libinsighttoolkit4-dev 4.9.0-4ubuntu1 / usr / include / ITK-4.9 / itkImageFileWriter.hxx

/*=========================================================================
 *
 *  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 itkImageFileWriter_hxx
#define itkImageFileWriter_hxx

#include "itkImageFileWriter.h"
#include "itkDataObject.h"
#include "itkObjectFactoryBase.h"
#include "itkImageIOFactory.h"
#include "itkCommand.h"
#include "vnl/vnl_vector.h"
#include "itkVectorImage.h"
#include "itkImageRegionIterator.h"
#include "itkRGBPixel.h"
#include "itkRGBAPixel.h"
#include "itkSymmetricSecondRankTensor.h"
#include "itkDiffusionTensor3D.h"
#include "itkMatrix.h"
#include "itkImageAlgorithm.h"
#include <complex>

namespace itk
{
//---------------------------------------------------------
template< typename TInputImage >
ImageFileWriter< TInputImage >
::ImageFileWriter():
  m_PasteIORegion(TInputImage::ImageDimension)
{
  m_UseCompression = false;
  m_UseInputMetaDataDictionary = true;
  m_FactorySpecifiedImageIO = false;
  m_UserSpecifiedIORegion = false;
  m_UserSpecifiedImageIO = false;
  m_NumberOfStreamDivisions = 1;
}

//---------------------------------------------------------
template< typename TInputImage >
ImageFileWriter< TInputImage >
::~ImageFileWriter()
{}

//---------------------------------------------------------
template< typename TInputImage >
void
ImageFileWriter< TInputImage >
::SetInput(const InputImageType *input)
{
  // ProcessObject is not const_correct so this cast is required here.
  this->ProcessObject::SetNthInput( 0,
                                    const_cast< TInputImage * >( input ) );
}

//---------------------------------------------------------
template< typename TInputImage >
const typename ImageFileWriter< TInputImage >::InputImageType *
ImageFileWriter< TInputImage >
::GetInput(void)
{
  return itkDynamicCastInDebugMode< TInputImage * >( this->GetPrimaryInput() );
}

//---------------------------------------------------------
template< typename TInputImage >
const typename ImageFileWriter< TInputImage >::InputImageType *
ImageFileWriter< TInputImage >
::GetInput(unsigned int idx)
{
  return itkDynamicCastInDebugMode< TInputImage * >( this->ProcessObject::GetInput(idx) );
}

//---------------------------------------------------------
template< typename TInputImage >
void
ImageFileWriter< TInputImage >
::SetIORegion(const ImageIORegion & region)
{
  itkDebugMacro("setting IORegion to " << region);
  if ( m_PasteIORegion != region )
    {
    m_PasteIORegion = region;
    this->Modified();
    m_UserSpecifiedIORegion = true;
    }
}

//---------------------------------------------------------
template< typename TInputImage >
void
ImageFileWriter< TInputImage >
::Write()
{
  const InputImageType *input = this->GetInput();

  itkDebugMacro(<< "Writing an image file");

  // Make sure input is available
  if ( input == ITK_NULLPTR )
    {
    itkExceptionMacro(<< "No input to writer!");
    }

  // Make sure that we can write the file given the name
  //
  if ( m_FileName == "" )
    {
    itkExceptionMacro(<< "No filename was specified");
    }

#if !defined(SPECIFIC_IMAGEIO_MODULE_TEST)
  if ( m_ImageIO.IsNull() ||
       ( m_FactorySpecifiedImageIO && !m_ImageIO->CanWriteFile( m_FileName.c_str() ) ) )
    {
    //try creating via factory
    if ( m_ImageIO.IsNull() )
      {
      itkDebugMacro(<< "Attempting factory creation of ImageIO for file: "
                    << m_FileName);
      }
    else // ( m_FactorySpecifiedImageIO && !m_ImageIO->CanWriteFile( m_FileName.c_str() )
      {
      itkDebugMacro(<< "ImageIO exists but doesn't know how to write file:"
                    << m_FileName);
      itkDebugMacro(<< "Attempting creation of ImageIO with a factory for file:"
                    << m_FileName);
      }
    m_ImageIO = ImageIOFactory::CreateImageIO(m_FileName.c_str(),
                                              ImageIOFactory::WriteMode);
    m_FactorySpecifiedImageIO = true;
    }
#endif

