PY: Added Python Code for Most Example Pipelines (#800)

Python code examples including pipelines, plugins and generic examples have been updated. Signed-off-by: Michael Jackson <[email protected]> Co-authored-by: Michael Jackson <[email protected]> Co-authored-by: Jared Duffey <[email protected]>
BlueQuartzSoftware · Jan 14, 2024 · f282e77 · f282e77
1 parent 6eef763
commit f282e77
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Showing 97 changed files with 6,494 additions and 309 deletions.
diff --git a/.gitignore b/.gitignore
@@ -29,3 +29,4 @@ test_data/
 CMakeUserPresets.json
 Workspace
 /__pycache__/
+/Data/
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -736,7 +736,7 @@ endforeach()
 
 set(SIMPLNX_GENERATED_PYTHON_HEADER ${SIMPLNX_GENERATED_HEADER_DIR}/SimplnxPython.hpp)
 set(SIMPLNX_PYTHON_MODULE "simplnx")
-configure_file(${simplnx_SOURCE_DIR}/wrapping/python/SimplnxPython.hpp.in ${SIMPLNX_GENERATED_PYTHON_HEADER})
+configure_file(${simplnx_SOURCE_DIR}/wrapping/python/CxPybind/SimplnxPython.hpp.in ${SIMPLNX_GENERATED_PYTHON_HEADER})
 
 list(APPEND SIMPLNX_GENERATED_HEADERS
   ${SIMPLNX_GENERATED_PYTHON_HEADER}

diff --git a/cmake/Summary.cmake b/cmake/Summary.cmake
@@ -49,8 +49,7 @@ OSInformation()
 message(STATUS "* -------------- Dependent Libraries -------------------------------------------")
 message(STATUS "* Eigen (${Eigen3_VERSION}) ${Eigen3_DIR}")
 message(STATUS "* HDF5 (${HDF5_VERSION}) ${HDF5_INSTALL}")
-# message(STATUS "* ITK (${ITK_VERSION}) ${ITK_DIR}")
-message(STATUS "* Pybind11 (${pybind11_VERSION}) ${pybind11_DIR}")
+message(STATUS "* ITK (${ITK_VERSION}) ${ITK_DIR}")
 message(STATUS "* TBB (${TBB_VERSION}) ${TBB_DIR}")
 message(STATUS "* fmt (${fmt_VERSION}) ${fmt_DIR}")
 message(STATUS "* nlohmann_json (${nlohmann_json_VERSION}) ${nlohmann_json_DIR}")
@@ -73,7 +72,9 @@ message(STATUS "* SIMPLNX_BUILD_DOCS: ${SIMPLNX_BUILD_DOCS}")
 message(STATUS "* DREAM3D_DATA_DIR: ${DREAM3D_DATA_DIR}")
 
 message(STATUS "* -------------- Simplnx Python Configuration Options -------------------------------------")
+message(STATUS "* Pybind11 (${pybind11_VERSION}) ${pybind11_DIR}")
 message(STATUS "* Python3_EXECUTABLE: ${Python3_EXECUTABLE}")
+message(STATUS "* PYTHON_EXECUTABLE: ${PYTHON_EXECUTABLE}")
 message(STATUS "* SIMPLNX_BUILD_PYTHON: ${SIMPLNX_BUILD_PYTHON}")
 message(STATUS "* SIMPLNX_BUILD_PYTHON_DOCS: ${SIMPLNX_BUILD_PYTHON_DOCS}")
 message(STATUS "* SIMPLNX_BUILD_PYTHON_TESTS: ${SIMPLNX_BUILD_PYTHON_TESTS}")

diff --git a/cmake/Utility.cmake b/cmake/Utility.cmake
@@ -275,7 +275,7 @@ function(create_pipeline_tests)
     get_filename_component(test_file_name ${pipeline_file_path} NAME_WE)
     string(REPLACE "/" "-" test_file_name "${test_file_name}")
 
