mitkImageWriter.cpp

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

The Medical Imaging Interaction Toolkit (MITK)

Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.

Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.

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

#include "mitkImageWriter.h"

#include "mitkImage.h"
#include "mitkImageAccessByItk.h"
#include "mitkImageReadAccessor.h"
#include "mitkImageTimeSelector.h"
#include "mitkItkPictureWrite.h"
#include <mitkLocaleSwitch.h>

#include <itkImageIOBase.h>
#include <itkImageIOFactory.h>

mitk::ImageWriter::ImageWriter() : m_UseCompression(true)
{
  this->SetNumberOfRequiredInputs(1);
  m_MimeType = "";
  SetDefaultExtension();
}

mitk::ImageWriter::~ImageWriter()
{
}

void mitk::ImageWriter::SetFileName(const char *fileName)
{
  if (fileName && (fileName == this->m_FileName))
  {
    return;
  }
  if (fileName)
  {
    this->m_FileName = fileName;
    this->m_FileNameWithoutExtension = this->m_FileName;
    this->m_Extension.clear();
    std::size_t pos = this->m_FileName.find_last_of("/\\");
    if (pos != std::string::npos)
    {
      std::size_t ppos = this->m_FileName.find_first_of('.', pos);
      if (ppos != std::string::npos)
      {
        this->m_FileNameWithoutExtension = this->m_FileName.substr(0, ppos);
        this->m_Extension = this->m_FileName.substr(ppos);
      }
    }
  }
  else
  {
    this->m_FileName.clear();
    this->m_FileNameWithoutExtension.clear();
    this->m_Extension.clear();
  }
  this->Modified();
}

void mitk::ImageWriter::SetFileName(const std::string &fileName)
{
  this->SetFileName(fileName.c_str());
}

void mitk::ImageWriter::SetExtension(const char *extension)
{
  if (extension && (extension == this->m_Extension))
  {
    return;
  }
  if (extension)
  {
    this->m_Extension = extension;
    this->m_FileName = this->m_FileNameWithoutExtension + this->m_Extension;
  }
  else
  {
    this->m_Extension.clear();
    this->m_FileName = this->m_FileNameWithoutExtension;
  }
  this->Modified();
}

void mitk::ImageWriter::SetExtension(const std::string &extension)
{
  this->SetFileName(extension.c_str());
}

void mitk::ImageWriter::SetDefaultExtension()
{
  this->m_Extension = ".mhd";
  this->m_FileName = this->m_FileNameWithoutExtension + this->m_Extension;
  this->Modified();
}

#include <vtkConfigure.h>
#include <vtkImageData.h>
#include <vtkXMLImageDataWriter.h>
static void writeVti(const char *filename, mitk::Image *image, int t = 0)
{
  vtkXMLImageDataWriter *vtkwriter = vtkXMLImageDataWriter::New();
  vtkwriter->SetFileName(filename);
  vtkwriter->SetInputData(image->GetVtkImageData(t));
  vtkwriter->Write();
  vtkwriter->Delete();
}

#include <itkRGBAPixel.h>

void mitk::ImageWriter::WriteByITK(mitk::Image *image, const std::string &fileName)
{
  MITK_INFO << "Writing image: " << fileName << std::endl;
  // Pictures and picture series like .png are written via a different mechanism then volume images.
  // So, they are still multiplexed and thus not support vector images.
  if (fileName.find(".png") != std::string::npos || fileName.find(".tif") != std::string::npos ||
      fileName.find(".jpg") != std::string::npos || fileName.find(".bmp") != std::string::npos)
  {
    try
    {
      // switch processing of single/multi-component images
      if (image->GetPixelType(0).GetNumberOfComponents() == 1)
      {
        AccessByItk_1(image, _mitkItkPictureWrite, fileName);
      }
      else
      {
        AccessFixedPixelTypeByItk_1(image,
                                    _mitkItkPictureWriteComposite,
                                    MITK_ACCESSBYITK_PIXEL_TYPES_SEQ MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES_SEQ,
                                    fileName);
      }
    }
    catch (itk::ExceptionObject &e)
    {
      std::cerr << "Caught " << e.what() << std::endl;
    }
    catch (std::exception &e)
    {
      std::cerr << "Caught std::exception " << e.what() << std::endl;
    }

    return;
  }

  // Implementation of writer using itkImageIO directly. This skips the use
  // of templated itkImageFileWriter, which saves the multiplexing on MITK side.

  unsigned int dimension = image->GetDimension();
  unsigned int *dimensions = image->GetDimensions();
  mitk::PixelType pixelType = image->GetPixelType();
  mitk::Vector3D mitkSpacing = image->GetGeometry()->GetSpacing();
  mitk::Point3D mitkOrigin = image->GetGeometry()->GetOrigin();

  // Due to templating in itk, we are forced to save a 4D spacing and 4D Origin, though they are not supported in MITK
  itk::Vector<double, 4u> spacing4D;
  spacing4D[0] = mitkSpacing[0];
  spacing4D[1] = mitkSpacing[1];
  spacing4D[2] = mitkSpacing[2];
  spacing4D[3] = 1; // There is no support for a 4D spacing. However, we should have an valid value here

  itk::Vector<double, 4u> origin4D;
  origin4D[0] = mitkOrigin[0];
  origin4D[1] = mitkOrigin[1];
  origin4D[2] = mitkOrigin[2];
  origin4D[3] = 0; // There is no support for a 4D origin. However, we should have an valid value here

  itk::ImageIOBase::Pointer imageIO =
    itk::ImageIOFactory::CreateImageIO(fileName.c_str(), itk::ImageIOFactory::WriteMode);

  if (imageIO.IsNull())
  {
    itkExceptionMacro(<< "Error: Could not create itkImageIO via factory for file " << fileName);
  }

  // Set the necessary information for imageIO
  imageIO->SetNumberOfDimensions(dimension);
  imageIO->SetPixelType(pixelType.GetPixelType());
  imageIO->SetComponentType(pixelType.GetComponentType() < PixelComponentUserType ?
                              static_cast<itk::ImageIOBase::IOComponentType>(pixelType.GetComponentType()) :
                              itk::ImageIOBase::UNKNOWNCOMPONENTTYPE);
  imageIO->SetNumberOfComponents(pixelType.GetNumberOfComponents());

  itk::ImageIORegion ioRegion(dimension);

  for (unsigned int i = 0; i < dimension; i++)
  {
    imageIO->SetDimensions(i, dimensions[i]);
    imageIO->SetSpacing(i, spacing4D[i]);
    imageIO->SetOrigin(i, origin4D[i]);

    mitk::Vector3D mitkDirection;
    mitkDirection.SetVnlVector(
      image->GetGeometry()->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(i));
    itk::Vector<double, 4u> direction4D;
    direction4D[0] = mitkDirection[0];
    direction4D[1] = mitkDirection[1];
    direction4D[2] = mitkDirection[2];

    // MITK only supports a 3x3 direction matrix. Due to templating in itk, however, we must
    // save a 4x4 matrix for 4D images. in this case, add an homogneous component to the matrix.
    if (i == 3)
      direction4D[3] = 1; // homogenous component
    else
      direction4D[3] = 0;

    vnl_vector<double> axisDirection(dimension);
    for (unsigned int j = 0; j < dimension; j++)
    {
      axisDirection[j] = direction4D[j] / spacing4D[i];
    }
    imageIO->SetDirection(i, axisDirection);

    ioRegion.SetSize(i, image->GetLargestPossibleRegion().GetSize(i));
    ioRegion.SetIndex(i, image->GetLargestPossibleRegion().GetIndex(i));
  }

  // use compression if available
  imageIO->SetUseCompression(m_UseCompression);

  imageIO->SetIORegion(ioRegion);
  imageIO->SetFileName(fileName);

  ImageReadAccessor imageAccess(image);
  imageIO->Write(imageAccess.GetData());
}

void mitk::ImageWriter::GenerateData()
{
  mitk::LocaleSwitch localeSwitch("C");

  if (m_FileName == "")
  {
    itkWarningMacro(<< "Sorry, filename has not been set!");
    return;
  }

  FILE *tempFile = fopen(m_FileName.c_str(), "w");
  if (tempFile == nullptr)
  {
    itkExceptionMacro(<< "File location not writeable");
    return;
  }
  fclose(tempFile);
  remove(m_FileName.c_str());

  // Creating clone of input image, since i might change the geometry
  mitk::Image::Pointer input = this->GetInput()->Clone();

  // Check if geometry information will be lost
  if (input->GetDimension() == 2)
  {
    if (!input->GetGeometry()->Is2DConvertable())
    {
      MITK_WARN << "Saving a 2D image with 3D geometry information. Geometry information will be lost! You might "
                   "consider using Convert2Dto3DImageFilter before saving.";

      // set matrix to identity
      mitk::AffineTransform3D::Pointer affTrans = mitk::AffineTransform3D::New();
      affTrans->SetIdentity();
      mitk::Vector3D spacing = input->GetGeometry()->GetSpacing();
      mitk::Point3D origin = input->GetGeometry()->GetOrigin();
      input->GetGeometry()->SetIndexToWorldTransform(affTrans);
      input->GetGeometry()->SetSpacing(spacing);
      input->GetGeometry()->SetOrigin(origin);
    }
  }

  bool vti = (m_Extension.find(".vti") != std::string::npos);

  // If the extension is NOT .pic and NOT .nrrd and NOT .nii and NOT .nii.gz the following block is entered
  if (m_Extension.find(".pic") == std::string::npos && m_Extension.find(".nrrd") == std::string::npos &&
      m_Extension.find(".nii") == std::string::npos && m_Extension.find(".nii.gz") == std::string::npos)
  {
    if (input->GetDimension() > 3)
    {
      int t, timesteps;

      timesteps = input->GetDimension(3);
      ImageTimeSelector::Pointer timeSelector = ImageTimeSelector::New();
      timeSelector->SetInput(input);
      mitk::Image::Pointer image = timeSelector->GetOutput();
      for (t = 0; t < timesteps; ++t)
      {
        std::ostringstream filename;
        timeSelector->SetTimeNr(t);
        timeSelector->Update();
        if (input->GetTimeGeometry()->IsValidTimeStep(t))
        {
          const mitk::TimeBounds &timebounds = input->GetTimeGeometry()->GetTimeBounds(t);
          filename << m_FileNameWithoutExtension << "_S" << std::setprecision(0) << timebounds[0] << "_E"
                   << std::setprecision(0) << timebounds[1] << "_T" << t << m_Extension;
        }
        else
        {
          itkWarningMacro(<< "Error on write: TimeGeometry invalid of image " << filename.str() << ".");
          filename << m_FileNameWithoutExtension << "_T" << t << m_Extension;
        }
        if (vti)
        {
          writeVti(filename.str().c_str(), input, t);
        }
        else
        {
          WriteByITK(image, filename.str());
        }
      }
    }
    else if (vti)
    {
      writeVti(m_FileName.c_str(), input);
    }
    else
    {
      WriteByITK(input, m_FileName);
    }
  }
  else
  {
    // use the PicFileWriter for the .pic data type
    if (m_Extension.find(".pic") != std::string::npos)
    {
         /*    PicFileWriter::Pointer picWriter = PicFileWriter::New();
         size_t found;
         found = m_FileName.find( m_Extension ); // !!! HAS to be at the very end of the filename (not somewhere in the middle)
         if( m_FileName.length() > 3 && found != m_FileName.length() - 4 )
         {
         //if Extension not in Filename
         std::ostringstream filename;
         filename <<  m_FileName.c_str() << m_Extension;
         picWriter->SetFileName( filename.str().c_str() );
         }
         else
         {
         picWriter->SetFileName( m_FileName.c_str() );
         }
         picWriter->SetInputImage( input );
         picWriter->Write();
         */    }

