Create CTest unit tests to run the Python example files.

Signed-off-by: Michael Jackson <[email protected]>
BlueQuartzSoftware · Nov 29, 2023 · 97e33d4 · 97e33d4
1 parent a06a6d5
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diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml
@@ -43,7 +43,7 @@ jobs:
           sudo apt-get -y install ninja-build
       - name: Install Sphinx
         run: |
-          sudo pip install sphinx myst-parser sphinx-markdown-tables sphinx_rtd_theme
+          sudo pip install sphinx myst-parser sphinx-markdown-tables sphinx_rtd_theme numpy
       - name: Setup NuGet Credentials
         shell: bash
         run: |

diff --git a/.github/workflows/macos.yml b/.github/workflows/macos.yml
@@ -32,7 +32,7 @@ jobs:
           brew install ninja
       - name: Install Sphinx
         run: |
-          sudo pip3 install sphinx myst-parser sphinx-markdown-tables sphinx_rtd_theme
+          sudo pip3 install sphinx myst-parser sphinx-markdown-tables sphinx_rtd_theme numpy
       - name: Setup NuGet Credentials
         shell: bash
         run: |

diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml
@@ -49,7 +49,7 @@ jobs:
           -source "https://nuget.pkg.github.com/BlueQuartzSoftware/index.json"
       - name: Install Sphinx
         run: |
-          pip install sphinx myst-parser sphinx-markdown-tables sphinx_rtd_theme
+          pip install sphinx myst-parser sphinx-markdown-tables sphinx_rtd_theme numpy
       - name: Configure
         run: |
           cmake --preset ci-windows-${{matrix.toolset}} ${{github.workspace}} -T ${{matrix.toolset}}

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -63,7 +63,7 @@ option(COMPLEX_ENABLE_INSTALL "Enables COMPLEX install rules" ON)
 file(TO_CMAKE_PATH "${CMAKE_COMMAND}" CMAKE_COMMAND_NORM)
 
 project(complex
-  VERSION 1.2.0
+  VERSION 1.2.1
   DESCRIPTION "SIMPL Redesign"
   HOMEPAGE_URL "https://github.com/BlueQuartzSoftware/complex"
   LANGUAGES CXX

diff --git a/CMakePresets.json b/CMakePresets.json
@@ -33,6 +33,10 @@
           "type": "BOOL",
           "value": "ON"
         },
+        "COMPLEX_ENABLE_PYTHON_TESTS": {
+          "type": "BOOL",
+          "value": "ON"
+        },
         "COMPLEX_EMBED_PYTHON": {
           "type": "BOOL",
           "value": "OFF"

diff --git a/cmake/Utility.cmake b/cmake/Utility.cmake
@@ -460,3 +460,86 @@ function(cmpBuildDateRevisionString)
   endif()
 
