From 49a6479b3bbc04153b486138d75ca34e87c518f2 Mon Sep 17 00:00:00 2001
From: Michael Jackson <mike.jackson@bluequartz.net>
Date: Mon, 22 Apr 2024 18:58:59 -0400
Subject: [PATCH] DOCS: Create a short tutorial about writing basic python +
 simplnx integration

Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>
---
 wrapping/python/ReadMe.md                     |  24 ++
 wrapping/python/docs/index_template.rst       |   5 +-
 .../docs/source/Images/Tutorial_1_Image_1.png | Bin 0 -> 23872 bytes
 wrapping/python/docs/source/Tutorial_1.rst    | 298 ++++++++++++++++++
 4 files changed, 325 insertions(+), 2 deletions(-)
 create mode 100644 wrapping/python/docs/source/Images/Tutorial_1_Image_1.png
 create mode 100644 wrapping/python/docs/source/Tutorial_1.rst

diff --git a/wrapping/python/ReadMe.md b/wrapping/python/ReadMe.md
index c410210dfa..87b0f531fc 100644
--- a/wrapping/python/ReadMe.md
+++ b/wrapping/python/ReadMe.md
@@ -95,3 +95,27 @@ cd simplnx/docs/
 make clean
 make html
 ```
+
+## Restructured Text Heading Levels
+
+=====================================
+Page Title
+=====================================
+
+###################################
+Part Title
+###################################
+
+Heading 1
+=========
+
+Heading 2
+---------
+
+Heading 3
+^^^^^^^^^
+
+Heading 4
+""""""""""
+
+ 
\ No newline at end of file
diff --git a/wrapping/python/docs/index_template.rst b/wrapping/python/docs/index_template.rst
index 34e0013c96..023b7de630 100644
--- a/wrapping/python/docs/index_template.rst
+++ b/wrapping/python/docs/index_template.rst
@@ -2,7 +2,7 @@
    compiling additional plugins, and you want the python docs
    generated, you will need to add those to the list below
 
-DREAM3D-NX Python Docs (v1.2.7)
+DREAM3D-NX Python Docs (v1.3.0)
 =================================
 
 Installation
@@ -47,6 +47,7 @@ How to use SIMPLNX from Python
    Overview
    DataObjects
    Geometry
+   Reference_Frame_Notes
 
 .. toctree::
    :maxdepth: 2
@@ -54,7 +55,7 @@ How to use SIMPLNX from Python
 
    Python_Introduction
    User_API
-   Reference_Frame_Notes
+   Tutorial_1
 
 .. toctree::
    :maxdepth: 1
diff --git a/wrapping/python/docs/source/Images/Tutorial_1_Image_1.png b/wrapping/python/docs/source/Images/Tutorial_1_Image_1.png
new file mode 100644
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diff --git a/wrapping/python/docs/source/Tutorial_1.rst b/wrapping/python/docs/source/Tutorial_1.rst
new file mode 100644
index 0000000000..b33903bd56
--- /dev/null
+++ b/wrapping/python/docs/source/Tutorial_1.rst
@@ -0,0 +1,298 @@
+.. Tutorial 1:
+
+=====================================
+Tutorial 1: Basic Python Integration
+=====================================
+
+###################################
+Anaconda Virtual Environment Setup
+###################################
+
+.. code:: shell
+
+      conda config --add channels conda-forge
+      conda config --set channel_priority strict
+      conda create -n nxpython python=3.12
+      conda activate nxpython
+      conda install -c bluequartzsoftware dream3dnx
+
+###################################
+Introduction
+###################################
+
+Setup your virtual environment following the directions from above. Then create a Tutorial_1.py file anywhere that you want and open that up in your Editor/IDE.
+
+
+###################################
+Necessary Import Statements
+###################################
+
+Just about every python source code that is written will need the following import Statements:
+
+.. code:: python
+
+    import simplnx as nx
+    import numpy as np
+
+If you will be using filters from DREAM3D-NX's other plugins, then you may additionally need the following:
+
+.. code:: python
+
+    import itkimageprocessing as nxitk
+    import orientationanalysis as nxor
+
+
+###################################
+Creating the DataStructure Object
+###################################
+
+If you will be interacting with data stored in DREAM3D-NX, you will need to instantiate a :ref:`DataStructure` object. This is 
+simply done with the following line of code:
+
+.. code:: python
+
+    # Create the DataStructure Object
+    data_structure = nx.DataStructure()
+
+A few caveats to take note of:
+1. You can have as many :ref:`DataStructure` objects as you want/need. Typically all data is stored in a single DataStructure object but there are use cases where having more than a single :ref:`DataStructure` object is needed.
