-/*-------------------------------------------------------------------------
-
- Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
- l'Image). All rights reserved. See Doc/License.txt or
- http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
-
+/*=========================================================================
+ 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://oncora1.lyon.fnclcc.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 above copyright notices for more information.
-
- -------------------------------------------------------------------------*/
+ 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 CLITKIMAGEARITHMGENERICFILTER_TXX
#define CLITKIMAGEARITHMGENERICFILTER_TXX
-/*-------------------------------------------------
- * @file clitkImageArithmGenericFilter.txx
- * @author David Sarrut <David.Sarrut@creatis.insa-lyon.fr>
- * @date 9 August 2006
- *
- -------------------------------------------------*/
+#include "clitkImageCommon.h"
+
+namespace clitk
+{
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+ImageArithmGenericFilter<args_info_type>::ImageArithmGenericFilter()
+ :ImageToImageGenericFilter<Self>("ImageArithmGenericFilter"),mTypeOfOperation(0)
+{
+ InitializeImageType<2>();
+ InitializeImageType<3>();
+ InitializeImageType<4>();
+ mIsOperationUseASecondImage = false;
+ mOverwriteInputImage = true;
+}
+//--------------------------------------------------------------------
+
//--------------------------------------------------------------------
+template<class args_info_type>
template<unsigned int Dim>
-void ImageArithmGenericFilter::Update_WithDim() {
-#define TRY_TYPE(TYPE) \
- if (IsSameType<TYPE>(mPixelTypeName)) { Update_WithDimAndPixelType<Dim, TYPE>(); return; }
- TRY_TYPE(char);
- TRY_TYPE(uchar);
- TRY_TYPE(short);
- TRY_TYPE(ushort);
- TRY_TYPE(int);
- TRY_TYPE(unsigned int);
- TRY_TYPE(float);
- TRY_TYPE(double);
-#undef TRY_TYPE
-
- std::string list = CreateListOfTypes<char, uchar, short, ushort, int, uint, float, double>();
- std::cerr << "Error, I don't know the type '" << mPixelTypeName << "' for the input image '"
- << mInputFilenames[0] << "'." << std::endl << "Known types are " << list << std::endl;
- exit(0);
+void ImageArithmGenericFilter<args_info_type>::InitializeImageType()
+{
+ ADD_DEFAULT_IMAGE_TYPES(Dim);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+void ImageArithmGenericFilter<args_info_type>::EnableOverwriteInputImage(bool b)
+{
+ mOverwriteInputImage = b;
}
//--------------------------------------------------------------------
+
//--------------------------------------------------------------------
-template<unsigned int Dim, class PixelType>
-void ImageArithmGenericFilter::Update_WithDimAndPixelType() {
+template<class args_info_type>
+void ImageArithmGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a)
+{
+ mArgsInfo=a;
+
+ // Set value
+ 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) AddInputFilename(mArgsInfo.input1_arg);
+ if (mArgsInfo.input2_given) {
+ mIsOperationUseASecondImage = true;
+ AddInputFilename(mArgsInfo.input2_arg);
+ }
+
+ if (mArgsInfo.output_given) 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 ImageArithmGenericFilter<args_info_type>::UpdateWithInputImageType()
+{
// Read input1
- typedef itk::Image<PixelType,Dim> ImageType;
- typename ImageType::Pointer input1 = clitk::readImage<ImageType>(mInputFilenames[0], mIOVerbose);
- typename ImageType::Pointer outputImage;
+ 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 = this->template GetInput<ImageType>(1);
+ IteratorType it2;
+
+ // Check dimension
+ if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input1, input2)) {
+ std::cerr << "* ERROR * the images (input and input2) must have the same size & spacing";
+ return;
+ }
- // Read input2 (float is ok altough it could take too memory ...)