  if ( m_ImageIO.IsNull() )
    {
    ImageFileWriterException e(__FILE__, __LINE__);
    std::ostringstream       msg;
    std::list< LightObject::Pointer > allobjects =
      ObjectFactoryBase::CreateAllInstance("itkImageIOBase");
    msg << " Could not create IO object for writing file "
        << m_FileName.c_str() << std::endl;
    if (allobjects.size() > 0)
      {
      msg << "  Tried to create one of the following:" << std::endl;
      for ( std::list< LightObject::Pointer >::iterator i = allobjects.begin();
            i != allobjects.end(); ++i )
        {
        ImageIOBase *io = dynamic_cast< ImageIOBase * >( i->GetPointer() );
        msg << "    " << io->GetNameOfClass() << std::endl;
        }
      msg << "  You probably failed to set a file suffix, or" << std::endl;
      msg << "    set the suffix to an unsupported type." << std::endl;
      }
    else
      {
      msg << "  There are no registered IO factories." << std::endl;
      msg << "  Please visit http://www.itk.org/Wiki/ITK/FAQ#NoFactoryException to diagnose the problem." << std::endl;
      }
    e.SetDescription( msg.str().c_str() );
    e.SetLocation(ITK_LOCATION);
    throw e;
    }

  // NOTE: this const_cast<> is due to the lack of const-correctness
  // of the ProcessObject.
  InputImageType *nonConstInput = const_cast< InputImageType * >( input );

  // Update the meta data if needed
  if ( !m_UserSpecifiedIORegion )
    {
    nonConstInput->UpdateOutputInformation();
    }
  else
    {
    // The user specified an io paste region.

    // If the input image is does not have an source filter, then we
    // do not want to update the output information, because it will
    // change the largest possible region to the buffered region. When
    // we are pasting the largest possible regions of the input must
    // match the file.
    if ( nonConstInput->GetSource() )
      {
      nonConstInput->UpdateOutputInformation();
      }

    }


  // Setup the ImageIO
  //
  m_ImageIO->SetNumberOfDimensions(TInputImage::ImageDimension);
  InputImageRegionType largestRegion = input->GetLargestPossibleRegion();
  const typename TInputImage::SpacingType & spacing = input->GetSpacing();
  const typename TInputImage::DirectionType & direction = input->GetDirection();
  // BUG 8436: Wrong origin when writing a file with non-zero index
  // origin = input->GetOrigin();
  const typename TInputImage::IndexType & startIndex = largestRegion.GetIndex();
  typename TInputImage::PointType origin;
  input->TransformIndexToPhysicalPoint(startIndex, origin);

  for ( unsigned int i = 0; i < TInputImage::ImageDimension; i++ )
    {
    m_ImageIO->SetDimensions( i, largestRegion.GetSize(i) );
    m_ImageIO->SetSpacing(i, spacing[i]);
    m_ImageIO->SetOrigin(i, origin[i]);
    vnl_vector< double > axisDirection(TInputImage::ImageDimension);
    // Please note: direction cosines are stored as columns of the
    // direction matrix
    for ( unsigned int j = 0; j < TInputImage::ImageDimension; j++ )
      {
      axisDirection[j] = direction[j][i];
      }
    m_ImageIO->SetDirection(i, axisDirection);
    }

  // configure compression
  m_ImageIO->SetUseCompression(m_UseCompression);

  // configure meta dictionary
  if ( m_UseInputMetaDataDictionary )
    {
    m_ImageIO->SetMetaDataDictionary( input->GetMetaDataDictionary() );
    }

  // Make sure that the image is the right type
  // confiugure pixel type
  if ( strcmp(input->GetNameOfClass(), "VectorImage") == 0 )
    {
    typedef typename InputImageType::InternalPixelType VectorImageScalarType;
    m_ImageIO->SetPixelTypeInfo(static_cast<const VectorImageScalarType *>(ITK_NULLPTR));
    typedef typename InputImageType::AccessorFunctorType AccessorFunctorType;
    m_ImageIO->SetNumberOfComponents( AccessorFunctorType::GetVectorLength(input) );
    }
  else
    {
    // Set the pixel and component type; the number of components.
    m_ImageIO->SetPixelTypeInfo(static_cast<const InputImagePixelType *>(ITK_NULLPTR));
    }

  // Setup the image IO for writing.
  //
  m_ImageIO->SetFileName( m_FileName.c_str() );

  // Notify start event observers
  this->InvokeEvent( StartEvent() );

  if ( m_NumberOfStreamDivisions > 1 || m_UserSpecifiedIORegion )
    {
    m_ImageIO->SetUseStreamedWriting(true);
    }

  ImageIORegion largestIORegion(TInputImage::ImageDimension);
  ImageIORegionAdaptor< TInputImage::ImageDimension >::
  Convert( largestRegion, largestIORegion, largestRegion.GetIndex() );

  // this pasteIORegion is the region we are going to write
  ImageIORegion pasteIORegion;
  if ( m_UserSpecifiedIORegion )
    {
    pasteIORegion = m_PasteIORegion;
    }
  else
    {
    pasteIORegion = largestIORegion;
    }

  // Check whether the paste region is fully contained inside the
  // largest region or not.
  if ( !largestIORegion.IsInside(pasteIORegion) )
    {
    itkExceptionMacro(
      << "Largest possible region does not fully contain requested paste IO region"
      << "Paste IO region: " << pasteIORegion
      << "Largest possible region: " << largestRegion);
    }

  // Determin the actual number of divisions of the input. This is determined
  // by what the ImageIO can do
  unsigned int numDivisions;

  // this may fail and throw an exception if the configuration is not supported
  numDivisions = m_ImageIO->GetActualNumberOfSplitsForWriting(m_NumberOfStreamDivisions,
                                                              pasteIORegion,
                                                              largestIORegion);

  /**
   * Loop over the number of pieces, execute the upstream pipeline on each
   * piece, and copy the results into the output image.
   */
  unsigned int piece;

  for ( piece = 0;
        piece < numDivisions && !this->GetAbortGenerateData();
        piece++ )
    {
    // get the actual piece to write
    ImageIORegion streamIORegion = m_ImageIO->GetSplitRegionForWriting(piece, numDivisions,
                                                                       pasteIORegion, largestIORegion);

    // Check whether the paste region is fully contained inside the
    // largest region or not.
    if ( !pasteIORegion.IsInside(streamIORegion) )
      {
      itkExceptionMacro(
        << "ImageIO returns streamable region that is not fully contain in paste IO region"
        << "Paste IO region: " << pasteIORegion
        << "Streamable region: " << streamIORegion);
      }

    InputImageRegionType streamRegion;
    ImageIORegionAdaptor< TInputImage::ImageDimension >::
    Convert( streamIORegion, streamRegion, largestRegion.GetIndex() );

    // execute the the upstream pipeline with the requested
    // region for streaming
    nonConstInput->SetRequestedRegion(streamRegion);
    nonConstInput->PropagateRequestedRegion();
    nonConstInput->UpdateOutputData();

    if( piece == 0 )
      {
      // initialize the progress here to mimic the progress behavior of the non
      // streaming filters, where the progress changes only when the other filters
      // are done.
      this->UpdateProgress( 0.0f );
      }

    // check to see if we tried to stream but got the largest possible region
    if ( piece == 0 && streamRegion != largestRegion )
      {
      InputImageRegionType bufferedRegion = input->GetBufferedRegion();
      if ( bufferedRegion == largestRegion )
        {
        // if so, then just write the entire image
        itkDebugMacro("Requested stream region  matches largest region input filter may not support streaming well.");
        itkDebugMacro("Writer is not streaming now!");
        numDivisions = 1;
        streamRegion = largestRegion;
        ImageIORegionAdaptor< TInputImage::ImageDimension >::
        Convert( streamRegion, streamIORegion, largestRegion.GetIndex() );
        }
      }

    m_ImageIO->SetIORegion(streamIORegion);

    // write the data
    this->GenerateData();

    this->UpdateProgress( static_cast<float>( piece + 1 ) / static_cast<float>( numDivisions ) );
    }

  // Notify end event observers
  this->InvokeEvent( EndEvent() );

  // Release upstream data if requested
  this->ReleaseInputs();
}

//---------------------------------------------------------
template< typename TInputImage >
void
ImageFileWriter< TInputImage >
::GenerateData(void)
{
  const InputImageType *input = this->GetInput();
  InputImageRegionType  largestRegion = input->GetLargestPossibleRegion();
  InputImagePointer     cacheImage;

  itkDebugMacro(<< "Writing file: " << m_FileName);

  // now extract the data as a raw buffer pointer
  const void *dataPtr = (const void *)input->GetBufferPointer();

  // check that the image's buffered region is the same as
  // ImageIO is expecting and we requested
  InputImageRegionType ioRegion;
  ImageIORegionAdaptor< TInputImage::ImageDimension >::
  Convert( m_ImageIO->GetIORegion(), ioRegion, largestRegion.GetIndex() );
  InputImageRegionType bufferedRegion = input->GetBufferedRegion();

  // before this test, bad stuff would happened when they don't match
  if ( bufferedRegion != ioRegion )
    {
    if ( m_NumberOfStreamDivisions > 1 || m_UserSpecifiedIORegion )
      {
      itkDebugMacro("Requested stream region does not match generated output");
      itkDebugMacro("input filter may not support streaming well");

      cacheImage = InputImageType::New();
      cacheImage->CopyInformation(input);
      cacheImage->SetBufferedRegion(ioRegion);
      cacheImage->Allocate();

      ImageAlgorithm::Copy( input, cacheImage.GetPointer(), ioRegion, ioRegion );

      dataPtr = (const void *)cacheImage->GetBufferPointer();
      }
    else
      {
      ImageFileWriterException e(__FILE__, __LINE__);
      std::ostringstream       msg;
      msg << "Did not get requested region!" << std::endl;
      msg << "Requested:" << std::endl;
      msg << ioRegion;
      msg << "Actual:" << std::endl;
      msg << bufferedRegion;
      e.SetDescription( msg.str().c_str() );
      e.SetLocation(ITK_LOCATION);
      throw e;
      }
    }

  m_ImageIO->Write(dataPtr);
}

//---------------------------------------------------------
template< typename TInputImage >
void
ImageFileWriter< TInputImage >
::PrintSelf(std::ostream & os, Indent indent) const
{
  Superclass::PrintSelf(os, indent);

  os << indent << "File Name: "
     << ( m_FileName.data() ? m_FileName.data() : "(none)" ) << std::endl;

  os << indent << "Image IO: ";
  if ( m_ImageIO.IsNull() )
    {
    os << "(none)\n";
    }
  else
    {
    os << m_ImageIO << "\n";
    }

  os << indent << "IO Region: " << m_PasteIORegion << "\n";
  os << indent << "Number of Stream Divisions: " << m_NumberOfStreamDivisions << "\n";

  if ( m_UseCompression )
    {
    os << indent << "Compression: On\n";
    }
  else
    {
    os << indent << "Compression: Off\n";
    }

  if ( m_UseInputMetaDataDictionary )
    {
    os << indent << "UseInputMetaDataDictionary: On\n";
    }
  else
    {
    os << indent << "UseInputMetaDataDictionary: Off\n";
    }

  if ( m_FactorySpecifiedImageIO )
    {
    os << indent << "FactorySpecifiedmageIO: On\n";
    }
  else
    {
    os << indent << "FactorySpecifiedmageIO: Off\n";
    }
}
} // end namespace itk

#endif