itkExtractImageFilter.hxx

/*=========================================================================
 *
 *  Copyright NumFOCUS
 *
 *  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
 *
 *         https://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 itkExtractImageFilter_hxx
#define itkExtractImageFilter_hxx

#include "itkImageAlgorithm.h"
#include "itkObjectFactory.h"
#include "itkProgressReporter.h"

namespace itk
{
/**
 *
 */
template <typename TInputImage, typename TOutputImage>
ExtractImageFilter<TInputImage, TOutputImage>::ExtractImageFilter()
{
  Superclass::InPlaceOff();
  this->DynamicMultiThreadingOn();
}

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

  os << indent << "ExtractionRegion: " << m_ExtractionRegion << std::endl;
  os << indent << "OutputImageRegion: " << m_OutputImageRegion << std::endl;
  os << indent << "DirectionCollapseStrategy: " << m_DirectionCollapseStrategy << std::endl;
}

template <typename TInputImage, typename TOutputImage>
void
ExtractImageFilter<TInputImage, TOutputImage>::CallCopyOutputRegionToInputRegion(
  InputImageRegionType &        destRegion,
  const OutputImageRegionType & srcRegion)
{
  ExtractImageFilterRegionCopierType extractImageRegionCopier;

  extractImageRegionCopier(destRegion, srcRegion, m_ExtractionRegion);
}

template <typename TInputImage, typename TOutputImage>
void
ExtractImageFilter<TInputImage, TOutputImage>::SetExtractionRegion(InputImageRegionType extractRegion)
{
  static_assert(InputImageDimension >= OutputImageDimension,
                "InputImageDimension must be greater than OutputImageDimension");
  m_ExtractionRegion = extractRegion;

  unsigned int        nonzeroSizeCount = 0;
  InputImageSizeType  inputSize = extractRegion.GetSize();
  OutputImageSizeType outputSize;
  outputSize.Fill(0);
  OutputImageIndexType outputIndex;
  outputIndex.Fill(0);

  /**
   * check to see if the number of non-zero entries in the extraction region
   * matches the number of dimensions in the output image.
   */
  for (unsigned int i = 0; i < InputImageDimension; ++i)
  {
    if (inputSize[i])
    {
      outputSize[nonzeroSizeCount] = inputSize[i];
      outputIndex[nonzeroSizeCount] = extractRegion.GetIndex()[i];
      ++nonzeroSizeCount;
    }
  }

  if (nonzeroSizeCount != OutputImageDimension)
  {
    itkExceptionMacro("The number of zero sized dimensions in the input image Extraction Region\n"
                      << "is not consistent with the dimensionality of the output image.\n"
                      << "Expected the extraction region size (" << extractRegion.GetSize() << ") to contain "
                      << InputImageDimension - OutputImageDimension << " zero sized dimensions to collapse.");
  }

  m_OutputImageRegion.SetSize(outputSize);
  m_OutputImageRegion.SetIndex(outputIndex);
  this->Modified();
}

/**
 * ExtractImageFilter can produce an image which is a different resolution
 * than its input image.  As such, ExtractImageFilter needs to provide an
 * implementation for GenerateOutputInformation() in order to inform
 * the pipeline execution model.  The original documentation of this
 * method is below.
 *
 * \sa ProcessObject::GenerateOutputInformaton()
 */
template <typename TInputImage, typename TOutputImage>
void
ExtractImageFilter<TInputImage, TOutputImage>::GenerateOutputInformation()
{
  // do not call the superclass' implementation of this method since
  // this filter allows the input and the output to be of different dimensions

  // get pointers to the input and output
  typename Superclass::OutputImagePointer     outputPtr = this->GetOutput();
  typename Superclass::InputImageConstPointer inputPtr = this->GetInput();

  if (!outputPtr || !inputPtr)
  {
    return;
  }

  // Set the output image size to the same value as the extraction region.
  outputPtr->SetLargestPossibleRegion(m_OutputImageRegion);

  // Set the output spacing and origin
  const ImageBase<InputImageDimension> * phyData;

  phyData = dynamic_cast<const ImageBase<InputImageDimension> *>(this->GetInput());

  if (phyData)
  {
    // Copy what we can from the image from spacing and origin of the input
    // This logic needs to be augmented with logic that select which
    // dimensions to copy

    const typename InputImageType::SpacingType &   inputSpacing = inputPtr->GetSpacing();
    const typename InputImageType::DirectionType & inputDirection = inputPtr->GetDirection();
    const typename InputImageType::PointType &     inputOrigin = inputPtr->GetOrigin();

    typename OutputImageType::SpacingType   outputSpacing;
    typename OutputImageType::DirectionType outputDirection;
    typename OutputImageType::PointType     outputOrigin;
    outputOrigin.Fill(0.0);

    if (static_cast<unsigned int>(OutputImageDimension) > static_cast<unsigned int>(InputImageDimension))
    {
      // copy the input to the output and fill the rest of the
      // output with zeros.
      for (unsigned int i = 0; i < InputImageDimension; ++i)
      {
        outputSpacing[i] = inputSpacing[i];
        outputOrigin[i] = inputOrigin[i];
        for (unsigned int dim = 0; dim < InputImageDimension; ++dim)
        {
          outputDirection[i][dim] = inputDirection[i][dim];
        }
      }
      for (unsigned int i = InputImageDimension; i < OutputImageDimension; ++i)
      {
        outputSpacing[i] = 1.0;
        outputOrigin[i] = 0.0;
        for (unsigned int dim = 0; dim < InputImageDimension; ++dim)
        {
          outputDirection[i][dim] = 0.0;
        }
        outputDirection[i][i] = 1.0;
      }
    }
    else
    {
      // copy the non-collapsed part of the input spacing and origin to the
      // output
      outputDirection.SetIdentity();
      int nonZeroCount = 0;
      for (unsigned int i = 0; i < InputImageDimension; ++i)
      {
        if (m_ExtractionRegion.GetSize()[i])
        {
          outputSpacing[nonZeroCount] = inputSpacing[i];
          outputOrigin[nonZeroCount] = inputOrigin[i];
          int nonZeroCount2 = 0;
          for (unsigned int dim = 0; dim < InputImageDimension; ++dim)
          {
            if (m_ExtractionRegion.GetSize()[dim])
            {
              outputDirection[nonZeroCount][nonZeroCount2] = inputDirection[i][dim];
              ++nonZeroCount2;
            }
          }
          ++nonZeroCount;
        }
      }
    }
    // if the filter changes from a higher to a lower dimension, or
    // if, after rebuilding the direction cosines, there's a zero
    // length cosine vector, reset the directions to identity
    // or throw an exception, depending on the collapse strategy.
    if (static_cast<int>(InputImageDimension) != static_cast<int>(OutputImageDimension))
    {
      switch (m_DirectionCollapseStrategy)
      {
        case DirectionCollapseStrategyEnum::DIRECTIONCOLLAPSETOIDENTITY:
        {
          outputDirection.SetIdentity();
        }
        break;
        case DirectionCollapseStrategyEnum::DIRECTIONCOLLAPSETOSUBMATRIX:
        {
          if (vnl_determinant(outputDirection.GetVnlMatrix()) == 0.0)
          {
            itkExceptionMacro("Invalid submatrix extracted for collapsed direction.");
          }
        }
        break;
        case DirectionCollapseStrategyEnum::DIRECTIONCOLLAPSETOGUESS:
        {
          if (vnl_determinant(outputDirection.GetVnlMatrix()) == 0.0)
          {
            outputDirection.SetIdentity();
          }
        }
        break;
        case DirectionCollapseStrategyEnum::DIRECTIONCOLLAPSETOUNKOWN:
        default:
        {
          itkExceptionMacro(
            << "It is required that the strategy for collapsing the direction matrix be explicitly specified. "
            << "Set with either myfilter->SetDirectionCollapseToIdentity() or "
               "myfilter->SetDirectionCollapseToSubmatrix() "
            << typeid(ImageBase<InputImageDimension> *).name());
        }
      }
    }
    // set the spacing and origin
    outputPtr->SetSpacing(outputSpacing);
    outputPtr->SetDirection(outputDirection);
    outputPtr->SetOrigin(outputOrigin);
    outputPtr->SetNumberOfComponentsPerPixel(inputPtr->GetNumberOfComponentsPerPixel());
  }
  else
  {
    // pointer could not be cast back down
    itkExceptionMacro("itk::ExtractImageFilter::GenerateOutputInformation "
                      << "cannot cast input to " << typeid(ImageBase<InputImageDimension> *).name());
  }
}

template <typename TInputImage, typename TOutputImage>
void
ExtractImageFilter<TInputImage, TOutputImage>::GenerateData()
{

  // InPlace::AllocateOutputs set the running in place ivar.
  // This method will be called again, by GenerateData, but there is
  // no harm done.
  this->AllocateOutputs();

  // The input matched the output, nothing to do.
  if (this->GetRunningInPlace())
  {
    OutputImageType * outputPtr = this->GetOutput();

    // the in-place grafting copies the meta data, this needs to be
    // set back.
    outputPtr->SetLargestPossibleRegion(m_OutputImageRegion);

    this->UpdateProgress(1.0);
    return;
  }

  this->Superclass::GenerateData();
}

/**
 * ExtractImageFilter can be implemented as a multithreaded filter.
 * Therefore, this implementation provides a DynamicThreadedGenerateData()
 * routine which is called for each processing thread. The output
 * image data is allocated automatically by the superclass prior to
 * calling DynamicThreadedGenerateData().  DynamicThreadedGenerateData can only
 * write to the portion of the output image specified by the
 * parameter "outputRegionForThread"
 *
 * \sa ImageToImageFilter::ThreadedGenerateData(),
 *     ImageToImageFilter::GenerateData()
 */
template <typename TInputImage, typename TOutputImage>
void
ExtractImageFilter<TInputImage, TOutputImage>::DynamicThreadedGenerateData(
  const OutputImageRegionType & outputRegionForThread)
{
  itkDebugMacro("Actually executing");

  const InputImageType * inputPtr = this->GetInput();
  OutputImageType *      outputPtr = this->GetOutput();


  // Define the portion of the input to walk for this thread
  InputImageRegionType inputRegionForThread;
  this->CallCopyOutputRegionToInputRegion(inputRegionForThread, outputRegionForThread);

  // copy the input pixel to the output
  ImageAlgorithm::Copy(inputPtr, outputPtr, inputRegionForThread, outputRegionForThread);
}

} // end namespace itk

#endif