ENH: Improvements and Bug Fixes to Orientation Analysis filters. (#1081)

* MergeTwins: Only get the LaueOps list once when the MergeTwins class is instantiated.
* ENH: Various updates to Compute Feature Face Curvature filters
    * Create parameter defaults for Feature Face Curvature filter
    *  Docs and new pipeline included.
* Update CMake Policies
* CMAKE: Check for proper version of CMake before setting policy
* BUG: Fix human name of ComputeFZQuaternions
* STYLE: Remove bad comment from WritePoleFigure
* Update TiffWriter to properly order the tiff tags in ascending order.
* Fix pole figure generation. Add improved IPF Legends
* COMP: Update to EbsdLib 1.0.33
* PY: Update conda build specs for newer EbsdLib 1.0.33
* DOC: Fix sphinx warnings

Signed-off-by: Michael Jackson <[email protected]>

---------

Signed-off-by: Michael Jackson <[email protected]>

CMakeLists.txt

@@ -1,5 +1,20 @@
 cmake_minimum_required(VERSION 3.26)
 
+cmake_policy(SET CMP0074 NEW) # ``find_package()`` uses ``<PackageName>_ROOT`` variables.
+cmake_policy(SET CMP0077 NEW) # ``option()`` honors normal variables.
+cmake_policy(SET CMP0080 NEW) # ``BundleUtilities`` cannot be included at configure time.
+
+# The ``FindPythonInterp`` and ``FindPythonLibs`` modules are removed.
+# if(CMAKE_VERSION VERSION_GREATER "3.27.0")
+#   cmake_policy(SET CMP0148 NEW)
+# endif()
+
+# resolves symlinks before collapsing ../ components.
+if(CMAKE_VERSION VERSION_GREATER "3.28.0")
+  cmake_policy(SET CMP0152 NEW)
+endif()
+
+
 include(${CMAKE_CURRENT_LIST_DIR}/cmake/Utility.cmake)
 
 # ------------------------------------------------------------------------------
@@ -123,9 +138,7 @@ file(WRITE ${FETCH_FILE_PATH} "# -----------------------------------------------
 # The WORKING_DIRECTORY is set to the following CMake code:
 # ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/$<$<CONFIG:Debug>:Debug>$<$<CONFIG:Release>:Release>
 # -----------------------------------------------------------------------\n
-cmake_policy(SET CMP0012 NEW)
-cmake_policy(SET CMP0054 NEW)\n
-")
+cmake_policy(SET CMP0012 NEW)\ncmake_policy(SET CMP0054 NEW)\ncmake_policy(SET CMP0152 NEW)\ncmake_policy(SET CMP0148 NEW)")
 
 set(TEST_WORKING_DIR "${CMAKE_LIBRARY_OUTPUT_DIRECTORY}")
 if(CMAKE_GENERATOR MATCHES "Visual Studio")

cmake/Summary.cmake

@@ -58,6 +58,7 @@ message(STATUS "* span-lite (${span-lite_VERSION}) ${span-lite_DIR}")
 message(STATUS "* boost_mp11 (${boost_mp11_VERSION}) ${boost_mp11_DIR}")
 message(STATUS "* nod (${nod_VERSION}) ${nod_DIR}")
 message(STATUS "* reproc++ (${reproc_VERSION}) ${reproc++_DIR}")
+message(STATUS "* EbsdLib (${EbsdLib_VERSION}) ${EbsdLib_DIR}")
 
 message(STATUS "* -------------- Simplnx Configuration Options -------------------------------------")
 message(STATUS "* SIMPLNX_BUILD_TESTS: ${SIMPLNX_BUILD_TESTS}")

