. The sampled point locations are then used to construct a **Vertex Geometry**. The number of point samples may either be specified manually or by inferring from another **Geometry**:
@@ -20,49 +20,20 @@ This **Filter** randomly samples point locations on **Triangles** in a **Triangl
In order to ensure an even sampling of the total surface are of the **Triangle Geometry**, the average number of points sampled per triangle is made proportional to the area of the triangle. Within a given **Triangle**, a point is chosen using the following approach:
-
![Equation 1](Images/PointSampleTriangleGeometry_Eqn1.png)
where ![](Images/PSTG_2.png) are the coordinates of the sampled point; ![](Images/PSTG_3.png), ![](Images/PSTG_4.png), and ![](Images/PSTG_5.png) are the coordinates of the vertices beloning to the **Triangle**; and ![](Images/PSTG_6.png) and ![](Images/PSTG_7.png) are random real numbers on the interval ![](Images/PSTG_8.png). This approach has the benefit of uniform sampling within the **Triangle** area, and functions correctly regardless of the dimensionality of the space embedding (i.e., whether the **Triangle** is in the plane or embedded in 3D).
The user may opt to use a mask to prevent certain **Triangles** from being sampled; where the mask is _false_, the **Triangle** will not be sampled. Additionally, the user may choose any number of **Face Attribute Arrays** to transfer to the created **Vertex Geometry**. The vertices in the new **Vertex Geometry** will gain the values of the **Faces** from which they were sampled.
-## Parameters ##
-
-| Name | Type | Description |
-|------|------|-------------|
-| Source for Number of Samples | Enumeration | Whether to input the number of samples manually or use another **Geometry** to determine the number of samples |
-| Number of Sample Points | int32_t | Number of sample points to use, if *Manual* is selected for *Source for Number of Samples* |
-| Use Mask | bool | Whether to use a boolean mask array to ignore certain **Trianlges** flagged as *false* from the sampling algorithm |
-
-## Required Geometry ###
-
-Triangle
-
-## Required Objects ##
+% Auto generated parameter table will be inserted here
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Data Container** | TriangleDataContainer | N/A | N/A | **Data Container** holding the **Triangle Geometry** to sample |
-| **Data Container** | None | N/A | N/A | **Data Container** holding the **Geometry** used to determine the number of samples, if *Other Geometry* is selected for *Source for Number of Samples* |
-| **Face Attribute Array** | FaceAreas | double | (1) | Specifies the area of each **Face** |
-| **Face Attribute Array** | Mask | bool | (1) | Specifies if the **Face** can be sampled, if *Use Mask* is checked |
+## Example Pipelines
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Data Container** | VertexDataContainer | N/A | N/A | **Data Container** holding the **Vertex Geometry** that represents the sampling points |
-| **Vertex Attribute Matrix** | VertexData | Vertex | N/A | **Vertex Attribute Matrix** for the created **Vertex Data Container** |
-
-## Example Pipelines ##
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/QuickSurfaceMeshFilter.md b/src/Plugins/ComplexCore/docs/QuickSurfaceMeshFilter.md
index ea45e4cf79..1d3ce15388 100644
--- a/src/Plugins/ComplexCore/docs/QuickSurfaceMeshFilter.md
+++ b/src/Plugins/ComplexCore/docs/QuickSurfaceMeshFilter.md
@@ -1,10 +1,10 @@
-# Quick Surface Mesh #
+# Quick Surface Mesh
-## Group (Subgroup) ##
+## Group (Subgroup)
Surface Meshing (Generation)
-## Description ##
+## Description
This **Filter** generates a **Triangle Geometry** from a grid **Geometry** (either an **Image Geometry** or a **RectGrid Geometry**) that represents a surface mesh of the present **Features**. The algorithm proceeds by creating a pair of **Triangles** for each face of the **Cell** where the neighboring **Cells** have a different **Feature** Id value. The meshing operation is extremely quick but can result in a surface mesh that is very "stair stepped". The user is encouraged to use a smoothing operation to reduce this "blockiness".
@@ -46,7 +46,7 @@ NodeType = 4
---------------
-### Node Types ###
+### Node Types
One of the arrays to come out of the algorithm is the "Node Type" vertex array. This array uses a value to label each vertex as to what kind of node it was determined to be during the meshing process.
@@ -59,46 +59,16 @@ One of the arrays to come out of the algorithm is the "Node Type" vertex array.
| 13 | Node that is on the exterior of the mesh and is a triple line |
| 14 | Node that is on the exterior of the mesh and is a quadruple point |
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Human Name | Description | Parameter Type |
-|--------------|-------------|----------------|
-| Attempt to Fix Problem Voxels | See help page. | complex.BoolParameter |
-| Generate Triple Lines | Experimental feature. May not work. Keep this off. | complex.BoolParameter |
-
-## Required Geometry ##
-
-Image/RectGrid
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Cell** belongs |
-| Any **Cell Attribute Array** | None | Any | Any | Specifies which **Cell Attribute Arrays** to transfer to the created **Triangle Geometry** |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Data Container** | TriangleDataContainer | N/A | N/A | Created **Data Container** name with a **Triangle Geometry** |
-| **Attribute Matrix** | VertexData | Vertex | N/A | Created **Vertex Attribute Matrix** name |
-| **Vertex Attribute Array** | NodeTypes | int8_t | (1) | Specifies the type of node in the **Geometry** |
-| **Attribute Matrix** | FaceData | Face | N/A | Created **Face Attribute Matrix** name |
-| **Face Attribute Array** | FaceLabels | int32_t | (2) | Specifies which **Features** are on either side of each **Face** |
-| **Attribute Matrix** | FaceFeatureData | Face Feature | N/A | **Feature Attribute Matrix** of the created *Face Labels* |
-| Any **Face Attribute Array** | None | Any | Any | The set of transferred **Cell Attribute Arrays** |
-
-## Example Pipelines ##
+## Example Pipelines
+ (01) SmallIN100 Quick Mesh
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/RawBinaryReaderFilter.md b/src/Plugins/ComplexCore/docs/RawBinaryReaderFilter.md
index 8c1fd9010c..5e93e40d48 100644
--- a/src/Plugins/ComplexCore/docs/RawBinaryReaderFilter.md
+++ b/src/Plugins/ComplexCore/docs/RawBinaryReaderFilter.md
@@ -1,19 +1,18 @@
-# Raw Binary Reader
+# Raw Binary Reader
-
-## Group (Subgroup) ##
+## Group (Subgroup)
IO (Input)
-## Description ##
+## Description
This **Filter** is designed to read data stored in files on the users system in *binary* form. The data file should **not** have any type of header before the data in the file. The user should know exactly how the data is stored in the file and properly define this in the user interface. Not correctly identifying the type of data can cause serious issues since this **Filter** is simply reading the data into a pre-allocated array interpreted as the user defines.
This **Filter** will error out and block the **Pipeline** from running if the total number of bytes that would need to be read from the file is larger than the actual file itself. The user can use an input file that is actually **larger** than the number of bytes required by the **Filter**; in this case, the **Filter** will only read the first part of the file unless an amount of bytes to skip is set.
-### Scalar Type ###
+### Scalar Type
-Computer data comes in 10 basic types on modern 32 bit and 64 bit operating systems. Data can be categorized as either *integer* or _floating point_. With each of these types, the number of bits that represent the data determine their maximum and minimum values. For integer values, the standard types are 8, 16, 32 and 64 bit (1, 2, 4, and 8 bytes). For floating point values, there are either 32 bit or 64 bit (4 or 8 bytes). Integer types can be either *signed* or _unsigned_. A signed integer can take negative values. An unsigned integer can only take positive values, but will have twice the positive value range as a signed integer.
+Computer data comes in 10 basic types on modern 32 bit and 64 bit operating systems. Data can be categorized as either *integer* or *floating point*. With each of these types, the number of bits that represent the data determine their maximum and minimum values. For integer values, the standard types are 8, 16, 32 and 64 bit (1, 2, 4, and 8 bytes). For floating point values, there are either 32 bit or 64 bit (4 or 8 bytes). Integer types can be either *signed* or *unsigned*. A signed integer can take negative values. An unsigned integer can only take positive values, but will have twice the positive value range as a signed integer.
The types of data that can be read with this **Filter** include:
@@ -30,12 +29,11 @@ The types of data that can be read with this **Filter** include:
---
+### Number of Components
-### Number of Components ###
-
-This parameter tells the program how many values are present for each _tuple_. For example, a grayscale image would typically have just a single value of type unsigned 8 bit integer at every pixel/voxel. A color image will have at least 3 components for red (R), breen (G) and blue (B), and sometimes 4 values if the alpha (A) channel is also stored. Euler angles are typically stored as a 3 component vector of 32 bit floating point values.
+This parameter tells the program how many values are present for each *tuple*. For example, a grayscale image would typically have just a single value of type unsigned 8 bit integer at every pixel/voxel. A color image will have at least 3 components for red (R), breen (G) and blue (B), and sometimes 4 values if the alpha (A) channel is also stored. Euler angles are typically stored as a 3 component vector of 32 bit floating point values.
-### Endian ###
+### Endian
This parameter tells the program which byte is *most significant* for multibyte values. Intel architecture computers are little endian while Power PC, Sun Sparc and DEC Alpha CPUs are big endian. Consider the following example:
@@ -48,48 +46,18 @@ This parameter tells the program which byte is *most significant* for multibyte
This setting is *crucial* to the correct interpretation of the binary data, so the user must be aware of how their binary data was encoded.
-
-### Skip Header Bytes ###
+### Skip Header Bytes
If the raw binary file you are reading has a *header* before the actual data begins, the user can instruct the **Filter** to skip this header portion of the file. The user needs to know how lond the header is in bytes. Another way to use this value is if the user wants to read data out of the interior of a file by skipping a defined number of bytes.
+% Auto generated parameter table will be inserted here
-## Parameters ##
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Input File | File Path | The input binary file path |
-| Scalar Type | Enumeration | Data type of the binary data |
-| Number of Components | int32_t | The number of values at each tuple |
-| Endian | Enumeration | The endianness of the data |
-| Skip Header Bytes | int32_t | Number of bytes to skip before reading data |
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-None
-
-## Created Objects ##
+## Example Pipelines
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| Any | None | Any | Any | Created **Attribute Array** name |
-
-
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/ReadTextDataArrayFilter.md b/src/Plugins/ComplexCore/docs/ReadTextDataArrayFilter.md
index 9a5b9c6f63..98b7226099 100644
--- a/src/Plugins/ComplexCore/docs/ReadTextDataArrayFilter.md
+++ b/src/Plugins/ComplexCore/docs/ReadTextDataArrayFilter.md
@@ -1,12 +1,10 @@
# Read Text Data Array
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Core (IO/Read)
-
-## Description ##
+## Description
This **Filter** allows the user to import a plain text file containing the contents of a single Attribute Array. The delimeters can be one of the following:
@@ -22,11 +20,10 @@ The filter does not care about how many values per line but only about reading t
+ Create AttributeMatrix: Give the AttributeMatrix a name and set the tuple dimensions to match the number of values in the input file.
+ OPTIONAL: If the data exists as a regular set of data on a grid then the user can also use the "Create Geometry (Image)" filter before importing the data.
-### Example Data ###
+### Example Data
The example data below has 50 elements. This means that it could successfully be read into an array that has 10 Tuples and 5 Componenets or 50 Tuples and 1 Component. The AttributeMatrix would need to have dimensions such that mulplying all the dimensions together yields 50. For example the AttributeMatrix could have X=5, Y=5 and Z=2 or X=10, Y=5 and Z=1. This filter does not require any type of Geometry as the filter is reading data directly into an array.
-
0 1 2 3 4 5 6 7 8 9
10 11 12 13 14 15 16 17 18 19
20 21 22 23 24 25 26 27 28 29
@@ -35,7 +32,7 @@ The example data below has 50 elements. This means that it could successfully be
![](Images/ImportAsciDataArray_ui.png)
-### Scalar Types ###
+### Scalar Types
| Value | Type |
|--|------|
@@ -50,7 +47,7 @@ The example data below has 50 elements. This means that it could successfully be
| 8 | Float 32 bit |
| 9 | Double 64 bit |
-### Delimeter Types ###
+### Delimeter Types
| Value | Type |
|--|------|
@@ -60,45 +57,14 @@ The example data below has 50 elements. This means that it could successfully be
| 3 | colon |
| 4 | tab |
+% Auto generated parameter table will be inserted here
+## Example Pipelines
-## Parameters ##
-
-| Name | Type | Description |
-|------|------| ----------- |
-| InputFile | String | The path to the input file including the filename |
-| ScalarType | int | See table above |
-| Number of Components | int | The number of components in the array. |
-| Skip Header Lines | int | If the file has some sort of a header, skip this many lines. |
-| Delimeter | int | See Table above |
-
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Attribute Matrix** | None | DataArrayPath | N/A | **Attribute Matrix** to store imported data into |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Attribute Array** | N/A | See Table above | based on number of components | The created Attribute Array |
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/RegularGridSampleSurfaceMesh.md b/src/Plugins/ComplexCore/docs/RegularGridSampleSurfaceMesh.md
index 49597c27e4..bdac2c49b0 100644
--- a/src/Plugins/ComplexCore/docs/RegularGridSampleSurfaceMesh.md
+++ b/src/Plugins/ComplexCore/docs/RegularGridSampleSurfaceMesh.md
@@ -16,7 +16,7 @@ This **Filter** "samples" a triangulated surface mesh on a rectilinear grid. The
## Parameters
| Name | Type | Description |
-|------|------|-------------|
+|------------|------| --------------------------------- |
| Dimensions | uint64 | Number of **Cells** along each axis |
| Resolution | float32 (3x) | The resolution values (dx, dy, dz) |
| Origin | float32 (3x) | The origin of the sampling volume |
@@ -27,19 +27,18 @@ Triangle
## Required Objects
-| Type | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|-----|
-| **Data Array** | Face Labels | int32 | (2) | Specifies which **Features** are on either side of each **Face**. |
+| Type | Default Name | Type | Comp Dims | Description |
+|------|--------------|-----|-----|-----------------------------------|
+| Data Array | Face Labels | int32 | (2) | Specifies which **Features** are on either side of each **Face**. |
## Created
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Image Geometry** | Image Geometry | N/A | N/A | Created **Image Geometry** name and *DataPath* |
-| **Attribute Matrix** | Cell Data | Cell | N/A | Created **Cell Attribute Matrix** name |
-| **Data Array** | Feature Ids | int32 | (1) | Specifies to which **Feature** each **Cell** belongs |
+| Kind | Default Name | Type | Comp Dims | Description |
+|---------------------------|--------------|----------|--------|---------------------------------------------|
+| Image Geometry | Image Geometry | N/A | N/A | Created **Image Geometry** name and *DataPath* |
+| Attribute Matrix | Cell Data | Cell | N/A | Created **Cell Attribute Matrix** name |
+| Data Array | Feature Ids | int32 | (1) | Specifies to which **Feature** each **Cell** belongs |
## License & Copyright
Please see the description file distributed with this **Plugin**
-
diff --git a/src/Plugins/ComplexCore/docs/RegularGridSampleSurfaceMeshFilter.md b/src/Plugins/ComplexCore/docs/RegularGridSampleSurfaceMeshFilter.md
index 29950d6f90..dd91203360 100644
--- a/src/Plugins/ComplexCore/docs/RegularGridSampleSurfaceMeshFilter.md
+++ b/src/Plugins/ComplexCore/docs/RegularGridSampleSurfaceMeshFilter.md
@@ -13,38 +13,12 @@ This **Filter** "samples" a triangulated surface mesh on a rectilinear grid. The
3. For each bounding box a **Cell** falls in, check against that **Feature's** **Triangle** list to determine if the **Cell** falls within that n-sided polyhedra (*Note:* if the surface mesh is conformal, then each **Cell** will only belong to one **Feature**, but if not, the last **Feature** the **Cell** is found to fall inside of will *own* the **Cell**)
4. Assign the **Feature** number that the **Cell** falls within to the *Feature Ids* array in the new rectilinear grid geometry
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| Dimensions | uint64 | Number of **Cells** along each axis |
-| Resolution | float32 (3x) | The resolution values (dx, dy, dz) |
-| Origin | float32 (3x) | The origin of the sampling volume |
-
-## Required Geometry
-
-Triangle
-
-## Required Objects
-
-| Type | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|-----|
-| **Data Array** | Face Labels | int32 | (2) | Specifies which **Features** are on either side of each **Face**. |
-
-## Created
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Image Geometry** | Image Geometry | N/A | N/A | Created **Image Geometry** name and *DataPath* |
-| **Attribute Matrix** | Cell Data | Cell | N/A | Created **Cell Attribute Matrix** name |
-| **Data Array** | Feature Ids | int32 | (1) | Specifies to which **Feature** each **Cell** belongs |
+% Auto generated parameter table will be inserted here
## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/RemoveFlaggedFeaturesFilter.md b/src/Plugins/ComplexCore/docs/RemoveFlaggedFeaturesFilter.md
index 2b28d80324..77b70277a9 100644
--- a/src/Plugins/ComplexCore/docs/RemoveFlaggedFeaturesFilter.md
+++ b/src/Plugins/ComplexCore/docs/RemoveFlaggedFeaturesFilter.md
@@ -1,43 +1,21 @@
-# Remove Flagged Features
+# Remove Flagged Features
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Processing (Cleanup)
-## Description ##
+## Description
This **Filter** will remove **Features** that have been flagged by another **Filter** from the structure. The **Filter** requires that the user point to a boolean array at the **Feature** level that tells the **Filter** whether the **Feature** should remain in the structure. If the boolean array is *false* for a **Feature**, then all **Cells** that belong to that **Feature** are temporarily *unassigned* and after all *undesired* **Features** are removed, the remaining **Features** are isotropically coarsened to fill in the gaps left by the removed **Features**.
-## Parameters ##
-
-None
-
-## Required Geometry ##
-
-Image
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Cell** belongs |
-| **Feature Attribute Array** | Active | bool | (1) | Specifies whether the **Feature** will remain in the structure or not |
+% Auto generated parameter table will be inserted here
-## Created Objects ##
+## Example Pipelines
-None
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/RemoveFlaggedVertices.md b/src/Plugins/ComplexCore/docs/RemoveFlaggedVertices.md
index 4c41cdcaa6..cb3d1b17bf 100644
--- a/src/Plugins/ComplexCore/docs/RemoveFlaggedVertices.md
+++ b/src/Plugins/ComplexCore/docs/RemoveFlaggedVertices.md
@@ -1,10 +1,10 @@
# Remove Flagged Vertices
-## Group (Subgroup) ##
+## Group (Subgroup)
DREAM3D Review (Geometry)
-## Description ##
+## Description
This **Filter** removes **Vertices** from the supplied **Vertex Geometry** that are flagged by a boolean mask array.
Specifically, **Vertices** flagged as *true* are removed from the **Geometry**. A new reduced **Vertex Geometry** is
@@ -16,39 +16,18 @@ tuples *removed* for any **Vertices** removed by the **Filter**. The user must s
Container**, but all other copied objects (**Attribute Matrices** and **Attribute Arrays**) will retain the same names
as the original source.
-_Note:_ Since it cannot be known before run time how many **Vertices** will be removed, the new **Vertex Geometry** and
+*Note:* Since it cannot be known before run time how many **Vertices** will be removed, the new **Vertex Geometry** and
all associated **Vertex** data to be copied will be initialized to have size 0. Any **Feature** or **Ensemble**
information will retain the same dimensions and size.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-None
+## Example Pipelines
-## Required Geometry ###
-
-Vertex
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|----------------------------|---------------------|------|----------------------|--------------------------------------------------------------|
-| **Data Container** | VertexDataContainer | N/A | N/A | **Data Container** holding the **Vertex Geometry** to reduce |
-| **Vertex Attribute Array** | Mask | bool | (1) | Mask array specifying which **Vertices* to remove |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|----------------------------|----------------------------|------|----------------------|---------------------------------------------------------------------------------------------------------------------------|
-| Reduced **Data Container** | ReducedVertexDataContainer | N/A | N/A | **Data Container** holding the reduced **Vertex Geometry** and any copied **Attribute Matrices** and **Attribute Arrays** |
-
-## Example Pipelines ##
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/RemoveMinimumSizeFeaturesFilter.md b/src/Plugins/ComplexCore/docs/RemoveMinimumSizeFeaturesFilter.md
index cd2e65b0a3..8e9099cecc 100644
--- a/src/Plugins/ComplexCore/docs/RemoveMinimumSizeFeaturesFilter.md
+++ b/src/Plugins/ComplexCore/docs/RemoveMinimumSizeFeaturesFilter.md
@@ -1,55 +1,30 @@
# Minimum Size
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Processing (Cleanup)
-## Description ##
+## Description
This **Filter** removes **Features** that have a total number of **Cells** below the minimum threshold defined by the user. Entering a number larger than the largest **Feature** generates an *error* (since all **Features** would be removed). Hence, a choice of threshold should be carefully be chosen if it is not known how many **Cells** are in the largest **Features**. After removing all the small **Features**, the remaining **Features** are isotropically coarsened to fill the gaps left by the small **Features**.
The **Filter** can be run in a mode where the minimum number of neighbors is applied to a single **Ensemble**. The user can select to apply the minimum to one specific **Ensemble**.
-## Notes ##
+## Notes
If any features are removed **and** the Cell Feature AttributeMatrix contains any *NeighborList* data arrays those arrays will be **REMOVED** because those lists are now invalid. Re-run the *Find Neighbors* filter to re-create the lists.
-## Parameters ##
-
-| Name | Type | Description |
-|------|------|-------------|
-| Minimum Allowed Feature Size | int32_t | Number of **Cells** that must be present in the **Feature** for it to remain in the sample |
-| Apply to Single Phase Only | bool | Tells the Filter whether to apply minimum to single ensemble or all ensembles |
-| Phase Index | int32_t | Which **Ensemble** to apply minimum to. Only needed if *Apply to Single Phase Only* is checked |
-
-## Required Geometry ##
-
-Image
-
-## Required Objects ##
+% Auto generated parameter table will be inserted here
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Cell** belongs |
-| **Feature Attribute Array** | Phases | int32_t | (1) | Specifies to which **Ensemble** each **Feature** belongs. Only required if *Apply to Single Phase Only* is checked |
-| **Feature Attribute Array** | NumCells | int32_t | (1) | Specifies the number of **Cells** belonging to each **Feature** |
-
-## Created Objects ##
-
-None
-
-## Example Pipelines ##
+## Example Pipelines
+ (10) SmallIN100 Full Reconstruction
+ (06) SmallIN100 Postsegmentation Processing
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/RenameDataObject.md b/src/Plugins/ComplexCore/docs/RenameDataObject.md
index 20ee9c9e6c..e50cf83073 100644
--- a/src/Plugins/ComplexCore/docs/RenameDataObject.md
+++ b/src/Plugins/ComplexCore/docs/RenameDataObject.md
@@ -1,43 +1,21 @@
# RenameDataObject
-## Group (Subgroup) ##
+## Group (Subgroup)
Core (Memory/Management)
-## Description ##
+## Description
This **Filter** renames a user chosen **Data Object** of any type.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------|------| ----------- |
-| New Data Object Name| String | New name for the selected **Data Object** |
+## Example Pipelines
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Data Object** | None | N/A | N/A | **Data Object** to rename |
-
-## Created Objects ##
-
-None
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/ReplaceElementAttributesWithNeighborValuesFilter.md b/src/Plugins/ComplexCore/docs/ReplaceElementAttributesWithNeighborValuesFilter.md
index 279bad8652..dfd47c773a 100644
--- a/src/Plugins/ComplexCore/docs/ReplaceElementAttributesWithNeighborValuesFilter.md
+++ b/src/Plugins/ComplexCore/docs/ReplaceElementAttributesWithNeighborValuesFilter.md
@@ -56,9 +56,9 @@ very large grains being similar most of the fine grains and twins are **NOT** re
### Oxford/Bruker (.ctf) File
Oxford Instruments and Bruker CTF data files do not include a "Confidence Index" measure. There are several measures
-such as _Mean Angular Deviation (MAD)_ or *Bands* but these values are not filled in or are defaulted to 0 (Zero) if the
+such as *Mean Angular Deviation (MAD)* or *Bands* but these values are not filled in or are defaulted to 0 (Zero) if the
scan point was not indexed. By using the *Error* value from the data file we can get the same effect as the EDAX
-_Confidence Index_. The user would use the following input values:
+*Confidence Index*. The user would use the following input values:
| Filter Parameter | Value |
|------------------|------------------------------------|
@@ -76,28 +76,7 @@ _Confidence Index_. The user would use the following input values:
Note the large areas of unindexed pixels in the original image (black pixels) and how they are all filled in. The filter
can act much like a generic "flood fill" image processing algorithm if used improperly.
-## Parameters
-
-| Name | Type | Description |
-|---------------------|----------|--------------------------------------------------------------------------------------------------|
-| Threshold Value | Any | Sets the threshold value a **Cell** must have to be considered for changing |
-| Comparison Operator | Int | Selects the operator to use. 0 = < (Less Than). 1 = > (Greater Than) |
-| Loop Until Gone | bool | Whether to iterate until all **Cells** are above the minimum tolerance or just run one iteration |
-| Image Geometry | DataPath | The path to the Image Geometry |
-
-## Required Geometry
-
-Image
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|--------------------------|--------------|------|----------------------|------------------------------------------------|
-| **Cell Attribute Array** | N/A | Any | (1) | The DataArray to use as input into the filter. |
-
-## Created Objects
-
-None
+% Auto generated parameter table will be inserted here
## Example Pipelines
@@ -107,13 +86,10 @@ The example pipeline (pipelines/Examples/ReplaceElementAttributesWithNeighbor.d3
|--|--|
| ![Original Data](Images/NeighborReplace_Small_IN100_Before.png) | ![Original Data](Images/NeighborReplace_Small_IN100_After.png) |
-
## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/ResampleImageGeomFilter.md b/src/Plugins/ComplexCore/docs/ResampleImageGeomFilter.md
index d5fc13ecd4..80e3bd81d1 100644
--- a/src/Plugins/ComplexCore/docs/ResampleImageGeomFilter.md
+++ b/src/Plugins/ComplexCore/docs/ResampleImageGeomFilter.md
@@ -1,14 +1,15 @@
# Resample Image Geometry
-## Group (Subgroup) ##
+## Group (Subgroup)
Sampling (Resample)
-## Description ##
+## Description
This **Filter** changes the **Cell** spacing/resolution based on inputs from the user. There are several resampling modes:
-### Spacing ###
+### Spacing
+
The values entered are the desired new spacings (not multiples of the current resolution). The number of **Cells** in the volume will change when the spacing values are changed and thus the user should be cautious of generating "too many" **Cells** by entering very small values (i.e., very high resolution).
**Example 1**:
@@ -23,7 +24,8 @@ Image Geometry with cell dimensions (524, 390, 164) and spacing (1, 1, 1).
If the new spacing value is (0.25, 0.7, 2.3), then the geometry will have cell dimensions (2096, 557, 71) and spacing (0.25, 0.7, 2.3).
-### Scale Factor ###
+### Scale Factor
+
The values entered are the desired scaling factor for each dimension, in percentages.
**Example 1**:
@@ -38,7 +40,8 @@ Image Geometry with cell dimensions (524, 390, 164) and spacing (1, 1, 1).
If the new scaling value is (120.4%, 50.74%, 68.12%), then the geometry will have cell dimensions (630, 197, 111) and spacing (0.830565, 1.97083, 1.468).
-### Exact Dimensions ###
+### Exact Dimensions
+
The values entered are the desired cell dimensions of the resampled geometry. (100, 100, 100) would resample the geometry so that there are 100 cells in each dimension.
**Example 1**:
@@ -55,51 +58,22 @@ If the new exact dimensions are (100, 500, 20), then the geometry will have cell
---
-A new grid of **Cells** is created and "overlaid" on the existing grid of **Cells**. There is currently no *interpolation* performed, rather the attributes of the old **Cell** that is closest to each new **Cell's** is assigned to that new **Cell**.
+A new grid of **Cells** is created and "overlaid" on the existing grid of **Cells**. There is currently no *interpolation* performed, rather the attributes of the old **Cell** that is closest to each new **Cell's** is assigned to that new **Cell**.
-*Note:* Present **Features** may disappear when down-sampling to coarse resolutions. If *Renumber Features* is checked, the **Filter** will check if this is the case and resize the corresponding **Feature Attribute Matrix** to comply with any changes. Additionally, the **Filter** will renumber **Features** such that they remain contiguous.
+*Note:* Present **Features** may disappear when down-sampling to coarse resolutions. If *Renumber Features* is checked, the **Filter** will check if this is the case and resize the corresponding **Feature Attribute Matrix** to comply with any changes. Additionally, the **Filter** will renumber **Features** such that they remain contiguous.
*Note:* This filter does NOT change the overall bounds of the volume, just the spacing and number of cells in the volume. To change the overall bounds of the volume, apply a scaling transformation with the [Apply Transformation To Geometry](./ApplyTransformationToGeometryFilter.md) filter.
-## Parameters ##
-
-| Name | Type | Description |
-|--------------------------|-------------|-------------------------------------------------------------------------------------------------------------|
-| Resampling Mode | int | The resampling mode used to resample the image geometry. Choices are Spacing, Scaling, or Exact Dimensions |
-| Spacing | float (3x) | The new resolution values (dx, dy, dz) |
-| Scale Factor | float (3x) | The scale factor (dx, dy, dz), in percentages. |
-| Exact Dimensions | uint64 (3x) | The exact dimensions (dx, dy, dz) to resample the geometry. |
-| Renumber Features | bool | Whether the **Features** should be renumbered |
-| Remove Original Geometry | bool | Whether the current **Geometry** should be removed after the resampling |
-
-## Required Geometry ##
-
-Image
+% Auto generated parameter table will be inserted here
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Attribute Matrix** | CellData | Cell | N/A | **Cell Attribute Matrix** that holds data for resolution change |
-| **Cell Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Cell** belongs. Only required if *Renumber Features* is checked |
-| **Attribute Matrix** | CellFeatureData | Cell Feature | N/A | **Feature Attribute Matrix** that corresponds to the **Feature** data for the selected _Feature Ids_. Only required if *Renumber Features* is checked |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Data Container** | NewImageDataContainer | N/A | N/A | Created **Data Container** name with an **Image Geometry**. |
-
-## Example Pipelines ##
+## Example Pipelines
ComplexCore/ResamplePorosityImage
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/ResampleRectGridToImageGeomFilter.md b/src/Plugins/ComplexCore/docs/ResampleRectGridToImageGeomFilter.md
index 0e9291d070..f2e2d729bd 100644
--- a/src/Plugins/ComplexCore/docs/ResampleRectGridToImageGeomFilter.md
+++ b/src/Plugins/ComplexCore/docs/ResampleRectGridToImageGeomFilter.md
@@ -1,10 +1,10 @@
# Resample RectGrid To ImageGeom
-## Group (Subgroup)
+## Group (Subgroup)
Sampling (Sampling)
-## Description
+## Description
This **Filter** will resample an existing RectilinearGrid onto a regular grid (Image Geometry) and copy cell data into the newly created Image Geometry Data Container during the process.
@@ -14,34 +14,14 @@ The algorithm logic is thus: If the ImageGeometry cell would contain multiple Re
The user can select which cell attribute matrix data arrays will be copied into the newly created Image Geometry Cell Attribute Matrix.
-## Parameters
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------|------|------|
-| Input Rectilinear Grid| DataPath | Path to the RectGrid Geometry to be re-sampled |
-| Selected Cell Attribute Arrays to Copy | Array of (DataPath) | Rect Grid Cell Data to possibly copy |
-| Image Geometry Voxel Dimensions | 3 x Int32 | The image geometry voxel dimensions in which to re-sample the rectilinear grid geometry |
+## Example Pipelines
-## Required Geometry
-
-Rectilinear Grid Geometry
-
-## Created Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|-----|
-| **Image Geometry** | Image Geometry | N/A | N/A | Path to the created Image Geometry |
-| **Attribute Matrix** | Cell Data | Element/Feature/Ensemble/etc. | N/A | The name of the cell data Attribute Matrix created with the Image Geometry |
-| **Element/Feature/Ensemble/etc. Attribute Array** | Copied from the input Data Container | int32_t/float/etc. | (1)/(3)/etc. | Cell level arrays copied over from the input to the resampled geometry |
-
-## Example Pipelines
-
-## License & Copyright
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/ReverseTriangleWindingFilter.md b/src/Plugins/ComplexCore/docs/ReverseTriangleWindingFilter.md
index 6c0fce1ca1..01f633a0c2 100644
--- a/src/Plugins/ComplexCore/docs/ReverseTriangleWindingFilter.md
+++ b/src/Plugins/ComplexCore/docs/ReverseTriangleWindingFilter.md
@@ -8,23 +8,7 @@ Surface Meshing (Connectivity/Arrangement)
This **Filter** reverses the *winding* for each **Triangle** in a **Triangle Geometry**. This will *reverse* the direction of calculated **Triangle** normals. Some analysis routines require the normals to be pointing "away" from the center of a **Feature**. This **Filter** allows for manipulation of this construct.
-## Parameters
-
-None
-
-## Required Geometry
-
-Triangle
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Data Container** | None | N/A | N/A | **Data Container** that holds the **Triangle Geometry** to reverse winding |
-
-## Created Objects
-
-None
+% Auto generated parameter table will be inserted here
## Example Pipelines
@@ -32,8 +16,6 @@ None
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/RobustAutomaticThreshold.md b/src/Plugins/ComplexCore/docs/RobustAutomaticThreshold.md
index 3f03a3fa82..3ff9199d86 100644
--- a/src/Plugins/ComplexCore/docs/RobustAutomaticThreshold.md
+++ b/src/Plugins/ComplexCore/docs/RobustAutomaticThreshold.md
@@ -1,10 +1,10 @@
# Robust Automatic Threshold
-## Group (Subgroup) ##
+## Group (Subgroup)
DREAM3D Review (Threshold)
-## Description ##
+## Description
This **Filter** automatically computes a threshold value for a scalar **Attribute Array** based on the array's gradient magnitude, producing a boolean array that is *false* where the input array is less than the threshold value and *true* otherwise. The threshold value is computed using the following equation:
@@ -12,37 +12,14 @@ This **Filter** automatically computes a threshold value for a scalar **Attribut
where \f$ a \f$ is the input array, \f$ g \f$ is the gradient magnitude array, \f$ n \f$ is the length of the input array, and \f$ T \f$ is the computed threshold value. Computing a threshold in this manner will generally partition the input array where its gradient is highest. Gradients may be computed using the Find Derivatives **Filter**. The gradient magnitude may then be found by computing the 2-norm of the gradient.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-None
+## Example Pipelines
-## Required Geometry ###
-
-None
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| Any **Attribute Array** | None | Any except bool | (1) | **Attribute Array** to threshold |
-| **Attribute Array** | None | float | (1) | Gradient magnitude of input **Attribute Array** |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Attribute Array** | Mask | bool | (1) | Mask array produced after application of the computed robust threshold to the input **Attribute Array** |
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/RotateSampleRefFrameFilter.md b/src/Plugins/ComplexCore/docs/RotateSampleRefFrameFilter.md
index 71351303bf..5d48dd6236 100644
--- a/src/Plugins/ComplexCore/docs/RotateSampleRefFrameFilter.md
+++ b/src/Plugins/ComplexCore/docs/RotateSampleRefFrameFilter.md
@@ -1,10 +1,10 @@
# Rotate Sample Reference Frame
-## Group (Subgroup) ##
+## Group (Subgroup)
Sampling (Rotating/Transforming)
-## Description ##
+## Description
**NOTE: As of July 2023, this filter is only verified to work with a rotation angle of 180 degrees, a rotation axis of (010), and a (0, 0, 0) origin.**
@@ -18,36 +18,15 @@ The equivalent rotation matrix for the above rotation would be the following:
| 1 | 0 | 0 |
| 0 | 0 | 1 |
-## Example ##
+## Example
When importing EBSD data from EDAX typically the user will need to rotate the sample reference frame about the <010> (Y) axis. This results in the image comparison below. Note that in the original image the origin of the data is at (0, 0) microns but after rotation the origin now becomes (-189, 0) microns. If you need to reset the origin back to (0,0) then the filter "Set Origin & Spacing" can be run.
![Imported EBSD Data Rotated about the <010> axis](Images/RotateSampleRefFrame_1.png)
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------|------|-------------|
-| Rotation Representation | Enumeration | Which form used to represent rotation (**axis angle** or **rotation matrix)** |
-| Rotation Axis (ijk) | float (3x) | Axis in sample reference frame to rotate about (if **axis angle**) |
-| Rotation Angle (Degrees) | float | Magnitude of rotation (in degrees) about the rotation axis (if **axis angle**) |
-| Rotation Matrix | float (3x3) | Axis in sample reference frame to rotate about (if **rotation matrix**) |
-
-## Required Geometry ##
-
-Image
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **DataArray** | N/A | Any | Same as geometry | List of **DataArrays** associated with the geometry |
-
-## Created Objects ##
-
-None
-
-## Example Pipelines ##
+## Example Pipelines
+ INL Export
+ Export Small IN100 ODF Data (StatsGenerator)
@@ -56,12 +35,10 @@ None
+ Edax IPF Colors
+ Confidence Index Histogram
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/ScalarSegmentFeaturesFilter.md b/src/Plugins/ComplexCore/docs/ScalarSegmentFeaturesFilter.md
index f17603a0cd..90fde6845a 100644
--- a/src/Plugins/ComplexCore/docs/ScalarSegmentFeaturesFilter.md
+++ b/src/Plugins/ComplexCore/docs/ScalarSegmentFeaturesFilter.md
@@ -1,11 +1,10 @@
-# Segment Features (Scalar)
+# Segment Features (Scalar)
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Reconstruction (Segmentation)
-## Description ##
+## Description
This **Filter** segments the **Features** by grouping neighboring **Cells** that satisfy the *scalar tolerance*, i.e., have a scalar difference less than the value set by the user. The process by which the **Features** are identified is given below and is a standard *burn algorithm*.
@@ -15,47 +14,20 @@ This **Filter** segments the **Features** by grouping neighboring **Cells** that
4. Remove the current **Cell** from the list and move to the next **Cell** and repeat 2. and 3.; continue until no **Cells** are left in the list
5. Increment the current **Feature** counter and repeat steps 1. through 4.; continue until no **Cells** remain unassigned in the dataset
-The user has the option to *Use Mask Array*, which allows the user to set a boolean array for the **Cells** that remove **Cells** with a value of *false* from consideration in the above algorithm. This option is useful if the user has an array that either specifies the domain of the "sample" in the "image" or specifies if the orientation on the **Cell** is trusted/correct.
+The user has the option to *Use Mask Array*, which allows the user to set a boolean array for the **Cells** that remove **Cells** with a value of *false* from consideration in the above algorithm. This option is useful if the user has an array that either specifies the domain of the "sample" in the "image" or specifies if the orientation on the **Cell** is trusted/correct.
After all the **Features** have been identified, an **Attribute Matrix** is created for the **Features** and each **Feature** is flagged as *Active* in a boolean array in the matrix.
-## Parameters ##
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Scalar Tolerance | float | Tolerance used to determine if neighboring **Cells** belong to the same **Feature** |
-| Use Mask Array | bool | Specifies whether to use a boolean array to exclude some **Cells** from the **Feature** identification process |
-
-## Required Geometry ##
-
-Image
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | None | Any | (1) | Scalar array used during segmentation |
-| **Cell Attribute Array** | Mask | bool | (1) | Specifies if the **Cell** is to be counted in the algorithm. Only required if *Use Mask Array* is checked |
+% Auto generated parameter table will be inserted here
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Cell** belongs. |
-| **Attribute Matrix** | CellFeatureData | Cell Feature | N/A | Created **Feature Attribute Matrix** name |
-| **Feature Attribute Array** | Active | bool | (1) | Specifies if the **Feature** is still in the sample (*true* if the **Feature** is in the sample and *false* if it is not). At the end of the **Filter**, all **Features** will be *Active* |
-
-
-## Example Pipelines ##
+## Example Pipelines
+ (09) Image Segmentation
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/SetImageGeomOriginScalingFilter.md b/src/Plugins/ComplexCore/docs/SetImageGeomOriginScalingFilter.md
index 45b1d37de1..620ef7e8de 100644
--- a/src/Plugins/ComplexCore/docs/SetImageGeomOriginScalingFilter.md
+++ b/src/Plugins/ComplexCore/docs/SetImageGeomOriginScalingFilter.md
@@ -1,11 +1,10 @@
# Set Origin & Spacing (Image Geometry)
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Core (Spatial)
-## Description ##
+## Description
This **Filter** changes the origin and/or the spacing of an **Image Geometry**. For example, if the current origin is at (0, 0, 0) and the user would like the origin to be (10, 4, 8), then the user should enter the following input values:
@@ -13,39 +12,14 @@ This **Filter** changes the origin and/or the spacing of an **Image Geometry**.
+ Y Origin: 4
+ Z Origin: 8
-## Parameters ##
-
-| Name | Type | Description |
-|---------|-----------|--------|
-| Origin | float (3x) | New origin for the **Image Geometry** |
-| Spacing | float (3x) | New spacing for the **Image Geometry** |
-| Change Origin | bool | Whether a new origin should be applied to the **Image Geometry** |
-| Change Spacing | bool | Whether a new spacing should be applied to the **Image Geometry** |
-
-## Required Geometry ##
-
-Image
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Data Container** | None | N/A | N/A | **Data Container** with an **Image Geometry** to modify |
+% Auto generated parameter table will be inserted here
-## Created Objects ##
+## Example Pipelines
-None
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/SharedFeatureFaceFilter.md b/src/Plugins/ComplexCore/docs/SharedFeatureFaceFilter.md
index bdcdb0b58c..f36497e8aa 100644
--- a/src/Plugins/ComplexCore/docs/SharedFeatureFaceFilter.md
+++ b/src/Plugins/ComplexCore/docs/SharedFeatureFaceFilter.md
@@ -12,49 +12,26 @@ boundary_ on which that **Triangle** resides. For example, if there were only tw
then the **Triangles** on that boundary would be labeled with a single unique Id. This procedure creates _unique groups_
of **Triangles**, which themselves are a set of **Features**. Thus, this **Filter** also creates a **Feature Attribute
Matrix** for this new set of **Features**, and creates **Attribute Arrays** for their Ids and number of **Triangles**. This
-process can be considered a **segmentation** where each unique id is the shared boundary between two features.
+process can be considered a **segmentation** where each unique id is the shared boundary between two features.