-    add_test(NAME "${ARGS_PLUGIN_NAME} ${padding}${test_index} ${test_file_name}"
+    add_test(NAME "PIPELINE::${ARGS_PLUGIN_NAME}::${padding}${test_index}_${test_file_name}"
             COMMAND "${PIPELINE_RUNNER_NAME}$<$<CONFIG:Debug>:${PIPELINE_RUNNER_DEBUG}>" --execute ${pipeline_file_path}
             #CONFIGURATIONS Debug
             WORKING_DIRECTORY ${TEST_WORKING_DIR})
@@ -473,7 +473,7 @@ function(AddPythonTest)
   set(oneValueArgs NAME FILE)
   set(multiValueArgs PYTHONPATH)
   cmake_parse_arguments(ARGS "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
-  message(STATUS "ARGS_FILE:${ARGS_FILE}")
+  # message(STATUS "ARGS_FILE:${ARGS_FILE}")
   if(SIMPLNX_BUILD_PYTHON)
     if(WIN32)
       add_test(NAME ${ARGS_NAME}

diff --git a/conda/conda_build_config.yaml b/conda/conda_build_config.yaml
@@ -2,10 +2,10 @@ cxx_compiler:
   - vs2019 # [win]
 
 c_compiler_version: # [unix]
-  - 9.3.0 # [linux]
+  - 10.4.0 # [linux]
 
 cxx_compiler_version:
-  - 9.3.0 # [linux]
+  - 10.4.0 # [linux]
 
 python:
     - 3.11

diff --git a/conda/meta.yaml b/conda/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "simplnx" %}
-{% set version = "1.2.2" %}
+{% set version = "1.2.3" %}
 
 package:
   name: {{ name|lower }}
@@ -40,7 +40,7 @@ build:
 requirements:
   build:
     - {{ compiler('cxx') }}
-    - cmake >=3.19
+    - cmake >=3.26
     - ninja
     - git
   host:

diff --git a/conda/recipe.yaml b/conda/recipe.yaml
@@ -1,5 +1,5 @@
 context:
-  version: "1.2.1"
+  version: "1.2.3"
   name: simplnx
 
 package:
@@ -26,7 +26,10 @@ 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: v5.2.1
+    folder: itk
+
 build:
   number: 0
   script_env:
@@ -38,7 +41,7 @@ build:
 requirements:
   build:
     - "{{ compiler('cxx') }}"
-    - cmake >=3.19
+    - cmake >=3.26
     - ninja
     - git
   host:
@@ -49,8 +52,6 @@ requirements:
     - eigen
     - fmt =10
     - hdf5 =1.12
-    - libitk =5.2
-    - libitk-devel =5.2
     - nlohmann_json
     - pybind11 >=2.10
     - reproc-cpp
@@ -66,7 +67,6 @@ requirements:
     - numpy
     - fmt =10
     - hdf5 =1.12
-    - libitk =5.2
     - reproc-cpp
     - tbb
     - zlib

diff --git a/src/Plugins/OrientationAnalysis/test/CMakeLists.txt b/src/Plugins/OrientationAnalysis/test/CMakeLists.txt
@@ -288,7 +288,7 @@ fi
     "${SIMPLNX_CTEST_TEST_DRIVER}" @ONLY)
 
   string(REPLACE "/" "_" test "${test}")
-  add_test(NAME ${PLUGIN_NAME}_${ARGS_TEST_INDEX} COMMAND "${SIMPLNX_CTEST_TEST_DRIVER}")
+  add_test(NAME "PIPELINE::${PLUGIN_NAME}::${ARGS_TEST_INDEX}" COMMAND "${SIMPLNX_CTEST_TEST_DRIVER}")
 endfunction()
 
 # ------------------------------------------------------------------------------

diff --git a/src/Plugins/OrientationAnalysis/test/MergeTwinsTest.cpp b/src/Plugins/OrientationAnalysis/test/MergeTwinsTest.cpp
@@ -64,7 +64,7 @@ TEST_CASE("Reconstruction::MergeTwinsFilter: Valid Execution", "[Reconstruction]
   {
     constexpr StringLiteral k_ImportFileData = "import_file_data";
 