cmake/UseEbsdLib.cmake

@@ -0,0 +1,26 @@
+# ------------------------------------------------------------------------------
+# Required EbsdLib and H5Support
+# ------------------------------------------------------------------------------
+
+if(SIMPLNX_BUILD_EBSDLIB)
+  find_package(H5Support REQUIRED)
+  find_package(EbsdLib REQUIRED)
+else()
+
+    if(NOT TARGET EbsdLib::EbsdLib)
+
+        if(EXISTS "${simplnx_SOURCE_DIR}/../EbsdLib")
+            set(EbsdLibProj_SOURCE_DIR "${simplnx_SOURCE_DIR}/../EbsdLib")
+        else()
+            message(FATAL_ERROR "EbsdLibProj_SOURCE_DIR was not set. Where is the EbsdLib project directory. Please set the EbsdLibProj_SOURCE_DIR variable to the EbsdLib directory.")
+        endif()
+        message(STATUS "EbsdLibProj_SOURCE_DIR: ${EbsdLibProj_SOURCE_DIR}")
+
+        set(EbsdLib_ENABLE_HDF5 ON)
+        set(EbsdLib_USE_PARALLEL_ALGORITHMS ${SIMPLNX_ENABLE_MULTICORE})
+        set(EbsdLib_BUILD_H5SUPPORT ON)
+        set(H5Support_INCLUDE_QT_API OFF)
+        add_subdirectory( ${EbsdLibProj_SOURCE_DIR} ${PROJECT_BINARY_DIR}/EbsdLib)
+    endif()
+endif()
+

conda/meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "simplnx" %}
-{% set version = "24.08.10" %}
+{% set version = "24.09.30" %}
 
 package:
   name: {{ name|lower }}
@@ -9,7 +9,7 @@ source:
   - path: ../
     folder: simplnx
   - git_url: https://github.com/BlueQuartzSoftware/EbsdLib
-    git_rev: v1.0.30
+    git_rev: v1.0.33
     folder: EbsdLib
   - git_url: https://github.com/BlueQuartzSoftware/H5Support
     git_rev: v1.0.13
@@ -25,9 +25,6 @@ source:
     folder: span-lite
   - url: https://raw.githubusercontent.com/BlueQuartzSoftware/simplnx-registry/9a5db7b5fa02b2495eb51654cbaab3c63820c779/ports/nod/CMakeLists.txt
     folder: nod
-  - git_url: https://github.com/insightsoftwareconsortium/ITK
-    git_rev: v5.4.0
-    folder: itk
 
 build:
   number: 0
@@ -78,4 +75,4 @@ test:
 about:
   home: https://www.dream3d.io/
   license: BSD
-  summary: DREAM3D-NX consists of data analysis tools (Filters) that allow for the construction of customized workflows (Pipelines) to analyze data.
+  summary: simplnx consists of data analysis tools (Filters) that allow for the construction of customized workflows (Pipelines) to analyze data.

src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/MergeTwins.cpp

@@ -8,7 +8,6 @@
 #include "EbsdLib/Core/EbsdLibConstants.h"
 #include "EbsdLib/Core/Orientation.hpp"
 #include "EbsdLib/Core/Quaternion.hpp"
-#include "EbsdLib/LaueOps/LaueOps.h"
 
 #include <random>
 
@@ -21,6 +20,7 @@ MergeTwins::MergeTwins(DataStructure& dataStructure, const IFilter::MessageHandl
 , m_ShouldCancel(shouldCancel)
 , m_MessageHandler(mesgHandler)
 {
+  m_OrientationOps = LaueOps::GetAllOrientationOps();
 }
 
 // -----------------------------------------------------------------------------
@@ -76,7 +76,6 @@ bool MergeTwins::determineGrouping(int32 referenceFeature, int32 neighborFeature
   auto axisToleranceRad = m_InputValues->AxisTolerance * numbers::pi_v<float32> / 180.0f;
 
   bool twin = false;
-  std::vector<LaueOps::Pointer> m_OrientationOps = LaueOps::GetAllOrientationOps();
 
   if(featureParentIds[neighborFeature] == -1 && phases[referenceFeature] > 0 && phases[neighborFeature] > 0)
   {

src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/MergeTwins.hpp

@@ -2,6 +2,7 @@
 
 #include "OrientationAnalysis/OrientationAnalysis_export.hpp"
 
+#include "EbsdLib/LaueOps/LaueOps.h"
 #include "simplnx/DataStructure/DataPath.hpp"
 #include "simplnx/DataStructure/DataStructure.hpp"
 #include "simplnx/Filter/IFilter.hpp"
@@ -50,6 +51,8 @@ class ORIENTATIONANALYSIS_EXPORT MergeTwins
   const MergeTwinsInputValues* m_InputValues = nullptr;
   const std::atomic_bool& m_ShouldCancel;
   const IFilter::MessageHandler& m_MessageHandler;
+
+  std::vector<LaueOps::Pointer> m_OrientationOps;
 };
 
