mitkItkImageFileReader.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 "mitkItkImageFileReader.h"
#include "mitkConfig.h"
#include "mitkException.h"
#include <mitkLocaleSwitch.h>
#include <mitkProportionalTimeGeometry.h>

#include <itkImage.h>
#include <itkImageFileReader.h>
#include <itksys/Directory.hxx>
#include <itksys/SystemTools.hxx>
//#include <itkImageSeriesReader.h>
#include <itkImageFileReader.h>
#include <itkImageIOFactory.h>
#include <itkImageIORegion.h>
#include <itkMetaDataObject.h>
//#include <itkImageSeriesReader.h>
//#include <itkDICOMImageIO2.h>
//#include <itkDICOMSeriesFileNames.h>
//#include <itkGDCMImageIO.h>
//#include <itkGDCMSeriesFileNames.h>
//#include <itkNumericSeriesFileNames.h>

void mitk::ItkImageFileReader::GenerateData()
{
  mitk::LocaleSwitch localeSwitch("C");
  mitk::Image::Pointer image = this->GetOutput();

  const unsigned int MINDIM = 2;
  const unsigned int MAXDIM = 4;

  MITK_INFO("mitkItkImageFileReader") << "loading " << m_FileName << " via itk::ImageIOFactory... " << std::endl;

  // Check to see if we can read the file given the name or prefix
  if (m_FileName == "")
  {
    mitkThrow() << "Empty filename in mitk::ItkImageFileReader ";
    return;
  }

  itk::ImageIOBase::Pointer imageIO =
    itk::ImageIOFactory::CreateImageIO(m_FileName.c_str(), itk::ImageIOFactory::ReadMode);
  if (imageIO.IsNull())
  {
    // itkWarningMacro( << "File Type not supported!" );
    mitkThrow() << "Could not create itk::ImageIOBase object for filename " << m_FileName;
    return;
  }

  // Got to allocate space for the image. Determine the characteristics of
  // the image.
  imageIO->SetFileName(m_FileName.c_str());
  imageIO->ReadImageInformation();

  unsigned int ndim = imageIO->GetNumberOfDimensions();
  if (ndim < MINDIM || ndim > MAXDIM)
  {
    itkWarningMacro(<< "Sorry, only dimensions 2, 3 and 4 are supported. The given file has " << ndim
                    << " dimensions! Reading as 4D.");
    ndim = MAXDIM;
  }

  itk::ImageIORegion ioRegion(ndim);
  itk::ImageIORegion::SizeType ioSize = ioRegion.GetSize();
  itk::ImageIORegion::IndexType ioStart = ioRegion.GetIndex();

  unsigned int dimensions[MAXDIM];
  dimensions[0] = 0;
  dimensions[1] = 0;
  dimensions[2] = 0;
  dimensions[3] = 0;

  ScalarType spacing[MAXDIM];
  spacing[0] = 1.0f;
  spacing[1] = 1.0f;
  spacing[2] = 1.0f;
  spacing[3] = 1.0f;

  Point3D origin;
  origin.Fill(0);

  unsigned int i;
  for (i = 0; i < ndim; ++i)
  {
    ioStart[i] = 0;
    ioSize[i] = imageIO->GetDimensions(i);
    if (i < MAXDIM)
    {
      dimensions[i] = imageIO->GetDimensions(i);
      spacing[i] = imageIO->GetSpacing(i);
      if (spacing[i] <= 0)
        spacing[i] = 1.0f;
    }
    if (i < 3)
    {
      origin[i] = imageIO->GetOrigin(i);
    }
  }

  ioRegion.SetSize(ioSize);
  ioRegion.SetIndex(ioStart);

  MITK_INFO("mitkItkImageFileReader") << "ioRegion: " << ioRegion << std::endl;
  imageIO->SetIORegion(ioRegion);
  void *buffer = new unsigned char[imageIO->GetImageSizeInBytes()];
  imageIO->Read(buffer);

  image->Initialize(MakePixelType(imageIO), ndim, dimensions);
  image->SetImportChannel(buffer, 0, Image::ManageMemory);

  // access direction of itk::Image and include spacing
  mitk::Matrix3D matrix;
  matrix.SetIdentity();
  unsigned int j, itkDimMax3 = (ndim >= 3 ? 3 : ndim);
  for (i = 0; i < itkDimMax3; ++i)
    for (j = 0; j < itkDimMax3; ++j)
      matrix[i][j] = imageIO->GetDirection(j)[i];

  // re-initialize PlaneGeometry with origin and direction
  PlaneGeometry *planeGeometry = static_cast<PlaneGeometry *>(image->GetSlicedGeometry(0)->GetPlaneGeometry(0));
  planeGeometry->SetOrigin(origin);
  planeGeometry->GetIndexToWorldTransform()->SetMatrix(matrix);

  // re-initialize SlicedGeometry3D
  SlicedGeometry3D *slicedGeometry = image->GetSlicedGeometry(0);
  slicedGeometry->InitializeEvenlySpaced(planeGeometry, image->GetDimension(2));
  slicedGeometry->SetSpacing(spacing);

  MITK_INFO("mitkItkImageFileReader") << slicedGeometry->GetCornerPoint(false, false, false);
  MITK_INFO("mitkItkImageFileReader") << slicedGeometry->GetCornerPoint(true, true, true);

  // re-initialize TimeGeometry
  ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New();
  timeGeometry->Initialize(slicedGeometry, image->GetDimension(3));
  image->SetTimeGeometry(timeGeometry);

  buffer = nullptr;
  MITK_INFO("mitkItkImageFileReader") << "number of image components: " << image->GetPixelType().GetNumberOfComponents()
                                      << std::endl;
  //  mitk::DataNode::Pointer node = this->GetOutput();
  //  node->SetData( image );

  // add level-window property
  // if ( image->GetPixelType().GetNumberOfComponents() == 1 )
  //{
  //  SetDefaultImageProperties( node );
  //}
  MITK_INFO("mitkItkImageFileReader") << "...finished!" << std::endl;
}

bool mitk::ItkImageFileReader::CanReadFile(const std::string filename,
                                           const std::string filePrefix,
                                           const std::string filePattern)
{
  // First check the extension
  if (filename == "")
    return false;

  // check if image is serie
  if (filePattern != "" && filePrefix != "")
    return false;

  itk::ImageIOBase::Pointer imageIO =
    itk::ImageIOFactory::CreateImageIO(filename.c_str(), itk::ImageIOFactory::ReadMode);
  if (imageIO.IsNull())
    return false;

  try
  {
    imageIO->SetFileName(filename.c_str());
    imageIO->ReadImageInformation();
    itk::MetaDataDictionary imgMetaDictionary = imageIO->GetMetaDataDictionary();
    std::vector<std::string> imgMetaKeys = imgMetaDictionary.GetKeys();
    std::vector<std::string>::const_iterator itKey = imgMetaKeys.begin();
    std::string metaString;

    for (; itKey != imgMetaKeys.end(); itKey++)
    {
      itk::ExposeMetaData<std::string>(imgMetaDictionary, *itKey, metaString);
      if (itKey->find("modality") != std::string::npos)
      {
        if (metaString.find("DWMRI") != std::string::npos)
        {
          return false; // DiffusionImageReader should handle this
        }
      }
    }
  }
  catch (...)
  {
    MITK_INFO("mitkItkImageFileReader") << "Could not read ImageInformation ";
  }

  return true;
}

mitk::ItkImageFileReader::ItkImageFileReader() : m_FileName(""), m_FilePrefix(""), m_FilePattern("")
{
}

mitk::ItkImageFileReader::~ItkImageFileReader()
{
}