tubeSegmentConnectedComponentsUsingParzenPDFs.h

/*=========================================================================

Library:   TubeTK

Copyright Kitware Inc.

All rights reserved.

Licensed under the Apache License, Version 2.0 ( the "License" );
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

    https://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

=========================================================================*/
#ifndef tubeSegmentConnectedComponentsUsingParzenPDFs_h
#define tubeSegmentConnectedComponentsUsingParzenPDFs_h

// ITK includes
#include "itkProcessObject.h"

// TubeTK includes
#include "tubeWrappingMacros.h"

#include "itktubePDFSegmenterParzen.h"


namespace tube
{
/** \class SegmentConnectedComponentsUsingParzenPDFs
 *
 *  \ingroup TubeTK
 */

template <class TImage, class TLabelMap = itk::Image<typename TImage::PixelType, TImage::ImageDimension>>
class SegmentConnectedComponentsUsingParzenPDFs : public itk::ProcessObject
{
public:
  using InputImageType = TImage;
  using InputImagePixelType = typename TImage::PixelType;

  using LabelMapType = TLabelMap;
  using LabelMapPixelType = typename TLabelMap::PixelType;

  /** Standard class type alias. */
  using Self = SegmentConnectedComponentsUsingParzenPDFs;
  using Superclass = itk::ProcessObject;
  using Pointer = itk::SmartPointer<Self>;
  using ConstPointer = itk::SmartPointer<const Self>;


  using FilterType = itk::tube::PDFSegmenterParzen<InputImageType, LabelMapType>;

  using PDFImageType = typename FilterType::PDFImageType;
  // using LabeledFeatureSpaceType = typename FilterType::LabeledFeatureSpaceType;

  using ProbabilityImageType = typename FilterType::ProbabilityImageType;
  using ProbabilityVectorType = typename FilterType::ProbabilityVectorType;
  using FeatureVectorType = typename FilterType::FeatureVectorType;
  using VectorDoubleType = typename FilterType::VectorDoubleType;
  using VectorUIntType = typename FilterType::VectorUIntType;
  using ObjectIdListType = typename FilterType::ObjectIdListType;

  /** Method for creation through the object factory. */
  itkNewMacro(Self);

  /** Run-time type information ( and related methods ). */
  itkOverrideGetNameOfClassMacro(SegmentConnectedComponentsUsingParzenPDFs);

  /** Set/Get input image */
  void
  SetFeatureImage(InputImageType * img);
  void
  AddFeatureImage(InputImageType * img);

  /** Set/Get mask image */
  tubeWrapSetObjectMacro(InputLabelMap, LabelMapType, Filter);
  tubeWrapGetObjectMacro(InputLabelMap, LabelMapType, Filter);

  tubeWrapForceSetMacro(ObjectId, LabelMapPixelType, Filter);
  tubeWrapAddMacro(ObjectId, LabelMapPixelType, Filter);
  tubeWrapGetMacro(ObjectId, ObjectIdListType, Filter);
  tubeWrapGetNthObjectMacro(ObjectId, LabelMapPixelType, Filter);

  tubeWrapSetMacro(VoidId, LabelMapPixelType, Filter);
  tubeWrapGetMacro(VoidId, LabelMapPixelType, Filter);

  tubeWrapSetMacro(IgnoreId, LabelMapPixelType, Filter);
  tubeWrapGetMacro(IgnoreId, LabelMapPixelType, Filter);

  tubeWrapSetMacro(ErodeDilateRadius, unsigned int, Filter);
  tubeWrapGetMacro(ErodeDilateRadius, unsigned int, Filter);

  tubeWrapSetMacro(DilateFirst, bool, Filter);
  tubeWrapGetMacro(DilateFirst, bool, Filter);

  tubeWrapSetMacro(HoleFillIterations, unsigned int, Filter);
  tubeWrapGetMacro(HoleFillIterations, unsigned int, Filter);