 } // namespace nx::core

src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/WritePoleFigure.cpp

@@ -72,7 +72,7 @@ class ComputeIntensityStereographicProjection
       float* xyzPtr = m_XYZCoords->getPointer(0);
       for(size_t i = 0; i < numCoords; i++)
       {
-        if(xyzPtr[i * 3 + 2] < 0.0f)
+        if(xyzPtr[i * 3 + 2] < 0.0f) // If the unit sphere data is in the southern hemisphere
         {
           xyzPtr[i * 3 + 0] *= -1.0f;
           xyzPtr[i * 3 + 1] *= -1.0f;
@@ -474,8 +474,6 @@ typename EbsdDataArray<T>::Pointer flipAndMirrorPoleFigure(EbsdDataArray<T>* src
 {
   typename EbsdDataArray<T>::Pointer converted = EbsdDataArray<T>::CreateArray(config.imageDim * config.imageDim, src->getComponentDimensions(), src->getName(), true);
   // We need to flip the image "vertically", which means the bottom row becomes
-  // the top row and convert from BGRA to RGBA ordering (This is a Little Endian code)
-  // If this is ever compiled on a BIG ENDIAN machine the colors will be off.
   for(int y = 0; y < config.imageDim; y++)
   {
     const int destY = config.imageDim - 1 - y;

src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/ComputeFZQuaternionsFilter.cpp

@@ -133,7 +133,7 @@ Uuid ComputeFZQuaternionsFilter::uuid() const
 //------------------------------------------------------------------------------
 std::string ComputeFZQuaternionsFilter::humanName() const
 {
-  return "Compute Reduction Orientations to Fundamental Zone";
+  return "Compute Fundamental Zone Orientations";
 }
 
 //------------------------------------------------------------------------------
@@ -279,7 +279,7 @@ Result<> ComputeFZQuaternionsFilter::executeImpl(DataStructure& dataStructure, c
     algArrays.push_back(maskArray);
   }
 
-  // Parallel algorithm to find duplicate nodes
+  // Parallel algorithm
   ParallelDataAlgorithm dataAlg;
   dataAlg.setRange(0ULL, static_cast<size_t>(quatArray.getNumberOfTuples()));
   dataAlg.requireArraysInMemory(algArrays);

src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/WritePoleFigureFilter.cpp

@@ -98,10 +98,10 @@ Parameters WritePoleFigureFilter::parameters() const
   params.insert(std::make_unique<Int32Parameter>(k_LambertSize_Key, "Lambert Image Size (Pixels)", "The height/width of the internal Lambert Square that is used for interpolation", 64));
   params.insert(std::make_unique<Int32Parameter>(k_NumColors_Key, "Number of Colors", "The number of colors to use for the Color Intensity pole figures", 32));
 
-  params.insertSeparator(Parameters::Separator{"Input Cell Data"});
-  params.insert(std::make_unique<ArraySelectionParameter>(k_CellEulerAnglesArrayPath_Key, "Cell Euler Angles", "Three angles defining the orientation of the Element in Bunge convention (Z-X-Z)",
+  params.insertSeparator(Parameters::Separator{"Input Orientation Data"});
+  params.insert(std::make_unique<ArraySelectionParameter>(k_CellEulerAnglesArrayPath_Key, "Euler Angles", "Three angles defining the orientation of the Element in Bunge convention (Z-X-Z)",
                                                           DataPath{}, ArraySelectionParameter::AllowedTypes{DataType::float32}, ArraySelectionParameter::AllowedComponentShapes{{3}}));
-  params.insert(std::make_unique<ArraySelectionParameter>(k_CellPhasesArrayPath_Key, "Cell Phases", "Specifies to which Ensemble each cell belongs", DataPath{},
+  params.insert(std::make_unique<ArraySelectionParameter>(k_CellPhasesArrayPath_Key, "Phases", "Specifies to which Ensemble each Euler angle belongs", DataPath{},
                                                           ArraySelectionParameter::AllowedTypes{DataType::int32}, ArraySelectionParameter::AllowedComponentShapes{{1}}));
   params.insertSeparator(Parameters::Separator{"Optional Data Mask"});
   params.insertLinkableParameter(std::make_unique<BoolParameter>(k_UseMask_Key, "Use Mask Array", "Should the algorithm use a mask array to remove non-indexed points", false));

