Fix failing unit tests.

API: Added name(), human_name(), uuid() to the IFilter python API BUG: Fixed nullptr crashes. Signed-off-by: Michael Jackson <[email protected]>
BlueQuartzSoftware · Dec 20, 2023 · f05f767 · f05f767
1 parent ff26535
commit f05f767
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Showing 20 changed files with 745 additions and 258 deletions.
diff --git a/CMakePresets.json b/CMakePresets.json
@@ -129,6 +129,10 @@
         "Python3_EXECUTABLE": {
           "type": "PATH",
           "value": "/Users/runner/hostedtoolcache/Python/3.10.13/x64/bin/python3.10"
+        },
+        "COMPLEX_PY_DISABLE_HIDDEN_VISIBILITY": {
+          "type": "BOOL",
+          "value": "ON"
         }
       }
     },
@@ -146,6 +150,14 @@
         "VCPKG_HOST_TRIPLET": {
           "type": "STRING",
           "value": "arm64-osx-dynamic"
+        },
+        "Python3_EXECUTABLE": {
+          "type": "PATH",
+          "value": "/Users/runner/hostedtoolcache/Python/3.10.13/x64/bin/python3.10"
+        },
+        "COMPLEX_PY_DISABLE_HIDDEN_VISIBILITY": {
+          "type": "BOOL",
+          "value": "ON"
         }
       }
     },

diff --git a/src/Plugins/ComplexCore/wrapping/python/complexpy.cpp b/src/Plugins/ComplexCore/wrapping/python/complexpy.cpp
@@ -544,8 +544,11 @@ PYBIND11_MODULE(complex, mod)
       std::vector<DataPath> outputPaths;
       for(const auto* object : self.getTopLevelData())
       {
-        auto topLevelPath = DataPath::FromString(object->getDataPaths()[0].getTargetName()).value();
-        outputPaths.push_back(topLevelPath);
+        if(object != nullptr)
+        {
+          auto topLevelPath = DataPath::FromString(object->getDataPaths()[0].getTargetName()).value();
+          outputPaths.push_back(topLevelPath);
+        }
       }
       return outputPaths;
     }

diff --git a/src/complex/Utilities/DataGroupUtilities.cpp b/src/complex/Utilities/DataGroupUtilities.cpp
@@ -186,7 +186,6 @@ std::optional<std::vector<DataPath>> GetAllChildDataPaths(const DataStructure& d
     {
       bool ignore = false;
       DataPath childPath = parentGroup.createChildPath(childName);
-      const DataObject* dataObject = dataStructure.getData(childPath);
       for(const auto& ignoredPath : ignoredDataPaths)
       {
         if(childPath == ignoredPath)
@@ -195,7 +194,8 @@ std::optional<std::vector<DataPath>> GetAllChildDataPaths(const DataStructure& d
           break;
         }
       }
-      if(!ignore && (dataObjectType == DataObject::Type::DataObject || dataObject->getDataObjectType() == dataObjectType))
+      const DataObject* dataObject = dataStructure.getData(childPath);
+      if(dataObject != nullptr && !ignore && (dataObjectType == DataObject::Type::DataObject || dataObject->getDataObjectType() == dataObjectType))
       {
         childDataObjects.push_back(childPath);
       }
@@ -211,7 +211,7 @@ std::optional<std::vector<DataPath>> GetAllChildDataPaths(const DataStructure& d
 {
   std::vector<DataPath> childDataObjects;
   const DataObject* dataObject1 = dataStructure.getData(parent);
-  if(dataObject1->getDataObjectType() == DataObject::Type::DataArray || dataObject1->getDataObjectType() == DataObject::Type::DynamicListArray ||
+  if(dataObject1 == nullptr || dataObject1->getDataObjectType() == DataObject::Type::DataArray || dataObject1->getDataObjectType() == DataObject::Type::DynamicListArray ||
      dataObject1->getDataObjectType() == DataObject::Type::NeighborList || dataObject1->getDataObjectType() == DataObject::Type::ScalarData ||
      dataObject1->getDataObjectType() == DataObject::Type::StringArray)
   {