Because the algorithm is essentially segmenting the triangles based on the unique combination of face labels, the filter will
-also generate a Feature level Attribute Matrix and place two additional *DataArrays* into that feature attribute matrix
-that store the following information:
-
+also generate a Feature level Attribute Matrix and place two additional _DataArrays_ into that feature attribute matrix
+that store the following information:
+
1. The number of triangles in each unique boundary
2. The pair of Face Label values that made up the unique boundary.
-### Generated Feature Boundaries *with* Randomization
+### Generated Feature Boundaries _with_ Randomization
![Example Surface Mesh Coloring By Feature Face Id](Images/SharedFeaturFace_1.png)
-### Generated Feature Boundaries *without* Randomization
+### Generated Feature Boundaries _without_ Randomization
![Example Surface Mesh Coloring By Feature Face Id](Images/SharedFeaturFace_2.png)
---------------
-## Parameters ##
-
-| Name | Type | Description |
-|--------------------------|---------|-------------------------------------------------------------------------------------|
-| Randomize Feature Values | boolean | Should the final 'FeatureFaceId' Array be randomized. This can aid in visualization |
-
-## Required Geometry
-
-Triangle
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|--------------------------|--------------|---------|----------------------|------------------------------------------------------------------|
-| **Face Attribute Array** | FaceLabels | int32_t | (2) | Specifies which **Features** are on either side of each **Face** |
-
-## Created Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|-----------------------------|-----------------|--------------|----------------------|--------------------------------------------------------------------------------------|
-| **Face Attribute Array** | FeatureFaceId | int32_t | (1) | Specifies to which **Feature** each **Face** belongs |
-| **Attribute Matrix** | FaceFeatureData | Face Feature | N/A | Created **Feature Attribute Matrix** name |
-| **Feature Attribute Array** | FaceLabels | int32_t | (2) | Specifies which *original* **Features** are on either side of each *new* **Feature** |
-| **Feature Attribute Array** | NumTriangles | int32_t | (1) | Number of **Triangles** in each **Feature** |
+% Auto generated parameter table will be inserted here
## Example Pipelines
@@ -64,8 +41,6 @@ Triangle
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/SilhouetteFilter.md b/src/Plugins/ComplexCore/docs/SilhouetteFilter.md
index 7b100ae350..1906113d8b 100644
--- a/src/Plugins/ComplexCore/docs/SilhouetteFilter.md
+++ b/src/Plugins/ComplexCore/docs/SilhouetteFilter.md
@@ -1,10 +1,10 @@
-# Silhouette #
+# Silhouette
-## Group (Subgroup) ##
+## Group (Subgroup)
DREAM3D Review (Clustering)
-## Description ##
+## Description
This **Filter** computes the silhouette for a clustered **Attribute Array**. The user must select both the original array that has been clustered and the array of cluster Ids. The silhouette represents a measure for the quality of a clustering. Specifically, the silhouette provides a measure for how strongly a given point belongs to its own cluster compared to all other clusters. The silhouette is computed as follows:
@@ -14,39 +14,14 @@ where \f$ a \f$ is the average distance between point \f$ i \f$ and all other po
The silhouette can be used to determine how well a particular clustering has performed, such as k means or k medoids.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------|------|-------------|
-| Distance Metric | Enumeration | The metric used to determine the distances between points |
-| Use Mask | bool | Whether to use a boolean mask array to ignore certain points flagged as *false* from the algorithm |
+## Example Pipelines
-## Required Geometry ###
-
-None
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| Any **Attribute Array** | None | Any| Any | The **Attribute Array** to silhouette |
-| **Attribute Array** | ClusterIds | int32_t | (1) | Specifies to which cluster each point belongs |
-| **Attribute Array** | Mask | bool | (1) | Specifies if the point is to be counted in the algorithm, if *Use Mask* is checked |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Attribute Array** | Silhouette | double | (1) | Silhouette value for each point |
-
-## Example Pipelines ##
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/SplitAttributeArrayFilter.md b/src/Plugins/ComplexCore/docs/SplitAttributeArrayFilter.md
index 892b2aa4ad..605c6c7bdc 100644
--- a/src/Plugins/ComplexCore/docs/SplitAttributeArrayFilter.md
+++ b/src/Plugins/ComplexCore/docs/SplitAttributeArrayFilter.md
@@ -1,11 +1,10 @@
-# Split Multicomponent Attribute Array
+# Split Multicomponent Attribute Array
-
-## Group (Subgroup) ##
+## Group (Subgroup)
DREAM3D Review (Memory/Management)
-## Description ##
+## Description
This **Filter** splits an n-component **Attribute Array** into **n** scalar arrays, where each array is one of the original components. Any arbitrary component array may be split in this manner, and the output arrays will have the same primitive type as the input array. The original array is not modified (unless the option to remove the original array is selected); instead, **n** new arrays are created. For example, consider an unsigned 8-bit array with three components:
@@ -23,38 +22,14 @@ There is an alternative option which allows the user to select a subset of compo
This **Filter** is the opposite operation of the Combine Attribute Arrays **Filter**, and the generalized version of the Extract Component as Attribute Array **Filter**.
-## Parameters ##
-
-| Name | Type | Description |
-|------|------|-------------|
-| Postfix | string | Postfix to add to the end of the split **Attribute Arrays**; this value may be empty |
-
-## Required Geometry ###
-
-None
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| Any **Attribute Array** | None | Any | > (1) | The multicomponent **Attribute Array** to split |
+% Auto generated parameter table will be inserted here
-## Created Objects ##
+## Example Pipelines
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Attribute Arrays** | Input array name + *Postfix* + component number | Same as input array | (1)| The set of scalar **Attribute Arrays**, equal to the number of components of the input **Attribute Array** |
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/StlFileReaderFilter.md b/src/Plugins/ComplexCore/docs/StlFileReaderFilter.md
index 9a621eaa70..4844791944 100644
--- a/src/Plugins/ComplexCore/docs/StlFileReaderFilter.md
+++ b/src/Plugins/ComplexCore/docs/StlFileReaderFilter.md
@@ -1,11 +1,10 @@
-# Read STL File
+# Read STL File
-
-## Group (Subgroup) ##
+## Group (Subgroup)
IO (Input)
-## Description ##
+## Description
This **Filter** will read a binary STL File and create a **Triangle Geometry** object in memory. The STL reader is very strict to the STL specification. An explanation of the STL file format can be found on [Wikipedia](https://en.wikipedia.org/wiki/STL). The structure of the file is as follows:
@@ -22,45 +21,14 @@ This **Filter** will read a binary STL File and create a **Triangle Geometry**
**It is very important that the "Attribute byte Count" is correct as DREAM.3D follows the specification strictly.** If you are writing an STL file be sure that the value for the "Attribute byte count" is *zero* (0). If you chose to encode additional data into a section after each triangle then be sure that the "Attribute byte count" is set correctly. DREAM.3D will obey the value located in the "Attribute byte count".
-## Parameters ##
-
-| Name | Type | Description |
-|------|------|------|
-| STL File | File Path | The input .stl file path |
-| Scale Output | Bool | Should the output vertex values be scaled |
-| Scale Factor | Float | Apply the scaling factor to each vertex |
-| Vertex Attribute Matrix | String | Name of the created Vertex Attribute Matrix |
-| Face Attribute Matrix | String | Name of the created Face Attribute Matrix |
-| Shared Vertex Attribute Matrix | String | Name of the created Shared Vertex Attribute Matrix |
-| Shared Face Attribute Matrix | String | Name of the created Shared Face Attribute Matrix |
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-None
-
-## Created Objects ##
+% Auto generated parameter table will be inserted here
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Data Container** | TriangleDataContainer | N/A | N/A | Created **Data Container** name with a **Triangle Geometry** |
-| **Attribute Matrix** | FaceData | Face | N/A | Created **Face Attribute Matrix** name |
-| **Face Attribute Array** | FaceNormals | double | (3) | Specifies the normal of each **Face** |
+## Example Pipelines
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/SurfaceNetsFilter.md b/src/Plugins/ComplexCore/docs/SurfaceNetsFilter.md
index 22f5f0e8ea..766b6b5c1a 100644
--- a/src/Plugins/ComplexCore/docs/SurfaceNetsFilter.md
+++ b/src/Plugins/ComplexCore/docs/SurfaceNetsFilter.md
@@ -1,10 +1,10 @@
-# SurfaceNets Filter #
+# SurfaceNets Filter
-## Group (Subgroup) ##
+## Group (Subgroup)
Surface Meshing (Generation)
-## Description ##
+## Description
This filter uses the algorithm from {1} to produce a triangle surface mesh. The code is directly based on the sample code from the paper but has been modified to
work with the complex library classes. This filter uses a different algorithm that aims to produce a mush that keeps sharp edges
@@ -35,55 +35,23 @@ SurfaceNets output **with** the built-in smoothing operation applied.
---------------
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Human Name | Description | Parameter Type |
-|--------------|-------------|----------------|
-| Apply Smoothing Operation | This will enable the built-in smoothing from the SurfaceNets algorithm | complex.BoolParameter |
-| Relaxation Iterations | The number of smoothing iterations to perform | complex.Int32Parameter |
-| Max Distance from Voxel | The maximum allowable distance that a node can move from the voxel center | complex.Float32Parameter |
-| Relaxation Factor | How far a node can move during each smoothing operation | complex.Float32Parameter |
-
-## Required Geometry ##
-
-Image/RectGrid
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------------------------------|--------------|---------|----------------------|--------------------------------------------------------------------------------------------|
-| **Cell Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Cell** belongs |
-| Any **Cell Attribute Array** | None | Any | Any | Specifies which **Cell Attribute Arrays** to transfer to the created **Triangle Geometry** |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------------------------------|-----------------------|------------------|----------------------|------------------------------------------------------------------|
-| **Data Container** | TriangleDataContainer | N/A | N/A | Created **Data Container** name with a **Triangle Geometry** |
-| **Attribute Matrix** | VertexData | Vertex | N/A | Created **Vertex Attribute Matrix** name |
-| **Vertex Attribute Array** | NodeTypes | int8_t | (1) | Specifies the type of node in the **Geometry** |
-| **Attribute Matrix** | FaceData | Face | N/A | Created **Face Attribute Matrix** name |
-| **Face Attribute Array** | FaceLabels | int32_t | (2) | Specifies which **Features** are on either side of each **Face** |
-| **Attribute Matrix** | FaceFeatureData | Face Feature | N/A | **Feature Attribute Matrix** of the created _Face Labels_ |
-| Any **Face Attribute Array** | None | List of DataPath | Any | The set of transferred **Cell Attribute Arrays** |
-
-## Example Pipelines ##
+## Example Pipelines
Pipelines/ComplexCore/SurfaceNets_Demo.d3dpipeline
-## Citations ##
+## Citations
{1}[SurfaceNets for Multi-Label Segmentations with Preservation of Sharp Boundaries](https://jcgt.org/published/0011/01/03/paper.pdf)
-## License & Copyright ##
+## License & Copyright
`Sarah F. Frisken, SurfaceNets for Multi-Label Segmentations with Preservation of Sharp
Boundaries, Journal of Computer Graphics Techniques (JCGT), vol. 11, no. 1, 34–54, 2022`
[http://jcgt.org/published/0011/01/03](http://jcgt.org/published/0011/01/03)
-## DREAM.3D Mailing Lists ##
+## DREAM.3D Mailing Lists
If you need more help with a **Filter**, please consider asking your question on
the [DREAM.3D Users Google group!](https://groups.google.com/forum/?hl=en#!forum/dream3d-users)
-
-
diff --git a/src/Plugins/ComplexCore/docs/TriangleCentroidFilter.md b/src/Plugins/ComplexCore/docs/TriangleCentroidFilter.md
index 1ba1e51386..f9546e7ae1 100644
--- a/src/Plugins/ComplexCore/docs/TriangleCentroidFilter.md
+++ b/src/Plugins/ComplexCore/docs/TriangleCentroidFilter.md
@@ -1,42 +1,24 @@
-Generate Triangle Centroids
+Generate Triangle Centroids
============
-## Group (Subgroup) ##
+## Group (Subgroup)
Surface Meshing (Misc)
-## Description ##
+## Description
This **Filter** computes the centroid of each **Triangle** in a **Triangle Geometry** by calculating the average position of all 3 **Vertices** that make up the **Triangle**.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-None
-
-## Required Geometry ##
-
-Triangle
-
-## Required Objects ##
-
-None
-
-## Created Objects ##
-| Kind | Default Name | Type | Component Dimensions | Description |
-|--------------------------|---------------|--------|----------------------|-----------------------------------------|
-| **Face Attribute Array** | FaceCentroids | float32 | (1) | Specifies the centroid of each **Face** |
-
-
-## Example Pipelines ##
+## Example Pipelines
+ Triangle_Face_Data_Demo.d3dpipeline
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/TriangleDihedralAngleFilter.md b/src/Plugins/ComplexCore/docs/TriangleDihedralAngleFilter.md
index 5f08000927..7c90b7d11c 100644
--- a/src/Plugins/ComplexCore/docs/TriangleDihedralAngleFilter.md
+++ b/src/Plugins/ComplexCore/docs/TriangleDihedralAngleFilter.md
@@ -1,44 +1,24 @@
# TriangleDihedralAngleFilter
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Surface Meshing (Misc)
-## Description ##
+## Description
This **Filter** computes the minimum dihedral angle of each **Triangle** in a **Triangle Geometry** by utilizing matrix mathematics
-## Parameters ##
-
-None
-
-## Required Geometry ##
-
-Triangle
-
-## Required Objects ##
-
-None
+% Auto generated parameter table will be inserted here
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Face Attribute Array** | dihedralAngles | double array | (1) | Specifies the minimum dihedral angle of each triangle of each **Face** |
-
-
-## Example Pipelines ##
+## Example Pipelines
+ (03) SmallIN100 Mesh Statistics
+ Triangle_Face_Data_Demo.d3dpipeline
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/TriangleNormalFilter.md b/src/Plugins/ComplexCore/docs/TriangleNormalFilter.md
index 63327b4a66..f05d60c171 100644
--- a/src/Plugins/ComplexCore/docs/TriangleNormalFilter.md
+++ b/src/Plugins/ComplexCore/docs/TriangleNormalFilter.md
@@ -1,14 +1,13 @@
# Calculate Triangle Normals
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Surface Meshing (Misc)
-## Description ##
+## Description
This **Filter** computes the normal of each **Triangle** in a **Triangle Geometry** by utilizing matrix subtraction, cross product, and normalization to implement the following theory:
- For a triangle with point1, point2, point3, if the vector U = point2 - point1 and the vector V = point3 - point1
+ For a triangle with point1, point2, point3, if the vector U = point2 - point1 and the vector V = point3 - point1
Nx = UyVz - UzVy
Ny = UzVx - UxVz
@@ -16,37 +15,17 @@ This **Filter** computes the normal of each **Triangle** in a **Triangle Geometr
Where "point#" represents a 3x1 Matrix of coordinates x, y, and z belonging to one of a Triangles vertexes and N represents the normal of the corresponding axis value
+% Auto generated parameter table will be inserted here
-## Parameters ##
-
-None
-
-## Required Geometry ##
-
-Triangle
-
-## Required Objects ##
-
-None
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Face Attribute Array** | FaceNormals | double array | (1) | Specifies the normal of each **Face** |
-
-
-## Example Pipelines ##
+## Example Pipelines
+ (03) SmallIN100 Mesh Statistics
+ Triangle_Face_Data_Demo.d3dpipeline
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/UncertainRegularGridSampleSurfaceMesh.md b/src/Plugins/ComplexCore/docs/UncertainRegularGridSampleSurfaceMesh.md
index eb846bbdc5..9ad3e584c0 100644
--- a/src/Plugins/ComplexCore/docs/UncertainRegularGridSampleSurfaceMesh.md
+++ b/src/Plugins/ComplexCore/docs/UncertainRegularGridSampleSurfaceMesh.md
@@ -19,13 +19,13 @@ This **Filter** "samples" a triangulated surface mesh on a rectilinear grid, but
## Parameters
| Name | Type | Description |
-|------|------|-------------|
+|------------|------| --------------------------------- |
| Use Seed | bool | If *true* user may set a set a seed for random generation |
| Seed | uint64 | This is the seed fed into the random generator |
| Dimensions | uint64 | Number of **Cells** along each axis |
| Resolution | float32 (3x) | The resolution values (dx, dy, dz) |
| Origin | float32 (3x) | The origin of the sampling volume |
-| Uncertainty | float32 (3x) | Vector of uncertainty values associated with X, Y and Z positions of **Cells** |
+| Uncertainty | float32 (3x) | Vector of uncertainty values associated with X, Y and Z positions of **Cells |
## Required Geometry
@@ -33,22 +33,22 @@ Triangle
## Required Objects
-| Type | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|-----|
-| **Data Array** | Face Labels | int32 | (2) | Specifies which **Features** are on either side of each **Face**. |
+| Type | Default Name | Type | Comp Dims | Description |
+|------|--------------|-----|-----|-----------------------------------|
+| Data Array | Face Labels | int32 | (2) | Specifies which **Features** are on either side of each **Face**. |
## Created Objects
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Image Geometry** | Image Geometry | N/A | N/A | Created **Image Geometry** name and *DataPath* |
-| **Attribute Matrix** | Cell Data | Cell | N/A | Created **Cell Attribute Matrix** name |
-| **Data Array** | Feature Ids | int32 | (1) | Specifies to which **Feature** each **Cell** belongs |
+| Kind | Default Name | Type | Comp Dims | Description |
+|---------------------------|--------------|----------|--------|---------------------------------------------|
+| Image Geometry | Image Geometry | N/A | N/A | Created **Image Geometry** name and *DataPath* |
+| Attribute Matrix | Cell Data | Cell | N/A | Created **Cell Attribute Matrix** name |
+| Data Array | Feature Ids | int32 | (1) | Specifies to which **Feature** each **Cell** belongs |
## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
+## DREAM3D-NX Help
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/UncertainRegularGridSampleSurfaceMeshFilter.md b/src/Plugins/ComplexCore/docs/UncertainRegularGridSampleSurfaceMeshFilter.md
index a5ef19dc3f..90ed738f08 100644
--- a/src/Plugins/ComplexCore/docs/UncertainRegularGridSampleSurfaceMeshFilter.md
+++ b/src/Plugins/ComplexCore/docs/UncertainRegularGridSampleSurfaceMeshFilter.md
@@ -16,41 +16,12 @@ This **Filter** "samples" a triangulated surface mesh on a rectilinear grid, but
**Note that the unperturbed grid is where the *Feature Ids* actually live, but the perturbed locations are where the Cells are sampled from. Essentially, the *Feature Ids* are stored where the user *thinks* the sampling took place, not where it actually took place!**
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| Use Seed | bool | If *true* user may set a set a seed for random generation |
-| Seed | uint64 | This is the seed fed into the random generator |
-| Dimensions | uint64 | Number of **Cells** along each axis |
-| Resolution | float32 (3x) | The resolution values (dx, dy, dz) |
-| Origin | float32 (3x) | The origin of the sampling volume |
-| Uncertainty | float32 (3x) | Vector of uncertainty values associated with X, Y and Z positions of **Cells** |
-
-## Required Geometry
-
-Triangle
-
-## Required Objects
-
-| Type | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|-----|
-| **Data Array** | Face Labels | int32 | (2) | Specifies which **Features** are on either side of each **Face**. |
-
-## Created Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Image Geometry** | Image Geometry | N/A | N/A | Created **Image Geometry** name and *DataPath* |
-| **Attribute Matrix** | Cell Data | Cell | N/A | Created **Cell Attribute Matrix** name |
-| **Data Array** | Feature Ids | int32 | (1) | Specifies to which **Feature** each **Cell** belongs |
+% Auto generated parameter table will be inserted here
## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/VtkRectilinearGridWriterFilter.md b/src/Plugins/ComplexCore/docs/VtkRectilinearGridWriterFilter.md
index 292c2a36ba..820ae1a9c0 100644
--- a/src/Plugins/ComplexCore/docs/VtkRectilinearGridWriterFilter.md
+++ b/src/Plugins/ComplexCore/docs/VtkRectilinearGridWriterFilter.md
@@ -1,56 +1,21 @@
-# Vtk Rectilinear Grid Exporter #
+# Vtk Rectilinear Grid Exporter
-
-## Group (Subgroup) ##
+## Group (Subgroup)
I/O Filters
-
-## Description ##
+## Description
This Filter reads the **Feature** and phase ids together with image parameters required by Vtk to an output file named by the user. The file is used to generate the image of the **Features** and phases of the **Features**.
+% Auto generated parameter table will be inserted here
-## Parameters ##
-
-| Name | Type |
-|------|------|
-| Output File | Output File |
-| Write **Feature** Ids | Boolean (On or Off) |
-| Write Phase Ids | Boolean (On or Off) |
-| Write Band Contrasts | Boolean (On or Off) |
-| Write KAM Value | Boolean (On or Off) |
-| Write GAM Values | Boolean (On or Off) |
-| Write LMG Values | Boolean (On or Off) |
-| Write Good **Cells** | Boolean (On or Off) |
-| Write IPF Colors | Boolean (On or Off) |
-| Write Binary File | Boolean (On or Off) |
-
-## Required DataContainers ##
-
-Voxel
-
-## Required Objects ##
-
-| Type | Default Name | Description | Comment | Filters Known to Create Data |
-|------|--------------|-------------|---------|-----|
-| Cell | GrainIds | Ids (ints) that specify to which **Feature** each **Cell** belongs. | Values should be present from segmentation of experimental data or synthetic generation and cannot be determined by this filter. Not having these values will result in the filter to fail/not execute. | Segment Features (Misorientation, C-Axis Misorientation, Scalar) (Reconstruction), Read Dx File (IO), Read Ph File (IO), Pack Primary Phases (SyntheticBuilding), Insert Precipitate Phases (SyntheticBuilding), Establish Matrix Phase (SyntheticBuilding)
-
-## Created Objects ##
+## Example Pipelines
-None
-
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/WriteASCIIDataFilter.md b/src/Plugins/ComplexCore/docs/WriteASCIIDataFilter.md
index 87c36743f7..1bcd70a57a 100644
--- a/src/Plugins/ComplexCore/docs/WriteASCIIDataFilter.md
+++ b/src/Plugins/ComplexCore/docs/WriteASCIIDataFilter.md
@@ -1,44 +1,19 @@
# Write ASCII Data
-
-## Group (Subgroup) ##
+## Group (Subgroup)
IO (Output) (Write) (Export) (Text) (CSV) (ASCII)
-## Description ##
+## Description
This **Filter** accepts DataArray(s) as input, extracts the data, creates the file(s), and writes it out according to parameter choices
-## Parameters ##
-
-| Name | Type | Decision |
-|-------|-----|----------|
-| Output Type | OutputSytle enum class | Whether data is printed to one file or multiple |
-| Output Path | Filesystem::path | Directory to store printed array files |
-| File Extension | string | The file extension used for generated files |
-| Maximum Tuples Per Line | int32 | Number of tuples printed before newline character is printed |
-| Delimiter | Delimiter enum class | ASCII character used to seperate values |
-
-## Required Geometry ##
-
-None
-
-## Required Objects ##
+% Auto generated parameter table will be inserted here
-| Kind | Default Name | Type | Component Dimensions | Description |
-|-----|-------|------|--------|------------------------------------------------------|
-| **DataArray** | Attribute Arrays to Export | DataArray | any | Specifies **DataArray** to have their values printed |
-
-## Created Objects ##
-
-None
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/WriteBinaryDataFilter.md b/src/Plugins/ComplexCore/docs/WriteBinaryDataFilter.md
index b5fb0dde71..6371651ccf 100644
--- a/src/Plugins/ComplexCore/docs/WriteBinaryDataFilter.md
+++ b/src/Plugins/ComplexCore/docs/WriteBinaryDataFilter.md
@@ -1,42 +1,19 @@
# WriteBinaryData
-
-## Group (Subgroup) ##
+## Group (Subgroup)
IO (Output) (Write) (Export) (Binary)
-## Description ##
+## Description
This **Filter** accepts DataArray(s) as input, extracts the data, creates the file(s), and writes it out to a single file in binary
-## Parameters ##
-
-| Name | Type | Decision |
-|-------|------|----------|
-| Endianess | Endianess enum class | Determines underlying ordering of binary, if unsure, use Little (most universal) |
-| Output Path | Filesystem::path | Directory to store printed array files |
-| File Extension | string | The file extension used for generated files |
-
-## Required Geometry ##
-
-None
-
-## Required Objects ##
+% Auto generated parameter table will be inserted here
-| Kind | Default Name | Type | Component Dimensions | Description |
-|---------------|-------|------|------|-----------------------------------------------------|
-| **DataArray** | Attribute Arrays to Export | DataArray | any | Specifies **DataArray** to have their values printed |
-
-## Created Objects ##
-
-None
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/docs/WriteStlFileFilter.md b/src/Plugins/ComplexCore/docs/WriteStlFileFilter.md
index 259a2bf0ad..2e5eeac52b 100644
--- a/src/Plugins/ComplexCore/docs/WriteStlFileFilter.md
+++ b/src/Plugins/ComplexCore/docs/WriteStlFileFilter.md
@@ -8,36 +8,12 @@ IO (Output)
This **Filter** will write a binary STL File for each unique **Feature** Id in the associated **Triangle** geometry. The STL files will be named with the [Feature_Id].stl. The user can designate an optional prefix for the files.
-## Parameters
-
-| Name | Type | Description |
-|------|------|------|
-| Group by Feature Phases | bool | When true this allows the STL files to be further broken down by Phases |
-| Output STL Directory | File Path | The output directory path where all of the individual STL files will be saved |
-| STL File Prefix | String | Optional Prefix to use when creating the STL file names |
-
-## Required Geometry
-
-Triangle
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Face Data Array** | Face Labels | int32 | (2) | Specifies which **Features** are on either side of each **Face** |
-| **Phases Data Array** | Feature Phases | int32 | (2) | Specifies which **Phases** of **Features** are on either side of each **Face** |
-| **Normals Data Array** | Face Normals | int32 | (2) | These are the face normals to be printed to the stl |
-
-## Created Objects
-
-None
+% Auto generated parameter table will be inserted here
## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/FeatureFaceCurvatureFilter.cpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/FeatureFaceCurvatureFilter.cpp
index e3855f20ed..d60eb6b2d7 100644
--- a/src/Plugins/ComplexCore/src/ComplexCore/Filters/FeatureFaceCurvatureFilter.cpp
+++ b/src/Plugins/ComplexCore/src/ComplexCore/Filters/FeatureFaceCurvatureFilter.cpp
@@ -71,7 +71,7 @@ Parameters FeatureFaceCurvatureFilter::parameters() const
params.insertLinkableParameter(std::make_unique(k_UseFaceNormals_Key, "Use Face Normals for Curve Fitting", "Use the face normals for curve fitting.", true));
- params.insertSeparator(Parameters::Separator{"Face Data"});
+ params.insertSeparator(Parameters::Separator{"Required Face Data"});
params.insert(std::make_unique(k_FaceAttribMatrix_Key, "Face Attribute Matrix", "The AttributeMatrix that holds the triangle face data.", DataPath()));
params.insert(std::make_unique(k_FaceLabels_Key, "Face Labels", "The DataPath to the 'Face Labels' DataArray", DataPath(),
ArraySelectionParameter::AllowedTypes{DataType::int32}, ArraySelectionParameter::AllowedComponentShapes{IArray::ShapeType{2}}));
@@ -82,6 +82,7 @@ Parameters FeatureFaceCurvatureFilter::parameters() const
params.insert(std::make_unique(k_FaceCentroids_Key, "Face Centroids", "The DataPath to the 'Face Centroids' DataArray", DataPath(),
ArraySelectionParameter::AllowedTypes{DataType::float64}, ArraySelectionParameter::AllowedComponentShapes{IArray::ShapeType{3}}));
+ params.insertSeparator(Parameters::Separator{"Created Face Data"});
params.insert(std::make_unique(k_PrincipalCurvature1_Key, "Principal Curvature 1", "Output DataPath to hold the 'Principal Curvature 1' values", DataPath()));
params.insert(std::make_unique(k_PrincipalCurvature2_Key, "Principal Curvature 2", "Output DataPath to hold the 'Principal Curvature 2' values", DataPath()));
params.insert(std::make_unique(k_PrincipalDirection1_Key, "Principal Direction 1", "Output DataPath to hold the 'Principal Direction 1' values", DataPath()));
diff --git a/src/Plugins/ITKImageProcessing/CMakeLists.txt b/src/Plugins/ITKImageProcessing/CMakeLists.txt
index 253327df58..9919338b92 100644
--- a/src/Plugins/ITKImageProcessing/CMakeLists.txt
+++ b/src/Plugins/ITKImageProcessing/CMakeLists.txt
@@ -230,6 +230,8 @@ set(AlgorithmList
)
endif()
+list(SORT FilterList ORDER ASCENDING)
+
# -----------------------------------------------------------------------------
# These are filters that need to be compiled but not exposed to a user
# -----------------------------------------------------------------------------
diff --git a/src/Plugins/ITKImageProcessing/PortingITKImageProcessingFilter.md b/src/Plugins/ITKImageProcessing/PortingITKImageProcessingFilter.md
index 14d9e0f01f..88a029d9aa 100644
--- a/src/Plugins/ITKImageProcessing/PortingITKImageProcessingFilter.md
+++ b/src/Plugins/ITKImageProcessing/PortingITKImageProcessingFilter.md
@@ -1,26 +1,28 @@
-# Porting ITK Image Processing Filter #
+# Porting ITK Image Processing Filter
-## Updating the Legacy UUID Maps ##
+## Updating the Legacy UUID Maps
-This **Plugin** contains three folders of filters instructions for porting to
+This **Plugin** contains three folders of filters instructions for porting to
and moving to ***Filters Folder*** are below:
-### If Porting From ***SIMPL*** to ***Filters Folder*** ###
- Use the **ComplexFilterGen** module distributed in ***SIMPL DREAM3D***. This
+### If Porting From ***SIMPL*** to ***Filters Folder***
+
+ Use the **ComplexFilterGen** module distributed in ***SIMPL DREAM3D***. This
module will automatically update the LegacyUUIDMapping for this **Plugin**.
- ### If Moving to ***Filters*** ###
+### If Moving to ***Filters***
+
- Open the LegacyUUIDMapping header file for this Plugin
- Uncomment the include statement for the filter being moved
- Uncomment the map entry for the filter being moved
- When working with the ***LegacyUUIDMapping*** header file in this **Plugin**
- be sure to make sure the commented out tokens are not removed. Their syntax is
+ When working with the ***LegacyUUIDMapping*** header file in this **Plugin**
+ be sure to make sure the commented out tokens are not removed. Their syntax is
one of the following:
- ***@@__HEADER__TOKEN__DO__NOT__DELETE__@@***
-
+ ***@@**HEADER__TOKEN__DO__NOT__DELETE**@@***
+
or
-
- ***@@__MAP__UPDATE__TOKEN__DO__NOT__DELETE__@@***
+
+ ***@@**MAP__UPDATE__TOKEN__DO__NOT__DELETE**@@***
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKAbsImage.md b/src/Plugins/ITKImageProcessing/docs/ITKAbsImage.md
index a064b1ed97..ffc44d2b39 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKAbsImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKAbsImage.md
@@ -1,4 +1,4 @@
-# ITK Abs Image Filter (ITKAbsImage)
+# ITK Abs Image Filter
Computes the absolute value of each pixel.
@@ -10,38 +10,14 @@ ITKImageIntensity (ImageIntensity)
itk::Math::abs() is used to perform the computation.
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKAcosImage.md b/src/Plugins/ITKImageProcessing/docs/ITKAcosImage.md
index 35af122127..5ab81b03b1 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKAcosImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKAcosImage.md
@@ -1,4 +1,4 @@
-# ITK Acos Image Filter (ITKAcosImage)
+# ITK Acos Image Filter
Computes the inverse cosine of each pixel.
@@ -12,47 +12,21 @@ This filter is templated over the pixel type of the input image and the pixel ty
The filter walks over all the pixels in the input image, and for each pixel does do the following:
-- cast the pixel value to double ,
-- apply the std::acos() function to the double value
-- cast the double value resulting from std::acos() to the pixel type of the output image
+- cast the pixel value to double ,
+- apply the std::acos() function to the double value
+- cast the double value resulting from std::acos() to the pixel type of the output image
- store the casted value into the output image.
-
-
The filter expects both images to have the same dimension (e.g. both 2D, or both 3D, or both ND).
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKAdaptiveHistogramEqualizationImage.md b/src/Plugins/ITKImageProcessing/docs/ITKAdaptiveHistogramEqualizationImage.md
index 84fc4fdc22..40e8da17fd 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKAdaptiveHistogramEqualizationImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKAdaptiveHistogramEqualizationImage.md
@@ -1,4 +1,4 @@
-# ITK Adaptive Histogram Equalization Image Filter (ITKAdaptiveHistogramEqualizationImage)
+# ITK Adaptive Histogram Equalization Image Filter
Power Law Adaptive Histogram Equalization.
@@ -22,41 +22,14 @@ The boundary condition ignores the part of the neighborhood outside the image, a
For detail description, reference "Adaptive Image Contrast Enhancement using Generalizations of Histogram Equalization." J.Alex Stark. IEEE Transactions on Image Processing, May 2000.
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| Radius | uint32 | |
-| Alpha | float32 | Set/Get the value of alpha. Alpha = 0 produces the adaptive histogram equalization (provided beta=0). Alpha = 1 produces an unsharp mask. Default is 0.3. |
-| Beta | float32 | Set/Get the value of beta. If beta = 1 (and alpha = 1), then the output image matches the input image. As beta approaches 0, the filter behaves as an unsharp mask. Default is 0.3. |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKAsinImage.md b/src/Plugins/ITKImageProcessing/docs/ITKAsinImage.md
index cf7e814626..2b430f8f31 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKAsinImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKAsinImage.md
@@ -1,4 +1,4 @@
-# ITK Asin Image Filter (ITKAsinImage)
+# ITK Asin Image Filter
Computes the sine of each pixel.
@@ -12,47 +12,21 @@ This filter is templated over the pixel type of the input image and the pixel ty
The filter walks over all the pixels in the input image, and for each pixel does the following:
-- cast the pixel value to double ,
-- apply the std::asin() function to the double value,
-- cast the double value resulting from std::asin() to the pixel type of the output image,
+- cast the pixel value to double ,
+- apply the std::asin() function to the double value,
+- cast the double value resulting from std::asin() to the pixel type of the output image,
- store the casted value into the output image.
-
-
The filter expects both images to have the same dimension (e.g. both 2D, or both 3D, or both ND)
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKAtanImage.md b/src/Plugins/ITKImageProcessing/docs/ITKAtanImage.md
index 6eae74faa8..6ed7d479e7 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKAtanImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKAtanImage.md
@@ -1,4 +1,4 @@
-# ITK Atan Image Filter (ITKAtanImage)
+# ITK Atan Image Filter
Computes the one-argument inverse tangent of each pixel.
@@ -12,43 +12,19 @@ This filter is templated over the pixel type of the input image and the pixel ty
The filter walks over all the pixels in the input image, and for each pixel does the following:
-- cast the pixel value to double ,
-- apply the std::atan() function to the double value,
-- cast the double value resulting from std::atan() to the pixel type of the output image,
+- cast the pixel value to double ,
+- apply the std::atan() function to the double value,
+- cast the double value resulting from std::atan() to the pixel type of the output image,
- store the cast value into the output image.
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKBinaryContourImage.md b/src/Plugins/ITKImageProcessing/docs/ITKBinaryContourImage.md
index e8e1a0eb0d..06d75c0e11 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKBinaryContourImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKBinaryContourImage.md
@@ -1,4 +1,4 @@
-# ITK Binary Contour Image Filter (ITKBinaryContourImage)
+# ITK Binary Contour Image Filter
Labels the pixels on the border of the objects in a binary image.
@@ -12,7 +12,7 @@ BinaryContourImageFilter takes a binary image as input, where the pixels in the
The connectivity can be changed to minimum or maximum connectivity with SetFullyConnected() . Full connectivity produces thicker contours.
-https://www.insight-journal.org/browse/publication/217
+
### Author
@@ -22,41 +22,14 @@ https://www.insight-journal.org/browse/publication/217
- LabelContourImageFilter BinaryErodeImageFilter SimpleContourExtractorImageFilter
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| FullyConnected | bool | Whether the connected components are defined strictly by face connectivity (False) or by face+edge+vertex connectivity (True). Default is False |
-| BackgroundValue | float64 | Set/Get the background value used to mark the pixels not on the border of the objects. |
-| ForegroundValue | float64 | Set/Get the foreground value used to identify the objects in the input and output images. |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching IntegerPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching IntegerPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKBinaryDilateImage.md b/src/Plugins/ITKImageProcessing/docs/ITKBinaryDilateImage.md
index 9585766d47..259db05507 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKBinaryDilateImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKBinaryDilateImage.md
@@ -1,4 +1,4 @@
-# ITK Binary Dilate Image Filter (ITKBinaryDilateImage)
+# ITK Binary Dilate Image Filter
Fast binary dilation of a single intensity value in the image.
@@ -23,43 +23,14 @@ N.Nikopoulos et al. "An efficient algorithm for 3d binary
morphological transformations with 3d structuring elements
for arbitrary size and shape". IEEE Transactions on Image Processing. Vol. 9. No. 3. 2000. pp. 283-286.* ImageToImageFilter BinaryErodeImageFilter BinaryMorphologyImageFilter
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| KernelRadius | uint32 | Set the radius of the kernel structuring element. |
-| KernelType | KernelEnum | Set the kernel or structuring element used for the morphology. |
-| BackgroundValue | float64 | The eroded pixels will receive the BackgroundValue. Default = non positive minimum |
-| ForegroundValue | float64 | The pixel value considered 'Foreground' that will be eroded |
-| BoundaryToForeground | bool | "Mark the boundary between foreground and background. |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching IntegerPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching IntegerPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKBinaryErodeImage.md b/src/Plugins/ITKImageProcessing/docs/ITKBinaryErodeImage.md
index b5cbf3aa93..4127f3651f 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKBinaryErodeImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKBinaryErodeImage.md
@@ -1,4 +1,4 @@
-# ITK Binary Erode Image Filter (ITKBinaryErodeImage)
+# ITK Binary Erode Image Filter
Fast binary erosion of a single intensity value in the image.
@@ -23,43 +23,14 @@ N.Nikopoulos et al. "An efficient algorithm for 3d binary
morphological transformations with 3d structuring elements
for arbitrary size and shape". IEEE Transactions on Image Processing. Vol. 9. No. 3. 2000. pp. 283-286.* ImageToImageFilter BinaryDilateImageFilter BinaryMorphologyImageFilter
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| KernelRadius | uint32 | Set the radius of the kernel structuring element. |
-| KernelType | KernelEnum | Set the kernel or structuring element used for the morphology. |
-| BackgroundValue | float64 | The eroded pixels will receive the BackgroundValue. Default = non positive minimum |
-| ForegroundValue | float64 | The pixel value considered 'Foreground' that will be eroded |
-| BoundaryToForeground | bool | "Mark the boundary between foreground and background. |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching IntegerPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching IntegerPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKBinaryMorphologicalClosingImage.md b/src/Plugins/ITKImageProcessing/docs/ITKBinaryMorphologicalClosingImage.md
index d01a78aed1..0356fe415e 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKBinaryMorphologicalClosingImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKBinaryMorphologicalClosingImage.md
@@ -1,4 +1,4 @@
-# ITK Binary Morphological Closing Image Filter (ITKBinaryMorphologicalClosingImage)
+# ITK Binary Morphological Closing Image Filter
binary morphological closing of an image.
@@ -12,7 +12,7 @@ This filter removes small (i.e., smaller than the structuring element) holes and
The structuring element is assumed to be composed of binary values (zero or one). Only elements of the structuring element having values > 0 are candidates for affecting the center pixel.
-This code was contributed in the Insight Journal paper: "Binary morphological closing and opening image filters" by Lehmann G. https://www.insight-journal.org/browse/publication/58
+This code was contributed in the Insight Journal paper: "Binary morphological closing and opening image filters" by Lehmann G.
### Author
@@ -22,42 +22,14 @@ This code was contributed in the Insight Journal paper: "Binary morphological cl
- MorphologyImageFilter , GrayscaleDilateImageFilter , GrayscaleErodeImageFilter
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| KernelRadius | uint32 | Set the radius of the kernel structuring element. |
-| KernelType | KernelEnum | Set the kernel or structuring element used for the morphology. |
-| ForegroundValue | float64 | Set the value in the image to consider as "foreground". Defaults to maximum value of InputPixelType. |
-| SafeBorder | bool | A safe border is added to input image to avoid borders effects and remove it once the closing is done |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching IntegerPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching IntegerPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKBinaryMorphologicalOpeningImage.md b/src/Plugins/ITKImageProcessing/docs/ITKBinaryMorphologicalOpeningImage.md
index 643c343a51..5b2db56e80 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKBinaryMorphologicalOpeningImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKBinaryMorphologicalOpeningImage.md
@@ -1,4 +1,4 @@
-# ITK Binary Morphological Opening Image Filter (ITKBinaryMorphologicalOpeningImage)
+# ITK Binary Morphological Opening Image Filter
binary morphological opening of an image.
@@ -12,7 +12,7 @@ This filter removes small (i.e., smaller than the structuring element) structure
The structuring element is assumed to be composed of binary values (zero or one). Only elements of the structuring element having values > 0 are candidates for affecting the center pixel.
-This code was contributed in the Insight Journal paper: "Binary morphological closing and opening image filters" by Lehmann G. https://www.insight-journal.org/browse/publication/58
+This code was contributed in the Insight Journal paper: "Binary morphological closing and opening image filters" by Lehmann G.
### Author
@@ -22,42 +22,14 @@ This code was contributed in the Insight Journal paper: "Binary morphological cl
- MorphologyImageFilter , GrayscaleDilateImageFilter , GrayscaleErodeImageFilter
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| KernelRadius | uint32 | Set the radius of the kernel structuring element. |
-| KernelType | KernelEnum | Set the kernel or structuring element used for the morphology. |
-| BackgroundValue | float64 | Set the value in eroded part of the image. Defaults to zero |
-| ForegroundValue | float64 | Set the value in the image to consider as "foreground". Defaults to maximum value of PixelType. |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching IntegerPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching IntegerPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKBinaryOpeningByReconstructionImage.md b/src/Plugins/ITKImageProcessing/docs/ITKBinaryOpeningByReconstructionImage.md
index 974b9f294e..975227c828 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKBinaryOpeningByReconstructionImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKBinaryOpeningByReconstructionImage.md
@@ -1,4 +1,4 @@
-# ITK Binary Opening By Reconstruction Image Filter (ITKBinaryOpeningByReconstructionImage)
+# ITK Binary Opening By Reconstruction Image Filter
binary morphological closing of an image.
