itkDCMTKFileReader.h

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/*=========================================================================
 *
 *  Copyright Insight Software Consortium
 *
 *  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
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  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 itkDCMTKFileReader_h
#define itkDCMTKFileReader_h

// XXX # Workaround bug in packaging of DCMTK 3.6.0 on Debian.
//     # See http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=637687
#ifndef HAVE_CONFIG_H
#define HAVE_CONFIG_H
#endif

#include <stack>
#include <vector>
#include "itkByteSwapper.h"
#include "itkIntTypes.h"
#include "vnl/vnl_vector.h"
#include "dcmtk/dcmdata/dcxfer.h"
#include "dcmtk/dcmdata/dcvrds.h"
#include "dcmtk/dcmdata/dcstack.h"
#include "dcmtk/dcmdata/dcdatset.h"
#include "itkMacro.h"
#include "itkImageIOBase.h"

class DcmSequenceOfItems;
class DcmFileFormat;
class DcmDictEntry;

// Don't print error messages if you're not throwing
// an exception
//     std::cerr body;
#define DCMTKException(body)                    \
  {                                             \
    if(throwException)                          \
      {                                         \
      itkGenericExceptionMacro(body);           \
      }                                         \
    else                                        \
      {                                         \
      return EXIT_FAILURE;                      \
      }                                         \
  }

namespace itk
{
class DCMTKSequence
{
public:
  DCMTKSequence()  = default;
  void SetDcmSequenceOfItems(DcmSequenceOfItems *seq);
  int card();
  int GetSequence(unsigned long index,
                  DCMTKSequence &target,bool throwException = true);
  int GetStack(unsigned short group,
               unsigned short element,
               DcmStack *resultStack, bool throwException = true);
  int GetElementCS(unsigned short group,
                   unsigned short element,
                   std::string &target,
                   bool throwException = true);
  int GetElementFD(unsigned short group,
                   unsigned short element,
                   double * &target,
                   bool throwException = true);
  int GetElementFD(unsigned short group,
                   unsigned short element,
                   double &target,
                   bool throwException = true);
  int GetElementDS(unsigned short group,
                   unsigned short element,
                   std::string &target,
                   bool throwException = true);
  int GetElementTM(unsigned short group,
                   unsigned short element,
                   std::string &target,
                   bool throwException = true);
  template <typename TType>
  int GetElementDS(unsigned short group,
                   unsigned short element,
                   unsigned short count,
                   TType  *target,
                   bool throwException)
    {
      DcmStack resultStack;
      this->GetStack(group,element,&resultStack);
      DcmDecimalString *dsItem =
        dynamic_cast<DcmDecimalString *>(resultStack.top());
      if(dsItem == nullptr)
        {
        DCMTKException(<< "Can't get DecimalString Element at tag "
                       << std::hex << group << " "
                       << element << std::dec);
        }

      OFVector<Float64> doubleVals;
      if(dsItem->getFloat64Vector(doubleVals) != EC_Normal)
        {
        DCMTKException(<< "Can't extract Array from DecimalString " << std::hex
                       << group << " " << std::hex
                       << element << std::dec);
        }
      if(doubleVals.size() != count)
        {
        DCMTKException(<< "DecimalString " << std::hex
                       << group << " " << std::hex
                       << element << " expected "
                       << count << "items, but found "
                       << doubleVals.size() << std::dec);

        }
      for(unsigned i = 0; i < count; i++)
        {
        target[i] = static_cast<TType>(doubleVals[i]);
        }
      return EXIT_SUCCESS;
    }
  int GetElementSQ(unsigned short group,
                   unsigned short element,
                   DCMTKSequence &target,
                   bool throwException = true);
private:
  DcmSequenceOfItems *m_DcmSequenceOfItems{nullptr};
};

class DCMTKFileReader
{
public:
  typedef DCMTKFileReader Self;

  DCMTKFileReader() = default;
  ~DCMTKFileReader();

  void SetFileName(const std::string &fileName);

  const std::string &GetFileName() const;

  void LoadFile();

  int GetElementLO(unsigned short group,
                   unsigned short element,
                   std::string &target,
                   bool throwException = true);
  int GetElementLO(unsigned short group,
                   unsigned short element,
                   std::vector<std::string> &target,
                   bool throwException = true);

  template <typename TType>
  int  GetElementDS(unsigned short group,
                    unsigned short element,
                    unsigned short count,
                    TType  *target,
                    bool throwException = true)
    {
      DcmTagKey tagkey(group,element);
      DcmElement *el;
      if(this->m_Dataset->findAndGetElement(tagkey,el) != EC_Normal)
        {
        DCMTKException(<< "Can't find tag " << std::hex
                       << group << " " << std::hex
                       << element << std::dec);
        }
      DcmDecimalString *dsItem = dynamic_cast<DcmDecimalString *>(el);
      if(dsItem == nullptr)
        {
        DCMTKException(<< "Can't find DecimalString element " << std::hex
                       << group << " " << std::hex
                       << element << std::dec);
        }
      OFVector<Float64> doubleVals;
      if(dsItem->getFloat64Vector(doubleVals) != EC_Normal)
        {
        DCMTKException(<< "Can't extract Array from DecimalString " << std::hex
                       << group << " " << std::hex
                       << element << std::dec);
        }
      if(doubleVals.size() != count)
        {
        DCMTKException(<< "DecimalString " << std::hex
                       << group << " " << std::hex
                       << element << " expected "
                       << count << "items, but found "
                       << doubleVals.size() << std::dec);

        }
      for(unsigned i = 0; i < count; i++)
        {
        target[i] = static_cast<TType>(doubleVals[i]);
        }
      return EXIT_SUCCESS;
    }

  template <typename TType>
  int  GetElementDSorOB(unsigned short group,
                        unsigned short element,
                        TType  &target,
                        bool throwException = true)
    {
      if(this->GetElementDS<TType>(group,element,1,&target,false) == EXIT_SUCCESS)
        {
        return EXIT_SUCCESS;
        }
      std::string val;
      if(this->GetElementOB(group,element,val) != EXIT_SUCCESS)
        {
        DCMTKException(<< "Can't find DecimalString element " << std::hex
                       << group << " " << std::hex
                       << element << std::dec);
        }
      const char *data = val.c_str();
      const TType *fptr = reinterpret_cast<const TType *>(data);
      target = *fptr;
      switch(this->GetTransferSyntax())
        {
        case EXS_LittleEndianImplicit:
        case EXS_LittleEndianExplicit:
          itk::ByteSwapper<TType>::SwapFromSystemToLittleEndian(&target);
          break;
        case EXS_BigEndianImplicit:
        case EXS_BigEndianExplicit:
          itk::ByteSwapper<TType>::SwapFromSystemToBigEndian(&target);
          break;
        default:
          break;
        }
      return EXIT_SUCCESS;

    }
  int  GetElementDS(unsigned short group,
                    unsigned short element,
                    std::string &target,
                    bool throwException = true);
  int  GetElementFD(unsigned short group,
                    unsigned short element,
                    double &target,
                    bool throwException = true);
  int  GetElementFD(unsigned short group,
                    unsigned short element,
                    double * &target,
                    bool throwException = true);
  int  GetElementFL(unsigned short group,
                    unsigned short element,
                    float &target,
                    bool throwException = true);
  int  GetElementFLorOB(unsigned short group,
                        unsigned short element,
                        float &target,
                        bool throwException = true);

  int  GetElementUS(unsigned short group,
                    unsigned short element,
                    unsigned short &target,
                    bool throwException = true);
  int  GetElementUS(unsigned short group,
                    unsigned short element,
                    unsigned short *&target,
                    bool throwException = true);
  int  GetElementCS(unsigned short group,
                    unsigned short element,
                    std::string &target,
                    bool throwException = true);

  int  GetElementPN(unsigned short group,
                    unsigned short element,
                    std::string &target,
                    bool throwException = true);

  int  GetElementIS(unsigned short group,
                    unsigned short element,
                    ::itk::int32_t  &target,
                    bool throwException = true);

  int  GetElementISorOB(unsigned short group,
                        unsigned short element,
                        ::itk::int32_t  &target,
                        bool throwException = true);
  int  GetElementOB(unsigned short group,
                    unsigned short element,
                    std::string &target,
                    bool throwException = true);

  int GetElementSQ(unsigned short group,
                   unsigned short entry,
                   DCMTKSequence &sequence,
                   bool throwException = true);

  int GetElementUI(unsigned short group,
                  unsigned short entry,
                  std::string &target,
                   bool throwException = true);

  int GetElementDA(unsigned short group,
                   unsigned short element,
                   std::string &target,
                   bool throwException = true);

  int GetElementTM(unsigned short group,
                   unsigned short element,
                   std::string &target,
                   bool throwException = true);

  int GetDirCosines(vnl_vector<double> &dir1,
                    vnl_vector<double> &dir2,
                    vnl_vector<double> &dir3);

  int GetFrameCount() const;

  int GetSlopeIntercept(double &slope, double &intercept);

  int GetDimensions(unsigned short &rows, unsigned short &columns);

  ImageIOBase::IOComponentType GetImageDataType();
  ImageIOBase::IOPixelType GetImagePixelType();

  int GetSpacing(double *spacing);
  int GetOrigin(double *origin);

  E_TransferSyntax GetTransferSyntax() const;

  long GetFileNumber() const;

  static void
  AddDictEntry(DcmDictEntry *entry);

private:
  static unsigned ascii2hex(char c);

  static std::string ConvertFromOB(OFString &toConvert);

  std::string          m_FileName;
  DcmFileFormat*       m_DFile{nullptr};
  DcmDataset *         m_Dataset{nullptr};
  E_TransferSyntax     m_Xfer{EXS_Unknown};
  Sint32               m_FrameCount{0};
  long                 m_FileNumber{-1L};
};

extern bool CompareDCMTKFileReaders(DCMTKFileReader *a, DCMTKFileReader *b);
}

#endif // itkDCMTKFileReader_h