From: tbaudier Date: Thu, 28 Feb 2019 13:26:46 +0000 (+0100) Subject: Merge branch 'master' of https://github.com/open-vv/vv X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=7f5fe9d1132d2fd6186dd33de41d5711ae32871d;hp=b50c4ae3e2850ad593d2c991b56e04ed22748f99;p=clitk.git Merge branch 'master' of https://github.com/open-vv/vv --- diff --git a/.travis.yml b/.travis.yml index 99db61b..a36890a 100644 --- a/.travis.yml +++ b/.travis.yml @@ -19,14 +19,14 @@ env: - WITH_CMAKE=true VTK_VERSION=v7.0.0 ITK_VERSION=v4.9.1 QT_VERSION=4.8.7 C11=false - WITH_CMAKE=true VTK_VERSION=v7.0.0 ITK_VERSION=v4.9.1 QT_VERSION=5.5.1 C11=false - WITH_CMAKE=true VTK_VERSION=v7.0.0 ITK_VERSION=v4.13.0 QT_VERSION=5.5.1 C11=false - - WITH_CMAKE=true VTK_VERSION=v8.1.1 ITK_VERSION=v5.0b01 QT_VERSION=5.5.1 C11=false + - WITH_CMAKE=true VTK_VERSION=v8.1.1 ITK_VERSION=v5.0rc01 QT_VERSION=5.5.1 C11=false - WITH_CMAKE=true VTK_VERSION=v6.3.0 ITK_VERSION=v4.9.1 QT_VERSION=4.8.7 C11=true - WITH_CMAKE=true VTK_VERSION=v6.3.0 ITK_VERSION=v4.9.1 QT_VERSION=5.5.1 C11=true - WITH_CMAKE=true VTK_VERSION=v6.3.0 ITK_VERSION=v4.13.0 QT_VERSION=5.5.1 C11=true - WITH_CMAKE=true VTK_VERSION=v7.0.0 ITK_VERSION=v4.9.1 QT_VERSION=4.8.7 C11=true - WITH_CMAKE=true VTK_VERSION=v7.0.0 ITK_VERSION=v4.9.1 QT_VERSION=5.5.1 C11=true - WITH_CMAKE=true VTK_VERSION=v7.0.0 ITK_VERSION=v4.13.0 QT_VERSION=5.5.1 C11=true - - WITH_CMAKE=true VTK_VERSION=v8.1.1 ITK_VERSION=v5.0b01 QT_VERSION=5.5.1 C11=true + - WITH_CMAKE=true VTK_VERSION=v8.1.1 ITK_VERSION=v5.0rc01 QT_VERSION=5.5.1 C11=true matrix: exclude: @@ -44,7 +44,7 @@ matrix: env: WITH_CMAKE=true VTK_VERSION=v6.3.0 ITK_VERSION=v4.13.0 QT_VERSION=5.5.1 C11=false - os: linux compiler: clang - env: WITH_CMAKE=true VTK_VERSION=v8.1.1 ITK_VERSION=v5.0b01 QT_VERSION=5.5.1 C11=false + env: WITH_CMAKE=true VTK_VERSION=v8.1.1 ITK_VERSION=v5.0rc01 QT_VERSION=5.5.1 C11=false - os: linux compiler: clang env: WITH_CMAKE=true VTK_VERSION=v7.0.0 ITK_VERSION=v4.13.0 QT_VERSION=5.5.1 C11=true @@ -53,19 +53,19 @@ matrix: env: WITH_CMAKE=true VTK_VERSION=v6.3.0 ITK_VERSION=v4.13.0 QT_VERSION=5.5.1 C11=true - os: linux compiler: clang - env: WITH_CMAKE=true VTK_VERSION=v8.1.1 ITK_VERSION=v5.0b01 QT_VERSION=5.5.1 C11=true + env: WITH_CMAKE=true VTK_VERSION=v8.1.1 ITK_VERSION=v5.0rc01 QT_VERSION=5.5.1 C11=true - os: osx env: WITH_CMAKE=true VTK_VERSION=v6.3.0 ITK_VERSION=v4.13.0 QT_VERSION=5.5.1 C11=false - os: osx env: WITH_CMAKE=true VTK_VERSION=v7.0.0 ITK_VERSION=v4.13.0 QT_VERSION=5.5.1 C11=false - os: osx - env: WITH_CMAKE=true VTK_VERSION=v8.1.1 ITK_VERSION=v5.0b01 QT_VERSION=5.5.1 C11=flase + env: WITH_CMAKE=true VTK_VERSION=v8.1.1 ITK_VERSION=v5.0rc01 QT_VERSION=5.5.1 C11=flase - os: osx env: WITH_CMAKE=true VTK_VERSION=v6.3.0 ITK_VERSION=v4.13.0 QT_VERSION=5.5.1 C11=true - os: osx env: WITH_CMAKE=true VTK_VERSION=v7.0.0 ITK_VERSION=v4.13.0 QT_VERSION=5.5.1 C11=true - os: osx - env: WITH_CMAKE=true VTK_VERSION=v8.1.1 ITK_VERSION=v5.0b01 QT_VERSION=5.5.1 C11=true + env: WITH_CMAKE=true VTK_VERSION=v8.1.1 ITK_VERSION=v5.0rc01 QT_VERSION=5.5.1 C11=true language: cpp diff --git a/common/clitkMatrix.cxx b/common/clitkMatrix.cxx index 2c09f31..e4afa7b 100644 --- a/common/clitkMatrix.cxx +++ b/common/clitkMatrix.cxx @@ -35,7 +35,7 @@ Get4x4MatrixDoubleAsString(vtkMatrix4x4 *matrix, for (unsigned int j = 0; j < 4; j++){ double absmax = 0.; for (unsigned int i = 0; i < 4; i++) - absmax = std::max(absmax, vnl_math_abs(matrix->GetElement(i, j))); + absmax = std::max(absmax, std::abs(matrix->GetElement(i, j))); unsigned ndigits = (unsigned)std::max(0.,std::log10(absmax))+1; width[j] = precision+ndigits+3; } diff --git a/itk/RelativePositionPropImageFilter.h b/itk/RelativePositionPropImageFilter.h index e876f9f..c2391e7 100644 --- a/itk/RelativePositionPropImageFilter.h +++ b/itk/RelativePositionPropImageFilter.h @@ -181,7 +181,7 @@ namespace itk { m_Alpha1 = 0; m_Alpha2 = 0; - m_K1 = vcl_acos(-1.0)/2; + m_K1 = std::acos(-1.0)/2; // m_K2 = 3.1417/2; m_Radius = 2; // DS m_Fast = true; // DS diff --git a/itk/clitkAddRelativePositionConstraintToLabelImageFilter.h b/itk/clitkAddRelativePositionConstraintToLabelImageFilter.h index 45f331e..df05283 100644 --- a/itk/clitkAddRelativePositionConstraintToLabelImageFilter.h +++ b/itk/clitkAddRelativePositionConstraintToLabelImageFilter.h @@ -149,7 +149,11 @@ namespace clitk { typename FloatImageType::Pointer GetFuzzyMap() { return m_FuzzyMap; } // I dont want to verify inputs information +#if ITK_VERSION_MAJOR <= 4 virtual void VerifyInputInformation() ITK_OVERRIDE { } +#else + virtual void VerifyInputInformation() const ITK_OVERRIDE { } +#endif // For debug void PrintOptions(); diff --git a/itk/clitkAddRelativePositionConstraintToLabelImageFilter.txx b/itk/clitkAddRelativePositionConstraintToLabelImageFilter.txx index c97ba0e..0e3581e 100644 --- a/itk/clitkAddRelativePositionConstraintToLabelImageFilter.txx +++ b/itk/clitkAddRelativePositionConstraintToLabelImageFilter.txx @@ -61,7 +61,7 @@ AddRelativePositionConstraintToLabelImageFilter(): FuzzyMapOnlyFlagOff(); FastFlagOff(); SetRadius(2.0); - SetK1(vcl_acos(-1.0)/2); + SetK1(std::acos(-1.0)/2); } //-------------------------------------------------------------------- diff --git a/itk/clitkBooleanOperatorLabelImageFilter.h b/itk/clitkBooleanOperatorLabelImageFilter.h index e7d1b73..523a179 100644 --- a/itk/clitkBooleanOperatorLabelImageFilter.h +++ b/itk/clitkBooleanOperatorLabelImageFilter.h @@ -99,8 +99,12 @@ namespace clitk { itkStaticConstMacro(OutputImageDimension, unsigned int, TOutputImage::ImageDimension); // I dont want to verify inputs information +#if ITK_VERSION_MAJOR <= 4 virtual void VerifyInputInformation() ITK_OVERRIDE { } - +#else + virtual void VerifyInputInformation() const ITK_OVERRIDE { } +#endif + protected: BooleanOperatorLabelImageFilter(); virtual ~BooleanOperatorLabelImageFilter() {} diff --git a/itk/clitkComposeVFFilter.txx b/itk/clitkComposeVFFilter.txx index 5cc5db1..e42c852 100644 --- a/itk/clitkComposeVFFilter.txx +++ b/itk/clitkComposeVFFilter.txx @@ -98,7 +98,7 @@ namespace clitk { // The following block is equivalent to the following line without // having to call floor. (Only for positive inputs, we already now that is in the image) - // baseIndex[dim] = (long) vcl_floor(contIndex[dim] ); + // baseIndex[dim] = (long) std::floor(contIndex[dim] ); baseIndex[dim] = (long) contIndex[dim]; distance[dim] = contIndex[dim] - double( baseIndex[dim] ); diff --git a/itk/clitkCropLikeImageFilter.h b/itk/clitkCropLikeImageFilter.h index 47ae445..6e63608 100644 --- a/itk/clitkCropLikeImageFilter.h +++ b/itk/clitkCropLikeImageFilter.h @@ -71,7 +71,11 @@ namespace clitk { itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension); // I dont want to verify inputs information +#if ITK_VERSION_MAJOR <= 4 virtual void VerifyInputInformation() ITK_OVERRIDE { } +#else + virtual void VerifyInputInformation() const ITK_OVERRIDE { } +#endif protected: CropLikeImageFilter(); diff --git a/itk/clitkForwardWarpImageFilter.h b/itk/clitkForwardWarpImageFilter.h index 7efac8f..ec46f0c 100644 --- a/itk/clitkForwardWarpImageFilter.h +++ b/itk/clitkForwardWarpImageFilter.h @@ -25,7 +25,11 @@ #include "itkImageRegionIterator.h" #include "itkImageRegionIteratorWithIndex.h" #include "itkNumericTraits.h" +#if ITK_VERSION_MAJOR <= 4 #include "itkSimpleFastMutexLock.h" +#else +#include +#endif namespace clitk { @@ -56,7 +60,9 @@ namespace clitk //Some other typedefs typedef double CoordRepType; typedef itk::Image WeightsImageType; +#if ITK_VERSION_MAJOR <= 4 typedef itk::Image MutexImageType; +#endif /** Point type */ typedef itk::Point PointType; diff --git a/itk/clitkForwardWarpImageFilter.txx b/itk/clitkForwardWarpImageFilter.txx index 4d49b4d..4c38b5a 100644 --- a/itk/clitkForwardWarpImageFilter.txx +++ b/itk/clitkForwardWarpImageFilter.txx @@ -53,7 +53,9 @@ public: //Typedefs typedef typename OutputImageType::PixelType OutputPixelType; typedef itk::Image WeightsImageType; - typedef itk::Image MutexImageType; +#if ITK_VERSION_MAJOR <= 4 + typedef itk::Image MutexImageType; +#endif //=================================================================================== //Set methods void SetWeights(const typename WeightsImageType::Pointer input) { @@ -64,11 +66,18 @@ public: m_DeformationField=input; this->Modified(); } +#if ITK_VERSION_MAJOR <= 4 void SetMutexImage(const typename MutexImageType::Pointer input) { m_MutexImage=input; this->Modified(); m_ThreadSafe=true; } +#else + void SetMutexImage() { + this->Modified(); + m_ThreadSafe=true; + } +#endif //Get methods typename WeightsImageType::Pointer GetWeights() { @@ -89,7 +98,11 @@ protected: //member data typename itk::Image< double, ImageDimension>::Pointer m_Weights; typename DeformationFieldType::Pointer m_DeformationField; +#if ITK_VERSION_MAJOR <= 4 typename MutexImageType::Pointer m_MutexImage; +#else + std::mutex m_Mutex; +#endif bool m_ThreadSafe; }; @@ -184,7 +197,7 @@ void HelperClass1::Thread for(dim = 0; dim < ImageDimension; dim++) { // The following block is equivalent to the following line without // having to call floor. For positive inputs!!! - // baseIndex[dim] = (long) vcl_floor(contIndex[dim] ); + // baseIndex[dim] = (long) std::floor(contIndex[dim] ); baseIndex[dim] = (long) contIndex[dim]; distance[dim] = contIndex[dim] - double( baseIndex[dim] ); } @@ -224,14 +237,22 @@ void HelperClass1::Thread } else { //Entering critilal section: shared memory +#if ITK_VERSION_MAJOR <= 4 m_MutexImage->GetPixel(neighIndex).Lock(); +#else + m_Mutex.lock(); +#endif //Set the pixel and weight at neighIndex outputPtr->SetPixel(neighIndex, outputPtr->GetPixel(neighIndex) + overlap * static_cast(inputIt.Get())); m_Weights->SetPixel(neighIndex, m_Weights->GetPixel(neighIndex) + overlap); //Unlock +#if ITK_VERSION_MAJOR <= 4 m_MutexImage->GetPixel(neighIndex).Unlock(); +#else + m_Mutex.unlock(); +#endif } //Add to total overlap @@ -459,11 +480,15 @@ void ForwardWarpImageFilterSetRegions(region); mutex->Allocate(); mutex->SetSpacing(inputPtr->GetSpacing()); helper1->SetMutexImage(mutex); +#else + helper1->SetMutexImage(); +#endif if (m_Verbose) std::cout <<"Forwarp warping using a thread-safe algorithm" < WeightsImageType; +#if ITK_VERSION_MAJOR <= 4 typedef itk::Image MutexImageType; +#endif /** Point type */ typedef itk::Point PointType; diff --git a/itk/clitkInvertVFFilter.txx b/itk/clitkInvertVFFilter.txx index b2485e0..6c91dbb 100644 --- a/itk/clitkInvertVFFilter.txx +++ b/itk/clitkInvertVFFilter.txx @@ -47,7 +47,9 @@ public: //Typedefs typedef typename OutputImageType::PixelType PixelType; typedef itk::Image WeightsImageType; - typedef itk::Image MutexImageType; +#if ITK_VERSION_MAJOR <= 4 + typedef itk::Image MutexImageType; +#endif //=================================================================================== //Set methods @@ -55,11 +57,18 @@ public: m_Weights = input; this->Modified(); } +#if ITK_VERSION_MAJOR <= 4 void SetMutexImage(const typename MutexImageType::Pointer input) { m_MutexImage=input; this->Modified(); m_ThreadSafe=true; } +#else + void SetMutexImage() { + this->Modified(); + m_ThreadSafe=true; + } +#endif //Get methods typename WeightsImageType::Pointer GetWeights() { @@ -79,7 +88,11 @@ protected: //member data typename WeightsImageType::Pointer m_Weights; +#if ITK_VERSION_MAJOR <= 4 typename MutexImageType::Pointer m_MutexImage; +#else + std::mutex m_Mutex; +#endif bool m_ThreadSafe; }; @@ -169,7 +182,7 @@ void HelperClass1::ThreadedGenerateData(const O for(dim = 0; dim < ImageDimension; dim++) { // The following block is equivalent to the following line without // having to call floor. (Only for positive inputs, we already now that is in the