@@ -18,47 +18,16 @@ The structuring element is assumed to be composed of binary values (zero or one)
### Related Filters
+This implementation was taken from the Insight Journal paper: * MorphologyImageFilter , OpeningByReconstructionImageFilter , BinaryClosingByReconstructionImageFilter
-
-This implementation was taken from the Insight Journal paper: https://www.insight-journal.org/browse/publication/176 * MorphologyImageFilter , OpeningByReconstructionImageFilter , BinaryClosingByReconstructionImageFilter
-
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| KernelRadius | uint32 | Set the radius of the kernel structuring element. |
-| KernelType | KernelEnum | Set the kernel or structuring element used for the morphology. |
-| ForegroundValue | float64 | Set the value in the image to consider as "foreground". Defaults to maximum value of PixelType. |
-| BackgroundValue | float64 | Set the value in eroded part of the image. Defaults to zero |
-| FullyConnected | bool | Whether the connected components are defined strictly by face connectivity (False) or by face+edge+vertex connectivity (True). Default is False |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching IntegerPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching IntegerPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKBinaryProjectionImage.md b/src/Plugins/ITKImageProcessing/docs/ITKBinaryProjectionImage.md
index a8fc252025..2209a5e34d 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKBinaryProjectionImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKBinaryProjectionImage.md
@@ -1,4 +1,4 @@
-# ITK Binary Projection Image Filter (ITKBinaryProjectionImage)
+# ITK Binary Projection Image Filter
Binary projection.
@@ -11,7 +11,7 @@ ITKImageStatistics (ImageStatistics)
Image projection is a very common task in image analysis to reduce the dimension of an image. A base
filter is provided with some specialized filters which implement different projection methods.
-This class was contributed to the Insight Journal by Gaetan Lehmann. The original paper can be found at https://www.insight-journal.org/browse/publication/71
+This class was contributed to the Insight Journal by Gaetan Lehmann. The original paper can be found at
### Author
@@ -19,50 +19,23 @@ This class was contributed to the Insight Journal by Gaetan Lehmann. The origina
### Related Filters
-- ProjectionImageFilter
-- MedianProjectionImageFilter
-- MeanProjectionImageFilter
-- MeanProjectionImageFilter
-- MaximumProjectionImageFilter
-- MinimumProjectionImageFilter
-- StandardDeviationProjectionImageFilter
+- ProjectionImageFilter
+- MedianProjectionImageFilter
+- MeanProjectionImageFilter
+- MeanProjectionImageFilter
+- MaximumProjectionImageFilter
+- MinimumProjectionImageFilter
+- StandardDeviationProjectionImageFilter
- SumProjectionImageFilter
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| ProjectionDimension | uint32 | The index of the projection dimension |
-| ForegroundValue | float64 | Set the value in the image to consider as "foreground". Defaults to maximum value of PixelType. Subclasses may alias this to DilateValue or ErodeValue. |
-| BackgroundValue | float64 | Set the value used as "background". Any pixel value which is not DilateValue is considered background. BackgroundValue is used for defining boundary conditions. Defaults to NumericTraits::NonpositiveMin() . |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKBinaryThinningImage.md b/src/Plugins/ITKImageProcessing/docs/ITKBinaryThinningImage.md
index 040ff1e6df..8f784b3d4c 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKBinaryThinningImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKBinaryThinningImage.md
@@ -1,4 +1,4 @@
-# ITK Binary Thinning Image Filter (ITKBinaryThinningImage)
+# ITK Binary Thinning Image Filter
This filter computes one-pixel-wide edges of the input image.
@@ -20,38 +20,14 @@ Rafael C. Gonzales and Richard E. Woods. Digital Image Processing. Addison Wesle
To do: Make this filter ND.* MorphologyImageFilter
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching IntegerPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching IntegerPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKBinaryThresholdImage.md b/src/Plugins/ITKImageProcessing/docs/ITKBinaryThresholdImage.md
index e88bc34a3c..3bcca950d2 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKBinaryThresholdImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKBinaryThresholdImage.md
@@ -1,4 +1,4 @@
-# ITK Binary Threshold Image Filter (ITKBinaryThresholdImage)
+# ITK Binary Threshold Image Filter
Binarize an input image by thresholding.
@@ -10,7 +10,7 @@ ITKThresholding (Thresholding)
This filter produces an output image whose pixels are either one of two values ( OutsideValue or InsideValue ), depending on whether the corresponding input image pixels lie between the two thresholds ( LowerThreshold and UpperThreshold ). Values equal to either threshold is considered to be between the thresholds.
-More precisely \f[ Output(x_i) = \begin{cases} InsideValue & \text{if \f$LowerThreshold \leq x_i \leq UpperThreshold\f$} \\ OutsideValue & \text{otherwise} \end{cases} \f]
+More precisely \f[ Output(x_i) = \begin{cases} InsideValue & \text{if \f$LowerThreshold \leq x_i \leq UpperThreshold\f$} \\ OutsideValue & \text{otherwise} \end{cases} \f]
This filter is templated over the input image type and the output image type.
@@ -19,42 +19,15 @@ The filter expect both images to have the same number of dimensions.
The default values for LowerThreshold and UpperThreshold are: LowerThreshold = NumericTraits::NonpositiveMin() ; UpperThreshold = NumericTraits::max() ; Therefore, generally only one of these needs to be set, depending on whether the user wants to threshold above or below the desired threshold.
Set the thresholds. The default lower threshold is NumericTraits::NonpositiveMin() . The default upper threshold is NumericTraits::max . An exception is thrown if the lower threshold is greater than the upper threshold.
-## Parameters
-| Name | Type | Description |
-|------|------|-------------|
-| LowerThreshold | float64 | The lower threshold that a pixel value could be and still be considered 'Inside Value' |
-| UpperThreshold | float64 | The upper threshold that a pixel value could be and still be considered 'Inside Value'|
-| InsideValue | uint8 | Set the "inside" pixel value. The default value NumericTraits::max() |
-| OutsideValue | uint8 | Set the "outside" pixel value. The default value NumericTraits::ZeroValue() . |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKBlackTopHatImage.md b/src/Plugins/ITKImageProcessing/docs/ITKBlackTopHatImage.md
index 754041430f..161cfabcac 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKBlackTopHatImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKBlackTopHatImage.md
@@ -1,4 +1,4 @@
-# ITK Black Top Hat Image Filter (ITKBlackTopHatImage)
+# ITK Black Top Hat Image Filter
Black top hat extracts local minima that are smaller than the structuring element.
@@ -18,42 +18,14 @@ Top-hats are described in Chapter 4.5 of Pierre Soille's book "Morphological Ima
### Related Filters
-
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| KernelRadius | uint32 | Set the radius of the kernel structuring element. |
-| KernelType | KernelEnum | Set the kernel or structuring element used for the morphology. |
-| SafeBorder | bool | A safe border is added to input image to avoid borders effects and remove it once the closing is done |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKClosingByReconstructionImage.md b/src/Plugins/ITKImageProcessing/docs/ITKClosingByReconstructionImage.md
index f87733d974..faea43eadc 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKClosingByReconstructionImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKClosingByReconstructionImage.md
@@ -1,4 +1,4 @@
-# ITK Closing By Reconstruction Image Filter (ITKClosingByReconstructionImage)
+# ITK Closing By Reconstruction Image Filter
Closing by reconstruction of an image.
@@ -25,42 +25,14 @@ Applications", Second Edition, Springer, 2003.
- GrayscaleMorphologicalClosingImageFilter
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| KernelRadius | uint32 | Set the radius of the kernel structuring element. |
-| KernelType | KernelEnum | Set the kernel or structuring element used for the morphology. |
-| FullyConnected | bool | Whether the connected components are defined strictly by face connectivity (False) or by face+edge+vertex connectivity (True). Default is False |
-| PreserveIntensities | bool | Set/Get whether the original intensities of the image retained for those pixels unaffected by the opening by reconstruction. If Off, the output pixel contrast will be reduced. |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKCosImage.md b/src/Plugins/ITKImageProcessing/docs/ITKCosImage.md
index 21579d987f..46bfb9b097 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKCosImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKCosImage.md
@@ -1,4 +1,4 @@
-# ITK Cos Image Filter (ITKCosImage)
+# ITK Cos Image Filter
Computes the cosine of each pixel.
@@ -12,47 +12,21 @@ This filter is templated over the pixel type of the input image and the pixel ty
The filter walks over all of the pixels in the input image, and for each pixel does the following:
-- cast the pixel value to double ,
-- apply the std::cos() function to the double value,
-- cast the double value resulting from std::cos() to the pixel type of the output image,
+- cast the pixel value to double ,
+- apply the std::cos() function to the double value,
+- cast the double value resulting from std::cos() to the pixel type of the output image,
- store the cast value into the output image.
-
-
The filter expects both images to have the same dimension (e.g. both 2D, or both 3D, or both ND)
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKDilateObjectMorphologyImage.md b/src/Plugins/ITKImageProcessing/docs/ITKDilateObjectMorphologyImage.md
index 8f97bfa533..5d48e71f5d 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKDilateObjectMorphologyImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKDilateObjectMorphologyImage.md
@@ -1,4 +1,4 @@
-# ITK Dilate Object Morphology Image Filter (ITKDilateObjectMorphologyImage)
+# ITK Dilate Object Morphology Image Filter
dilation of an object in an image
@@ -10,44 +10,18 @@ ITKBinaryMathematicalMorphology (BinaryMathematicalMorphology)
Dilate an image using binary morphology. Pixel values matching the object value are considered the "foreground" and all other pixels are "background". This is useful in processing mask images containing only one object.
-If a pixel's value is equal to the object value and the pixel is adjacent to a non-object valued pixel, then the kernel is centered on the object-value pixel and neighboring pixels covered by the kernel are assigned the object value. The structuring element is assumed to be composed of binary values (zero or one).* ObjectMorphologyImageFilter , ErodeObjectMorphologyImageFilter
-- BinaryDilateImageFilter
-
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| KernelRadius | uint32 | Set the radius of the kernel structuring element. |
-| KernelType | KernelEnum | Set the kernel or structuring element used for the morphology. |
-| ObjectValue | float64 | The pixel value of the 'Object' to be dilated |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
+If a pixel's value is equal to the object value and the pixel is adjacent to a non-object valued pixel, then the kernel is centered on the object-value pixel and neighboring pixels covered by the kernel are assigned the object value. The structuring element is assumed to be composed of binary values (zero or one).* ObjectMorphologyImageFilter , ErodeObjectMorphologyImageFilter
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
+- BinaryDilateImageFilter
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKDiscreteGaussianImage.md b/src/Plugins/ITKImageProcessing/docs/ITKDiscreteGaussianImage.md
index 2ef35ad1e5..3672ba877e 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKDiscreteGaussianImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKDiscreteGaussianImage.md
@@ -1,4 +1,4 @@
-# ITK Discrete Gaussian Image Filter (ITKDiscreteGaussianImage)
+# ITK Discrete Gaussian Image Filter
Blurs an image by separable convolution with discrete gaussian kernels. This filter performs Gaussian blurring by separable convolution of an image and a discrete Gaussian operator (kernel).
@@ -12,48 +12,21 @@ The Gaussian operator used here was described by Tony Lindeberg (Discrete Scale-
The variance or standard deviation (sigma) will be evaluated as pixel units if SetUseImageSpacing is off (false) or as physical units if SetUseImageSpacing is on (true, default). The variance can be set independently in each dimension.
-When the Gaussian kernel is small, this filter tends to run faster than itk::RecursiveGaussianImageFilter .* GaussianOperator
-- Image
-- Neighborhood
-- NeighborhoodOperator
-- RecursiveGaussianImageFilter
-
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| Variance | float64 | |
-| MaximumKernelWidth | uint32 | Set the kernel to be no wider than MaximumKernelWidth pixels, even if MaximumError demands it. The default is 32 pixels. |
-| MaximumError | float64 | |
-| UseImageSpacing | bool | Set/Get whether or not the filter will use the spacing of the input image in its calculations. Use On to take the image spacing information into account and to specify the Gaussian variance in real world units; use Off to ignore the image spacing and to specify the Gaussian variance in voxel units. Default is On. |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
+When the Gaussian kernel is small, this filter tends to run faster than itk::RecursiveGaussianImageFilter .* GaussianOperator
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
+- Image
+- Neighborhood
+- NeighborhoodOperator
+- RecursiveGaussianImageFilter
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKErodeObjectMorphologyImage.md b/src/Plugins/ITKImageProcessing/docs/ITKErodeObjectMorphologyImage.md
index 7b317baf78..9c784a131f 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKErodeObjectMorphologyImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKErodeObjectMorphologyImage.md
@@ -1,4 +1,4 @@
-# ITK Erode Object Morphology Image Filter (ITKErodeObjectMorphologyImage)
+# ITK Erode Object Morphology Image Filter
Erosion of an object in an image.
@@ -10,45 +10,18 @@ ITKBinaryMathematicalMorphology (BinaryMathematicalMorphology)
Erosion of an image using binary morphology. Pixel values matching the object value are considered the "object" and all other pixels are "background". This is useful in processing mask images containing only one object.
-If the pixel covered by the center of the kernel has the pixel value ObjectValue and the pixel is adjacent to a non-object valued pixel, then the kernel is centered on the object-value pixel and neighboring pixels covered by the kernel are assigned the background value. The structuring element is assumed to be composed of binary values (zero or one).* ObjectMorphologyImageFilter , BinaryFunctionErodeImageFilter
-- BinaryErodeImageFilter
-
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| KernelRadius | uint32 | Set the radius of the kernel structuring element. |
-| KernelType | KernelEnum | Set the kernel or structuring element used for the morphology. |
-| ObjectValue | float64 | The pixel value of the 'Object' to be eroded |
-| BackgroundValue | float64 | Set the value to be assigned to eroded pixels |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
+If the pixel covered by the center of the kernel has the pixel value ObjectValue and the pixel is adjacent to a non-object valued pixel, then the kernel is centered on the object-value pixel and neighboring pixels covered by the kernel are assigned the background value. The structuring element is assumed to be composed of binary values (zero or one).* ObjectMorphologyImageFilter , BinaryFunctionErodeImageFilter
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
+- BinaryErodeImageFilter
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKExpImage.md b/src/Plugins/ITKImageProcessing/docs/ITKExpImage.md
index 3b10c19a31..38963c2a43 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKExpImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKExpImage.md
@@ -1,4 +1,4 @@
-# ITK Exp Image Filter (ITKExpImage)
+# ITK Exp Image Filter
Computes the exponential function of each pixel.
@@ -10,38 +10,14 @@ ITKImageIntensity (ImageIntensity)
The computation is performed using std::exp(x).
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKExpNegativeImage.md b/src/Plugins/ITKImageProcessing/docs/ITKExpNegativeImage.md
index a9ea7264db..db7a8e1da9 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKExpNegativeImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKExpNegativeImage.md
@@ -1,4 +1,4 @@
-# ITK Exp Negative Image Filter (ITKExpNegativeImage)
+# ITK Exp Negative Image Filter
Computes the function exp(-K.x) for each input pixel.
@@ -10,38 +10,14 @@ ITKImageIntensity (ImageIntensity)
Every output pixel is equal to std::exp(-K.x ). where x is the intensity of the homologous input pixel, and K is a user-provided constant.
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKGradientMagnitudeImage.md b/src/Plugins/ITKImageProcessing/docs/ITKGradientMagnitudeImage.md
index b5ee3a023b..39a0a25c2e 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKGradientMagnitudeImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKGradientMagnitudeImage.md
@@ -1,4 +1,4 @@
-# ITK Gradient Magnitude Image Filter (ITKGradientMagnitudeImage)
+# ITK Gradient Magnitude Image Filter
Computes the gradient magnitude of an image region at each pixel.
@@ -17,39 +17,14 @@ Computes the gradient magnitude of an image region at each pixel.
- NeighborhoodOperator
- NeighborhoodIterator
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| UseImageSpacing | bool | Set/Get whether or not the filter will use the spacing of the input image in the computation of the derivatives. Use On to compute the gradient in physical space; use Off to ignore image spacing and to compute the gradient in isotropic voxel space. Default is On. |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKGrayscaleDilateImage.md b/src/Plugins/ITKImageProcessing/docs/ITKGrayscaleDilateImage.md
index 36e61eece6..e46a6c0a20 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKGrayscaleDilateImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKGrayscaleDilateImage.md
@@ -1,4 +1,4 @@
-# ITK Grayscale Dilate Image Filter (ITKGrayscaleDilateImage)
+# ITK Grayscale Dilate Image Filter
Grayscale dilation of an image.
@@ -12,40 +12,14 @@ Dilate an image using grayscale morphology. Dilation takes the maximum of all th
The structuring element is assumed to be composed of binary values (zero or one). Only elements of the structuring element having values > 0 are candidates for affecting the center pixel.* MorphologyImageFilter , GrayscaleFunctionDilateImageFilter , BinaryDilateImageFilter
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| KernelRadius | uint32 | Set the radius of the kernel structuring element. |
-| KernelType | KernelEnum | Set the kernel or structuring element used for the morphology. |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKGrayscaleErodeImage.md b/src/Plugins/ITKImageProcessing/docs/ITKGrayscaleErodeImage.md
index 91de8eb8f1..749267516b 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKGrayscaleErodeImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKGrayscaleErodeImage.md
@@ -1,4 +1,4 @@
-# ITK Grayscale Erode Image Filter (ITKGrayscaleErodeImage)
+# ITK Grayscale Erode Image Filter
Grayscale erosion of an image.
@@ -12,40 +12,14 @@ Erode an image using grayscale morphology. Erosion takes the maximum of all the
The structuring element is assumed to be composed of binary values (zero or one). Only elements of the structuring element having values > 0 are candidates for affecting the center pixel.* MorphologyImageFilter , GrayscaleFunctionErodeImageFilter , BinaryErodeImageFilter
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| KernelRadius | uint32 | Set the radius of the kernel structuring element. |
-| KernelType | KernelEnum | Set the kernel or structuring element used for the morphology. |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKGrayscaleFillholeImage.md b/src/Plugins/ITKImageProcessing/docs/ITKGrayscaleFillholeImage.md
index 99026cde97..750eaf26cd 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKGrayscaleFillholeImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKGrayscaleFillholeImage.md
@@ -1,4 +1,4 @@
-# ITK Grayscale Fillhole Image Filter (ITKGrayscaleFillholeImage)
+# ITK Grayscale Fillhole Image Filter
Remove local minima not connected to the boundary of the image.
@@ -15,42 +15,18 @@ This filter is used to smooth over local minima without affecting the values of
This filter uses the ReconstructionByErosionImageFilter . It provides its own input as the "mask" input to the geodesic erosion. The "marker" image for the geodesic erosion is constructed such that boundary pixels match the boundary pixels of the input image and the interior pixels are set to the maximum pixel value in the input image.
Geodesic morphology and the Fillhole algorithm is described in Chapter 6 of Pierre Soille's book "Morphological Image Analysis:
-Principles and Applications", Second Edition, Springer, 2003.* ReconstructionByErosionImageFilter
-- MorphologyImageFilter , GrayscaleErodeImageFilter , GrayscaleFunctionErodeImageFilter , BinaryErodeImageFilter
-
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| FullyConnected | bool | Whether the connected components are defined strictly by face connectivity (False) or by face+edge+vertex connectivity (True). Default is False |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
+Principles and Applications", Second Edition, Springer, 2003.* ReconstructionByErosionImageFilter
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
+- MorphologyImageFilter , GrayscaleErodeImageFilter , GrayscaleFunctionErodeImageFilter , BinaryErodeImageFilter
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKGrayscaleGrindPeakImage.md b/src/Plugins/ITKImageProcessing/docs/ITKGrayscaleGrindPeakImage.md
index eb239b6c5d..83c26fcf3c 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKGrayscaleGrindPeakImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKGrayscaleGrindPeakImage.md
@@ -1,4 +1,4 @@
-# ITK Grayscale Grind Peak Image Filter (ITKGrayscaleGrindPeakImage)
+# ITK Grayscale Grind Peak Image Filter
Remove local maxima not connected to the boundary of the image.
@@ -17,42 +17,18 @@ This filter uses the GrayscaleGeodesicDilateImageFilter . It provides its own in
This filter is the dual to the GrayscaleFillholeImageFilter which implements the Fillhole algorithm. Since it is a dual, it is somewhat superfluous but is provided as a convenience.
Geodesic morphology and the Fillhole algorithm is described in Chapter 6 of Pierre Soille's book "Morphological Image Analysis:
-Principles and Applications", Second Edition, Springer, 2003.* GrayscaleGeodesicDilateImageFilter
-- MorphologyImageFilter , GrayscaleDilateImageFilter , GrayscaleFunctionDilateImageFilter , BinaryDilateImageFilter
-
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| FullyConnected | bool | Whether the connected components are defined strictly by face connectivity (False) or by face+edge+vertex connectivity (True). Default is False |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
+Principles and Applications", Second Edition, Springer, 2003.* GrayscaleGeodesicDilateImageFilter
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
+- MorphologyImageFilter , GrayscaleDilateImageFilter , GrayscaleFunctionDilateImageFilter , BinaryDilateImageFilter
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKGrayscaleMorphologicalClosingImage.md b/src/Plugins/ITKImageProcessing/docs/ITKGrayscaleMorphologicalClosingImage.md
index e9690dbd67..7417889967 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKGrayscaleMorphologicalClosingImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKGrayscaleMorphologicalClosingImage.md
@@ -1,4 +1,4 @@
-# ITK Grayscale Morphological Closing Image Filter (ITKGrayscaleMorphologicalClosingImage)
+# ITK Grayscale Morphological Closing Image Filter
Grayscale closing of an image.
@@ -12,41 +12,14 @@ Close an image using grayscale morphology.
The structuring element is assumed to be composed of binary values (zero or one). Only elements of the structuring element having values > 0 are candidates for affecting the center pixel.* MorphologyImageFilter , GrayscaleFunctionErodeImageFilter , BinaryErodeImageFilter
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| KernelRadius | uint32 | Set the radius of the kernel structuring element. |
-| KernelType | KernelEnum | Set the kernel or structuring element used for the morphology. |
-| SafeBorder | bool | A safe border is added to input image to avoid borders effects and remove it once the closing is done |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKGrayscaleMorphologicalOpeningImage.md b/src/Plugins/ITKImageProcessing/docs/ITKGrayscaleMorphologicalOpeningImage.md
index 591616c16a..37a540b806 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKGrayscaleMorphologicalOpeningImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKGrayscaleMorphologicalOpeningImage.md
@@ -1,4 +1,4 @@
-# ITK Grayscale Morphological Opening Image Filter (ITKGrayscaleMorphologicalOpeningImage)
+# ITK Grayscale Morphological Opening Image Filter
Grayscale opening of an image.
@@ -12,41 +12,14 @@ Open an image using grayscale morphology.
The structuring element is assumed to be composed of binary values (zero or one). Only elements of the structuring element having values > 0 are candidates for affecting the center pixel.* MorphologyImageFilter , GrayscaleFunctionDilateImageFilter , BinaryDilateImageFilter
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| KernelRadius | uint32 | Set the radius of the kernel structuring element. |
-| KernelType | KernelEnum | Set the kernel or structuring element used for the morphology. |
-| SafeBorder | bool | A safe border is added to input image to avoid borders effects and remove it once the closing is done |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKHConvexImage.md b/src/Plugins/ITKImageProcessing/docs/ITKHConvexImage.md
index 5466339ec4..625ac22323 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKHConvexImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKHConvexImage.md
@@ -1,4 +1,4 @@
-# ITK H Convex Image Filter (ITKHConvexImage)
+# ITK H Convex Image Filter
Identify local maxima whose height above the baseline is greater than h.
@@ -13,43 +13,18 @@ HConvexImageFilter extract local maxima that are more than h intensity units abo
This filter uses the HMaximaImageFilter .
Geodesic morphology and the H-Convex algorithm is described in Chapter 6 of Pierre Soille's book "Morphological Image Analysis:
-Principles and Applications", Second Edition, Springer, 2003.* GrayscaleGeodesicDilateImageFilter , HMinimaImageFilter
-- MorphologyImageFilter , GrayscaleDilateImageFilter , GrayscaleFunctionDilateImageFilter , BinaryDilateImageFilter
-
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| Height | float64 | Set/Get the height that a local maximum must be above the local background (local contrast) in order to survive the processing. Local maxima below this value are replaced with an estimate of the local background. |
-| FullyConnected | bool | Whether the connected components are defined strictly by face connectivity (False) or by face+edge+vertex connectivity (True). Default is False |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
+Principles and Applications", Second Edition, Springer, 2003.* GrayscaleGeodesicDilateImageFilter , HMinimaImageFilter
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
+- MorphologyImageFilter , GrayscaleDilateImageFilter , GrayscaleFunctionDilateImageFilter , BinaryDilateImageFilter
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKHMaximaImage.md b/src/Plugins/ITKImageProcessing/docs/ITKHMaximaImage.md
index d48c8e1e10..0362322d49 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKHMaximaImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKHMaximaImage.md
@@ -1,4 +1,4 @@
-# ITK H Maxima Image Filter (ITKHMaximaImage)
+# ITK H Maxima Image Filter
Suppress local maxima whose height above the baseline is less than h.
@@ -17,42 +17,18 @@ This filter uses the ReconstructionByDilationImageFilter . It provides its own i
Geodesic morphology and the H-Maxima algorithm is described in Chapter 6 of Pierre Soille's book "Morphological Image Analysis:
Principles and Applications", Second Edition, Springer, 2003.
-The height parameter is set using SetHeight.* ReconstructionByDilationImageFilter , HMinimaImageFilter , HConvexImageFilter
-- MorphologyImageFilter , GrayscaleDilateImageFilter , GrayscaleFunctionDilateImageFilter , BinaryDilateImageFilter
-
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| Height | float64 | Set/Get the height that a local maximum must be above the local background (local contrast) in order to survive the processing. Local maxima below this value are replaced with an estimate of the local background. |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
+The height parameter is set using SetHeight.* ReconstructionByDilationImageFilter , HMinimaImageFilter , HConvexImageFilter
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
+- MorphologyImageFilter , GrayscaleDilateImageFilter , GrayscaleFunctionDilateImageFilter , BinaryDilateImageFilter
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKHMinimaImage.md b/src/Plugins/ITKImageProcessing/docs/ITKHMinimaImage.md
index 94ef860935..2424b9a4db 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKHMinimaImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKHMinimaImage.md
@@ -1,4 +1,4 @@
-# ITK H Minima Image Filter (ITKHMinimaImage)
+# ITK H Minima Image Filter
Suppress local minima whose depth below the baseline is less than h.
@@ -15,43 +15,18 @@ If original image is subtracted from the output of HMinimaImageFilter , the sign
This filter uses the GrayscaleGeodesicErodeImageFilter . It provides its own input as the "mask" input to the geodesic dilation. The "marker" image for the geodesic dilation is the input image plus the height parameter h.
Geodesic morphology and the H-Minima algorithm is described in Chapter 6 of Pierre Soille's book "Morphological Image Analysis:
-Principles and Applications", Second Edition, Springer, 2003.* GrayscaleGeodesicDilateImageFilter , HMinimaImageFilter , HConvexImageFilter
-- MorphologyImageFilter , GrayscaleDilateImageFilter , GrayscaleFunctionDilateImageFilter , BinaryDilateImageFilter
-
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| Height | float64 | Set/Get the height that a local maximum must be above the local background (local contrast) in order to survive the processing. Local maxima below this value are replaced with an estimate of the local background. |
-| FullyConnected | bool | Whether the connected components are defined strictly by face connectivity (False) or by face+edge+vertex connectivity (True). Default is False |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
+Principles and Applications", Second Edition, Springer, 2003.* GrayscaleGeodesicDilateImageFilter , HMinimaImageFilter , HConvexImageFilter
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
+- MorphologyImageFilter , GrayscaleDilateImageFilter , GrayscaleFunctionDilateImageFilter , BinaryDilateImageFilter
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKImageReader.md b/src/Plugins/ITKImageProcessing/docs/ITKImageReader.md
index 2d861e628f..c73e0baa26 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKImageReader.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKImageReader.md
@@ -2,38 +2,24 @@
This filter directly wraps an ITK filter of the same name.
-## Group (Subgroup) ##
+## Group (Subgroup)
ITKImageProcessing (ITKImageProcessing)
-## Description ##
+## Description
Reads images through ITK
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type |
-|------------------|------|
-| Input File | String | Path to the input file to read. |
-
-## Required Objects ##
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Data Container** | Data Container Name | N/A | N/A | Description of object... |
-
-## Example Pipelines ##
+## Example Pipelines
+ Image Histogram
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKImageWriter.md b/src/Plugins/ITKImageProcessing/docs/ITKImageWriter.md
index aa4cd0012f..d988d050a6 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKImageWriter.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKImageWriter.md
@@ -1,51 +1,29 @@
# ITK::Image Writer (KW)
-## Group (Subgroup) ##
+## Group (Subgroup)
ITKImageProcessing (ITKImageProcessing)
-## Description ##
+## Description
This **Filter** will save images based on an array that represents grayscale, RGB or ARGB color values. If the input array represents a 3D volume, the **Filter** will output a series of slices along one of the orthogonal axes. The options are to produce XY slices along the Z axis, XZ slices along the Y axis or YZ slices along the X axis. The user has the option to save in one of 3 standard image formats: TIF, BMP, or PNG. The output files will be numbered sequentially starting at zero (0) and ending at the total dimensions for the chosen axis. For example, if the Z axis has 117 dimensions, 117 XY image files will be produced and numbered 0 to 116. Unless the data is a single slice then only a single image will be produced using the name given in the Output File parameter.
-An example of a **Filter** that produces color data that can be used as input to this **Filter** is the [Generate IPF Colors](generateipfcolors.html) **Filter**, which will generate RGB values for each voxel in the volume.
+An example of a **Filter** that produces color data that can be used as input to this **Filter**
+is the {ref}`Generate IFP Colors ` **Filter**, which will generate RGB values for each voxel in the volume.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------------------|------| --------------|
-| Output File | String | Path to the output file to write. |
-| Plane | Enumeration | Selection for plane normal for writing the images (XY, XZ, or YZ) |
-| Index Offeset | Integer | Default=0, This is the starting index when writing mulitple images |
-
-## Required Geometry ##
-
-Image
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | None| uint8_t | (n) | Selected color data for output image. The data should represent grayscale, RGB or ARGB color values. The dimensionality of the array depends on the kind of image read: (1) for grayscale, (3) for RGB, and (4) for ARGB |
-
-
-## Created Objects ##
-
-None
-
-## Example Pipelines ##
+## Example Pipelines
+ INL Export
+ TxCopper_Exposed
+ TxCopper_Unexposed
+ Edax IPF Colors
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKImportFijiMontageFilter.md b/src/Plugins/ITKImageProcessing/docs/ITKImportFijiMontageFilter.md
index 34f9ed641a..c63f4e43f9 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKImportFijiMontageFilter.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKImportFijiMontageFilter.md
@@ -1,16 +1,16 @@
-# Import Fiji Montage #
+# Import Fiji Montage
-## Group (Subgroup) ##
+## Group (Subgroup)
Import/Export (Import)
-## Description ##
+## Description
Imports multiple images for the purpose of montage assembly. Each image is stored in it's own *DataContaner/AttributeMatrix/AttributeArray* where the name of the *DataContainer* is based off the row & column index of the montage. The filter assumes that the Configuration File is in the same folder as the images. The created *AttributeMatrix* and *AttributeArray* will have the same name. The image files **MUST** be located in the same directory as the Fiji Configuration File.
Utilizes the *itkReadImage* and *ColorToGrayScale* filters
-## Example Registration File ##
+## Example Registration File
# Define the number of dimensions we are working on
dim = 2 <===== THIS LINE IS REQUIRED
@@ -23,23 +23,8 @@ Utilizes the *itkReadImage* and *ColorToGrayScale* filters
SampleMosaic_p4.bmp; ; (0.23675, 1839.55)
SampleMosaic_p5.bmp; ; (1227.31, 1839.55)
-## Parameters ##
-| Name | Type | Comment |
-|------------------|------|---------|
-| Input Fiji Tile Configuration File | String | The configuration file in the same directory as all of the identified geometries |
-| Name of Created DataGroup | String | Name of the overarching parent DataGroup |
-| Length Unit | Int | Selected from predefined list. See table below |
-| Parent DataGroup | Bool = ON | Parent all imported geometries under a DataGroup |
-| Change Origin | Bool = OFF | Set the origin of the mosaic to a user defined value |
-| Origin | Float 3 Vect | The new origin of the mosaic |
-| Convert to GrayScale | Bool | The filter will show an error if the images are already in grayscale format |
-| Color Weighting | Float 3 Vect | The luminosity values for the conversion |
-| Data Container Prefix | String | A prefix that can be used for each data container. |
-| Cell Attribute Matrix Name | String | The name of the Cell Attribute Matrix. |
-| Image Data Array Name | String | The name of the import image data |
-
-### Color To Gray Scale Notes ###
+### Color To Gray Scale Notes
The luminosity method is a more sophisticated version of the average method. It also averages the values, but it forms a weighted average to account for human perception. We re more sensitive to green than other colors, so green is weighted most heavily. The default formula for luminosity is BT709 Gray scale:
@@ -47,7 +32,7 @@ The luminosity method is a more sophisticated version of the average method. It
The user can set the weightings to what ever values they would like.
-### Lenght Unit ###
+### Lenght Unit
Yoctometer = 0
Zeptometer = 1
@@ -79,35 +64,17 @@ The user can set the weightings to what ever values they would like.
Unspecified = 100U
Unknown = 101U
-## Required DataContainers ##
-
-NONE
-
-## Required Objects ##
-
-NONE
+% Auto generated parameter table will be inserted here
-## Created Objects ##
-
-This filter will create one data container for each image tile that is in the xml file. That created Data Container will have a Cell Attribute Matrix which will also hold a single Attribute Array of the same type of the image (unless the user selects to convert images to Gray Scale images.)
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| DataGroup | Zen DataGroup | N/A | N/A | Parent DataGroup created in the datastructure |
-| Image Geometry | Mosaic- | N/A | N/A | The prefix for all created Image Geometries |
-| AttributeMatrix | Tile Data | N/A | N/A | The name of every created Attribute Matrix |
-| DataArray | Image | N/A | N/A | The name of the created DataArray in each Image Geometry |
-
-## Example Pipelines ##
+## Example Pipelines
Prebuilt Pipelines / Examples / ITKImageProcessing / Fiji Import
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3D Mailing Lists ##
+## DREAM3D Mailing Lists
If you need more help with a filter, please consider asking your question on the DREAM3D Users mailing list:
-
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKImportImageStack.md b/src/Plugins/ITKImageProcessing/docs/ITKImportImageStack.md
index 5605ecae10..a91ad4ed87 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKImportImageStack.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKImportImageStack.md
@@ -2,47 +2,28 @@
This filter directly wraps an ITK filter of the same name.
-## Group (Subgroup) ##
+## Group (Subgroup)
ITKImageProcessing (ITKImageProcessing)
-## Description ##
+## Description
Read in a stack of 2D images into a 3D volume with ITK. Supports most common
scalar pixel types and the many file formats supported by ITK.
Images are read in as an **Image Geomotry**. The user must specify the origin
in physical space and resolution (uniform physical size of the resulting **Cells**).
-## Parameters ##
+% Auto generated parameter table will be inserted here
-- Input Directory
-- File Ordering (Ascending or Descending)
-- Origin
-- Resolution
+## Example Pipelines
-## Required Objects ##
+- (08) Image Initial Visualization
+- (09) Image Segmentation
-None
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Data Container** | ImageDataContainer | N/A | N/A | Created **Data Container** name **Image Geometry** |
-| **Attribute Matrix** | CellData | Cell | N/A | Created **Cell Attribute Matrix** name |
-| **Cell Attribute Array** | ImageData | Varies based on input | (n) | |
-
-## Example Pipelines ##
-
-+ (08) Image Initial Visualization
-+ (09) Image Segmentation
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKIntensityWindowingImage.md b/src/Plugins/ITKImageProcessing/docs/ITKIntensityWindowingImage.md
index dd5e76ad38..1bfc9d2a9a 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKIntensityWindowingImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKIntensityWindowingImage.md
@@ -1,4 +1,4 @@
-# ITK Intensity Windowing Image Filter (ITKIntensityWindowingImage)
+# ITK Intensity Windowing Image Filter
Applies a linear transformation to the intensity levels of the input Image that are inside a user-defined interval. Values below this interval are mapped to a constant. Values over the interval are mapped to another constant.
@@ -12,42 +12,14 @@ IntensityWindowingImageFilter applies pixel-wise a linear transformation to the
All computations are performed in the precision of the input pixel's RealType. Before assigning the computed value to the output pixel.* RescaleIntensityImageFilter
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| WindowMinimum | float64 | Set/Get the values of the maximum and minimum intensities of the input intensity window. |
-| WindowMaximum | float64 | Set/Get the values of the maximum and minimum intensities of the input intensity window. |
-| OutputMinimum | float64 | Set/Get the values of the maximum and minimum intensities of the output image. |
-| OutputMaximum | float64 | Set/Get the values of the maximum and minimum intensities of the output image. |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKInvertIntensityImage.md b/src/Plugins/ITKImageProcessing/docs/ITKInvertIntensityImage.md
index 34e32aac90..aeca74fd26 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKInvertIntensityImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKInvertIntensityImage.md
@@ -1,4 +1,4 @@
-# ITK Invert Intensity Image Filter (ITKInvertIntensityImage)
+# ITK Invert Intensity Image Filter
Invert the intensity of an image.
@@ -18,39 +18,14 @@ InvertIntensityImageFilter inverts intensity of pixels by subtracting pixel valu
- IntensityWindowingImageFilter ShiftScaleImageFilter
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| Maximum | float64 | Set/Get the maximum intensity value for the inversion. |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKLabelContourImage.md b/src/Plugins/ITKImageProcessing/docs/ITKLabelContourImage.md
index f546f74893..2beed3ce0d 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKLabelContourImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKLabelContourImage.md
@@ -1,4 +1,4 @@
-# ITK Label Contour Image Filter (ITKLabelContourImage)
+# ITK Label Contour Image Filter
Labels the pixels on the border of the objects in a labeled image.
@@ -12,7 +12,7 @@ LabelContourImageFilter takes a labeled image as input, where the pixels in the
The connectivity can be changed to minimum or maximum connectivity with SetFullyConnected() . Full connectivity produces thicker contours.
-https://www.insight-journal.org/browse/publication/217
+
### Author
@@ -22,40 +22,14 @@ https://www.insight-journal.org/browse/publication/217
- BinaryContourImageFilter
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| FullyConnected | bool | Whether the connected components are defined strictly by face connectivity (False) or by face+edge+vertex connectivity (True). Default is False |
-| BackgroundValue | float64 | Set/Get the background value used to identify the objects and mark the pixels not on the border of the objects. |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching IntegerPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching IntegerPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKLog10Image.md b/src/Plugins/ITKImageProcessing/docs/ITKLog10Image.md
index 1571696d5d..61f678acc3 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKLog10Image.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKLog10Image.md
@@ -1,4 +1,4 @@
-# ITK Log10 Image Filter (ITKLog10Image)
+# ITK Log10 Image Filter
Computes the log10 of each pixel.
@@ -10,38 +10,14 @@ ITKImageIntensity (ImageIntensity)
The computation is performed using std::log10(x).
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKLogImage.md b/src/Plugins/ITKImageProcessing/docs/ITKLogImage.md
index bb91a41548..d7758d62bf 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKLogImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKLogImage.md
@@ -1,4 +1,4 @@
-# ITK Log Image Filter (ITKLogImage)
+# ITK Log Image Filter
Computes the log() of each pixel.
@@ -8,40 +8,14 @@ ITKImageIntensity (ImageIntensity)
## Description
-
-
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKMaskImage.md b/src/Plugins/ITKImageProcessing/docs/ITKMaskImage.md
index 1151e5f143..cdac541ede 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKMaskImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKMaskImage.md
@@ -2,11 +2,11 @@
This filter directly wraps an ITK filter of the same name.
-## Group (Subgroup) ##
+## Group (Subgroup)
ITKImageProcessing (ITKImageProcessing)
-## Description ##
+## Description
Mask an image with a mask.
@@ -22,57 +22,29 @@ The pixel type of the input 2 image must have a valid definition of the operator
*
```
-
The pixel from the input 1 is cast to the pixel type of the output image.
Note that the input and the mask images must be of the same size.
*WARNING* Any pixel value other than masking value (0 by default) will not be masked out.* MaskNegatedImageFilter
- Wiki Examples:* All Examples* Apply a mask to an image
-
-## Parameters ##
-
-| Name | Type | Description |
-|------|------|-------------|
-| OutsideValue | double| Method to explicitly set the outside value of the mask. Defaults to 0 |
-
-
-## Required Geometry ##
-
-Image
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | None | N/A | (1) | Array containing input image
+ Wiki Examples:*All Examples* Apply a mask to an image
-## Created Objects ##
+% Auto generated parameter table will be inserted here
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | None | | (1) | Array containing filtered image
-
-## References ##
+## References
[1] T.S. Yoo, M. J. Ackerman, W. E. Lorensen, W. Schroeder, V. Chalana, S. Aylward, D. Metaxas, R. Whitaker. Engineering and Algorithm Design for an Image Processing API: A Technical Report on ITK - The Insight Toolkit. In Proc. of Medicine Meets Virtual Reality, J. Westwood, ed., IOS Press Amsterdam pp 586-592 (2002).
[2] H. Johnson, M. McCormick, L. Ibanez. The ITK Software Guide: Design and Functionality. Fourth Edition. Published by Kitware Inc. 2015 ISBN: 9781-930934-28-3
[3] H. Johnson, M. McCormick, L. Ibanez. The ITK Software Guide: Introduction and Development Guidelines. Fourth Edition. Published by Kitware Inc. 2015 ISBN: 9781-930934-27-6
-## Example Pipelines ##
-
+## Example Pipelines
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3D Mailing Lists ##
+## DREAM3D Mailing Lists
If you need more help with a filter, please consider asking your question on the DREAM3D Users mailing list:
-https://groups.google.com/forum/?hl=en#!forum/dream3d-users
-
-
-
-
+
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKMedianImage.md b/src/Plugins/ITKImageProcessing/docs/ITKMedianImage.md
index 83cae05934..15b7b79b16 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKMedianImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKMedianImage.md
@@ -1,4 +1,4 @@
-# ITK Median Image Filter (ITKMedianImage)
+# ITK Median Image Filter
Applies a median filter to an image.
@@ -12,44 +12,20 @@ Computes an image where a given pixel is the median value of the the pixels in a
A median filter is one of the family of nonlinear filters. It is used to smooth an image without being biased by outliers or shot noise.