src/Plugins/OrientationAnalysis/src/OrientationAnalysis/utilities/TiffWriter.cpp

@@ -56,27 +56,29 @@ std::pair<int32_t, std::string> TiffWriter::WriteImage(const std::string& filepa
   // Generate the offset into the Image File Directory (ifd) which we are going to write first
   constexpr uint32_t ifdOffset = 8;
   outputFile.write(reinterpret_cast<const char*>(&ifdOffset), sizeof(ifdOffset));
-
+  const int k_NumTags = 12;
   std::vector<TIFTAG> tags;
-  tags.push_back(TIFTAG{0x00FE, 0x0004, 1, 0x00000000});                       // NewSubfileType
-  tags.push_back(TIFTAG{0x0100, 0x0004, 1, width});                            // ImageWidth
-  tags.push_back(TIFTAG{0x0101, 0x0004, 1, height});                           // ImageLength
-  tags.push_back(TIFTAG{0x0102, 0x0003, 1, 8 * sizeof(char)});                 // BitsPerSample
-  tags.push_back(TIFTAG{0x0103, 0x0003, 1, 0x0001});                           // Compression
-  tags.push_back(TIFTAG{0x0106, 0x0003, 1, photometricInterpretation});        // PhotometricInterpretation  // For SamplesPerPixel = 3 or 4 (RGB or RGBA)
+  tags.push_back(TIFTAG{0x00FE, 0x0004, 1, 0x00000000});                // NewSubfileType
+  tags.push_back(TIFTAG{0x0100, 0x0004, 1, width});                     // ImageWidth
+  tags.push_back(TIFTAG{0x0101, 0x0004, 1, height});                    // ImageLength
+  tags.push_back(TIFTAG{0x0102, 0x0003, 1, 8 * sizeof(char)});          // BitsPerSample
+  tags.push_back(TIFTAG{0x0103, 0x0003, 1, 0x0001});                    // Compression
+  tags.push_back(TIFTAG{0x0106, 0x0003, 1, photometricInterpretation}); // PhotometricInterpretation  // For SamplesPerPixel = 3 or 4 (RGB or RGBA)
+  // Now compute the offset to the image data so that we can put that into the tag.
+  // The math on this ONLY Works if we have 11 total Tags.
+  // IF YOU ADD MORE TAGS, YOU NEED TO ADJUST THE NEXT LINE OF CODE
+  int32_t imageDataOffset = static_cast<int32_t>(8 + (k_NumTags * 12) + 6); // Header + tags + IDF Tag entry count and Next IFD Offset
+  tags.push_back(TIFTAG{0x0111, 0x0004, 1, imageDataOffset});               // StripOffsets
+
   tags.push_back(TIFTAG{0x0112, 0x0003, 1, 1});                                // Orientation
   tags.push_back(TIFTAG{0x0115, 0x0003, 1, samplesPerPixel});                  // SamplesPerPixel
   tags.push_back(TIFTAG{0x0116, 0x0004, 1, height});                           // RowsPerStrip
   tags.push_back(TIFTAG{0x0117, 0x0004, 1, width * height * samplesPerPixel}); // StripByteCounts
+
   // TIFTAG XResolution;
   // TIFTAG YResolution;
   // TIFTAG ResolutionUnit;
-  tags.push_back(TIFTAG{0x011c, 0x0003, 1, 0x0001}); // PlanarConfiguration
-
-  // Now compute the offset to the image data so that we can put that into the tag.
-  // THESE NEXT 2 LINES MUST BE THE LAST TAG TO BE PUSHED BACK INTO THE VECTOR OR THE MATH WILL BE WRONG
-  const int32_t imageDataOffset = static_cast<int32_t>(8 + ((tags.size() + 1) * 12) + 6); // Header + tags + IDF Tag entry count and Next IFD Offset
-  tags.push_back(TIFTAG{0x0111, 0x0004, 1, imageDataOffset});                             // StripOffsets
+  tags.push_back(TIFTAG{0x011c, 0x0003, 1, 0x0001}); // PlanarConfiguration // 284
 
   // Write the number of tags to the IFD section
   uint16_t numEntries = static_cast<uint16_t>(tags.size());

src/Plugins/SimplnxCore/docs/AppendImageGeometryFilter.md

@@ -13,11 +13,11 @@ This filter also has an option to mirror the resulting geometry in the chosen di
 
 ### X Direction Examples
 
-#### Example 1
+#### Example 1 (X)
 If the user has an already existing **Image Geometry** that is 100 voxels in the *Y* direction by 300 pixels in the
 *Z* direction and composed of 10 *X* slices, then if the user appends another three data sets in the X direction that are the same dimensions in Y & Z but contain 20 *X* slices each, the resulting **Image Geometry** will have a total of 70 *X* slices.
 