diff --git a/wrapping/python/CMakeLists.txt b/wrapping/python/CMakeLists.txt
@@ -300,18 +300,19 @@ if(COMPLEX_ENABLE_PYTHON_TESTS)
     set(PYTHON_TEST_INPUT_DIR "${complex_SOURCE_DIR}/wrapping/python/examples")
 
     set(COMPLEX_PYTHON_TESTS
+      "angle_conversion" 
+      "basic_arrays" 
       "basic_ebsd_ipf"
-      "import_d3d" 
-      # "angle_conversion" 
-      # "basic_arrays" 
-      # "basic_numpy" 
-      # "create_ensemble_info" 
-      # "generated_file_list" 
-      # "geometry_examples" 
-      # "import_hdf5" 
-      # "output_file" 
-      # "pipeline" 
-      # "read_csv_file"
+      "basic_numpy" 
+      "create_ensemble_info" 
+      "generated_file_list" 
+      "geometry_examples" 
+      "import_d3d"      # Dependent on 'basic_ebsd_ipf' running first
+      "import_hdf5"     # Dependent on 'basic_ebsd_ipf' running first
+      "output_file" 
+      "pipeline" 
+      "read_csv_file"
+    #  "read_esprit_data"
     )
 
     CreatePythonTests(PREFIX "PY_COMPLEX"

diff --git a/wrapping/python/CxPybind/CxPybind/CxPybind.hpp b/wrapping/python/CxPybind/CxPybind/CxPybind.hpp
@@ -397,7 +397,18 @@ auto BindFilter(py::handle scope, const Internals& internals)
 
     std::string executeSig = MakePythonSignature<FilterT>("execute", internals);
     std::string executeDocString = fmt::format("{}\n\nExecutes the filter\n", executeSig);
-
+    filter.def_static("human_name", [&internals]() {
+      FilterT filter;
+      return filter.humanName();
+    });
+    filter.def_static("name", [&internals]() {
+      FilterT filter;
+      return filter.name();
+    });
+    filter.def_static("uuid", [&internals]() {
+      FilterT filter;
+      return filter.uuid();
+    });
     filter.def_static(
         "execute",
         [&internals](DataStructure& dataStructure, const py::kwargs& kwargs) {

diff --git a/wrapping/python/complex_test_dirs.in.py b/wrapping/python/complex_test_dirs.in.py
@@ -6,6 +6,21 @@
 
  '''
 
+
+import complex as cx
+
+def check_filter_result(filter: cx.IFilter, result: cx.IFilter.ExecuteResult):
+  if len(result.warnings) != 0:
+    print(f'{filter.name()} ::  Warnings: {result.warnings}')
+
+  has_errors = len(result.errors) != 0 
+  if has_errors:
+    print(f'{filter.name()} :: Errors: {result.errors}')
+    raise RuntimeError(result)
+
+  print(f"{filter.name()} :: No errors running the filter")
+
+
 def GetBuildDirectory():
   return '${CMAKE_LIBRARY_OUTPUT_DIRECTORY}'
 
@@ -23,3 +38,13 @@ def GetComplexPythonSourceDir():
 