-This filter requires that the input pixel type provides an operator<() (LessThan Comparable).* Image
-- Neighborhood
-- NeighborhoodOperator
-- NeighborhoodIterator
-
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| Radius | uint32 | |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
+This filter requires that the input pixel type provides an operator<() (LessThan Comparable).* Image
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
+- Neighborhood
+- NeighborhoodOperator
+- NeighborhoodIterator
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKMhaFileReader.md b/src/Plugins/ITKImageProcessing/docs/ITKMhaFileReader.md
index a9a4555a68..1dfb2f4e7a 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKMhaFileReader.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKMhaFileReader.md
@@ -4,46 +4,24 @@ This filter reads the image data from an MHA file.
The transformation matrix from the MHA file can be optionally read and saved as a data array and/or applied to the created image geometry.
-## Group (Subgroup) ##
+## Group (Subgroup)
ITKImageProcessing (ITKImageProcessing)
-## Description ##
+## Description
Reads MHA images and their transformation matrices using ITK
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------------------|------|-------------|
-| Input MHA File | String | Path to the input .mha file to read. |
-| Save Image Transformation As Array | Boolean | Determines whether or not to read and save the transformation matrix found in the .mha file to a data array. |
-| Apply Image Transformation To Geometry | Boolean | Determines whether or not to read and apply the transformation matrix found in the .mha file to the created image geometry. |
-| Interpolation Type | Choice | The interpolation type used when transforming the cell data arrays in the created image geometry. Only available if **Apply Image Transformation To Geometry** is set to True.|
-
-## Required Objects ##
-
-None.
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Image Geometry** | ImageDataContainer | N/A | N/A | The created image geometry that contains the image data from the .mha file. |
-| **Cell Attribute Matrix** | Cell Data | N/A | N/A | The created cell attribute matrix that contains the image data from the .mha file. |
-| **Data Array** | ImageData | uint16 | 1 | The created data array that contains the image data from the .mha file. |
-| **Data Array** | TransformationMatrix | float32 | 16 | 4x4 transformation matrix read from the .mha input file. Only available if **Save Image Transformation As Array** is set to True. |
-
-## Example Pipelines ##
+## Example Pipelines
None.
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKMorphologicalGradientImage.md b/src/Plugins/ITKImageProcessing/docs/ITKMorphologicalGradientImage.md
index afbf761d63..116e7a17ad 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKMorphologicalGradientImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKMorphologicalGradientImage.md
@@ -1,4 +1,4 @@
-# ITK Morphological Gradient Image Filter (ITKMorphologicalGradientImage)
+# ITK Morphological Gradient Image Filter
Compute the gradient of a grayscale image.
@@ -10,40 +10,14 @@ ITKMathematicalMorphology (MathematicalMorphology)
The structuring element is assumed to be composed of binary values (zero or one). Only elements of the structuring element having values > 0 are candidates for affecting the center pixel.* MorphologyImageFilter , GrayscaleFunctionDilateImageFilter , BinaryDilateImageFilter
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| KernelRadius | uint32 | Set the radius of the kernel structuring element. |
-| KernelType | KernelEnum | Set the kernel or structuring element used for the morphology. |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKMorphologicalWatershedImage.md b/src/Plugins/ITKImageProcessing/docs/ITKMorphologicalWatershedImage.md
index 3b1bb42785..06ed151f33 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKMorphologicalWatershedImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKMorphologicalWatershedImage.md
@@ -1,4 +1,4 @@
-# ITK Morphological Watershed Image Filter (ITKMorphologicalWatershedImage)
+# ITK Morphological Watershed Image Filter
Watershed segmentation implementation with morphological operators.
@@ -13,7 +13,7 @@ Watershed pixel are labeled 0. TOutputImage should be an integer type. Labels of
The morphological watershed transform algorithm is described in Chapter 9.2 of Pierre Soille's book "Morphological Image Analysis:
Principles and Applications", Second Edition, Springer, 2003.
-This code was contributed in the Insight Journal paper: "The watershed transform in ITK - discussion and new developments" by Beare R., Lehmann G. https://www.insight-journal.org/browse/publication/92
+This code was contributed in the Insight Journal paper: "The watershed transform in ITK - discussion and new developments" by Beare R., Lehmann G.
### Author
@@ -23,41 +23,14 @@ This code was contributed in the Insight Journal paper: "The watershed transform
- WatershedImageFilter , MorphologicalWatershedFromMarkersImageFilter
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| Level | float64 | Set the 'level' variable to the filter |
-| MarkWatershedLine | bool | Set/Get whether the watershed pixel must be marked or not. Default is true. Set it to false do not only avoid writing watershed pixels, it also decrease algorithm complexity. |
-| FullyConnected | bool | Whether the connected components are defined strictly by face connectivity (False) or by face+edge+vertex connectivity (True). Default is False |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching ScalarPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching ScalarPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKNormalizeImage.md b/src/Plugins/ITKImageProcessing/docs/ITKNormalizeImage.md
index f297f028cf..0384e94869 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKNormalizeImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKNormalizeImage.md
@@ -1,4 +1,4 @@
-# ITK Normalize Image Filter (ITKNormalizeImage)
+# ITK Normalize Image Filter
Normalize an image by setting its mean to zero and variance to one.
@@ -12,38 +12,14 @@ NormalizeImageFilter shifts and scales an image so that the pixels in the image
NB: since this filter normalizes the data such that the mean is at 0, and \f$-\sigma\f$ to \f$+\sigma\f$ is mapped to -1.0 to 1.0, output image integral types will produce an image that DOES NOT HAVE a unit variance due to 68% of the intensity values being mapped to the real number range of -1.0 to 1.0 and then cast to the output integral value.* NormalizeToConstantImageFilter
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKNotImage.md b/src/Plugins/ITKImageProcessing/docs/ITKNotImage.md
index 9def2716d6..b6270bcae1 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKNotImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKNotImage.md
@@ -1,4 +1,4 @@
-# ITK Not Image Filter (ITKNotImage)
+# ITK Not Image Filter
Implements the NOT logical operator pixel-wise on an image.
@@ -27,41 +27,16 @@ return this->m_BackgroundValue;
```
-
Where "!" is the unary Logical NOT operator in C++.
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching IntegerPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching IntegerPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKOpeningByReconstructionImage.md b/src/Plugins/ITKImageProcessing/docs/ITKOpeningByReconstructionImage.md
index a02785028d..44a649db04 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKOpeningByReconstructionImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKOpeningByReconstructionImage.md
@@ -1,4 +1,4 @@
-# ITK Opening By Reconstruction Image Filter (ITKOpeningByReconstructionImage)
+# ITK Opening By Reconstruction Image Filter
Opening by reconstruction of an image.
@@ -25,42 +25,14 @@ Applications", Second Edition, Springer, 2003.
- GrayscaleMorphologicalOpeningImageFilter
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| KernelRadius | uint32 | Set the radius of the kernel structuring element. |
-| KernelType | KernelEnum | Set the kernel or structuring element used for the morphology. |
-| FullyConnected | bool | Whether the connected components are defined strictly by face connectivity (False) or by face+edge+vertex connectivity (True). Default is False |
-| PreserveIntensities | bool | Set/Get whether the original intensities of the image retained for those pixels unaffected by the opening by reconstruction. If Off, the output pixel contrast will be reduced. |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKOtsuMultipleThresholdsImage.md b/src/Plugins/ITKImageProcessing/docs/ITKOtsuMultipleThresholdsImage.md
index b9d9b3e159..f9250d4cca 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKOtsuMultipleThresholdsImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKOtsuMultipleThresholdsImage.md
@@ -1,4 +1,4 @@
-# ITK Otsu Multiple Thresholds Image Filter (ITKOtsuMultipleThresholdsImage)
+# ITK Otsu Multiple Thresholds Image Filter
Threshold an image using multiple Otsu Thresholds.
@@ -10,47 +10,19 @@ ITKThresholding (Thresholding)
This filter creates a labeled image that separates the input image into various classes. The filter computes the thresholds using the OtsuMultipleThresholdsCalculator and applies those thresholds to the input image using the ThresholdLabelerImageFilter . The NumberOfHistogramBins and NumberOfThresholds can be set for the Calculator. The LabelOffset can be set for the ThresholdLabelerImageFilter .
-This filter also includes an option to use the valley emphasis algorithm from H.F. Ng, "Automatic thresholding for defect detection", Pattern Recognition Letters, (27): 1644-1649, 2006. The valley emphasis algorithm is particularly effective when the object to be thresholded is small. See the following tests for examples: itkOtsuMultipleThresholdsImageFilterTest3 and itkOtsuMultipleThresholdsImageFilterTest4 To use this algorithm, simple call the setter: SetValleyEmphasis(true) It is turned off by default.* ScalarImageToHistogramGenerator
-- OtsuMultipleThresholdsCalculator
-- ThresholdLabelerImageFilter
-
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| NumberOfThresholds | uint8 | Set/Get the number of thresholds. Default is 1. |
-| LabelOffset | uint8 | Set/Get the offset which labels have to start from. Default is 0. |
-| NumberOfHistogramBins | uint32 | Set/Get the number of histogram bins. Default is 128. |
-| ValleyEmphasis | bool | Set/Get the use of valley emphasis. Default is false. |
-| ReturnBinMidpoint | bool | Should the threshold value be mid-point of the bin or the maximum? Default is to return bin maximum. |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
+This filter also includes an option to use the valley emphasis algorithm from H.F. Ng, "Automatic thresholding for defect detection", Pattern Recognition Letters, (27): 1644-1649, 2006. The valley emphasis algorithm is particularly effective when the object to be thresholded is small. See the following tests for examples: itkOtsuMultipleThresholdsImageFilterTest3 and itkOtsuMultipleThresholdsImageFilterTest4 To use this algorithm, simple call the setter: SetValleyEmphasis(true) It is turned off by default.* ScalarImageToHistogramGenerator
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
+- OtsuMultipleThresholdsCalculator
+- ThresholdLabelerImageFilter
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKRelabelComponentImage.md b/src/Plugins/ITKImageProcessing/docs/ITKRelabelComponentImage.md
index 97ca012614..35e3041a8d 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKRelabelComponentImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKRelabelComponentImage.md
@@ -1,4 +1,4 @@
-# ITK Relabel Component Image Filter (ITKRelabelComponentImage)
+# ITK Relabel Component Image Filter
Relabel the components in an image such that consecutive labels are used.
@@ -20,40 +20,14 @@ If user sets a minimum object size, all objects with fewer pixels than the minim
RelabelComponentImageFilter can be run as an "in place" filter, where it will overwrite its output. The default is run out of place (or generate a separate output). "In place" operation can be controlled via methods in the superclass, InPlaceImageFilter::InPlaceOn() and InPlaceImageFilter::InPlaceOff().* ConnectedComponentImageFilter , BinaryThresholdImageFilter , ThresholdImageFilter
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| MinimumObjectSize | uint64 | Set the minimum size in pixels for an object. All objects smaller than this size will be discarded and will not appear in the output label map. NumberOfObjects will count only the objects whose pixel counts are greater than or equal to the minimum size. Call GetOriginalNumberOfObjects to find out how many objects were present in the original label map. |
-| SortByObjectSize | bool | Controls whether the object labels are sorted by size. If false, initial order of labels is kept. |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching IntegerPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching IntegerPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKRescaleIntensityImage.md b/src/Plugins/ITKImageProcessing/docs/ITKRescaleIntensityImage.md
index 0ab0657ca0..dfa61c2731 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKRescaleIntensityImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKRescaleIntensityImage.md
@@ -1,4 +1,4 @@
-# ITK Rescale Intensity Image Filter (ITKRescaleIntensityImage)
+# ITK Rescale Intensity Image Filter
Applies a linear transformation to the intensity levels of the input Image .
@@ -12,49 +12,20 @@ RescaleIntensityImageFilter applies pixel-wise a linear transformation to the in
The following equation gives the mapping of the intensity values
-
-
- \f[ outputPixel = ( inputPixel - inputMin) \cdot \frac{(outputMax - outputMin )}{(inputMax - inputMin)} + outputMin \f]
-
+ \f[ outputPixel = ( inputPixel - inputMin) \cdot \frac{(outputMax - outputMin )}{(inputMax - inputMin)} + outputMin \f]
All computations are performed in the precision of the input pixel's RealType. Before assigning the computed value to the output pixel.
NOTE: In this filter the minimum and maximum values of the input image are computed internally using the MinimumMaximumImageCalculator . Users are not supposed to set those values in this filter. If you need a filter where you can set the minimum and maximum values of the input, please use the IntensityWindowingImageFilter . If you want a filter that can use a user-defined linear transformation for the intensity, then please use the ShiftScaleImageFilter .* IntensityWindowingImageFilter
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| OutputMinimum | float64 | |
-| OutputMaximum | float64 | |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKSigmoidImage.md b/src/Plugins/ITKImageProcessing/docs/ITKSigmoidImage.md
index faabb7a388..b0005d9d39 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKSigmoidImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKSigmoidImage.md
@@ -1,4 +1,4 @@
-# ITK Sigmoid Image Filter (ITKSigmoidImage)
+# ITK Sigmoid Image Filter
Computes the sigmoid function pixel-wise.
@@ -14,42 +14,14 @@ A linear transformation is applied first on the argument of the sigmoid function
Every output pixel is equal to f(x). Where x is the intensity of the homologous input pixel, and alpha and beta are user-provided constants.
-## Parameters
-
-| Name | Type | Description |
-|------|------|--------------------------|
-| Alpha | float64 | Alpha in the above equation |
-| Beta | float64 | Beta in the abvove equation |
-| OutputMaximum | float64 | The maximum output value |
-| OutputMinimum | float64 | The minimum output value |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKSignedMaurerDistanceMapImage.md b/src/Plugins/ITKImageProcessing/docs/ITKSignedMaurerDistanceMapImage.md
index 201bc2ed45..96b9d4f198 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKSignedMaurerDistanceMapImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKSignedMaurerDistanceMapImage.md
@@ -1,4 +1,4 @@
-# ITK Signed Maurer Distance Map Image Filter (ITKSignedMaurerDistanceMapImage)
+# ITK Signed Maurer Distance Map Image Filter
This filter calculates the Euclidean distance transform of a binary image in linear time for arbitrary dimensions.
@@ -8,58 +8,26 @@ ITKDistanceMap (DistanceMap)
## Description
-
Inputs and Outputs
This is an image-to-image filter. The dimensionality is arbitrary. The only dimensionality constraint is that the input and output images be of the same dimensions and size. To maintain integer arithmetic within the filter, the default output is the signed squared distance. This implies that the input image should be of type "unsigned int" or "int" whereas the output image is of type "int". Obviously, if the user wishes to utilize the image spacing or to have a filter with the Euclidean distance (as opposed to the squared distance), output image types of float or double should be used.
-
The inside is considered as having negative distances. Outside is treated as having positive distances. To change the convention, use the InsideIsPositive(bool) function.
-
Parameters
Set/GetBackgroundValue specifies the background of the value of the input binary image. Normally this is zero and, as such, zero is the default value. Other than that, the usage is completely analogous to the itk::DanielssonDistanceImageFilter class except it does not return the Voronoi map.
-
Reference: C. R. Maurer, Jr., R. Qi, and V. Raghavan, "A Linear Time Algorithm
for Computing Exact Euclidean Distance Transforms of Binary Images in
Arbitrary Dimensions", IEEE - Transactions on Pattern Analysis and Machine Intelligence, 25(2): 265-270, 2003.
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| InsideIsPositive | bool | Set if the inside represents positive values in the signed distance map. By convention ON pixels are treated as inside pixels. |
-| SquaredDistance | bool | Set if the distance should be squared. |
-| UseImageSpacing | bool | Set if image spacing should be used in computing distances. |
-| BackgroundValue | float64 | Set the background value which defines the object. Usually this value is = 0. |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching IntegerPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching IntegerPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKSinImage.md b/src/Plugins/ITKImageProcessing/docs/ITKSinImage.md
index 14a3ee298d..59949d837e 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKSinImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKSinImage.md
@@ -1,4 +1,4 @@
-# ITK Sin Image Filter (ITKSinImage)
+# ITK Sin Image Filter
Computes the sine of each pixel.
@@ -10,38 +10,14 @@ ITKImageIntensity (ImageIntensity)
The computations are performed using std::sin(x).
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKSqrtImage.md b/src/Plugins/ITKImageProcessing/docs/ITKSqrtImage.md
index ad0a9dc7db..b4078e06e0 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKSqrtImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKSqrtImage.md
@@ -1,4 +1,4 @@
-# ITK Sqrt Image Filter (ITKSqrtImage)
+# ITK Sqrt Image Filter
Computes the square root of each pixel.
@@ -10,38 +10,14 @@ ITKImageIntensity (ImageIntensity)
The computations are performed using std::sqrt(x).
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKSquareImage.md b/src/Plugins/ITKImageProcessing/docs/ITKSquareImage.md
index ec3efe3384..69cf75ea15 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKSquareImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKSquareImage.md
@@ -1,4 +1,4 @@
-# ITK Square Image Filter (ITKSquareImage)
+# ITK Square Image Filter
Computes the square of the intensity values pixel-wise.
@@ -8,40 +8,14 @@ ITKImageIntensity (ImageIntensity)
## Description
-
-
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKTanImage.md b/src/Plugins/ITKImageProcessing/docs/ITKTanImage.md
index 063431d92c..aab9915c28 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKTanImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKTanImage.md
@@ -1,4 +1,4 @@
-# ITK Tan Image Filter (ITKTanImage)
+# ITK Tan Image Filter
Computes the tangent of each input pixel.
@@ -10,38 +10,14 @@ ITKImageIntensity (ImageIntensity)
The computations are performed using std::tan(x).
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKThresholdImage.md b/src/Plugins/ITKImageProcessing/docs/ITKThresholdImage.md
index 16f11eb534..a5e318100c 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKThresholdImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKThresholdImage.md
@@ -1,4 +1,4 @@
-# ITK Threshold Image Filter (ITKThresholdImage)
+# ITK Threshold Image Filter
Set image values to a user-specified value if they are below, above, or between simple threshold values.
@@ -22,41 +22,14 @@ Note that these definitions indicate that pixels equal to the threshold value ar
The pixels must support the operators >= and <=.
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| Lower | float64 | Set/Get methods to set the lower threshold. |
-| Upper | float64 | Set/Get methods to set the upper threshold. |
-| OutsideValue | float64 | The pixel type must support comparison operators. Set the "outside" pixel value. The default value NumericTraits::ZeroValue() . |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKValuedRegionalMaximaImage.md b/src/Plugins/ITKImageProcessing/docs/ITKValuedRegionalMaximaImage.md
index a0cd67cd92..03fcdb1877 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKValuedRegionalMaximaImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKValuedRegionalMaximaImage.md
@@ -1,4 +1,4 @@
-# ITK Valued Regional Maxima Image Filter (ITKValuedRegionalMaximaImage)
+# ITK Valued Regional Maxima Image Filter
Transforms the image so that any pixel that is not a regional maxima is set to the minimum value for the pixel type. Pixels that are regional maxima retain their value.
@@ -18,7 +18,7 @@ ITKMathematicalMorphology (MathematicalMorphology)
Regional maxima are flat zones surrounded by pixels of lower value. A completely flat image will be marked as a regional maxima by this filter.
-This code was contributed in the Insight Journal paper: "Finding regional extrema - methods and performance" by Beare R., Lehmann G. https://www.insight-journal.org/browse/publication/65
+This code was contributed in the Insight Journal paper: "Finding regional extrema - methods and performance" by Beare R., Lehmann G.
### Author
@@ -26,43 +26,18 @@ This code was contributed in the Insight Journal paper: "Finding regional extrem
### Related Filters
-- ValuedRegionalMinimaImageFilter
-- ValuedRegionalExtremaImageFilter
+- ValuedRegionalMinimaImageFilter
+- ValuedRegionalExtremaImageFilter
- HMinimaImageFilter
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| FullyConnected | bool | Whether the connected components are defined strictly by face connectivity (False) or by face+edge+vertex connectivity (True). Default is False |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching ScalarPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching ScalarPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKValuedRegionalMinimaImage.md b/src/Plugins/ITKImageProcessing/docs/ITKValuedRegionalMinimaImage.md
index 11e207d149..3f4071ddcc 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKValuedRegionalMinimaImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKValuedRegionalMinimaImage.md
@@ -1,4 +1,4 @@
-# ITK Valued Regional Minima Image Filter (ITKValuedRegionalMinimaImage)
+# ITK Valued Regional Minima Image Filter
Transforms the image so that any pixel that is not a regional minima is set to the maximum value for the pixel type. Pixels that are regional minima retain their value.
@@ -10,7 +10,7 @@ ITKMathematicalMorphology (MathematicalMorphology)
Regional minima are flat zones surrounded by pixels of higher value. A completely flat image will be marked as a regional minima by this filter.
-This code was contributed in the Insight Journal paper: "Finding regional extrema - methods and performance" by Beare R., Lehmann G. https://www.insight-journal.org/browse/publication/65
+This code was contributed in the Insight Journal paper: "Finding regional extrema - methods and performance" by Beare R., Lehmann G.
### Author
@@ -18,42 +18,17 @@ This code was contributed in the Insight Journal paper: "Finding regional extrem
### Related Filters
-- ValuedRegionalMaximaImageFilter , ValuedRegionalExtremaImageFilter ,
+- ValuedRegionalMaximaImageFilter , ValuedRegionalExtremaImageFilter ,
- HMinimaImageFilter
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| FullyConnected | bool | Whether the connected components are defined strictly by face connectivity (False) or by face+edge+vertex connectivity (True). Default is False |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching ScalarPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching ScalarPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/docs/ITKWhiteTopHatImage.md b/src/Plugins/ITKImageProcessing/docs/ITKWhiteTopHatImage.md
index 51a0cc0d8b..5548c250e1 100644
--- a/src/Plugins/ITKImageProcessing/docs/ITKWhiteTopHatImage.md
+++ b/src/Plugins/ITKImageProcessing/docs/ITKWhiteTopHatImage.md
@@ -1,4 +1,4 @@
-# ITK White Top Hat Image Filter (ITKWhiteTopHatImage)
+# ITK White Top Hat Image Filter
White top hat extracts local maxima that are larger than the structuring element.
@@ -16,42 +16,14 @@ Top-hats are described in Chapter 4.5 of Pierre Soille's book "Morphological Ima
### Related Filters
-
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| KernelRadius | uint32 | Set the radius of the kernel structuring element. |
-| KernelType | KernelEnum | Set the kernel or structuring element used for the morphology. |
-| SafeBorder | bool | A safe border is added to input image to avoid borders effects and remove it once the closing is done |
-
-## Required Geometry
-
-Image Geometry
-
-## Required Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Input Image Geometry | DataPath | DataPath to the Input Image Geometry |
-| Input Image Data Array | DataPath | Path to input image with pixel type matching BasicPixelIDTypeList |
-
-## Created Objects
-
-| Name |Type | Description |
-|-----|------|-------------|
-| Output Image Data Array | DataPath | Path to output image with pixel type matching BasicPixelIDTypeList |
+% Auto generated parameter table will be inserted here
## Example Pipelines
-
## License & Copyright
Please see the description file distributed with this plugin.
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/ITKImageProcessing/tools/ReadMe.md b/src/Plugins/ITKImageProcessing/tools/ReadMe.md
index b72eaab1e8..103299662f 100644
--- a/src/Plugins/ITKImageProcessing/tools/ReadMe.md
+++ b/src/Plugins/ITKImageProcessing/tools/ReadMe.md
@@ -7,7 +7,6 @@ From the file `itk_filter_generator.py`, you will need to update the python vari
Then you can run the `itk_filter_generator.py` file to generate the filters.
-
An example usage of the python script is this:
````
diff --git a/src/Plugins/OrientationAnalysis/PortingOrientationAnalysisFilter.md b/src/Plugins/OrientationAnalysis/PortingOrientationAnalysisFilter.md
index 16486e2f38..40c6777377 100644
--- a/src/Plugins/OrientationAnalysis/PortingOrientationAnalysisFilter.md
+++ b/src/Plugins/OrientationAnalysis/PortingOrientationAnalysisFilter.md
@@ -1,25 +1,27 @@
-# Porting Orientation Analysis Filter #
+# Porting Orientation Analysis Filter
-## Updating the Legacy UUID Maps ##
+## Updating the Legacy UUID Maps
This **Plugin** contains two folders of filters instructions for both are below:
-> ### If Porting From ***SIMPL*** to ***Filters Folder*** ###
-> Use the **ComplexFilterGen** module distributed in ***SIMPL DREAM3D***. This
+> ### If Porting From ***SIMPL*** to ***Filters Folder***
+>
+> Use the **ComplexFilterGen** module distributed in ***SIMPL DREAM3D***. This
module will automatically update the LegacyUUIDMapping for this **Plugin**.
>
-> ### If Moving to ***Filters*** ###
+> ### If Moving to ***Filters***
+>
>
- Open the LegacyUUIDMapping header file for this Plugin
- Uncomment the include statement for the filter being moved
- Uncomment the map entry for the filter being moved
- When working with the ***LegacyUUIDMapping*** header file in this **Plugin**
- be sure to make sure the commented out tokens are not removed. Their syntax is
+ When working with the ***LegacyUUIDMapping*** header file in this **Plugin**
+ be sure to make sure the commented out tokens are not removed. Their syntax is
one of the following:
- > ***@@__HEADER__TOKEN__DO__NOT__DELETE__@@***
-
+ > ***@@**HEADER__TOKEN__DO__NOT__DELETE**@@***
+
or
-
- > ***@@__MAP__UPDATE__TOKEN__DO__NOT__DELETE__@@***
+
+ > ***@@**MAP__UPDATE__TOKEN__DO__NOT__DELETE**@@***
diff --git a/src/Plugins/OrientationAnalysis/Support/GMT/UsingGMT.md b/src/Plugins/OrientationAnalysis/Support/GMT/UsingGMT.md
index 4335c8a2dc..5ed2b4f138 100644
--- a/src/Plugins/OrientationAnalysis/Support/GMT/UsingGMT.md
+++ b/src/Plugins/OrientationAnalysis/Support/GMT/UsingGMT.md
@@ -1,79 +1,82 @@
-# Using GMT With DREAM3D #
+# Using GMT With DREAM3D
-
-## Tools Needed ##
+## Tools Needed
+ GMT version 5.x
+ ImageMagick installed (which has the "convert" utility)
+ Ghostscript installed (to convert postscript files to image files)
-+ Shell environment that can run 'bash'. This means "MSys" on windows.
-
++ Shell environment that can run 'bash'. This means "MSys" on windows.
-## Windows Setup ##
+## Windows Setup
-### Install ImageMagick ###
+### Install ImageMagick
Download the zip version of *ImageMagick* from [http://www.imagemagick.org/script/binary-releases.php](http://www.imagemagick.org/script/binary-releases.php). Select the type if release that you are allowed to install. Note for windows that there is a .zip which does not require an installer to be executed. This is probably the best route for those without sys-admin privileges on their machines.
-
-### Install Ghostscript ###
+### Install Ghostscript
Download Ghostscript from [http://www.ghostscript.com/download/gsdnld.html](http://www.ghostscript.com/download/gsdnld.html). **NOTE:** Download the **32bit** version regardless of what version of Windows you are running. The ImageMagick installation seems to default to using a 32 bit version of Ghostscript. There are ways around this that involve hacking the ImageMagick Installation.
-### Install an MSys Environment ###
+### Install an MSys Environment
+
I just used the MSys that came with "Git-Bash" for windows.
-### Install GMT Version 5.x ###
+### Install GMT Version 5.x
Download and install GMT version 5.x from the GMT website [http://gmt.soest.hawaii.edu/projects/gmt/wiki/Download](http://gmt.soest.hawaii.edu/projects/gmt/wiki/Download). Again select what works best for your system and access privileges.
-### Getting started with GMT ###
+### Getting started with GMT
+
Launch a "Git Bash" shell which is an MSys shell. Now we need to export the paths to all the packages we just got done installing. For example I have installed all the packages (GMT, ImageMagick, Ghostscript) into C:/Applications so I would need to do the following:
+```console
export PATH=/c/Applications/gmt5/bin:$PATH
export PATH=/c/Applications/gs/gs9.10/bin:$PATH
export PATH=/c/Applications/ImageMagick-6.8.8-4:$PATH
+```
After you have executed those commands (Which you could put in your .bashrc file) you can then verify that the executables are in the path:
+```console
$ which gmt
/c/Applications/gmt5/bin/gmt
$ which convert
/c/Applications/gs/gs9.10/bin/convert
$ which gswin32c
/c/Applications/ImageMagick-6.8.8-4/gswin32c
+```
-
-## Unix/Linux Setup ##
+## Unix/Linux Setup
Use your package manager to install/verify that GMT5, ImageMagick and Ghostscript are all installed.
-## OS X Setup ##
+## OS X Setup
+
Download the GMT standalone installer which is a .dmg file. Double click the .dmg, copy the gmt.app into your applications folder.
### Use Homebrew to install ImageMagick
Download the HomeBrew installer
-```
-brew install imagemagick
-```
+```console
+brew install imagemagick
export PATH=$PATH:/Applications/
+```
-## Command Line 5D Parameter GBCD ##
+## Command Line 5D Parameter GBCD
+ Generate the GMT .dat file from DREAM.3D
+ Make sure the GMT environment is setup completely
+ Execute the following:
+```console
+./DrawStereograms [number_of_files] [Stereo_file_name] 5d rainbow [Lo] [Hi] [step] stereo HEX|CUBIC
+```
- ./DrawStereograms [number_of_files] [Stereo_file_name] 5d rainbow [Lo] [Hi] [step] stereo HEX|CUBIC
-
-
-### Example ###
+### Example
- ./Draw_stereograms 1 gbcd_Mg_9bins_gmt_ 5d rainbow 0.79 9.71 0.89
-
+```console
+./Draw_stereograms 1 gbcd_Mg_9bins_gmt_ 5d rainbow 0.79 9.71 0.89
+```
Note the actual input file is named *gbcd_Mg_9bins_gmt_1.dat* but we are using a substring of that file name as the argument to the script
-
diff --git a/src/Plugins/OrientationAnalysis/data/ReadMe.md b/src/Plugins/OrientationAnalysis/data/ReadMe.md
index 96a8e3ebb5..69207a461a 100644
--- a/src/Plugins/OrientationAnalysis/data/ReadMe.md
+++ b/src/Plugins/OrientationAnalysis/data/ReadMe.md
@@ -3,6 +3,6 @@
| FileName | Type | Dims | Notes | MD5 |
|----------|------|------|-------|-----|
| fz_quats.raw | Float 32 | 100 x 100 x 2 x 4 | Quaternions from Small IN100 converted to Fundamental Zone **| 7a69b4d01447fcdb59d32f416be22492 |
-| quats.raw | Float 32 | 100 x 100 x 2 x 4 | Quaternions from Small IN100 Data Set ** | f163cc7930c6f19a83c2b9cd1dd26938 |
+| quats.raw | Float 32 | 100 x 100 x 2 x 4 | Quaternions from Small IN100 Data Set | f163cc7930c6f19a83c2b9cd1dd26938 |
** Cropped from X 41-140 (inclusive), Y 41-140 (inclusive), Z 0-1 (inclusive) for a dim of 100 x 100 x 2
diff --git a/src/Plugins/OrientationAnalysis/docs/AlignSectionsMisorientationFilter.md b/src/Plugins/OrientationAnalysis/docs/AlignSectionsMisorientationFilter.md
index 6f23cf1df2..c7d652935e 100644
--- a/src/Plugins/OrientationAnalysis/docs/AlignSectionsMisorientationFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/AlignSectionsMisorientationFilter.md
@@ -1,11 +1,10 @@
-# Align Sections (Misorientation)
+# Align Sections (Misorientation)
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Reconstruction (Alignment)
-## Description ##
+## Description
This **Filter** attempts to align consecutive 'sections' perpendicular to the Z-direction of the sample by determining the position that results in the minimum amount of misorientation between **Cells** directly above-below each other. The algorithm of this **Filter** is as follows:
@@ -14,7 +13,7 @@ This **Filter** attempts to align consecutive 'sections' perpendicular to the Z-
3. Repeat steps 1 and 2 for each position when shifting the second slice (relative to the first) from three (3) **Cells** to the left to three (3) **Cells** to the right, as well as from three (3) **Cells** up to three (3) **Cells** down. *Note that this creates a 7x7 grid*
4. Determine the position in the 7x7 grid that has the lowest misalignment value. (It will be the position with the fewest different **Cell** pairs)
5. Repeat steps 1-4 with the center of each (new) 7x7 grid at the best position from the last 7x7 grid until the best position in the current/new 7x7 grid is the same as the last 7x7 grid
-6) Repeat steps 1-5 for each pair of neighboring sections
+6. Repeat steps 1-5 for each pair of neighboring sections
**Note that this is similar to a downhill simplex and can get caught in a local minimum!**
@@ -24,45 +23,17 @@ The user can choose to write the determined shift to an output file by enabling
The user can also decide to remove a *background shift* present in the sample. The process for this is to fit a line to the X and Y shifts along the Z-direction of the sample. The individual shifts are then modified to make the slope of the fit line be 0. Effectively, this process is trying to keep the top and bottom section of the sample fixed. Some combinations of sample geometry and internal features can result in this algorithm introducing a 'shear' in the sample and the *Linear Background Subtraction* will attempt to correct for this.
-## Parameters ##
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Misorientation Tolerance | float | Tolerance used to decide if **Cells** above/below one another should be considered to be _the same_. The value selected should be similar to the tolerance one would use to define **Features** (i.e., 2-10 degrees) |
-| Write Alignment Shift File | bool | Whether to write the shifts applied to each section to a file |
-| Alignment File | File Path | The output file path where the user would like the shifts applied to the section to be written. Only needed if *Write Alignment Shifts File* is checked |
-| Linear Background Subtraction | bool | Whether to remove a *background shift* present in the alignment |
-| Use Mask Array | bool | Whether to remove some **Cells** from consideration in the alignment process |
-
-
-## Required Geometry ##
-
-Image
-
-## Required Objects ##
+% Auto generated parameter table will be inserted here
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | Quats | float | (4) | Specifies the orientation of the **Cell** in quaternion representation |
-| **Cell Attribute Array** | Phases | int32_t | (1) | Specifies to which **Ensemble** each **Cell** belongs |
-| **Cell Attribute Array** | Mask | bool | (1) | Specifies if the **Cell** is to be counted in the algorithm. Only required if *Use Mask Array* is checked |
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
-
-## Created Objects ##
-
-None
-
-## Example Pipelines ##
+## Example Pipelines
+ (10) SmallIN100 Full Reconstruction
+ (03) SmallIN100 Alignment
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/AlignSectionsMutualInformationFilter.md b/src/Plugins/OrientationAnalysis/docs/AlignSectionsMutualInformationFilter.md
index 9acd2865d9..2371317c04 100644
--- a/src/Plugins/OrientationAnalysis/docs/AlignSectionsMutualInformationFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/AlignSectionsMutualInformationFilter.md
@@ -1,21 +1,21 @@
-# Align Sections (Mutual Information) #
+# Align Sections (Mutual Information)
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Reconstruction (Alignment)
-## Description ##
+## Description
This **Filter** segments each 2D slice, creating *Feature Ids* that are used when determining the *mutual information* between neighboring slices. The slices are shifted relative to one another until the position of maximum *mutual information* is determined for each section. The *Feature Ids* are temporary, they apply to this **Filter** only and are not related to the *Feature Ids* generated in other **Filters**. The algorithm of this **Filter** is listed below:
1. Segment *Features* on each 'section' of the sample perpendicular to the Z-direction. This is done using the same algorithm in the [Segment Features (Misorientation)](@ref alignsectionsmisorientation) **Filter** (only in 2D on each section)
2. Calculate the *mutual information* between neighboring sections and store that as the misalignment value for that position. *Mutual information* is related to the ratio of joint probability to individual probabilities of variables (i.e., p(x,y)/p(x)p(y) ). Details of the actual *mutual information* calculation can be found in the references below, but can be thought of as the inherent dependence between variables (here the *Feature Ids* on neighboring sections).
-3. Repeat step 2 for each position when shifting the second slice (relative to the first) from three (3) **Cells** to the left
+3. Repeat step 2 for each position when shifting the second slice (relative to the first) from three (3) **Cells** to the left
to three (3) **Cells** to the right, as well as from three (3) **Cells** up to three (3) **Cells** down
*Note that this creates a 7x7 grid*
4. Determine the position in the 7x7 grid that has the highest *mutual information* value
5. Repeat steps 2-4 with the center of each (new) 7x7 grid at the best position from the last 7x7 grid until the best position in the current/new 7x7 grid is the same as the last 7x7 grid
+
6) Repeat steps 2-5 for each pair of neighboring sections
**Note that this is similar to a downhill simplex and can get caught in a local minimum!**
@@ -28,55 +28,28 @@ If the user elects to use a mask array, the **Cells** flagged as *false* in the
The user can choose to write the determined shift to an output file by enabling *Write Alignment Shifts File* and providing a file path.
+% Auto generated parameter table will be inserted here
-## Parameters ##
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Misorientation Tolerance | float | Tolerance used to decide if **Cells** above/below one another should be considered to be _the same_. The value selected should be similar to the tolerance one would use to define **Features** (i.e., 2-10 degrees) |
-| Write Alignment Shift File | bool | Whether to write the shifts applied to each section to a file |
-| Alignment File | File Path | The output file path where the user would like the shifts applied to the section to be written. Only needed if *Write Alignment Shifts File* is checked |
-| Use Mask Array | bool | Whether to remove some **Cells** from consideration in the alignment process |
-
-## Required Geometry ##
-
-Image
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | Quats | float | (4) | Specifies the orientation of the **Cell** in quaternion representation |
-| **Cell Attribute Array** | Phases | int32_t | (1) | Specifies to which **Ensemble** each **Cell** belongs |
-| **Cell Attribute Array** | Mask | bool | (1) | Specifies if the **Cell** is to be counted in the algorithm. Only required if *Use Mask Array* is checked |
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
-
-## Created Objects ##
-
-None
-
-## References ##
+## References
[Scholar Pedia](http://www.scholarpedia.org/article/Mutual_information)
Journal articles on *Mutual Information* that are useful:
-+ _Elements of information theory_. John Wiley & Sons, New York, NY.Gray, R.M. (1990).
-+ _Entropy and Information Theory_. Springer-Verlag, New York, NY. Nirenberg, S. and Latham, P.E. (2003).
-+ _Decoding neuronal spike trains: how important are correlations?_ Proc. Natl. Acad. Sci. 100:7348-7353. Shannon, C.E. and Weaver, W. (1949).
-+ _The mathematical theory of communication_. University of Illinois Press, Urbana, Illinois. M zard, M. and Monatanari, A. (2009).
-+ _Information, Physics, and Computation_. Oxford University Press, Oxford.
++ *Elements of information theory*. John Wiley & Sons, New York, NY.Gray, R.M. (1990).
++ *Entropy and Information Theory*. Springer-Verlag, New York, NY. Nirenberg, S. and Latham, P.E. (2003).
++ *Decoding neuronal spike trains: how important are correlations?* Proc. Natl. Acad. Sci. 100:7348-7353. Shannon, C.E. and Weaver, W. (1949).
++ *The mathematical theory of communication*. University of Illinois Press, Urbana, Illinois. M zard, M. and Monatanari, A. (2009).
++ *Information, Physics, and Computation*. Oxford University Press, Oxford.
-## Example Pipelines ##
+## Example Pipelines
AlignSectionsMutualInformation
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/BadDataNeighborOrientationCheckFilter.md b/src/Plugins/OrientationAnalysis/docs/BadDataNeighborOrientationCheckFilter.md
index 2e27a11bd0..e087f31af5 100644
--- a/src/Plugins/OrientationAnalysis/docs/BadDataNeighborOrientationCheckFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/BadDataNeighborOrientationCheckFilter.md
@@ -1,11 +1,10 @@
-# Neighbor Orientation Comparison (Bad Data) #
+# Neighbor Orientation Comparison (Bad Data)
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Orientation Analysis (Cleanup)
-## Description ##
+## Description
This **Filter** compares the orientations of *bad* **Cells** with their neighbor **Cells**. If the misorientation is below a user defined tolerance for a user defined number of neighbor **Cells** , then the *bad* **Cell** will be changed to a *good* **Cell**.
@@ -13,43 +12,19 @@ This **Filter** compares the orientations of *bad* **Cells** with their neighbor
*Note:* The **Filter** will iteratively reduce the required number of neighbors from 6 until it reaches the user defined number. So, if the user selects a required number of neighbors of 4, then the **Filter** will run with a required number of neighbors of 6, then 5, then 4 before finishing.
-## Parameters ##
-
-| Name | Type | Description |
-|------|------|-------------|
-| Misorientation Tolerance (Degrees) | float | Angular tolerance used to compare with neighboring **Cells** |
-| Required Number of Neighbors | int32_t | Minimum number of neighbor **Cells** that must have orientations within above tolerace to allow **Cell** to be changed |
-
-## Required Geometry ##
-
-Image
-
-## Required Objects ##
+% Auto generated parameter table will be inserted here
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | Quaternions | flaot | (4) | Specifies the orientation of the **Cell** in quaternion representation |
-| **Cell Attribute Array** | Mask | bool | (1) | Used to define **Cells** as *good* or *bad* |
-| **Cell Attribute Array** | Cell Phases | int32_t | (1) | Specifies to which **Ensemble** each **Cell** belongs |
-| **Ensemble Attribute Array** | Crystal Structures | uint32_t | (1) | Enumeration representing the crystal structure for each phase |
-
-## Created Objects ##
-
-None
-
-## Example Pipelines ##
+## Example Pipelines
+ (10) SmallIN100 Full Reconstruction
+ (04) SmallIN100 Presegmentation Processing
+ INL Export
+ 04_Steiner Compact
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/CAxisSegmentFeaturesFilter.md b/src/Plugins/OrientationAnalysis/docs/CAxisSegmentFeaturesFilter.md
index 981199f9b9..84ece2f2d1 100644
--- a/src/Plugins/OrientationAnalysis/docs/CAxisSegmentFeaturesFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/CAxisSegmentFeaturesFilter.md
@@ -1,11 +1,10 @@
-# Segment Features (C-Axis Misalignment)
+# Segment Features (C-Axis Misalignment)
-
-## Group (Subgroup)
+## Group (Subgroup)
Reconstruction (Segmentation)
-## Description
+## Description
This **Filter** segments the **Features** by grouping neighboring **Cells** that satisfy the *C-axis misalignment tolerance*, i.e., have misalignment angle less than the value set by the user. The *C-axis misalignment* refers to the angle between the <001> directions (C-axis in the hexagonal system) that is present between neighboring **Cells**. The process by which the **Features** are identified is given below and is a standard *burn algorithm*.