-    auto filter = filterList->createFilter(k_ImportDream3dFilterHandle);
+    auto filter = filterList->createFilter(k_ReadDREAM3DFilterHandle);
     REQUIRE(nullptr != filter);
 
     Dream3dImportParameter::ImportData parameter;

diff --git a/src/Plugins/OrientationAnalysis/test/OrientationAnalysisTestUtils.hpp b/src/Plugins/OrientationAnalysis/test/OrientationAnalysisTestUtils.hpp
@@ -43,8 +43,8 @@ namespace nx::core
 const Uuid k_ReadTextDataArrayFilterId = *Uuid::FromString("25f7df3e-ca3e-4634-adda-732c0e56efd4");
 const FilterHandle k_ReadTextDataArrayFilterHandle(k_ReadTextDataArrayFilterId, k_SimplnxCorePluginId);
 // Make sure we can instantiate the Read DREAM3D Data File
-const Uuid k_ImportDream3dFilterId = *Uuid::FromString("0dbd31c7-19e0-4077-83ef-f4a6459a0e2d");
-const FilterHandle k_ImportDream3dFilterHandle(k_ImportDream3dFilterId, k_SimplnxCorePluginId);
+const Uuid k_ReadDREAM3DFilterId = *Uuid::FromString("0dbd31c7-19e0-4077-83ef-f4a6459a0e2d");
+const FilterHandle k_ReadDREAM3DFilterHandle(k_ReadDREAM3DFilterId, k_SimplnxCorePluginId);
 // Make sure we can instantiate the Read RenameDataObject
 const Uuid k_RenameDataObjectFilterId = *Uuid::FromString("911a3aa9-d3c2-4f66-9451-8861c4b726d5");
 const FilterHandle k_RenameDataObjectFilterHandle(k_RenameDataObjectFilterId, k_SimplnxCorePluginId);