 endfunction()
+
+
+#-------------------------------------------------------------------------------
+# @Brief function AddPythonTest
+# @ NAME
+# @ FILE
+# @ PYTHONPATH
+#-------------------------------------------------------------------------------
+function(AddPythonTest)
+  set(options )
+  set(oneValueArgs NAME FILE)
+  set(multiValueArgs PYTHONPATH)
+  cmake_parse_arguments(ARGS "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+
+  if(COMPLEX_BUILD_PYTHON)
+    if(WIN32)
+      add_test(NAME ${ARGS_NAME}
+        COMMAND ${complex_SOURCE_DIR}/wrapping/python/testing/anaconda_test.bat
+      )
+
+      set_property(TEST ${ARGS_NAME}
+        PROPERTY
+          ENVIRONMENT
+            "PYTHON_TEST_FILE=${ARGS_FILE}"
+      )
+    else()
+      add_test(NAME ${ARGS_NAME}
+        COMMAND ${complex_SOURCE_DIR}/wrapping/python/testing/anaconda_test.sh
+      )
+
+      set_property(TEST ${ARGS_NAME}
+        PROPERTY
+          ENVIRONMENT
+            "PYTHON_TEST_FILE=${ARGS_FILE}"
+      )
+    endif()
+  else()
+    add_test(NAME ${ARGS_NAME}
+      COMMAND ${PYTHON_EXECUTABLE} ${ARGS_FILE}
+    )
+  endif()
+
+  if(WIN32)
+    string(REPLACE ";" "\\;" ARGS_PYTHONPATH "${ARGS_PYTHONPATH}")
+  else()
+    string(REPLACE ";" ":" ARGS_PYTHONPATH "${ARGS_PYTHONPATH}")
+  endif()
+
+  set_property(TEST ${ARGS_NAME}
+    APPEND
+    PROPERTY
+      ENVIRONMENT
+      "PYTHONPATH=${ARGS_PYTHONPATH}"
+      "${complex_PYTHON_TEST_ENV}"
+  )
+endfunction()
+
+#-------------------------------------------------------------------------------
+# @Brief function CreatePythonTests
+# @ PREFIX
+# @ INPUT_DIR
+# @ TEST_NAMES
+#-------------------------------------------------------------------------------
+function(CreatePythonTests)
+  set(options)
+  set(oneValueArgs PREFIX INPUT_DIR)
+  set(multiValueArgs TEST_NAMES)
+  cmake_parse_arguments(ARGS "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+
+  set(TESTS_PYTHONPATH
+    "$<TARGET_FILE_DIR:complex>"
+  )
+
+  foreach(test ${ARGS_TEST_NAMES})
+    string(REPLACE "/" "_" test_name ${test})
+    set(PY_TEST_NAME ${ARGS_PREFIX}_${test_name})
+
+    AddPythonTest(NAME ${PY_TEST_NAME}
+      FILE ${ARGS_INPUT_DIR}/${test}.py
+      PYTHONPATH ${TESTS_PYTHONPATH}
+    )
+  endforeach()
+endfunction()
diff --git a/conda/meta.yaml b/conda/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "complex" %}
-{% set version = "1.2.0" %}
+{% set version = "1.2.1" %}
 
 package:
   name: {{ name|lower }}

diff --git a/conda/recipe.yaml b/conda/recipe.yaml
@@ -1,5 +1,5 @@
 context:
-  version: "1.2.0"
+  version: "1.2.1"
   name: complex
 
 package:

diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/CreateDataArray.cpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/CreateDataArray.cpp
@@ -134,7 +134,8 @@ IFilter::PreflightResult CreateDataArray::preflightImpl(const DataStructure& dat
     if(!useDims)
     {
       return MakePreflightErrorResult(
-          -78602, "The DataArray to be created is not within an AttributeMatrix, so the dimensions cannot be determined implicitly. Check Set Tuple Dimensions to set the dimensions");
+          -78602, fmt::format("The DataArray to be created '{}'is not within an AttributeMatrix, so the dimensions cannot be determined implicitly. Check Set Tuple Dimensions to set the dimensions",
+                              dataArrayPath.toString()));
     }
     else
     {

diff --git a/src/Plugins/ComplexCore/src/ComplexCore/Filters/ReadTextDataArrayFilter.cpp b/src/Plugins/ComplexCore/src/ComplexCore/Filters/ReadTextDataArrayFilter.cpp
@@ -106,7 +106,8 @@ IFilter::PreflightResult ReadTextDataArrayFilter::preflightImpl(const DataStruct
     if(!useDims)
     {
       return MakePreflightErrorResult(
-          -77602, "The DataArray to be created is not within an AttributeMatrix, so the dimensions cannot be determined implicitly. Check Set Tuple Dimensions to set the dimensions");
+          -78602, fmt::format("The DataArray to be created '{}'is not within an AttributeMatrix, so the dimensions cannot be determined implicitly. Check Set Tuple Dimensions to set the dimensions",
+                              arrayPath.toString()));
     }
     else
     {

diff --git a/src/Plugins/ComplexCore/wrapping/python/complexpy.cpp b/src/Plugins/ComplexCore/wrapping/python/complexpy.cpp
@@ -10,7 +10,6 @@
 #include "ComplexCore/ComplexCoreFilterBinding.hpp"
 
 #include <ComplexCore/ComplexCorePlugin.hpp>
-
 #include <complex/DataStructure/AttributeMatrix.hpp>
 #include <complex/DataStructure/DataArray.hpp>
 #include <complex/DataStructure/DataGroup.hpp>
@@ -80,6 +79,7 @@
 #include <complex/Pipeline/AbstractPipelineNode.hpp>
 #include <complex/Pipeline/Pipeline.hpp>
 #include <complex/Pipeline/PipelineFilter.hpp>
+#include <complex/Utilities/DataGroupUtilities.hpp>
 