@@ -15,50 +14,20 @@ This **Filter** segments the **Features** by grouping neighboring **Cells** that
4. Remove the current **Cell** from the list and move to the next **Cell** and repeat 2. and 3.; continue until no **Cells** are left in the list
5. Increment the current **Feature** counter and repeat steps 1. through 4.; continue until no **Cells** remain unassigned in the dataset
-The user has the option to *Use Mask Array*, which allows the user to set a boolean array for the **Cells** that remove **Cells** with a value of *false* from consideration in the above algorithm. This option is useful if the user has an array that either specifies the domain of the "sample" in the "image" or specifies if the orientation on the **Cell** is trusted/correct.
+The user has the option to *Use Mask Array*, which allows the user to set a boolean array for the **Cells** that remove **Cells** with a value of *false* from consideration in the above algorithm. This option is useful if the user has an array that either specifies the domain of the "sample" in the "image" or specifies if the orientation on the **Cell** is trusted/correct.
After all the **Features** have been identified, a **Feature Attribute Matrix** is created for the **Features** and each **Feature** is flagged as *Active* in a boolean array in the matrix.
-## Parameters
-
-| Name | Type | Description |
-|------|------| ----------- |
-| C-Axis Misorientation Tolerance (Degrees) | float | Tolerance (in degrees) used to determine if neighboring **Cells** belong to the same **Feature** |
-| Use Mask Array | bool | Specifies whether to use a boolean array to exclude some **Cells** from the **Feature** identification process |
-
-## Required Geometry
-
-Image
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | Quats | float | (4) | Specifies the orientation of the **Cell** in quaternion representation |
-| **Cell Attribute Array** | Phases | int32_t | (1) | Specifies to which **Ensemble** each **Cell** belongs |
-| **Cell Attribute Array** | Mask | bool | (1) | Specifies if the **Cell** is to be counted in the algorithm. Only required if *Use Mask Array* is checked |
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
+% Auto generated parameter table will be inserted here
-## Created Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Cell** belongs. |
-| **Attribute Matrix** | CellFeatureData | Cell Feature | N/A | Created **Feature Attribute Matrix** name |
-| **Feature Attribute Array** | Active | bool | (1) | Specifies if the **Feature** is still in the sample (*true* if the **Feature** is in the sample and *false* if it is not). At the end of the **Filter**, all **Features** will be *Active* |
-
-
-
-## Example Pipelines
+## Example Pipelines
Combo-EBSD-osc_r0c0
-## License & Copyright
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/ConvertOrientations.md b/src/Plugins/OrientationAnalysis/docs/ConvertOrientations.md
index 63400f2288..5a459a9ee4 100644
--- a/src/Plugins/OrientationAnalysis/docs/ConvertOrientations.md
+++ b/src/Plugins/OrientationAnalysis/docs/ConvertOrientations.md
@@ -1,15 +1,14 @@
-# Convert Orientation Representations #
+# Convert Orientation Representations
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Orientation Analysis (Conversion)
-## Description ##
+## Description
This **Filter** generates a new orientation representation (see Data Layout Table below) for each **Element**, given the *Input Orientation Representation* for the **Element**. The following table lists the various orientation representations that are supported. DREAM3D is capable of converting between any representation with some caveats.
-#### Data Layout ####
+### Data Layout
| Orientation Representation | No. of Components | Representation Type | Data Layout |
|----------------------------|----------|---------------------|-------------|
@@ -22,9 +21,7 @@ This **Filter** generates a new orientation representation (see Data Layout Tabl
| Cubochoric | 3 | 6 | \[x, y, z\] |
| StereoGraphic | 3 | 7 | \[x, y, z\] |
-
-
-#### Data Range ####
+### Data Range
The valid range for Euler angles is (Degrees):
@@ -32,41 +29,17 @@ The valid range for Euler angles is (Degrees):
+ Phi : 0 to 180
+ phi-2: 0 to 360
-#### Data Conversion Notes ####
+### Data Conversion Notes
If the angles fall outside of this range the **original** Euler Input data **WILL BE CHANGED** to ensure they are within this range.
-## Precision Notes ##
+## Precision Notes
While every effort has been made to ensure the correctness of each transformation algorithm, certain situations may arise where the initial precision of the input data is not large enough for the algorithm to calculate an answer that is intuitive. The user should be acutely aware of their input data and if their data may cause these situations to occur. Combinations of Euler angles close to 0, 180 and 360 can cause these issues to be hit. For instance an Euler angle of [180, 56, 360] is symmetrically the same as [180, 56, 0] and due to calculation errors and round off errors converting that Euler angle between representations may not give the numerical answer the user was anticipating but will give a symmetrically equivalent angle.
-## Parameters ##
-
-| Name | Type | Description |
-|------------------|------|-------------|
-| Input Orientation Type | Enumeration | Specifies the incoming orientation representation |
-| Output Orientation Type | Enumeration | Specifies to which orientation representation to convert the incoming data |
-| Output Orientations | String | The name of the data array with the converted orientation representation |
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
+% Auto generated parameter table will be inserted here
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| Any **Data Array** | Input Orientations | float | See above table | Incoming orientation representation |
-
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|-------------------|
-| Any **Data Array** | *Output Orientations* | float | See above table | Converted orientation representation |
-
-
-## Example Pipelines ##
+## Example Pipelines
+ 02_Adaptive Alignment - Misorientation - Zero Shifts
+ (10) SmallIN100 Full Reconstruction
@@ -77,12 +50,10 @@ Not Applicable
+ 04_Steiner Compact
+ (03) SmallIN100 Alignment
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/ConvertQuaternionFilter.md b/src/Plugins/OrientationAnalysis/docs/ConvertQuaternionFilter.md
index 98b9c912b6..b458ed857e 100644
--- a/src/Plugins/OrientationAnalysis/docs/ConvertQuaternionFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/ConvertQuaternionFilter.md
@@ -1,48 +1,23 @@
# Convert Quaternion Order
-## Group (Subgroup) ##
+## Group (Subgroup)
OrientationAnalysis (Conversions)
-## Description ##
+## Description
Internally DREAM.3D assumes that a quaternion is laid out in the order such that < x, y, z >, w or Vector-Scalar ordering. Codes and algorithms external to DREAM.3D may store quaternions in the opposite or Scalar-Vector order (w < x,y,z >). This filter will allow the user to easily convert imported Quaternions into the representation that DREAM.3D expects.
For Example if the user has imported quaternion data in the form of Scalar-Vector then they would run this filter using a conversion type of **ToVectorScalar** and using the generated quaternions in subsequent filters. If the user wanted to then write out the Quaternions in the Scalar-Vector form then could add this filter again to the end of the pipeline (but before writing out data) to convert the Vector-Scalar quaternions array (assuming something modified the array).
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------|------|------|
-| Delete Original Array | Boolean | Set this to TRUE/ON to have the original 3 component data array deleted at the end of the filter. |
-| Conversion Type | Integer | 0=ToScalarVector, 1=ToVectorScalar |
+## Example Pipelines
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|-----|
-| **Attribute Array** | Quaternion Input | float | (4) | |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|-----|
-| **Attribute Array** | Quaternion Ouput | float | (4) | |
-
-
-## Example Pipelines ##
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/CreateEnsembleInfoFilter.md b/src/Plugins/OrientationAnalysis/docs/CreateEnsembleInfoFilter.md
index 15d8e51e4a..3258519d29 100644
--- a/src/Plugins/OrientationAnalysis/docs/CreateEnsembleInfoFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/CreateEnsembleInfoFilter.md
@@ -1,13 +1,12 @@
# Create Ensemble Info
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Processing (Generation)
-## Description ##
+## Description
-This **Filter** allows the user to enter basic crystallographic information about each phase. The Laue class, Phase Type, and Phase Name can all be entered by the user. The information is stored in an EnsembleAttributeMatrix. These values are needed to allow the calculation of certain kinds of crystallographic statistics on the volume, if they have not already been provided by some other means. Each row in the table lists the __Crystal Structure__, __Phase Type__, and __Phase Name__. The proper values for the crystal structure and phase type come from internal constants within DREAM.3D and are listed here:
+This **Filter** allows the user to enter basic crystallographic information about each phase. The Laue class, Phase Type, and Phase Name can all be entered by the user. The information is stored in an EnsembleAttributeMatrix. These values are needed to allow the calculation of certain kinds of crystallographic statistics on the volume, if they have not already been provided by some other means. Each row in the table lists the **Crystal Structure**, **Phase Type**, and **Phase Name**. The proper values for the crystal structure and phase type come from internal constants within DREAM.3D and are listed here:
### Crystal Structure
@@ -37,41 +36,16 @@ This **Filter** allows the user to enter basic crystallographic information abou
| BoundaryPhase | 4 |
| UnknownPhaseType | 999 |
+% Auto generated parameter table will be inserted here
-## Parameters ##
-
-| Name | Type | Description |
-|------|------|-------------|
-| Ensemble | Create Ensemble Info | The created Ensemble crystal structures, phase types, and phase names |
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-None
+## Example Pipelines
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimension | Description |
-|------|--------------|-------------|---------|--------------|
-| **Attribute Matrix** | EnsembleAttributeMatrix | Ensemble | N/A | Created **Ensemble Attribute Matrix** name |
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
-| **Ensemble Attribute Array** | PhaseTypes | uint32_t | (1) | Enumeration representing the phase type for each **Ensemble** |
-| **String Data Array** | PhaseNames | String | (1) | The phase names for each **Ensemble** |
-
-
-## Example Pipelines ##
Import_ASCII
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/EBSDSegmentFeaturesFilter.md b/src/Plugins/OrientationAnalysis/docs/EBSDSegmentFeaturesFilter.md
index dee58ec126..9abd375431 100644
--- a/src/Plugins/OrientationAnalysis/docs/EBSDSegmentFeaturesFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/EBSDSegmentFeaturesFilter.md
@@ -1,11 +1,10 @@
-# Segment Features (Misorientation)
+# Segment Features (Misorientation)
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Reconstruction (Segmentation)
-## Description ##
+## Description
This **Filter** segments the **Features** by grouping neighboring **Cells** that satisfy the *misorientation tolerance*, i.e., have misorientation angle less than the value set by the user. The process by which the **Features** are identified is given below and is a standard *burn algorithm*.
@@ -15,53 +14,23 @@ This **Filter** segments the **Features** by grouping neighboring **Cells** that
4. Remove the current **Cell** from the list and move to the next **Cell** and repeat 2. and 3.; continue until no **Cells** are left in the list
5. Increment the current **Feature** counter and repeat steps 1. through 4.; continue until no **Cells** remain unassigned in the dataset
-The user has the option to *Use Mask Array*, which allows the user to set a boolean array for the **Cells** that remove **Cells** with a value of *false* from consideration in the above algorithm. This option is useful if the user has an array that either specifies the domain of the "sample" in the "image" or specifies if the orientation on the **Cell** is trusted/correct.
+The user has the option to *Use Mask Array*, which allows the user to set a boolean array for the **Cells** that remove **Cells** with a value of *false* from consideration in the above algorithm. This option is useful if the user has an array that either specifies the domain of the "sample" in the "image" or specifies if the orientation on the **Cell** is trusted/correct.
After all the **Features** have been identified, a **Feature Attribute Matrix** is created for the **Features** and each **Feature** is flagged as *Active* in a boolean array in the matrix.
-## Parameters ##
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Misorientation Tolerance (Degrees) | float | Tolerance (in degrees) used to determine if neighboring **Cells** belong to the same **Feature** |
-| Use Mask Array | bool | Specifies whether to use a boolean array to exclude some **Cells** from the **Feature** identification process |
-
-## Required Geometry ##
-
-Image
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | Quats | float | (4) | Specifies the orientation of the **Cell** in quaternion representation |
-| **Cell Attribute Array** | Phases | int32_t | (1) | Specifies to which **Ensemble** each **Cell** belongs |
-| **Cell Attribute Array** | Mask | bool | (1) | Specifies if the **Cell** is to be counted in the algorithm. Only required if *Use Mask Array* is checked |
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
+% Auto generated parameter table will be inserted here
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Cell** belongs. |
-| **Attribute Matrix** | CellFeatureData | Cell Feature | N/A | Created **Feature Attribute Matrix** name |
-| **Feature Attribute Array** | Active | bool | (1) | Specifies if the **Feature** is still in the sample (*true* if the **Feature** is in the sample and *false* if it is not). At the end of the **Filter**, all **Features** will be *Active* |
-
-
-
-## Example Pipelines ##
+## Example Pipelines
+ (10) SmallIN100 Full Reconstruction
+ INL Export
+ (05) SmallIN100 Segmentation
+ 04_Steiner Compact
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/EbsdToH5EbsdFilter.md b/src/Plugins/OrientationAnalysis/docs/EbsdToH5EbsdFilter.md
index f11f0bfb9e..65bc067d56 100644
--- a/src/Plugins/OrientationAnalysis/docs/EbsdToH5EbsdFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/EbsdToH5EbsdFilter.md
@@ -1,61 +1,49 @@
# Import Orientation File(s) to H5EBSD
-## Group (Subgroup) ##
+## Group (Subgroup)
IO (Input)
-## Description ##
+## Description
This **Filter** will convert orientation data obtained from Electron Backscatter Diffraction (EBSD) experiments into a single file archive based on the [HDF5](http://www.hdfgroup.org) file specification. See the **Supported File Formats** section below for information on file compatibility. This **Filter** is typically run as a single **Filter** **Pipeline** to perform the conversion. All subsequent **Pipelines** should then use the Read H5EBSD File **Filter** to import the H5EBSD file into DREAM.3D for analysis, as opposed to re-importing the raw EBSD files. The primary purpose of this **Filter** is to import a stack of data that forms a 3D volume. If the user wishes to import a single data file, then the **Filters** Read EDAX EBSD Data (.ang), Read EDAX EBSD Data (.h5), or Read Oxford Instr. EBSD Data (.ctf) should be used for EDAX .ang, EDAX .h5, or Oxford .ctf files, respectively.
-### Converting Orientation Data to H5EBSD Archive ###
+### Converting Orientation Data to H5EBSD Archive
In order to work with orientation data, DREAM.3D needs to read the data from an archive file based on the [HDF5](http://www.hdfgroup.org) specification. In order to convert the data, the user will first build a single **Filter** **Pipeline** by selecting the Import Orientation File(s) to H5EBSD **Filter**. This **Filter** will convert a directory of sequentially numbered files into a single [HDF5](http://www.hdfgroup.org) file that retains all the meta data from the header(s) of the files. The user selects the directory that contains all the files to be imported then uses the additional input widgets on the **Filter** interface (_File Prefix_, _File Suffix_, _File Extension_, and _Padding Digits_) to make adjustments to the generated file name until the correct number of files is found. The user may also select starting and ending indices to import. The user interface indicates through red and green icons if an expected file exists on the file system and will also display a warning message at the bottom of the **Filter** interface if any of the generated file names do not appear on the file system.
-### Stacking Order ###
+### Stacking Order
-Due to different experimental setups, the definition of the *bottom* slice or the **Z=0** slice can be different. The user should verify that the proper button box is checked for their data set.
+Due to different experimental setups, the definition of the _bottom_ slice or the **Z=0** slice can be different. The user should verify that the proper button box is checked for their data set.
+ **Low to High** This means that the file with the lowest index, closest to zero (0), will be considered the Z=0 slice.
+ **High to Low** This means that the file with the highest index, farthest from zero (0), will be considered the Z=0 slice.
-### Z Resolution ###
+### Z Resolution
Many serial sectioning systems are inherently a series of 2D scans stacked together to form a 3D volume of material. Therefore, the experimental systems have no knowledge of the amount of material that was removed between each slice and so the user is responsible for setting this value correctly for their data set.
------
-
![Import Orientation Files User Interface](Images/EbsdToH5Ebsd_Image_1.png)
------
-
-## Orientations, Reference Frames and Coordinate Systems ##
+## Orientations, Reference Frames and Coordinate Systems
DREAM.3D's origin follows the specimen's coordinate system so that the physical location of the 0 row and 0 column voxel should visually appear in the lower left corner of a computer graphics display as shown in the figure below, where the specimen coordinate system (white) overlaid with EBSD coordinate system (yellow).
------
-
![TSL Coordinate System (Spatial)](Images/EbsdToH5Ebsd_CoordinateSystem.png)
------
-
Commercial EBSD acquisition systems do not typically follow this convention, and DREAM.3D needs input from the user so that the proper transformations to the data can be applied during subsequent analysis. Commercial EBSD software packages allow for some initial transformations of the data, in which case the DREAM.3D environment does not have any way of determining if those transformations have already occurred. During the import process the user is asked a few questions regarding the orientation of the EBSD data in relation to the specimen coordinate system.
-### Setting the Spatial Reference Frame ###
+### Setting the Spatial Reference Frame
-The user needs to click the *Set Reference Frame* button to set the proper reference frame for the data set which will be written to the H5EBSD file as meta data. Below are a number of examples showing the differences in the data sets due to the selection of different reference frames.
+The user needs to click the _Set Reference Frame_ button to set the proper reference frame for the data set which will be written to the H5EBSD file as meta data. Below are a number of examples showing the differences in the data sets due to the selection of different reference frames.
| No Sample Transform | Edax/HKL Sample Transform |
|--|--|
| ![No Transform or Unknown Manufacturer or HEDM Data](Images/EbsdToH5Ebsd_NoUnknown_HEDM_RefFrame.png) | ![TSL or HKL Transform](Images/EbsdToH5Ebsd_EDAX_HKL_RefFrame.png) |
+### Preset Transformations
-### Preset Transformations ###
-
------
![Selecting the Reference Frame](Images/EbsdToH5Ebsd_ReferenceFrameDialog.png)
------
-
| Manufacturer | Sample Reference Transformation | Euler Transformation |
| ------| ------| ------|
| Edax - TSL | 180 @ <010> | 90 @ <001> |
@@ -63,7 +51,7 @@ The user needs to click the *Set Reference Frame* button to set the proper refer
| No Transform | 0 @ <001> | 0 @ <001>
| HEDM - IceNine| 0 @ <001> | 0 @ <001>
-### Supported File Formats ###
+### Supported File Formats
| Manufacturer | File Extension | Comments |
|---------------|----------------|----------|
@@ -71,37 +59,21 @@ The user needs to click the *Set Reference Frame* button to set the proper refer
| Oxford Instruments | .ctf | Euler Angles can be stored in Degrees or Radians. |
| HEDM from APS | .mic | A .config file with the same name is needed for each .mic file |
-### Completing the Conversion ###
+### Completing the Conversion
Once all the inputs are correct the user can click the **Go** button to start the conversion. Progress will be displayed at the bottom of the DREAM3D user interface during the conversion.
-## Parameters ##
-
-See Description
-
-## Required Geometry ##
+% Auto generated parameter table will be inserted here
-Not Applicable
-
-## Required Objects ##
-
-None
-
-## Created Objects ##
-
-None
-
-## Example Pipelines ##
+## Example Pipelines
+ (01) SmallIN100 Archive
+ 01_Import Data
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/EnsembleInfoReaderFilter.md b/src/Plugins/OrientationAnalysis/docs/EnsembleInfoReaderFilter.md
index 6c18f35093..3c39595454 100644
--- a/src/Plugins/OrientationAnalysis/docs/EnsembleInfoReaderFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/EnsembleInfoReaderFilter.md
@@ -1,13 +1,12 @@
-# Import Ensemble Info File
+# Import Ensemble Info File
-
-## Group (Subgroup)
+## Group (Subgroup)
IO (Input)
-## Description
+## Description
-This **Filter** reads in information about the crystal structure and phase types of all the **Features** that are contained in a **Cell** based volume. These values are needed to allow the calculation of statistics on the volume, if they have not already been provided by some other means. The format of the input file is a simple ASCII text file with the extension .ini or .txt. The first group in the file is the name [EnsembleInfo] in square brackets with the key Number_Phases=*number of phases* that are contained in the volume. Subsequent groups in the file list the __Phase Number__, __Crystal Structure__ and __Phase Type__. The proper values for the crystal structure and phase type come from internal constants within DREAM.3D and are listed here:
+This **Filter** reads in information about the crystal structure and phase types of all the **Features** that are contained in a **Cell** based volume. These values are needed to allow the calculation of statistics on the volume, if they have not already been provided by some other means. The format of the input file is a simple ASCII text file with the extension .ini or .txt. The first group in the file is the name [EnsembleInfo] in square brackets with the key Number_Phases=*number of phases* that are contained in the volume. Subsequent groups in the file list the **Phase Number**, **Crystal Structure** and **Phase Type**. The proper values for the crystal structure and phase type come from internal constants within DREAM.3D and are listed here:
**Crystal Structure**
@@ -37,9 +36,9 @@ This **Filter** reads in information about the crystal structure and phase types
| BoundaryPhase | 4 |
| UnknownPhaseType | 999 |
-## Example Input
+## Example Input
-__Phase numbering starts at One (1). Phase Zero (0) is reserved for internal use in DREAM.3D__
+**Phase numbering starts at One (1). Phase Zero (0) is reserved for internal use in DREAM.3D**
For example, if you have a structure that has 2 phases that consist of a Cubic Primary phase and a Hexagonal Matrix phase the file would be the following:
[EnsembleInfo]
@@ -53,38 +52,14 @@ For example, if you have a structure that has 2 phases that consist of a Cubic P
CrystalStructure=Hexagonal_High
PhaseType=MatrixPhase
+% Auto generated parameter table will be inserted here
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| Input Ensemble Info File | File Path | The input file path |
-
-## Required Geometry
-
-Not Applicable
-
-## Required Objects
-
-None
+## Example Pipelines
-## Created Objects
-
-| Kind | Default Name | Type | Component Dimension | Description |
-|------|--------------|-------------|---------|--------------|
-| **Attribute Matrix** | EnsembleAttributeMatrix | Ensemble | N/A | Created **Ensemble Attribute Matrix** name |
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
-| **Ensemble Attribute Array** | PhaseTypes | uint32_t | (1) | Enumeration representing the phase type for each **Ensemble** |
-
-
-## Example Pipelines
-
-## License & Copyright
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/ExportGBCDGMTFileFilter.md b/src/Plugins/OrientationAnalysis/docs/ExportGBCDGMTFileFilter.md
index fe8762a1a6..f285d2d8ae 100644
--- a/src/Plugins/OrientationAnalysis/docs/ExportGBCDGMTFileFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/ExportGBCDGMTFileFilter.md
@@ -1,53 +1,25 @@
# Write GBCD Pole Figure (GMT 5)
-
-## Group (Subgroup) ##
+## Group (Subgroup)
IO (Output)
-## Description ##
-
-This **Filter** creates a .dat file that can be used in conjunction with [GMT](http://gmt.soest.hawaii.edu/) to generate a grain boundary character distribution (GBCD) pole figure. The user must select the relevant phase for which to write the pole figure by entering the *phase index*.
+## Description
------
+This **Filter** creates a .dat file that can be used in conjunction with [GMT](http://gmt.soest.hawaii.edu/) to generate a grain boundary character distribution (GBCD) pole figure. The user must select the relevant phase for which to write the pole figure by entering the *phase index*.
![GMT Visualization of the Small IN100 GBCD Results](Images/ExportGBCDGMTFile.png)
------
-
-## Parameters ##
-
-| Name | Type | Description |
-|------|------|-------------|
-| Phase of Interest | int32_t | Index of the **Ensemble** for which to plot the pole figure |
-| Crystal Structure | Enumeration | Crystal structure for GBCD. Currently supports from Hexagonal-High 6/mmm or Cubic-High m-3m symmetries |
-| Misorientation Axis-Angle | float (4x) | Axis-Angle pair values for drawing GBCD |
-| Output GMT File | File Path | The output .dat file path |
-
-## Required Geometry ##
-
-Triangle
+% Auto generated parameter table will be inserted here
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Ensemble Attribute Array** | GBDC | double | (n,m,l,o,q,r) | 5 parameter GBCD data. The 6th component is used internally to track the northern vs. southern hemisphere of the Lambert sphere |
-
-## Created Objects ##
-
-None
-
-## Example Pipelines ##
+## Example Pipelines
+ (04) SmallIN100 GBCD
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/ExportGBCDTriangleDataFilter.md b/src/Plugins/OrientationAnalysis/docs/ExportGBCDTriangleDataFilter.md
index 323cac02b6..cbf8799e98 100644
--- a/src/Plugins/OrientationAnalysis/docs/ExportGBCDTriangleDataFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/ExportGBCDTriangleDataFilter.md
@@ -1,15 +1,14 @@
-# Write GBCD Triangles File
+# Write GBCD Triangles File
-
-## Group (Subgroup) ##
+## Group (Subgroup)
IO (Output)
-## Description ##
+## Description
This **Filter** writes relevant information about the Grain Boundary Character Distribution (GBCD) on an existing set of triangles. The information written includes the inward and outward Euler angles, normals, and areas for each triangle. The file format was originally defined by Prof. Greg Rohrer (CMU).
-## Example Output ##
+## Example Output ##
# Triangles Produced from DREAM3D version 5.2
# Column 1-3: right hand average orientation (phi1, PHI, phi2 in RADIANS)
@@ -28,39 +27,14 @@ This **Filter** writes relevant information about the Grain Boundary Character D
3.4109 0.6178 1.0586 0.2662 0.6970 4.4347 0.9822 0.1328 0.1328 0.0256
..
-## Parameters ##
-
-| Name | Type | Description |
-|------|------|-------------|
-| Output File | File Path | The output GBCD triangle file path |
-
-## Required Geometry ##
-
-Image + Triangle
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Face Attribute Array** | FaceLabels | int32_t | (2) | Specifies which **Features** are on either side of each **Face** |
-| **Face Attribute Array** | FaceNormals | double | (3) | Specifies the normal of each **Face** |
-| **Face Attribute Array** | FaceAreas | double | (1) | Specifies the area of each **Face** |
-| **Feature Attribute Array** | AvgEulerAngles | float | (3) | Three angles defining the orientation of the **Feature** in Bunge convention (Z-X-Z). |
+% Auto generated parameter table will be inserted here
-## Created Objects ##
+## Example Pipelines
-None
-
-## Example Pipelines ##
-
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/FindAvgCAxesFilter.md b/src/Plugins/OrientationAnalysis/docs/FindAvgCAxesFilter.md
index 8d017393c0..56afefbf33 100644
--- a/src/Plugins/OrientationAnalysis/docs/FindAvgCAxesFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/FindAvgCAxesFilter.md
@@ -1,54 +1,29 @@
-# Find Average C-Axis Orientations
+# Find Average C-Axis Orientations
-
-## Group (Subgroup)
+## Group (Subgroup)
Statistics (Crystallographic)
-## Description
+## Description
This **Filter** determines the average C-axis location of each **Feature** by the following algorithm:
1. Gather all **Elements** that belong to the **Feature**
2. Determine the location of the c-axis in the sample *reference frame* for the rotated quaternions for all **Elements**
-3. Average the locations and store as the average for the **Feature**
-
-*Note:* This **Filter** will only work properly for *Hexagonal* materials. The **Filter** does not apply any symmetry operators because there is only one c-axis (<001>) in *Hexagonal* materials and thus all symmetry operators will leave the c-axis in the same position in the sample *reference frame*. However, in *Cubic* materials, for example, the {100} family of directions are all equivalent and the <001> direction will change location in the sample *reference frame* when symmetry operators are applied.
-
-## Parameters
-
-None
-
-## Required Geometry
-
-Not Applicable
+3. Average the locations and store as the average for the **Feature**
-## Required Objects
+*Note:* This **Filter** will only work properly for *Hexagonal* materials. The **Filter** does not apply any symmetry operators because there is only one c-axis (<001>) in *Hexagonal* materials and thus all symmetry operators will leave the c-axis in the same position in the sample *reference frame*. However, in *Cubic* materials, for example, the {100} family of directions are all equivalent and the <001> direction will change location in the sample *reference frame* when symmetry operators are applied.
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Element Attribute Array** | Quats | float | (4) | Specifies the orientation of the **Element** in quaternion representation |
-| **Element Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Element** belongs. |
-| **Cell Attribute Array** | Phases | int32_t | (1) | Specifies to which **Ensemble** each **Cell** belongs |
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
+% Auto generated parameter table will be inserted here
-## Created Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | AvgCAxes | float | (3) | The direction of the **Feature's** C-axis in the sample reference frame |
-
-
-## Example Pipelines
+## Example Pipelines
Combo-EBSD-osc_r0c0
-## License & Copyright
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/FindAvgOrientationsFilter.md b/src/Plugins/OrientationAnalysis/docs/FindAvgOrientationsFilter.md
index 6d1e026f9c..47f73780f4 100644
--- a/src/Plugins/OrientationAnalysis/docs/FindAvgOrientationsFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/FindAvgOrientationsFilter.md
@@ -1,11 +1,10 @@
-# Find Feature Average Orientations
+# Find Feature Average Orientations
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Statistics (Crystallographic)
-## Description ##
+## Description
This **Filter** determines the average orientation of each **Feature** by the following algorithm:
@@ -18,32 +17,9 @@ This **Filter** determines the average orientation of each **Feature** by the fo
*Note:* The quaternions can be averaged with a simple average because the quaternion space is not distorted like Euler space.
-## Parameters ##
-
-None
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Element Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Element** belongs |
-| **Element Attribute Array** | Phases | int32_t | (1) | Specifies the **Ensemble** of the **Element** |
-| **Element Attribute Array** | Quats | float | (4) | Specifies the orientation of the **Element** in quaternion representation |
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
+% Auto generated parameter table will be inserted here
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | AvgQuats | float | (4) | Specifies the average orientation of the **Feature** in quaternion representation |
-| **Feature Attribute Array** | AvgEulerAngles | float | (3) | Specifies the orientation of each **Feature** in Bunge convention (Z-X-Z) |
-
-
-## Example Pipelines ##
+## Example Pipelines
+ (10) SmallIN100 Full Reconstruction
+ InsertTransformationPhase
@@ -51,12 +27,10 @@ Not Applicable
+ (05) SmallIN100 Crystallographic Statistics
+ (06) SmallIN100 Synthetic
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/FindBoundaryStrengthsFilter.md b/src/Plugins/OrientationAnalysis/docs/FindBoundaryStrengthsFilter.md
index 4baab9ed00..d994fba6a9 100644
--- a/src/Plugins/OrientationAnalysis/docs/FindBoundaryStrengthsFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/FindBoundaryStrengthsFilter.md
@@ -1,6 +1,5 @@
# Find Feature Boundary Strength Metrics
-
## Group (Subgroup)
Statistics (Crystallographic)
@@ -17,33 +16,7 @@ This **Filter** calculates the same metrics as in the Find Neighbor Slip Transmi
*Note:* Each metric is calculated twice for the two different directions slip could approach the boundary. The values are stored on each **Face** in the **Face** map in a way that notes the direction (i.e., when **Feature** 1 has neighbor **Feature** 2 and when **Feature** 2 has neighbor **Feature** 1) because the direction across the boundary between the **Features** affects the value of the metric.
-## Parameters
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Loading Direction | float32 (3x) | The loading axis for the sample |
-
-## Required Geometry
-
-Image + Triangle
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Face Attribute Array** | FaceLabels | int32 | (2) | Specifies which **Features** are on either side of each **Face** |
-| **Feature Attribute Array** | AvgQuats | float32 | (4) | Specifies the average orientation of each **Feature** in quaternion representation |
-| **Feature Attribute Array** | Phases | int32 | (1) | Specifies to which **Ensemble** each **Feature** belongs |
-| **Ensemble Attribute Array** | CrystalStructures | uint32 | (1) | Enumeration representing the crystal structure for each phase |
-
-## Created Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Face Attribute Array** | F1s | float32 | (2) | |
-| **Face Attribute Array** | F1spts | float32 | (2) | |
-| **Face Attribute Array** | F7s | float32 | (2) | |
-| **Face Attribute Array** | mPrimes | float32 | (2) | |
+% Auto generated parameter table will be inserted here
## Example Pipelines
@@ -51,8 +24,6 @@ Image + Triangle
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/FindCAxisLocationsFilter.md b/src/Plugins/OrientationAnalysis/docs/FindCAxisLocationsFilter.md
index d219e27243..61743bcf94 100644
--- a/src/Plugins/OrientationAnalysis/docs/FindCAxisLocationsFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/FindCAxisLocationsFilter.md
@@ -1,6 +1,5 @@
# Find C-Axis Locations
-
## Group (Subgroup)
Statistics (Crystallographic)
@@ -9,30 +8,9 @@ Statistics (Crystallographic)
This **Filter** determines the direction of the C-axis for each **Element** by applying the quaternion of the **Element** to the <001> direction, which is the C-axis for *Hexagonal* materials. This will tell where the C-axis of the **Element** sits in the *sample reference frame*.
-*Note:* This **Filter** will only work properly for *Hexagonal* materials. The **Filter** does not apply any symmetry operators because there is only one c-axis (<001>) in *Hexagonal* materials and thus all symmetry operators will leave the c-axis in the same position in the sample *reference frame*. However, in *Cubic* materials, for example, the {100} family of directions are all equivalent and the <001> direction will change location in the *sample reference frame* when symmetry operators are applied.
-
-## Parameters
-
-None
-
-## Required Geometry
-
-Not Applicable
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Element Attribute Array** | Quats | float | (4) | Specifies the orientation of the **Element** in quaternion representation |
-| **Cell Attribute Array** | Phases | int32_t | (1) | Specifies to which **Ensemble** each **Cell** belongs |
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
-
-## Created Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Element Attribute Array** | CAxisLocation | float | (3) | Direction of the C-axis for each **Element** in the sample reference frame |
+*Note:* This **Filter** will only work properly for *Hexagonal* materials. The **Filter** does not apply any symmetry operators because there is only one c-axis (<001>) in *Hexagonal* materials and thus all symmetry operators will leave the c-axis in the same position in the sample *reference frame*. However, in *Cubic* materials, for example, the {100} family of directions are all equivalent and the <001> direction will change location in the *sample reference frame* when symmetry operators are applied.
+% Auto generated parameter table will be inserted here
## Example Pipelines
@@ -42,8 +20,6 @@ Combo-EBSD-osc_r0c0
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/FindFeatureNeighborCAxisMisalignmentsFilter.md b/src/Plugins/OrientationAnalysis/docs/FindFeatureNeighborCAxisMisalignmentsFilter.md
index f53268968b..c14e548c91 100644
--- a/src/Plugins/OrientationAnalysis/docs/FindFeatureNeighborCAxisMisalignmentsFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/FindFeatureNeighborCAxisMisalignmentsFilter.md
@@ -1,7 +1,6 @@
-# Find Feature Neighbor C-Axis Misalignments
+# Find Feature Neighbor C-Axis Misalignments
-
-## Group (Subgroup)
+## Group (Subgroup)
Statistics (Crystallographic)
@@ -9,47 +8,20 @@ Statistics (Crystallographic)
This **Filter** determines, for each **Feature**, the C-axis misalignments with the **Features** that are in contact with it. The C-axis misalignments are stored as a list (for each **Feature**) of angles (in degrees).
-### Notes
-
-__NOTE:__ Only features with identical phase values and a crystal structure of **Hexagonal_High** will be calculated. If two features have different phase values or a crystal structure that is *not* Hexagonal_High then a value of NaN is set for the misorientation.
-
-## Parameters
-
-| Name | Type | Description |
-|------|------| ----------- |
-|Find Average Misalignment Per Feature | bool | Whether the *average* of the C-axis misalignments with the neighboring **Features** should be stored for each **Feature** |
-
-## Required Geometry
-
-Not Applicable
+### Notes
-## Required Objects
+**NOTE:** Only features with identical phase values and a crystal structure of **Hexagonal_High** will be calculated. If two features have different phase values or a crystal structure that is *not* Hexagonal_High then a value of NaN is set for the misorientation.
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | NeighborLists | List of int32_t | (1) | List of the contiguous neighboring **Features** for a given **Feature** |
-| **Feature Attribute Array** | AvgQuats | float | (4) | Defines the average orientation of the **Feature** in quaternion representation |
-| **Feature Attribute Array** | Phases | int32_t | (1) | Specifies to which **Ensemble** each **Feature** belongs |
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
+% Auto generated parameter table will be inserted here
-## Created Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | CAxisMisalignmentList | List of float | (1) | List of the C-axis misalignment angles (in degrees) with the contiguous neighboring **Features** for a given **Feature** |
-| **Feature Attribute Array** | AvgCAxisMisalignments | float | (1) | Number weighted average of neighbor C-axis misalignments. Only created if *Find Average Misalignment Per Feature* is checked |
-
-
-## Example Pipelines
+## Example Pipelines
Combo-EBSD-osc_r0c0
-## License & Copyright
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/FindFeatureReferenceCAxisMisorientationsFilter.md b/src/Plugins/OrientationAnalysis/docs/FindFeatureReferenceCAxisMisorientationsFilter.md
index 1790301a68..5a16e1ec2a 100644
--- a/src/Plugins/OrientationAnalysis/docs/FindFeatureReferenceCAxisMisorientationsFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/FindFeatureReferenceCAxisMisorientationsFilter.md
@@ -1,53 +1,25 @@
-# Find Feature Reference C-Axis Misalignments
+# Find Feature Reference C-Axis Misalignments
-
-## Group (Subgroup)
+## Group (Subgroup)
Statistics (Crystallographic)
-## Description
+## Description
This **Filter** calculates the misorientation angle between the C-axis of each **Cell** within a **Feature** and the average C-axis for that **Feature** and stores that value for each **Cell**. The average and standard deviation of those values for all **Cells** belonging to the same **Feature** is also stored for each **Feature**.
This filter requires at least one Hexagonal crystal structure phase (Hexagonal-Low 6/m or Hexagonal-High 6/mmm). Although it is not recommended, you can give input data with mixed phase types and all non hexagonal phases will be skipped in the calculations.
-## Parameters
-
-None
-
-## Required Geometry
-
-Image
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Cell** belongs |
-| **Cell Attribute Array** | Quats | float | (4) | Specifies the orientation of the **Cell** in quaternion representation |
-| **Cell Attribute Array** | Phases | int32_t | (1) | Specifies to which **Ensemble** each **Cell** belongs |
-| **Feature Attribute Array** | AvgCAxes | float | (3) | The direction of the **Feature's** C-axis in the sample reference frame |
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
+% Auto generated parameter table will be inserted here
-## Created Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | FeatureReferenceCAxisMisorientations | float | (1) | Misorientation angle (in degrees) between **Cell's** C-axis and the C-axis of the **Feature** that owns that **Cell** |
-| **Feature Attribute Array** | FeatureAvgCAxisMisorientations | float | (1) | Average of the *FeatureReferenceCAxisMisorientation* values for all of the **Cells** that belong to the **Feature** |
-| **Feature Attribute Array** | FeatureStdevCAxisMisorientations | float | (1) | Standard deviation of the *FeatureReferenceCAxisMisorientation* values for all of the **Cells** that belong to the **Feature** |
-
-
-## Example Pipelines
+## Example Pipelines
Combo-EBSD-osc_r0c0
-## License & Copyright
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/FindFeatureReferenceMisorientationsFilter.md b/src/Plugins/OrientationAnalysis/docs/FindFeatureReferenceMisorientationsFilter.md
index f419420a3c..f5201ade16 100644
--- a/src/Plugins/OrientationAnalysis/docs/FindFeatureReferenceMisorientationsFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/FindFeatureReferenceMisorientationsFilter.md
@@ -1,55 +1,25 @@
-# Find Feature Reference Misorientations
+# Find Feature Reference Misorientations
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Statistics (Crystallographic)
-## Description ##
+## Description
This **Filter** calculates the misorientation angle between each **Cell** within a **Feature** and a *reference orientation* for that **Feature**. The user can choose the *reference orientation* to be used for the **Features** from a drop-down menu. The options for the *reference orientation* are the average orientation of the **Feature** or the orientation of the **Cell** that is furthest from the *boundary* of the **Feature**.
Note: the average orientation of the **Feature** is a typical choice, but if the **Feature** has undergone plastic deformation and the amount of lattice rotation developed is of interest, then it may be more reasonable to use the orientation *near the center* of the **Feature** as it may not have rotated and thus serve as a better *reference orientation*.
-## Parameters ##
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Reference Orientation | Enumeration | Specifies the *reference orientation* to use when comparing to each **Cell** |
-
-## Required Geometry ##
-
-Image
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Cell** belongs |
-| **Cell Attribute Array** | Phases | int32_t | (1) | Specifies to which **Ensemble** each **Cell** belongs |
-| **Cell Attribute Array** | Quats | float | (4) | Specifies the orientation of the **Cell** in quaternion representation |
-| **Feature Attribute Array** | AvgQuats | float | (4) | Specifies the average orientation of the **Feature** in quaternion representation (, w). Only required if the *reference orientation* is selected to be the average of the **Feature** |
-| **Cell Attribute Array** | GBEuclideanDistances | float | (1) | Distance the **Cells** are from the *boundary* of the **Feature** they belong to. Only required if the *reference orientation* is selected to be the orientation at the **Feature** centroid |
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
+% Auto generated parameter table will be inserted here
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | FeatureReferenceMisorientations | float | (1) | Misorientation angle (in degrees) between **Cell's** orientation and the reference orientation of the **Feature** that owns that **Cell** |
-| **Feature Attribute Array** | FeatureAvgMisorientations | float | (1) | Average of the *FeatureReferenceMisorientation* values for all of the **Cells** that belong to the **Feature** |
-
-
-## Example Pipelines ##
+## Example Pipelines
+ (05) SmallIN100 Crystallographic Statistics
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/FindGBCDFilter.md b/src/Plugins/OrientationAnalysis/docs/FindGBCDFilter.md
index 253efd61c4..d7e5be75b7 100644
--- a/src/Plugins/OrientationAnalysis/docs/FindGBCDFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/FindGBCDFilter.md
@@ -1,57 +1,23 @@
-# Find GBCD
+# Find GBCD
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Statistics (Crystallographic)
-## Description ##
+## Description
This **Filter** computes the 5D grain boundary character distribution (GBCD) for a **Triangle Geometry**, which is the relative area of grain boundary for a given misorientation and normal. The GBCD can be visualized by using either the **Write GBCD Pole Figure (GMT)** or the **Write GBCD Pole Figure (VTK)** **Filters**.
-## Parameters ##
-
-| Name | Type | Description |
-|------|------| ----------- |
-| GBCD Resolution (Degrees) | float | The resolution in degrees for the GBCD calculation |
-
-## Required Geometry ##
-
-Image + Triangle
-
-## Required Objects (From Triangle Geometry) ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Face Attribute Array** | FaceLabels | int32_t | (2) | Specifies which **Features** are on either side of each **Face** |
-| **Face Attribute Array** | FaceNormals | double | (3) | Specifies the normal of each **Face** |
-| **Face Attribute Array** | FaceAreas | double | (1) | Specifies the area of each **Face** |
-
-## Required Objects (From Image Geometry) ##
+% Auto generated parameter table will be inserted here
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | AvgEulerAngles | float | (3) | Three angles defining the orientation of the **Feature** in Bunge convention (Z-X-Z) |
-| **Feature Attribute Array** | Phases | int32_t | (1) | Specifies to which phase each **Feature** belongs |
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Ensemble Attribute Array** | GBDC | Double | (n,m,l,o,q,r) | 5 parameter GBCD data. The 6th component is used internally to track the northern vs. southern hemisphere of the Lambert sphere |
-
-
-## Example Pipelines ##
+## Example Pipelines
+ (04) SmallIN100 GBCD
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/FindGBCDMetricBasedFilter.md b/src/Plugins/OrientationAnalysis/docs/FindGBCDMetricBasedFilter.md
index 53c5a852af..8ad3ff6fd9 100644
--- a/src/Plugins/OrientationAnalysis/docs/FindGBCDMetricBasedFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/FindGBCDMetricBasedFilter.md
@@ -1,24 +1,22 @@
-# Find GBCD (Metric-Based Approach)
+# Find GBCD (Metric-Based Approach)
-
-## Group (Subgroup)
+## Group (Subgroup)
Statistics (Crystallographic)
-## Description
+## Description
This **Filter** computes a section through the five-dimensional grain boundary distirbution for a fixed misorientation. An example of such a section is shown in Fig. 1. Differently than **Find GBCD Filter**, which uses a method based on partition of the boundary space into bins, this **Filter** implements an alternative metric-based approach described by K. Glowinski and A. Morawiec in [Analysis of experimental grain boundary distributions based on boundary-space metrics, Metall. Mater. Trans. A 45, 3189-3194 (2014)](https://link.springer.com/article/10.1007/s11661-014-2325-y)
![Fig. 1: Section for the 17.9 deg./[111] misorientation through the grain boundary distribution obtained using this Filter for the small IN100 data set. Units are multiples of random distribution (MRDs).](Images/FindGBCDMetricBased_dist.png)
-Metrics in the boundary space can be defined in a number of ways, but it is essential that two boundaries are close (distant) if they have similar (different) geometric features, and that symmetrically equivalent representations of boundaries are taken into consideration. Formally, the boundary space is a Cartesian product of the misorientation and boundary-normal subspaces. For computational reasons and because of considerably different resolutions in determinination of grain misorientation and boundary-plane parameters, it is convenient to use a separate metric in each subspace. With separate metrics, the procedure for computing distribution values for a selected misorientation has two stages. First, boundary segments with misorientations located not farther from the fixed misorientation than a limiting distance ρm are selected. In the second stage, the distribution is probed at evenly distributed normal directions (see Fig. 2), and areas of boundaries whose normals deviate from a given direction by less than ρp are summed. (The radii ρm and ρp should be tailored to resolution, amount, and quality of data and set.) Eventually, the obtained distribution is normalized in order to express it in the conventional units, i.e., multiples of the random distribution.
+Metrics in the boundary space can be defined in a number of ways, but it is essential that two boundaries are close (distant) if they have similar (different) geometric features, and that symmetrically equivalent representations of boundaries are taken into consideration. Formally, the boundary space is a Cartesian product of the misorientation and boundary-normal subspaces. For computational reasons and because of considerably different resolutions in determinination of grain misorientation and boundary-plane parameters, it is convenient to use a separate metric in each subspace. With separate metrics, the procedure for computing distribution values for a selected misorientation has two stages. First, boundary segments with misorientations located not farther from the fixed misorientation than a limiting distance ρm are selected. In the second stage, the distribution is probed at evenly distributed normal directions (see Fig. 2), and areas of boundaries whose normals deviate from a given direction by less than ρp are summed. (The radii ρm and ρp should be tailored to resolution, amount, and quality of data and set.) Eventually, the obtained distribution is normalized in order to express it in the conventional units, i.e., multiples of the random distribution.
| Image |
|-------|
| ![](Images/FindGBCDMetricBased_samplpts.png)|
|Fig. 2: End-points (drawn in stereographic projection) of sampling directions used for probing distribution values; the number of points here is about 1500. Additionally, distributions are probed at points lying at the equator (marked with red); this is helpful for some plotting software.|
-
This **Filter** also calculates statistical errors of the distributions using the formula
ε = ( *f* *n* *v* )1/2
@@ -30,9 +28,7 @@ where ε is the relative error of the distribution function at a given po
| ![](Images/FindGBCDMetricBased_err2.png)|
|![Fig. 3: (a) Errors (absolute values of one standard deviation) corresponding to the distribution shown in Fig. 1. Levels are given in MRDs. (b) Relative errors (given in %) of the distribution from Fig. 1.](Images/FindGBCDMetricBased_err2.png)|
-
-
-## Format of Output Files
+## Format of Output Files
Output files are formatted to be readable by GMT plotting program. The first line contains the fixed misorientation axis and angle. Each of the remaining lines contains three numbers. The first two columns are angles (in degrees) describing a given sampling direction; let us denote them *col*1 and *col*2, respectively. The third column is either the value of the GBCD (in MRD) for that direction or its error (in MRD or %, depending on user's selection). If you use other software, you can retrive spherical angles θ and φ of the sampling directions in the following way:
@@ -42,56 +38,26 @@ Output files are formatted to be readable by GMT plotting program. The first lin
Then, the directions are given as [ sin θ × cos φ , sin θ × sin φ , cos θ ].
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| Phase of Interest | int32_t | Index of the **Ensemble** for which to compute GBCD; boundaries having grains of this phase on both its sides will only be taken into account |
-| Fixed Misorientation | float (4x) | Axis-angle representation of the misorientation of interest. Angle value should be in degrees. |
-| Limiting Distances | float | ρm and ρp as defined above |
-| Number of Sampling Points | int32_t | The **approximate** number of sampling directions |
-| Exclude Triangles Directly Neighboring Triple Lines | bool | If checked, only interiors of **Faces** are included in GBCD |
-| Output Distribution File | File Path | The output file path (extension .dat, GMT format) |
-| Output Distribution Errors File | File Path | The output file path (extension .dat, GMT format) |
-| Save Relative Errors Instead of Their Absolute Values | bool | What type of errors to save (see above description for more detail) |
-
-## Required Geometry
-Image + Triangle
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|-------|--------------|-------------|---------|-----|
-| **Vertex Attribute Array** | NodeTypes | int8_t | (1) | Specifies the type of node in the Geometry
-| **Face Attribute Array** | FaceLabels | int32_t | (2) | Specifies which **Features** are on either side of each **Face** |
-| **Face Attribute Array** | FaceNormals | double | (3) | Specifies the normal of each **Face** |
-| **Face Attribute Array** | FaceAreas | double | (1) | Specifies the area of each **Face** |
-| **Feature Attribute Array** | FaceLabels | int32_t | (2) | Specifies which *original* **Features** are on either side of each boundary **Feature** |
-| **Feature Attribute Array** | AvgEulerAngles | float | (3) | Three angles defining the orientation of the **Feature** in Bunge convention (Z-X-Z) |
-| **Feature Attribute Array** | Phases | int32_t | (1) | Specifies to which phase each **Feature** belongs |
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
-
-## Feedback
+## Feedback
In the case of any questions, suggestions, bugs, etc., please feel free to email the author of this **Filter** at kglowinski *at* ymail.com
+% Auto generated parameter table will be inserted here
-## References
+## References
-[1] K. Glowinski and A. Morawiec, Analysis of experimental grain boundary distributions based on boundary-space metrics, Metall. Mater. Trans. A 45, 3189-3194 (2014)
+[1] K. Glowinski and A. Morawiec, Analysis of experimental grain boundary distributions based on boundary-space metrics, Metall. Mater. Trans. A 45, 3189-3194 (2014)
-## Example Pipelines
+## Example Pipelines
`(05) SmallIN100 GBCD Metric.d3dpipeline`
This pipeline depends on previous pipelines in the Small IN100 reconstruction pipeline series.
-## License & Copyright
+## License & Copyright
Please see the description file distributed with this **Plugin**.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/FindGBPDMetricBasedFilter.md b/src/Plugins/OrientationAnalysis/docs/FindGBPDMetricBasedFilter.md
index ae0253dbce..72134d7388 100644
--- a/src/Plugins/OrientationAnalysis/docs/FindGBPDMetricBasedFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/FindGBPDMetricBasedFilter.md
@@ -1,13 +1,12 @@
-# Find GBPD (Metric-Based Approach)
+# Find GBPD (Metric-Based Approach)
-
-## Group (Subgroup)
+## Group (Subgroup)
Statistics (Crystallographic)
-## Description
+## Description
-This **Filter** computes the grain boundary plane distribution (GBPD) like that shown in Fig. 1. It should be noted that most GBPDs presented so far in literature were obtained using a method based on partition of the grain boundary space into bins, similar to that implemented in the *Find GBCD* **Filter**. This **Filter** calculates the GBPD using an alternative approach adapted from the one included in the *Find GBCD (Metric-based Approach)* **Filter** and described by K. Glowinski and A. Morawiec in [Analysis of experimental grain boundary distributions based on boundary-space metrics, Metall. Mater. Trans. A 45, 3189-3194 (2014)](http://link.springer.com/article/10.1007%2Fs11661-014-2325-y). Briefly, the GBPD is probed at evenly distributed sampling directions (similarly to *Find GBCD (Metric-based Approach)* **Filter**) and areas of mesh segments with their normal vectors deviated by less than a limiting angle ρp from a given direction are summed. If *n*S is the number of crystal symmetry transformations, each boundary plane segment is represented by up to 4 × *n*S equivalent vectors, and all of them are processed. It is enough to sample the distribution at directions corresponding to the standard stereographic triangle (or, in general, to a fundamental region corresponding to a considered crystallographic point group); values at remaining points are obtained based on crystal symmetries. After summing the boundary areas, the distribution is normalized. First, the values at sampling vectors are divided by the total area of all segments. Then, in order to express the distribution in the conventional units, i.e., multiples of random distribution (MRDs), the obtained fractional values are divided by the volume *v* = (*A* nS) / (4π), where *A* is the area of a spherical cap determined by ρp.
+This **Filter** computes the grain boundary plane distribution (GBPD) like that shown in Fig. 1. It should be noted that most GBPDs presented so far in literature were obtained using a method based on partition of the grain boundary space into bins, similar to that implemented in the *Find GBCD* **Filter**. This **Filter** calculates the GBPD using an alternative approach adapted from the one included in the *Find GBCD (Metric-based Approach)* **Filter** and described by K. Glowinski and A. Morawiec in [Analysis of experimental grain boundary distributions based on boundary-space metrics, Metall. Mater. Trans. A 45, 3189-3194 (2014)](http://link.springer.com/article/10.1007%2Fs11661-014-2325-y). Briefly, the GBPD is probed at evenly distributed sampling directions (similarly to *Find GBCD (Metric-based Approach)* **Filter**) and areas of mesh segments with their normal vectors deviated by less than a limiting angle ρp from a given direction are summed. If *n*S is the number of crystal symmetry transformations, each boundary plane segment is represented by up to 4 × *n*S equivalent vectors, and all of them are processed. It is enough to sample the distribution at directions corresponding to the standard stereographic triangle (or, in general, to a fundamental region corresponding to a considered crystallographic point group); values at remaining points are obtained based on crystal symmetries. After summing the boundary areas, the distribution is normalized. First, the values at sampling vectors are divided by the total area of all segments. Then, in order to express the distribution in the conventional units, i.e., multiples of random distribution (MRDs), the obtained fractional values are divided by the volume *v* = (*A* nS) / (4π), where *A* is the area of a spherical cap determined by ρp.
![Fig. 1: GBPD obtained for Small IN100 with the limiting distance set to 7° and with triangles adjacent to triple lines removed. Units are MRDs.](Images/FindGBPDMetricBased_example.png)
@@ -17,38 +16,10 @@ This **Filter** also calculates statistical errors of the distributions using th
is the relative error of the distribution function at a given point, *f* is the value of the function at that point, and *n* stands for the number of grain boundaries (**not** the number of mesh triangles) in the considered network. The errors can be calculated either as their absolute values, i.e., ε × *f* or as relative errors, i.e., 100% × ε. The latter are computed in a way that if the relative error exceeds 100%, it is rounded down to 100%.
-See also the documentation for [Find GBCD (Metric-based Approach)](../FindGBCDMetricBasedFilter/index.html) **Filter** for additional information.
-
-## Parameters
-
-| Name | Type | Description |
-|------|------|-------------|
-| Phase of Interest | int32_t | Index of the **Ensemble** for which to compute GBPD; boundaries having grains of this phase on both its sides will only be taken into account |
-| Limiting Distance | float | ρp as defined above |
-| Number of Sampling Points | int32_t | The **approximate** number of sampling directions |
-| Exclude Triangles Directly Neighboring Triple Lines | bool | Only interiors of **Faces** are included in GBPD |
-| Output Distribution File | File Path | The output file path (extension .dat, GMT format) |
-| Output Distribution Errors File | File Path | The output file path (extension .dat, GMT format) |
-| Save Relative Errors Instead of Their Absolute Values | bool | What type of errors to save (see above description for more detail) |
-
-## Required Geometry
-
-Image + Triangle
+See also the documentation for {ref}`Find GBCD (Metric-based Approach) Filter ` for additional information.
-## Required Objects
-| Kind | Default Name | Type | Component Dimensions | Description |
-|-------|--------------|-------------|---------|-----|
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
-| **Feature Attribute Array** | AvgEulerAngles | float | (3) | Three angles defining the orientation of the **Feature** in Bunge convention (Z-X-Z) |
-| **Feature Attribute Array** | Phases | int32_t | (1) | Specifies to which phase each **Feature** belongs |
-| **Face Attribute Array** | FaceLabels | int32_t | (2) | Specifies which **Features** are on either side of each **Face** |
-| **Face Attribute Array** | FaceNormals | double | (3) | Specifies the normal of each **Face** |
-| **Face Attribute Array** | FaceAreas | double | (1) | Specifies the area of each **Face** |
-| **Feature Face Attribute Array** | FaceLabels | int32_t | (2) | Specifies to which phase each **Face Feature** belongs |
-| **Vertex Attribute Array** | NodeTypes | int8_t | (1) | Specifies the type of node in the Geometry
-
-## Format of Output Files ##
+## Format of Output Files
Output files are formatted to be readable by GMT plotting program. The first line is always "0.0 0.0 0.0 0.0". Each of the remaining lines contains three numbers. The first two columns are angles (in degrees) describing a given sampling direction; let us denote them *col*1 and *col*2, respectively. The third column is either the value of the GBCD (in MRD) for that direction or its error (in MRD or %, depending on user's selection). If you use other software, you can retrive spherical angles θ and φ of the sampling directions in the following way:
@@ -58,24 +29,21 @@ Output files are formatted to be readable by GMT plotting program. The first lin
Then, the directions are given as [ sin θ × cos φ , sin θ × sin φ , cos θ ].
-## Feedback
+## Feedback
In the case of any questions, suggestions, bugs, etc., please feel free to email the author of this **Filter** at kglowinski *at* ymail.com
+% Auto generated parameter table will be inserted here
-## References
-
-[1] K. Glowinski and A. Morawiec, Analysis of experimental grain boundary distributions based on boundary-space metrics, Metall. Mater. Trans. A 45, 3189-3194 (2014)
-
-## Example Pipelines
+## References
+[1] K. Glowinski and A. Morawiec, Analysis of experimental grain boundary distributions based on boundary-space metrics, Metall. Mater. Trans. A 45, 3189-3194 (2014)
+## Example Pipelines
-## License & Copyright
+## License & Copyright
Please see the description file distributed with this **Plugin**.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/FindKernelAvgMisorientationsFilter.md b/src/Plugins/OrientationAnalysis/docs/FindKernelAvgMisorientationsFilter.md
index 3d2881e278..13d33f12be 100644
--- a/src/Plugins/OrientationAnalysis/docs/FindKernelAvgMisorientationsFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/FindKernelAvgMisorientationsFilter.md
@@ -1,10 +1,10 @@
# Find Kernel Average Misorientations
-## Group (Subgroup) ##
+## Group (Subgroup)
Statistics (Crystallographic)
-## Description ##
+## Description
This **Filter** determines the Kernel Average Misorientation (KAM) for each **Cell**. The user can select the size of the kernel to be used in the calculation. The kernel size entered by the user is the *radius* of the kernel (i.e., entering values of *1*, *2*, *3* will result in a kernel that is *3*, *5*, and *7* **Cells** in size in the X, Y and Z directions, respectively). The algorithm for determination of KAM is as follows:
@@ -13,42 +13,17 @@ This **Filter** determines the Kernel Average Misorientation (KAM) for each **Ce
*Note:* All **Cells** in the kernel are weighted equally during the averaging, though they are not equidistant from the central **Cell**.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------|------| ----------- |
-| Kernel Radius | int32_t (3x) | Size of the kernel in the X, Y and Z directions (in number of **Cells**) |
-
-## Required Geometry ##
-
-Image
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Cell** belongs |
-| **Cell Attribute Array** | Phases | int32_t | (1) | Specifies to which **Ensemble** each **Cell** belongs |
-| **Cell Attribute Array** | Quats | float | (4) | Specifies the orientation of the **Cell** in quaternion representation |
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | KernelAverageMisorientations | float | (1) | Average misorientation (in Degrees) for all **Cells** within the kernel and the central **Cell** |
-
-## Example Pipelines ##
+## Example Pipelines
+ MassifPipeline
+ (05) SmallIN100 Crystallographic Statistics
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/FindMisorientationsFilter.md b/src/Plugins/OrientationAnalysis/docs/FindMisorientationsFilter.md
index 93d1d6ed1d..a2cfa2b46a 100644
--- a/src/Plugins/OrientationAnalysis/docs/FindMisorientationsFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/FindMisorientationsFilter.md
@@ -1,57 +1,29 @@
-# Find Feature Neighbor Misorientations
+# Find Feature Neighbor Misorientations
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Statistics (Crystallographic)
-## Description ##
+## Description
This **Filter** determines, for each **Feature**, the misorientations with each of the **Features** that are in contact with it. The misorientations are stored as a list (for each **Feature**) of angles (in degrees). The axis of the misorientation is not stored by this **Filter**.
The user can also calculate the average misorientation between the feature and all contacting features.
-### Notes ###
-
-__NOTE:__ Only features with identical crystal structures will be calculated. If two features have different crystal structures then a value of NaN is set for the misorientation.
-
-## Parameters ##
-
-| Name | Type | Description |
-|------|------|-------------|
-| Find Average Misorientation Per Feature | bool | Specifies if the *average* of the misorienations with the neighboring **Features** should be stored for each **Feature** |
-
-## Required Geometry ##
-
-Not Applicable
+### Notes
-## Required Objects ##
+**NOTE:** Only features with identical crystal structures will be calculated. If two features have different crystal structures then a value of NaN is set for the misorientation.
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | NeighborLists | List of int32_t | (1) | List of the contiguous neighboring **Features** for a given **Feature** |
-| **Feature Attribute Array** | AvgQuats | float | (4) | Defines the average orientation of the **Feature** in quaternion representation |
-| **Feature Attribute Array** | Phases | int32_t | (1) | Specifies to which **Ensemble** each **Feature** belongs |
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
+% Auto generated parameter table will be inserted here
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | MisorientationLists | List of float | (1) | List of the misorientation angles with the contiguous neighboring **Features** for a given **Feature** |
-| **Feature Attribute Array** | AvgMisorientation | float | (1) | Number weighted average of neighbor misorientations. Only created if *Find Average Misorientation Per Feature* is checked |
-
-
-## Example Pipelines ##
+## Example Pipelines
+ (05) SmallIN100 Crystallographic Statistics
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/FindSchmidsFilter.md b/src/Plugins/OrientationAnalysis/docs/FindSchmidsFilter.md
index fa3a51e47e..7500f03888 100644
--- a/src/Plugins/OrientationAnalysis/docs/FindSchmidsFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/FindSchmidsFilter.md
@@ -1,63 +1,29 @@
-# Find Schmid Factors
+# Find Schmid Factors
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Statistics (Crystallographic)
-## Description ##
+## Description
This **Filter** calculates the Schmid factor of each **Feature** given its average orientation and a user defined loading axis. The Schmid Factor is the combination of the component of the axial force *F* that lies parallel to the slip direction and the component that lies perpendicular to the slip plane. The equation for the Schmid Factor is given as:
Schmid Factor = (cos φ cos λ)
*The angle φ is the angle between the tensile axis and the slip plane normal, and λ is the angle between the tensile axis and the slip direction in the slip plane.*
-
-The **Filter** determines the Schmid factor for each **Feature** by using the above equation for all possible slip systems (given the **Feature's** crystal structure). The largest Schmid factor from all of the slip systems is stored for the **Feature**. Only the Schmid factor is used in determining which slip system's Schmid factor to report. The critical resolved shear stress for the different slip systems is not considered.
-
-## Parameters ##
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Loading Direction | float (3x) | The loading axis for the sample |
-| Store Angle Components of Schmid Factor | bool | Whether to store the φ and λ for each **Feature** |
-| Override Default Slip System | bool | Allows the user to manually input the slip plane and slip direction |
-| Slip Plane | float (3x) | Vector defining the slip plane normal. Only needed if *Override Default Slip System* is checked |
-| Slip Direction | float (3x) | Vector defining the slip direction. Only needed if *Override Default Slip System* is checked |
-
-## Required Geometry ##
-
-Not Applicable
-## Required Objects ##
+The **Filter** determines the Schmid factor for each **Feature** by using the above equation for all possible slip systems (given the **Feature's** crystal structure). The largest Schmid factor from all of the slip systems is stored for the **Feature**. Only the Schmid factor is used in determining which slip system's Schmid factor to report. The critical resolved shear stress for the different slip systems is not considered.
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | Phases | int32_t | (1) | Specifies to which **Ensemble** each **Feature** belongs |
-| **Feature Attribute Array** | AvgQuats | float | (4) | Specifies the average orienation of each **Feature** in quaternion representation |
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
+% Auto generated parameter table will be inserted here
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | Schmids | Float | (1) | Value of the Schmid factor for the most favorably oriented slip system (i.e., the one with the highest Schmid factor) |
-| **Feature Attribute Array** | SlipSystems | Int | (1) | Enumeration of the slip system that has the highest Schmid factor |
-| **Feature Attribute Array** | Poles | Ints | (3) | Specifies the crystallographic pole that points along the user defined loading direction |
-| **Feature Attribute Array** | SchmidPhis | Float | (1) | Angle between tensile axis and slip plane normal. Only created if *Store Angle Components of Schmid Factor* is checked |
-| **Feature Attribute Array** | SchmidLambdas | Float | (1) | Angle between tensile axis and splid drirection. Only created if *Store Angle Components of Schmid Factor* is checked |
-
-
-## Example Pipelines ##
+## Example Pipelines
+ (05) SmallIN100 Crystallographic Statistics
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/FindShapesFilter.md b/src/Plugins/OrientationAnalysis/docs/FindShapesFilter.md
index 035c4fd41e..493c7a267e 100644
--- a/src/Plugins/OrientationAnalysis/docs/FindShapesFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/FindShapesFilter.md
@@ -1,11 +1,10 @@
-# Find Feature Shapes
+# Find Feature Shapes
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Statistics (Morphological)
-## Description ##
+## Description
This **Filter** calculates the second-order moments of each **Feature** in order to determine the *principal axis lengths, principal axis directions, aspect ratios and moment invariant Omega3s*. The *principal axis lengths* are those of a "best-fit" ellipsoid. The algorithm for determining the moments and these values is as follows:
@@ -18,33 +17,9 @@ This **Filter** calculates the second-order moments of each **Feature** in order
7. Determine the Euler angles required to represent the *principal axis directions* in the *sample reference frame* and store them as the **Feature**'s *Axis Euler Angles*.
8. Calculate the moment variant Omega3 as definied in [2] and is discussed further in [1] and [3]
-## Parameters ##
-
-None
-
-## Required Geometry ##
-
-Image
-
-## Required Objects ##
+% Auto generated parameter table will be inserted here
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Cell** belongs |
-| **Feature Attribute Array** | Centroids | float | (3) | X, Y, Z coordinates of **Feature** center of mass |
-| **Attribute Matrix** | CellFeatureData | Cell Feature | N/A | **Feature Attribute Matrix** of the selected *Feature Ids* |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | AspectRatios | float | (2) | Ratio of semi-axis lengths (b/a and c/a) for best-fit ellipsoid to **Feature** |
-| **Feature Attribute Array** | AxisEulerAngles | float | (3) | Euler angles (in radians) necessary to rotate the sample reference frame to the reference frame of the **Feature**, where the prinicpal axes of the best-fit ellipsoid are (X, Y, Z) |
-| **Feature Attribute Array** | SemiAxisLengths | float | (3) | Semi-axis lengths (a, b, c) for best-fit ellipsoid to **Feature** |
-| **Feature Attribute Array** | Omega3s | float | (1) | 3rd invariant of the second-order moment matrix for the **Feature**, does not assume a shape type (i.e., ellipsoid) |
-| **Feature Attribute Array** | Volumes | float | (1) | The volume of each **Feature** |
-
-## References ##
+## References ##
[1] Representation and Reconstruction of Three-dimensional Microstructures in Ni-based Superalloys, AFOSR FA9550-07-1-0179 Final Report, 20 Dec 2010.
@@ -52,19 +27,17 @@ Image
[3] n-Dimensional Moment Invariants and Conceptual Mathematical Theory of Recognition n-Dimensional Solids, Alexander G. Mamistvalov, IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE, VOL. 20, NO. 8, AUGUST 1998, p. 819-831.
-[4] M. Groeber, M. Uchic, D. Dimiduk, and S. Ghosh. A Framework for Automated Analysis and Simulation of 3D Polycrystalline Microstructures, Part 1: Statistical Characterization Acta Materialia, 56 (2008), 1257-1273.
+[4] M. Groeber, M. Uchic, D. Dimiduk, and S. Ghosh. A Framework for Automated Analysis and Simulation of 3D Polycrystalline Microstructures, Part 1: Statistical Characterization Acta Materialia, 56 (2008), 1257-1273.
-## Example Pipelines ##
+## Example Pipelines
+ (01) SmallIN100 Morphological Statistics
+ (06) SmallIN100 Synthetic
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/FindSlipTransmissionMetricsFilter.md b/src/Plugins/OrientationAnalysis/docs/FindSlipTransmissionMetricsFilter.md
index a0c805a03e..cfbaf5453c 100644
--- a/src/Plugins/OrientationAnalysis/docs/FindSlipTransmissionMetricsFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/FindSlipTransmissionMetricsFilter.md
@@ -1,10 +1,10 @@
-# Find Neighbor Slip Transmission Metrics #
+# Find Neighbor Slip Transmission Metrics
-## Group (Subgroup) ##
+## Group (Subgroup)
Statistics (Crystallographic)
-## Description ##
+## Description
This **Filter** calculates a suite of *slip transmission metrics* that are related to the alignment of slip directions and planes across **Feature** boundaries. The algorithm for calculation of these metrics is as follows:
@@ -17,40 +17,14 @@ This **Filter** calculates a suite of *slip transmission metrics* that are relat
*Note:* The transmission metrics are calculated using the average orientations for neighboring **Features** and not the local orientation near the boundary. Also, the metrics are calculated twice (i.e., when **Feature** 1 has neighbor **Feature** 2 and when **Feature** 2 has neighbor **Feature** 1) because the direction across the boundary between the **Features** affects the value of the metric.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-None
+## Example Pipelines
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | NeighborList | List of int32 | (1) | List of the contiguous neighboring **Features** for a given **Feature** |
-| **Feature Attribute Array** | AvgQuats | float32 | (4) | Specifies the average orienation of each **Feature** in quaternion representation |
-| **Feature Attribute Array** | Phases | int32 | (1) | Specifies to which **Ensemble** each **Feature** belongs |
-| **Ensemble Attribute Array** | CrystalStructures | uint32 | (1) | Enumeration representing the crystal structure for each **Ensemble** |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | F1s | float32 | (2) | |
-| **Feature Attribute Array** | F1spts | float32 | (2) | |
-| **Feature Attribute Array** | F7s | float32 | (2) | |
-| **Feature Attribute Array** | mPrimes | float32 | (2) | |
-
-## Example Pipelines ##
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/FindTriangleGeomShapesFilter.md b/src/Plugins/OrientationAnalysis/docs/FindTriangleGeomShapesFilter.md
index 5a505cff14..78e160bdb8 100644
--- a/src/Plugins/OrientationAnalysis/docs/FindTriangleGeomShapesFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/FindTriangleGeomShapesFilter.md
@@ -1,10 +1,10 @@
# Find Feature Shapes from Triangle Geometry
-## Group (Subgroup) ##
+## Group (Subgroup)
Statistics (Morphological)
-## Description ##
+## Description
This **Filter** calculates the second-order moments of each enclosed **Feature** in a **Triangle Geometry**. The
second-order moments allow for the determination of the *principal axis lengths, principal axis directions, aspect
@@ -30,33 +30,9 @@ for determining the moments and these values is as follows:
represented, resulting in inaccurate Omega3 values. This problem is especially apparent for perfect rectangular prisms,
but any shape with clear sharp corners may be affected.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-None
-
-## Required Geometry ##
-
-Triangle
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|-----------------------------|-----------------|--------------|----------------------|--------------------------------------------------------------------|
-| **Face Attribute Array** | FaceLabels | int32_t | (2) | Specifies which **Features** are on either side of each **Face** |
-| **Feature Attribute Array** | Centroids | float | (3) | Coordinates of the center of mass for a given enclosed **Feature** |
-| **Feature Attribute Array** | Volumes | float | (1) | Volume of the enclosed **Feature** |
-| **Attribute Matrix** | FaceFeatureData | Face Feature | N/A | **Feature Attribute Matrix** of the selected _Face Labels |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|-----------------------------|-----------------|-------|----------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| **Feature Attribute Array** | AspectRatios | float | (2) | Ratio of axis lengths (b/a and c/a) for best-fit ellipsoid to enclosed **Feature** |
-| **Feature Attribute Array** | AxisEulerAngles | float | (3) | Euler angles (in radians) necessary to rotate the sample reference frame to the reference frame of the enclosed **Feature**, where the principal axes of the best-fit ellipsoid are (X, Y, Z) |
-| **Feature Attribute Array** | AxisLengths | float | (3) | Axis lengths (a, b, c) for best-fit ellipsoid to enclosed **Feature** |
-| **Feature Attribute Array** | Omega3s | float | (1) | 3rd invariant of the second-order moment matrix for the enclosed **Feature**, does not assume a shape type (i.e., ellipsoid) |
-
-## References ##
+## References ##
[1] Representation and Reconstruction of Three-dimensional Microstructures in Ni-based Superalloys, AFOSR
FA9550-07-1-0179 Final Report, 20 Dec 2010.
@@ -70,14 +46,12 @@ Mamistvalov, IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE, VOL
[4] M. Groeber, M. Uchic, D. Dimiduk, and S. Ghosh. A Framework for Automated Analysis and Simulation of 3D
Polycrystalline Microstructures, Part 1: Statistical Characterization Acta Materialia, 56 (2008), 1257-1273.
-## Example Pipelines ##
+## Example Pipelines
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/GenerateFZQuaternions.md b/src/Plugins/OrientationAnalysis/docs/GenerateFZQuaternions.md
index f7f7372193..05fe3e61ca 100644
--- a/src/Plugins/OrientationAnalysis/docs/GenerateFZQuaternions.md
+++ b/src/Plugins/OrientationAnalysis/docs/GenerateFZQuaternions.md
@@ -1,17 +1,15 @@
-# GenerateFZQuaternions
+# GenerateFZQuaternions
-
-## Group (Subgroup) ##
+## Group (Subgroup)
OrientationAnalysis (OrientationAnalysis)
-## Description ##
+## Description
This **Filter** reduces input orientations (Quaternions) into the fundamental zone for the given Laue group.
The following figures represent a BCC Interstitial steel EBSD data set courtesy of [1].
-
| | |
|----|----|
| ![ ](Images/ReadH5Ebsd_Right.png) | ![ ](Images/Cubic_m3m_IPFLegend.png) |
@@ -19,28 +17,7 @@ The following figures represent a BCC Interstitial steel EBSD data set courtesy
| ![ ](Images/GenerateFZQuats_1.png) | ![ ](Images/GenerateFZQuats_2.png) |
| EBSD Dataset **before** the filter. IPF Colors are using a reference direction of < 001 >. The data is visualized in the 3D stereographic unit spheres with a superimposed Rodrigues Fundamental Zone. | EBSD Dataset **after** the filter. IPF Colors are using a reference direction of < 001 >. The data is visualized in the 3D stereographic unit spheres with a superimposed Rodrigues Fundamental Zone. |
-
-## Parameters ##
-
-| Name | Type | Description |
-|------|------|------|
-| Apply to Good Elements Only (Bad Elements Will Be Black) | bool | Whether to assign a black color to "bad" **Elements** |
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|-----|
-| **Element Attribute Array** | Quaternions | float | (4) | Quaternions ordered as (< x, y, z >, w) |
-| **Element Attribute Array** | Phases | int32_t | (1) | Phase Id specifying the phase of the **Element** |
-| **Element Attribute Array** | Mask | bool | (1) | Used to define **Elements** as *good* or *bad*. Only required if _Apply to Good Elements Only (Bad Elements Will Be Black)_ is checked |
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble**. |
-
-
-**Crystal Structure Table**
+### Crystal Structure Table
| String Name | Internal Value | Laue Name |
| ------------|----------------|----------|
@@ -57,29 +34,19 @@ Not Applicable
| Trigonal_High | 10 | Trigonal-High -3m |
| UnknownCrystalStructure | 999 | Undefined Crystal Structure |
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|-----|
-| **Element Attribute Array** | FZ Quaternions | float | (4) | The Quaternion that represents an orientation within the fundamental zone for each **Element** |
-
-## References ##
+% Auto generated parameter table will be inserted here
-[1]: N. Allain-Bonasso, F. Wagner, S. Berbenni, D.P. Field, A study of the heterogeneity of plastic deformation in IF steel by EBSD, Materials Science and Engineering: A, Volume 548, 30 June 2012, Pages 56-63, ISSN 0921-5093, http://dx.doi.org/10.1016/j.msea.2012.03.068.
-(http://www.sciencedirect.com/science/article/pii/S0921509312004388)
+## References
-[2]: http://reference.iucr.org/dictionary/Laue_classes
+[1]: N. Allain-Bonasso, F. Wagner, S. Berbenni, D.P. Field, A study of the heterogeneity of plastic deformation in IF steel by EBSD, Materials Science and Engineering: A, Volume 548, 30 June 2012, Pages 56-63, ISSN 0921-5093, .
+()
-## Example Pipelines ##
+## Example Pipelines
-
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/GenerateFaceIPFColoringFilter.md b/src/Plugins/OrientationAnalysis/docs/GenerateFaceIPFColoringFilter.md
index e0d12a23d4..f421cb4449 100644
--- a/src/Plugins/OrientationAnalysis/docs/GenerateFaceIPFColoringFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/GenerateFaceIPFColoringFilter.md
@@ -1,13 +1,12 @@
# Generate IPF Colors (Face)
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Processing (Crystallography)
-## Description ##
+## Description
-This **Filter** generates a pair of colors for each **Triangle** in a **Triangle Geometry** based on the inverse pole figure (IPF) color scheme for the present crystal structure. Each **Triangle** has 2 colors since any **Face** sits at a boundary between 2 **Features** for a well-connected set of **Features** that represent _grains_. The reference direction used for the IPF color generation is the *normal* of the **Triangle**.
+This **Filter** generates a pair of colors for each **Triangle** in a **Triangle Geometry** based on the inverse pole figure (IPF) color scheme for the present crystal structure. Each **Triangle** has 2 colors since any **Face** sits at a boundary between 2 **Features** for a well-connected set of **Features** that represent _grains_. The reference direction used for the IPF color generation is the _normal_ of the **Triangle**.
------------
@@ -15,41 +14,16 @@ This **Filter** generates a pair of colors for each **Triangle** in a **Triangle
------------
-## Parameters ##
-
-None
-
-## Required Geometry ##
-
-Image + Triangle
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Face Attribute Array** | FaceLabels | int32_t | (2) | Specifies which **Features** are on either side of each **Face** |
-| **Face Attribute Array** | FaceNormals | double | (3) | Specifies the normal of each **Face** |
-| **Feature Attribute Array** | AvgEulerAngles | float | (3) | Three angles defining the orientation of the **Feature** in Bunge convention (Z-X-Z) |
-| **Feature Attribute Array** | Phases | int32_t | (1) | Specifies to which phase each **Feature** belongs |
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
+% Auto generated parameter table will be inserted here
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Face Attribute Array** | IPFColors | uint8_t | (6) | A set of two RGB color schemes encoded as unsigned chars for each **Face** |
-
-
-## Example Pipelines ##
+## Example Pipelines
+ (03) SmallIN100 Mesh Statistics
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/GenerateFaceMisorientationColoringFilter.md b/src/Plugins/OrientationAnalysis/docs/GenerateFaceMisorientationColoringFilter.md
index f82faf944d..e62d9e8596 100644
--- a/src/Plugins/OrientationAnalysis/docs/GenerateFaceMisorientationColoringFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/GenerateFaceMisorientationColoringFilter.md
@@ -1,49 +1,23 @@
# Generate Misorientation Colors (Face)
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Processing (Crystallography)
-## Description ##
+## Description
This **Filter** generates a 3 component vector for each **Triangle** in a **Triangle Geometry** that is the axis-angle of the misorientation associated with the **Features** that lie on either side of the **Triangle**. The axis is normalized, so if the magnitude of the vector is viewed, it will be the *misorientation angle* in degrees.
-## Parameters ##
-
-None
-
-## Required Geometry ##
-
-Image + Triangle
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Face Attribute Array** | FaceLabels | int32_t | (2) | Specifies which **Features** are on either side of each **Face** |
-| **Feature Attribute Array** | AvgQuats | float | (4) | Specifies the average orientation of each **Feature** in quaternion representation |
-| **Feature Attribute Array** | Phases | int32_t | (1) | Specifies to which phase each **Feature** belongs |
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
+% Auto generated parameter table will be inserted here
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Face Attribute Array** | MisorientationColors | float | (3) | A set of RGB color schemes encoded as floats for each **Face** |
-
-
-## Example Pipelines ##
+## Example Pipelines
+ (03) SmallIN100 Mesh Statistics
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/GenerateGBCDPoleFigureFilter.md b/src/Plugins/OrientationAnalysis/docs/GenerateGBCDPoleFigureFilter.md
index 30b04ca2fa..1ddbd6ae8f 100644
--- a/src/Plugins/OrientationAnalysis/docs/GenerateGBCDPoleFigureFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/GenerateGBCDPoleFigureFilter.md
@@ -1,59 +1,27 @@
-# Generate GBCD Pole Figure
+# Generate GBCD Pole Figure
-
-## Group (Subgroup) ##
+## Group (Subgroup)
IO (Output)
-## Description ##
+## Description
This **Filter** creates a pole figure from the Grain Boundary Character Distribution (GBCD) data. The user must select the relevant phase for which to generate the pole figure by entering the *phase index*.
------
-
![Regular Grid Visualization of the Small IN100 GBCD results](Images/Small_IN00_GBCD_RegularGrid.png)
![Using ParaView's Threshold filter + Cells to Points + Delaunay2D Filters](Images/Small_IN100_GBCD_Delaunay2D.png)
------
-
-## Parameters ##
-
-| Name | Type | Description |
-|------|------|-------------|
-| Phase of Interest | int32 | Index of the **Ensemble** for which to plot the pole figure |
-| Misorientation Axis-Angle | float (4x) | Axis-Angle pair values for drawing GBCD in the order of Axis (Degrees) then Axis (Normalized)|
-| Output Image Dimension | int32 | The value to use for the x and y dimensions of the created Image Geometry |
-
-## Required Geometry ##
-
-Triangle
+% Auto generated parameter table will be inserted here
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Ensemble Attribute Array** | GBDC | double | (n,m,l,o,q,r) | 5 parameter GBCD data. The 6th component is used internally to track the northern vs. southern hemisphere of the Lambert sphere |
-| Crystal Structure | CrystalStructures | Enumeration | 1 | Crystal structure for GBCD. Currently supports from Hexagonal-High 6/mmm or Cubic-High m-3m symmetries |
-
-## Created Objects ##
-
-| Kind | Default Name | Description |
-|------|--------------|-------------|
-| Image Geometry | [ImageGeometry] | The Image Geometry to be created |
-| Cell Attribute Matrix | Cell Data | The name of the cell attribute matrix created for the Image Geometry |
-| Cell Intensity Array | Intensity | The data array to be created from the pole figures and stored in the Image Geometry cell attribute matrix |
-
-## Example Pipelines ##
+## Example Pipelines
+ (04) SmallIN100 GBCD
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/GenerateIPFColorsFilter.md b/src/Plugins/OrientationAnalysis/docs/GenerateIPFColorsFilter.md
index 10a44b23a4..3e4ba1d82b 100644
--- a/src/Plugins/OrientationAnalysis/docs/GenerateIPFColorsFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/GenerateIPFColorsFilter.md
@@ -1,61 +1,29 @@
# Generate IPF Colors
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Processing (Crystallography)
-## Description ##
+## Description
This **Filter** will generate *inverse pole figure* (IPF) colors for cubic, hexagonal or trigonal crystal structures. The user can enter the *Reference Direction*, which defaults to [001]. The **Filter** also has the option to apply a black color to all "bad" **Elements**, as defined by a boolean *mask* array, which can be generated using the Threshold Objects **Filter**.
-### Originating Data Notes ###
+### Originating Data Notes
+ TSL (.ang file)
- - If the data originates from a TSL .ang file, then **Elements** that the TSL software could not reliably identify the Euler angles for will have a "Fit of Solution" = 180 and/or an "Image Quality" = 0.0.
- - This means that when the user runs some sort of threshold **Filter** the *mask* will be those **Elements** that have an Image Quality > 0 and/or Fit < 180.0
+ + If the data originates from a TSL .ang file, then **Elements** that the TSL software could not reliably identify the Euler angles for will have a "Fit of Solution" = 180 and/or an "Image Quality" = 0.0.