+2. Only a **single** :ref:`DataStructure` object can be stored in a .dream3d file. 
+
+
+################################################
+First Steps: Create a Group in the DataStructure
+################################################
+
+As in the user interface of DREAM3D-NX, you as the developer can execute any of filter from DREAM3D-NX using only Python codes. This is performed
+by instantiating the filter and then calling the `execute()` method with the appropriate parameters used in the call. With the current API, we are tending to
+inline instantiate the filter and execute it all in the same line. Some things to note with this small piece of code:
+
+- There will **always** be a required :ref:`DataStructure` object. All arguments in the `execute()` method are named arguments. None are positional. This means that each argument must be in the form of 'name=value'.
+- The 2nd argument shows an use of the :ref:`DataPath` object. Lots of filters will require a :ref:`DataPath` object so this is a common use.
+- There is a method called `hierarchy_to_str()` that is a part of the :ref:`DataStructure` class which will print the heirarchy of the DataStructure.
+
+
+.. code:: python
+
+    result = nx.CreateDataGroup.execute(data_structure=data_structure, 
+                                    data_object_path=nx.DataPath("Top Level Group"))
+    print(f'{data_structure.hierarchy_to_str()}')
+
+If we were to run this code we would get the following:
+
+.. code:: text
+
+    |--Top Level Group
+
+
+Let's try to add a bunch of groups to the :ref:`DataStructure` object by using a loop:
+
+.. code:: python
+
+    for i in range(1, 6):
+    
+        current_data_group_path = nx.DataPath(f"Top Level Group {i}")
+        result = nx.CreateDataGroup.execute(data_structure=data_structure, 
+                                            data_object_path=current_data_group_path)
+    print(f'{data_structure.hierarchy_to_str()}')
+
+And the output would look like the following:
+
+.. code:: text
+
+    |--Top Level Group 1
+    |--Top Level Group 2
+    |--Top Level Group 3
+    |--Top Level Group 4
+    |--Top Level Group 5
+
+  
+
+################################################
+Result Objects
+################################################
+
+Each time a filter is executed, it will return an `nx.ExecuteResult` object. This 
+object can be interrogated for both warnings and errors that occured while the 
+filter was executing. A typical function that can be written to properly error
+check the 'result' value is the following:
+
+.. code:: python
+
+    def check_filter_result(filter: nx.IFilter, result: nx.IFilter.ExecuteResult) -> None:
+        """
+        This function will check the `result` for any errors. If errors do exist then a 
+        `RuntimeError` will be thrown. Your own code to modify this to return something
+        else that doesn't just stop your script in its tracks.
+        """
+        if len(result.warnings) != 0:
+            for w in result.warnings:
+            print(f'Warning: ({w.code}) {w.message}')
+        
+        has_errors = len(result.errors) != 0 
+        if has_errors:
+            for err in result.errors:
+            print(f'Error: ({err.code}) {err.message}')
+            raise RuntimeError(result)
+        
+        print(f"{filter.name()} :: No errors running the filter")
+
+If you were to integrate this into your own code, then we would get the following when we wanted to execute a filter:
+
+.. code:: python
+
+    result = nx.CreateDataGroup.execute(data_structure=data_structure, 
+                                    data_object_path=nx.DataPath("Top Level Group"))
+    check_filter_result( nx.CreateDataGroup(), result)
+
+
+################################################
+Creating a DataArray Object
+################################################
+
+Raw data is stored in a :ref:`DataArray` object within the :ref:`DataStructure`. The DREAM3D-NX python bindings only expose a subset of functionality
+from the :ref:`DataArray`, enough to get the name, tuple shape and component shape. **ALL** interactions to modify a :ref:`DataArray` are done via a 
+`numpy view <https://numpy.org/doc/stable/user/basics.copies.html>`_. Let us first create a :ref:`DataArray` object within the :ref:`DataStructure` by using the
+:ref:`CreateDataArray` filter. Adding into the current python source file... 
