mitkDICOMSegmentationIO.h

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/*============================================================================
 
The Medical Imaging Interaction Toolkit (MITK)
 
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
 
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
 
============================================================================*/
 
#ifndef mitkDICOMSegmentationIO_h
#define mitkDICOMSegmentationIO_h
 
#include <mitkAbstractFileIO.h>
#include <mitkLabelSetImage.h>
 
#include <mitkDICOMTagsOfInterestAddHelper.h>
 
#include <dcmqi/Dicom2ItkConverterBase.h>
#include <dcmqi/JSONSegmentationMetaInformationHandler.h>
 
#include <dcmtk/dcmdata/dcitem.h>
 
#include <memory>
#include <vector>
 
namespace mitk
{
  class DICOMSegmentationIO : public mitk::AbstractFileIO
  {
  public:
    typedef mitk::MultiLabelSegmentation InputType;
    typedef itk::Image<unsigned short, 3> itkInputImageType;
    typedef itk::Image<short, 3> itkInternalImageType;
 
    DICOMSegmentationIO();
 
    // -------------- AbstractFileReader -------------
 
    using AbstractFileReader::Read;
 
    ConfidenceLevel GetReaderConfidenceLevel() const override;
 
    // -------------- AbstractFileWriter -------------
 
    void Write() override;
 
    ConfidenceLevel GetWriterConfidenceLevel() const override;
 
  protected:
    std::vector<itk::SmartPointer<BaseData>> DoRead() override;
 
  private:
    DICOMSegmentationIO *IOClone() const override;
 
    // -------------- DICOMSegmentationIO specific functions -------------
 
    void BuildMetaInfoHandler(const MultiLabelSegmentation *input,
                              int layer,
                              dcmqi::JSONSegmentationMetaInformationHandler &handler) const;
    void SetLabelProperties(Label *label, dcmqi::SegmentAttributes *segmentAttribute);
 
    MultiLabelSegmentation::Pointer ReadLabelmapSegmentation(
      dcmqi::Dicom2ItkConverterBase &converter,
      dcmqi::JSONSegmentationMetaInformationHandler &metaInfo);
 
    MultiLabelSegmentation::Pointer ReadBinarySegmentation(
      dcmqi::Dicom2ItkConverterBase &converter,
      dcmqi::JSONSegmentationMetaInformationHandler &metaInfo,
      bool assumeOverlappingSegments);
  };
} // end of namespace mitk
 
#endif