--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+#ifndef CLITKVectorArithmGENERICFILTER_TXX
+#define CLITKVectorArithmGENERICFILTER_TXX
+
+#include "clitkImageCommon.h"
+
+#include "itkMinimumMaximumImageCalculator.h"
+
+namespace clitk
+{
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+VectorArithmGenericFilter<args_info_type>::VectorArithmGenericFilter()
+ :ImageToImageGenericFilter<Self>("VectorArithmGenericFilter"),mTypeOfOperation(0)
+{
+ InitializeImageType<3>();
+ mIsOperationUseASecondImage = false;
+ mIsOutputScalar = false;
+ mOverwriteInputImage = true;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+template<unsigned int Dim>
+void VectorArithmGenericFilter<args_info_type>::InitializeImageType()
+{
+ ADD_VEC_IMAGE_TYPE(Dim,3u,float);
+ ADD_VEC_IMAGE_TYPE(Dim,3u,double);
+ ADD_VEC_IMAGE_TYPE(Dim,2u,float);
+ ADD_VEC_IMAGE_TYPE(Dim,2u,double);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+void VectorArithmGenericFilter<args_info_type>::EnableOverwriteInputImage(bool b)
+{
+ mOverwriteInputImage = b;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+void VectorArithmGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a)
+{
+ mArgsInfo=a;
+
+ // Set value
+ this->SetIOVerbose(mArgsInfo.verbose_flag);
+ mTypeOfOperation = mArgsInfo.operation_arg;
+ mDefaultPixelValue = mArgsInfo.pixelValue_arg;
+ mScalar = mArgsInfo.scalar_arg;
+ mOutputIsFloat = mArgsInfo.setFloatOutput_flag;
+
+ if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
+
+ if (mArgsInfo.input1_given) this->AddInputFilename(mArgsInfo.input1_arg);
+ if (mArgsInfo.input2_given) {
+ mIsOperationUseASecondImage = true;
+ this->AddInputFilename(mArgsInfo.input2_arg);
+ if (mArgsInfo.operation_arg == 1)
+ mIsOutputScalar = true;
+ }
+ else if (mArgsInfo.operation_arg == 5 || mArgsInfo.operation_arg == 6)
+ mIsOutputScalar = true;
+
+ if (mArgsInfo.output_given) this->SetOutputFilename(mArgsInfo.output_arg);
+
+ // Check type of operation (with scalar or with other image)
+ if ((mArgsInfo.input2_given) && (mArgsInfo.scalar_given)) {
+ std::cerr << "ERROR : you cannot provide both --scalar and --input2 option" << std::endl;
+ exit(-1);
+ }
+ if ((!mArgsInfo.input2_given) && (!mArgsInfo.scalar_given)) {
+ if (mArgsInfo.operation_arg < 5) {
+ std::cerr << "Such operation need the --scalar option." << std::endl;
+ exit(-1);
+ }
+ }
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+template<class ImageType>
+void VectorArithmGenericFilter<args_info_type>::UpdateWithInputImageType()
+{
+ // Read input1
+ typename ImageType::Pointer input1 = this->template GetInput<ImageType>(0);
+
+ // Set input image iterator
+ typedef itk::ImageRegionIterator<ImageType> IteratorType;
+ IteratorType it(input1, input1->GetLargestPossibleRegion());
+
+ // typedef input2
+ typename ImageType::Pointer input2 = NULL;
+ IteratorType it2;
+
+ // Special case for normalisation
+ /*
+ if (mTypeOfOperation == 12) {
+ typedef itk::MinimumMaximumImageCalculator<ImageType> MinMaxFilterType;
+ typename MinMaxFilterType::Pointer ff = MinMaxFilterType::New();