if (mIsOperationUseASecondImage) {
- typedef itk::Image<float,Dim> ImageType2;
- typename ImageType2::Pointer input2 = clitk::readImage<ImageType2>(mInputFilenames[1], mIOVerbose);
- outputImage = ComputeImage<ImageType, ImageType2>(input1, input2);
+ // Read input2
+ input2 = this->template GetInput<ImageType>(1);
+ // Set input image iterator
+ it2 = IteratorType(input2, input2->GetLargestPossibleRegion());
}
- else {
- outputImage = ComputeImage<ImageType>(input1);
+
+ // 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) {
+ // 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);
}
- // Write results
- this->SetNextOutput<ImageType>(outputImage);
- //clitk::writeImage<ImageType>(outputImage, mOutputFilename, mIOVerbose);
+ // ---------------- Create new output Image ---------------------
+ else {
+ if (mOutputIsFloat) {
+ // Create output image
+ typedef itk::Image<float,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) ComputeImage(it, it2, ito);
+ else ComputeImage(it, ito);
+ this->template SetNextOutput<OutputImageType>(output);
+ } else {
+ // Create output image
+ 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);
+ }
+ }
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-template<class ImageType>
-typename ImageType::Pointer
-ImageArithmGenericFilter::ComputeImage(typename ImageType::Pointer inputImage) {
+template<class args_info_type>
+template<class Iter1, class Iter2, class Iter3>
+void ImageArithmGenericFilter<args_info_type>::ComputeImage(Iter1 it1, Iter2 it2, Iter3 ito)
+{
+ it1.GoToBegin();
+ it2.GoToBegin();
+ ito.GoToBegin();
+ typedef typename Iter3::PixelType PixelType;
- typedef typename ImageType::PixelType PixelType;
- typedef itk::ImageRegionIterator<ImageType> IteratorType;
- IteratorType it(inputImage, inputImage->GetLargestPossibleRegion());
+ switch (mTypeOfOperation) {
+ case 0: // Addition
+ while (!ito.IsAtEnd()) {
+ ito.Set(PixelTypeDownCast<double, PixelType>((double)it1.Get() + (double)it2.Get()) );
+ ++it1;
+ ++it2;
+ ++ito;
+ }
+ break;
+ case 1: // Multiply
+ while (!ito.IsAtEnd()) {
+ ito.Set(PixelTypeDownCast<double, PixelType>((double)it1.Get() * (double)it2.Get()) );
+ ++it1;
+ ++it2;
+ ++ito;
+ }
+ break;
+ case 2: // Divide
+ while (!ito.IsAtEnd()) {
+ if (it1.Get() != 0)
+ ito.Set(PixelTypeDownCast<double, PixelType>((double)it1.Get() / (double)it2.Get()));
+ else ito.Set(mDefaultPixelValue);
+ ++it1;
+ ++it2;
+ ++ito;
+ }
+ break;
+ case 3: // Max
+ while (!ito.IsAtEnd()) {
+ if (it1.Get() < it2.Get()) ito.Set(PixelTypeDownCast<double, PixelType>(it2.Get()));
+ ++it1;
+ ++it2;
+ ++ito;
+ }
+ break;
+ case 4: // Min
+ while (!ito.IsAtEnd()) {
+ if (it1.Get() > it2.Get()) ito.Set(PixelTypeDownCast<double, PixelType>(it2.Get()));
+ ++it1;
+ ++it2;
+ ++ito;
+ }
+ break;
+ case 5: // Absolute difference
+ DD("AbsoluteDifff");
+ while (!ito.IsAtEnd()) {
+ ito.Set(PixelTypeDownCast<double, PixelType>(fabs((double)it2.Get()-(double)it1.Get())));
+ ++it1;
+ ++it2;
+ ++ito;
+ }
+ break;
+ case 6: // Squared differences
+ while (!ito.IsAtEnd()) {
+ ito.Set(PixelTypeDownCast<double, PixelType>(pow((double)it1.Get()-(double)it2.Get(),2)));
+ ++it1;
+ ++it2;
+ ++ito;
+ }
+ break;
+ case 7: // Difference
+ while (!ito.IsAtEnd()) {
+ ito.Set(PixelTypeDownCast<double, PixelType>((double)it1.Get()-(double)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;
+ 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::ImageArithmGenericFilter<args_info_type>::ComputeImage(Iter1 it, Iter2 ito)
+{
+ ito.GoToBegin();
it.GoToBegin();
-
+ typedef typename Iter2::PixelType PixelType;
+
+ // Perform operation
switch (mTypeOfOperation) {
case 0: // Addition
while (!it.IsAtEnd()) {
- it.Set(PixelTypeDownCast<double, PixelType>((double)it.Get() + mScalar) );
+ ito.Set(clitk::PixelTypeDownCast<double, PixelType>((double)it.Get() + mScalar) );
++it;
+ ++ito;
}
break;
case 1: // Multiply
while (!it.IsAtEnd()) {
- it.Set(PixelTypeDownCast<double, PixelType>((double)it.Get() * mScalar) );
+ ito.Set(PixelTypeDownCast<double, PixelType>((double)it.Get() * mScalar) );
++it;
+ ++ito;
}
break;
case 2: // Inverse
while (!it.IsAtEnd()) {
if (it.Get() != 0)
- it.Set(PixelTypeDownCast<double, PixelType>(mScalar / (double)it.Get()));
- else it.Set(mDefaultPixelValue);
+ ito.Set(PixelTypeDownCast<double, PixelType>(mScalar / (double)it.Get()));
+ else ito.Set(mDefaultPixelValue);
++it;
+ ++ito;
}
break;
- case 3: // Max
+ case 3: // Max
while (!it.IsAtEnd()) {
- if (it.Get() < mScalar) it.Set(PixelTypeDownCast<double, PixelType>(mScalar));
+ 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) it.Set(PixelTypeDownCast<double, PixelType>(mScalar));
+ 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
+ case 5: // Absolute value
while (!it.IsAtEnd()) {
- if (it.Get() <= 0) it.Set(PixelTypeDownCast<double, PixelType>(-it.Get()));
+ if (it.Get() <= 0) ito.Set(PixelTypeDownCast<double, PixelType>(-it.Get()));
// <= zero to avoid warning for unsigned types
+ else ito.Set(PixelTypeDownCast<double, PixelType>(it.Get()));
++it;
+ ++ito;
}
break;
case 6: // Squared value
while (!it.IsAtEnd()) {
- it.Set(PixelTypeDownCast<double, PixelType>((double)it.Get()*(double)it.Get()));
+ ito.Set(PixelTypeDownCast<double, PixelType>((double)it.Get()*(double)it.Get()));
++it;
+ ++ito;
}
break;
case 7: // Log
while (!it.IsAtEnd()) {
- if (it.Get() > 0)
- it.Set(PixelTypeDownCast<double, PixelType>(log((double)it.Get())));
- else it.Set(mDefaultPixelValue);
+ 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()) {
- it.Set(PixelTypeDownCast<double, PixelType>(exp((double)it.Get())));
+ ito.Set(PixelTypeDownCast<double, PixelType>(exp((double)it.Get())));
++it;
+ ++ito;
}
break;
case 9: // sqrt
while (!it.IsAtEnd()) {
- if (it.Get() > 0)
- it.Set(PixelTypeDownCast<double, PixelType>(sqrt((double)it.Get())));
+ if (it.Get() > 0)
+ ito.Set(PixelTypeDownCast<double, PixelType>(sqrt((double)it.Get())));
else {
- if (it.Get() ==0) it.Set(0);
- else it.Set(mDefaultPixelValue);
+ if (it.Get() ==0) ito.Set(0);
+ else ito.Set(mDefaultPixelValue);
}
++it;
+ ++ito;
}
break;
default: // error ?
std::cerr << "ERROR : the operation number (" << mTypeOfOperation << ") is not known." << std::endl;
exit(-1);
}
-
- return inputImage;
}
//--------------------------------------------------------------------
-//--------------------------------------------------------------------
-template<class ImageType1, class ImageType2>
-typename ImageType1::Pointer
-ImageArithmGenericFilter::ComputeImage(typename ImageType1::Pointer inputImage1,
- typename ImageType2::Pointer inputImage2) {
-
- typedef typename ImageType1::PixelType PixelType;
- typedef itk::ImageRegionIterator<ImageType1> IteratorType;
- IteratorType it1(inputImage1, inputImage1->GetLargestPossibleRegion());
- it1.GoToBegin();
-
- typedef itk::ImageRegionConstIterator<ImageType2> ConstIteratorType;
- ConstIteratorType it2(inputImage2, inputImage2->GetLargestPossibleRegion());
- it2.GoToBegin();
-
- switch (mTypeOfOperation) {
- case 0: // Addition
- while (!it1.IsAtEnd()) {
- it1.Set(PixelTypeDownCast<double, PixelType>((double)it1.Get() + (double)it2.Get()) );
- ++it1; ++it2;
- }
- break;
- case 1: // Multiply
- while (!it1.IsAtEnd()) {
- it1.Set(PixelTypeDownCast<double, PixelType>((double)it1.Get() * (double)it2.Get()) );
- ++it1; ++it2;
- }
- break;
- case 2: // Divide
- while (!it1.IsAtEnd()) {
- if (it1.Get() != 0)
- it1.Set(PixelTypeDownCast<double, PixelType>((double)it1.Get() / (double)it2.Get()));
- else it1.Set(mDefaultPixelValue);
- ++it1; ++it2;
- }
- break;
- case 3: // Max
- while (!it1.IsAtEnd()) {
- if (it1.Get() < it2.Get()) it1.Set(PixelTypeDownCast<double, PixelType>(it2.Get()));
- ++it1; ++it2;
- }
- break;
- case 4: // Min
- while (!it1.IsAtEnd()) {
- if (it1.Get() > it2.Get()) it1.Set(PixelTypeDownCast<double, PixelType>(it2.Get()));
- ++it1; ++it2;
- }
- break;
- case 5: // Absolute difference
- while (!it1.IsAtEnd()) {
- it1.Set(PixelTypeDownCast<double, PixelType>(fabs(it2.Get()-it1.Get())));
- ++it1; ++it2;
- }
- break;
- case 6: // Squared differences
- while (!it1.IsAtEnd()) {
- it1.Set(PixelTypeDownCast<double, PixelType>(pow((double)it1.Get()-(double)it2.Get(),2)));
- ++it1; ++it2;
- }
- break;
- case 7: // Difference
- while (!it1.IsAtEnd()) {
- it1.Set(PixelTypeDownCast<double, PixelType>((double)it1.Get()-(double)it2.Get()));
- ++it1; ++it2;
- }
- break;
- case 8: // Relative Difference
- while (!it1.IsAtEnd()) {
- if (it1.Get() != 0) it1.Set(PixelTypeDownCast<double, PixelType>(((double)it1.Get()-(double)it2.Get()))/(double)it1.Get());
- else it1.Set(0.0);
- ++it1; ++it2;
- }
- break;
- default: // error ?
- std::cerr << "ERROR : the operation number (" << mTypeOfOperation << ") is not known." << std::endl;
- exit(-1);
- }
-
- return inputImage1;
-}
-//--------------------------------------------------------------------
+} // end namespace
#endif //#define CLITKIMAGEARITHMGENERICFILTER_TXX
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff