mitkDICOMITKSeriesGDCMReader.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 mitkDICOMITKSeriesGDCMReader_h
#define mitkDICOMITKSeriesGDCMReader_h

#include <stack>
#include "itkMutexLock.h"
#include "mitkDICOMFileReader.h"
#include "mitkDICOMDatasetSorter.h"
#include "mitkDICOMGDCMImageFrameInfo.h"
#include "mitkEquiDistantBlocksSorter.h"
#include "mitkNormalDirectionConsistencySorter.h"
#include "MitkDICOMExports.h"


namespace itk
{
  class TimeProbesCollectorBase;
}

namespace mitk
{

class MITKDICOM_EXPORT DICOMITKSeriesGDCMReader : public DICOMFileReader
{
  public:

    mitkClassMacro( DICOMITKSeriesGDCMReader, DICOMFileReader );
    mitkCloneMacro( DICOMITKSeriesGDCMReader );
    itkFactorylessNewMacro( DICOMITKSeriesGDCMReader );
    mitkNewMacro1Param( DICOMITKSeriesGDCMReader, unsigned int );
    mitkNewMacro2Param( DICOMITKSeriesGDCMReader, unsigned int, bool );

    void AnalyzeInputFiles() override;

    // void AllocateOutputImages();
    bool LoadImages() override;

    // re-implemented from super-class
    bool CanHandleFile(const std::string& filename) override;

    virtual void AddSortingElement(DICOMDatasetSorter* sorter, bool atFront = false);

    typedef const std::list<DICOMDatasetSorter::ConstPointer> ConstSorterList;
    ConstSorterList GetFreelyConfiguredSortingElements() const;

    void SetFixTiltByShearing(bool on);

    bool GetFixTiltByShearing() const;

    void SetAcceptTwoSlicesGroups(bool accept) const;
    bool GetAcceptTwoSlicesGroups() const;

    void SetToleratedOriginOffsetToAdaptive(double fractionOfInterSliceDistanct = 0.3) const;

    void SetToleratedOriginOffset(double millimeters = 0.005) const;

    void SetSimpleVolumeReading(bool read)
    {
      m_SimpleVolumeReading = read;
    };

    bool GetSimpleVolumeReading()
    {
      return m_SimpleVolumeReading;
    };

    double GetToleratedOriginError() const;
    bool IsToleratedOriginOffsetAbsolute() const;

    double GetDecimalPlacesForOrientation() const;

    bool operator==(const DICOMFileReader& other) const override;

    DICOMTagPathList GetTagsOfInterest() const override;

    static int GetDefaultDecimalPlacesForOrientation()
    {
      return m_DefaultDecimalPlacesForOrientation;
    }

    static bool GetDefaultSimpleVolumeImport()
    {
      return m_DefaultSimpleVolumeImport;
    }

    static bool GetDefaultFixTiltByShearing()
    {
      return m_DefaultFixTiltByShearing;
    }

  protected:

    void InternalPrintConfiguration(std::ostream& os) const override;

  static std::string GetActiveLocale();
    void PushLocale() const;
    void PopLocale() const;

    const static int m_DefaultDecimalPlacesForOrientation = 5;
    const static bool m_DefaultSimpleVolumeImport = false;
    const static bool m_DefaultFixTiltByShearing = true;

    DICOMITKSeriesGDCMReader(unsigned int decimalPlacesForOrientation = m_DefaultDecimalPlacesForOrientation, bool simpleVolumeImport = m_DefaultSimpleVolumeImport);
    ~DICOMITKSeriesGDCMReader() override;

    DICOMITKSeriesGDCMReader(const DICOMITKSeriesGDCMReader& other);
    DICOMITKSeriesGDCMReader& operator=(const DICOMITKSeriesGDCMReader& other);

    typedef std::vector<DICOMDatasetAccessingImageFrameList> SortingBlockList;
    virtual SortingBlockList Condense3DBlocks(SortingBlockList& resultOf3DGrouping);

    virtual DICOMTagCache::Pointer GetTagCache() const;
    void SetTagCache( const DICOMTagCache::Pointer& ) override;

  static SortingBlockList InternalExecuteSortingStep(
        unsigned int sortingStepIndex,
        const DICOMDatasetSorter::Pointer& sorter,
        const SortingBlockList& input);

    virtual bool LoadMitkImageForOutput(unsigned int o);

    virtual bool LoadMitkImageForImageBlockDescriptor(DICOMImageBlockDescriptor& block) const;

  static ReaderImplementationLevel GetReaderImplementationLevel(const std::string sopClassUID);
  private:

    void EnsureMandatorySortersArePresent(unsigned int decimalPlacesForOrientation, bool simpleVolumeImport = false);

  protected:

    // NOT nice, made available to ThreeDnTDICOMSeriesReader due to lack of time
    bool m_FixTiltByShearing; // could be removed by ITKDICOMSeriesReader NOT flagging tilt unless requested to fix it!

    bool m_SimpleVolumeReading;

  private:

    SortingBlockList m_SortingResultInProgress;

    typedef std::list<DICOMDatasetSorter::Pointer> SorterList;
    SorterList m_Sorter;

  protected:

    // NOT nice, made available to ThreeDnTDICOMSeriesReader and ClassicDICOMSeriesReader due to lack of time
    mitk::EquiDistantBlocksSorter::Pointer m_EquiDistantBlocksSorter;

    mitk::NormalDirectionConsistencySorter::Pointer m_NormalDirectionConsistencySorter;

  private:

    static itk::MutexLock::Pointer s_LocaleMutex;

    mutable std::stack<std::string> m_ReplacedCLocales;
    mutable std::stack<std::locale> m_ReplacedCinLocales;

    double m_DecimalPlacesForOrientation;

    DICOMTagCache::Pointer m_TagCache;
    bool m_ExternalCache;
};

}

#endif