diff --git a/src/Plugins/SimplnxCore/pipelines/Import_ASCII.d3dpipeline b/src/Plugins/SimplnxCore/pipelines/Import_ASCII.d3dpipeline
@@ -7,9 +7,9 @@
       "args": {
         "cell_data_name": "CellData",
         "dimensions": [
-          189,
-          201,
-          1
+          60,
+          40,
+          100
         ],
         "geometry_data_path": "[Image Geometry]",
         "origin": [
@@ -33,54 +33,36 @@
     {
       "args": {
         "created_data_group": "",
-        "selected_data_group": "[Image Geometry]/CellData",
-        "tuple_dimensions": [
-          [
-            1.0,
-            201.0,
-            189.0
-          ]
-        ],
-        "use_existing_group": true,
-        "wizard_data": {
-          "Begin Index": 33,
-          "Comma As Delimiter": false,
-          "Consecutive Delimiters": true,
-          "Data Headers": [
+        "read_csv_data": {
+          "Consecutive Delimiters": false,
+          "Custom Headers": [
             "phi1",
             "Phi",
-            "phi2",
-            "x",
-            "y",
-            "Image Quality",
-            "Confidence Index",
-            "Phase",
-            "SEM Signal",
-            "Fit"
+            "phi2"
           ],
           "Data Types": [
             8,
             8,
-            8,
-            8,
-            8,
-            8,
-            8,
-            4,
-            8,
             8
           ],
           "Delimiters": [
-            32
+            ","
           ],
           "Header Line": 1,
           "Header Mode": 1,
-          "Input File Path": "Data/Small_IN100/Slice_1.ang",
-          "Number of Lines": 38021,
-          "Semicolon As Delimiter": false,
-          "Space As Delimiter": true,
-          "Tab As Delimiter": false
-        }
+          "Input File Path": "C:/Users/alejo/Downloads/DREAM3DNX-7.0.0-RC-7-UDRI-20231027.2-windows-AMD64/DREAM3DNX-7.0.0-RC-7-UDRI-20231027.2-windows-AMD64/Data/ASCIIData/EulersRotated.csv",
+          "Skipped Array Mask": [
+            false,
+            false,
+            false
+          ],
+          "Start Import Row": 1,
+          "Tuple Dimensions": [
+            480001
+          ]
+        },
+        "selected_data_group": "[Image Geometry]/CellData",
+        "use_existing_group": true
       },
       "comments": "",
       "filter": {
@@ -91,7 +73,7 @@
     },
     {
       "args": {
-        "move_values": false,
+        "move_values": true,
         "normalize_data": false,
         "selected_data_array_paths": [
           "[Image Geometry]/CellData/phi1",
@@ -107,21 +89,6 @@
       },
       "isDisabled": false
     },
-    {
-      "args": {
-        "removed_data_path": [
-          "[Image Geometry]/CellData/phi1",
-          "[Image Geometry]/CellData/Phi",
-          "[Image Geometry]/CellData/phi2"
-        ]
-      },
-      "comments": "",
-      "filter": {
-        "name": "simplnx::DeleteData",
-        "uuid": "bf286740-e987-49fe-a7c8-6e566e3a0606"
-      },
-      "isDisabled": false
-    },
     {
       "args": {
         "cell_ensemble_attribute_matrix_name": "[Image Geometry]/CellEnsembleData",
@@ -143,11 +110,32 @@
       },
       "isDisabled": false
     },
+    {
+      "args": {
+        "advanced_options": true,
+        "component_count": 1,
+        "data_format": "",
+        "initialization_value": "1",
+        "numeric_type": 4,
+        "output_data_array": "[Image Geometry]/CellData/Phases",
+        "tuple_dimensions": [
+          [
+            0.0
+          ]
+        ]
+      },
+      "comments": "",
+      "filter": {
+        "name": "complex::CreateDataArray",
+        "uuid": "67041f9b-bdc6-4122-acc6-c9fe9280e90d"
+      },
+      "isDisabled": false
+    },
     {
       "args": {
         "cell_euler_angles_array_path": "[Image Geometry]/CellData/Eulers",
         "cell_ipf_colors_array_name": "IPFColors",
-        "cell_phases_array_path": "[Image Geometry]/CellData/Phase",
+        "cell_phases_array_path": "[Image Geometry]/CellData/Phases",
         "crystal_structures_array_path": "[Image Geometry]/CellEnsembleData/CrystalStructures",
         "mask_array_path": "",
         "reference_dir": [
@@ -192,5 +180,6 @@
       "isDisabled": true
     }
   ],
+  "version": 1,
   "workflowParams": []
 }
diff --git a/src/Plugins/SimplnxCore/src/SimplnxCore/Filters/ReadVolumeGraphicsFileFilter.cpp b/src/Plugins/SimplnxCore/src/SimplnxCore/Filters/ReadVolumeGraphicsFileFilter.cpp
@@ -329,13 +329,13 @@ Result<ReadVolumeGraphicsFileFilter::HeaderMetadata> ReadHeaderMetaData(const st
   return {metadata};
 }
 
-struct ImportVolumeGraphicsFileFilterCache
+struct ReadVolumeGraphicsFileFilterCache
 {
   fs::path VgiDataFilePath;
 };
 
 std::atomic_int32_t s_InstanceId = 0;
-std::map<int32, ImportVolumeGraphicsFileFilterCache> s_HeaderCache;
+std::map<int32, ReadVolumeGraphicsFileFilterCache> s_HeaderCache;
 
 } // namespace
 

diff --git a/src/Plugins/TestOne/test/ErrorWarningFilterTest.cpp b/src/Plugins/TestOne/test/ErrorWarningFilterTest.cpp
@@ -15,7 +15,7 @@ constexpr int32 k_ExecuteWarning = -666000;
 constexpr int32 k_ExecuteError = -666001;
 } // namespace
 
-TEST_CASE("ErrorWarningFilter: Instantiate Filter", "[ErrorWarningFilter]")
+TEST_CASE("ErrorWarningFilter::Instantiate Filter", "[ErrorWarningFilter]")
 {
   DataStructure dataStructure;