ImageBase/src/itkImageIOBase.cxx

/*=========================================================================
 *
 *  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.
 *
 *=========================================================================*/

#include "itkImageIOBase.h"
#include "itkImageRegionSplitterSlowDimension.h"
#include <mutex>
#include "itksys/SystemTools.hxx"
#include "itkPrintHelper.h"


namespace itk
{
ImageIOBase::ImageIOBase()

{
  Reset(false);
}

void ImageIOBase::Reset(const bool)
{
  m_Initialized = false;
  m_FileName = "";
  m_NumberOfComponents = 1;
  for ( unsigned int i = 0; i < m_NumberOfDimensions; i++ )
    {
    m_Dimensions[i] = 0;
    m_Strides[i] = 0;
    }
  m_NumberOfDimensions = 0;

  m_UseStreamedReading = false;
  m_UseStreamedWriting = false;
  m_ExpandRGBPalette   = true;
  m_IsReadAsScalarPlusPalette  = false;

}

ImageIOBase::~ImageIOBase() = default;

const ImageIOBase::ArrayOfExtensionsType &
ImageIOBase::GetSupportedWriteExtensions() const
{
  return this->m_SupportedWriteExtensions;
}

const ImageIOBase::ArrayOfExtensionsType &
ImageIOBase::GetSupportedReadExtensions() const
{
  return this->m_SupportedReadExtensions;
}

void ImageIOBase::AddSupportedReadExtension(const char *extension)
{
  this->m_SupportedReadExtensions.push_back(extension);
}

void ImageIOBase::AddSupportedWriteExtension(const char *extension)
{
  this->m_SupportedWriteExtensions.push_back(extension);
}

void ImageIOBase::Resize(const unsigned int numDimensions,
                         const unsigned int *dimensions)
{
  m_NumberOfDimensions = numDimensions;
  if ( dimensions != nullptr )
    {
    for ( unsigned int i = 0; i < m_NumberOfDimensions; i++ )
      {
      m_Dimensions[i] = dimensions[i];
      }
    ComputeStrides();
    }
}

void ImageIOBase::SetDimensions(unsigned int i, SizeValueType dim)
{
  if ( i >= m_Dimensions.size() )
    {
    itkWarningMacro( "Index: " << i
                               << " is out of bounds, expected maximum is "
                               << m_Dimensions.size() );
    itkExceptionMacro( "Index: " << i
                                 << " is out of bounds, expected maximum is "
                                 << m_Dimensions.size() );
    }
  this->Modified();
  m_Dimensions[i] = dim;
}

void ImageIOBase::SetOrigin(unsigned int i, double origin)
{
  if ( i >= m_Origin.size() )
    {
    itkWarningMacro( "Index: " << i
                               << " is out of bounds, expected maximum is "
                               << m_Origin.size() );
    itkExceptionMacro( "Index: " << i
                                 << " is out of bounds, expected maximum is "
                                 << m_Origin.size() );
    }
  this->Modified();
  m_Origin[i] = origin;
}

void ImageIOBase::SetSpacing(unsigned int i, double spacing)
{
  if ( i >= m_Spacing.size() )
    {
    itkWarningMacro( "Index: " << i
                               << " is out of bounds, expected maximum is "
                               << m_Spacing.size() );
    itkExceptionMacro( "Index: " << i
                                 << " is out of bounds, expected maximum is "
                                 << m_Spacing.size() );
    }
  this->Modified();
  m_Spacing[i] = spacing;
}

void ImageIOBase::SetDirection(unsigned int i, const std::vector< double > & direction)
{
  if ( i >= m_Direction.size() )
    {
    itkWarningMacro( "Index: " << i
                               << " is out of bounds, expected maximum is "
                               << m_Direction.size() );
    itkExceptionMacro( "Index: " << i
                                 << " is out of bounds, expected maximum is "
                                 << m_Direction.size() );
    }
  this->Modified();
  m_Direction[i] = direction;
}