 def GetComplexSourceDir():
     return '${complex_SOURCE_DIR}'
+
+def print_all_paths():
+    print(f'#### Important Filesystem Paths ####')
+    print(f'  GetBuildDirectory:         {GetBuildDirectory()}')
+    print(f'  GetTestDirectory:          {GetTestDirectory()}')
+    print(f'  GetTestTempDirectory:      {GetTestTempDirectory()}')
+    print(f'  GetDataDirectory:          {GetDataDirectory()}')
+    print(f'  GetComplexPythonSourceDir: {GetComplexPythonSourceDir()}')
+    print(f'  GetComplexSourceDir:       {GetComplexSourceDir()}')
+    print('#######################################')
diff --git a/wrapping/python/docs/source/Overview.rst b/wrapping/python/docs/source/Overview.rst
@@ -181,7 +181,49 @@ form a **Pipeline**, in which the data structure flows through the set of **Filt
 being modified along the way. If a **Filter** reads in data from outside of DREAM3D-NX, 
 then the new data will be incorporated into the existing data structure. Or, if no 
 data structure yet exists (e.g, starting from a “blank slate”), a new one will be 
-created. 
+created.
+
+.. py:class:: complex.IFilter
+
+   This class holds an instantiation of a DREAM3D-NX filter. The filter can be
+   preflighted, executed or just held for later execution. 
+
+   .. py:method:: name()
+
+      :return: The C++ classname of the filter
+      :rtype: str
+
+   .. py:method:: human_name()
+
+      :return: What the user would see in the DREAM3D-NX application
+      :rtype: str
+
+   .. py:method:: uuid()
+
+      :return: The unique identifier of the filter
+      :rtype: str
+
+   .. py:method:: execute()
+
+      :return: A complex.IFilter.Result object that contains any warnings or errors
+      that were encountered during the execution of the filter.
+      :rtype: complex.IFilter.Result
+
+   .. py:method:: preflight()
+
+      :return: A complex.IFilter.Result object that contains any warnings or errors
+      that were encountered during the preflight of the filter.
+      :rtype: complex.IFilter.Result
+
+.. code:: python
+
+   create_array_filter = cx.CreateDataArray()
+   print(f'{create_array_filter.name()}')
+   print(f'{create_array_filter.human_name()}')
+   print(f'{create_array_filter.uuid()}')
+
+For examles of executing a filter, please see any of the example python files included
+with the source package.
 
 .. _Pipeline:
 .. _Plugin:

diff --git a/wrapping/python/examples/angle_conversion.py b/wrapping/python/examples/angle_conversion.py
@@ -1,4 +1,40 @@
-# Import the DREAM3D Base library and Plugins
+"""
+Important Note
+==============
+
+This python file can be used as an example of how to execute a number of DREAM3D-NX
+filters one after another, if you plan to use the codes below (and you are welcome to),
+there are a few things that you, the developer, should take note of:
+
+Import Statements
+-----------------
+
+You will most likely *NOT* need to include the following code:
+
+   .. code:: python
+      
+      import complex_test_dirs as cxtest
+
+Filter Error Detection
+----------------------
+
+In each section of code a filter is created and executed immediately. This may or
+may *not* be what you want to do. You can also preflight the filter to verify the
+correctness of the filters before executing the filter **although** this is done
+for you when the filter is executed. As such, you will want to check the 'result'
+variable to see if there are any errors or warnings. If there **are** any then
+you, as the developer, should act appropriately on the errors or warnings. 
+More specifically, this bit of code:
+
+   .. code:: python
+
+      cxtest.check_filter_result(cxor.ReadAngDataFilter, result)
+
+is used by the simplnx unit testing framework and should be replaced by your own
+error checking code. You are welcome to look up the function definition and use
+that.
+
+"""
 import complex as cx
 
 import itkimageprocessing as cxitk
@@ -7,6 +43,10 @@
 
 import numpy as np
 
+#------------------------------------------------------------------------------
+# Print the various filesystem paths that are pregenerated for this machine.
+#------------------------------------------------------------------------------
+cxtest.print_all_paths()
 
 
 # ------------------------------------------------------------------------------
@@ -22,11 +62,8 @@
                                     tuple_dimensions=[[99]],
                                     output_data_array=array_path,
                                     initialization_value='0')
-if len(result.errors) != 0:
-    print('Errors: {}', result.errors)
-    print('Warnings: {}', result.warnings)
-else:
-    print("No errors running the CreateDataArray")
+cxtest.check_filter_result(cx.CreateDataArray, result)
+
 
 # Get a numpy.view into the newly created DataArray
 data_array = data_structure[array_path]
@@ -48,11 +85,8 @@
                                           input_type=0,
                                           output_orientation_array_name='Quaternions',
                                           output_type=2)
-if len(result.errors) != 0:
-    print('Errors: {}', result.errors)
-    print('Warnings: {}', result.warnings)
-else:
-    print("No errors running the ConvertOrientations")
+cxtest.check_filter_result(cxor.ConvertOrientations, result)
+
 
 # Get the Quaternions and print them out.
 data_array = data_structure[quat_path]