itkTestingExtractSliceImageFilter.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 itkTestingExtractSliceImageFilter_hxx
#define itkTestingExtractSliceImageFilter_hxx

#include "itkImageRegionIterator.h"
#include "itkObjectFactory.h"
#include "itkTotalProgressReporter.h"

namespace itk
{
namespace Testing
{

template <typename TInputImage, typename TOutputImage>
ExtractSliceImageFilter<TInputImage, TOutputImage>::ExtractSliceImageFilter()
{
  this->DynamicMultiThreadingOn();
  this->ThreaderUpdateProgressOff();
}


template <typename TInputImage, typename TOutputImage>
void
ExtractSliceImageFilter<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 << "DirectionCollaspeStrategy: " << m_DirectionCollaspeStrategy << std::endl;
}


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

  extractImageRegionCopier(destRegion, srcRegion, m_ExtractionRegion);
}


template <typename TInputImage, typename TOutputImage>
void
ExtractSliceImageFilter<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])
    {
      if (nonzeroSizeCount < OutputImageDimension)
      {
        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();
}


template <typename TInputImage, typename TOutputImage>
void
ExtractSliceImageFilter<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
  TOutputImage *      outputPtr = this->GetOutput();
  const TInputImage * 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 == nullptr)
  {
    // pointer could not be cast back down
    itkExceptionMacro("itk::ExtractSliceImageFilter::GenerateOutputInformation "
                      << "cannot cast input to " << typeid(ImageBase<InputImageDimension> *).name());
  }
  // 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[nonZeroCount][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.
  switch (m_DirectionCollaspeStrategy)
  {
    case TestExtractSliceImageFilterCollapseStrategyEnum::DIRECTIONCOLLAPSETOIDENTITY:
    {
      outputDirection.SetIdentity();
    }
    break;
    case TestExtractSliceImageFilterCollapseStrategyEnum::DIRECTIONCOLLAPSETOSUBMATRIX:
    {
      if (vnl_determinant(outputDirection.GetVnlMatrix()) == 0.0)
      {
        itkExceptionMacro("Invalid submatrix extracted for collapsed direction.");
      }
    }
    break;
    case TestExtractSliceImageFilterCollapseStrategyEnum::DIRECTIONCOLLAPSETOGUESS:
    {
      if (vnl_determinant(outputDirection.GetVnlMatrix()) == 0.0)
      {
        outputDirection.SetIdentity();
      }
    }
    break;
    case TestExtractSliceImageFilterCollapseStrategyEnum::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());
}


template <typename TInputImage, typename TOutputImage>
void
ExtractSliceImageFilter<TInputImage, TOutputImage>::DynamicThreadedGenerateData(
  const OutputImageRegionType & outputRegionForThread)
{

  itkDebugMacro("Actually executing");

  // Get the input and output pointers
  const TInputImage * inputPtr = this->GetInput();
  TOutputImage *      outputPtr = this->GetOutput();

  TotalProgressReporter progress(this, outputPtr->GetRequestedRegion().GetNumberOfPixels());

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

  using OutputIterator = ImageRegionIterator<TOutputImage>;
  using InputIterator = ImageRegionConstIterator<TInputImage>;

  OutputIterator outIt(outputPtr, outputRegionForThread);
  InputIterator  inIt(inputPtr, inputRegionForThread);

  // walk the output region, and sample the input image
  while (!outIt.IsAtEnd())
  {
    // copy the input pixel to the output
    outIt.Set(static_cast<OutputImagePixelType>(inIt.Get()));
    ++outIt;
    ++inIt;
    progress.CompletedPixel();
  }
}


template <typename TInputImage, typename TOutputImage>
void
ExtractSliceImageFilter<TInputImage, TOutputImage>::SetInput(const TInputImage * input)
{
  // Process object is not const-correct so the const_cast is required here
  this->ProcessObject::SetNthInput(0, const_cast<TInputImage *>(input));
}


template <typename TInputImage, typename TOutputImage>
const TInputImage *
ExtractSliceImageFilter<TInputImage, TOutputImage>::GetInput() const
{
  return itkDynamicCastInDebugMode<const TInputImage *>(this->GetPrimaryInput());
}

} // end namespace Testing
} // end namespace itk

#endif