void ImageIOBase::SetDirection(unsigned int i, const vnl_vector< double > & direction)
{
  if ( i >= m_Direction.size() )
    {
    itkWarningMacro( "Index: " << i
                               << " is out of bounds, expected maximum is "
                               << m_Direction.size() );
    itkExceptionMacro( "Index: " << i
                                 << " is out of bounds, expected maximum is "
                                 << m_Direction.size() );
    }
  this->Modified();
  std::vector< double > v;
  v.resize( m_Direction.size() );
  // Note: direction.size() <= v.size().
  for ( unsigned int j = 0; j < direction.size(); j++ )
    {
    v[j] = direction[j];
    }
  m_Direction[i] = v;
}

const std::type_info & ImageIOBase::GetComponentTypeInfo() const
{
  switch ( m_ComponentType )
    {
    case UCHAR:
      return typeid( unsigned char );
    case CHAR:
      return typeid( char );
    case USHORT:
      return typeid( unsigned short );
    case SHORT:
      return typeid( short );
    case UINT:
      return typeid( unsigned int );
    case INT:
      return typeid( int );
    case ULONG:
      return typeid( unsigned long );
    case LONG:
      return typeid( long );
    case ULONGLONG:
      return typeid( unsigned long long );
    case LONGLONG:
      return typeid( long long);
    case FLOAT:
      return typeid( float );
    case DOUBLE:
      return typeid( double );
    case UNKNOWNCOMPONENTTYPE:
    default:
      itkExceptionMacro ("Unknown component type: " << m_ComponentType);
    }
}

void ImageIOBase::ComputeStrides()
{
  m_Strides[0] = this->GetComponentSize();
  m_Strides[1] = m_NumberOfComponents * m_Strides[0];
  for ( unsigned int i = 2; i <= ( m_NumberOfDimensions + 1 ); i++ )
    {
    m_Strides[i] = static_cast<SizeType>(m_Dimensions[i - 2]) * m_Strides[i - 1];
    }
}

// Calculates the image size in PIXELS
ImageIOBase::SizeType
ImageIOBase
::GetImageSizeInPixels() const
{
  unsigned int i;
  SizeType     numPixels = 1;

  for ( i = 0; i < m_NumberOfDimensions; i++ )
    {
    numPixels *= m_Dimensions[i];
    }

  return numPixels;
}

ImageIOBase::SizeType
ImageIOBase
::GetImageSizeInComponents() const
{
  return ( this->GetImageSizeInPixels() * m_NumberOfComponents );
}

ImageIOBase::SizeType
ImageIOBase
::GetImageSizeInBytes() const
{
  return ( this->GetImageSizeInComponents() * this->GetComponentSize() );
}

ImageIOBase::SizeType
ImageIOBase
::GetComponentStride() const
{
  return m_Strides[0];
}

ImageIOBase::SizeType
ImageIOBase
::GetPixelStride() const
{
  return m_Strides[1];
}

ImageIOBase::SizeType
ImageIOBase
::GetRowStride() const
{
  return m_Strides[2];
}

ImageIOBase::SizeType
ImageIOBase
::GetSliceStride() const
{
  return m_Strides[3];
}

void ImageIOBase::SetNumberOfDimensions(unsigned int dim)
{
  if ( dim != m_NumberOfDimensions )
    {
    m_Origin.resize(dim);
    m_Spacing.resize(dim);
    m_Direction.resize(dim);
    m_Strides.resize(dim + 2);
    m_NumberOfDimensions = dim;
    m_Dimensions.resize(dim);
    m_Direction.resize(dim);
    std::vector< double > axis(dim);
    for ( unsigned int i = 0; i < dim; i++ )
      {
      for ( unsigned int j = 0; j < dim; j++ )
        {
        if ( i == j )
          {
          axis[j] = 1.0;
          }
        else
          {
          axis[j] = 0.0;
          }
        }
      this->SetDirection(i, axis);
      this->SetOrigin(i, 0.0);
      this->SetSpacing(i, 1.0);
      }
    this->Modified();
    }
}

bool
ImageIOBase
::ReadBufferAsBinary(std::istream & is, void *buffer, ImageIOBase::SizeType num)
{
  const auto numberOfBytesToBeRead = Math::CastWithRangeCheck< std::streamsize >(num);

  is.read(static_cast< char * >( buffer ), numberOfBytesToBeRead);

  const std::streamsize numberOfBytesRead = is.gcount();

#ifdef __APPLE_CC__
  // fail() is broken in the Mac. It returns true when reaches eof().
  if ( numberOfBytesRead != numberOfBytesToBeRead )
#else
  if ( ( numberOfBytesRead != numberOfBytesToBeRead )  || is.fail() )
#endif
    {
    return false; // read failed
    }

  return true;
}

unsigned int ImageIOBase::GetPixelSize() const
{
  if ( m_ComponentType == UNKNOWNCOMPONENTTYPE
       || m_PixelType == UNKNOWNPIXELTYPE )
    {
    itkExceptionMacro ("Unknown pixel or component type: ("
                       << m_PixelType << ", " << m_ComponentType << ")");
    }

  return this->GetComponentSize() * this->GetNumberOfComponents();
}


void ImageIOBase::SetCompressor( std::string _c )
{
  if ( this->m_Compressor != _c )
    {
    this->m_Compressor = _c;
    this->Modified();

    std::transform(_c.begin(), _c.end(), _c.begin(), ::toupper);
    this->InternalSetCompressor(_c);
    }
}

void ImageIOBase::SetMaximumCompressionLevel( int _MaximumCompressionLevel )
{
  this->m_MaximumCompressionLevel = _MaximumCompressionLevel;
  this->SetCompressionLevel( this->GetCompressionLevel() );
}

void ImageIOBase::InternalSetCompressor(const std::string &_compressor)
{
  if (_compressor != "")
    {
    itkWarningMacro("Unknown compressor: \"" << _compressor << "\", setting to default.");
    this->SetCompressor("");
    }
}

unsigned int ImageIOBase::GetComponentSize() const
{
  switch ( m_ComponentType )
    {
    case UCHAR:
      return sizeof( unsigned char );
    case CHAR:
      return sizeof( char );
    case USHORT:
      return sizeof( unsigned short );
    case SHORT:
      return sizeof( short );
    case UINT:
      return sizeof( unsigned int );
    case INT:
      return sizeof( int );
    case ULONG:
      return sizeof( unsigned long );
    case LONG:
      return sizeof( long );
    case ULONGLONG:
      return sizeof( unsigned long long );
    case LONGLONG:
      return sizeof( long long );
    case FLOAT:
      return sizeof( float );
    case DOUBLE:
      return sizeof( double );
    case UNKNOWNCOMPONENTTYPE:
    default:
      itkExceptionMacro ("Unknown component type: " << m_ComponentType);
    }
}

std::string ImageIOBase::GetFileTypeAsString(FileType t) const
{
  switch ( t )
    {
    case ASCII:
      return std::string( "ASCII");
    case Binary:
      return std::string( "Binary");
    case TypeNotApplicable:
    default:
      return std::string( "TypeNotApplicable");
    }
  //Not reachable return s = "TypeNotApplicable";
}

std::string ImageIOBase::GetByteOrderAsString(ByteOrder t) const
{
  switch ( t )
    {
    case BigEndian:
      return std::string( "BigEndian");
    case LittleEndian:
      return std::string( "LittleEndian");
    case OrderNotApplicable:
    default:
      return std::string( "OrderNotApplicable");
    }
}

std::string ImageIOBase::GetComponentTypeAsString(IOComponentType t)
{
  switch ( t )
    {
    case UCHAR:
      return std::string( "unsigned_char" );
    case CHAR:
      return std::string( "char" );
    case USHORT:
      return std::string( "unsigned_short" );
    case SHORT:
      return std::string( "short" );
    case UINT:
      return std::string( "unsigned_int" );
    case INT:
      return std::string( "int" );
    case ULONG:
      return std::string( "unsigned_long" );
    case LONG:
      return std::string( "long" );
    case ULONGLONG:
      return std::string( "unsigned_long_long" );
    case LONGLONG:
      return std::string( "long_long" );
    case FLOAT:
      return std::string( "float" );
    case DOUBLE:
      return std::string( "double" );
    case UNKNOWNCOMPONENTTYPE:
      return std::string( "unknown" );
    default:
      return std::string( "unknown" );
    }
}

ImageIOBase::IOComponentType ImageIOBase::GetComponentTypeFromString(const std::string &typeString)
{
  if(typeString.compare("unsigned_char") == 0)
    {
    return UCHAR;
    }
  else if(typeString.compare("char") == 0)
    {
    return CHAR;
    }
  else if(typeString.compare("unsigned_short") == 0)
    {
    return USHORT;
    }
  else if(typeString.compare("short") == 0)
    {
    return SHORT;
    }
  else if(typeString.compare("unsigned_int") == 0)
    {
    return UINT;
    }
  else if(typeString.compare("int") == 0)
    {
    return INT;
    }
  else if(typeString.compare("unsigned_long") == 0)
    {
    return ULONG;
    }
  else if(typeString.compare("long") == 0)
    {
    return LONG;
    }
  else if(typeString.compare("unsigned_long_long") == 0)
    {
    return ULONGLONG;
    }
  else if(typeString.compare("long_long") == 0)
    {
    return LONGLONG;
    }
  else if(typeString.compare("float") == 0)
    {
    return FLOAT;
    }
  else if(typeString.compare("double") == 0)
    {
    return DOUBLE;
    }
  else
    {
    return UNKNOWNCOMPONENTTYPE;
    }
}

std::string ImageIOBase::GetPixelTypeAsString(IOPixelType t)
{
  switch ( t )
    {
    case SCALAR:
      return std::string( "scalar" );
    case VECTOR:
      return std::string( "vector" );
    case COVARIANTVECTOR:
      return std::string( "covariant_vector" );
    case POINT:
      return std::string( "point" );
    case OFFSET:
      return std::string( "offset" );
    case RGB:
      return std::string( "rgb" );
    case RGBA:
      return std::string( "rgba" );
    case SYMMETRICSECONDRANKTENSOR:
      return std::string( "symmetric_second_rank_tensor" );
    case DIFFUSIONTENSOR3D:
      return std::string( "diffusion_tensor_3D" );
    case COMPLEX:
      return std::string( "complex" );
    case FIXEDARRAY:
      return std::string( "fixed_array" );
    case MATRIX:
      return std::string( "matrix" );
    case UNKNOWNPIXELTYPE:
      return std::string( "unknown" );
    default:
      return std::string( "unknown" );
    }
}

ImageIOBase::IOPixelType ImageIOBase::GetPixelTypeFromString(const std::string &pixelString)
{
  if(pixelString.compare("scalar") == 0)
    {
    return SCALAR;
    }
  else if(pixelString.compare("vector") == 0)
    {
    return VECTOR;
    }
  else if(pixelString.compare("covariant_vector") == 0)
    {
    return COVARIANTVECTOR;
    }
  else if(pixelString.compare("point") == 0)
    {
    return POINT;
    }
  else if(pixelString.compare("offset") == 0)
    {
    return OFFSET;
    }
  else if(pixelString.compare("rgb") == 0)
    {
    return RGB;
    }
  else if(pixelString.compare("rgba") == 0)
    {
    return RGBA;
    }
  else if(pixelString.compare("symmetric_second_rank_tensor") == 0)
    {
    return SYMMETRICSECONDRANKTENSOR;
    }
  else if(pixelString.compare("diffusion_tensor_3D") == 0)
    {
    return DIFFUSIONTENSOR3D;
    }
  else if(pixelString.compare("complex") == 0)
    {
    return COMPLEX;
    }
  else if(pixelString.compare("fixed_array") == 0)
    {
    return FIXEDARRAY;
    }
  else if(pixelString.compare("matrix") == 0)
    {
    return MATRIX;
    }
  else
    {
    return UNKNOWNPIXELTYPE;
    }
}

void ImageIOBase::OpenFileForReading(std::ifstream & inputStream, const std::string & filename,
                                     bool ascii)
{
  // Make sure that we have a file to
  if ( filename.empty() )
    {
    itkExceptionMacro( << "A FileName must be specified." );
    }

  // Close file from any previous image
  if ( inputStream.is_open() )
    {
    inputStream.close();
    }

  // Open the new file for reading
  itkDebugMacro( << "Opening file for reading: " << filename );

  std::ios::openmode mode = std::ios::in;
  if ( !ascii )
    {
    mode |= std::ios::binary;
    }

  inputStream.open( filename.c_str(), mode );

  if ( !inputStream.is_open() || inputStream.fail() )
    {
    itkExceptionMacro( << "Could not open file: "
                       << filename << " for reading."
                       << std::endl
                       << "Reason: "
                       << itksys::SystemTools::GetLastSystemError() );
    }
}

void ImageIOBase::OpenFileForWriting(std::ofstream & outputStream, const std::string & filename,
                                     bool truncate, bool ascii)
{
  // Make sure that we have a file to
  if ( filename.empty() )
    {
    itkExceptionMacro( << "A FileName must be specified." );
    }

  // Close file from any previous image
  if ( outputStream.is_open() )
    {
    outputStream.close();
    }

  // Open the new file for writing
  itkDebugMacro( << "Opening file for writing: " << filename );

  std::ios::openmode mode = std::ios::out;
  if ( truncate )
    {
    // typically, ios::out also implies ios::trunc, but being explicit is safer
    mode |= std::ios::trunc;
    }
  else
    {
    mode |= std::ios::in;
    // opening a nonexistent file for reading + writing is not allowed on some platforms
    if ( !itksys::SystemTools::FileExists( filename.c_str() ) )
      {
      itksys::SystemTools::Touch( filename.c_str(), true );
      // don't worry about failure here, errors should be detected later when the file
      // is "actually" opened, unless there is a race condition
      }
    }
  if ( !ascii )
    {
    mode |= std::ios::binary;
    }

  outputStream.open( filename.c_str(), mode );

  if ( !outputStream.is_open() || outputStream.fail() )
    {
    itkExceptionMacro( << "Could not open file: "
                       << filename << " for writing."
                       << std::endl
                       << "Reason: "
                       << itksys::SystemTools::GetLastSystemError() );
    }
}

namespace
{
template< typename TComponent >
void WriteBuffer(std::ostream & os, const TComponent *buffer, ImageIOBase::SizeType num)
{
  const TComponent *ptr = buffer;

  using PrintType = typename itk::NumericTraits< TComponent >::PrintType;
  for ( ImageIOBase::SizeType i = 0; i < num; i++ )
    {
    if ( !( i % 6 ) && i )
      {
      os << "\n";
      }
    os << PrintType(*ptr++) << " ";
    }
}
}
void ImageIOBase::WriteBufferAsASCII(std::ostream & os, const void *buffer,
                                     IOComponentType ctype,
                                     ImageIOBase::SizeType numComp)
{
  switch ( ctype )
    {
    case UCHAR:
      {
      using Type = const unsigned char *;
      auto buf = reinterpret_cast< Type >( buffer );
      WriteBuffer(os, buf, numComp);
      }
      break;
    case CHAR:
      {
      using Type = const char *;
      auto buf = reinterpret_cast< Type >( buffer );
      WriteBuffer(os, buf, numComp);
      }
      break;

    case USHORT:
      {
      using Type = const unsigned short *;
      auto buf = reinterpret_cast< Type >( buffer );
      WriteBuffer(os, buf, numComp);
      }
      break;

    case SHORT:
      {
      using Type = const short *;
      auto buf = reinterpret_cast< Type >( buffer );
      WriteBuffer(os, buf, numComp);
      }
      break;

    case UINT:
      {
      using Type = const unsigned int *;
      auto buf = reinterpret_cast< Type >( buffer );
      WriteBuffer(os, buf, numComp);
      }
      break;

    case INT:
      {
      using Type = const int *;
      auto buf = reinterpret_cast< Type >( buffer );
      WriteBuffer(os, buf, numComp);
      }
      break;

    case ULONG:
      {
      using Type = const unsigned long *;
      auto buf = reinterpret_cast< Type >( buffer );
      WriteBuffer(os, buf, numComp);
      }
      break;

    case LONG:
      {
      using Type = const long *;
      auto buf = reinterpret_cast< Type >( buffer );
      WriteBuffer(os, buf, numComp);
      }
      break;

    case ULONGLONG:
      {
      using Type = const unsigned long long *;
      auto buf = reinterpret_cast< Type >( buffer );
      WriteBuffer(os, buf, numComp);
      }
      break;

    case LONGLONG:
      {
      using Type = const long long *;
      auto buf = reinterpret_cast< Type >( buffer );
      WriteBuffer(os, buf, numComp);
      }
      break;

    case FLOAT:
      {
      using Type = const float *;
      auto buf = reinterpret_cast< Type >( buffer );
      WriteBuffer(os, buf, numComp);
      }
      break;

    case DOUBLE:
      {
      using Type = const double *;
      auto buf = reinterpret_cast< Type >( buffer );
      WriteBuffer(os, buf, numComp);
      }
      break;

    default:
      break;
    }
}

namespace
{
template< typename TComponent >
void ReadBuffer(std::istream & is, TComponent *buffer, ImageIOBase::SizeType num)
{
  using PrintType = typename itk::NumericTraits< TComponent >::PrintType;
  PrintType   temp;
  TComponent *ptr = buffer;
  for ( ImageIOBase::SizeType i = 0; i < num; i++, ptr++ )
    {
    is >> temp;
    *ptr = static_cast< TComponent >( temp );
    }
}
}
void ImageIOBase::ReadBufferAsASCII(std::istream & is, void *buffer,
                                    IOComponentType ctype,
                                    ImageIOBase::SizeType numComp)
{
  switch ( ctype )
    {
    case UCHAR:
      {
      auto * buf = reinterpret_cast< unsigned char * >( buffer );
      ReadBuffer(is, buf, numComp);
      }
      break;
    case CHAR:
      {
      auto * buf = reinterpret_cast< char * >( buffer );
      ReadBuffer(is, buf, numComp);
      }
      break;

    case USHORT:
      {
      auto * buf = reinterpret_cast< unsigned short * >( buffer );
      ReadBuffer(is, buf, numComp);
      }
      break;

    case SHORT:
      {
      auto * buf = reinterpret_cast< short * >( buffer );
      ReadBuffer(is, buf, numComp);
      }
      break;

    case UINT:
      {
      auto * buf = reinterpret_cast< unsigned int * >( buffer );
      ReadBuffer(is, buf, numComp);
      }
      break;

    case INT:
      {
      auto * buf = reinterpret_cast< int * >( buffer );
      ReadBuffer(is, buf, numComp);
      }
      break;

    case ULONG:
      {
      auto * buf = reinterpret_cast< unsigned long * >( buffer );
      ReadBuffer(is, buf, numComp);
      }
      break;

    case LONG:
      {
      auto * buf = reinterpret_cast< long * >( buffer );
      ReadBuffer(is, buf, numComp);
      }
      break;

    case ULONGLONG:
      {
      auto * buf = reinterpret_cast< unsigned long long * >( buffer );
      ReadBuffer(is, buf, numComp);
      }
      break;

    case LONGLONG:
      {
      auto * buf = reinterpret_cast< long long * >( buffer );
      ReadBuffer(is, buf, numComp);
      }
      break;

    case FLOAT:
      {
      auto * buf = reinterpret_cast< float * >( buffer );
      ReadBuffer(is, buf, numComp);
      }
      break;

    case DOUBLE:
      {
      auto * buf = reinterpret_cast< double * >( buffer );
      ReadBuffer(is, buf, numComp);
      }
      break;

    default:
      break;
    }
}

namespace
{
std::mutex ioDefaultSplitterLock;
ImageRegionSplitterBase::Pointer ioDefaultSplitter;

}

const ImageRegionSplitterBase*
ImageIOBase::GetImageRegionSplitter() const
{
  if ( ioDefaultSplitter.IsNull() )
    {
    // thread safe lazy initialization,  prevent race condition on
    // setting, with an atomic set if null.
    std::lock_guard< std::mutex > lock( ioDefaultSplitterLock );
    if ( ioDefaultSplitter.IsNull() )
      {
      ioDefaultSplitter = ImageRegionSplitterSlowDimension::New().GetPointer();
      }
    }
  return ioDefaultSplitter;
}


bool
ImageIOBase::HasSupportedReadExtension( const char *fileName, bool ignoreCase )
{
  return this->HasSupportedExtension( fileName,
                                      this->GetSupportedReadExtensions(),
                                      ignoreCase );
}


bool
ImageIOBase::HasSupportedWriteExtension( const char *fileName, bool ignoreCase )
{

  return this->HasSupportedExtension( fileName,
                                      this->GetSupportedWriteExtensions(),
                                      ignoreCase );
}


bool
ImageIOBase::HasSupportedExtension( const char * filename,
                                    const ImageIOBase::ArrayOfExtensionsType &supportedExtensions,
                                    bool ignoreCase )
{

  std::string ext = itksys::SystemTools::GetFilenameLastExtension(filename);
  if ( ignoreCase )
    {
    std::transform(ext.begin(), ext.end(), ext.begin(), ::tolower);
    }

  for ( auto && candidate : supportedExtensions )
    {
    if ( ignoreCase )
      {
      size_t n = candidate.size();
      if ( n == ext.size() && n > 0)
        {

        while ( true )
          {
          --n;
          if (ext[n] != ::tolower(candidate[n]))
            {
            break;
            }
          if ( n == 0 )
            {
            return true;
            }
          }

        }
      }
    else
      {
      if ( candidate == ext )
        {
        return true;
        }
      }
    }
  return false;
}

unsigned int
ImageIOBase::GetActualNumberOfSplitsForWritingCanStreamWrite(unsigned int numberOfRequestedSplits,
                                                             const ImageIORegion & pasteRegion) const
{
  const ImageRegionSplitterBase* splitter = this->GetImageRegionSplitter();
  return splitter->GetNumberOfSplits(pasteRegion, numberOfRequestedSplits);
}

unsigned int
ImageIOBase::GetActualNumberOfSplitsForWriting(unsigned int numberOfRequestedSplits,
                                               const ImageIORegion & pasteRegion,
                                               const ImageIORegion & largestPossibleRegion)
{
  if ( this->CanStreamWrite() )
    {
    return GetActualNumberOfSplitsForWritingCanStreamWrite(numberOfRequestedSplits, pasteRegion);
    }
  if ( pasteRegion != largestPossibleRegion )
    {
    itkExceptionMacro( "Pasting is not supported! Can't write:" << this->GetFileName() );
    }
  if ( numberOfRequestedSplits != 1 )
    {
    itkDebugMacro("Requested more then 1 splits for streaming");
    itkDebugMacro("This IO class does not support streaming!");
    }
  return 1;
}

ImageIORegion
ImageIOBase::GetSplitRegionForWritingCanStreamWrite(unsigned int ithPiece,
                                                    unsigned int numberOfActualSplits,
                                                    const ImageIORegion & pasteRegion) const
{
  ImageIORegion splitRegion = pasteRegion;

  const ImageRegionSplitterBase* splitter = this->GetImageRegionSplitter();
  splitter->GetSplit( ithPiece, numberOfActualSplits, splitRegion );

  return splitRegion;
}

ImageIORegion
ImageIOBase::GetSplitRegionForWriting(unsigned int ithPiece,
                                      unsigned int numberOfActualSplits,
                                      const ImageIORegion & pasteRegion,
                                      const ImageIORegion & largestPossibleRegion)
{
  if ( this->CanStreamWrite() )
    {
    return GetSplitRegionForWritingCanStreamWrite(ithPiece, numberOfActualSplits, pasteRegion);
    }
  return largestPossibleRegion;
}

/** Given a requested region, determine what could be the region that we can
 * read from the file. This is called the streamable region, which will be
 * smaller than the LargestPossibleRegion and greater or equal to the
 * RequestedRegion */
ImageIORegion
ImageIOBase
::GenerateStreamableReadRegionFromRequestedRegion(
  const ImageIORegion & requested) const
{
  //
  // The default implementations determines that the streamable region is
  // equal to the minimal size of the image in the file. That is two
  // say the return ImageIORegion::GetImageSizeInPixels() is equal to
  // the number in the file.
  //

  // Since the image in the file may have a lower or higher dimension
  // than the image type over which the ImageFileReader is
  // being instantiated we must choose an image dimension which will
  // represent all the pixels. That is we can trim trailing 1s.

  unsigned int minIODimension = this->m_NumberOfDimensions;

  while ( minIODimension )
    {
    if ( this->m_Dimensions[minIODimension - 1] == 1 )
      {
      --minIODimension;
      }
    else
      {
      break;
      }
    }

  // dimension size we use to represent the region
  unsigned int maxDimension =
    minIODimension > requested.GetImageDimension() ? minIODimension : requested.GetImageDimension();

  // First: allocate with the correct dimensions
  ImageIORegion streamableRegion(maxDimension);

  // Second: copy only the number of dimension that the file has.
  for ( unsigned int i = 0; i < minIODimension; i++ )
    {
    streamableRegion.SetSize(i, this->m_Dimensions[i]);
    streamableRegion.SetIndex(i, 0);
    }

  // Third: set the rest to the default : start = 0, size = 1
  for ( unsigned int j = minIODimension; j < streamableRegion.GetImageDimension(); j++ )
    {
    streamableRegion.SetSize(j, 1);
    streamableRegion.SetIndex(j, 0);
    }

  // Finally: return the streamable region
  return streamableRegion;
}

/** Return the directions that this particular ImageIO would use by default
 *  in the case the recipient image dimension is smaller than the dimension
 *  of the image in file. */
std::vector< double >
ImageIOBase
::GetDefaultDirection(unsigned int k) const
{
  std::vector< double > axis;
  axis.resize( this->GetNumberOfDimensions() );

  // Fill up with the equivalent of a line from an Identity matrix
  for (double & axi : axis)
    {
    axi = 0.0;
    }

  axis[k] = 1.0;

  return axis;
}

void ImageIOBase::PrintSelf(std::ostream & os, Indent indent) const
{
  using namespace print_helper;

  Superclass::PrintSelf(os, indent);

  os << indent << "FileName: " << m_FileName << std::endl;
  os << indent << "FileType: " << this->GetFileTypeAsString(m_FileType) << std::endl;
  os << indent << "ByteOrder: " << this->GetByteOrderAsString(m_ByteOrder) << std::endl;
  os << indent << "IORegion: " << std::endl;
  m_IORegion.Print( os, indent.GetNextIndent() );
  os << indent << "Number of Components/Pixel: " << m_NumberOfComponents << "\n";
  os << indent << "Pixel Type: " << this->GetPixelTypeAsString(m_PixelType) << std::endl;
  os << indent << "Component Type: " << this->GetComponentTypeAsString(m_ComponentType)
     << std::endl;
  os << indent << "Dimensions: " << m_Dimensions << std::endl;
  os << indent << "Origin: " << m_Origin << std::endl;
  os << indent << "Spacing: " << m_Spacing << std::endl;
  os << indent << "Direction: " << std::endl;
  for( const auto & direction : m_Direction )
    {
    os << indent << direction << std::endl;
    }
  if( m_UseCompression )
    {
    os << indent << "UseCompression: On" << std::endl;
    }
  else
    {
    os << indent << "UseCompression: Off" << std::endl;
    }
  os << indent << "CompressionLevel: " << m_CompressionLevel << std::endl;
  os << indent << "MaximumCompressionLevel: " << m_MaximumCompressionLevel << std::endl;
  os << indent << "Compressor: " << m_Compressor << std::endl;
  if( m_UseStreamedReading )
    {
    os << indent << "UseStreamedReading: On" << std::endl;
    }
  else
    {
    os << indent << "UseStreamedReading: Off" << std::endl;
    }
  if( m_UseStreamedWriting )
    {
    os << indent << "UseStreamedWriting: On" << std::endl;
    }
  else
    {
    os << indent << "UseStreamedWriting: Off" << std::endl;
    }
  if( m_ExpandRGBPalette )
    {
    os << indent << "ExpandRGBPalette: On" << std::endl;
    }
  else
    {
    os << indent << "ExpandRGBPalette: Off" << std::endl;
    }
  if( m_IsReadAsScalarPlusPalette )
    {
    os << indent << "IsReadAsScalarPlusPalette: True" << std::endl;
    }
  else
    {
    os << indent << "IsReadAsScalarPlusPalette: False" << std::endl;
    }
}

} //namespace itk