  tubeWrapSetNthMacro(ObjectPDFWeight, double, Filter);
  tubeWrapGetNthObjectMacro(ObjectPDFWeight, double, Filter);
  tubeWrapSetMacro(ObjectPDFWeight, VectorDoubleType, Filter);
  tubeWrapGetMacro(ObjectPDFWeight, VectorDoubleType, Filter);

  tubeWrapSetMacro(ProbabilityImageSmoothingStandardDeviation, double, Filter);
  tubeWrapGetMacro(ProbabilityImageSmoothingStandardDeviation, double, Filter);

  tubeWrapSetMacro(HistogramSmoothingStandardDeviation, double, Filter);
  tubeWrapGetMacro(HistogramSmoothingStandardDeviation, double, Filter);

  tubeWrapSetMacro(OutlierRejectPortion, double, Filter);
  tubeWrapGetMacro(OutlierRejectPortion, double, Filter);

  tubeWrapSetMacro(ReclassifyNotObjectLabels, bool, Filter);
  tubeWrapGetMacro(ReclassifyNotObjectLabels, bool, Filter);

  tubeWrapSetMacro(ReclassifyObjectLabels, bool, Filter);
  tubeWrapGetMacro(ReclassifyObjectLabels, bool, Filter);

  tubeWrapSetMacro(ForceClassification, bool, Filter);
  tubeWrapGetMacro(ForceClassification, bool, Filter);

  tubeWrapSetMacro(NumberOfBinsPerFeature, VectorUIntType, Filter);
  tubeWrapGetMacro(NumberOfBinsPerFeature, VectorUIntType, Filter);

  tubeWrapSetMacro(BinMin, VectorDoubleType, Filter);
  tubeWrapGetMacro(BinMin, VectorDoubleType, Filter);

  tubeWrapSetMacro(BinSize, VectorDoubleType, Filter);
  tubeWrapGetMacro(BinSize, VectorDoubleType, Filter);

  tubeWrapSetNthObjectMacro(ClassPDFImage, PDFImageType, Filter);
  tubeWrapGetNthObjectMacro(ClassPDFImage, PDFImageType, Filter);

  tubeWrapCallMacro(GenerateLabeledFeatureSpace, Filter);

  // tubeWrapSetObjectMacro( LabeledFeatureSpace, LabeledFeatureSpaceType, Filter );
  // tubeWrapGetObjectMacro( LabeledFeatureSpace, LabeledFeatureSpaceType, Filter );

  ProbabilityVectorType
  GetProbabilityVector(const FeatureVectorType & fv) const
  {
    return m_Filter->GetProbabilityVector(fv);
  };

  tubeWrapCallMacro(ClassifyImages, Filter);

  tubeWrapGetMacro(NumberOfClasses, unsigned int, Filter);

  tubeWrapGetNthObjectMacro(ClassProbabilityImage, ProbabilityImageType, Filter);

  void
  Update(void) override;

  /** Get output segmentation mask */
  tubeWrapGetObjectMacro(OutputLabelMap, LabelMapType, Filter);

protected:
  SegmentConnectedComponentsUsingParzenPDFs(void);
  ~SegmentConnectedComponentsUsingParzenPDFs() {}
  void
  PrintSelf(std::ostream & os, itk::Indent indent) const override;

private:
  /** itkSegmentConnectedComponentsUsingParzenPDFs parameters **/
  SegmentConnectedComponentsUsingParzenPDFs(const Self &);
  void
  operator=(const Self &);

  // To remove warning "was hidden [-Woverloaded-virtual]"
  void
  SetInput(const DataObjectIdentifierType &, itk::DataObject *) override {};

  using FeatureVectorGeneratorType = itk::tube::FeatureVectorGenerator<InputImageType>;

  typename FilterType::Pointer                 m_Filter;
  typename FeatureVectorGeneratorType::Pointer m_FVGenerator;
};

} // End namespace tube


#ifndef ITK_MANUAL_INSTANTIATION
#  include "tubeSegmentConnectedComponentsUsingParzenPDFs.hxx"
#endif

#endif // End !defined( __tubeSegmentConnectedComponentsUsingParzenPDFs_h )