-#### Example 2 (Visual Example)
+#### Example 2 (Visual Example) (X)
 Here's the SmallIN100 dataset example sliced into three pieces in the X direction:
 
 ![](Images/AppendImageGeometry/x_direction_pieces.png)
@@ -28,11 +28,11 @@ And here is what the geometry looks like after appending the three pieces togeth
 
 ### Y Direction Examples
 
-#### Example 1
+#### Example 1 (Y)
 If the user has an already existing **Image Geometry** that is 400 voxels in the *X* direction by 200 pixels in the
 *Z* direction and composed of 50 *Y* slices, then if the user appends another two data sets in the Y direction that are the same dimensions in X & Z but contain 40 *Y* slices each, the resulting **Image Geometry** will have a total of 130 *Y* slices.
 
-#### Example 2 (Visual Example)
+#### Example 2 (Visual Example) (Y)
 Here's the SmallIN100 dataset example sliced into three pieces in the Y direction:
 
 ![](Images/AppendImageGeometry/y_direction_pieces.png)
@@ -43,11 +43,11 @@ And here is what the geometry looks like after appending the three pieces togeth
 
 ### Z Direction Examples
 
-#### Example 1
+#### Example 1 (Z)
 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 if the user appends one other data set in the Z direction that is the same dimensions in X & Y but contains 10 *Z* slices, the resulting **Image Geometry** will have a total of 15 *Z* slices.
 
-#### Example 2 (Visual Example)
+#### Example 2 (Visual Example) (Z)
 Here's the SmallIN100 dataset example sliced into three pieces in the Z direction:
 
 ![](Images/AppendImageGeometry/z_direction_pieces.png)

src/Plugins/SimplnxCore/docs/ComputeSurfaceFeaturesFilter.md

@@ -15,13 +15,13 @@ 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.
 
-### WARNING
+### WARNING - Feature ID=0 Voxels
 
 If there are voxels within the volume that have **Feature ID=0** then any feature touching those voxels will be considered a *Surface* feature.
 
-### WARNING
+### WARNING - Fixed bugs
 
-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.
+The version of this filter in legacy DREAM.3D (version 6.x) had two bugs: one that indexed into neighboring features incorrectly [DREAM.3D repo issue #988](https://github.com/BlueQuartzSoftware/DREAM3D/issues/988), and another that incorrectly labeled feature 0 as a surface feature when feature 0 exists in the feature ids array [DREAM.3D repo issue #989](https://github.com/BlueQuartzSoftware/DREAM3D/issues/989). Both of these bugs have been fixed in this new version.
 
 ### 2D Image Geometry
 

src/Plugins/SimplnxCore/docs/FeatureFaceCurvatureFilter.md

@@ -15,9 +15,20 @@ The values of the principal directions can have their signs flipped. They are ca
 
 *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)
+![Curvature Coloring](Images/FeatureFaceCurvatureFilter_3.png)
 @image latex FeatureFaceCurvatureFilter.png "Curvature Coloring of a Feature" width = 6in
 
+## Ring Neighbor Schematic
+
+![Ring Neighbor Schematic](Images/FeatureFaceCurvatureFilter_1.png)
+
+## Parameter Notes:
+
+- The "Feature Face Ids" input data can be computed from the "Compute Triangle Face Ids" filter
+- The "Face Normals" input data can be computed from the "Compute Triangle Normals" filter
+- The "Face Centroids" input data can be computed from the "Compute Triangle Centroids" filter
+
+
 % Auto generated parameter table will be inserted here
 
 ## References
@@ -26,6 +37,9 @@ The values of the principal directions can have their signs flipped. They are ca
 
 ## Example Pipelines
 
+- Pipelines -> SimplnxCore -> Compute_Feature_Face_Curvature
+- Pipelines -> SimplnxCore -> Compute_Feature_Face_Curvature_2
+
 ## License & Copyright
 
 Please see the description file distributed with this**Plugin**