Add wrapping and tests for PhasedArray3DSpecialCoordinatesImage

.github/workflows/build-test-package.yml

@@ -4,13 +4,13 @@ on: [push,pull_request]
 
 jobs:
   cxx-build-workflow:
-    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-cxx.yml@f2191a014a93c0d0e7b9e7ffb32d2e1118fb2876
+    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-cxx.yml@edd0a4350396f533e9ec3755ed6c5af5ddfedb97
     with:
       itk-module-deps: '[email protected]:[email protected]:[email protected]:[email protected]:[email protected]'
       warnings-to-ignore: "\"pointer is null\" \"in a call to non-static member function\""
 
   python-build-workflow:
-    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-package-python.yml@f2191a014a93c0d0e7b9e7ffb32d2e1118fb2876
+    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-package-python.yml@edd0a4350396f533e9ec3755ed6c5af5ddfedb97
     with:
       itk-module-deps: 'InsightSoftwareConsortium/[email protected]:InsightSoftwareConsortium/[email protected]:InsightSoftwareConsortium/[email protected]:InsightSoftwareConsortium/[email protected]:KitwareMedical/[email protected]'
     secrets:

setup.py

@@ -5,7 +5,7 @@
 
 setup(
     name='itk-ultrasound',
-    version='0.6.1',
+    version='0.6.2',
     author='Matthew McCormick',
     author_email='[email protected]',
     packages=['itk'],

test/Baseline/ScanConvertPhasedArray3DITKNearestNeighborTestOutput.mha.sha512

@@ -0,0 +1 @@
+8fc8129454b6ec93fb5c133d9835f8a49df0ab14584d44b3454e1b36dee60ef92e29bb9e8c3b9a1340129877fc0ec81d7beb5022eaf3bcbbed8fa3ebab8e6c74

test/Baseline/ScanConvertPhasedArray3DITKWindowedSincTestOutput.mha.sha512

@@ -0,0 +1 @@
+cf4bac01a2692100f1c2b2445f3468b26c754e380f4d0119b466c079639f309ad18f775106f341a72c6126a7a636d55c494ed40edf441de262418ff65b2a792e

test/Baseline/ScanConvertPhasedArray3DTestOutput.mha.sha512

@@ -0,0 +1 @@
+6e589887b660f79513d1c09479cc70bd815e532e013fcb3bb185a21c641e417210d6a8286199a265b8e6b9159254e6237108539d0c5eb865a7bedb03d64cbf50

test/Input/ScanConvertPhasedArray3DTestInput.mha.sha512

@@ -0,0 +1 @@
+7d5e6c2b070107a279277c48ead400bab15edd7aaa1b1b2238a8437da1435c41f75c3b2323fdba17f6415d10ea37992ff053f52a5f6d7a0937f78cfaf1f3687a

wrapping/CMakeLists.txt

@@ -11,6 +11,7 @@ set(WRAPPER_SUBMODULE_ORDER
   itkCurvilinearArraySpecialCoordinatesImage
   itkImageUltrasound # Extra itk::Image wrappings for SupportWindow filters
   itkCurvilinearArraySpecialCoordinatesImageFilters
+  itkPhasedArray3DSpecialCoordinatesImage # CASCI needs to come before
   itkAttenuationImageFilter
   itkBlockMatchingMetricImageFilter
   itkBlockMatchingNormalizedCrossCorrelationMetricImageFilter

wrapping/itkCurvilinearArraySpecialCoordinatesImage.wrap

@@ -29,27 +29,19 @@ string(APPEND ITK_WRAP_PYTHON_SWIG_EXT "
 
