DWIConverterFactory.cxx

//
// Created by Hui Xie on 12/19/16.
//

#include "DWIConverterFactory.h"

DWIConverterFactory::DWIConverterFactory( const std::string DicomDirectory, const bool UseBMatrixGradientDirections,
                                          const double smallGradientThreshold )
  : m_DicomDirectory( DicomDirectory )
  , m_UseBMatrixGradientDirections( UseBMatrixGradientDirections )
  , m_SmallGradientThreshold( smallGradientThreshold )
{}

DWIConverterFactory::~DWIConverterFactory()
{
  for ( std::vector< itk::DCMTKFileReader * >::iterator it = this->m_Headers.begin(); it != this->m_Headers.end();
        ++it )
  {
    delete ( *it );
  }
}

bool
DWIConverterFactory::isNIIorNrrd( const std::string & filename )
{
  constexpr size_t NUMEXT = 4;
  const char *     extensions[NUMEXT] = { ".nii", ".nii.gz", ".nhdr", ".nrrd" };
  for ( size_t i = 0; i < NUMEXT; ++i )
  {
    if ( filename.find( extensions[i] ) != std::string::npos )
    {
      return true; // Return true if one of the valid extensions found
    }
  }
  return false;
}

DWIConverter *
DWIConverterFactory::New()
{

  // Directory of DICOM slices?
  if ( itksys::SystemTools::FileIsDirectory( m_DicomDirectory.c_str() ) )
  {
    DWIDICOMConverterBase::InputNamesGeneratorType::Pointer inputNames =
      DWIDICOMConverterBase::InputNamesGeneratorType::New();
    inputNames->SetUseSeriesDetails( true );
    inputNames->SetLoadSequences( true );
    inputNames->SetLoadPrivateTags( true );
    inputNames->SetInputDirectory( m_DicomDirectory );
    m_InputFileNames = inputNames->GetInputFileNames();
  }
  // single file multiSlice Volume?
  else if ( itksys::SystemTools::FileExists( m_DicomDirectory.c_str() ) )
  {
    m_InputFileNames.push_back( m_DicomDirectory );
  }

  DWIConverter * converter( nullptr );
  // nothing at all found?
  if ( m_InputFileNames.size() < 1 )
  {
    std::cerr << "Error: no DICOMfiles found in inputDirectory: " << m_DicomDirectory << std::endl;
    return nullptr;
  }

  // there is a logic error below --huixie
  else if ( m_InputFileNames.size() == 1 && isNIIorNrrd( m_InputFileNames[0] ) ) // FSL Reader or NRRD Reader
  {
    itkGenericExceptionMacro( << "INVALID PATH, create FSLDWIConverter in main program" << std::endl );
    converter = new FSLDWIConverter( m_InputFileNames, "", "" );
  }
  else // Assume multi file dicom file reading
  {

    // below code has logic error, it has empty hole in the tail of m_Headers when HasPixelData == false;
    /*
     *
     * m_Headers.resize(m_InputFileNames.size());
    int                                 headerCount = 0;
    for( unsigned i = 0; i < m_Headers.size(); ++i )
    {
      itk::DCMTKFileReader *curReader = new itk::DCMTKFileReader;
      curReader->SetFileName(m_InputFileNames[i]);
      try
      {
        curReader->LoadFile();
      }
      catch( ... )
      {
        std::cerr << "Error reading slice" << m_InputFileNames[i] << std::endl;
        delete curReader;
        curReader = nullptr;
      }
      // check for pixel data.
      if(curReader)
      {
        if(!curReader->HasPixelData() )
        {
          delete curReader;
        }
        else
        {
          this->m_Headers[headerCount] = curReader;
          headerCount++;
        }
      }
    }*/

    // modified by HuiXie
    m_Headers.clear();
    int headerCount = 0;
    for ( unsigned i = 0; i < m_InputFileNames.size(); ++i )
    {
      itk::DCMTKFileReader * curReader = new itk::DCMTKFileReader;
      curReader->SetFileName( m_InputFileNames[i] );
      try
      {
        curReader->LoadFile();
      }
      catch ( ... )
      {
        std::cerr << "Error reading slice" << m_InputFileNames[i] << std::endl;
        delete curReader;
        curReader = nullptr;
      }
      // check for pixel data.
      if ( curReader )
      {
        if ( !curReader->HasPixelData() )
        {
          delete curReader;
        }
        else
        {
          m_Headers.push_back( curReader );
          headerCount++;
        }
      }
    }
    // end of modified by HuiXie


    // no headers found, nothing to do.
    if ( headerCount == 0 )
    {
      std::cerr << "No pixel data in series " << m_DicomDirectory << std::endl;
      return nullptr;
    }
    m_InputFileNames.resize( 0 );
    //
    // clean the filename by traversing the header vector
    for ( unsigned int i = 0; i < this->m_Headers.size(); ++i )
    {
      m_InputFileNames.push_back( m_Headers[i]->GetFileName() );
    }
    try
    {
      m_Headers[0]->GetElementLO( 0x0008, 0x0070, this->m_Vendor );
      strupper( this->m_Vendor );
    }
    catch ( itk::ExceptionObject & excp )
    {
      std::cerr << "Can't get vendor name from DICOM file" << excp << std::endl;
      return nullptr;
    }

    if ( StringContains( this->m_Vendor, "PHILIPS" ) )
    {
      converter = new PhilipsDWIConverter( m_Headers, m_InputFileNames, m_UseBMatrixGradientDirections );
    }
    else if ( StringContains( this->m_Vendor, "SIEMENS" ) )
    {
      converter = new SiemensDWIConverter(
        m_Headers, m_InputFileNames, m_UseBMatrixGradientDirections, m_SmallGradientThreshold );
    }
    else if ( StringContains( this->m_Vendor, "GE" ) )
    {
      converter = new GEDWIConverter( m_Headers, m_InputFileNames, m_UseBMatrixGradientDirections );
    }
    else if ( StringContains( this->m_Vendor, "HITACHI" ) )
    {
      converter = new HitachiDWIConverter( m_Headers, m_InputFileNames, m_UseBMatrixGradientDirections );
    }
    else
    {
      // generic converter can't do anything except load a DICOM
      // directory
      converter = new GenericDWIConverter( m_InputFileNames );
      this->m_Vendor = "GENERIC";
    }
  }
  return converter;
}
std::string
DWIConverterFactory::GetVendor()
{
  return m_Vendor;
}