+
+.. code:: python
+
+    result = nx.CreateDataArray().execute(data_structure=data_structure, 
+                                            component_count=1, 
+                                            initialization_value_str="0", 
+                                            numeric_type_index=nx.NumericType.float32, 
+                                            output_array_path=nx.DataPath("Top Level Group/2D Array"), 
+                                            tuple_dimensions=[[5,4]])
+    nxutility.check_filter_result( nx.CreateDataArray(), result)
+    print(f'{data_structure.hierarchy_to_str()}')
+
+Note how we are creating the array inside the very first :ref:`DataGroup` that we created. If we run the file from start to finish we now get the following output:
+
+.. code:: text
+
+    |--Top Level Group
+      |--2D Array
+    |--Top Level Group 1
+    |--Top Level Group 2
+    |--Top Level Group 3
+    |--Top Level Group 4
+    |--Top Level Group 5
+
+As you can see we have successfully created an array that can hold some data. The next step is to interact with that :ref:`DataArray` and use numpy to modify the array in place.
+
+################################################
+Modifying the DataArray Object using Numpy
+################################################
+
+The method from :ref:`DataStructure` that we will be using is item selection using the '[]' operator paired with an 
+immediate call to the '.npview()' method. This will retrieve the a numpy view of the DataArray that was created in the last step.
+
+.. code:: python
+
+    array_view = data_structure["Top Level Group/2D Array"].npview()
+
+Now that we have a numpy view we can do anything to the array that numpy (or any other package that accepts numpy views) can do for us. For example, we can
+create random data in the array using the following:
+
+.. code:: python
+
+    # Fill the numpy data view with random numbers
+    rng = np.random.default_rng()
+    rng.standard_normal(out=array_view, dtype=np.float32)
+    print(f'{array_view}')
+
+The output from this code would print something similar to:
+
+.. code:: text
+
+    [[[-1.3746183 ]
+    [-0.08409024]
+    [ 1.2792562 ]
+    [-0.37265882]
+    [ 0.05201177]]
+
+    [[-0.11597582]
+    [-0.35329401]
+    [-0.88307136]
+    [-0.98040694]
+    [ 0.28385338]]
+
+    [[ 0.7635286 ]
+    [-1.3911186 ]
+    [ 0.5670461 ]
+    [ 0.11915083]
+    [-0.8656706 ]]
+
+    [[ 2.1133974 ]
+    [ 1.3168721 ]
+    [ 2.6951575 ]
+    [ 0.10712756]
+    [-0.07898012]]]
+
+And if you wanted to use `matplotlib <https://matplotlib.org/>`_ to view the data, that is easily done in the usual manner:
+
+.. code:: python
+
+    # Show the result
+    plt.imshow(array_view)
+    plt.title("Random Data")
+    plt.axis('off')  # to turn off axes
+    plt.show()
+
+
+.. figure:: Images/Tutorial_1_Image_1.png
+   :alt: MatPlotLib output
+
+
+################################################
+Complete Source Code
+################################################
+
+.. code:: python
+    
+    import simplnx as nx
+    import numpy as np
+    import matplotlib.pyplot as plt
+    import nxutility
+
+    # Create the DataStructure instance
+    data_structure = nx.DataStructure()
+
+    result = nx.CreateDataGroup.execute(data_structure=data_structure, 
+                                        data_object_path=nx.DataPath("Top Level Group"))
+
+    # Loop to create a bunch of DataGroups.
+    for i in range(1, 6):
+        current_data_group_path = nx.DataPath(f"Top Level Group {i}")
+        result = nx.CreateDataGroup.execute(data_structure=data_structure, 
+                                            data_object_path=current_data_group_path)
+
+    # Execute the filter
+    result = nx.CreateDataArray().execute(data_structure=data_structure, 
+                                        component_count=1, 
+                                        initialization_value_str="0", 
+                                        numeric_type_index=nx.NumericType.float32, 
+                                        output_array_path=nx.DataPath("Top Level Group/2D Array"), 
+                                        tuple_dimensions=[[4,5]])
+    nxutility.check_filter_result( nx.CreateDataArray(), result)
+    print(f'{data_structure.hierarchy_to_str()}')
+
+    # Try to get the array from the DataStructure
+    try:
+        array_view = data_structure["Top Level Group/2D Array"].npview()
+    except AttributeError as attrerr:
+        print(f'{attrerr}')
+        quit(1) # This is pretty harsh! Maybe something more elegant to unwind from this error
+    
+    # Fill the numpy data view with random numbers
+    rng = np.random.default_rng()
+    rng.standard_normal(out=array_view, dtype=np.float32)
+
+    print(f'{array_view}')
+
+    # Show the result
+    plt.imshow(array_view)
+    plt.title("Random Data")
+    plt.axis('off')  # to turn off axes
+    plt.show()
+