   %extend swig_name {
       itkIndex##template_params TransformPhysicalPointToIndex(const itkPointD##template_params & point ) {
-          itkIndex##template_params idx;
-          self->TransformPhysicalPointToIndex<double>( point, idx );
-          return idx;
+          return self->TransformPhysicalPointToIndex<double>( point );
         }
 
       itkContinuousIndexD##template_params TransformPhysicalPointToContinuousIndex(const itkPointD##template_params & point ) {
-          itkContinuousIndexD##template_params idx;
-          self->TransformPhysicalPointToContinuousIndex<double>( point, idx );
-          return idx;
+          return self->TransformPhysicalPointToContinuousIndex<double>( point );
       }
 
       itkPointD##template_params TransformContinuousIndexToPhysicalPoint(const itkContinuousIndexD##template_params & idx ) {
-          itkPointD##template_params point;
-          self->TransformContinuousIndexToPhysicalPoint<double>( idx, point );
-          return point;
+          return self->TransformContinuousIndexToPhysicalPoint<double>( idx );
       }
 
       itkPointD##template_params TransformIndexToPhysicalPoint(const itkIndex##template_params & idx ) {
-          itkPointD##template_params point;
-          self->TransformIndexToPhysicalPoint<double>( idx, point );
-          return point;
+          return self->TransformIndexToPhysicalPoint<double>( idx );
       }
   }
 

wrapping/itkCurvilinearArraySpecialCoordinatesImageFilters.wrap

@@ -1,10 +1,11 @@
 # ITK image filters wrapped for ITKUltrasound `itk::CurvilinearArraySpecialCoordinatesImage` inputs.
-# Must be wrapped in a separate file after `itkCurvilinearArraySpecialCoordinates.wrap` so that
+# Must be wrapped in a separate file after `itkCurvilinearArraySpecialCoordinatesImage.wrap` so that
 # SWIG does not implicitly define erroneous overrides for template methods such as
 # `TransformPhysicalPointToContinuousIndex`, etc.
 
-# See `WRAPPER_SUBMODULE_ORDER` in CMakeLists.txt for where `itkCASCIFilters.wrap` is set to
-# always be wrapped after `itkCurvilinearArraySpecialCoordinatesImage.wrap`.
+# See `WRAPPER_SUBMODULE_ORDER` in CMakeLists.txt for where
+# `itkCurvilinearArraySpecialCoordinatesImageFilters.wrap` is set to
+# be wrapped after `itkCurvilinearArraySpecialCoordinatesImage.wrap`.
 
 itk_wrap_include("itkCurvilinearArraySpecialCoordinatesImage.h")
 itk_wrap_class("itk::ImageSource" POINTER)

wrapping/itkPhasedArray3DSpecialCoordinatesImage.wrap

@@ -0,0 +1,50 @@
+itk_wrap_include("list")
+itk_wrap_include("complex")
+
+# Explicitly override template method wrappings so that implicit
+# scalar type is always `double` for greatest precision.
+# Adds wrapping overrides to `itkPhasedArray3DSpecialCoordinatesImage_ext.i` configured with
+# CMake for input to SWIG wrapping generation.
+# See `DECL_PYTHON_IMAGEBASE_CLASS` definition in `ITK/Wrapping/Generators/Python/PyBase/pyBase.i`
+# for precedent.
+string(APPEND ITK_WRAP_PYTHON_SWIG_EXT "
+%inline %{
+#include \"itkContinuousIndexSwigInterface.h\"
+%}
+
+%define DECL_PYTHON_PHASEDARRAY3DSPECIALCOORDINATESIMAGE_CLASS(swig_name, template_params)
+
+  %extend swig_name {
+      itkIndex##template_params TransformPhysicalPointToIndex(const itkPointD##template_params & point ) {
+          return self->TransformPhysicalPointToIndex<double>( point );
+        }
+
+      itkContinuousIndexD##template_params TransformPhysicalPointToContinuousIndex(const itkPointD##template_params & point ) {
+          return self->TransformPhysicalPointToContinuousIndex<double>( point );
+      }
+
+      itkPointD##template_params TransformContinuousIndexToPhysicalPoint(const itkContinuousIndexD##template_params & idx ) {
+          return self->TransformContinuousIndexToPhysicalPoint<double>( idx );
+      }
+
+      itkPointD##template_params TransformIndexToPhysicalPoint(const itkIndex##template_params & idx ) {
+          return self->TransformIndexToPhysicalPoint<double>( idx );
+      }
+  }
+
+%enddef
+")
+
+# Wrap class for real and complex pixel types. Dimension is always 3.
+itk_wrap_class("itk::PhasedArray3DSpecialCoordinatesImage" POINTER_WITH_SUPERCLASS)
+  foreach(t ${WRAP_ITK_SCALAR})
+    itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}")
+    string(APPEND ITK_WRAP_PYTHON_SWIG_EXT "DECL_PYTHON_PHASEDARRAY3DSPECIALCOORDINATESIMAGE_CLASS(${WRAPPER_SWIG_NAME}${ITKM_${t}}, 3)\n")
+  endforeach()
+  foreach(t3 ${WRAP_ITK_COMPLEX_REAL})
+    itk_wrap_template("${ITKM_${t3}}" "${ITKT_${t3}}")
+    string(APPEND ITK_WRAP_PYTHON_SWIG_EXT "DECL_PYTHON_PHASEDARRAY3DSPECIALCOORDINATESIMAGE_CLASS(${WRAPPER_SWIG_NAME}${ITKM_${t3}}, 3)\n")
+  endforeach()
+itk_end_wrap_class()
+
+# Then wrap consuming filters in itkPhasedArray3DSpecialCoordinatesImageFilters.wrap

wrapping/itkPhasedArray3DSpecialCoordinatesImageFilters.wrap

@@ -0,0 +1,150 @@
+# ITK image filters wrapped for ITKUltrasound `itk::PhasedArray3DSpecialCoordinatesImage` inputs.
+# Must be wrapped in a separate file after `itkPhasedArray3DSpecialCoordinatesImage.wrap` so that
+# SWIG does not implicitly define erroneous overrides for template methods such as
+# `TransformPhysicalPointToContinuousIndex`, etc.
+
+# See `WRAPPER_SUBMODULE_ORDER` in CMakeLists.txt for where
+# `itkPhasedArray3DSpecialCoordinatesImageFilters.wrap` is set to
+# be wrapped after `itkPhasedArray3DSpecialCoordinatesImage.wrap`.
+
+itk_wrap_include("itkPhasedArray3DSpecialCoordinatesImage.h")
+itk_wrap_class("itk::ImageSource" POINTER)
+  foreach(real_type ${WRAP_ITK_SCALAR})
+    itk_wrap_template("PA3DSCI${ITKM_${real_type}}" "itk::PhasedArray3DSpecialCoordinatesImage<${ITKT_${real_type}}>")
+  endforeach()
+  foreach(complex_type ${WRAP_ITK_COMPLEX_REAL})
+    itk_wrap_template("PA3DSCI${ITKM_${complex_type}}" "itk::PhasedArray3DSpecialCoordinatesImage<${ITKT_${complex_type}}>")
+  endforeach()
+itk_end_wrap_class()
+
+itk_wrap_include("itkImage.h")
+itk_wrap_class("itk::ImageToImageFilter" POINTER)
+  foreach(t ${WRAP_ITK_SCALAR})
+    foreach(ut ${WRAP_ITK_INT})
+      itk_wrap_template("I${ITKM_${t}}3PA3DSCI${ITKM_${ut}}"
+        "itk::Image< ${ITKT_${t}}, 3 >, itk::PhasedArray3DSpecialCoordinatesImage< ${ITKT_${ut}} >")
+    endforeach()
+    foreach(t2 ${WRAP_ITK_SCALAR})
+      itk_wrap_template("PA3DSCI${ITKM_${t}}PA3DSCI${ITKM_${t2}}"
+        "itk::PhasedArray3DSpecialCoordinatesImage< ${ITKT_${t}} >, itk::PhasedArray3DSpecialCoordinatesImage< ${ITKT_${t2}} >")
+    endforeach()
+    itk_wrap_template("PA3DSCI${ITKM_${t}}I${ITKM_${t}}3"
+      "itk::PhasedArray3DSpecialCoordinatesImage< ${ITKT_${t}} >, itk::Image< ${ITKT_${t}}, 3>")
+  endforeach()
+
+  foreach(rt ${WRAP_ITK_REAL})
+    foreach(ct ${WRAP_ITK_COMPLEX_REAL})
+      itk_wrap_template("PA3DSCI${ITKM_${rt}}PA3DSCI${ITKM_${ct}}"
+      "itk::PhasedArray3DSpecialCoordinatesImage<  ${ITKT_${rt}} >, itk::PhasedArray3DSpecialCoordinatesImage<  ${ITKT_${ct}} >")
+      itk_wrap_template("PA3DSCI${ITKM_${ct}}PA3DSCI${ITKM_${rt}}"
+      "itk::PhasedArray3DSpecialCoordinatesImage<  ${ITKT_${ct}} >, itk::PhasedArray3DSpecialCoordinatesImage<  ${ITKT_${rt}} >")
