Add ProxTVImage filter (BlueQuartzSoftware#182)

* Git on Linux really want this file to have LF line endings

* Updating the filter creation script to parse with Python 3

This update just avoids syntax errors on reading the script.
Trying to run this script using Python 3 causes an exception.

* ENH: generate ProxTVImage filter, add it to source and test lists

CMakeLists.txt

@@ -75,7 +75,7 @@ if(ITK_VERSION_MAJOR EQUAL 4)
 elseif(ITK_VERSION_MAJOR EQUAL 5)
   #message(STATUS "Using ITK v5")
   # Put ITK 5 Specific Modyles in here
-  set( ADDITIONAL_ITK_MODULES ${ADDITIONAL_ITK_MODULES} Montage)
+  set( ADDITIONAL_ITK_MODULES ${ADDITIONAL_ITK_MODULES} Montage TotalVariation)
 endif()
 
 option(${PLUGIN_NAME}_ENABLE_SCIFIO "Enable SCIFIO ITK Modules" OFF)

Documentation/ITKImageProcessingFilters/ITKProxTVImage.md

@@ -0,0 +1,56 @@
+ITK::Prox T V Image Filter (KW) {#itkproxtvimage}
+==============
+
+## Group (Subgroup) ##
+
+ITKImageProcessing (ITKImageProcessing)
+
+## Description ##
+
+Applies a total variation noise reduction filter to an image.
+
+ProxTVImageFilter from https://github.com/InsightSoftwareConsortium/ITKTotalVariation
+
+## Parameters ##
+
+| Name | Type | Description |
+|------|------|-------------|
+| MaximumNumberOfIterations | double| Get and set the maximum number of iterations. |
+| Weights | FloatVec3Type| N/A |
+| Norms | FloatVec3Type| N/A |
+
+
+## Required Geometry ##
+
+Image
+
+## Required Objects ##
+
+| Kind | Default Name | Type | Component Dimensions | Description |
+|------|--------------|------|----------------------|-------------|
+| **Cell Attribute Array** | None | N/A | (1)  | Array containing input image
+
+## Created Objects ##
+
+| Kind | Default Name | Type | Component Dimensions | Description |
+|------|--------------|------|----------------------|-------------|
+| **Cell Attribute Array** | None |  | (1)  | Array containing filtered image
+
+## References ##
+
+[1] T.S. Yoo, M. J. Ackerman, W. E. Lorensen, W. Schroeder, V. Chalana, S. Aylward, D. Metaxas, R. Whitaker. Engineering and Algorithm Design for an Image Processing API: A Technical Report on ITK - The Insight Toolkit. In Proc. of Medicine Meets Virtual Reality, J. Westwood, ed., IOS Press Amsterdam pp 586-592 (2002). 
+[2] H. Johnson, M. McCormick, L. Ibanez. The ITK Software Guide: Design and Functionality. Fourth Edition. Published by Kitware Inc. 2015 ISBN: 9781-930934-28-3
+[3] H. Johnson, M. McCormick, L. Ibanez. The ITK Software Guide: Introduction and Development Guidelines. Fourth Edition. Published by Kitware Inc. 2015 ISBN: 9781-930934-27-6
+
+## Example Pipelines ##
+
+
+
+## License & Copyright ##
+
+Please see the description file distributed with this plugin.
+
+## DREAM3D Mailing Lists ##
+
+If you need more help with a filter, please consider asking your question on the DREAM3D Users mailing list:
+https://groups.google.com/forum/?hl=en#!forum/dream3d-users

ITKImageProcessingFilters/ITKProxTVImage.cpp

@@ -0,0 +1,167 @@
+// File automatically generated
+
+/*
+ * Your License or Copyright can go here
+ */
+
+#include "ITKImageProcessing/ITKImageProcessingFilters/ITKProxTVImage.h"
+#include "SIMPLib/ITK/SimpleITKEnums.h"
+
+#include "SIMPLib/Common/Constants.h"
+#include "SIMPLib/FilterParameters/AbstractFilterParametersReader.h"
+#include "SIMPLib/FilterParameters/DataArraySelectionFilterParameter.h"
+#include "SIMPLib/FilterParameters/LinkedBooleanFilterParameter.h"
+#include "SIMPLib/FilterParameters/SeparatorFilterParameter.h"
+#include "SIMPLib/FilterParameters/StringFilterParameter.h"
+
+#include "SIMPLib/Geometry/ImageGeom.h"
+
+#include "SIMPLib/ITK/Dream3DTemplateAliasMacro.h"
+#include "SIMPLib/ITK/itkDream3DImage.h"
+
+// -----------------------------------------------------------------------------
+//
+// -----------------------------------------------------------------------------
+ITKProxTVImage::ITKProxTVImage()
+{
+  m_MaximumNumberOfIterations = StaticCastScalar<double, double, double>(10u);
+  m_Weights = CastStdToVec3<std::vector<double>, FloatVec3Type, float>(std::vector<double>(3, 1.0));
+  m_Norms = CastStdToVec3<std::vector<double>, FloatVec3Type, float>(std::vector<double>(3, 1.0));
+
+  setupFilterParameters();
+}
+
+// -----------------------------------------------------------------------------
+//
+// -----------------------------------------------------------------------------
+ITKProxTVImage::~ITKProxTVImage() = default;
+
+// -----------------------------------------------------------------------------
+//
+// -----------------------------------------------------------------------------
+void ITKProxTVImage::setupFilterParameters()
+{
+  FilterParameterVectorType parameters;
+
+    parameters.push_back(SIMPL_NEW_DOUBLE_FP("MaximumNumberOfIterations", MaximumNumberOfIterations, FilterParameter::Parameter, ITKProxTVImage));
+  parameters.push_back(SIMPL_NEW_FLOAT_VEC3_FP("Weights", Weights, FilterParameter::Parameter, ITKProxTVImage));
+  parameters.push_back(SIMPL_NEW_FLOAT_VEC3_FP("Norms", Norms, FilterParameter::Parameter, ITKProxTVImage));
+
+
+  QStringList linkedProps;
+  linkedProps << "NewCellArrayName";
+  parameters.push_back(SIMPL_NEW_LINKED_BOOL_FP("Save as New Array", SaveAsNewArray, FilterParameter::Parameter, ITKProxTVImage, linkedProps));
+  parameters.push_back(SeparatorFilterParameter::New("Cell Data", FilterParameter::RequiredArray));
+  {
+    DataArraySelectionFilterParameter::RequirementType req =
+        DataArraySelectionFilterParameter::CreateRequirement(SIMPL::Defaults::AnyPrimitive, SIMPL::Defaults::AnyComponentSize, AttributeMatrix::Type::Cell, IGeometry::Type::Image);
+    parameters.push_back(SIMPL_NEW_DA_SELECTION_FP("Attribute Array to filter", SelectedCellArrayPath, FilterParameter::RequiredArray, ITKProxTVImage, req));
+  }
+  parameters.push_back(SeparatorFilterParameter::New("Cell Data", FilterParameter::CreatedArray));
+  parameters.push_back(SIMPL_NEW_STRING_FP("Filtered Array", NewCellArrayName, FilterParameter::CreatedArray, ITKProxTVImage));
+
+  setFilterParameters(parameters);
+}
+
+// -----------------------------------------------------------------------------
+//
+// -----------------------------------------------------------------------------
+void ITKProxTVImage::readFilterParameters(AbstractFilterParametersReader* reader, int index)
+{
+  reader->openFilterGroup(this, index);
+  setSelectedCellArrayPath(reader->readDataArrayPath("SelectedCellArrayPath", getSelectedCellArrayPath()));
+  setNewCellArrayName(reader->readString("NewCellArrayName", getNewCellArrayName()));
+  setSaveAsNewArray(reader->readValue("SaveAsNewArray", getSaveAsNewArray()));
+  setMaximumNumberOfIterations(reader->readValue("MaximumNumberOfIterations", getMaximumNumberOfIterations()));
+  setWeights(reader->readFloatVec3("Weights", getWeights()));
+  setNorms(reader->readFloatVec3("Norms", getNorms()));
+
+  reader->closeFilterGroup();
+}
+
+// -----------------------------------------------------------------------------
+//
+// -----------------------------------------------------------------------------
+template <typename InputPixelType, typename OutputPixelType, unsigned int Dimension> void ITKProxTVImage::dataCheck()
+{
+  clearErrorCode();
+  clearWarningCode();
+
+  // Check consistency of parameters
+  this->CheckIntegerEntry<unsigned int, double>(m_MaximumNumberOfIterations, "MaximumNumberOfIterations", 1);
+  this->CheckVectorEntry<double, FloatVec3Type>(m_Weights, "Weights", 0);
+  this->CheckVectorEntry<double, FloatVec3Type>(m_Norms, "Norms", 0);
+
+  ITKImageProcessingBase::dataCheck<InputPixelType, OutputPixelType, Dimension>();
+}
+
+// -----------------------------------------------------------------------------
+//
+// -----------------------------------------------------------------------------
+void ITKProxTVImage::dataCheckInternal()
+{
+  Dream3DArraySwitchMacro(this->dataCheck, getSelectedCellArrayPath(), -4);
+}
+
+// -----------------------------------------------------------------------------
+//
+// -----------------------------------------------------------------------------
+
+template <typename InputPixelType, typename OutputPixelType, unsigned int Dimension> void ITKProxTVImage::filter()
+{
+  typedef itk::Dream3DImage<InputPixelType, Dimension> InputImageType;
+  typedef itk::Dream3DImage<OutputPixelType, Dimension> OutputImageType;
+  // define filter
+  typedef itk::ProxTVImageFilter<InputImageType, OutputImageType> FilterType;
+  typename FilterType::Pointer filter = FilterType::New();
+  filter->SetMaximumNumberOfIterations(static_cast<unsigned int>(m_MaximumNumberOfIterations));
+  filter->SetWeights(CastVec3ToITK<FloatVec3Type, typename FilterType::ArrayType, typename FilterType::ArrayType::ValueType>(m_Weights, FilterType::ArrayType::Dimension));
+  filter->SetNorms(CastVec3ToITK<FloatVec3Type, typename FilterType::ArrayType, typename FilterType::ArrayType::ValueType>(m_Norms, FilterType::ArrayType::Dimension));
+  this->ITKImageProcessingBase::filter<InputPixelType, OutputPixelType, Dimension, FilterType>(filter);
+
+}
+
+// -----------------------------------------------------------------------------
+//
+// -----------------------------------------------------------------------------
+void ITKProxTVImage::filterInternal()
+{
+  Dream3DArraySwitchMacro(this->filter, getSelectedCellArrayPath(), -4);
+}
+
+// -----------------------------------------------------------------------------
+//
+// -----------------------------------------------------------------------------
+AbstractFilter::Pointer ITKProxTVImage::newFilterInstance(bool copyFilterParameters) const
+{
+  ITKProxTVImage::Pointer filter = ITKProxTVImage::New();
+  if(copyFilterParameters)
+  {
+    copyFilterParameterInstanceVariables(filter.get());
+  }
+  return filter;
+}
+
+// -----------------------------------------------------------------------------
+//
+// -----------------------------------------------------------------------------
+const QString ITKProxTVImage::getHumanLabel() const
+{
+  return "ITK::Prox T V Image Filter";
+}
+
+// -----------------------------------------------------------------------------
+//
+// -----------------------------------------------------------------------------
+const QUuid ITKProxTVImage::getUuid()
+{
+  return QUuid("{d3856d4c-5651-5eab-8740-489a87fa8bdd}");
+}
+
+// -----------------------------------------------------------------------------
+//
+// -----------------------------------------------------------------------------
+const QString ITKProxTVImage::getSubGroupName() const
+{
+  return "ITK NoModule";
+}

ITKImageProcessingFilters/ITKProxTVImage.h

@@ -0,0 +1,111 @@
+// File automatically generated
+
+/*
+ * Your License or Copyright can go here
+ */
+#pragma once
+
+
+#ifdef __clang__
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Winconsistent-missing-override"
+#endif
+
+#include "ITKImageProcessingBase.h"
+
+#include "SIMPLib/Common/SIMPLibSetGetMacros.h"
+#include "SIMPLib/SIMPLib.h"
+
+// Auto includes
+#include <SIMPLib/FilterParameters/DoubleFilterParameter.h>
+#include <SIMPLib/FilterParameters/FloatVec3FilterParameter.h>
+#include <itkProxTVImageFilter.h>
+
+
+/**
+ * @brief The ITKProxTVImage class. See [Filter documentation](@ref ITKProxTVImage) for details.
+ */
+class ITKProxTVImage : public ITKImageProcessingBase
+{
+  Q_OBJECT
+
+public:
+  SIMPL_SHARED_POINTERS(ITKProxTVImage)
+  SIMPL_FILTER_NEW_MACRO(ITKProxTVImage)
+  SIMPL_TYPE_MACRO_SUPER_OVERRIDE(ITKProxTVImage, AbstractFilter)
+
+  ~ITKProxTVImage() override;
+
+  SIMPL_FILTER_PARAMETER(double, MaximumNumberOfIterations)
+  Q_PROPERTY(double MaximumNumberOfIterations READ getMaximumNumberOfIterations WRITE setMaximumNumberOfIterations)
+
+  SIMPL_FILTER_PARAMETER(FloatVec3Type, Weights)
+  Q_PROPERTY(FloatVec3Type Weights READ getWeights WRITE setWeights)
+
+  SIMPL_FILTER_PARAMETER(FloatVec3Type, Norms)
+  Q_PROPERTY(FloatVec3Type Norms READ getNorms WRITE setNorms)
+
+
+  /**
+   * @brief newFilterInstance Reimplemented from @see AbstractFilter class
+   */
+  AbstractFilter::Pointer
+  newFilterInstance(bool copyFilterParameters) const override;
+
+  /**
+   * @brief getHumanLabel Reimplemented from @see AbstractFilter class
+   */
+  const QString getHumanLabel() const override;
+
+  /**
+   * @brief getSubGroupName Reimplemented from @see AbstractFilter class
+   */
+  const QString getSubGroupName() const override;
+
+  /**
+   * @brief getUuid Return the unique identifier for this filter.
+   * @return A QUuid object.
+   */
+  const QUuid getUuid() override;
+
+  /**
+   * @brief setupFilterParameters Reimplemented from @see AbstractFilter class
+   */
+  void setupFilterParameters() override;
+
+  /**
+   * @brief readFilterParameters Reimplemented from @see AbstractFilter class
+   */
+  void readFilterParameters(AbstractFilterParametersReader * reader, int index) override;
+
+protected:
+  ITKProxTVImage();
+
+  /**
+   * @brief dataCheckInternal overloads dataCheckInternal in ITKImageBase and calls templated dataCheck
+   */
+  void dataCheckInternal() override;
+
+  /**
+   * @brief dataCheck Checks for the appropriate parameter values and availability of arrays
+   */
+  template <typename InputImageType, typename OutputImageType, unsigned int Dimension> void dataCheck();
+
+  /**
+  * @brief filterInternal overloads filterInternal in ITKImageBase and calls templated filter
+  */
+  void filterInternal() override;
+
+  /**
+  * @brief Applies the filter
+  */
+  template <typename InputImageType, typename OutputImageType, unsigned int Dimension> void filter();
+
+private:
+  ITKProxTVImage(const ITKProxTVImage&) = delete;    // Copy Constructor Not Implemented
+  void operator=(const ITKProxTVImage&) = delete;   // Move assignment Not Implemented
+};
+
+#ifdef __clang__
+#pragma clang diagnostic pop
+#endif

ITKImageProcessingFilters/SourceList.cmake

@@ -151,6 +151,7 @@ if(NOT ITKImageProcessing_LeanAndMean)
     ITKFFTNormalizedCorrelationImage
     ITKVectorRescaleIntensityImage
     ITKPatchBasedDenoisingImage
+    ITKProxTVImage
   )
 endif()
 

Test/CMakeLists.txt

@@ -126,6 +126,7 @@ if(NOT ITKImageProcessing_LeanAndMean)
     ITKFFTNormalizedCorrelationImageTest
     ITKVectorRescaleIntensityImageTest
     ITKPatchBasedDenoisingImageTest
+    ITKProxTVImageTest
   )
 endif()