image) - // baseIndex[dim] = (long) vcl_floor(contIndex[dim] ); + // baseIndex[dim] = (long) std::floor(contIndex[dim] ); baseIndex[dim] = (long) contIndex[dim]; distance[dim] = contIndex[dim] - double( baseIndex[dim] ); @@ -215,14 +228,22 @@ void HelperClass1::ThreadedGenerateData(const O else { //Entering critilal section: shared memory +#if ITK_VERSION_MAJOR <= 4 m_MutexImage->GetPixel(neighIndex).Lock(); +#else + m_Mutex.lock(); +#endif //Set the pixel and weight at neighIndex outputPtr->SetPixel(neighIndex, outputPtr->GetPixel(neighIndex) - (displacement*overlap)); m_Weights->SetPixel(neighIndex, m_Weights->GetPixel(neighIndex) + overlap); //Unlock +#if ITK_VERSION_MAJOR <= 4 m_MutexImage->GetPixel(neighIndex).Unlock(); +#else + m_Mutex.unlock(); +#endif } //Add to total overlap @@ -451,11 +472,15 @@ template void InvertVFFilterSetRegions(region); mutex->Allocate(); mutex->SetSpacing(inputPtr->GetSpacing()); helper1->SetMutexImage(mutex); +#else + helper1->SetMutexImage(); +#endif if (m_Verbose) std::cout <<"Inverting using a thread-safe algorithm" < { public: +#if ITK_VERSION_MAJOR <= 4 virtual void VerifyInputInformation() ITK_OVERRIDE { } +#else + virtual void VerifyInputInformation() const ITK_OVERRIDE { } +#endif /** Standard class typedefs. */ typedef PasteImageFilter Self; diff --git a/itk/clitkSliceBySliceRelativePositionFilter.txx b/itk/clitkSliceBySliceRelativePositionFilter.txx index 16571ea..fc820be 100644 --- a/itk/clitkSliceBySliceRelativePositionFilter.txx +++ b/itk/clitkSliceBySliceRelativePositionFilter.txx @@ -43,7 +43,7 @@ SliceBySliceRelativePositionFilter(): SetObjectCCLSelectionDirection(1); ObjectCCLSelectionIgnoreSingleCCLFlagOff(); VerboseSlicesFlagOff(); - this->SetK1(vcl_acos(-1.0)/2); + this->SetK1(std::acos(-1.0)/2); } //-------------------------------------------------------------------- diff --git a/itk/clitkVectorBSplineDecompositionImageFilter.txx b/itk/clitkVectorBSplineDecompositionImageFilter.txx index 7031745..90bfa5c 100644 --- a/itk/clitkVectorBSplineDecompositionImageFilter.txx +++ b/itk/clitkVectorBSplineDecompositionImageFilter.txx @@ -131,7 +131,7 @@ VectorBSplineDecompositionImageFilter switch (m_SplineOrder) { case 3: m_NumberOfPoles = 1; - m_SplinePoles[0] = vcl_sqrt(3.0) - 2.0; + m_SplinePoles[0] = std::sqrt(3.0) - 2.0; break; case 0: m_NumberOfPoles = 0; @@ -141,18 +141,18 @@ VectorBSplineDecompositionImageFilter break; case 2: m_NumberOfPoles = 1; - m_SplinePoles[0] = vcl_sqrt(8.0) - 3.0; + m_SplinePoles[0] = std::sqrt(8.0) - 3.0; break; case 4: m_NumberOfPoles = 2; - m_SplinePoles[0] = vcl_sqrt(664.0 - vcl_sqrt(438976.0)) + vcl_sqrt(304.0) - 19.0; - m_SplinePoles[1] = vcl_sqrt(664.0 + vcl_sqrt(438976.0)) - vcl_sqrt(304.0) - 19.0; + m_SplinePoles[0] = std::sqrt(664.0 - std::sqrt(438976.0)) + std::sqrt(304.0) - 19.0; + m_SplinePoles[1] = std::sqrt(664.0 + std::sqrt(438976.0)) - std::sqrt(304.0) - 19.0; break; case 5: m_NumberOfPoles = 2; - m_SplinePoles[0] = vcl_sqrt(135.0 / 2.0 - vcl_sqrt(17745.0 / 4.0)) + vcl_sqrt(105.0 / 4.0) + m_SplinePoles[0] = std::sqrt(135.0 / 2.0 - std::sqrt(17745.0 / 4.0)) + std::sqrt(105.0 / 4.0) - 13.0 / 2.0; - m_SplinePoles[1] = vcl_sqrt(135.0 / 2.0 + vcl_sqrt(17745.0 / 4.0)) - vcl_sqrt(105.0 / 4.0) + m_SplinePoles[1] = std::sqrt(135.0 / 2.0 + std::sqrt(17745.0 / 4.0)) - std::sqrt(105.0 / 4.0) - 13.0 / 2.0; break; default: @@ -182,7 +182,7 @@ VectorBSplineDecompositionImageFilter horizon = m_DataLength[m_IteratorDirection]; zn = z; if (m_Tolerance > 0.0) { - horizon = (long)vcl_ceil(log(m_Tolerance) / vcl_log(fabs(z))); + horizon = (long)std::ceil(log(m_Tolerance) / std::log(fabs(z))); } if (horizon < m_DataLength[m_IteratorDirection]) { /* accelerated loop */ @@ -195,7 +195,7 @@ VectorBSplineDecompositionImageFilter } else { /* full loop */ iz = 1.0 / z; - z2n = vcl_pow(z, (double)(m_DataLength[m_IteratorDirection] - 1L)); + z2n = std::pow(z, (double)(m_DataLength[m_IteratorDirection] - 1L)); sum = m_Scratch[0] + z2n * m_Scratch[m_DataLength[m_IteratorDirection] - 1L]; z2n *= z2n * iz; for (unsigned int n = 1; n <= (m_DataLength[m_IteratorDirection] - 2); n++) { diff --git a/itk/clitkVectorBSplineDecompositionImageFilterWithOBD.txx b/itk/clitkVectorBSplineDecompositionImageFilterWithOBD.txx index 7bc3165..51e6361 100644 --- a/itk/clitkVectorBSplineDecompositionImageFilterWithOBD.txx +++ b/itk/clitkVectorBSplineDecompositionImageFilterWithOBD.txx @@ -138,7 +138,7 @@ VectorBSplineDecompositionImageFilterWithOBD switch (m_SplineOrder) { case 3: m_NumberOfPoles = 1; - m_SplinePoles[0] = vcl_sqrt(3.0) - 2.0; + m_SplinePoles[0] = std::sqrt(3.0) - 2.0; break; case 0: m_NumberOfPoles = 0; @@ -148,18 +148,18 @@ VectorBSplineDecompositionImageFilterWithOBD break; case 2: m_NumberOfPoles = 1; - m_SplinePoles[0] = vcl_sqrt(8.0) - 3.0; + m_SplinePoles[0] = std::sqrt(8.0) - 3.0; break; case 4: m_NumberOfPoles = 2; - m_SplinePoles[0] = vcl_sqrt(664.0 - vcl_sqrt(438976.0)) + vcl_sqrt(304.0) - 19.0; - m_SplinePoles[1] = vcl_sqrt(664.0 + vcl_sqrt(438976.0)) - vcl_sqrt(304.0) - 19.0; + m_SplinePoles[0] = std::sqrt(664.0 - std::sqrt(438976.0)) + std::sqrt(304.0) - 19.0; + m_SplinePoles[1] = std::sqrt(664.0 + std::sqrt(438976.0)) - std::sqrt(304.0) - 19.0; break; case 5: m_NumberOfPoles = 2; - m_SplinePoles[0] = vcl_sqrt(135.0 / 2.0 - vcl_sqrt(17745.0 / 4.0)) + vcl_sqrt(105.0 / 4.0) + m_SplinePoles[0] = std::sqrt(135.0 / 2.0 - std::sqrt(17745.0 / 4.0)) + std::sqrt(105.0 / 4.0) - 13.0 / 2.0; - m_SplinePoles[1] = vcl_sqrt(135.0 / 2.0 + vcl_sqrt(17745.0 / 4.0)) - vcl_sqrt(105.0 / 4.0) + m_SplinePoles[1] = std::sqrt(135.0 / 2.0 + std::sqrt(17745.0 / 4.0)) - std::sqrt(105.0 / 4.0) - 13.0 / 2.0; break; default: @@ -189,7 +189,7 @@ VectorBSplineDecompositionImageFilterWithOBD horizon = m_DataLength[m_IteratorDirection]; zn = z; if (m_Tolerance > 0.0) { - horizon = (long)vcl_ceil(log(m_Tolerance) / vcl_log(fabs(z))); + horizon = (long)std::ceil(log(m_Tolerance) / std::log(fabs(z))); } if (horizon < m_DataLength[m_IteratorDirection]) { /* accelerated loop */ @@ -202,7 +202,7 @@ VectorBSplineDecompositionImageFilterWithOBD } else { /* full loop */ iz = 1.0 / z; - z2n = vcl_pow(z, (double)(m_DataLength[m_IteratorDirection] - 1L)); + z2n = std::pow(z, (double)(m_DataLength[m_IteratorDirection] - 1L)); sum = m_Scratch[0] + z2n * m_Scratch[m_DataLength[m_IteratorDirection] - 1L]; z2n *= z2n * iz; for (unsigned int n = 1; n <= (m_DataLength[m_IteratorDirection] - 2); n++) { diff --git a/itk/clitkVectorBSplineInterpolateImageFunction.txx b/itk/clitkVectorBSplineInterpolateImageFunction.txx index 2599b80..935f257 100644 --- a/itk/clitkVectorBSplineInterpolateImageFunction.txx +++ b/itk/clitkVectorBSplineInterpolateImageFunction.txx @@ -484,12 +484,12 @@ VectorBSplineInterpolateImageFunction // compute the interpolation indexes for (unsigned int n = 0; n< ImageDimension; n++) { if (splineOrder & 1) { // Use this index calculation for odd splineOrder - indx = (long)vcl_floor((float)x[n]) - splineOrder / 2; + indx = (long)std::floor((float)x[n]) - splineOrder / 2; for (unsigned int k = 0; k <= splineOrder; k++) { evaluateIndex[n][k] = indx++; } } else { // Use this index calculation for even splineOrder - indx = (long)vcl_floor((float)(x[n] + 0.5)) - splineOrder / 2; + indx = (long)std::floor((float)(x[n] + 0.5)) - splineOrder / 2; for (unsigned int k = 0; k <= splineOrder; k++) { evaluateIndex[n][k] = indx++; } diff --git a/itk/clitkVectorBSplineInterpolateImageFunctionWithLUT.txx b/itk/clitkVectorBSplineInterpolateImageFunctionWithLUT.txx index a237a35..7096224 100644 --- a/itk/clitkVectorBSplineInterpolateImageFunctionWithLUT.txx +++ b/itk/clitkVectorBSplineInterpolateImageFunctionWithLUT.txx @@ -206,7 +206,7 @@ GetSampleIndexOfPixelPosition(const ContinuousIndexType & x, IndexType & Evaluat for(int l=0; lm_SplineOrder / 2; + indx = (long)std::floor(x[l]) - mSplineOrders[l] / 2 ; //this->m_SplineOrder / 2; evaluateIndex[l] = indx; } else { // Use this index calculation for even splineOrder if (mSplineOrders[l] == 0) evaluateIndex[l] = itk::Math::Round(x[l]); else { - indx = (long)vcl_floor((x[l]+ 0.5)) - mSplineOrders[l] / 2; //this->m_SplineOrder / 2; + indx = (long)std::floor((x[l]+ 0.5)) - mSplineOrders[l] / 2; //this->m_SplineOrder / 2; evaluateIndex[l] = indx; } } @@ -355,12 +355,12 @@ EvaluateWeightsAtContinuousIndex(const ContinuousIndexType& x, const TCoeffici long indx; for (unsigned int l=0; lm_SplineOrder / 2; + indx = (long)std::floor(x[l]) - mSplineOrders[l] / 2 ; //this->m_SplineOrder / 2; evaluateIndex[l] = indx; } else { // Use this index calculation for even splineOrder if (mSplineOrders[l] == 0) evaluateIndex[l] = itk::Math::Round(x[l]); else { - indx = (long)vcl_floor((x[l]+ 0.5)) - mSplineOrders[l] / 2; //this->m_SplineOrder / 2; + indx = (long)std::floor((x[l]+ 0.5)) - mSplineOrders[l] / 2; //this->m_SplineOrder / 2; evaluateIndex[l] = indx; } } diff --git a/itk/itkBSplineDecompositionImageFilterWithOBD.txx b/itk/itkBSplineDecompositionImageFilterWithOBD.txx index 8041409..46af359 100644 --- a/itk/itkBSplineDecompositionImageFilterWithOBD.txx +++ b/itk/itkBSplineDecompositionImageFilterWithOBD.txx @@ -146,7 +146,7 @@ BSplineDecompositionImageFilterWithOBD case 3: m_NumberOfPoles = 1; - m_SplinePoles[0] = vcl_sqrt(3.0) - 2.0; + m_SplinePoles[0] = std::sqrt(3.0) - 2.0; break; case 0: m_NumberOfPoles = 0; @@ -156,18 +156,18 @@ BSplineDecompositionImageFilterWithOBD break; case 2: m_NumberOfPoles = 1; - m_SplinePoles[0] = vcl_sqrt(8.0) - 3.0; + m_SplinePoles[0] = std::sqrt(8.0) - 3.0; break; case 4: m_NumberOfPoles = 2; - m_SplinePoles[0] = vcl_sqrt(664.0 - vcl_sqrt(438976.0)) + vcl_sqrt(304.0) - 19.0; - m_SplinePoles[1] = vcl_sqrt(664.0 + vcl_sqrt(438976.0)) - vcl_sqrt(304.0) - 19.0; + m_SplinePoles[0] = std::sqrt(664.0 - std::sqrt(438976.0)) + std::sqrt(304.0) - 19.0; + m_SplinePoles[1] = std::sqrt(664.0 + std::sqrt(438976.0)) - std::sqrt(304.0) - 19.0; break; case 5: m_NumberOfPoles = 2; - m_SplinePoles[0] = vcl_sqrt(135.0 / 2.0 - vcl_sqrt(17745.0 / 4.0)) + vcl_sqrt(105.0 / 4.0) + m_SplinePoles[0] = std::sqrt(135.0 / 2.0 - std::sqrt(17745.0 / 4.0)) + std::sqrt(105.0 / 4.0) - 13.0 / 2.0; - m_SplinePoles[1] = vcl_sqrt(135.0 / 2.0 + vcl_sqrt(17745.0 / 4.0)) - vcl_sqrt(105.0 / 4.0) + m_SplinePoles[1] = std::sqrt(135.0 / 2.0 + std::sqrt(17745.0 / 4.0)) - std::sqrt(105.0 / 4.0) - 13.0 / 2.0; break; default: @@ -196,7 +196,7 @@ BSplineDecompositionImageFilterWithOBD horizon = m_DataLength[m_IteratorDirection]; zn = z; if (m_Tolerance > 0.0) { - horizon = (long)vcl_ceil(log(m_Tolerance) / vcl_log(fabs(z))); + horizon = (long)std::ceil(log(m_Tolerance) / std::log(fabs(z))); } if (horizon < m_DataLength[m_IteratorDirection]) { /* accelerated loop */ @@ -209,7 +209,7 @@ BSplineDecompositionImageFilterWithOBD } else { /* full loop */ iz = 1.0 / z; - z2n = vcl_pow(z, (double)(m_DataLength[m_IteratorDirection] - 1L)); + z2n = std::pow(z, (double)(m_DataLength[m_IteratorDirection] - 1L)); sum = m_Scratch[0] + z2n * m_Scratch[m_DataLength[m_IteratorDirection] - 1L]; z2n *= z2n * iz; for (unsigned int n = 1; n <= (m_DataLength[m_IteratorDirection] - 2); n++) { diff --git a/itk/itkBSplineInterpolateImageFunctionWithLUT.txx b/itk/itkBSplineInterpolateImageFunctionWithLUT.txx index b9354a5..58a173a 100644 --- a/itk/itkBSplineInterpolateImageFunctionWithLUT.txx +++ b/itk/itkBSplineInterpolateImageFunctionWithLUT.txx @@ -187,7 +187,7 @@ namespace itk for(int l=0; lm_SplineOrder / 2; + indx = (long)std::floor(x[l]) - mSplineOrders[l] / 2 ; //this->m_SplineOrder / 2; evaluateIndex[l] = indx; } else { // Use this index calculation for even splineOrder if (mSplineOrders[l] == 0) evaluateIndex[l] = Math::Round(x[l]); else { - indx = (long)vcl_floor((x[l]+ 0.5)) - mSplineOrders[l] / 2; //this->m_SplineOrder / 2; + indx = (long)std::floor((x[l]+ 0.5)) - mSplineOrders[l] / 2; //this->m_SplineOrder / 2; evaluateIndex[l] = indx; } } diff --git a/itk/itkBSplineInterpolateImageFunctionWithLUT.txx.original b/itk/itkBSplineInterpolateImageFunctionWithLUT.txx.original index 3a8744f..877a784 100644 --- a/itk/itkBSplineInterpolateImageFunctionWithLUT.txx.original +++ b/itk/itkBSplineInterpolateImageFunctionWithLUT.txx.original @@ -259,7 +259,7 @@ GetSampleIndexOfPixelPosition(const ContinuousIndexType & x, IndexType & Evaluat // bool mChange = false; // Compute t1 = distance to floor - TCoefficientType t1 = x[l]- vcl_floor(x[l]); + TCoefficientType t1 = x[l]- std::floor(x[l]); // Compute index in precomputed weights table TCoefficientType t2 = mSamplingFactors[l]*t1; @@ -311,13 +311,13 @@ EvaluateAtContinuousIndex(const ContinuousIndexType & x) const { long indx; for (unsigned int l=0; lm_SplineOrder / 2; + indx = (long)std::floor(x[l]) - mSplineOrders[l] / 2 ; //this->m_SplineOrder / 2; EvaluateIndex[l] = indx; } else { // Use this index calculation for even splineOrder if (mSplineOrders[l] == 0) EvaluateIndex[l] = (long)rint(x[l]); else { - indx = (long)vcl_floor((x[l]+ 0.5)) - mSplineOrders[l] / 2; //this->m_SplineOrder / 2; + indx = (long)std::floor((x[l]+ 0.5)) - mSplineOrders[l] / 2; //this->m_SplineOrder / 2; EvaluateIndex[l] = indx; } } diff --git a/itk/itkRayCastInterpolateImageFunctionWithOrigin.txx b/itk/itkRayCastInterpolateImageFunctionWithOrigin.txx index ebf73cf..d173a48 100644 --- a/itk/itkRayCastInterpolateImageFunctionWithOrigin.txx +++ b/itk/itkRayCastInterpolateImageFunctionWithOrigin.txx @@ -129,7 +129,7 @@ public: typename InputImageType::SpacingType spacing=this->m_Image->GetSpacing(); if (m_ValidRay) - return vcl_sqrt(m_VoxelIncrement[0]*spacing[0]*m_VoxelIncrement[0]*spacing[0] + return std::sqrt(m_VoxelIncrement[0]*spacing[0]*m_VoxelIncrement[0]*spacing[0] + m_VoxelIncrement[1]*spacing[1]*m_VoxelIncrement[1]*spacing[1] + m_VoxelIncrement[2]*spacing[2]*m_VoxelIncrement[2]*spacing[2] ); else @@ -470,10 +470,10 @@ RayCastHelper + C*m_BoundingCorner[c1][2] ); // initialise plane value and normalise - m_BoundingPlane[j][0] = A/vcl_sqrt(A*A + B*B + C*C); - m_BoundingPlane[j][1] = B/vcl_sqrt(A*A + B*B + C*C); - m_BoundingPlane[j][2] = C/vcl_sqrt(A*A + B*B + C*C); - m_BoundingPlane[j][3] = D/vcl_sqrt(A*A + B*B + C*C); + m_BoundingPlane[j][0] = A/std::sqrt(A*A + B*B + C*C); + m_BoundingPlane[j][1] = B/std::sqrt(A*A + B*B + C*C); + m_BoundingPlane[j][2] = C/std::sqrt(A*A + B*B + C*C); + m_BoundingPlane[j][3] = D/std::sqrt(A*A + B*B + C*C); if ( (A*A + B*B + C*C) == 0 ) { itk::ExceptionObject err(__FILE__, __LINE__); @@ -799,9 +799,9 @@ RayCastHelper // Calculate the number of voxels in each direction - xNum = vcl_fabs(m_RayVoxelStartPosition[0] - m_RayVoxelEndPosition[0]); - yNum = vcl_fabs(m_RayVoxelStartPosition[1] - m_RayVoxelEndPosition[1]); - zNum = vcl_fabs(m_RayVoxelStartPosition[2] - m_RayVoxelEndPosition[2]); + xNum = std::fabs(m_RayVoxelStartPosition[0] - m_RayVoxelEndPosition[0]); + yNum = std::fabs(m_RayVoxelStartPosition[1] - m_RayVoxelEndPosition[1]); + zNum = std::fabs(m_RayVoxelStartPosition[2] - m_RayVoxelEndPosition[2]); // The direction iterated in is that with the greatest number of voxels // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -991,9 +991,9 @@ RayCastHelper startOK = false; endOK = false; - Istart[0] = (int) vcl_floor(m_RayVoxelStartPosition[0]); - Istart[1] = (int) vcl_floor(m_RayVoxelStartPosition[1]); - Istart[2] = (int) vcl_floor(m_RayVoxelStartPosition[2]); + Istart[0] = (int) std::floor(m_RayVoxelStartPosition[0]); + Istart[1] = (int) std::floor(m_RayVoxelStartPosition[1]); + Istart[2] = (int) std::floor(m_RayVoxelStartPosition[2]); if( (Istart[0] >= 0) && (Istart[0] + Idirn[0] < m_NumberOfVoxelsInX) && (Istart[1] >= 0) && (Istart[1] + Idirn[1] < m_NumberOfVoxelsInY) && @@ -1008,13 +1008,13 @@ RayCastHelper m_TotalRayVoxelPlanes--; } - Istart[0] = (int) vcl_floor(m_RayVoxelStartPosition[0] + Istart[0] = (int) std::floor(m_RayVoxelStartPosition[0] + m_TotalRayVoxelPlanes*m_VoxelIncrement[0]); - Istart[1] = (int) vcl_floor(m_RayVoxelStartPosition[1] + Istart[1] = (int) std::floor(m_RayVoxelStartPosition[1] + m_TotalRayVoxelPlanes*m_VoxelIncrement[1]); - Istart[2] = (int) vcl_floor(m_RayVoxelStartPosition[2] + Istart[2] = (int) std::floor(m_RayVoxelStartPosition[2] + m_TotalRayVoxelPlanes*m_VoxelIncrement[2]); if( (Istart[0] >= 0) && (Istart[0] + Idirn[0] < m_NumberOfVoxelsInX) && @@ -1286,18 +1286,18 @@ RayCastHelper switch( m_TraversalDirection ) { case TRANSVERSE_IN_X: { - y = m_Position3Dvox[1] - vcl_floor(m_Position3Dvox[1]); - z = m_Position3Dvox[2] - vcl_floor(m_Position3Dvox[2]); + y = m_Position3Dvox[1] - std::floor(m_Position3Dvox[1]); + z = m_Position3Dvox[2] - std::floor(m_Position3Dvox[2]); break; } case TRANSVERSE_IN_Y: { - y = m_Position3Dvox[0] - vcl_floor(m_Position3Dvox[0]); - z = m_Position3Dvox[2] - vcl_floor(m_Position3Dvox[2]); + y = m_Position3Dvox[0] - std::floor(m_Position3Dvox[0]); + z = m_Position3Dvox[2] - std::floor(m_Position3Dvox[2]); break; } case TRANSVERSE_IN_Z: { - y = m_Position3Dvox[0] - vcl_floor(m_Position3Dvox[0]); - z = m_Position3Dvox[1] - vcl_floor(m_Position3Dvox[1]); + y = m_Position3Dvox[0] - std::floor(m_Position3Dvox[0]); + z = m_Position3Dvox[1] - std::floor(m_Position3Dvox[1]); break; } default: { @@ -1322,7 +1322,7 @@ void RayCastHelper ::IncrementIntensities(double increment) { - short inc = (short) vcl_floor(increment + 0.5); + short inc = (short) std::floor(increment + 0.5); if (! m_ValidRay) { return; diff --git a/registration/clitkAffineRegistrationGenericFilter.cxx b/registration/clitkAffineRegistrationGenericFilter.cxx index d034912..2c94379 100644 --- a/registration/clitkAffineRegistrationGenericFilter.cxx +++ b/registration/clitkAffineRegistrationGenericFilter.cxx @@ -20,6 +20,45 @@ #define CLITKAFFINEREGISTRATIONGENERICFILTER_CXX #include "clitkAffineRegistrationGenericFilter.h" +// clitk include +#include "clitkIO.h" +#include "clitkCommon.h" +#include "clitkImageCommon.h" +#include "clitkAffineRegistration_ggo.h" +#include "clitkImageArithm_ggo.h" +#include "clitkCorrelationRatioImageToImageMetric.h" +#include "clitkTransformUtilities.h" +#include "clitkGenericMetric.h" +#include "clitkGenericOptimizer.h" +#include "clitkGenericInterpolator.h" +#include "clitkGenericAffineTransform.h" +#include "clitkImageToImageGenericFilter.h" + + +//itk include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +// other includes +#include +#include +#include + namespace clitk { diff --git a/registration/clitkAffineRegistrationGenericFilter.h b/registration/clitkAffineRegistrationGenericFilter.h index 22b9f52..94890dd 100644 --- a/registration/clitkAffineRegistrationGenericFilter.h +++ b/registration/clitkAffineRegistrationGenericFilter.h @@ -20,43 +20,11 @@ #define CLITKAFFINEREGISTRATIONGENERICFILTER_H // clitk include -#include "clitkIO.h" -#include "clitkCommon.h" -#include "clitkImageCommon.h" #include "clitkAffineRegistration_ggo.h" -#include "clitkImageArithm_ggo.h" -#include "clitkCorrelationRatioImageToImageMetric.h" -#include "clitkTransformUtilities.h" -#include "clitkGenericMetric.h" -#include "clitkGenericOptimizer.h" -#include "clitkGenericInterpolator.h" -#include "clitkGenericAffineTransform.h" #include "clitkImageToImageGenericFilter.h" -//itk include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include - -// other includes -#include -#include -#include + namespace clitk { diff --git a/registration/clitkBSplineDeformableTransform.txx b/registration/clitkBSplineDeformableTransform.txx index 60a2136..151c259 100644 --- a/registration/clitkBSplineDeformableTransform.txx +++ b/registration/clitkBSplineDeformableTransform.txx @@ -296,7 +296,7 @@ namespace clitk // when spline order is even. // The valid interval for evaluation is [start+offset, last-offset) // when spline order is odd. - // Where offset = vcl_floor(spline / 2 ). + // Where offset = std::floor(spline / 2 ). // Note that the last pixel is not included in the valid region // with odd spline orders. typename RegionType::SizeType size = m_GridRegion.GetSize(); diff --git a/registration/clitkCorrelationRatioImageToImageMetric.txx b/registration/clitkCorrelationRatioImageToImageMetric.txx index 1454539..d76f020 100644 --- a/registration/clitkCorrelationRatioImageToImageMetric.txx +++ b/registration/clitkCorrelationRatioImageToImageMetric.txx @@ -168,7 +168,7 @@ CorrelationRatioImageToImageMetric //check in which bin the fixed value belongs, get the index const double fixedImageBinTerm = (fixedValue - m_FixedImageMin) / m_FixedImageBinSize; - const unsigned int fixedImageBinIndex = static_cast( vcl_floor(fixedImageBinTerm ) ); + const unsigned int fixedImageBinIndex = static_cast( std::floor(fixedImageBinTerm ) ); //adapt the measures per bin this->m_mMSVPB[fixedImageBinIndex]+=movingSquaredValue; this->m_mSMVPB[fixedImageBinIndex]+=movingValue; @@ -289,7 +289,7 @@ CorrelationRatioImageToImageMetric typename MovingImageType::IndexType mappedIndex; for( unsigned int j = 0; j < MovingImageType::ImageDimension; j++ ) { - mappedIndex[j] = static_cast( vnl_math_rnd( tempIndex[j] ) ); + mappedIndex[j] = static_cast( std::round( tempIndex[j] ) ); } const GradientPixelType gradient = @@ -409,7 +409,7 @@ CorrelationRatioImageToImageMetric typename MovingImageType::IndexType mappedIndex; for( unsigned int j = 0; j < MovingImageType::ImageDimension; j++ ) { - mappedIndex[j] = static_cast( vnl_math_rnd( tempIndex[j] ) ); + mappedIndex[j] = static_cast( std::round( tempIndex[j] ) ); } const GradientPixelType gradient = diff --git a/registration/clitkDeformationListStatisticsFilter.h b/registration/clitkDeformationListStatisticsFilter.h index 1a224ec..1651094 100644 --- a/registration/clitkDeformationListStatisticsFilter.h +++ b/registration/clitkDeformationListStatisticsFilter.h @@ -27,7 +27,11 @@ #include "itkImageRegionIterator.h" #include "itkImageRegionIteratorWithIndex.h" #include "itkNumericTraits.h" +#if ITK_VERSION_MAJOR <= 4 #include "itkSimpleFastMutexLock.h" +#else +#include +#endif #include "itkImageMaskSpatialObject.h" namespace clitk diff --git a/registration/clitkMultiResolutionPDEDeformableRegistration.txx b/registration/clitkMultiResolutionPDEDeformableRegistration.txx index c8312e6..73cb497 100644 --- a/registration/clitkMultiResolutionPDEDeformableRegistration.txx +++ b/registration/clitkMultiResolutionPDEDeformableRegistration.txx @@ -21,7 +21,6 @@ #include "itkRecursiveMultiResolutionPyramidImageFilter.h" #include "itkImageRegionIterator.h" -#include "vnl/vnl_math.h" namespace clitk { @@ -260,10 +259,10 @@ MultiResolutionPDEDeformableRegistrationGetNumberOfLevels() ); - unsigned int fixedLevel = vnl_math_min( (int) m_CurrentLevel, + unsigned int fixedLevel = std::min( (int) m_CurrentLevel, (int) m_FixedImagePyramid->GetNumberOfLevels() ); DeformationFieldPointer tempField = ITK_NULLPTR; @@ -387,9 +386,9 @@ MultiResolutionPDEDeformableRegistrationGetNumberOfLevels() ); - fixedLevel = vnl_math_min( (int) m_CurrentLevel, + fixedLevel = std::min( (int) m_CurrentLevel, (int) m_FixedImagePyramid->GetNumberOfLevels() ); // We can release data from pyramid which are no longer required. diff --git a/registration/clitkMultiResolutionPyramidRegionFilter.txx b/registration/clitkMultiResolutionPyramidRegionFilter.txx index 17c63d4..eeee602 100644 --- a/registration/clitkMultiResolutionPyramidRegionFilter.txx +++ b/registration/clitkMultiResolutionPyramidRegionFilter.txx @@ -68,14 +68,14 @@ namespace clitk const float scaleFactor = static_cast( m_Schedule[ level ][ dim ] ); size[ dim ] = static_cast( - vcl_floor(static_cast( inputSize[ dim ] ) / scaleFactor ) ); + std::floor(static_cast( inputSize[ dim ] ) / scaleFactor ) ); if( size[ dim ] < 1 ) { size[ dim ] = 1; } start[ dim ] = static_cast( - vcl_ceil(static_cast( inputStart[ dim ] ) / scaleFactor ) ); + std::ceil(static_cast( inputStart[ dim ] ) / scaleFactor ) ); } m_RegionPyramid[ level ].SetSize( size ); m_RegionPyramid[ level ].SetIndex( start ); diff --git a/registration/clitkOptNormalizedCorrelationImageToImageMetric.h b/registration/clitkOptNormalizedCorrelationImageToImageMetric.h index 067cd87..ea06571 100644 --- a/registration/clitkOptNormalizedCorrelationImageToImageMetric.h +++ b/registration/clitkOptNormalizedCorrelationImageToImageMetric.h @@ -24,8 +24,6 @@ #include "itkPoint.h" #include "itkIndex.h" -#include "itkMultiThreader.h" - namespace clitk { diff --git a/registration/clitkOptNormalizedCorrelationImageToImageMetric.txx b/registration/clitkOptNormalizedCorrelationImageToImageMetric.txx index ea2c52a..fbb52ca 100644 --- a/registration/clitkOptNormalizedCorrelationImageToImageMetric.txx +++ b/registration/clitkOptNormalizedCorrelationImageToImageMetric.txx @@ -310,7 +310,7 @@ NormalizedCorrelationImageToImageMetric } - const RealType denom = -1.0 * vcl_sqrt(sff * smm ); + const RealType denom = -1.0 * std::sqrt(sff * smm ); MeasureType measure; if( this->m_NumberOfPixelsCounted > 0 && denom != 0.0) { measure = sfm / denom; @@ -400,7 +400,7 @@ NormalizedCorrelationImageToImageMetric } - m_Denom = -1.0 * vcl_sqrt(m_SFF * m_SMM ); + m_Denom = -1.0 * std::sqrt(m_SFF * m_SMM ); MeasureType measure; if( this->m_NumberOfPixelsCounted > 0 && m_Denom != 0.0) { measure = m_SFM / m_Denom; diff --git a/registration/clitkOptNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.h b/registration/clitkOptNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.h index 208cb38..3afd1b6 100644 --- a/registration/clitkOptNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.h +++ b/registration/clitkOptNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.h @@ -24,8 +24,6 @@ #include "itkPoint.h" #include "itkIndex.h" -#include "itkMultiThreader.h" - namespace clitk { diff --git a/registration/clitkOptNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.txx b/registration/clitkOptNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.txx index 042b4b7..494c61a 100644 --- a/registration/clitkOptNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.txx +++ b/registration/clitkOptNormalizedCorrelationImageToImageMetricFor3DBLUTFFD.txx @@ -310,7 +310,7 @@ NormalizedCorrelationImageToImageMetricFor3DBLUTFFD } - const RealType denom = -1.0 * vcl_sqrt(sff * smm ); + const RealType denom = -1.0 * std::sqrt(sff * smm ); MeasureType measure; if( this->m_NumberOfPixelsCounted > 0 && denom != 0.0) { measure = sfm / denom; @@ -400,7 +400,7 @@ NormalizedCorrelationImageToImageMetricFor3DBLUTFFD } - m_Denom = -1.0 * vcl_sqrt(m_SFF * m_SMM ); + m_Denom = -1.0 * std::sqrt(m_SFF * m_SMM ); MeasureType measure; if( this->m_NumberOfPixelsCounted > 0 && m_Denom != 0.0) { measure = m_SFM / m_Denom; diff --git a/registration/clitkRecursiveSpatioTemporalMultiResolutionPyramidImageFilter.txx b/registration/clitkRecursiveSpatioTemporalMultiResolutionPyramidImageFilter.txx index c1dd208..822c4ef 100644 --- a/registration/clitkRecursiveSpatioTemporalMultiResolutionPyramidImageFilter.txx +++ b/registration/clitkRecursiveSpatioTemporalMultiResolutionPyramidImageFilter.txx @@ -27,8 +27,6 @@ #include "itkShrinkImageFilter.h" #include "itkIdentityTransform.h" -#include "vnl/vnl_math.h" - namespace clitk { @@ -147,7 +145,7 @@ RecursiveSpatioTemporalMultiResolutionPyramidImageFilterGetSchedule()[ilevel][idim] / this->GetSchedule()[ilevel+1][idim]; } - variance[idim] = vnl_math_sqr( 0.5 * + variance[idim] = std::sqr( 0.5 * static_cast( factors[idim] ) ); if( factors[idim] != 1 ) { @@ -314,7 +312,7 @@ RecursiveSpatioTemporalMultiResolutionPyramidImageFilter 1 ) { oper->SetDirection( idim ); - oper->SetVariance( vnl_math_sqr( 0.5 * + oper->SetVariance( std::sqr( 0.5 * static_cast( factors[idim] ) ) ); oper->CreateDirectional(); radius[idim] = oper->GetRadius()[idim]; @@ -352,7 +350,7 @@ RecursiveSpatioTemporalMultiResolutionPyramidImageFilter 1 ) { oper->SetDirection( idim ); - oper->SetVariance( vnl_math_sqr( 0.5 * + oper->SetVariance( std::sqr( 0.5 * static_cast( factors[idim] ) ) ); oper->CreateDirectional(); radius[idim] = oper->GetRadius()[idim]; @@ -367,14 +365,14 @@ RecursiveSpatioTemporalMultiResolutionPyramidImageFilter( vcl_floor( + requestedSize[idim] = static_cast( std::floor( static_cast(requestedSize[idim]) / static_cast(factors[idim]) ) ); if( requestedSize[idim] < 1 ) { requestedSize[idim] = 1; } - requestedIndex[idim] = static_cast( vcl_ceil( + requestedIndex[idim] = static_cast( std::ceil( static_cast(requestedIndex[idim]) / static_cast(factors[idim]) ) ); @@ -450,7 +448,7 @@ RecursiveSpatioTemporalMultiResolutionPyramidImageFilterSetDirection(idim); - oper->SetVariance( vnl_math_sqr( 0.5 * static_cast( + oper->SetVariance( std::sqr( 0.5 * static_cast( this->GetSchedule()[refLevel][idim] ) ) ); oper->SetMaximumError( this->GetMaximumError() ); oper->CreateDirectional(); diff --git a/registration/clitkShapedBLUTSpatioTemporalDeformableTransform.txx b/registration/clitkShapedBLUTSpatioTemporalDeformableTransform.txx index 7cc0107..a57ead0 100644 --- a/registration/clitkShapedBLUTSpatioTemporalDeformableTransform.txx +++ b/registration/clitkShapedBLUTSpatioTemporalDeformableTransform.txx @@ -478,7 +478,7 @@ namespace clitk // when spline order is even. // The valid interval for evaluation is [start+offset, last-offset) // when spline order is odd. - // Where offset = vcl_floor(spline / 2 ). + // Where offset = std::floor(spline / 2 ). // Note that the last pixel is not included in the valid region // with odd spline orders. typename RegionType::SizeType size = m_PaddedGridRegion.GetSize(); diff --git a/registration/clitkSpatioTemporalMultiResolutionImageRegistrationMethod.txx b/registration/clitkSpatioTemporalMultiResolutionImageRegistrationMethod.txx index 4d67baf..405b2c6 100644 --- a/registration/clitkSpatioTemporalMultiResolutionImageRegistrationMethod.txx +++ b/registration/clitkSpatioTemporalMultiResolutionImageRegistrationMethod.txx @@ -280,14 +280,14 @@ SpatioTemporalMultiResolutionImageRegistrationMethod const float scaleFactor = static_cast( schedule[ level ][ dim ] ); size[ dim ] = static_cast( - vcl_floor(static_cast( inputSize[ dim ] ) / scaleFactor ) ); + std::floor(static_cast( inputSize[ dim ] ) / scaleFactor ) ); if( size[ dim ] < 1 ) { size[ dim ] = 1; } start[ dim ] = static_cast( - vcl_ceil(static_cast( inputStart[ dim ] ) / scaleFactor ) ); + std::ceil(static_cast( inputStart[ dim ] ) / scaleFactor ) ); } m_FixedImageRegionPyramid[ level ].SetSize( size ); m_FixedImageRegionPyramid[ level ].SetIndex( start ); diff --git a/registration/clitkSpatioTemporalMultiResolutionPyramidImageFilter.txx b/registration/clitkSpatioTemporalMultiResolutionPyramidImageFilter.txx index 4c01738..d6b3c88 100644 --- a/registration/clitkSpatioTemporalMultiResolutionPyramidImageFilter.txx +++ b/registration/clitkSpatioTemporalMultiResolutionPyramidImageFilter.txx @@ -26,8 +26,6 @@ #include "itkShrinkImageFilter.h" #include "itkIdentityTransform.h" -#include "vnl/vnl_math.h" - namespace clitk { @@ -218,7 +216,7 @@ SpatioTemporalMultiResolutionPyramidImageFilter // schedule[level-1] ); if( level > 0 ) { - m_Schedule[level][dim] = vnl_math_min( m_Schedule[level][dim], m_Schedule[level-1][dim] ); + m_Schedule[level][dim] = std::min( m_Schedule[level][dim], m_Schedule[level-1][dim] ); } if( m_Schedule[level][dim] < 1 ) @@ -331,7 +329,7 @@ SpatioTemporalMultiResolutionPyramidImageFilter for( idim = 0; idim < ImageDimension; idim++ ) { factors[idim] = m_Schedule[ilevel][idim]; - variance[idim] = vnl_math_sqr( 0.5 * + variance[idim] = std::sqr( 0.5 * static_cast( factors[idim] ) ); } @@ -433,11 +431,11 @@ SpatioTemporalMultiResolutionPyramidImageFilter outputSpacing[idim] = inputSpacing[idim] * shrinkFactor; outputSize[idim] = static_cast( - vcl_floor(static_cast(inputSize[idim]) / shrinkFactor ) ); + std::floor(static_cast(inputSize[idim]) / shrinkFactor ) ); if( outputSize[idim] < 1 ) { outputSize[idim] = 1; } outputStartIndex[idim] = static_cast( - vcl_ceil(static_cast(inputStartIndex[idim]) / shrinkFactor ) ); + std::ceil(static_cast(inputStartIndex[idim]) / shrinkFactor ) ); } //Now compute the new shifted origin for the updated levels; const typename OutputImageType::PointType::VectorType outputOriginOffset @@ -528,11 +526,11 @@ SpatioTemporalMultiResolutionPyramidImageFilter double factor = static_cast( m_Schedule[ilevel][idim] ); outputSize[idim] = static_cast( - vcl_floor(static_cast(baseSize[idim]) / factor ) ); + std::floor(static_cast(baseSize[idim]) / factor ) ); if( outputSize[idim] < 1 ) { outputSize[idim] = 1; } outputIndex[idim] = static_cast( - vcl_ceil(static_cast(baseIndex[idim]) / factor ) ); + std::ceil(static_cast(baseIndex[idim]) / factor ) ); } @@ -605,7 +603,7 @@ SpatioTemporalMultiResolutionPyramidImageFilter for( idim = 0; idim < TInputImage::ImageDimension; idim++ ) { oper->SetDirection(idim); - oper->SetVariance( vnl_math_sqr( 0.5 * static_cast( + oper->SetVariance( std::sqr( 0.5 * static_cast( m_Schedule[refLevel][idim] ) ) ); oper->SetMaximumError( m_MaximumError ); oper->CreateDirectional(); diff --git a/registration/itkOptMattesMutualInformationImageToImageMetricFor3DBLUTFFD.h b/registration/itkOptMattesMutualInformationImageToImageMetricFor3DBLUTFFD.h index c51414e..79bd1c1 100644 --- a/registration/itkOptMattesMutualInformationImageToImageMetricFor3DBLUTFFD.h +++ b/registration/itkOptMattesMutualInformationImageToImageMetricFor3DBLUTFFD.h @@ -46,8 +46,6 @@ #include "itkBSplineDeformableTransform.h" #include "itkArray2D.h" -#include "itkMultiThreader.h" - namespace itk { diff --git a/registration/itkOptMattesMutualInformationImageToImageMetricFor3DBLUTFFD.txx b/registration/itkOptMattesMutualInformationImageToImageMetricFor3DBLUTFFD.txx index ef4257e..9f71766 100644 --- a/registration/itkOptMattesMutualInformationImageToImageMetricFor3DBLUTFFD.txx +++ b/registration/itkOptMattesMutualInformationImageToImageMetricFor3DBLUTFFD.txx @@ -768,9 +768,9 @@ MattesMutualInformationImageToImageMetricFor3DBLUTFFD // check for non-zero bin contribution if( jointPDFValue > 1e-16 && movingImagePDFValue > 1e-16 ) { - double pRatio = vcl_log(jointPDFValue / movingImagePDFValue ); + double pRatio = std::log(jointPDFValue / movingImagePDFValue ); if( fixedImagePDFValue > 1e-16) { - sum += jointPDFValue * ( pRatio - vcl_log(fixedImagePDFValue ) ); + sum += jointPDFValue * ( pRatio - std::log(fixedImagePDFValue ) ); } } // end if-block to check non-zero bin contribution @@ -1093,10 +1093,10 @@ MattesMutualInformationImageToImageMetricFor3DBLUTFFD // check for non-zero bin contribution if( jointPDFValue > 1e-16 && movingImagePDFValue > 1e-16 ) { - double pRatio = vcl_log(jointPDFValue / movingImagePDFValue ); + double pRatio = std::log(jointPDFValue / movingImagePDFValue ); if( fixedImagePDFValue > 1e-16) { - sum += jointPDFValue * ( pRatio - vcl_log(fixedImagePDFValue ) ); + sum += jointPDFValue * ( pRatio - std::log(fixedImagePDFValue ) ); } if( this->m_UseExplicitPDFDerivatives ) { diff --git a/registration/itkOptMeanSquaresImageToImageMetricFor3DBLUTFFD.h b/registration/itkOptMeanSquaresImageToImageMetricFor3DBLUTFFD.h index e12b42f..d23a9cd 100644 --- a/registration/itkOptMeanSquaresImageToImageMetricFor3DBLUTFFD.h +++ b/registration/itkOptMeanSquaresImageToImageMetricFor3DBLUTFFD.h @@ -40,8 +40,6 @@ #include "itkPoint.h" #include "itkIndex.h" -#include "itkMultiThreader.h" - namespace itk {