+    endforeach()
+  endforeach()
+
+  foreach(t3 ${WRAP_ITK_COMPLEX_REAL})
+    itk_wrap_template("PA3DSCI${ITKM_${t3}}PA3DSCI${ITKM_${t3}}"
+      "itk::PhasedArray3DSpecialCoordinatesImage<  ${ITKT_${t3}} >, itk::PhasedArray3DSpecialCoordinatesImage<  ${ITKT_${t3}} >")
+  endforeach()
+itk_end_wrap_class()
+
+itk_wrap_class("itk::ImageFileReader" POINTER_WITH_SUPERCLASS)
+  foreach(t ${WRAP_ITK_SCALAR})
+    itk_wrap_template("PA3DSCI${ITKM_${t}}"
+      "itk::PhasedArray3DSpecialCoordinatesImage< ${ITKT_${t}} >")
+  endforeach()
+itk_end_wrap_class()
+
+itk_wrap_class("itk::ImageFileWriter" POINTER)
+  foreach(t ${WRAP_ITK_SCALAR})
+    itk_wrap_template("PA3DSCI${ITKM_${t}}"
+      "itk::PhasedArray3DSpecialCoordinatesImage< ${ITKT_${t}} >")
+  endforeach()
+itk_end_wrap_class()
+
+itk_wrap_class("itk::CastImageFilter" POINTER_WITH_2_SUPERCLASSES)
+  foreach(t1 ${WRAP_ITK_SCALAR})
+    foreach(t2 ${WRAP_ITK_SCALAR})
+      itk_wrap_template("PA3DSCI${ITKM_${t1}}PA3DSCI${ITKM_${t2}}"
+        "itk::PhasedArray3DSpecialCoordinatesImage< ${ITKT_${t1}} >, itk::PhasedArray3DSpecialCoordinatesImage< ${ITKT_${t2}} >")
+      itk_wrap_template("PA3DSCI${ITKM_${t1}}I${ITKM_${t2}}3"
+        "itk::PhasedArray3DSpecialCoordinatesImage< ${ITKT_${t1}} >, itk::Image< ${ITKT_${t2}}, 3 >")
+    endforeach()
+  endforeach()
+itk_end_wrap_class()
+
+itk_wrap_class("itk::RescaleIntensityImageFilter" POINTER_WITH_2_SUPERCLASSES)
+  foreach(t ${WRAP_ITK_SCALAR})
+    foreach(ut ${WRAP_ITK_INT})
+      itk_wrap_template("I${ITKM_${t}}3PA3DSCI${ITKM_${ut}}"
+        "itk::Image< ${ITKT_${t}}, 3 >, itk::PhasedArray3DSpecialCoordinatesImage< ${ITKT_${ut}} >")
+    endforeach()
+  endforeach()
+itk_end_wrap_class()
+
+itk_wrap_include("itkSpectra1DSupportWindowToMaskImageFilter.h")
+itk_wrap_class("itk::Spectra1DSupportWindowToMaskImageFilter" POINTER_WITH_2_SUPERCLASSES)
+    foreach(t ${WRAP_ITK_INT})
+      itk_wrap_template("IlistitkIndex33PA3DSCI${ITKM_${t}}"
+        "itk::Image< std::list< itk::Index< 3 > >, 3 >, itk::PhasedArray3DSpecialCoordinatesImage< ${ITKT_${t}} >")
+    endforeach()
+itk_end_wrap_class()
+
+# The rest is needed for ResampleImageFilter and interpolator functions
+set(resample_filter_pixel_types "F")
+if(ITK_WRAP_unsigned_char)
+  list(APPEND resample_filter_pixel_types "UC")
+endif()
+itk_wrap_include("itkResampleImageFilter.h")
+itk_wrap_class("itk::ResampleImageFilter" POINTER)
+  foreach(t ${resample_filter_pixel_types})
+    itk_wrap_template("PA3DSCI${ITKM_${t}}I${ITKM_${t}}3"
+      "itk::PhasedArray3DSpecialCoordinatesImage< ${ITKT_${t}} >, itk::Image< ${ITKT_${t}}, 3 >")
+  endforeach()
+itk_end_wrap_class()
+
+itk_wrap_class("itk::ImageFunction" POINTER)
+  foreach(t ${resample_filter_pixel_types})
+    itk_wrap_template("PA3DSCI${ITKM_${t}}${ITKM_D}"
+      "itk::PhasedArray3DSpecialCoordinatesImage< ${ITKT_${t}} >, ${ITKT_D}, ${ITKT_D}")
+  endforeach()
+itk_end_wrap_class()
+
+itk_wrap_class("itk::InterpolateImageFunction" POINTER)
+  foreach(t ${resample_filter_pixel_types})
+    itk_wrap_template("PA3DSCI${ITKM_${t}}${ITKM_D}" "itk::PhasedArray3DSpecialCoordinatesImage< ${ITKT_${t}} >, ${ITKT_D}")
+  endforeach()
+itk_end_wrap_class()
+
+itk_wrap_class("itk::NearestNeighborInterpolateImageFunction" POINTER)
+  foreach(t ${resample_filter_pixel_types})
+    itk_wrap_template("PA3DSCI${ITKM_${t}}${ITKM_D}"
+      "itk::PhasedArray3DSpecialCoordinatesImage< ${ITKT_${t}} >, ${ITKT_D}")
+  endforeach()
+itk_end_wrap_class()
+
+itk_wrap_class("itk::LinearInterpolateImageFunction" POINTER)
+  foreach(t ${resample_filter_pixel_types})
+    itk_wrap_template("PA3DSCI${ITKM_${t}}${ITKM_D}"
+      "itk::PhasedArray3DSpecialCoordinatesImage< ${ITKT_${t}} >, ${ITKT_D}")
+  endforeach()
+itk_end_wrap_class()
+
+itk_wrap_class("itk::GaussianInterpolateImageFunction" POINTER)
+  foreach(t ${resample_filter_pixel_types})
+    itk_wrap_template("PA3DSCI${ITKM_${t}}${ITKM_D}"
+      "itk::PhasedArray3DSpecialCoordinatesImage< ${ITKT_${t}} >, ${ITKT_D}")
+  endforeach()
+itk_end_wrap_class()
+
+itk_wrap_include("itkWindowedSincInterpolateImageFunction.h")
+set(window_functions "Hamming" "Cosine" "Welch" "Lanczos")
+set(radii 2 3)
+itk_wrap_class("itk::WindowedSincInterpolateImageFunction" POINTER)
+  foreach(t ${resample_filter_pixel_types})
+    foreach(r ${radii}) # radius
+      foreach(function ${window_functions})
+        itk_wrap_template("PA3DSCI${ITKM_${t}}${r}${function}" "itk::PhasedArray3DSpecialCoordinatesImage< ${ITKT_${t}} >, ${r}, itk::Function::${function}WindowFunction< ${r} >")
+      endforeach()
+    endforeach()
+  endforeach()
+itk_end_wrap_class()

