vtkITKArchetypeImageSeriesReader.h

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

Copyright Brigham and Women's Hospital (BWH) All Rights Reserved.

See COPYRIGHT.txt
or http://www.slicer.org/copyright/copyright.txt for details.

Program:   vtkITK
Module:    $HeadURL$
Date:      $Date$
Version:   $Revision$

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

#ifndef __vtkITKArchetypeImageSeriesReader_h
#define __vtkITKArchetypeImageSeriesReader_h

// VTKITK includes
#include "vtkITK.h"

// VTK includes
#include "vtkImageAlgorithm.h"
class vtkMatrix4x4;

// ITK includes
#include "itkImageIOBase.h"
#include "itkMetaDataDictionary.h"
#include "itkSpatialOrientation.h"

// STD includes
#include <algorithm>
#include <string>
#include <vector>

class VTK_ITK_EXPORT vtkITKArchetypeImageSeriesReader : public vtkImageAlgorithm
{
public:
  static vtkITKArchetypeImageSeriesReader *New();
  vtkTypeMacro(vtkITKArchetypeImageSeriesReader,vtkImageAlgorithm);
  void PrintSelf(ostream& os, vtkIndent indent) override;

  typedef itk::SpatialOrientation::ValidCoordinateOrientationFlags CoordinateOrientationCode;

  vtkSetStringMacro(Archetype);
  vtkGetStringMacro(Archetype);

  unsigned int GetNumberOfFileNames();
  const std::vector<std::string>& GetFileNames();

  unsigned int AddFileName( const char* filename );
  const char* GetFileName( unsigned int n );
  void ResetFileNames();

  vtkSetVector3Macro(DefaultDataSpacing,double);
  vtkGetVector3Macro(DefaultDataSpacing,double);

  vtkSetVector3Macro(DefaultDataOrigin,double);
  vtkGetVector3Macro(DefaultDataOrigin,double);

  vtkSetMacro(FileNameSliceOffset,int);
  vtkGetMacro(FileNameSliceOffset,int);

  vtkSetMacro(FileNameSliceSpacing,int);
  vtkGetMacro(FileNameSliceSpacing,int);

  vtkSetMacro(FileNameSliceCount,int);
  vtkGetMacro(FileNameSliceCount,int);

  virtual int CanReadFile(const char* filename);

  void SetDesiredCoordinateOrientationToAxial ()
    {
    this->DesiredCoordinateOrientation =
      itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_RAI;
    this->UseNativeCoordinateOrientation = 0;
    this->Modified();
    }
  void SetDesiredCoordinateOrientationToCoronal ()
    {
    this->DesiredCoordinateOrientation =
      itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_RSA;
    this->UseNativeCoordinateOrientation = 0;
    this->Modified();
    }
  void SetDesiredCoordinateOrientationToSagittal ()
  {
    this->DesiredCoordinateOrientation =
      itk::SpatialOrientation::ITK_COORDINATE_ORIENTATION_ASL;
    this->UseNativeCoordinateOrientation = 0;
    this->Modified();
  }
  void SetDesiredCoordinateOrientationToNative ()
    {
    this->UseNativeCoordinateOrientation = 1;
    this->Modified();
    }
  vtkGetMacro(DesiredCoordinateOrientation, CoordinateOrientationCode);
  vtkGetMacro(UseNativeCoordinateOrientation, char);

  virtual void SetOutputScalarTypeToDouble()
    {
    UseNativeScalarType = 0;
    this->SetOutputScalarType(VTK_DOUBLE);
    }
  virtual void SetOutputScalarTypeToFloat()
    {
    UseNativeScalarType = 0;
    this->SetOutputScalarType(VTK_FLOAT);
    }
  virtual void SetOutputScalarTypeToLong()
    {
    UseNativeScalarType = 0;
    this->SetOutputScalarType(VTK_LONG);
    }
  virtual void SetOutputScalarTypeToUnsignedLong()
    {
    UseNativeScalarType = 0;
    this->SetOutputScalarType(VTK_UNSIGNED_LONG);
    }
  virtual void SetOutputScalarTypeToInt()
    {
    UseNativeScalarType = 0;
    this->SetOutputScalarType(VTK_INT);
    }
  virtual void SetOutputScalarTypeToUnsignedInt()
    {
    UseNativeScalarType = 0;
    this->SetOutputScalarType(VTK_UNSIGNED_INT);
    }
  virtual void SetOutputScalarTypeToShort()
    {
    UseNativeScalarType = 0;
    this->SetOutputScalarType(VTK_SHORT);
    }
  virtual void SetOutputScalarTypeToUnsignedShort()
    {
    UseNativeScalarType = 0;
    this->SetOutputScalarType(VTK_UNSIGNED_SHORT);
    }
  virtual void SetOutputScalarTypeToChar()
    {
    UseNativeScalarType = 0;
    this->SetOutputScalarType(VTK_CHAR);
    }
  virtual void SetOutputScalarTypeToUnsignedChar()
    {
    UseNativeScalarType = 0;
    this->SetOutputScalarType(VTK_UNSIGNED_CHAR);
    }
  virtual void SetOutputScalarTypeToNative()
    {
    UseNativeScalarType = 1;
    this->Modified();
    }

  void SetUseNativeOriginOn()
    {
    UseNativeOrigin = true;
    }

  void SetUseNativeOriginOff()
    {
    UseNativeOrigin = false;
    }

  enum
    {
    GDCM = 0,
    DCMTK
    };
  vtkSetClampMacro(DICOMImageIOApproach, int, vtkITKArchetypeImageSeriesReader::GDCM, vtkITKArchetypeImageSeriesReader::DCMTK);
  vtkGetMacro(DICOMImageIOApproach, int);
  void SetDICOMImageIOApproachToGDCM() {this->SetDICOMImageIOApproach(vtkITKArchetypeImageSeriesReader::GDCM);};
  void SetDICOMImageIOApproachToDCMTK() {this->SetDICOMImageIOApproach(vtkITKArchetypeImageSeriesReader::DCMTK);};

  vtkSetMacro(OutputScalarType, int);
  vtkGetMacro(OutputScalarType, int);

  vtkSetMacro(NumberOfComponents, unsigned int);
  vtkGetMacro(NumberOfComponents, unsigned int);

  vtkSetMacro(SingleFile, int);
  vtkGetMacro(SingleFile, int);

  vtkSetMacro(AnalyzeHeader, bool);
  vtkGetMacro(AnalyzeHeader, bool);

  vtkSetMacro(UseOrientationFromFile, int);
  vtkGetMacro(UseOrientationFromFile, int);

  vtkMatrix4x4* GetRasToIjkMatrix();

  vtkMatrix4x4* GetMeasurementFrameMatrix();

  vtkSetMacro(VoxelVectorType, int);
  vtkGetMacro(VoxelVectorType, int);

  const itk::MetaDataDictionary &GetMetaDataDictionary() const;
  std::vector<std::string> Tags;
  std::vector<std::string> TagValues;
  void ParseDictionary();

  unsigned int GetNumberOfItemsInDictionary();
  bool HasKey( char* tag );
  const char* GetNthKey( unsigned int n );
  const char* GetNthValue( unsigned int n );
  const char* GetTagValue( char* tag );

  bool GetGroupingByTags()
    {
    return GroupingByTags;
    }

  void SetGroupingByTagsOn()
    {
    GroupingByTags = true;
    }

  void SetGroupingByTagsOff()
    {
    GroupingByTags = false;
    }

  int GetSelectedUID()
    {
    return SelectedUID;
    }

  void SetSelectedUID( int v )
    {
    SelectedUID = v;
    SetGroupingByTagsOn();
    }

  int GetSelectedContentTime()
    {
    return SelectedContentTime;
    }

  void SetSelectedContentTime( int v )
    {
    SelectedContentTime = v;
    SetGroupingByTagsOn();
    }

  int GetSelectedTriggerTime()
    {
    return SelectedTriggerTime;
    }

  void SetSelectedTriggerTime( int v )
    {
    SelectedTriggerTime = v;
    SetGroupingByTagsOn();
    }

  int GetSelectedEchoNumbers()
    {
    return SelectedEchoNumbers;
    }

  void SetSelectedEchoNumbers( int v )
    {
    SelectedEchoNumbers = v;
    SetGroupingByTagsOn();
    }


  int GetSelectedDiffusion()
    {
    return SelectedDiffusion;
    }

  void SetSelectedDiffusion( int v )
    {
    SelectedDiffusion = v;
    SetGroupingByTagsOn();
    }

  int GetSelectedSlice()
    {
    return SelectedSlice;
    }

  void SetSelectedSlice( int v )
    {
    SelectedSlice = v;
    SetGroupingByTagsOn();
    }

  int GetSelectedOrientation()
    {
    return SelectedOrientation;
    }

  void SetSelectedOrientation( int v )
    {
    SelectedOrientation = v;
    SetGroupingByTagsOn();
    }

  unsigned int GetNumberOfSeriesInstanceUIDs()
    {
    return this->SeriesInstanceUIDs.size();
    }

  unsigned int GetNumberOfContentTime()
    {
    return this->ContentTime.size();
    }

  unsigned int GetNumberOfTriggerTime()
    {
    return this->TriggerTime.size();
    }

  unsigned int GetNumberOfEchoNumbers()
    {
    return this->EchoNumbers.size();
    }

  unsigned int GetNumberOfSliceLocation()
    {
    return this->SliceLocation.size();
    }

  unsigned int GetNumberOfDiffusionGradientOrientation()
    {
    return this->DiffusionGradientOrientation.size();
    };

  unsigned int GetNumberOfImageOrientationPatient()
    {
    return this->ImageOrientationPatient.size();
    };

  unsigned int GetNumberOfImagePositionPatient()
    {
    return this->ImagePositionPatient.size();
    }

  int ExistSeriesInstanceUID( const char* SeriesInstanceUID )
    {
    for (unsigned int k = 0; k < GetNumberOfSeriesInstanceUIDs(); k++)
      {
      if ( this->SeriesInstanceUIDs[k].find(SeriesInstanceUID) != std::string::npos )
        {
        return k;
        }
      }
    return -1;
    }

  int ExistContentTime( const char* contentTime )
    {
      for (unsigned int k = 0; k < GetNumberOfContentTime(); k++)
        {
        if ( this->ContentTime[k].find(contentTime) != std::string::npos )
          {
          return k;
          }
        }
      return -1;
    }

  int ExistTriggerTime( const char* triggerTime )
    {
      for (unsigned int k = 0; k < GetNumberOfTriggerTime(); k++)
        {
        if ( this->TriggerTime[k].find(triggerTime) != std::string::npos )
          {
          return k;
          }
        }
      return -1;
    }

  int ExistEchoNumbers( const char* echoNumbers )
    {
      for (unsigned int k = 0; k < GetNumberOfEchoNumbers(); k++)
        {
        if ( this->EchoNumbers[k].find(echoNumbers) != std::string::npos )
          {
          return k;
          }
        }
      return -1;
    }

  int ExistDiffusionGradientOrientation( float* dgo )
    {
      float a = 0;
      for (int n = 0; n < 3; n++)
        {
        a += dgo[n]*dgo[n];
        }

      for (unsigned int k = 0; k < GetNumberOfDiffusionGradientOrientation(); k++)
        {
        float b = 0;
        float c = 0;
        for (int n = 0; n < 3; n++)
          {
          b += this->DiffusionGradientOrientation[k][n] * this->DiffusionGradientOrientation[k][n];
          c += this->DiffusionGradientOrientation[k][n] * dgo[n];
          }
        c = fabs(c)/sqrt(a*b);

        if ( c > 0.99999 )
          {
          return k;
          }
        }
      return -1;
    }

  int ExistSliceLocation( float sliceLocation )
    {
    std::vector<float>::iterator iter =
      std::find(this->SliceLocation.begin(), this->SliceLocation.end(), sliceLocation);
    return iter != this->SliceLocation.end() ?
      std::distance(this->SliceLocation.begin(), iter) : -1;
    }

  int ExistImageOrientationPatient( float * directionCosine )
    {
      float a = sqrt( directionCosine[0]*directionCosine[0] + directionCosine[1]*directionCosine[1] + directionCosine[2]*directionCosine[2] );
      for (int k = 0; k < 3; k++)
        {
        directionCosine[k] /= a;
        }
      a = sqrt( directionCosine[3]*directionCosine[3] + directionCosine[4]*directionCosine[4] + directionCosine[5]*directionCosine[5] );
      for (int k = 3; k < 6; k++)
        {
        directionCosine[k] /= a;
        }

      for (unsigned int k = 0; k < GetNumberOfImageOrientationPatient(); k++)
        {
        std::vector<float> aVec = ImageOrientationPatient[k];
        a = sqrt( aVec[0]*aVec[0] + aVec[1]*aVec[1] + aVec[2]*aVec[2] );
        float b = (directionCosine[0]*aVec[0] + directionCosine[1]*aVec[1] + directionCosine[2]*aVec[2])/a;
        if ( b < 0.99999 )
          {
          continue;
          }

        a = sqrt( aVec[3]*aVec[3] + aVec[4]*aVec[4] + aVec[5]*aVec[5] );
        b = (directionCosine[3]*aVec[3] + directionCosine[4]*aVec[4] + directionCosine[5]*aVec[5])/a;
        if ( b > 0.99999 )
          {
          return k;
          }
        }
      return -1;
    }

  int ExistImagePositionPatient( float* ipp )
    {
      float a = 0;
      for (int n = 0; n < 3; n++)
        {
        a += ipp[n]*ipp[n];
        }

      for (unsigned int k = 0; k < GetNumberOfImagePositionPatient(); k++)
        {
        float b = 0;
        float c = 0;
        for (int n = 0; n < 3; n++)
          {
          b += this->ImagePositionPatient[k][n] * this->ImagePositionPatient[k][n];
          c += this->ImagePositionPatient[k][n] * ipp[n];
          }
        c = fabs(c)/sqrt(a*b);
        if ( c > 0.99999 )
          {
          return k;
          }
        }
      return -1;
    }

  const char* GetNthSeriesInstanceUID( unsigned int n )
    {
      if ( n >= this->GetNumberOfSeriesInstanceUIDs() )
        {
        return nullptr;
        }
      return this->SeriesInstanceUIDs[n].c_str();
    }

  const char* GetNthContentTime( unsigned int n )
    {
      if ( n >= this->GetNumberOfContentTime() )
        {
        return nullptr;
        }
      return this->ContentTime[n].c_str();
    }

  const char* GetNthTriggerTime( unsigned int n )
    {
      if ( n >= this->GetNumberOfTriggerTime() )
        {
        return nullptr;
        }
      return this->TriggerTime[n].c_str();
    }

  const char* GetNthEchoNumbers( unsigned int n )
    {
      if ( n >= this->GetNumberOfEchoNumbers() )
        {
        return nullptr;
        }
      return this->EchoNumbers[n].c_str();
    }

  float* GetNthDiffusionGradientOrientation( unsigned int n )
    {
      if ( n >= this->GetNumberOfDiffusionGradientOrientation() )
        {
        return nullptr;
        }
      float *dgo = new float [3];
      for (int k = 0; k <3; k++)
        {
        dgo[k] = this->DiffusionGradientOrientation[n][k];
        }
      return dgo;
    }

  float GetNthSliceLocation( unsigned int n )
    {
      if ( n >= this->GetNumberOfSliceLocation() )
        {
        return this->SliceLocation[0];
        }
      return this->SliceLocation[0];
    }

  float* GetNthImageOrientationPatient( unsigned int n )
    {
      if ( n >= this->GetNumberOfImageOrientationPatient() )
        {
        return nullptr;
        }
      float *dgo = new float [6];
      for (int k = 0; k <6; k++)
        {
        dgo[k] = this->ImageOrientationPatient[n][k];
        }
      return dgo;
    }

  float* GetNthImagePositionPatient( unsigned int n )
    {
      if (n >= this->GetNumberOfImagePositionPatient() )
        {
        return nullptr;
        }
      float *ipp = new float [3];
      for (int k = 0; k <3; k++)
        {
        ipp[k] = this->ImagePositionPatient[n][k];
        }
      return ipp;
    }

  int InsertSeriesInstanceUIDs ( const char * aUID )
    {
      int k = ExistSeriesInstanceUID( aUID );
      if ( k >= 0 )
        {
        return k;
        }

      std::string aVector(aUID);
      this->SeriesInstanceUIDs.push_back( aVector );
      return (this->SeriesInstanceUIDs.size()-1);
    }

  int InsertContentTime ( const char * aTime )
    {
      int k = ExistContentTime( aTime );
      if ( k >= 0 )
        {
        return k;
        }

      std::string aVector(aTime);
      this->ContentTime.push_back( aVector );
      return (this->ContentTime.size()-1);
    }

  int InsertTriggerTime ( const char * aTime )
    {
      int k = ExistTriggerTime( aTime );
      if ( k >= 0 )
        {
        return k;
        }

      std::string aVector(aTime);
      this->TriggerTime.push_back( aVector );
      return (this->TriggerTime.size()-1);
    }

  int InsertEchoNumbers ( const char * aEcho )
    {
      int k = ExistEchoNumbers( aEcho );
      if ( k >= 0 )
        {
        return k;
        }

      std::string aVector(aEcho);
      this->EchoNumbers.push_back( aVector );
      return (this->EchoNumbers.size()-1);
    }

  int InsertDiffusionGradientOrientation ( float *a )
    {
      int k = ExistDiffusionGradientOrientation( a );
      if ( k >= 0 )
        {
        return k;
        }
      std::vector< float > aVector(3);
      float aMag = sqrt(a[0]*a[0]+a[1]*a[1]+a[2]*a[2]);
      for (k = 0; k < 3; k++)
        {
        aVector[k] = a[k]/aMag;
        }

      this->DiffusionGradientOrientation.push_back( aVector );
      return (this->DiffusionGradientOrientation.size()-1);
    }

  int InsertSliceLocation ( float a )
    {
      int k = ExistSliceLocation( a );
      if ( k >= 0 )
        {
        return k;
        }

      this->SliceLocation.push_back( a );
      return (this->SliceLocation.size()-1);
    }
  int InsertNextSliceLocation( )
    {
    int size = this->SliceLocation.size();
    this->SliceLocation.push_back(
      size > 0 ? this->SliceLocation.back() + 1 : 0.f);
    return size;
    }

  int InsertImageOrientationPatient ( float *a )
    {
      int k = ExistImageOrientationPatient( a );
      if ( k >= 0 )
        {
        return k;
        }
      std::vector< float > aVector(6);
      float aMag = sqrt(a[0]*a[0]+a[1]*a[1]+a[2]*a[2]);
      float bMag = sqrt(a[3]*a[3]+a[4]*a[4]+a[5]*a[5]);
      for (k = 0; k < 3; k++)
        {
        aVector[k] = a[k]/aMag;
        aVector[k+3] = a[k+3]/bMag;
        }

      this->ImageOrientationPatient.push_back( aVector );
      return (this->ImageOrientationPatient.size()-1);
    }

  int InsertImagePositionPatient ( float *a )
    {
      int k = ExistImagePositionPatient( a );
      if ( k >= 0 )
        {
        return k;
        }

      std::vector< float > aVector(3);
      for ( unsigned int i = 0; i < 3; i++ ) aVector[i] = a[i];
      this->ImagePositionPatient.push_back( aVector );
      return (this->ImagePositionPatient.size()-1);
    }

  void AnalyzeDicomHeaders( );

  void AssembleNthVolume( int n );
  int AssembleVolumeContainingArchetype();

  void GroupFiles ( int idxSeriesInstanceUID,
                    int idxContentTime,
                    int idxTriggerTime,
                    int idxEchoNumbers,
                    int idxDiffusionGradientOrientation,
                    int idxSliceLocation,
                    int idxImageOrientationPatient );

  const char* GetNthFileName ( int idxSeriesInstanceUID,
                               int idxContentTime,
                               int idxTriggerTime,
                               int idxEchoNumbers,
                               int idxDiffusionGradientOrientation,
                               int idxSliceLocation,
                               int idxImageOrientationPatient,
                               int n );


protected:
  vtkITKArchetypeImageSeriesReader();
  ~vtkITKArchetypeImageSeriesReader() override;

  static std::string GetMetaDataWithoutSpaces(const itk::MetaDataDictionary &dict, const std::string& tag);

  itk::ImageIOBase::Pointer GetImageIO(const char* filename);

  char *Archetype;
  int SingleFile;
  int UseOrientationFromFile;
  int DataExtent[6];

  int          OutputScalarType;
  unsigned int NumberOfComponents;

  std::vector<double> MetaDataScalarRangeMinima;
  std::vector<double> MetaDataScalarRangeMaxima;
  void GetScalarRangeMetaDataKeys(itk::ImageIOBase::Pointer imageIO,
                                  std::string range_keys[2]);
  void SetMetaDataScalarRangeToPointDataInfo(vtkImageData* data);

  double DefaultDataSpacing[3];
  double DefaultDataOrigin[3];
  float ScanAxis[3];
  float ScanOrigin[3];

  int FileNameSliceOffset;
  int FileNameSliceSpacing;
  int FileNameSliceCount;

  vtkMatrix4x4* RasToIjkMatrix;
  vtkMatrix4x4* MeasurementFrameMatrix;

  char UseNativeCoordinateOrientation;
  char UseNativeScalarType;
  bool UseNativeOrigin;

  int DICOMImageIOApproach;

  bool GroupingByTags;
  int SelectedUID;
  int SelectedContentTime;
  int SelectedTriggerTime;
  int SelectedEchoNumbers;
  int SelectedDiffusion;
  int SelectedSlice;
  int SelectedOrientation;

  unsigned int IndexArchetype;

  std::vector<std::string> FileNames;
  std::vector<std::pair <double, int> > FileNameSliceKey;
  CoordinateOrientationCode DesiredCoordinateOrientation;
  int RequestInformation(vtkInformation *, vtkInformationVector **, vtkInformationVector *) override;

  itk::MetaDataDictionary Dictionary;


  std::vector<std::string> AllFileNames;
  bool AnalyzeHeader;
  bool IsOnlyFile;
  bool ArchetypeIsDICOM;

  std::vector<std::string> SeriesInstanceUIDs;
  std::vector<std::string> ContentTime;
  std::vector<std::string> TriggerTime;
  std::vector<std::string> EchoNumbers;
  std::vector< std::vector<float> > DiffusionGradientOrientation;
  std::vector<float> SliceLocation;
  std::vector< std::vector<float> > ImageOrientationPatient;
  std::vector< std::vector<float> > ImagePositionPatient;

  std::vector<long int> IndexSeriesInstanceUIDs;
  std::vector<long int> IndexContentTime;
  std::vector<long int> IndexTriggerTime;
  std::vector<long int> IndexEchoNumbers;
  std::vector<long int> IndexDiffusionGradientOrientation;
  std::vector<long int> IndexSliceLocation;
  std::vector<long int> IndexImageOrientationPatient;
  std::vector<long int> IndexImagePositionPatient;

  int VoxelVectorType;

private:
  vtkITKArchetypeImageSeriesReader(const vtkITKArchetypeImageSeriesReader&) = delete;
  void operator=(const vtkITKArchetypeImageSeriesReader&) = delete;
};

#endif