LegacyIO/mitkRawImageFileReader.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 "mitkRawImageFileReader.h"
#include "mitkImageCast.h"

#include <itkImage.h>
#include <itkImageFileReader.h>
#include <itkRawImageIO.h>

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

mitk::RawImageFileReader::~RawImageFileReader()
{
}

void mitk::RawImageFileReader::SetDimensions(unsigned int i, unsigned int dim)
{
  if (i > 2)
    return;

  this->Modified(); // TODO: this order (first modified, then set the variable) is intended??
  m_Dimensions[i] = dim;
}

unsigned int mitk::RawImageFileReader::GetDimensions(unsigned int i) const
{
  if (i > 2)
    return 0;

  return m_Dimensions[i];
}

bool mitk::RawImageFileReader::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;

  return true;
}

void mitk::RawImageFileReader::GenerateData()
{
  mitk::Image::Pointer output = this->GetOutput();

  if (this->GetOutput() == nullptr)
  {
    MITK_INFO << "Error" << std::endl;
  }

  // Check to see if we can read the file given the name or prefix
  if (m_FileName == "")
  {
    itkWarningMacro(<< "File Type not supported!");
    return;
  }

  // check file dimensionality and pixel type and perform reading according to it
  if (m_Dimensionality == 2)
  {
    if (m_PixelType == SCHAR)
      TypedGenerateData<signed char, 2>();
    else if (m_PixelType == UCHAR)
      TypedGenerateData<unsigned char, 2>();
    else if (m_PixelType == SSHORT)
      TypedGenerateData<signed short int, 2>();
    else if (m_PixelType == USHORT)
      TypedGenerateData<unsigned short int, 2>();
    else if (m_PixelType == UINT)
      TypedGenerateData<unsigned int, 2>();
    else if (m_PixelType == SINT)
      TypedGenerateData<signed int, 2>();
    else if (m_PixelType == FLOAT)
      TypedGenerateData<float, 2>();
    else if (m_PixelType == DOUBLE)
      TypedGenerateData<double, 2>();
    else
    {
      MITK_INFO << "Error while reading raw file: Dimensionality or pixel type not supported or not properly set"
                << std::endl;
      return;
    }
  }
  else if (m_Dimensionality == 3)
  {
    if (m_PixelType == SCHAR)
      TypedGenerateData<signed char, 3>();
    else if (m_PixelType == UCHAR)
      TypedGenerateData<unsigned char, 3>();
    else if (m_PixelType == SSHORT)
      TypedGenerateData<signed short int, 3>();
    else if (m_PixelType == USHORT)
      TypedGenerateData<unsigned short int, 3>();
    else if (m_PixelType == UINT)
      TypedGenerateData<unsigned int, 3>();
    else if (m_PixelType == SINT)
      TypedGenerateData<signed int, 3>();
    else if (m_PixelType == FLOAT)
      TypedGenerateData<float, 3>();
    else if (m_PixelType == DOUBLE)
      TypedGenerateData<double, 3>();
    else
    {
      MITK_INFO << "Error while reading raw file: Dimensionality or pixel type not supported or not properly set"
                << std::endl;
      return;
    }
  }
  else
  {
    MITK_INFO << "Error while reading raw file: Dimensionality not supported" << std::endl;
    return;
  }

  MITK_INFO << "...reading raw finished!" << std::endl;
}

template <typename TPixel, unsigned int VImageDimensions>
void mitk::RawImageFileReader::TypedGenerateData()
{
  mitk::Image::Pointer output = this->GetOutput();

  if (this->GetOutput() == nullptr)
  {
    MITK_INFO << "Error" << std::endl;
  }

  MITK_INFO << "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 == "")
  {
    itkWarningMacro(<< "File Type not supported!");
    return;
  }

  typedef itk::Image<TPixel, VImageDimensions> ImageType;
  typedef itk::ImageFileReader<ImageType> ReaderType;
  typedef itk::RawImageIO<TPixel, VImageDimensions> IOType;

  typename ReaderType::Pointer reader = ReaderType::New();
  typename IOType::Pointer io = IOType::New();

  io->SetFileDimensionality(VImageDimensions);

  for (unsigned short int dim = 0; dim < VImageDimensions; ++dim)
  {
    io->SetDimensions(dim, m_Dimensions[dim]);
  }

  if (m_Endianity == LITTLE)
  {
    io->SetByteOrderToLittleEndian();
  }
  else if (m_Endianity == BIG)
  {
    io->SetByteOrderToBigEndian();
  }
  else
  {
    MITK_INFO << "Warning: endianity not properly set. Resulting image might be incorrect";
  }

  reader->SetImageIO(io);
  reader->SetFileName(m_FileName.c_str());

  try
  {
    reader->Update();
  }
  catch (itk::ExceptionObject &err)
  {
    MITK_ERROR << "An error occurred during the raw image reading process: ";
    MITK_INFO << err << std::endl;
  }

  mitk::Image::Pointer image = mitk::Image::New();
  mitk::CastToMitkImage(reader->GetOutput(), image);
  output->Initialize(image);
  output->SetVolume(reader->GetOutput()->GetBufferPointer());
}