 #include <fmt/ranges.h>
 
@@ -504,12 +504,118 @@ PYBIND11_MODULE(complex, mod)
 
   dataObject.def_property_readonly("id", &DataObject::getId);
   dataObject.def_property_readonly("name", &DataObject::getName);
+  dataObject.def_property_readonly("type", &DataObject::getDataObjectType);
 
   dataStructure.def(py::init<>());
   dataStructure.def("__getitem__", py::overload_cast<const DataPath&>(&DataStructure::getSharedData));
+  dataStructure.def("__getitem__", [](DataStructure& self, const std::string& path) {
+    auto pathConversionResult = DataPath::FromString(path);
+    if(!pathConversionResult)
+    {
+      return std::shared_ptr<DataObject>(nullptr);
+    }
+    return self.getSharedData(pathConversionResult.value());
+  });
   dataStructure.def_property_readonly("size", &DataStructure::getSize);
   dataStructure.def("__len__", &DataStructure::getSize);
   dataStructure.def("remove", py::overload_cast<const DataPath&>(&DataStructure::removeData));
+  dataStructure.def("remove", [](DataStructure& self, const std::string& path) {
+    auto pathConversionResult = DataPath::FromString(path);
+    if(!pathConversionResult)
+    {
+      return false;
+    }
+    return self.removeData(pathConversionResult.value());
+  });
+  dataStructure.def("hierarchy_to_str", [](DataStructure& self) {
+    std::stringstream ss;
+    self.exportHierarchyAsText(ss);
+    return ss.str();
+  });
+  dataStructure.def("hierarchy_to_graphviz", [](DataStructure& self) {
+    std::stringstream ss;
+    self.exportHierarchyAsGraphViz(ss);
+    return ss.str();
+  });
+  dataStructure.def("get_children", [](DataStructure& self, complex::DataPath& parentPath) {
+    if(parentPath.empty())
+    {
+      std::vector<DataPath> outputPaths;
+      for(const auto* object : self.getTopLevelData())
+      {
+        auto topLevelPath = DataPath::FromString(object->getDataPaths()[0].getTargetName()).value();
+        outputPaths.push_back(topLevelPath);
+      }
+      return outputPaths;
+    }
+    else
+    {
+      auto result = complex::GetAllChildDataPaths(self, parentPath);
+      if(result)
+      {
+        return result.value();
+      }
+      return std::vector<DataPath>{};
+    }
+  });
+  dataStructure.def("get_children", [](DataStructure& self, const std::string& parentPath) {
+    if(parentPath.empty())
+    {
+      std::vector<DataPath> outputPaths;
+      for(const auto* object : self.getTopLevelData())
+      {
+        auto topLevelPath = DataPath::FromString(object->getDataPaths()[0].getTargetName()).value();
+        outputPaths.push_back(topLevelPath);
+      }
+      return outputPaths;
+    }
+    else
+    {
+      auto pathConversionResult = DataPath::FromString(parentPath);
+      if(!pathConversionResult)
+      {
+        return std::vector<DataPath>{};
+      }
+
+      auto result = complex::GetAllChildDataPaths(self, pathConversionResult.value());
+      if(result)
+      {
+        return result.value();
+      }
+      return std::vector<DataPath>{};
+    }
+  });
+
+  auto dataObjectType = py::enum_<DataObject::Type>(dataObject, "DataObjectType");
+  dataObjectType.value("DataObject", DataObject::Type::DataObject);
+  dataObjectType.value("DynamicListArray", DataObject::Type::DynamicListArray);
+  dataObjectType.value("ScalarData", DataObject::Type::ScalarData);
+  dataObjectType.value("BaseGroup", DataObject::Type::BaseGroup);
+  dataObjectType.value("AttributeMatrix", DataObject::Type::AttributeMatrix);
+  dataObjectType.value("DataGroup", DataObject::Type::DataGroup);
+  dataObjectType.value("IDataArray", DataObject::Type::IDataArray);
+  dataObjectType.value("DataArray", DataObject::Type::DataArray);
+  dataObjectType.value("IGeometry", DataObject::Type::IGeometry);
+  dataObjectType.value("IGridGeometry", DataObject::Type::IGridGeometry);
+  dataObjectType.value("RectGridGeom", DataObject::Type::RectGridGeom);
+  dataObjectType.value("ImageGeom", DataObject::Type::ImageGeom);
+  dataObjectType.value("INodeGeometry0D", DataObject::Type::INodeGeometry0D);
+  dataObjectType.value("VertexGeom", DataObject::Type::VertexGeom);
+  dataObjectType.value("INodeGeometry1D", DataObject::Type::INodeGeometry1D);
+  dataObjectType.value("EdgeGeom", DataObject::Type::EdgeGeom);
+  dataObjectType.value("INodeGeometry2D", DataObject::Type::INodeGeometry2D);
+  dataObjectType.value("QuadGeom", DataObject::Type::QuadGeom);
+  dataObjectType.value("TriangleGeom", DataObject::Type::TriangleGeom);
+  dataObjectType.value("INodeGeometry3D", DataObject::Type::INodeGeometry3D);
+  dataObjectType.value("HexahedralGeom", DataObject::Type::HexahedralGeom);
+  dataObjectType.value("TetrahedralGeom", DataObject::Type::TetrahedralGeom);
+  dataObjectType.value("INeighborList", DataObject::Type::INeighborList);
+  dataObjectType.value("NeighborList", DataObject::Type::NeighborList);
+  dataObjectType.value("StringArray", DataObject::Type::StringArray);
+  dataObjectType.value("AbstractMontage", DataObject::Type::AbstractMontage);
+  dataObjectType.value("GridMontage", DataObject::Type::GridMontage);
+  dataObjectType.value("Unknown", DataObject::Type::Unknown);
+  dataObjectType.value("Any", DataObject::Type::Any);
 
