diff --git a/Modules/MatchPointRegistration/include/itkStitchImageFilter.tpp b/Modules/MatchPointRegistration/include/itkStitchImageFilter.tpp index 1ec8334ada..5e8e7529c9 100644 --- a/Modules/MatchPointRegistration/include/itkStitchImageFilter.tpp +++ b/Modules/MatchPointRegistration/include/itkStitchImageFilter.tpp @@ -1,639 +1,639 @@ /*============================================================================ 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. ============================================================================*/ #ifndef itkStitchImageFilter_hxx #define itkStitchImageFilter_hxx #include "itkStitchImageFilter.h" #include "itkObjectFactory.h" #include "itkIdentityTransform.h" #include "itkProgressReporter.h" #include "itkImageRegionIteratorWithIndex.h" #include "itkImageScanlineIterator.h" #include "itkSpecialCoordinatesImage.h" #include "itkDefaultConvertPixelTraits.h" #include "itkSimpleDataObjectDecorator.h" #include namespace itk { template< typename TInputImage, typename TOutputImage, typename TInterpolatorPrecisionType, typename TTransformPrecisionType > StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType > ::StitchImageFilter() : m_OutputSpacing( 1.0 ), m_OutputOrigin( 0.0 ), m_UseReferenceImage( false ), m_StitchStrategy(StitchStrategy::Mean) { m_Size.Fill( 0 ); m_OutputStartIndex.Fill( 0 ); m_OutputDirection.SetIdentity(); // Pipeline input configuration // implicit input index set: // #1 "ReferenceImage" optional Self::AddOptionalInputName("ReferenceImage"); m_DefaultPixelValue = NumericTraits::ZeroValue( m_DefaultPixelValue ); } template< typename TInputImage, typename TOutputImage, typename TInterpolatorPrecisionType, typename TTransformPrecisionType > void StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType > ::SetInput(const InputImageType* image) { this->SetInput(0, image, itk::IdentityTransform< TTransformPrecisionType, ImageDimension>::New().GetPointer(), LinearInterpolatorType::New().GetPointer()); } template< typename TInputImage, typename TOutputImage, typename TInterpolatorPrecisionType, typename TTransformPrecisionType > void StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType > ::SetInput(unsigned int index, const InputImageType* image) { this->SetInput(index, image, itk::IdentityTransform< TTransformPrecisionType, ImageDimension>::New().GetPointer(), LinearInterpolatorType::New().GetPointer()); } template< typename TInputImage, typename TOutputImage, typename TInterpolatorPrecisionType, typename TTransformPrecisionType > void StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType > ::SetInput(unsigned int index, const InputImageType* image, const TransformType* transform) { this->SetInput(index, image, transform, LinearInterpolatorType::New().GetPointer()); } template< typename TInputImage, typename TOutputImage, typename TInterpolatorPrecisionType, typename TTransformPrecisionType > void StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType > ::SetInput(unsigned int index, const InputImageType* image, const TransformType* transform, InterpolatorType* interpolator) { Superclass::SetInput(index, image); m_Interpolators[image] = interpolator; this->SetTransform(index, transform); } template< typename TInputImage, typename TOutputImage, typename TInterpolatorPrecisionType, typename TTransformPrecisionType > void StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType > ::SetTransform(unsigned int index, const TransformType* transform) { const auto transformName = this->GetTransformInputName(index); typedef SimpleDataObjectDecorator< TransformPointerType > DecoratorType; const DecoratorType* oldInput = itkDynamicCastInDebugMode< const DecoratorType* >(this->ProcessObject::GetInput(transformName)); if (!oldInput || oldInput->Get() != transform) { typename DecoratorType::Pointer newInput = DecoratorType::New(); // Process object is not const-correct so the const_cast is required here newInput->Set(const_cast(transform)); this->ProcessObject::SetInput(transformName, newInput); } } template< typename TInputImage, typename TOutputImage, typename TInterpolatorPrecisionType, typename TTransformPrecisionType > const typename StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >::TransformType* StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType > ::GetTransform(unsigned int index) const { typedef SimpleDataObjectDecorator< TransformPointerType > DecoratorType; const DecoratorType* input = itkDynamicCastInDebugMode< const DecoratorType* >(this->ProcessObject::GetInput(this->GetTransformInputName(index))); if (nullptr != input) { return input->Get(); } return nullptr; } template< typename TInputImage, typename TOutputImage, typename TInterpolatorPrecisionType, typename TTransformPrecisionType > const typename StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType >::InterpolatorType* StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType > ::GetInterpolator(unsigned int index) const { auto input = this->GetInput(index); if (m_Interpolators.find(input) != std::end(m_Interpolators)) { return m_Interpolators[input]; } return nullptr; } template< typename TInputImage, typename TOutputImage, typename TInterpolatorPrecisionType, typename TTransformPrecisionType > void StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType > ::SetOutputSpacing(const double *spacing) { SpacingType s; for(unsigned int i = 0; i < TOutputImage::ImageDimension; ++i) { s[i] = static_cast< typename SpacingType::ValueType >(spacing[i]); } this->SetOutputSpacing(s); } template< typename TInputImage, typename TOutputImage, typename TInterpolatorPrecisionType, typename TTransformPrecisionType > void StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType > ::SetOutputOrigin(const double *origin) { OriginPointType p(origin); this->SetOutputOrigin(p); } template< typename TInputImage, typename TOutputImage, typename TInterpolatorPrecisionType, typename TTransformPrecisionType > void StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType > ::SetOutputParametersFromImage(const ImageBaseType *image) { this->SetOutputOrigin ( image->GetOrigin() ); this->SetOutputSpacing ( image->GetSpacing() ); this->SetOutputDirection ( image->GetDirection() ); this->SetOutputStartIndex ( image->GetLargestPossibleRegion().GetIndex() ); this->SetSize ( image->GetLargestPossibleRegion().GetSize() ); } template< typename TInputImage, typename TOutputImage, typename TInterpolatorPrecisionType, typename TTransformPrecisionType > void StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType > ::BeforeThreadedGenerateData() { this->EnsureInterpolators(); this->EnsureTransforms(); for (const auto& interpolator : m_Interpolators) { interpolator.second->SetInputImage(interpolator.first); } unsigned int nComponents = DefaultConvertPixelTraits::GetNumberOfComponents( m_DefaultPixelValue ); if (nComponents == 0) { PixelComponentType zeroComponent - = NumericTraits::ZeroValue( zeroComponent ); + = NumericTraits::ZeroValue(); nComponents = this->GetInput()->GetNumberOfComponentsPerPixel(); NumericTraits::SetLength(m_DefaultPixelValue, nComponents ); for (unsigned int n=0; n void StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType > ::AfterThreadedGenerateData() { // Disconnect input image from the interpolator for (auto& interpolator : m_Interpolators) { interpolator.second->SetInputImage(ITK_NULLPTR); } } template< typename TInputImage, typename TOutputImage, typename TInterpolatorPrecisionType, typename TTransformPrecisionType > void StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType > ::ThreadedGenerateData(const OutputImageRegionType & outputRegionForThread, ThreadIdType threadId) { if( outputRegionForThread.GetNumberOfPixels() == 0 ) { return; } // Get the output pointers OutputImageType* outputPtr = this->GetOutput(); // Get this input pointers InputImageVectorType inputs = this->GetInputs(); TransformMapType transforms = this->GetTransforms(); std::map lowerIndices; std::map upperIndices; for (const auto& input : inputs) { const auto largestRegion = input->GetLargestPossibleRegion(); lowerIndices[input] = largestRegion.GetIndex(); upperIndices[input] = largestRegion.GetUpperIndex(); } // Create an iterator that will walk the output region for this thread. typedef ImageRegionIteratorWithIndex< OutputImageType > OutputIterator; OutputIterator outIt(outputPtr, outputRegionForThread); // Define a few indices that will be used to translate from an input pixel // to an output pixel PointType outputPoint; // Coordinates of current output pixel PointType inputPoint; // Coordinates of current input pixel ContinuousInputIndexType inputIndex; // Support for progress methods/callbacks ProgressReporter progress(this, threadId, outputRegionForThread.GetNumberOfPixels()); // Min/max values of the output pixel type AND these values // represented as the output type of the interpolator const PixelComponentType