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/*=========================================================================
*
* 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 itkJoinSeriesImageFilter_hxx
#define itkJoinSeriesImageFilter_hxx
#include "itkProgressReporter.h"
#include "itkImageAlgorithm.h"
#include "itkTotalProgressReporter.h"
namespace itk
{
template <typename TInputImage, typename TOutputImage>
JoinSeriesImageFilter<TInputImage, TOutputImage>::JoinSeriesImageFilter()
{
this->DynamicMultiThreadingOn();
this->ThreaderUpdateProgressOff();
}
template <typename TInputImage, typename TOutputImage>
void
JoinSeriesImageFilter<TInputImage, TOutputImage>::VerifyInputInformation() ITKv5_CONST
{
Superclass::VerifyInputInformation();
// Verify that all input have the same number of components
typename InputImageType::ConstPointer image = this->GetInput();
if (image.IsNull())
{
itkExceptionMacro("Input not set as expected!");
}
const unsigned int numComponents = image->GetNumberOfComponentsPerPixel();
typename Superclass::DataObjectPointerArraySizeType idx = 1;
for (; idx < this->GetNumberOfIndexedInputs(); ++idx)
{
image = this->GetInput(idx);
// If the input was not set it could still be null
if (image.IsNull())
{
// An invalid requested region exception will be generated later.
continue;
}
if (numComponents != image->GetNumberOfComponentsPerPixel())
{
itkExceptionMacro("Primary input has " << numComponents << " numberOfComponents "
<< "but input " << idx << " has " << image->GetNumberOfComponentsPerPixel()
<< '!');
}
}
}
template <typename TInputImage, typename TOutputImage>
void
JoinSeriesImageFilter<TInputImage, TOutputImage>::GenerateOutputInformation()
{
// Do not call the superclass' implementation of this method since
// this filter allows the input 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 largest possible region. Use a RegionCopier
// so that the input and output images can be different dimensions.
OutputImageRegionType outputLargestPossibleRegion;
this->CallCopyInputRegionToOutputRegion(outputLargestPossibleRegion, inputPtr->GetLargestPossibleRegion());
// for the new dimension, assuming the index has been set 0.
outputLargestPossibleRegion.SetSize(static_cast<unsigned int>(InputImageDimension),
static_cast<SizeValueType>(this->GetNumberOfIndexedInputs()));
outputPtr->SetLargestPossibleRegion(outputLargestPossibleRegion);
// 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
unsigned int ii;
const typename InputImageType::SpacingType & inputSpacing = inputPtr->GetSpacing();
const typename InputImageType::PointType & inputOrigin = inputPtr->GetOrigin();
typename OutputImageType::SpacingType outputSpacing;
typename OutputImageType::PointType outputOrigin;
// Copy the input to the output and fill the rest of the
// output with zeros.
for (ii = 0; ii < InputImageDimension; ++ii)
{
outputSpacing[ii] = inputSpacing[ii];
outputOrigin[ii] = inputOrigin[ii];
}
for (; ii < OutputImageDimension; ++ii)
{
outputSpacing[ii] = 1.0;
outputOrigin[ii] = 0.0;
}
// For the new dimension
outputSpacing[InputImageDimension] = this->GetSpacing();
outputOrigin[InputImageDimension] = this->GetOrigin();
// Set the spacing and origin
outputPtr->SetSpacing(outputSpacing);
outputPtr->SetOrigin(outputOrigin);
//
// Copy the direction cosines from the input to the output.
// On join, the output dim is always >= input dim
using InputDirectionType = typename InputImageType::DirectionType;
using OutputDirectionType = typename OutputImageType::DirectionType;
InputDirectionType inputDir = inputPtr->GetDirection();
unsigned int inputdim = InputImageType::GetImageDimension();
unsigned int outputdim = OutputImageType::GetImageDimension();
OutputDirectionType outputDir = outputPtr->GetDirection();
for (unsigned int i = 0; i < outputdim; ++i)
{
for (unsigned int j = 0; j < outputdim; ++j)
{
if (j < inputdim && i < inputdim)
{
outputDir[i][j] = inputDir[i][j];
}
else
{
outputDir[i][j] = i == j ? 1.0 : 0.0;
}
}
}
outputPtr->SetDirection(outputDir);
}
else
{
// Pointer could not be cast back down
itkExceptionMacro("itk::JoinSeriesImageFilter::GenerateOutputInformation "
<< "cannot cast input to " << typeid(ImageBase<InputImageDimension> *).name());
}
// Support VectorImages by setting number of components on output.
const unsigned int numComponents = inputPtr->GetNumberOfComponentsPerPixel();
if (numComponents != outputPtr->GetNumberOfComponentsPerPixel())
{
outputPtr->SetNumberOfComponentsPerPixel(numComponents);
}
}
template <typename TInputImage, typename TOutputImage>
void
JoinSeriesImageFilter<TInputImage, TOutputImage>::GenerateInputRequestedRegion()
{
Superclass::GenerateInputRequestedRegion();
if (!this->GetOutput())
{
return;
}
OutputImageRegionType outputRegion = this->GetOutput()->GetRequestedRegion();
IndexValueType begin = outputRegion.GetIndex(InputImageDimension);
IndexValueType end = begin + outputRegion.GetSize(InputImageDimension);
for (IndexValueType idx = 0; idx < this->GetNumberOfIndexedInputs(); ++idx)
{
InputImagePointer inputPtr = const_cast<InputImageType *>(this->GetInput(idx));
if (!inputPtr)
{
// Because DataObject::PropagateRequestedRegion() allows only
// InvalidRequestedRegionError, it's impossible to write simply:
// itkExceptionMacro("Missing input " << idx);
InvalidRequestedRegionError e(__FILE__, __LINE__);
e.SetLocation(ITK_LOCATION);
e.SetDescription("Missing input.");
e.SetDataObject(this->GetOutput());
throw e;
}
InputImageRegionType inputRegion;
if (begin <= idx && idx < end)
{
this->CallCopyOutputRegionToInputRegion(inputRegion, outputRegion);
}
else
{
// Tell the pipeline that updating this input is unnecessary
inputRegion = inputPtr->GetBufferedRegion();
}
inputPtr->SetRequestedRegion(inputRegion);
}
}
template <typename TInputImage, typename TOutputImage>
void
JoinSeriesImageFilter<TInputImage, TOutputImage>::DynamicThreadedGenerateData(
const OutputImageRegionType & outputRegionForThread)
{
OutputImageRegionType outputRegion = outputRegionForThread;
outputRegion.SetSize(InputImageDimension, 1);
InputImageRegionType inputRegion;
this->CallCopyOutputRegionToInputRegion(inputRegion, outputRegionForThread);
const IndexValueType begin = outputRegionForThread.GetIndex(InputImageDimension);
const IndexValueType end = begin + outputRegionForThread.GetSize(InputImageDimension);
TOutputImage * output = this->GetOutput();
TotalProgressReporter progress(this, output->GetRequestedRegion().GetNumberOfPixels());
for (IndexValueType idx = begin; idx < end; ++idx)
{
outputRegion.SetIndex(InputImageDimension, idx);
ImageAlgorithm::Copy(this->GetInput(idx), output, inputRegion, outputRegion);
progress.Completed(outputRegion.GetNumberOfPixels());
}
}
template <typename TInputImage, typename TOutputImage>
void
JoinSeriesImageFilter<TInputImage, TOutputImage>::PrintSelf(std::ostream & os, Indent indent) const
{
Superclass::PrintSelf(os, indent);
os << indent << "Spacing: " << m_Spacing << std::endl;
os << indent << "Origin: " << m_Origin << std::endl;
}
} // end namespace itk
#endif
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