wrapping/test/CMakeLists.txt

@@ -40,7 +40,7 @@ itk_python_add_test(NAME PythonCurvilinearArraySpecialCoordinatesImageTemplateMe
   COMMAND PythonCurvilinearArraySpecialCoordinatesImageTemplateMethodsTest.py
   )
 
-itk_python_expression_add_test(NAME PythonInstantiateGaussianInterpolateImageFunction
+itk_python_expression_add_test(NAME PythonInstantiateGaussianInterpolateImageFunctionCASCI
   EXPRESSION "iFunc = itk.GaussianInterpolateImageFunction[itk.CurvilinearArraySpecialCoordinatesImage[itk.UC, 2], itk.D].New()"
   )
 
@@ -58,6 +58,58 @@ itk_python_add_test(NAME PythonCurvilinearResampleTest
     --first-sample-distance 26.4
   )
 
+itk_python_expression_add_test(NAME PythonInstantiateGaussianInterpolateImageFunctionPA3DSCI
+  EXPRESSION "iFunc = itk.GaussianInterpolateImageFunction[itk.PhasedArray3DSpecialCoordinatesImage[itk.F], itk.D].New()"
+  )
+
+itk_python_add_test(NAME PythonPhasedArray3DResampleNearestTest
+  TEST_DRIVER_ARGS
+  --compareIntensityTolerance 1
+  --compare
+    DATA{${test_baseline_dir}/ScanConvertPhasedArray3DITKNearestNeighborTestOutput.mha}
+    ${ITK_TEST_OUTPUT_DIR}/ScanConvertPhasedArray3DITKNearestNeighborTestOutput.mha
+  COMMAND PythonPhasedArray3DResample.py
+    -i DATA{${test_input_dir}/ScanConvertPhasedArray3DTestInput.mha}
+    -o ${ITK_TEST_OUTPUT_DIR}/ScanConvertPhasedArray3DITKNearestNeighborTestOutput.mha
+    --azimuth-angular-separation 0.0872665
+    --elevation-angular-separation 0.0174533
+    --radius-sample-size 0.2
+    --first-sample-distance 8.0
+    --interpolation-type nearest
+  )
+
+itk_python_add_test(NAME PythonPhasedArray3DResampleLinearTest
+  TEST_DRIVER_ARGS
+  --compareIntensityTolerance 1
+  --compare
+    DATA{${test_baseline_dir}/ScanConvertPhasedArray3DTestOutput.mha}
+    ${ITK_TEST_OUTPUT_DIR}/ScanConvertPhasedArray3DTestOutput.mha
+  COMMAND PythonPhasedArray3DResample.py
+    -i DATA{${test_input_dir}/ScanConvertPhasedArray3DTestInput.mha}
+    -o ${ITK_TEST_OUTPUT_DIR}/ScanConvertPhasedArray3DTestOutput.mha
+    --azimuth-angular-separation 0.0872665
+    --elevation-angular-separation 0.0174533
+    --radius-sample-size 0.2
+    --first-sample-distance 8.0
+    # --interpolation-type linear  # linear is the default
+  )
+
+itk_python_add_test(NAME PythonPhasedArray3DResampleSincTest
+  TEST_DRIVER_ARGS
+  --compareIntensityTolerance 1
+  --compare
+    DATA{${test_baseline_dir}/ScanConvertPhasedArray3DITKWindowedSincTestOutput.mha}
+    ${ITK_TEST_OUTPUT_DIR}/ScanConvertPhasedArray3DITKWindowedSincTestOutput.mha
+  COMMAND PythonPhasedArray3DResample.py
+    -i DATA{${test_input_dir}/ScanConvertPhasedArray3DTestInput.mha}
+    -o ${ITK_TEST_OUTPUT_DIR}/ScanConvertPhasedArray3DITKWindowedSincTestOutput.mha
+    --azimuth-angular-separation 0.0872665
+    --elevation-angular-separation 0.0174533
+    --radius-sample-size 0.2
+    --first-sample-distance 8.0
+    --interpolation-type sinc
+  )
+
 itk_python_add_test(NAME PythonBackscatterImageFilterTest0
   TEST_DRIVER_ARGS
   --compareIntensityTolerance 0.01