minValue = NumericTraits< PixelComponentType >::NonpositiveMin(); const PixelComponentType maxValue = NumericTraits< PixelComponentType >::max(); typedef typename InterpolatorType::OutputType OutputType; const ComponentType minOutputValue = static_cast(minValue); const ComponentType maxOutputValue = static_cast(maxValue); // Walk the output region outIt.GoToBegin(); while (!outIt.IsAtEnd()) { // Determine the index of the current output pixel outputPtr->TransformIndexToPhysicalPoint(outIt.GetIndex(), outputPoint); std::vector pixvals; std::vector pixDistance; for (const auto& input : inputs) { // Compute corresponding input pixel position inputPoint = transforms[input]->TransformPoint(outputPoint); const bool isInsideInput = input->TransformPhysicalPointToContinuousIndex(inputPoint, inputIndex); // Evaluate input at right position and copy to the output if (m_Interpolators[input]->IsInsideBuffer(inputIndex) && isInsideInput) { OutputType value = m_Interpolators[input]->EvaluateAtContinuousIndex(inputIndex); pixvals.emplace_back(this->CastPixelWithBoundsChecking(value, minOutputValue, maxOutputValue)); ContinuousInputIndexType indexDistance; const auto spacing = input->GetSpacing(); double minBorderDistance = std::numeric_limits::max(); for (unsigned int i = 0; i < ImageDimension; ++i) { minBorderDistance = std::min(minBorderDistance, std::min(std::abs(lowerIndices[input][i] - inputIndex[i]) * spacing[i], std::abs(upperIndices[input][i] - inputIndex[i]) * spacing[i])); } pixDistance.emplace_back(minBorderDistance); } } if (!pixvals.empty()) { //at least one input provided a value if (StitchStrategy::Mean == m_StitchStrategy) { double sum = std::accumulate(pixvals.begin(), pixvals.end(), 0.0); outIt.Set(sum / pixvals.size()); } else { auto finding = std::max_element(pixDistance.begin(), pixDistance.end()); outIt.Set(pixvals[std::distance(pixDistance.begin(), finding)]); } } else { outIt.Set(m_DefaultPixelValue); // default background value } progress.CompletedPixel(); ++outIt; } } template< typename TInputImage, typename TOutputImage, typename TInterpolatorPrecisionType, typename TTransformPrecisionType > typename StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType > ::PixelType StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType > ::CastPixelWithBoundsChecking(const InterpolatorOutputType value, const ComponentType minComponent, const ComponentType maxComponent ) const { const unsigned int nComponents = InterpolatorConvertType::GetNumberOfComponents(value); PixelType outputValue; NumericTraits::SetLength( outputValue, nComponents ); for (unsigned int n = 0; n < nComponents; n++) { ComponentType component = InterpolatorConvertType::GetNthComponent( n, value ); if ( component < minComponent ) { PixelConvertType::SetNthComponent( n, outputValue, static_cast( minComponent ) ); } else if ( component > maxComponent ) { PixelConvertType::SetNthComponent( n, outputValue, static_cast( maxComponent ) ); } else { PixelConvertType::SetNthComponent(n, outputValue, static_cast( component ) ); } } return outputValue; } template typename StitchImageFilter::InputImageVectorType StitchImageFilter ::GetInputs() { InputImageVectorType inputs; for (unsigned int i = 0; i < this->GetNumberOfIndexedInputs(); ++i) { auto input = this->GetInput(i); if (nullptr != input) { inputs.push_back(input); } } return inputs; } template typename StitchImageFilter::TransformMapType StitchImageFilter ::GetTransforms() { TransformMapType transforms; for (unsigned int i = 0; i < this->GetNumberOfIndexedInputs(); ++i) { auto input = this->GetInput(i); auto transform = this->GetTransform(i); transforms[input] = transform; } return transforms; } template< typename TInputImage, typename TOutputImage, typename TInterpolatorPrecisionType, typename TTransformPrecisionType > void StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType > ::GenerateInputRequestedRegion() { // Call the superclass' implementation of this method Superclass::GenerateInputRequestedRegion(); if ( !this->GetInput() ) { return; } // Get pointers to the input auto inputs = this->GetInputs(); for (auto& input : inputs) { InputImagePointer inputPtr = const_cast(input); // Determining the actual input region is non-trivial, especially // when we cannot assume anything about the transform being used. // So we do the easy thing and request the entire input image. // inputPtr->SetRequestedRegionToLargestPossibleRegion(); } } template< typename TInputImage, typename TOutputImage, typename TInterpolatorPrecisionType, typename TTransformPrecisionType > void StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType > ::GenerateOutputInformation() { // Call the superclass' implementation of this method Superclass::GenerateOutputInformation(); // Get pointers to the input and output OutputImageType *outputPtr = this->GetOutput(); if ( !outputPtr ) { return; } const ReferenceImageBaseType *referenceImage = this->GetReferenceImage(); // Set the size of the output region if ( m_UseReferenceImage && referenceImage ) { outputPtr->SetLargestPossibleRegion( referenceImage->GetLargestPossibleRegion() ); } else { typename TOutputImage::RegionType outputLargestPossibleRegion; outputLargestPossibleRegion.SetSize(m_Size); outputLargestPossibleRegion.SetIndex(m_OutputStartIndex); outputPtr->SetLargestPossibleRegion(outputLargestPossibleRegion); } // Set spacing and origin if ( m_UseReferenceImage && referenceImage ) { outputPtr->SetSpacing( referenceImage->GetSpacing() ); outputPtr->SetOrigin( referenceImage->GetOrigin() ); outputPtr->SetDirection( referenceImage->GetDirection() ); } else { outputPtr->SetSpacing(m_OutputSpacing); outputPtr->SetOrigin(m_OutputOrigin); outputPtr->SetDirection(m_OutputDirection); } } template< typename TInputImage, typename TOutputImage, typename TInterpolatorPrecisionType, typename TTransformPrecisionType > ModifiedTimeType StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType > ::GetMTime(void) const { ModifiedTimeType latestTime = Object::GetMTime(); for (const auto& interpolator : m_Interpolators) { if (interpolator.second.GetPointer()) { if (latestTime < interpolator.second->GetMTime()) { latestTime = interpolator.second->GetMTime(); } } } return latestTime; } template< typename TInputImage, typename TOutputImage, typename TInterpolatorPrecisionType, typename TTransformPrecisionType > void StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType > ::PrintSelf(std::ostream & os, Indent indent) const { Superclass::PrintSelf(os, indent); os << indent << "DefaultPixelValue: " << static_cast< typename NumericTraits< PixelType >::PrintType > ( m_DefaultPixelValue ) << std::endl; os << indent << "Size: " << m_Size << std::endl; os << indent << "OutputStartIndex: " << m_OutputStartIndex << std::endl; os << indent << "OutputSpacing: " << m_OutputSpacing << std::endl; os << indent << "OutputOrigin: " << m_OutputOrigin << std::endl; os << indent << "OutputDirection: " << m_OutputDirection << std::endl; for (const auto& interpolator : m_Interpolators) { os << indent << "Interpolator: " << interpolator.second.GetPointer() << std::endl; } os << indent << "UseReferenceImage: " << ( m_UseReferenceImage ? "On" : "Off" ) << std::endl; } template< typename TInputImage, typename TOutputImage, typename TInterpolatorPrecisionType, typename TTransformPrecisionType > void StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType > ::EnsureTransforms() { const auto inputCount = this->GetNumberOfIndexedInputs(); for (unsigned int i = 0; i < inputCount; ++i) { auto input = this->GetInput(i); if (nullptr == input) { itkExceptionMacro(<< "Nth input image is not set (n: " << i << ")."); } auto transform = this->GetTransform(i); if (nullptr == transform) { this->SetTransform(i, itk::IdentityTransform< TTransformPrecisionType, ImageDimension>::New().GetPointer()); } } } template< typename TInputImage, typename TOutputImage, typename TInterpolatorPrecisionType, typename TTransformPrecisionType > void StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType > ::EnsureInterpolators() { const auto inputCount = this->GetNumberOfIndexedInputs(); InterpolatorMapType newInterpolatorMap; for (unsigned int i = 0; i < inputCount; ++i) { auto input = this->GetInput(i); if (nullptr == input) { itkExceptionMacro(<< "Nth input image is not set (n: " << i << ")."); } if (m_Interpolators[input].IsNull()) { newInterpolatorMap[input] = LinearInterpolatorType::New().GetPointer(); } else { newInterpolatorMap[input] = m_Interpolators[input]; } } m_Interpolators = newInterpolatorMap; } template< typename TInputImage, typename TOutputImage, typename TInterpolatorPrecisionType, typename TTransformPrecisionType > std::string StitchImageFilter< TInputImage, TOutputImage, TInterpolatorPrecisionType, TTransformPrecisionType > ::GetTransformInputName(unsigned int index) { return "transform_" + std::to_string(index); } } // end namespace itk #endif