+ + This means that when the user runs some sort of threshold **Filter** the *mask* will be those **Elements** that have an Image Quality > 0 and/or Fit < 180.0
+ HKL (.ctf file)
- - If the data originates from an HKL (or Bruker) system (.ctf file) then bad voxels can typically be found by setting "Error" > 0
- - This means that when the user runs some sort of threshold **Filter** the *mask* will be those **Elements** that have an Error = 0
-
-
------
+ + If the data originates from an HKL (or Bruker) system (.ctf file) then bad voxels can typically be found by setting "Error" > 0
+ + This means that when the user runs some sort of threshold **Filter** the *mask* will be those **Elements** that have an Error = 0
![IPF Color Triangle](Images/IPFFilterLegend.png)
------
-
![Example Data Set](Images/IPFColor_1.png)
------
-
-## Parameters ##
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Reference Direction | float (3x) | The reference axis with respect to compute the IPF colors |
-| Apply to Good Elements Only (Bad Elements Will Be Black) | bool | Whether to assign a black color to "bad" **Elements** |
-
-## Required Geometry ##
+% Auto generated parameter table will be inserted here
-Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Element Data Array** | Euler Angles | float | (3) | Three angles defining the orientation of the **Element** in Bunge convention (Z-X-Z) |
-| **Element Data Array** | Phases | int32 | (1) | Phase Id specifying the phase of the **Element** |
-| **Element Data Array** | Mask | bool | (1) | Used to define **Elements** as *good* or *bad*. Only required if _Apply to Good Elements Only (Bad Elements Will Be Black)_ is checked |
-| **Ensemble Data Array** | Crystal Structures | uint32 | (1) | Enumeration representing the crystal structure for each **Ensemble** |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Element Data Array** | IPFColor | uint8 | (3) | The RGB colors encoded as unsigned chars for each **Element** |
-
-## Example Pipelines ##
+## Example Pipelines
+ (10) SmallIN100 Full Reconstruction
+ (04) SmallIN100 Presegmentation Processing
@@ -72,12 +40,10 @@ Not Applicable
+ (03) SmallIN100 Alignment
+ (06) SmallIN100 Synthetic
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/GeneratePoleFigureFilter.md b/src/Plugins/OrientationAnalysis/docs/GeneratePoleFigureFilter.md
index 2825bbe1cd..6e329a8cf7 100644
--- a/src/Plugins/OrientationAnalysis/docs/GeneratePoleFigureFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/GeneratePoleFigureFilter.md
@@ -8,25 +8,22 @@ IO (Output)
This **Filter** creates a standard pole figure image for each **Ensemble** in a selected **Data Container** with an **Image Geometry**. The **Filter** uses Euler angles in radians and requires the crystal structures for each **Ensemble** array and the corresponding **Ensemble** Ids on the **Cells**. The **Filter** also requires a *mask* array to determine which **Cells** are valid for the pole figure computation.
-### Algorithm Choice ###
+### Algorithm Choice
+
1: The pole figure algorithm uses a *modified Lambert square* to perform the interpolations onto the circle. This is an alternate type of interpolation that the EBSD OEMs do not perform which may make the output from DREAM.3D look slightly different than output obtained from the OEM programs.
**Only an advanced user with intimate knowledge of the modified Lambert projection should attempt to change the value for the "Lambert Image Size (Pixels)" input parameter.**
2: Discrete Pole Figure
------
-
| Lambert Projection | Discrete |
|-----|--------|
| ![Example Pole Figure Using Square Layout](Images/PoleFigure_Example.png) | ![Example Pole Figure Using Square Layout](Images/Pole_Figure_Discrete_Example.png) |
------
-
## Parameters
| Name | Type | Description |
-|------|------| ----------- |
+|------------|------| --------------------------------- |
| Pole Figure Type | Enumeration: 0=Lambert, 1=Discrete | Controls the type of pole figure |
| Image Format | Enumeration | Image file format to write. Currently supports .tif, .bmp, and .png file formats |
| Lambert Image Size (Pixels) | int32_t | Size of the Lambert square in pixels |
@@ -43,18 +40,17 @@ NONE
## Required Objects
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | EulerAngles | float | (3) | Three angles defining the orientation of the **Cell** in Bunge convention (Z-X-Z) |
-| **Cell Attribute Array** | Phases | int32_t | (1) | Specifies to which **Ensemble** each **Cell** belongs |
-| **Cell Attribute Array** | Mask | bool | (1) | Used to define **Cells** as *good* or *bad* |
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
+| Kind | Default Name | Type | Comp Dims | Description |
+|---------------------------|--------------|----------|--------|---------------------------------------------|
+| Cell Attribute Array | EulerAngles | float | (3) | Three angles defining the orientation of the **Cell** in Bunge convention (Z-X-Z) |
+| Cell Attribute Array | Phases | int32_t | (1) | Specifies to which **Ensemble** each **Cell** belongs |
+| Cell Attribute Array | Mask | bool | (1) | Used to define **Cells** as *good* or *bad* |
+| Ensemble Attribute Array | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each Ensemble |
## Created Objects
None
-
## Example Pipelines
+ TxCopper_Exposed
@@ -64,6 +60,6 @@ None
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
+## DREAM3D-NX Help
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/GenerateQuaternionConjugateFilter.md b/src/Plugins/OrientationAnalysis/docs/GenerateQuaternionConjugateFilter.md
index c4fc339efc..e69b2167c0 100644
--- a/src/Plugins/OrientationAnalysis/docs/GenerateQuaternionConjugateFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/GenerateQuaternionConjugateFilter.md
@@ -1,10 +1,10 @@
# Generate Quaternion Conjugate
-## Group (Subgroup) ##
+## Group (Subgroup)
Processing (OrientationAnalysis)
-## Description ##
+## Description
This filter will generate the transpose of a [1x4] *Quaternion* laid out in memory such that < x, y, z >, w. This can be
handy when the user wants to convert the orientation transformation to an opposite effect. The algorihtm will calculate
@@ -15,36 +15,14 @@ transformation. If the incoming data was collected in such a way that the orient
Quats, Eulers, Orientation Matrix, Rodrigues) was assumed to be a **Crystal to Sample** transformation then this filter
can be applied to a quaternion to convert into a reference frame that DREAM.3D assumes.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|-----------------------|---------|---------------------------------------------------------------------------------------------------|
-| Delete Original Array | Boolean | Set this to TRUE/ON to have the original 3 component data array deleted at the end of the filter. |
+## Example Pipelines
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|---------------------|------------------|-------|----------------------|-------------|
-| **Attribute Array** | Quaternion Input | float | (4) | |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|---------------------|------------------|-------|----------------------|-------------|
-| **Attribute Array** | Quaternion Ouput | float | (4) | |
-
-## Example Pipelines ##
-
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/INLWriterFilter.md b/src/Plugins/OrientationAnalysis/docs/INLWriterFilter.md
index 21e311ebd5..7d7981a18c 100644
--- a/src/Plugins/OrientationAnalysis/docs/INLWriterFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/INLWriterFilter.md
@@ -1,10 +1,10 @@
-# Export INL File #
+# Export INL File
-## Group (Subgroup) ##
+## Group (Subgroup)
IO (Output)
-## Description ##
+## Description
This **Filter** writes out **Cell** data from an **Image Geometry** to a file format used by the Idaho National Laboratory (INL). The format is columnar and space delimited, with header lines denoted by the "#" character. The columns are the following:
@@ -20,7 +20,7 @@ This **Filter** writes out **Cell** data from an **Image Geometry** to a file fo
Some information about the phase is included in the header section of the file in addition to values for the origin, step size, dimensions and number of **Features** in the file.
-## Example Output ##
+## Example Output
# File written from DREAM3DLib Version 5.2.1789.6419a8d
# DateTime: Fri Jun 19 10:13:25 2015
@@ -64,41 +64,16 @@ Some information about the phase is included in the header section of the file i
0.266234 0.697020 4.434729 -34.750004 10.250000 -29.000000 639 1 43
0.266234 0.697020 4.434729 -34.500004 10.250000 -29.000000 639 1 43
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------|------|-------------|
-| Output File | File Path | The output .inl file path |
-
-## Required Geometry ##
-
-Image
-
-## Required Objects ##
-
-| Kind | Default Name |Type | Component Dimensions | Description |
-|------|--------------|-------------|---------|-----|
-| **Cell Attribute Array** | FeatureIds | int32 | (1) | Specifies to which **Feature** each **Cell** belongs |
-| **Cell Attribute Array** | Phases | int32 | (1) | Specifies to which **Ensemble** each **Cell** belongs |
-| **Cell Attribute Array** | EulerAngles | float32 | (3) | Three angles defining the orientation of the **Cell** in Bunge convention (Z-X-Z) |
-| **Ensemble Attribute Array** | CrystalStructures | uint32 | (1) | Enumeration representing the crystal structure for each **Ensemble** |
-| **Ensemble Attribute Array** | Material Names | String | (1) | Name of each **Ensemble** |
-| **Ensemble Attribute Array** | Number of Features | int32 | (1) | The number of **Features** per **Ensemble** |
-
-## Created Objects ##
-
-None
-
-## Example Pipelines ##
+## Example Pipelines
- INL Export
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/Images/IPFColor_1.png b/src/Plugins/OrientationAnalysis/docs/Images/IPFColor_1.png
new file mode 100644
index 0000000000..909e76a166
Binary files /dev/null and b/src/Plugins/OrientationAnalysis/docs/Images/IPFColor_1.png differ
diff --git a/src/Plugins/OrientationAnalysis/docs/Images/IPFFilterLegend.png b/src/Plugins/OrientationAnalysis/docs/Images/IPFFilterLegend.png
new file mode 100644
index 0000000000..fab7d7ae26
Binary files /dev/null and b/src/Plugins/OrientationAnalysis/docs/Images/IPFFilterLegend.png differ
diff --git a/src/Plugins/OrientationAnalysis/docs/Images/ReadH5Ebsd_UI.png b/src/Plugins/OrientationAnalysis/docs/Images/ReadH5Ebsd_UI.png
new file mode 100644
index 0000000000..55fcccce1b
Binary files /dev/null and b/src/Plugins/OrientationAnalysis/docs/Images/ReadH5Ebsd_UI.png differ
diff --git a/src/Plugins/OrientationAnalysis/docs/Images/ReadH5Ebsd_Wrong.png b/src/Plugins/OrientationAnalysis/docs/Images/ReadH5Ebsd_Wrong.png
new file mode 100644
index 0000000000..7eaaa00b39
Binary files /dev/null and b/src/Plugins/OrientationAnalysis/docs/Images/ReadH5Ebsd_Wrong.png differ
diff --git a/src/Plugins/OrientationAnalysis/docs/ImportH5EspritDataFilter.md b/src/Plugins/OrientationAnalysis/docs/ImportH5EspritDataFilter.md
index 44be26cd1e..5493adfbc0 100644
--- a/src/Plugins/OrientationAnalysis/docs/ImportH5EspritDataFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/ImportH5EspritDataFilter.md
@@ -1,112 +1,43 @@
# Import Bruker Nano Esprit EBSD Data (.h5)
-
-## Group (Subgroup)
+## Group (Subgroup)
Import/Export (Import)
-## Description
+## Description
-This **Filter** will read a single .h5 file into a new **Image Geometry**, allowing the immediate use of **Filters** on the data instead of having to generate the intermediate .h5ebsd file. A **Cell Attribute Matrix** and **Ensemble Attribute Matrix** will also be created to hold the imported EBSD information. Currently, the user has no control over the names of the created **Attribute Arrays**.
+This **Filter** will read a single .h5 file into a new **Image Geometry**, allowing the immediate use of **Filters** on the data instead of having to generate the intermediate .h5ebsd file. A **Cell Attribute Matrix** and Ensemble Attribute Matrix** will also be created to hold the imported EBSD information. Currently, the user has no control over the names of the created **Attribute Arrays**.
| User interface before entering a proper "Z Spacing" value and selecting which scans to include. |
|-------|
|![](Images/ReadEspritH5_1.png)|
-
| User interface AFTER setting the "Z Spacing" and selecting files. |
|-------|
|![](Images/ReadEspritH5_2.png)|
-
-## Notes About Reference Frames
+## Notes About Reference Frames
The user should be aware that simply reading the file then performing operations that are dependent on the proper crystallographic and sample reference frame will be undefined or simply **wrong**. In order to bring the crystal reference frame and sample reference frame into coincidence, rotations will need to be applied to the data. The recommended filters are:
-+ [Rotate Euler Reference Frame](../RotateEulerRefFrameFilter/index.html)
-+ [Rotate Sample Reference Frame](../RotateSampleRefFrameFilter/index.html)
++ {ref}`Rotate Euler Reference Frame `
++ {ref}`Rotate Sample Reference Frame `
If the data has come from a TSL acquisition system and the settings of the acquisition software were in the default modes, the following reference frame transformations may need to be performed based on the version of the OIM Analysis software being used to collect the data:
+ Sample Reference Frame: 180o about the <010> Axis
+ Crystal Reference Frame: 90o about the <001> Axis
-The user also may want to assign un-indexed pixels to be ignored by flagging them as "bad". The [Threshold Objects](../MultiThresholdObjects/index.html) **Filter** can be used to define this *mask* by thresholding on values such as *MAD* > xx.
-
-## Parameters
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Input File | File Path | The input .h5 file path |
-| Scan Name | Enumeration | The name of the scan in the .h5 file. EDAX can store multiple scans in a single file |
-| Z Spacing | float | The spacing in microns between each layer. |
-| Origin | float (3x1) | The origin of the volume |
-| Read Pattern Data | bool | Default=OFF |
-| Combine phi1, PHI, phi2 into Single Euler Angles Attribute Array | bool | Default=ON |
-| Convert Euler Angles to Radians | bool | Default=ON |
-
-## Required Geometry
-
-Not Applicable
-
-## Required Objects
-
-None
-
-## Created Objects
-
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Data Container** | ImageDataContainer | N/A | N/A | Created **Data Container** name with an **Image Geometry** |
-| **Attribute Matrix** | CellData | Cell | N/A | Created **Cell Attribute Matrix** name |
-| **Attribute Matrix** | CellEnsembleData | Cell Ensemble | N/A | Created **Cell Ensemble Attribute Matrix** name |
+The user also may want to assign un-indexed pixels to be ignored by flagging them as "bad". The {ref}`Threshold Objects ` Filter can be used to define this *mask* by thresholding on values such as *MAD* > xx.
-### Created Cell Attribute Arrays
+% Auto generated parameter table will be inserted here
-These arrays will **most likely** be created but is not guaranteed. Additional arrays (unknown at the time of writing) may also be created.
+## Example Pipelines
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | DD | float | (1) | |
-| **Cell Attribute Array** | MAD | float | (1) | Mean Angular Deviation |
-| **Cell Attribute Array** | MADPhase | int | (1) | |
-| **Cell Attribute Array** | NIndexedBands | int | (1) | |
-| **Cell Attribute Array** | PCX | float | (1) | Pattern Center X |
-| **Cell Attribute Array** | PCY | float | (1) | Pattern Center Y |
-| **Cell Attribute Array** | Phase | int | (1) | |
-| **Cell Attribute Array** | RadonBandCount | int | (1) | |
-| **Cell Attribute Array** | RadonQuality | float | (1) | |
-| **Cell Attribute Array** | RawPatterns | float | (1) | |
-| **Cell Attribute Array** | XBEAM | int | (1) | |
-| **Cell Attribute Array** | YBEAM | int | (1) | |
-| **Cell Attribute Array** | XSAMPLE | float | (1) | |
-| **Cell Attribute Array** | YSAMPLE | float | (1) | |
-| **Cell Attribute Array** | Euler Angles | float | (3) | Note the filter will create the Euler Angles array by interleaving the phi1, PHI and phi2 data arrays from the data file. |
-| **Cell Attribute Array** | Pattern | uint8_t | (NxM) | The pattern data may be very large. There is an option to NOT read it into DREAM.3D if it is not needed by the analysis. |
-
-
-### Created Ensemble Attribute Arrays
-
-These arrays will **most likely** be created but is not guaranteed. Additional arrays (unknown at the time of writing) may also be created.
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
-| **Ensemble Attribute Array** | LatticeConstants | float | (6) | The 6 values that define the lattice constants for each **Ensemble**|
-| **Ensemble Attribute Array** | MaterialName | String | (1) | Name of each **Ensemble** |
-
-
-
-## Example Pipelines
-
-
-## License & Copyright
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/ImportH5OimDataFilter.md b/src/Plugins/OrientationAnalysis/docs/ImportH5OimDataFilter.md
index b776190c3d..e7a7ce7643 100644
--- a/src/Plugins/OrientationAnalysis/docs/ImportH5OimDataFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/ImportH5OimDataFilter.md
@@ -1,33 +1,28 @@
# Import EDAX EBSD Data (.h5)
-
-## Group (Subgroup)
+## Group (Subgroup)
Import/Export (Import)
## Description
-This **Filter** will read a single .h5 file into a new **Image Geometry**, allowing the immediate use of **Filters** on the data instead of having to generate the intermediate .h5ebsd file. A **Cell Attribute Matrix** and **Ensemble Attribute Matrix** will also be created to hold the imported EBSD information. Currently, the user has no control over the names of the created **Attribute Arrays**.
+This **Filter** will read a single .h5 file into a new **Image Geometry**, allowing the immediate use of **Filters** on the data instead of having to generate the intermediate .h5ebsd file. A **Cell Attribute Matrix** and Ensemble Attribute Matrix** will also be created to hold the imported EBSD information. Currently, the user has no control over the names of the created **Attribute Arrays**.
-| User interface before entering a proper "Z Spacing" value and selecting which scans to include. |
-|-------|
-|![](Images/ReadEDAXH5_1.png)|
+![User interface before entering a proper "Z Spacing" value and selecting which scans to include.](Images/ReadEDAXH5_1.png)
-| User interface AFTER setting the "Z Spacing" and selecting files. |
-|-------|
-|![](Images/ReadEDAXH5_2.png)|
+![User interface AFTER setting the "Z Spacing" and selecting files.](Images/ReadEDAXH5_2.png)
## Notes About Reference Frames
The user should be aware that simply reading the file then performing operations that are dependent on the proper crystallographic and sample reference frame will be undefined or simply **wrong**. In order to bring the crystal reference frame and sample reference frame into coincidence, rotations will need to be applied to the data. The recommended filters are:
-+ [Rotate Euler Reference Frame](../RotateEulerRefFrameFilter/index.html)
-+ [Rotate Sample Reference Frame](../RotateSampleRefFrameFilter/index.html)
+- {ref}`Rotate Euler Reference Frame `
+- {ref}`Rotate Sample Reference Frame `
If the data has come from a TSL acquisition system and the settings of the acquisition software were in the default modes, the following reference frame transformations may need to be performed based on the version of the OIM Analysis software being used to collect the data:
-+ Crystal Reference Frame: 90o about the <001> Axis
-+ Sample Reference Frame: 180o about the <010> Axis
+- Crystal Reference Frame: 90o about the <001> Axis
+- Sample Reference Frame: 180o about the <010> Axis
### Important Consideration for Sample Reference Frame
@@ -36,74 +31,16 @@ the user should **CHECK** the option **ON** for "Perform Slice By Slice Transfor
## Thresholding out Unindexed Scan Points
-The user also may want to assign un-indexed pixels to be ignored by flagging them as "bad". The [Threshold Objects](../MultiThresholdObjects/index.html) **Filter** can be used to define this *mask* by thresholding on values such as *Confidence Index* > xx or *Image Quality* > desired quality.
-
-## Parameters
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Input File | File Path | The input .h5 file path |
-| Scan Name | Enumeration | The name of the scan in the .h5 file. EDAX can store multiple scans in a single file |
-| Z Spacing | float | The spacing in microns between each layer. |
-| Origin | float (3x1) | The origin of the volume |
-| Read Pattern Data | bool | Default=OFF |
-
-## Required Geometry
-
-Not Applicable
-
-## Required Objects
-
-None
-
-## Created Objects
-
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Data Container** | ImageDataContainer | N/A | N/A | Created **Data Container** name with an **Image Geometry** |
-| **Attribute Matrix** | CellData | Cell | N/A | Created **Cell Attribute Matrix** name |
-| **Attribute Matrix** | CellEnsembleData | Cell Ensemble | N/A | Created **Cell Ensemble Attribute Matrix** name |
-
-### Created Cell Attribute Arrays
+The user also may want to assign un-indexed pixels to be ignored by flagging them as "bad". The {ref}`Threshold Objects ` **Filter** can be used to define this *mask* by thresholding on values such as *Confidence Index* > xx or *Image Quality* > desired quality.
-These arrays will **most likely** be created but is not guaranteed. Additional arrays (unknown at the time of writing) may also be created.
+% Auto generated parameter table will be inserted here
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | Confidence Index | float |(1) | Confidence of indexing |
-| **Cell Attribute Array** | EulerAngles | float |(3) | Three angles defining the orientation of the **Cell** in Bunge convention (Z-X-Z) |
-| **Cell Attribute Array** | Fit | float |(1) | Quality of fit for indexing |
-| **Cell Attribute Array** | Image Quality | float |(1) | Quality of image |
-| **Cell Attribute Array** | Phases | int32_t | (1) | Specifies to which phase each **Cell** belongs |
-| **Cell Attribute Array** | SEM Signal | float |(1) | Value of SEM signal |
-| **Cell Attribute Array** | X Position | float |(1) | X coordinate of **Cell** |
-| **Cell Attribute Array** | Y Position | float |(1) | Y coordinate of **Cell** |
-| **Cell Attribute Array** | Pattern | uint8_t | (NxM) | The pattern data may be very large. There is an option to NOT read it into DREAM.3D if it is not needed by the analysis. |
+## Example Pipelines
-
-### Created Ensemble Attribute Arrays
-
-These arrays will **most likely** be created but is not guaranteed. Additional arrays (unknown at the time of writing) may also be created.
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
-| **Ensemble Attribute Array** | LatticeConstants | float | (6) | The 6 values that define the lattice constants for each **Ensemble**|
-| **Ensemble Attribute Array** | MaterialName | String | (1) | Name of each **Ensemble** |
-
-
-
-## Example Pipelines
-
-
-
-## License & Copyright
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/MergeTwinsFilter.md b/src/Plugins/OrientationAnalysis/docs/MergeTwinsFilter.md
index 5686e47e72..c41f90024d 100644
--- a/src/Plugins/OrientationAnalysis/docs/MergeTwinsFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/MergeTwinsFilter.md
@@ -1,60 +1,26 @@
-# Merge Twins
+# Merge Twins
-
-## Group (Subgroup) ##
+## Group (Subgroup)
Reconstruction (Grouping)
-## Description ##
+## Description
*THIS FILTER ONLY WORKS ON CUBIC-HIGH (m3m) Laue Classes.*
This **Filter** groups neighboring **Features** that are in a twin relationship with each other (currently only FCC σ = 3 twins). The algorithm for grouping the **Features** is analogous to the algorithm for segmenting the **Features** - only the average orientation of the **Features** are used instead of the orientations of the individual **Elements**. The user can specify a tolerance on both the *axis* and the *angle* that defines the twin relationship (i.e., a tolerance of 1 degree for both tolerances would allow the neighboring **Features** to be grouped if their misorientation was between 59-61 degrees about an axis within 1 degree of <111>, since the Sigma 3 twin relationship is 60 degrees about <111>).
+% Auto generated parameter table will be inserted here
-## Parameters ##
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Axis Tolerance (Degrees) | float | Tolerance allowed when comparing the axis part of the axis-angle representation of the misorientation |
-| Angle Tolerance (Degrees) | float | Tolerance allowed when comparing the angle part of the axis-angle representation of the misorientation |
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Feature Attribute Array** | NonContiguousNeighbors | List of int32_t | (1) | List of non-contiguous neighbors for each **Feature**. Only needed if _Use Non-Contiguous Neighbors_ is checked |
-| **Feature Attribute Array** | NeighborList | List of int32_t | (1) | List of neighbors for each **Feature** |
-| **Element Attribute Array** | FeatureIds | int32_t | (1) | Specifies to which **Feature** each **Element** belongs |
-| **Feature Attribute Array** | Phases | int32_t | (1) | Specifies to which **Ensemble** each **Feature** belongs |
-| **Feature Attribute Array** | AvgQuats | float| (4) | Specifies the average orientation of the **Feature** in quaternion representation |
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Element Attribute Array** | ParentIds | int32_t | (1) | Specifies to which *parent* each **Element** belongs |
-| **Attribute Matrix** | NewFeatureData | Feature | N/A | Created **Feature Attribute Matrix** name |
-| **Feature Attribute Array** | ParentIds | int32_t | (1) | Specifies to which *parent* each **Feature** belongs |
-| **Feature Attribute Array** | Active | bool | (1) | Specifies if the **Feature** is still in the sample (*true* if the **Feature** is in the sample and *false* if it is not). At the end of the **Filter**, all **Features** will be *Active* |
-
-
-## Example Pipelines ##
+## Example Pipelines
+ (10) SmallIN100 Full Reconstruction
+ (06) SmallIN100 Postsegmentation Processing
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/NeighborOrientationCorrelationFilter.md b/src/Plugins/OrientationAnalysis/docs/NeighborOrientationCorrelationFilter.md
index 7bb6d5e1b3..74f14f3bd0 100644
--- a/src/Plugins/OrientationAnalysis/docs/NeighborOrientationCorrelationFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/NeighborOrientationCorrelationFilter.md
@@ -1,19 +1,18 @@
# Neighbor Orientation Correlation
-## Group (Subgroup) ##
+## Group (Subgroup)
Processing (Cleanup)
-## Description ##
+## Description
This **Filter** first identifies all **Cells** that have a *confidence index* below the minimum set by the user. Then, for each of those **Cells**, their neighboring **Cells** are checked to determine the number of neighbor **Cells** with orientations different than the reference **Cell** by more than the user defined *misorientation tolerance*. In addition the neighboring **Cells** are compared with each other to determine the number of neighboring **Cells** that have the same orientation (again within the user defined tolerance). The *Cleanup Level* set by the user is then used to determine which **Cells** are replaced. If a level of 5 is set, then at least 5 of the neighboring **Cells** must be different than the reference **Cell** and at least 5 of the neighboring **Cells** must be the same as each other (and so on for other *Cleanup Level*). If a **Cell** meets the replacement criteria, then all of its attributes are replaced with the attributes of one of the neighboring **Cells** that are the same as each other.
*Note:* The **Filter** will iteratively reduce the *Cleanup Level* from 6 until it reaches the user defined number. So, if the user selects a level of 4, then the **Filter** will run with a level of 6, then 5, then 4 before finishing.
-
Neighbors are defined as a the "nearest neighbors" which share a "face". For 3D structures it is 6 neighbors that share a common face with the current cell.
-### Example ###
+### Example
| | 0 | 1 | 2 |
|---|---|---|---|
@@ -25,45 +24,19 @@ Schematic layout of the neighboring cells. Only the In-Plane neighbors are shown
In this example cell (1,1) has a confidence index < 0.1 and the surrounding cells all have a misorientation tolerance not greater than 5 degrees. Comparing cell (1,1) with its neighbor cells we can see that the misorientation is greater than 5 Degrees. In this case the central cell (1,1) would have all of its attributes replaced with the "best" neighbor based on the phase of a neighbor cell matching the central cell.
-## Parameters ##
-
-| Name | Type | Description |
-|------|------|-------------|
-| Minimum Confidence Index | float32 | Sets the minimum value of 'confidence' a **Cell** must have |
-| Misorientation Tolerance (Degrees) | Float32 | Angular tolerance used to compare with neighboring **Cells** |
-| Cleanup Level | int32 | Minimum number of neighbor **Cells** that must have orientations within above tolerace to allow **Cell** to be changed |
-
-## Required Geometry ##
-
-Image
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | Confidence Index | float32 | (1) | Specifies the confidence in the orientation of the **Cell** (TSL data) |
-| **Cell Attribute Array** | Cell Phases | int32 | (1) | Specifies to which **Ensemble** each **Cell** belongs |
-| **Cell Attribute Array** | Quaternions | float32 | (4) | Specifies the orientation of the **Cell** in quaternion representation |
-| **Ensemble Attribute Array** | Crystal Structures | uint32 | (1) | Enumeration representing the crystal structure for each **Ensemble** |
+% Auto generated parameter table will be inserted here
-## Created Objects ##
-
-None
-
-
-## Example Pipelines ##
+## Example Pipelines
+ (10) SmallIN100 Full Reconstruction
+ (04) SmallIN100 Presegmentation Processing
+ INL Export
+ 04_Steiner Compact
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/ReadAngDataFilter.md b/src/Plugins/OrientationAnalysis/docs/ReadAngDataFilter.md
index 3ad8f0d312..faad519864 100644
--- a/src/Plugins/OrientationAnalysis/docs/ReadAngDataFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/ReadAngDataFilter.md
@@ -1,15 +1,14 @@
-# Import EDAX EBSD Data (.ang)
+# Import EDAX EBSD Data (.ang)
-
-## Group (Subgroup) ##
+## Group (Subgroup)
IO (Input)
-## Description ##
+## Description
-This **Filter** will read a single .ang file into a new **Image Geometry**, allowing the immediate use of **Filters** on the data instead of having to generate the intermediate .h5ebsd file. A **Cell Attribute Matrix** and **Ensemble Attribute Matrix** will also be created to hold the imported EBSD information. Currently, the user has no control over the names of the created **Attribute Arrays**. The user should be aware that simply reading the file then performing operations that are dependent on the proper crystallographic and sample reference frame will be undefined or simply **wrong**. In order to bring the crystal reference frame and sample reference frame into coincidence, rotations will need to be applied to the data.
+This **Filter** will read a single .ang file into a new **Image Geometry**, allowing the immediate use of **Filters** on the data instead of having to generate the intermediate .h5ebsd file. A **Cell Attribute Matrix** and Ensemble Attribute Matrix** will also be created to hold the imported EBSD information. Currently, the user has no control over the names of the created **Attribute Arrays**. The user should be aware that simply reading the file then performing operations that are dependent on the proper crystallographic and sample reference frame will be undefined or simply **wrong**. In order to bring the crystal reference frame and sample reference frame into coincidence, rotations will need to be applied to the data.
-### Default TSL Transformations ###
+### Default TSL Transformations
If the data has come from a TSL acquisition system and the settings of the acquisition software were in the default modes, he following reference frame transformations may need to be performed based on the version of the OIM Analysis software being used to collect the data:
@@ -18,51 +17,19 @@ If the data has come from a TSL acquisition system and the settings of the acqui
The user also may want to assign un-indexed pixels to be ignored by flagging them as "bad". The Threshold Objects **Filter** can be used to define this *mask* by thresholding on values such as *Confidence Index* > 0.1 or *Image Quality* > desired quality.
-## Parameters ##
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Input File | File Path | The input .ang file path |
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
+% Auto generated parameter table will be inserted here
-None
-
-## Created Objects ##
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Data Container** | ImageDataContainer | N/A | N/A | Created **Data Container** name with an **Image Geometry** |
-| **Attribute Matrix** | CellData | Cell | N/A | Created **Cell Attribute Matrix** name |
-| **Attribute Matrix** | CellEnsembleData | Cell Ensemble | N/A | Created **Cell Ensemble Attribute Matrix** name |
-| **Cell Attribute Array** | Confidence Index | float |(1) | Confidence of indexing |
-| **Cell Attribute Array** | EulerAngles | float |(3) | Three angles defining the orientation of the **Cell** in Bunge convention (Z-X-Z) |
-| **Cell Attribute Array** | Fit | float |(1) | Quality of fit for indexing |
-| **Cell Attribute Array** | Image Quality | float |(1) | Quality of image |
-| **Cell Attribute Array** | Phases | int32_t | (1) | Specifies to which phase each **Cell** belongs |
-| **Cell Attribute Array** | SEM Signal | float |(1) | Value of SEM signal |
-| **Cell Attribute Array** | X Position | float |(1) | X coordinate of **Cell** |
-| **Cell Attribute Array** | Y Position | float |(1) | Y coordinate of **Cell** |
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
-| **Ensemble Attribute Array** | LatticeConstants | float | (6) | The 6 values that define the lattice constants for each **Ensemble**|
-| **Ensemble Attribute Array** | MaterialName | String | (1) | Name of each **Ensemble** |
-
-## Example Pipelines ##
+## Example Pipelines
+ INL Export
+ Export Small IN100 ODF Data (StatsGenerator)
+ Edax IPF Colors
+ Confidence Index Histogram
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/ReadCtfDataFilter.md b/src/Plugins/OrientationAnalysis/docs/ReadCtfDataFilter.md
index e3bf089583..615f1ee4df 100644
--- a/src/Plugins/OrientationAnalysis/docs/ReadCtfDataFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/ReadCtfDataFilter.md
@@ -1,16 +1,15 @@
-# Import Oxford Instr. Ebsd Data
+# Import Oxford Instr. Ebsd Data
-
-## Group (Subgroup) ##
+## Group (Subgroup)
IO (Input)
-## Description ##
+## Description
-This **Filter** will read a single .ctf file into a new **Image Geometry**, allowing the immediate use of **Filters** on the data instead of having to generate the intermediate .h5ebsd file. A **Cell Attribute Matrix** and **Ensemble Attribute Matrix** will also be created to hold the imported EBSD information. Currently, the user has no control over the names of the created **Attribute Arrays**. The user should be aware that simply reading the file then performing operations that are dependent on the proper crystallographic and sample reference frame will be **undefined, inaccurate and/or wrong**. In order to bring the crystal reference frame and sample reference frame into coincidence, rotations will need to be applied to the data. An excellant reference for this is the following PDF file:
+This **Filter** will read a single .ctf file into a new **Image Geometry**, allowing the immediate use of **Filters** on the data instead of having to generate the intermediate .h5ebsd file. A **Cell Attribute Matrix** and Ensemble Attribute Matrix** will also be created to hold the imported EBSD information. Currently, the user has no control over the names of the created **Attribute Arrays**. The user should be aware that simply reading the file then performing operations that are dependent on the proper crystallographic and sample reference frame will be **undefined, inaccurate and/or wrong**. In order to bring the crystal reference frame and sample reference frame into coincidence, rotations will need to be applied to the data. An excellant reference for this is the following PDF file:
[http://pajarito.materials.cmu.edu/rollett/27750/L17-EBSD-analysis-31Mar16.pdf](http://pajarito.materials.cmu.edu/rollett/27750/L17-EBSD-analysis-31Mar16.pdf)
-### Default HKL Transformations ###
+### Default HKL Transformations
If the data has come from a HKL acquisition system and the settings of the acquisition software were in the default modes, then the following reference frame transformations need to be performed:
@@ -19,11 +18,11 @@ If the data has come from a HKL acquisition system and the settings of the acqui
The user also may want to assign un-indexed pixels to be ignored by flagging them as "bad". The Threshold Objects **Filter** can be used to define this *mask* by thresholding on values such as *Error* = 0.
-### Radians and Degrees ###
+### Radians and Degrees
Most 2D .ctf files have their angles in **degrees** where as DREAM.3D expects radians. The filter provides an option to convert the Euler Angles to Radians and is turned on by default. The user is encouraged to create an IPF Image of their EBSD data to ensure that they do in-fact need to have this option enabled.
-### The Axis Alignment Issue for Hexagonal Symmetry [1] ###
+### The Axis Alignment Issue for Hexagonal Symmetry [1]
+ The issue with hexagonal materials is the alignment of the Cartesian coordinate system used for calculations with the crystal coordinate system (the Bravais lattice).
+ In one convention (e.g. EDAX.TSL), the x-axis, i.e. [1,0,0], is aligned with the crystal a1 axis, i.e. the [2,-1,-1,0] direction. In this case, the y-axis is aligned with the [0,1,-1,0] direction. (Green Axis in Figure 1)
@@ -32,64 +31,28 @@ Most 2D .ctf files have their angles in **degrees** where as DREAM.3D expects ra
+ Caution: it appears that the axis alignment is a choice that must be made when installing TSL software so determination of which convention is in use must be made on a case-by-case basis. It is fixed to the y-convention in the HKL software.
+ The main clue that something is wrong in a conversion is that either the 2110 & 1010 pole figures are transposed, or that a peak in the inverse pole figure that should be present at 2110 has shifted over to 1010.
+ DREAM.3D uses the TSL/EDAX convention.
-+ __The result of this is that the filter will by default add 30 degrees to the second Euler Angle (phi2) when reading Oxford Instr (.ctf) files. This can be disabled by the user if necessary.__
++ **The result of this is that the filter will by default add 30 degrees to the second Euler Angle (phi2) when reading Oxford Instr (.ctf) files. This can be disabled by the user if necessary.**
| Figure 1 |
|--------|
| ![Figure showing 30 Degree conversions](Images/Hexagonal_Axis_Alignment.png) |
-| **Figure 1:** showing TSL and Oxford Instr. conventions. EDAX/TSL is in **Green**. Oxford Inst. is in **Red** |
-
-## Parameters ##
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Input File | File Path |The input .ctf file path |
-| Convert to Radians | bool | Should the filter convert the Eulers to Radians (Default = true)|
-| Hexagonal Axis Alignment | bool | Should the filter convert a Hexagonal phase to the EDAX standard for x-axis alignment |
-
-## Required Geometry ##
-
-Not Applicable
+| Figure 1:**showing TSL and Oxford Instr. conventions. EDAX/TSL is in **Green**. Oxford Inst. is in**Red |
-## Required Objects ##
+% Auto generated parameter table will be inserted here
-None
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Data Container** | ImageDataContainer | N/A | N/A | Created **Data Container** name with an **Image Geometry** |
-| **Attribute Matrix** | CellData | Cell | N/A | Created **Cell Attribute Matrix** name |
-| **Attribute Matrix** | CellEnsembleData | Cell Ensemble | N/A | Created **Cell Ensemble Attribute Matrix** name |
-| **Cell Attribute Array** | BC | float | (1) | Band contrast levels |
-| **Cell Attribute Array** | EulerAngles | float | (3) | Three angles defining the orientation of the **Cell** in Bunge convention (Z-X-Z) |
-| **Cell Attribute Array** | BS | float | (1) | Band saturation levels |
-| **Cell Attribute Array** | Bands | float | (1) | Number of bands |
-| **Cell Attribute Array** | Phases | int32_t | (1) | Specifies to which phase each **Cell** belongs |
-| **Cell Attribute Array** | MAD | float | (1) | Mean angular deviation. Typical threshold value is < 1.8 |
-| **Cell Attribute Array** | X Position | float |(1) | X coordinate of **Cell** |
-| **Cell Attribute Array** | Y Position | float |(1) | Y coordinate of **Cell** |
-| **Cell Attribute Array** | Error | int32_t | (1) | Value = 0 is a well indexed scan point |
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
-| **Ensemble Attribute Array** | LatticeConstants | float | (6) | The 6 values that define the lattice constants for each **Ensemble**|
-| **Ensemble Attribute Array** | MaterialName | String | (1) | Name of each **Ensemble** |
-
-## Example Pipelines ##
+## Example Pipelines
+ TxCopper_Exposed
+ TxCopper_Unexposed
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## References ##
+## References
[1] Rollett, A.D. Lecture Slides located at [http://pajarito.materials.cmu.edu/rollett/27750/L17-EBSD-analysis-31Mar16.pdf](http://pajarito.materials.cmu.edu/rollett/27750/L17-EBSD-analysis-31Mar16.pdf)
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/ReadH5EbsdFilter.md b/src/Plugins/OrientationAnalysis/docs/ReadH5EbsdFilter.md
index 76b0b53f39..aaf77140f1 100644
--- a/src/Plugins/OrientationAnalysis/docs/ReadH5EbsdFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/ReadH5EbsdFilter.md
@@ -1,88 +1,55 @@
# ReadH5Ebsd
-## Group (Subgroup) ##
+## Group (Subgroup)
IO (Input)
-## Description ##
+## Description
-This **Filter** reads from the .h5ebsd file that was generated with the *Import Orientation File(s) to H5EBSD* **Filter**.
-
------
+This **Filter** reads from the .h5ebsd file that was generated with the *Import Orientation File(s) to H5EBSD* **Filter**.
![Read H5Ebsd File User Interface](Images/ReadH5Ebsd_UI.png)
------
-
-
+ The user can use the checkboxes under the *Data Arrays to Read* section to select which specific data arrays they are interested in importing.
+ The user can select a subset of the slices if they do not wish to import the entire volume.
+ The type of transformations that are recommended based on the manufacturer of the data are also listed with a checkbox that allows the user to toggle the recommended transformations on and off.
+ The user should select the Euler angle representation. (This is **only** available if the **Use Recommended Transformations** is turned **on**.)
-### Notes About Transformations ###
+### Notes About Transformations
The **user** is solely responsible for knowing any sample reference frame transformations, crystal reference frame transformations and how the Euler angles are represented in the file. DREAM.3D provides historically correct transformations from a few of the EBSD manufacturers under the assumption that the EBSD instrument has been setup according to their guidelines. The **user** is strongly encouraged to discuss these topics with the person(s) who were responsible for collecting the data. For example the IPF images presented below were generated from an H5Ebsd file that was generated using a CTF file. The difference is that the **Incorrect** image did not correctly select the **Angle Representation** combo box on the filter's user interface. The Euler angles were actually in degrees but were treated as if the values were in radians. The correct image is on the right.
If the user does not want the **Read H5Ebsd** filter to perform any transformations then the checkbox can be unchecked and the user can manually perform any desired transformations by inserting the appropriate filters into the pipeline. The suggested filters are:
-+ [Rotate Euler Reference Frame](rotateeulerrefframe.html)
-+ [Rotate Sample Reference Frame](rotatesamplerefframe.html)
-+ [Convert Angles to Degrees or Radians](changeanglerepresentation.html)
++ {ref}`Rotate Euler Reference Frame `
++ {ref}`Rotate Sample Reference Frame `
++ {ref}`Convert Angles to Degrees or Radians `
An excellant reference for this is the following PDF file:
[http://pajarito.materials.cmu.edu/rollett/27750/L17-EBSD-analysis-31Mar16.pdf](http://pajarito.materials.cmu.edu/rollett/27750/L17-EBSD-analysis-31Mar16.pdf)
-
| Incorrect | Correct |
|---------|---------|
|![Read H5Ebsd File User Interface](Images/ReadH5Ebsd_Wrong.png) | ![Read H5Ebsd File User Interface](Images/ReadH5Ebsd_Right.png) |
| Euler angles were treated as Radians | Euler angles were converted from Degrees to Radians |
|"Interstitial Free (IF) Steel courtesy of [1]"| |
-### The Axis Alignment Issue for Hexagonal Symmetry [2] ###
+### The Axis Alignment Issue for Hexagonal Symmetry [2]
+ The issue with hexagonal materials is the alignment of the Cartesian coordinate system used for calculations with the crystal coordinate system (the Bravais lattice).
+ In one convention (e.g. EDAX.TSL), the x-axis, i.e. [1,0,0], is aligned with the crystal a1 axis, i.e. the [2,-1,-1,0] direction. In this case, the y-axis is aligned with the [0,1,-1,0] direction. (Green Axis in Figure 1)
+ In the other convention, (e.g. Oxford Instr, Univ. Metz software), the x-axis, i.e. [1,0,0], is aligned with the crystal [1,0,-1,0] direction. In this case, the y-axis is aligned with the [-1,2,-1,0] direction. (Red Axis in Figure 1)
-+ This is important because texture analysis can lead to an ambiguity as to the alignment of [2,-1,-1,0] versus [1,0,-1,0], with apparent **30 ** shifts in the data.