         // use the ITK .nrrd Image writer
         if (m_Extension.find(".nrrd") != std::string::npos || m_Extension.find(".nii") != std::string::npos ||
             m_Extension.find(".nii.gz") != std::string::npos)
         {
           WriteByITK(input, this->m_FileName);
         }
  }
  m_MimeType = "application/MITK.Pic";
}

bool mitk::ImageWriter::CanWriteDataType(DataNode *input)
{
  if (input)
  {
    return this->CanWriteBaseDataType(input->GetData());
  }
  return false;
}

void mitk::ImageWriter::SetInput(DataNode *input)
{
  if (input && CanWriteDataType(input))
    this->ProcessObject::SetNthInput(0, dynamic_cast<mitk::Image *>(input->GetData()));
}

std::string mitk::ImageWriter::GetWritenMIMEType()
{
  return m_MimeType;
}

std::vector<std::string> mitk::ImageWriter::GetPossibleFileExtensions()
{
  std::vector<std::string> possibleFileExtensions;
  possibleFileExtensions.push_back(".pic");
  possibleFileExtensions.push_back(".pic.gz");
  possibleFileExtensions.push_back(".bmp");
  possibleFileExtensions.push_back(".dcm");
  possibleFileExtensions.push_back(".DCM");
  possibleFileExtensions.push_back(".dicom");
  possibleFileExtensions.push_back(".DICOM");
  possibleFileExtensions.push_back(".gipl");
  possibleFileExtensions.push_back(".gipl.gz");
  possibleFileExtensions.push_back(".mha");
  possibleFileExtensions.push_back(".nii");
  possibleFileExtensions.push_back(".nii.gz");
  possibleFileExtensions.push_back(".nrrd");
  possibleFileExtensions.push_back(".nhdr");
  possibleFileExtensions.push_back(".png");
  possibleFileExtensions.push_back(".PNG");
  possibleFileExtensions.push_back(".spr");
  possibleFileExtensions.push_back(".mhd");
  possibleFileExtensions.push_back(".vtk");
  possibleFileExtensions.push_back(".vti");
  possibleFileExtensions.push_back(".hdr");
  possibleFileExtensions.push_back(".img");
  possibleFileExtensions.push_back(".img.gz");
  possibleFileExtensions.push_back(".png");
  possibleFileExtensions.push_back(".tif");
  possibleFileExtensions.push_back(".jpg");
  return possibleFileExtensions;
}

std::string mitk::ImageWriter::GetSupportedBaseData() const
{
  return Image::GetStaticNameOfClass();
}

std::string mitk::ImageWriter::GetFileExtension()
{
  return m_Extension;
}

void mitk::ImageWriter::SetInput(mitk::Image *image)
{
  this->ProcessObject::SetNthInput(0, image);
}

const mitk::Image *mitk::ImageWriter::GetInput()
{
  if (this->GetNumberOfInputs() < 1)
  {
    return nullptr;
  }
  else
  {
    return static_cast<const mitk::Image *>(this->ProcessObject::GetInput(0));
  }
}

const char *mitk::ImageWriter::GetDefaultFilename()
{
  return "Image.nrrd";
}

const char *mitk::ImageWriter::GetFileDialogPattern()
{
  return "Nearly Raw Raster Data (*.nrrd);;"
         "NIfTI format (*.nii *.nii.gz);;"
         "VTK Image Data Files (*.vti);;"
         "NRRD with detached header (*.nhdr);;"
         "Analyze Format (*.hdr);;"
         "MetaImage (*.mhd);;"
         "Sets of 2D slices (*.png *.tiff *.jpg *.jpeg *.bmp);;"
         "DICOM (*.dcm *.DCM *.dicom *.DICOM);;"
         "UMDS GIPL Format Files (*.gipl *.gipl.gz)";
}

const char *mitk::ImageWriter::GetDefaultExtension()
{
  return ".nrrd";
}

bool mitk::ImageWriter::CanWriteBaseDataType(BaseData::Pointer data)
{
  return dynamic_cast<mitk::Image *>(data.GetPointer());
}

void mitk::ImageWriter::DoWrite(BaseData::Pointer data)
{
  if (this->CanWriteBaseDataType(data))
  {
    this->SetInput(dynamic_cast<mitk::Image *>(data.GetPointer()));
    this->Update();
  }
}

void mitk::ImageWriter::SetUseCompression(bool useCompression)
{
  m_UseCompression = useCompression;
}