   py::class_<BaseGroup, DataObject, std::shared_ptr<BaseGroup>> baseGroup(mod, "BaseGroup");
   baseGroup.def("contains", py::overload_cast<const std::string&>(&BaseGroup::contains, py::const_));

diff --git a/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/ReadH5EspritDataFilter.cpp b/src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/ReadH5EspritDataFilter.cpp
@@ -65,7 +65,7 @@ Parameters ReadH5EspritDataFilter::parameters() const
   Parameters params;
   // Create the parameter descriptors that are needed for this filter
   params.insertSeparator(Parameters::Separator{"Input Parameters"});
-  params.insert(std::make_unique<OEMEbsdScanSelectionParameter>(k_SelectedScanNames_Key, "Scan Names", "The name of the scan in the .h5 file. EDAX can store multiple scans in a single file",
+  params.insert(std::make_unique<OEMEbsdScanSelectionParameter>(k_SelectedScanNames_Key, "Scan Names", "The name of the scan in the .h5 file. Esprit can store multiple scans in a single file",
                                                                 OEMEbsdScanSelectionParameter::ValueType{},
                                                                 /* OEMEbsdScanSelectionParameter::AllowedManufacturers{EbsdLib::OEM::Bruker, EbsdLib::OEM::DREAM3D},*/
                                                                 OEMEbsdScanSelectionParameter::EbsdReaderType::Esprit, OEMEbsdScanSelectionParameter::ExtensionsType{".h5", ".hdf5"}));
@@ -134,7 +134,10 @@ IFilter::PreflightResult ReadH5EspritDataFilter::preflightImpl(const DataStructu
   const std::vector<usize> tupleDims = {dims[2], dims[1], dims[0]};
   {
     CreateImageGeometryAction::SpacingType spacing = {static_cast<float32>(reader->getXStep()), static_cast<float32>(reader->getYStep()), pZSpacingValue};
-
+    for(float& value : spacing)
+    {
+      value = (value == 0.0f ? 1.0f : value);
+    }
     auto createDataGroupAction = std::make_unique<CreateImageGeometryAction>(pImageGeometryNameValue, dims, pOriginValue, spacing, pCellAttributeMatrixNameValue);
     resultOutputActions.value().appendAction(std::move(createDataGroupAction));
   }