++ This is important because texture analysis can lead to an ambiguity as to the alignment of [2,-1,-1,0] versus [1,0,-1,0], with apparent **30** shifts in the data.
+ Caution: it appears that the axis alignment is a choice that must be made when installing TSL software so determination of which convention is in use must be made on a case-by-case basis. It is fixed to the y-convention in the HKL software.
+ The main clue that something is wrong in a conversion is that either the 2110 & 1010 pole figures are transposed, or that a peak in the inverse pole figure that should be present at 2110 has shifted over to 1010.
+ DREAM.3D uses the TSL/EDAX convention.
-+ **The result of this is that the filter will *AUTOMATICALLY* add 30 to phi2 when reading Oxford Instr (.ctf) files or .h5ebsd files denoted with the HKL manufacturer ID. There is no way to turn off this behavior. **
++ **The result of this is that the filter will *AUTOMATICALLY* add 30 to phi2 when reading Oxford Instr (.ctf) files or .h5ebsd files denoted with the HKL manufacturer ID. There is no way to turn off this behavior.**
![Figure 1 showing TSL \& Oxford Instr. conventions.](Images/Hexagonal_Axis_Alignment.png)
-## Parameters ##
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Input File | File Path | The input .h5ebsd file path |
-| Start Slice | Int | The first slice of data to read |
-| End Slice | Int | The last slice of data to read |
-| Use Recommended Transformations | bool | Whether to apply the listed recommended transformations |
-| Data Arrays to Read | Bool(s) | Whether to read the listed arrays |
-| Angle Representation | Int (0=Radians, 1=Degrees) | How the Euler Angles are represented. |
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
+% Auto generated parameter table will be inserted here
-None
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Geometry** | ImageGeometry | Image | N/A | Created **Image Geometry** |
-| **Attribute Matrix** | CellData | Cell | N/A | Created **Cell Attribute Matrix** name |
-| **Attribute Matrix** | CellEnsembleData | Cell Ensemble | N/A | Created **Cell Ensemble Attribute Matrix** name |
-
-An array for each of the arrays selected in the *Data Arrays to Read* section will also be created.
-
-## Example Pipelines ##
+## Example Pipelines
+ 02_Adaptive Alignment - Misorientation - Zero Shifts
+ (10) SmallIN100 Full Reconstruction
@@ -91,20 +58,17 @@ An array for each of the arrays selected in the *Data Arrays to Read* section wi
+ (02) SmallIN100 Initial Visualization
+ (03) SmallIN100 Alignment
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## References ##
+## References
-[1] N. Allain-Bonasso, F. Wagner, S. Berbenni, D.P. Field, A study of the heterogeneity of plastic deformation in IF steel by EBSD, Materials Science and Engineering: A, Volume 548, 30 June 2012, Pages 56-63, ISSN 0921-5093, http://dx.doi.org/10.1016/j.msea.2012.03.068.
-(http://www.sciencedirect.com/science/article/pii/S0921509312004388)
+[1] N. Allain-Bonasso, F. Wagner, S. Berbenni, D.P. Field, A study of the heterogeneity of plastic deformation in IF steel by EBSD, Materials Science and Engineering: A, Volume 548, 30 June 2012, Pages 56-63, ISSN 0921-5093, .
+()
[2] Rollett, A.D. Lecture Slides located at [http://pajarito.materials.cmu.edu/rollett/27750/L17-EBSD-analysis-31Mar16.pdf](http://pajarito.materials.cmu.edu/rollett/27750/L17-EBSD-analysis-31Mar16.pdf)
+## DREAM3D-NX Help
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
-
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/RodriguesConvertorFilter.md b/src/Plugins/OrientationAnalysis/docs/RodriguesConvertorFilter.md
index 834b3d3d27..f6e0101386 100644
--- a/src/Plugins/OrientationAnalysis/docs/RodriguesConvertorFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/RodriguesConvertorFilter.md
@@ -1,10 +1,10 @@
# Rodrigues Convertor
-## Group (Subgroup) ##
+## Group (Subgroup)
OrientationAnalysis (Processing)
-## Description ##
+## Description
This *filter* will convert a 3 component Rodrigues vector into a 4 component vector that DREAM.3D expects in its
equations and algorithms. The algorithm is the following:
@@ -13,38 +13,16 @@ equations and algorithms. The algorithm is the following:
+ Divide each component by the length
+ Store the length as the 4th component in the output array
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|-----------------------|---------|---------------------------------------------------------------------------------------------------|
-| Delete Original Array | Boolean | Set this to TRUE/ON to have the original 3 component data array deleted at the end of the filter. |
-
-## Required Geometry ##
-
-Required Geometry Type -or- Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|---------------------|------------------------|-------|----------------------|-------------|
-| **Attribute Array** | Rodrigues Input Vector | float | (3) | |
-
-## Created Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|---------------------|------------------------|-------|----------------------|-------------|
-| **Attribute Array** | Rodrigues Ouput Vector | float | (4) | |
-
-## Example Pipelines ##
+## Example Pipelines
List the names of the example pipelines where this filter is used.
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this plugin.
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/RotateEulerRefFrameFilter.md b/src/Plugins/OrientationAnalysis/docs/RotateEulerRefFrameFilter.md
index cb13c9f2af..4a80354457 100644
--- a/src/Plugins/OrientationAnalysis/docs/RotateEulerRefFrameFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/RotateEulerRefFrameFilter.md
@@ -1,46 +1,26 @@
# RotateEulerRefFrame
-## Group (Subgroup) ##
+## Group (Subgroup)
Orientation Analysis (Conversion)
-## Description ##
+## Description
This **Filter** performs a passive rotation (Right hand rule) of the Euler Angles about a user defined axis. The *reference frame* is being rotated and thus the *Euler Angles* necessary to represent the same orientation must change to account for the new *reference frame*. The user can set an *angle* and an *axis* to define the rotation of the *reference frame*.
-## Parameters ##
+% Auto generated parameter table will be inserted here
-| Name | Type | Description |
-|------|------|-------------|
-| Rotation Axis-Angle | float (4x) | Axis-Angle in sample reference frame to rotate about. |
-
-## Required Geometry ##
-
-Not Applicable
-
-## Required Objects ##
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Element Data Array** | EulerAngles | float | (3) | Three angles defining the orientation of the **Cell** in Bunge convention (Z-X-Z) |
-
-## Created Objects ##
-
-None
-
-## Example Pipelines ##
+## Example Pipelines
+ INL Export
+ Export Small IN100 ODF Data (StatsGenerator)
+ Edax IPF Colors
+ Confidence Index Histogram
-## License & Copyright ##
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/WritePoleFigureFilter.md b/src/Plugins/OrientationAnalysis/docs/WritePoleFigureFilter.md
index df2cc6e3ed..8688e14746 100644
--- a/src/Plugins/OrientationAnalysis/docs/WritePoleFigureFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/WritePoleFigureFilter.md
@@ -16,56 +16,15 @@ This **Filter** creates a standard pole figure image for each **Ensemble** in a
2: Discrete Pole figure. The algorithm will simply mark each pixel that had at least 1 count as a black pixel.
-
### Layout
The 3 pole figures can be laid out in a Square, Horizontal row or vertical column. Supporting informatio (including the color bar legend for color pole figures) will also be printed on the image.
------
-
| Lambert Projection | Discrete |
|--------------------|----------|
| ![Example Pole Figure Using Square Layout](Images/PoleFigure_Example.png) | ![Example Pole Figure Using Square Layout](Images/Pole_Figure_Discrete_Example.png) |
------
-
-## Parameters
-
-| Name | Type | Description |
-|------|------| ----------- |
-| Figure Title | String | The title of the figure. |
-| Pole Figure Type | Enumeration: 0=Lambert, 1=Discrete | Controls the type of pole figure |
-| Lambert Image Size (Pixels) | int32_t | Size of the Lambert square in pixels |
-| Number of Colors | int32_t | Number of colors to use to make the pole figure |
-| Image Layout | Enumeration | Layout for the resulting pole figure images, either square, horizontal, or vertical |
-| Image Prefix | String | Prefix the prepend each pole figure file with |
-| Output Path | File Path | Output directory path for images |
-| Image Size (Square Pixels) | int32_t | Size of the output image in square pixels |
-| Use Mask Array | bool | Specifies whether to use a boolean array to exclude some **Cells**. Only those cells that have a *Mask Array* value of 1 will be used. |
-| Save as Image Geometry | Bool | Save the created Pole Figure as an Image Geometry |
-| Output Image Geometry Path | DataPath | The DataPath to the created image geometry |
-
-## Required Geometry
-
-NONE
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Cell Attribute Array** | EulerAngles | float | (3) | Three angles defining the orientation of the **Cell** in Bunge convention (Z-X-Z) |
-| **Cell Attribute Array** | Phases | int32_t | (1) | Specifies to which **Ensemble** each **Cell** belongs |
-| **Cell Attribute Array** | Mask | bool | (1) | Used to define **Cells** as *good* or *bad* |
-| **Ensemble Attribute Array** | CrystalStructures | uint32_t | (1) | Enumeration representing the crystal structure for each **Ensemble** |
-
-## Created Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|------|--------------|------|----------------------|-------------|
-| **Geometry** | ImageGeometry | Image | N/A | Created **Image Geometry** |
-| **Attribute Matrix** | CellData | Cell | N/A | Created **Cell Attribute Matrix** name |
-| **DataArray** | Image | Data Array (uint8) | 4 | Created **DataArray** name |
-
+% Auto generated parameter table will be inserted here
## Example Pipelines
@@ -76,8 +35,6 @@ NONE
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/src/Plugins/OrientationAnalysis/docs/WriteStatsGenOdfAngleFileFilter.md b/src/Plugins/OrientationAnalysis/docs/WriteStatsGenOdfAngleFileFilter.md
index 4bdafc4ff4..1e6c21dde4 100644
--- a/src/Plugins/OrientationAnalysis/docs/WriteStatsGenOdfAngleFileFilter.md
+++ b/src/Plugins/OrientationAnalysis/docs/WriteStatsGenOdfAngleFileFilter.md
@@ -4,7 +4,7 @@
IO (Output)
-## Description
+## Description
This **Filter** is used in a workflow where the user would like to generate a synthetic microstructure with an ODF that matches (as closely as possible) an existing experimental data set or other data set that is being mimicked. The basic workflow is the following:
@@ -19,19 +19,18 @@ This **Filter** is used in a workflow where the user would like to generate a sy
9. Select the file that was just written
10. Load the data and inspect the ODF that was generated
+## Important Change from Earlier Versions of StatsGenerator
-## Important Change from Earlier Versions of StatsGenerator
+StatsGenerator can not load data from standard .ang or .ctf files. If you want to get the ODF from an existing experimental data set and you have one of those files then you must use the functionality of this filter
-**StatsGenerator can not load data from standard .ang or .ctf files. If you want to get the ODF from an existing experimental data set and you have one of those files then you must use the functionality of this filter**
-
-## Notes on Implementation
+## Notes on Implementation
+ A separate file is written for each phase
+ Spaces are the default as the delimiters between values. The user can select another value
-+ Default values of 1.0 are used for both the *weight* and _sigma_. **If the user needs a stronger texture due to a low number of angles then larger values should be used such as 10, 100 or even 1000.**
++ Default values of 1.0 are used for both the *weight* and *sigma*. **If the user needs a stronger texture due to a low number of angles then larger values should be used such as 10, 100 or even 1000.**
+ The user has the option to convert the supplied Euler angles to degrees. **StatsGenerator** is able to import Euler angles as either degrees or radians based on user input, so the output type from this **Filter** could remain as radians or be converted to degrees. The user should remain cognizant of what representation their angles are in so that the correct option is chosen during the import process in **StatsGenerator**
-## Example File
+## Example File
The file written is a simple text file that contains a short comment section and a single *Header* line of data. All comment lines should come **BEFORE** the actual header line. There is a single header line in the form of "Key:Value" and then the lines of data.
@@ -46,15 +45,14 @@ The file written is a simple text file that contains a short comment section and
7.2 3.6 7.2 1 1
10.8 5.4 10.8 1 1
14.4 7.2 14.4 1 1
-
+
The **only** required header line is:
Angle Count:100
There are 5 columns of data which are the 3 Euler Angles, the Weight Value and the Sigma Value.
-
-### Delimiter
+### Delimiter
Choice of delimiter is as follows:
@@ -64,41 +62,16 @@ Choice of delimiter is as follows:
3 = : (colon)
4 = \t (tab)
+% Auto generated parameter table will be inserted here
-## Parameters
-
-| Name | Type | Description |
-|---------|---------| --------------- |
-| Output File | File Path | Output angles file path |
-| Default Weight | float | This value will be used for the Weight column |
-| Default Sigma | int | This value will be used for the Sigma column |
-| Delimiter | Enumeration | The delimiter separating the data |
-| Convert to Degrees | bool | Whether to convert the Euler angles from radians to degrees. If the Euler angles are already in degrees, this option will "convert" the data again, resulting in garbage orientations! |
-| Only Write Good Elements | bool | Whether to only write the Euler angles for those elements denoted as true in the supplied mask array |
-
-
-## Required Objects
-
-| Kind | Default Name | Type | Component Dimensions | Description |
-|-------|---------------------|--------|---------------------------------|-----------------|
-| **Element Attribute Array** | EulerAngles | float | (3) | Three angles defining the orientation of the **Element** in Bunge convention (Z-X-Z) |
-| **Element Attribute Array** | Phases | int32_t | (1) | Specifies to which **Ensemble** each **Element** belongs |
-| **Element Attribute Array** | Mask | bool | (1) | Used to define **Elements** as *good* or *bad*. Only required if *Only Write Good Elements* is checked |
-
-## Created Objects
-
-None
-
-## Example Pipelines
+## Example Pipelines
+ Export Small IN100 ODF Data (StatsGenerator)
-## License & Copyright
+## License & Copyright
Please see the description file distributed with this **Plugin**
-## DREAM3DNX Help
-
-Check out our GitHub community page at [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) to report bugs, ask the community for help, discuss features, or get help from the developers.
-
+## DREAM3D-NX Help
+If you need help, need to file a bug report or want to request a new feature, please head over to the [DREAM3DNX-Issues](https://github.com/BlueQuartzSoftware/DREAM3DNX-Issues) GItHub site where the community of DREAM3D-NX users can help answer your questions.
diff --git a/wrapping/python/docs/CMakeLists.txt b/wrapping/python/docs/CMakeLists.txt
index a086649b08..04dcf9f0ca 100644
--- a/wrapping/python/docs/CMakeLists.txt
+++ b/wrapping/python/docs/CMakeLists.txt
@@ -51,7 +51,7 @@ add_custom_target(sphinx_copy_sources ALL
DEPENDS generate_sphinx_docs
COMMAND ${CMAKE_COMMAND} -E remove_directory "${COMPLEX_SPHINX_DOCS_DIR}/source"
COMMAND ${CMAKE_COMMAND} -E copy_directory "${CMAKE_CURRENT_SOURCE_DIR}/source" "${COMPLEX_SPHINX_DOCS_DIR}/source"
- COMMENT "SPHINX: Copying static doc files to build directory at ${COMPLEX_SPHINX_DOCS_DIR}"
+ COMMENT "COMPLEX Python Docs: Copying static doc files to build directory at ${COMPLEX_SPHINX_DOCS_DIR}"
)
#------------------------------------------------------------------------------
@@ -60,7 +60,7 @@ add_custom_target(sphinx_copy_sources ALL
add_custom_target(sphinx_generate_plugin_rst ALL
DEPENDS sphinx_copy_sources
COMMAND "$"
- COMMENT "SPHINX: Generated Plugin .rst docs file"
+ COMMENT "COMPLEX Python Docs: Generated Plugin .rst docs file"
)
#------------------------------------------------------------------------------
@@ -91,7 +91,7 @@ if(WIN32)
DEPENDS sphinx_generate_plugin_rst
COMMAND "${SPHINX_MAKE_BAT_FILE}" clean
COMMAND "${SPHINX_MAKE_BAT_FILE}" html
- COMMENT "SPHINX: Generating Python HTML Documentation"
+ COMMENT "COMPLEX Python Docs: Generating Python HTML Documentation"
WORKING_DIRECTORY "${COMPLEX_SPHINX_DOCS_DIR}"
)
else()
@@ -99,7 +99,7 @@ else()
DEPENDS sphinx_generate_plugin_rst
COMMAND "/usr/bin/make" clean
COMMAND "/usr/bin/make" html
- COMMENT "SPHINX: Generating Python HTML Documentation"
+ COMMENT "COMPLEX Python Docs: Generating Python HTML Documentation"
WORKING_DIRECTORY "${COMPLEX_SPHINX_DOCS_DIR}"
)
endif()
diff --git a/wrapping/python/docs/generate_sphinx_docs.cpp b/wrapping/python/docs/generate_sphinx_docs.cpp
index 597311c48d..96618a3eef 100644
--- a/wrapping/python/docs/generate_sphinx_docs.cpp
+++ b/wrapping/python/docs/generate_sphinx_docs.cpp
@@ -1,6 +1,12 @@
+#include "complex/Common/Types.hpp"
+#include "complex/Common/TypesUtility.hpp"
#include "complex/Core/Application.hpp"
#include "complex/Filter/FilterHandle.hpp"
#include "complex/Filter/IFilter.hpp"
+#include "complex/Parameters/ArraySelectionParameter.hpp"
+#include "complex/Parameters/GeometrySelectionParameter.hpp"
+#include "complex/Parameters/VectorParameter.hpp"
+#include "complex/Utilities/DataObjectUtilities.hpp"
#include "complex/Utilities/FilterUtilities.hpp"
#include "complex/Utilities/StringUtilities.hpp"
@@ -46,16 +52,30 @@ void GenerateParameterList()
ADD_PARAMETER_TRAIT(complex.DataTypeParameter, "d31358d5-3253-4c69-aff0-eb98618f851b")
ADD_PARAMETER_TRAIT(complex.EnsembleInfoParameter, "10d3924f-b4c9-4e06-9225-ce11ec8dff89")
ADD_PARAMETER_TRAIT(complex.ArrayThresholdsParameter, "e93251bc-cdad-44c2-9332-58fe26aedfbe")
- ADD_PARAMETER_TRAIT(complex.MultiArraySelectionParameter, "d11e0bd8-f227-4fd1-b618-b6f16b259fc8")
ADD_PARAMETER_TRAIT(complex.GenerateColorTableParameter, "7b0e5b25-564e-4797-b154-4324ef276bf0")
ADD_PARAMETER_TRAIT(complex.DataObjectNameParameter, "fbc89375-3ca4-4eb2-8257-aad9bf8e1c94")
ADD_PARAMETER_TRAIT(complex.NeighborListSelectionParameter, "ab0b7a7f-f9ab-4e6f-99b5-610e7b69fc5b")
ADD_PARAMETER_TRAIT(complex.ChoicesParameter, "ee4d5ce2-9582-48fa-b182-8a766ce0feff")
ADD_PARAMETER_TRAIT(complex.GeneratedFileListParameter, "aac15aa6-b367-508e-bf73-94ab6be0058b")
- ADD_PARAMETER_TRAIT(complex.DataGroupCreationParameter, "bff2d4ac-04a6-5251-b188-4f83f7865074")
ADD_PARAMETER_TRAIT(complex.DataPathSelectionParameter, "cd12d081-fbf0-46c4-8f4a-15e2e06e98b8")
ADD_PARAMETER_TRAIT(complex.CalculatorParameter, "ba2d4937-dbec-5536-8c5c-c0a406e80f77")
ADD_PARAMETER_TRAIT(complex.ReadCSVFileParameter, "4f6d6a33-48da-427a-8b17-61e07d1d5b45")
+
+ ADD_PARAMETER_TRAIT(complex.MultiArraySelectionParameter, "d11e0bd8-f227-4fd1-b618-b6f16b259fc8")
+ ADD_PARAMETER_TRAIT(complex.ArraySelectionParameter, "ab047a7f-f9ab-4e6f-99b5-610e7b69fc5b")
+ ADD_PARAMETER_TRAIT(complex.DataGroupSelectionParameter, "bff3d4ac-04a6-5251-b178-4f83f7865074")
+ ADD_PARAMETER_TRAIT(complex.AttributeMatrixSelectionParameter, "a3619d74-a1d9-4bc2-9e03-ca001d65b119")
+ ADD_PARAMETER_TRAIT(complex.GeometrySelectionParameter, "3804cd7f-4ee4-400f-80ad-c5af17735de2")
+
+ ADD_PARAMETER_TRAIT(complex.DataGroupCreationParameter, "bff2d4ac-04a6-5251-b188-4f83f7865074")
+ ADD_PARAMETER_TRAIT(complex.ArrayCreationParameter, "ab047a7d-f81b-4e6f-99b5-610e7b69fc5b")
+
+ ADD_PARAMETER_TRAIT(complex.FileSystemPathParameter, "f9a93f3d-21ef-43a1-a958-e57cbf3b2909")
+ ADD_PARAMETER_TRAIT(complex.BoolParameter, "b6936d18-7476-4855-9e13-e795d717c50f")
+ ADD_PARAMETER_TRAIT(complex.ImportHDF5DatasetParameter, "32e83e13-ee4c-494e-8bab-4e699df74a5a")
+ ADD_PARAMETER_TRAIT(complex.Dream3dImportParameter, "170a257d-5952-4854-9a91-4281cd06f4f5")
+ ADD_PARAMETER_TRAIT(complex.DynamicTableParameter, "eea76f1a-fab9-4704-8da5-4c21057cf44e")
+
ADD_PARAMETER_TRAIT(complex.Int8Parameter, "cae73834-68f8-4235-b010-8bea87d8ff7a")
ADD_PARAMETER_TRAIT(complex.UInt8Parameter, "6c3efeff-ce8f-47c0-83d1-262f2b2dd6cc")
ADD_PARAMETER_TRAIT(complex.Int16Parameter, "44ae56e8-e6e7-4e4d-8128-dd3dc2c6696e")
@@ -66,11 +86,7 @@ void GenerateParameterList()
ADD_PARAMETER_TRAIT(complex.UInt64Parameter, "36d91b23-5500-4ed4-bdf3-d680f54ee5d1")
ADD_PARAMETER_TRAIT(complex.Float32Parameter, "e4452dfe-2f70-4833-819e-0cbbec21289b")
ADD_PARAMETER_TRAIT(complex.Float64Parameter, "f2a18fff-a095-47d7-b436-ede41b5ea21a")
- ADD_PARAMETER_TRAIT(complex.ArraySelectionParameter, "ab047a7f-f9ab-4e6f-99b5-610e7b69fc5b")
- ADD_PARAMETER_TRAIT(complex.FileSystemPathParameter, "f9a93f3d-21ef-43a1-a958-e57cbf3b2909")
- ADD_PARAMETER_TRAIT(complex.DataGroupSelectionParameter, "bff3d4ac-04a6-5251-b178-4f83f7865074")
- ADD_PARAMETER_TRAIT(complex.GeometrySelectionParameter, "3804cd7f-4ee4-400f-80ad-c5af17735de2")
- ADD_PARAMETER_TRAIT(complex.BoolParameter, "b6936d18-7476-4855-9e13-e795d717c50f")
+
ADD_PARAMETER_TRAIT(complex.VectorInt8Parameter, "9f5f9683-e492-4a79-8378-79d727b2356a")
ADD_PARAMETER_TRAIT(complex.VectorUInt8Parameter, "bff78ff3-35ef-482a-b3b1-df8806e7f7ef")
ADD_PARAMETER_TRAIT(complex.VectorInt16Parameter, "43810a29-1a5f-4472-bec6-41de9ffe27f7")
@@ -81,13 +97,177 @@ void GenerateParameterList()
ADD_PARAMETER_TRAIT(complex.VectorUInt64Parameter, "17309744-c4e8-4d1e-807e-e7012387f1ec")
ADD_PARAMETER_TRAIT(complex.VectorFloat32Parameter, "88f231a1-7956-41f5-98b7-4471705d2805")
ADD_PARAMETER_TRAIT(complex.VectorFloat64Parameter, "57cbdfdf-9d1a-4de8-95d7-71d0c01c5c96")
- ADD_PARAMETER_TRAIT(complex.AttributeMatrixSelectionParameter, "a3619d74-a1d9-4bc2-9e03-ca001d65b119")
- ADD_PARAMETER_TRAIT(complex.ImportHDF5DatasetParameter, "32e83e13-ee4c-494e-8bab-4e699df74a5a")
- ADD_PARAMETER_TRAIT(complex.Dream3dImportParameter, "170a257d-5952-4854-9a91-4281cd06f4f5")
- ADD_PARAMETER_TRAIT(complex.DynamicTableParameter, "eea76f1a-fab9-4704-8da5-4c21057cf44e")
- ADD_PARAMETER_TRAIT(complex.ArrayCreationParameter, "ab047a7d-f81b-4e6f-99b5-610e7b69fc5b")
}
+std::string ParseScalarType(const std::string& paramType)
+{
+ std::string temp = complex::StringUtilities::replace(paramType, "complex.", "Scalar Value |");
+ temp = complex::StringUtilities::replace(temp, "Parameter", "");
+ // temp = complex::StringUtilities::replace(temp, "Vector", " (Vector)");
+ return temp;
+}
+
+// std::string ParseVectorType(const std::string& paramType)
+//{
+// std::string temp = complex::StringUtilities::replace(paramType, "complex.", "");
+// temp = complex::StringUtilities::replace(temp, "Vector", "Vector of Values |");
+// temp = complex::StringUtilities::replace(temp, "Parameter", "");
+//
+// return temp;
+// }
+
+bool CheckScalarPrimitive(std::ostream& rstStream, const complex::AnyParameter& paramValue)
+{
+
+ static const std::set scalarPrimitives = {
+ complex::Uuid::FromString("a8ff9dbd-45e7-4ed6-8537-12dd53069bce").value(), complex::Uuid::FromString("44ae56e8-e6e7-4e4d-8128-dd3dc2c6696e").value(),
+ complex::Uuid::FromString("156a6f46-77e5-41d8-8f5a-65ba1da52f2a").value(), complex::Uuid::FromString("21acff45-a653-45db-a0d1-f43cd344b93a").value(),
+ complex::Uuid::FromString("e9521130-276c-40c7-95d7-0b4cb4f80649").value(), complex::Uuid::FromString("b2039349-bd3a-4dbb-93d2-b4b5c633e697").value(),
+ complex::Uuid::FromString("36d91b23-5500-4ed4-bdf3-d680f54ee5d1").value(), complex::Uuid::FromString("e4452dfe-2f70-4833-819e-0cbbec21289b").value(),
+ complex::Uuid::FromString("f2a18fff-a095-47d7-b436-ede41b5ea21a").value(), complex::Uuid::FromString("e9521130-276c-40c7-95d7-0b4cb4f80649").value()};
+
+ if(scalarPrimitives.find(paramValue->uuid()) != scalarPrimitives.end())
+ {
+ rstStream << "| " << paramValue->humanName() << " | " << ParseScalarType(s_ParameterMap[paramValue->uuid()]) << " | " << paramValue->helpText() << " |\n";
+ return true;
+ }
+ return false;
+}
+
+bool CheckVectorPrimitive(std::ostream& rstStream, const complex::AnyParameter& paramValue)
+{
+ static const std::set vectorPrimitives = {
+ complex::Uuid::FromString("9f5f9683-e492-4a79-8378-79d727b2356a").value(), complex::Uuid::FromString("bff78ff3-35ef-482a-b3b1-df8806e7f7ef").value(),
+ complex::Uuid::FromString("43810a29-1a5f-4472-bec6-41de9ffe27f7").value(), complex::Uuid::FromString("2f1ba2f4-c5d5-403c-8b90-0bf60d2bde9b").value(),
+ complex::Uuid::FromString("d3188e18-e383-4727-ab32-88b5fda56ae8").value(), complex::Uuid::FromString("37322aa6-1a2f-4ecb-9aa1-8922d7ac1e49").value(),
+ complex::Uuid::FromString("4ceaffc1-7326-4f65-a33a-eae263dc22d1").value(), complex::Uuid::FromString("17309744-c4e8-4d1e-807e-e7012387f1ec").value(),
+ complex::Uuid::FromString("88f231a1-7956-41f5-98b7-4471705d2805").value(), complex::Uuid::FromString("57cbdfdf-9d1a-4de8-95d7-71d0c01c5c96").value()};
+
+ std::string paramTypeName = complex::StringUtilities::replace(s_ParameterMap[paramValue->uuid()], "complex.", "");
+ paramTypeName = complex::StringUtilities::replace(paramTypeName, "Vector", "");
+ paramTypeName = complex::StringUtilities::replace(paramTypeName, "Parameter", "");
+
+ if(vectorPrimitives.find(paramValue->uuid()) != vectorPrimitives.end())
+ {
+ const VectorParameterBase* paramPtr = dynamic_cast(paramValue.get());
+ rstStream << "| " << paramValue->humanName() << " | Vector of " << paramTypeName << " Values | Order=";
+
+ auto names = paramPtr->names();
+ int i = 0;
+ for(const auto& name : names)
+ {
+ rstStream << name;
+ i++;
+ if(i != names.size())
+ {
+ rstStream << ",";
+ }
+ }
+
+ rstStream << " | " << paramValue->helpText() << " |\n";
+ return true;
+ }
+ return false;
+}
+
+/**
+ *
+ * @param rstStream
+ * @param paramValue
+ * @return
+ */
+bool CheckArraySelectionParameter(std::ostream& rstStream, const complex::AnyParameter& paramValue)
+{
+ static const std::set param = {complex::Uuid::FromString("ab047a7f-f9ab-4e6f-99b5-610e7b69fc5b").value()};
+
+ std::string paramTypeName = s_ParameterMap[paramValue->uuid()];
+ paramTypeName = complex::StringUtilities::replace(paramTypeName, "complex.", "");
+ paramTypeName = complex::StringUtilities::replace(paramTypeName, "Parameter", "");
+ paramTypeName = complex::StringUtilities::replace(paramTypeName, "Selection", " Selection");
+ const ArraySelectionParameter* paramPtr = dynamic_cast(paramValue.get());
+ if(paramPtr != nullptr)
+ {
+ rstStream << "| " << paramValue->humanName() << " | " << paramTypeName << " | Allowed Types: ";
+ auto allowedTypes = paramPtr->allowedTypes();
+ int i = 0;
+ for(const auto& allowedType : allowedTypes)
+ {
+ rstStream << complex::DataTypeToString(allowedType).str();
+ i++;
+ if(i != allowedTypes.size())
+ {
+ rstStream << ", ";
+ }
+ }
+ auto compShapes = paramPtr->requiredComponentShapes();
+ if(!compShapes.empty())
+ {
+ rstStream << " Comp. Shape: ";
+ }
+ for(const auto& compShape : compShapes)
+ {
+ rstStream << fmt::format("{}", fmt::join(compShape, ","));
+ }
+ rstStream << " | " << paramValue->helpText() << " |\n";
+ return true;
+ }
+
+ return false;
+}
+
+bool CheckGeometrySelectionParameter(std::ostream& rstStream, const complex::AnyParameter& paramValue)
+{
+ static const std::set param = {complex::Uuid::FromString("d11e0bd8-f227-4fd1-b618-b6f16b259fc8").value()};
+
+ std::string paramTypeName = s_ParameterMap[paramValue->uuid()];
+ paramTypeName = complex::StringUtilities::replace(paramTypeName, "complex.", "");
+ paramTypeName = complex::StringUtilities::replace(paramTypeName, "Parameter", "");
+ paramTypeName = complex::StringUtilities::replace(paramTypeName, "Selection", " Selection");
+ const GeometrySelectionParameter* paramPtr = dynamic_cast(paramValue.get());
+ if(paramPtr != nullptr)
+ {
+
+ rstStream << "| " << paramValue->humanName() << " | " << paramTypeName << " | ";
+
+ auto allowedTypes = paramPtr->allowedTypes();
+ int i = 0;
+ for(const auto& allowedType : allowedTypes)
+ {
+ rstStream << complex::GeometryTypeToString(allowedType).str();
+ i++;
+ if(i != allowedTypes.size())
+ {
+ rstStream << ", ";
+ }
+ }
+
+ rstStream << " | " << paramValue->helpText() << " |\n";
+ return true;
+ }
+
+ return false;
+}
+
+/**
+ *
+ * @param rstStream
+ * @param paramValue
+ */
+void CheckParameter(std::ostream& rstStream, const complex::AnyParameter& paramValue)
+{
+ std::string paramTypeName = s_ParameterMap[paramValue->uuid()];
+ paramTypeName = complex::StringUtilities::replace(paramTypeName, "complex.", "");
+ paramTypeName = complex::StringUtilities::replace(paramTypeName, "Parameter", " | ");
+
+ rstStream << "| " << paramValue->humanName() << " | " << paramTypeName << " | " << paramValue->helpText() << " |\n";
+}
+
+/**
+ *
+ * @param filePath
+ * @param trimLine
+ * @return
+ */
std::vector ReadFile(const std::filesystem::path& filePath, bool trimLine)
{
std::ifstream file = std::ifstream(filePath);
@@ -298,10 +478,197 @@ std::vector FindTableColumnWidths(const Parameters& parameters)
return {maxUIDisplay, maxPythonArg};
}
+std::vector ConvertFilterDoc(const std::filesystem::path& docFilePath)
+{
+ // Open the existing doc file
+ // Extract out the first paragraph of the Filter's markdown documentation after the ## Description section marker
+ std::vector mdLines = ReadFile(docFilePath, false);
+ std::vector outputLines;
+ std::stringstream mdStream;
+ bool extractLines = true;
+ for(const auto& line : mdLines)
+ {
+ if(complex::StringUtilities::starts_with(line, "## Parameters"))
+ {
+ extractLines = false;
+ continue;
+ }
+
+ if(complex::StringUtilities::starts_with(line, "## Example Pipelines"))
+ {
+ extractLines = true;
+ outputLines.push_back("@PARAMETER_TABLE@");
+ }
+
+ if(!extractLines && complex::StringUtilities::starts_with(line, "## License & Copyright"))
+ {
+ extractLines = true;
+ outputLines.push_back("@PARAMETER_TABLE@");
+ }
+ if(extractLines)
+ {
+ outputLines.push_back(line);
+ }
+ }
+
+ return outputLines;
+}
+
+void GenerateMarkdownFilterParameterTable()
+{
+ auto* filterListPtr = Application::Instance()->getFilterList();
+
+ // Loop over each plugin and create a .rst file
+ const auto pluginListPtr = Application::Instance()->getPluginList();
+ for(const auto& plugin : pluginListPtr)
+ {
+ std::string plugName = plugin->getName();
+ const std::string pluginRootDir = fmt::format("{}", s_PluginDirMap[plugName]);
+ if(pluginRootDir.empty())
+ {
+ continue;
+ }
+
+ // This will alphabetize the filter list
+ const auto& pluginFilterHandles = plugin->getFilterHandles();
+ std::map> filterHandles;
+ for(const auto& filterHandle : pluginFilterHandles)
+ {
+ filterHandles[filterHandle.getClassName()] = {filterHandle.getFilterId(), filterHandle.getPluginId()};
+ }
+
+ // Loop on each Filter
+ for(const auto& filterHandleIter : filterHandles)
+ {
+ std::string filterClassName = filterHandleIter.first;
+ FilterHandle const filterHandle(filterHandleIter.second.first, filterHandleIter.second.second);
+ IFilter::UniquePointer filter = filterListPtr->createFilter(filterHandle);
+
+ std::stringstream pTableStream;
+
+ // std::vector columnWidths = FindTableColumnWidths(parameters);
+ int needTableHeader = 0;
+
+ const auto& parameters = filter->parameters();
+
+ for(const auto& layoutObj : parameters.getLayout())
+ {
+ if(std::holds_alternative(layoutObj))
+ {
+
+ if(needTableHeader == 0)
+ {
+ pTableStream << "### Filter Parameters\n\n";
+ pTableStream << "| Parameter Name | Parameter Type | Parameter Notes | Description |\n";
+ pTableStream << "|----------------|----------------|-----------------|-------------|\n";
+ }
+
+ std::string key = std::get(layoutObj).key;
+ const auto& paramValue = parameters.at(key);
+ if(CheckScalarPrimitive(pTableStream, paramValue))
+ {
+ continue;
+ }
+ if(CheckVectorPrimitive(pTableStream, paramValue))
+ {
+ continue;
+ }
+ if(CheckArraySelectionParameter(pTableStream, paramValue))
+ {
+ continue;
+ }
+ if(CheckGeometrySelectionParameter(pTableStream, paramValue))
+ {
+ continue;
+ }
+ CheckParameter(pTableStream, paramValue);
+ }
+ else
+ {
+ std::string key = std::get(layoutObj).name;
+ pTableStream << "\n";
+ pTableStream << "### " << key << "\n\n";
+ pTableStream << "| Parameter Name | Parameter Type | Parameter Notes | Description |\n";
+ pTableStream << "|----------------|----------------|-----------------|-------------|\n";
+ }
+ needTableHeader++;
+ }
+
+#if SOMETHING
+ for(const auto& parameter : parameters)
+ {
+ auto const& paramValue = parameter.second;
+ if(paramValue->helpText().empty())
+ {
+ std::cout << filter->name() << "::" << paramValue->name() << " HELP Text is empty\n";
+ }
+ for(const auto& letter : paramValue->name())
+ {
+ if(::isupper(letter) != 0)
+ {
+ std::cout << filter->name() << "::" << paramValue->name() << " HAS CAPS. Should be lower snake case\n";
+ break;
+ }
+ }
+
+ if(CheckScalarPrimitive(pTableStream, paramValue))
+ {
+ continue;
+ }
+ if(CheckVectorPrimitive(pTableStream, paramValue))
+ {
+ continue;
+ }
+ if(CheckArraySelectionParameter(pTableStream, paramValue))
+ {
+ continue;
+ }
+ if(CheckGeometrySelectionParameter(pTableStream, paramValue))
+ {
+ continue;
+ }
+ CheckParameter(pTableStream, paramValue);
+ }
+#endif
+
+ pTableStream << '\n';
+
+ // Read the Current Filter's Documentation File
+ const std::filesystem::path docFilePath = fmt::format("{}/docs/{}.md", pluginRootDir, filterClassName);
+ std::vector filterDocContents = ConvertFilterDoc(docFilePath);
+
+ // Create a new output file
+ const std::filesystem::path rstFilePath = fmt::format("{}/nx_docs/source/{}/{}.md", COMPLEX_BUILD_DIR, plugName, filterClassName);
+ const Result<> createDirectoriesResult = complex::CreateOutputDirectories(rstFilePath.parent_path());
+
+ std::ofstream rstStream = std::ofstream(rstFilePath, std::ios_base::binary | std::ios_base::trunc);
+ if(!rstStream.is_open())
+ {
+ std::cout << "ERROR:" << rstFilePath << "\n";
+ return;
+ }
+
+ rstStream << "```{index} single: Filters; " << filter->humanName() << "\n```\n";
+
+ for(const auto& line : filterDocContents)
+ {
+ if(line == "@PARAMETER_TABLE@")
+ {
+ rstStream << pTableStream.str();
+ }
+ else
+ {
+ rstStream << line << "\n";
+ }
+ }
+ }
+ }
+}
+
/**
* @brief
*/
-void GenerateRstFilterDocs()
+void GeneratePythonRstFiles()
{
auto* filterListPtr = Application::Instance()->getFilterList();
@@ -466,7 +833,7 @@ std::string ReadIndexTemplateFile(const std::filesystem::path& path)
/**
* @brief Generates the index.rst file for the sphinx docs
*/
-void GenerateIndexRstFile()
+void GeneratePythonSphinxIndex()
{
std::string indexTemplate;
{
@@ -515,18 +882,21 @@ void GenerateIndexRstFile()
*/
int main(int32_t argc, char** argv)
{
- try
+ // try
{
GenerateParameterList();
Application app;
app.loadPlugins(COMPLEX_BIN_DIR, true);
- GenerateRstFilterDocs();
- GenerateIndexRstFile();
- } catch(const std::exception& except)
+ GeneratePythonRstFiles();
+ GeneratePythonSphinxIndex();
+
+ GenerateMarkdownFilterParameterTable();
+ }
+ // catch(const std::exception& except)
{
- std::cout << "RST Doc Generator threw a runtime exception which should NOT happen" << std::endl;
+ // std::cout << "RST Doc Generator threw a runtime exception which should NOT happen" << std::endl;
}
return 0;
}
diff --git a/wrapping/python/docs/index_template.rst b/wrapping/python/docs/index_template.rst
index 86830c4dc4..d98a189cde 100644
--- a/wrapping/python/docs/index_template.rst
+++ b/wrapping/python/docs/index_template.rst
@@ -5,6 +5,17 @@
DREAM3D-NX Python Docs
================================
+The *complex* library can be installed through an Anaconda packages from the *BlueQuartzSoftware* channel. This can be achieved
+by creating a new virtual environment
+
+.. code:: shell
+
+ conda config --add channels conda-forge
+ conda config --set channel_priority strict
+ conda create -n cxpython python=3.9
+ conda activate cxpython
+ conda install -c bluequartzsoftware complex
+
.. toctree::
:maxdepth: 3
:caption: Contents:
@@ -23,6 +34,3 @@ Indices and tables
* :ref:`genindex`
* :ref:`modindex`
-* :ref:`search`
-
-
diff --git a/wrapping/python/docs/source/DataObjects.rst b/wrapping/python/docs/source/DataObjects.rst
index 7697eab748..8527f1b16e 100644
--- a/wrapping/python/docs/source/DataObjects.rst
+++ b/wrapping/python/docs/source/DataObjects.rst
@@ -30,6 +30,20 @@ This is the abstract base class for all other objects that can be inserted into
DataStructure_ . It should never be used as the appropriate class from the list
below should be used instead.
+
+DataPath
+---------
+
+A DataPath is a complex class that describes the path to a :ref:`DataObject` within
+the DataStructure_ . The path is constructed as a python list of string objects.
+For example if we have a top level group called **MyGroup** and a `DataArray`
+called *Euler Angles* within that group the **DataPath** object that would be constructed is the following
+
+.. code:: python
+
+ array_path = cx.DataPath(['MyGroup', 'Euler Angles'])
+
+
.. _DataGroup:
DataGroup
@@ -48,17 +62,6 @@ any needed DataGroups.
.. _DataPath:
-DataPath
----------
-
-A DataPath is a complex class that describes the path to a :ref:`DataObject` within
-the DataStructure_ . The path is constructed as a python list of string objects.
-For example if we have a top level group called **MyGroup** and a `DataArray`
-called *Euler Angles* within that group the **DataPath** object that would be constructed is the following
-
-.. code:: python
-
- array_path = cx.DataPath(['MyGroup', 'Euler Angles'])
.. _DataArray: