ENH: Add option to save the Counts or MRD values to an array for Pole…

… Figures (BlueQuartzSoftware#995)

* ENH: Add ability to save intensity data arrays as image geometries
* ENH: Add option to NormalizeToMRD. Add Metadata DataArray
* Use the RTree.hpp from simplnx/Utilities

---------

Signed-off-by: Michael Jackson <[email protected]>
Co-authored-by: Jared Duffey <[email protected]>

CMakeLists.txt

@@ -118,6 +118,7 @@ set_property(GLOBAL PROPERTY USE_FOLDERS ON)
 set(FETCH_FILE_PATH "${simplnx_BINARY_DIR}/simplnx_fetch_remote_files.cmake")
 set_property(GLOBAL PROPERTY FETCH_FILE_PATH "${FETCH_FILE_PATH}")
 file(WRITE ${FETCH_FILE_PATH} "# -----------------------------------------------------------------------
+# This file is programmatically generated from the CMake file ${CMAKE_CURRENT_LIST_FILE}
 # This file has the commands to download each of the test files.
 # The WORKING_DIRECTORY is set to the following CMake code:
 # ${CMAKE_LIBRARY_OUTPUT_DIRECTORY}/$<$<CONFIG:Debug>:Debug>$<$<CONFIG:Release>:Release>

src/Plugins/OrientationAnalysis/CMakeLists.txt

@@ -243,6 +243,9 @@ set(PLUGIN_EXTRA_SOURCES
   "${${PLUGIN_NAME}_SOURCE_DIR}/src/${PLUGIN_NAME}/utilities/SIMPLConversion.hpp"
   "${${PLUGIN_NAME}_SOURCE_DIR}/src/${PLUGIN_NAME}/utilities/TiffWriter.hpp"
   "${${PLUGIN_NAME}_SOURCE_DIR}/src/${PLUGIN_NAME}/utilities/TiffWriter.cpp"
+  "${${PLUGIN_NAME}_SOURCE_DIR}/src/${PLUGIN_NAME}/utilities/delaunator.cpp"
+  "${${PLUGIN_NAME}_SOURCE_DIR}/src/${PLUGIN_NAME}/utilities/delaunator.h"
+  "${${PLUGIN_NAME}_SOURCE_DIR}/src/${PLUGIN_NAME}/utilities/IntersectionUtilities.hpp"
 )
 target_sources(${PLUGIN_NAME} PRIVATE ${PLUGIN_EXTRA_SOURCES})
 source_group(TREE "${${PLUGIN_NAME}_SOURCE_DIR}/src/${PLUGIN_NAME}/utilities" PREFIX ${PLUGIN_NAME} FILES ${PLUGIN_EXTRA_SOURCES})

src/Plugins/OrientationAnalysis/docs/WritePoleFigureFilter.md

@@ -6,9 +6,9 @@ IO (Output)
 
 ## Description
 
-This **Filter** creates a standard crystallographic pole figure image for each **Ensemble** (phase)in a selected **Data Container**. The **Filter** uses Euler angles in radians and requires the crystal structures and material names for each **Ensemble** array and the corresponding **Ensemble** Ids on the **Cells**. The **Filter** also optionally can use a *mask* array to determine which **Cells** are valid for the pole figure computation.
+This **Filter** creates a standard crystallographic pole figure image for each **Ensemble** (phase) in a selected **Data Container**. The **Filter** uses Euler angles in radians and requires the crystal structures and material names for each **Ensemble** array and the corresponding **Ensemble** Ids on the **Cells**. The **Filter** also optionally can use a *mask* array to determine which angles are valid for the pole figure computation.
 
-In a practicale sense, this means that the following information is available to the filter:
+In a practical sense, this means that the following information is available to the filter:
 
 - Cell Level
 
@@ -23,17 +23,36 @@ In a practicale sense, this means that the following information is available to
 
 ### Algorithm Choice
 
-1: The pole figure algorithm uses a *modified Lambert square* to perform the interpolations onto the unit 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.
+1: The pole figure algorithm uses a *modified Lambert square* to perform the interpolations onto the unit 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.**
+**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. The algorithm will simply mark each pixel that had at least 1 count as a black pixel.
 
-### Layout
+## Output Options
+
+### Write Image to Disk
+
+The user can select to have the combined set of pole figures written to disk as a tiff image file
+
+### Save Pole Figure as Image Geometry
+
+The combined pole figure image will be saved into the DataStructure as an Image Geometry
+
+### Save Raw Intensity Data
+
+The normalized count data is saved for each pole figure into a Data Array that is stored inside an Image Geometry. This allows
+the user to select their own color plots. The Image Geometry will also have a string DataArray that lists the pertinent
+data that went into the creation: Number of points, which hemisphere, Phase Name, etc.
+
+### Image Layout
 
 The 3 pole figures can be laid out in a Square, Horizontal row or vertical column. Supporting information (including the color bar legend for color pole figures) will also be printed on the image.
 
-| Lambert Projection | Discrete |
+| Colorized Intensity | Discrete |
 |--------------------|----------|
 | ![Example Pole Figure Using Square Layout](Images/PoleFigure_Example.png) | ![Example Pole Figure Using Square Layout](Images/Pole_Figure_Discrete_Example.png) |