+ ff->SetImage(input1);
+ ff->ComputeMaximum();
+ mScalar = ff->GetMaximum();
+ mTypeOfOperation = 11; // divide
+ }
+ */
+
+ if (mIsOperationUseASecondImage) {
+ // Read input2
+ input2 = this->template GetInput<ImageType>(1);
+ // Set input image iterator
+ it2 = IteratorType(input2, input2->GetLargestPossibleRegion());
+ // Check dimension
+ if (!clitk::HaveSameSize<ImageType, ImageType>(input1, input2)) {
+ itkExceptionMacro(<< "The images (input and input2) must have the same size");
+ }
+ if(!clitk::HaveSameSpacing<ImageType, ImageType>(input1, input2)) {
+ itkWarningMacro(<< "The images (input and input2) do not have the same spacing. "
+ << "Using first input's information.");
+ }
+ }
+
+ // Check if overwrite and outputisfloat and pixeltype is not float -> do not overwrite
+ if (mOverwriteInputImage && mOutputIsFloat && (typeid(typename ImageType::PixelType) != typeid(float))) {
+ // std::cerr << "Warning. Could not use both mOverwriteInputImage and mOutputIsFloat, because input is "
+ // << typeid(PixelType).name()
+ // << std::endl;
+ mOverwriteInputImage = false;
+ }
+
+ // ---------------- Overwrite input Image ---------------------
+ if (mOverwriteInputImage && !mIsOutputScalar) {
+ // Set output iterator (to input1)
+ IteratorType ito = IteratorType(input1, input1->GetLargestPossibleRegion());
+ if (mIsOperationUseASecondImage) ComputeImage(it, it2, ito);
+ else ComputeImage(it, ito);
+ this->template SetNextOutput<ImageType>(input1);
+ }
+
+ // ---------------- Create new output Image ---------------------
+ else {
+ // Create output image
+ if (!mIsOutputScalar) {
+ typedef ImageType OutputImageType;
+ typename OutputImageType::Pointer output = OutputImageType::New();
+ output->SetRegions(input1->GetLargestPossibleRegion());
+ output->SetOrigin(input1->GetOrigin());
+ output->SetSpacing(input1->GetSpacing());
+ output->Allocate();
+ // Set output iterator
+ typedef itk::ImageRegionIterator<OutputImageType> IteratorOutputType;
+ IteratorOutputType ito = IteratorOutputType(output, output->GetLargestPossibleRegion());
+ if (mIsOperationUseASecondImage) ComputeImage(it, it2, ito);
+ else ComputeImage(it, ito);
+ this->template SetNextOutput<OutputImageType>(output);
+ }
+ else {
+ // Create scalar output image
+ typedef itk::Image<typename ImageType::PixelType::ValueType, ImageType::ImageDimension> OutputImageType;
+ typename OutputImageType::Pointer output = OutputImageType::New();
+ output->SetRegions(input1->GetLargestPossibleRegion());
+ output->SetOrigin(input1->GetOrigin());
+ output->SetSpacing(input1->GetSpacing());
+ output->Allocate();
+ // Set output iterator
+ typedef itk::ImageRegionIterator<OutputImageType> IteratorOutputType;
+ IteratorOutputType ito = IteratorOutputType(output, output->GetLargestPossibleRegion());
+ if (mIsOperationUseASecondImage) ComputeScalarImage(it, it2, ito);
+ else ComputeScalarImage(it, ito);
+ this->template SetNextOutput<OutputImageType>(output);
+ }
+ }
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+template<class Iter1, class Iter2, class Iter3>
+void VectorArithmGenericFilter<args_info_type>::ComputeImage(Iter1 it1, Iter2 it2, Iter3 ito)
+{
+ it1.GoToBegin();
+ it2.GoToBegin();
+ ito.GoToBegin();
+ typedef typename Iter3::PixelType PixelType;
+
+ switch (mTypeOfOperation) {
+ case 0: // Addition
+ while (!ito.IsAtEnd()) {
+ ito.Set(it1.Get() + it2.Get());
+ ++it1;
+ ++it2;
+ ++ito;
+ }
+ break;
+ /*
+ case 1: // Multiply
+ while (!ito.IsAtEnd()) {
+ ito.Set(it1.Get() * it2.Get()) );
+ ++it1;
+ ++it2;
+ ++ito;
+ }
+ break;
+ */
+ /*
+ case 2: // Divide
+ while (!ito.IsAtEnd()) {
+ if (it1.Get() != 0)
+ ito.Set(it1.Get() / it2.Get()));
+ else ito.Set(mDefaultPixelValue);
+ ++it1;
+ ++it2;
+ ++ito;
+ }
+ break;
+ case 3: // Max
+ while (!ito.IsAtEnd()) {
+ if (it1.Get() < it2.Get()) ito.Set(it2.Get());
+ ++it1;
+ ++it2;
+ ++ito;
+ }
+ break;
+ case 4: // Min
+ while (!ito.IsAtEnd()) {
+ if (it1.Get() > it2.Get()) ito.Set(it2.Get());
+ ++it1;
+ ++it2;
+ ++ito;
+ }
+ break;
+ */
+ /*
+ case 5: // Absolute difference
+ while (!ito.IsAtEnd()) {
+ ito.Set(it2.Get()-it1.Get());
+ ++it1;
+ ++it2;
+ ++ito;
+ }
+ break;
+ */
+ /*
+ case 6: // Squared differences
+ while (!ito.IsAtEnd()) {
+ ito.Set(pow(it1.Get()-it2.Get(),2)));
+ ++it1;
+ ++it2;
+ ++ito;
+ }
+ break;
+ */
+ case 7: // Difference
+ while (!ito.IsAtEnd()) {
+ ito.Set(it1.Get()-it2.Get());
+ ++it1;
+ ++it2;
+ ++ito;
+ }
+ break;
+ /*
+ case 8: // Relative Difference
+ while (!ito.IsAtEnd()) {
+ if (it1.Get() != 0) ito.Set(PixelTypeDownCast<double, PixelType>(((double)it1.Get()-(double)it2.Get()))/(double)it1.Get());
+ else ito.Set(0.0);
+ ++it1;
+ ++it2;
+ ++ito;
+ }
+ break;
+ */
+ /*
+ case 9: // CrossProduct
+ while (!ito.IsAtEnd()) {
+ ito.Set(it1.Get()^it2.Get());
+ ++it1;
+ ++it2;
+ ++ito;
+ }
+ break;
+ */
+ default: // error ?
+ std::cerr << "ERROR : the operation number (" << mTypeOfOperation << ") is not known." << std::endl;
+ exit(-1);
+ }
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+template<class Iter1, class Iter2>
+void clitk::VectorArithmGenericFilter<args_info_type>::ComputeImage(Iter1 it, Iter2 ito)
+{
+ ito.GoToBegin();
+ it.GoToBegin();
+
+ typedef typename Iter1::PixelType PixelType;
+
+ PixelType scalar_vector;
+ scalar_vector.Fill(mScalar);
+
+ // Perform operation
+ switch (mTypeOfOperation) {
+ case 0: // Addition
+ while (!it.IsAtEnd()) {
+ ito.Set(it.Get() + scalar_vector);
+ ++it;
+ ++ito;
+ }
+ break;
+ case 1: // Multiply
+ while (!it.IsAtEnd()) {
+ ito.Set(it.Get() * mScalar);
+ ++it;
+ ++ito;
+ }
+ break;
+ /*
+ case 2: // Inverse
+ while (!it.IsAtEnd()) {
+ if (it.Get() != 0)
+ ito.Set(mScalar / it.Get()));
+ else ito.Set(mDefaultPixelValue);
+ ++it;
+ ++ito;
+ }
+ break;
+ case 3: // Max
+ while (!it.IsAtEnd()) {
+ if (it.Get() < mScalar) ito.Set(PixelTypeDownCast<double, PixelType>(mScalar));
+ else ito.Set(PixelTypeDownCast<double, PixelType>(it.Get()));
+ ++it;
+ ++ito;
+ }
+ break;
+ case 4: // Min
+ while (!it.IsAtEnd()) {
+ if (it.Get() > mScalar) ito.Set(PixelTypeDownCast<double, PixelType>(mScalar));
+ else ito.Set(PixelTypeDownCast<double, PixelType>(it.Get()));
+ ++it;
+ ++ito;
+ }
+ break;
+ */
+ /*
+ case 5: // Absolute value
+ while (!it.IsAtEnd()) {
+ ito.Set(PixelTypeDownCast<double, PixelType>(it.GetNorm()));
+ ++it;
+ ++ito;
+ }
+ break;
+ case 6: // Squared value
+ while (!it.IsAtEnd()) {
+ ito.Set(PixelTypeDownCast<double, PixelType>(it.GetSquaredNorm());
+ ++it;
+ ++ito;
+ }
+ break;
+ */
+ /*
+ case 7: // Log
+ while (!it.IsAtEnd()) {
+ if (it.Get() > 0)
+ ito.Set(PixelTypeDownCast<double, PixelType>(log((double)it.Get())));
+ else ito.Set(mDefaultPixelValue);
+ ++it;
+ ++ito;
+ }
+ break;
+ case 8: // exp
+ while (!it.IsAtEnd()) {
+ ito.Set(PixelTypeDownCast<double, PixelType>(exp((double)it.Get())));
+ ++it;
+ ++ito;
+ }
+ break;
+ case 9: // sqrt
+ while (!it.IsAtEnd()) {
+ if (it.Get() > 0)
+ ito.Set(PixelTypeDownCast<double, PixelType>(sqrt((double)it.Get())));
+ else {
+ if (it.Get() ==0) ito.Set(0);
+ else ito.Set(mDefaultPixelValue);
+ }
+ ++it;
+ ++ito;
+ }
+ break;
+ case 10: // exp
+ while (!it.IsAtEnd()) {
+ ito.Set(PixelTypeDownCast<double, PixelType>((0x10000 - (double)it.Get())/mScalar));
+ ++it;
+ ++ito;
+ }
+ break;
+ */
+ case 11: // divide
+ while (!it.IsAtEnd()) {
+ ito.Set(it.Get() / mScalar);
+ ++it;
+ ++ito;
+ }
+ break;
+ case 12: // normalize
+ while (!it.IsAtEnd()) {
+ PixelType n = it.Get();
+ n.Normalize();
+ ito.Set(n);
+ ++it;
+ ++ito;
+ }
+ break;
+ default: // error ?
+ std::cerr << "ERROR : the operation number (" << mTypeOfOperation << ") is not known." << std::endl;
+ exit(-1);
+ }
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+template<class Iter1, class Iter2, class Iter3>
+void VectorArithmGenericFilter<args_info_type>::ComputeScalarImage(Iter1 it1, Iter2 it2, Iter3 ito)
+{
+ it1.GoToBegin();
+ it2.GoToBegin();
+ ito.GoToBegin();
+ typedef typename Iter3::PixelType PixelType;
+
+ switch (mTypeOfOperation) {
+ case 1: // Multiply
+ while (!ito.IsAtEnd()) {
+ ito.Set(it1.Get() * it2.Get());
+ ++it1;
+ ++it2;
+ ++ito;
+ }
+ break;
+ default: // error ?
+ std::cerr << "ERROR : the operation number (" << mTypeOfOperation << ") is not known." << std::endl;
+ exit(-1);
+ }
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+template<class Iter1, class Iter2>
+void clitk::VectorArithmGenericFilter<args_info_type>::ComputeScalarImage(Iter1 it, Iter2 ito)
+{
+ ito.GoToBegin();
+ it.GoToBegin();
+
+ typedef typename Iter2::PixelType PixelType;
+
+
+ // Perform operation
+ switch (mTypeOfOperation) {
+ case 5: // Absolute value
+ while (!it.IsAtEnd()) {
+ ito.Set(PixelTypeDownCast<double, PixelType>(it.Get().GetNorm()));
+ ++it;
+ ++ito;
+ }
+ break;
+ case 6: // Squared value
+ while (!it.IsAtEnd()) {
+ ito.Set(PixelTypeDownCast<double, PixelType>(it.Get().GetSquaredNorm()));
+ ++it;
+ ++ito;
+ }
+ break;
+ default: // error ?
+ std::cerr << "ERROR : the operation number (" << mTypeOfOperation << ") is not known." << std::endl;
+ exit(-1);
+ }
+}
+//--------------------------------------------------------------------
+
+
+} // end namespace
+
+#endif //#define CLITKVectorArithmGENERICFILTER_TXX
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff