1 /*=========================================================================
2 Program: vv http://www.creatis.insa-lyon.fr/rio/vv
5 - University of LYON http://www.universite-lyon.fr/
6 - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
7 - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
9 This software is distributed WITHOUT ANY WARRANTY; without even
10 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
11 PURPOSE. See the copyright notices for more information.
13 It is distributed under dual licence
15 - BSD See included LICENSE.txt file
16 - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
17 ======================================================================-====*/
19 #ifndef CLITKAFFINEREGISTRATIONGENERICFILTER_TXX
20 #define CLITKAFFINEREGISTRATIONGENERICFILTER_TXX
25 //==============================================================================
26 //Creating an observer class that allows us to monitor the registration
27 //================================================================================
28 class CommandIterationUpdate : public itk::Command
31 typedef CommandIterationUpdate Self;
32 typedef itk::Command Superclass;
33 typedef itk::SmartPointer<Self> Pointer;
36 CommandIterationUpdate() {};
38 typedef clitk::GenericOptimizer<args_info_clitkAffineRegistration> OptimizerType;
39 typedef const OptimizerType * OptimizerPointer;
41 // Set the generic optimizer
42 void SetOptimizer(OptimizerPointer o) {
47 void Execute(itk::Object *caller, const itk::EventObject & event) {
48 Execute( (const itk::Object *)caller, event);
51 void Execute(const itk::Object * object, const itk::EventObject & event) {
52 if ( !(itk::IterationEvent().CheckEvent( &event )) ) {
56 m_Optimizer->OutputIterationInfo();
59 OptimizerPointer m_Optimizer;
61 //==================================================================================================================================//
63 //===================================================================================================================================//
65 template<class args_info_clitkAffineRegistration>
66 AffineRegistrationGenericFilter<args_info_clitkAffineRegistration>::AffineRegistrationGenericFilter():
67 ImageToImageGenericFilter<Self>("Register")
70 InitializeImageType<2>();
71 InitializeImageType<3>();
74 //==========================================================================================================//
75 //============================================================================================================//
76 //--------------------------------------------------------------------
77 template<class args_info_type>
78 template<unsigned int Dim>
79 void AffineRegistrationGenericFilter<args_info_type>::InitializeImageType()
81 ADD_DEFAULT_IMAGE_TYPES(Dim);
83 //--------------------------------------------------------------------
86 //==============================================================================
87 //Creating an observer class that allows us to change parameters at subsequent levels
88 //==============================================================================
89 template <typename TRegistration, class args_info_clitkAffineRegistration>
90 class RegistrationInterfaceCommand : public itk::Command
93 typedef RegistrationInterfaceCommand Self;
94 typedef itk::Command Superclass;
95 typedef itk::SmartPointer<Self> Pointer;
98 RegistrationInterfaceCommand() {};
102 typedef TRegistration RegistrationType;
103 typedef RegistrationType * RegistrationPointer;
106 typedef typename RegistrationType::FixedImageType InternalImageType;
107 typedef clitk::GenericMetric<args_info_clitkAffineRegistration, InternalImageType, InternalImageType> GenericMetricType;
109 // Two arguments are passed to the Execute() method: the first
110 // is the pointer to the object which invoked the event and the
111 // second is the event that was invoked.
112 void Execute(itk::Object * object, const itk::EventObject & event) {
113 if ( !(itk::IterationEvent().CheckEvent( &event )) ) {
118 RegistrationPointer registration = dynamic_cast<RegistrationPointer>( object );
119 unsigned int numberOfLevels=registration->GetNumberOfLevels();
120 unsigned int currentLevel=registration->GetCurrentLevel()+1;
123 std::cout<<std::endl;
124 std::cout<<"========================================"<<std::endl;
125 std::cout<<"Starting resolution level "<<currentLevel<<" of "<<numberOfLevels<<"..."<<std::endl;
126 std::cout<<"========================================"<<std::endl;
127 std::cout<<std::endl;
130 if (currentLevel>1) {
131 // Reinitialize the metric (!= number of samples)
132 typename GenericMetricType::Pointer genericMetric= GenericMetricType::New();
133 genericMetric->SetArgsInfo(m_ArgsInfo);
134 genericMetric->SetFixedImage(registration->GetFixedImagePyramid()->GetOutput(registration->GetCurrentLevel()));
135 if (m_ArgsInfo.referenceMask_given) genericMetric->SetFixedImageMask(registration->GetMetric()->GetFixedImageMask());
136 typedef itk::ImageToImageMetric< InternalImageType, InternalImageType > MetricType;
137 typename MetricType::Pointer metric=genericMetric->GetMetricPointer();
138 registration->SetMetric(metric);
142 void Execute(const itk::Object * , const itk::EventObject & ) {
146 void SetArgsInfo(args_info_clitkAffineRegistration a) {
149 args_info_clitkAffineRegistration m_ArgsInfo;
152 //==============================================================================================//
154 //==============================================================================================//
155 template<class args_info_clitkAffineRegistration>
156 void AffineRegistrationGenericFilter<args_info_clitkAffineRegistration>::SetArgsInfo(const args_info_clitkAffineRegistration & a)
159 if (m_ArgsInfo.reference_given) AddInputFilename(m_ArgsInfo.reference_arg);
160 if (m_ArgsInfo.target_given) {
161 AddInputFilename(m_ArgsInfo.target_arg);
164 if (m_ArgsInfo.output_given) SetOutputFilename(m_ArgsInfo.output_arg);
166 //==============================================================================
167 // Update with the number of dimensions and pixeltype
168 //==============================================================================
169 template<class args_info_clitkAffineRegistration>
170 template<class InputImageType>
171 void AffineRegistrationGenericFilter<args_info_clitkAffineRegistration>::UpdateWithInputImageType()
173 //=============================================================================
175 //=============================================================================
177 typedef typename InputImageType::PixelType PixelType;
178 //typedef typename InputImageType::ImageDimension Dimension;
181 bool threadsGiven=m_ArgsInfo.threads_given;
182 int threads=m_ArgsInfo.threads_arg;
184 //Coordinate Representation
185 typedef double TCoordRep;
188 typename InputImageType::Pointer fixedImage = this->template GetInput<InputImageType>(0);
190 typename InputImageType::Pointer inputFixedImage = this->template GetInput<InputImageType>(0);
193 typename InputImageType::Pointer movingImage = this->template GetInput<InputImageType>(1);
195 typename InputImageType::Pointer inputMovingImage = this->template GetInput<InputImageType>(1);
199 //The pixeltype of the fixed image will be used for output
200 typedef itk::Image< PixelType, InputImageType::ImageDimension > FixedImageType;
202 //Whatever the pixel type, internally we work with an image represented in float
203 typedef typename InputImageType::PixelType InternalPixelType;
204 typedef itk::Image< InternalPixelType, InputImageType::ImageDimension > InternalImageType;
206 //Read in the reference/fixed image
207 // typedef itk::ImageFileReader< InternalImageType > ReaderType;
208 // typename ReaderType::Pointer fixedImageReader = ReaderType::New();
209 // fixedImageReader->SetFileName( m_ArgsInfo.reference_arg);
212 //Read in the object/moving image
213 // typename ReaderType::Pointer movingImageReader = ReaderType::New();
214 // movingImageReader->SetFileName( m_ArgsInfo.target_arg );
215 if (m_Verbose) std::cout<<"Reading images..."<<std::endl;
216 // fixedImageReader->Update();
217 // movingImageReader->Update();
219 if (m_Verbose) std::cout << "Reading images... " << std::endl;
221 //we connect pointers to these internal images
222 // typedef typename fixedImageReader fixedImage;
223 // typedef typename movingImageReader movingImage;
225 //We keep the images used for input for possible output
226 // typedef typename fixedImageReader inputFixedImage;
227 // typedef typename movingImageReader inputMovingImage;
230 //============================================================================
232 //============================================================================
234 //If given, the intensities of both images are first normalized to a zero mean and SD of 1
235 // (usefull for MI, not necessary for Mattes' MI but performed anyway for the ouput)
236 if ( m_ArgsInfo.normalize_flag ) {
237 typedef itk::NormalizeImageFilter< InternalImageType,InternalImageType > NormalizeFilterType;
239 typename NormalizeFilterType::Pointer fixedNormalizeFilter = NormalizeFilterType::New();
240 typename NormalizeFilterType::Pointer movingNormalizeFilter = NormalizeFilterType::New();
242 fixedNormalizeFilter->SetInput( fixedImage );
243 movingNormalizeFilter->SetInput( movingImage );
245 fixedNormalizeFilter->Update();
246 movingNormalizeFilter->Update();
248 //We keep the images used for input for possible output
249 inputFixedImage= fixedNormalizeFilter->GetOutput();
250 inputMovingImage= movingNormalizeFilter->GetOutput();
252 //the pointers are reconnected for further output
253 fixedImage=fixedNormalizeFilter->GetOutput();
254 movingImage=movingNormalizeFilter->GetOutput();
256 if (m_Verbose) std::cout << "Normalizing image intensities to zero mean and SD of 1..." << std::endl;
260 //If given, the images are blurred before processing
261 if ( m_ArgsInfo.blur_arg!= 0) {
262 typedef itk::DiscreteGaussianImageFilter<InternalImageType,InternalImageType> GaussianFilterType;
263 typename GaussianFilterType::Pointer fixedSmoother = GaussianFilterType::New();
264 typename GaussianFilterType::Pointer movingSmoother = GaussianFilterType::New();
265 fixedSmoother->SetVariance( m_ArgsInfo.blur_arg );
266 movingSmoother->SetVariance(m_ArgsInfo.blur_arg );
268 fixedSmoother->SetInput( fixedImage );
269 movingSmoother->SetInput( movingImage );
271 fixedSmoother->Update();
272 movingSmoother->Update();
274 fixedImage=fixedSmoother->GetOutput();
275 movingImage=movingSmoother->GetOutput();
277 if (m_Verbose) std::cout << "Blurring images with a Gaussian with standard deviation of " << m_ArgsInfo.blur_arg <<"..." << std::endl;
281 //============================================================================
282 // Setting up the moving image in a reference system
283 //============================================================================
284 const itk::Vector<double, InputImageType::ImageDimension> movingResolution = movingImage->GetSpacing();
285 typename InternalImageType::RegionType movingRegion = movingImage->GetLargestPossibleRegion();
286 typename InternalImageType::RegionType::SizeType movingSize = movingRegion.GetSize();
288 // Print the parameters of the moving image
290 std::cout << "Object or Moving image:"<<std::endl;
291 std::cout << "Size: " << movingSize[0] << ", " << movingSize[1];
292 if (InputImageType::ImageDimension==3) std::cout<<", " << movingSize[2];
293 std::cout << std::endl;
295 std::cout<< "Resolution: "<< movingResolution[0] << ", " << movingResolution[1];
296 if (InputImageType::ImageDimension==3) std::cout<< ", " << movingResolution[2];
297 std::cout << std::endl;
301 //============================================================================
302 // Setting up the fixed image in a reference system
303 //============================================================================
304 const itk::Vector<double, InputImageType::ImageDimension> fixedResolution = fixedImage->GetSpacing();
305 typename InternalImageType::RegionType fixedRegion = fixedImage->GetLargestPossibleRegion();
306 typename InternalImageType::RegionType::SizeType fixedSize = fixedRegion.GetSize();
308 // Print the parameters of the moving image and the transform
310 std::cout << "Target or Moving image:"<<std::endl;
311 std::cout << "Size: " << fixedSize[0] << ", " << fixedSize[1];
312 if (InputImageType::ImageDimension==3) std::cout<<", " << fixedSize[2];
313 std::cout << std::endl;
315 std::cout<< "Resolution: "<< fixedResolution[0] << ", " << fixedResolution[1];
316 if (InputImageType::ImageDimension==3) std::cout<< ", " << fixedResolution[2];
317 std::cout << std::endl;
322 //===========================================================================
323 // If given, we connect a mask to reference or target
324 //============================================================================
325 typedef itk::ImageMaskSpatialObject< InputImageType::ImageDimension > MaskType;
326 typename MaskType::Pointer fixedMask=NULL;
327 if (m_ArgsInfo.referenceMask_given) {
328 fixedMask= MaskType::New();
329 typedef itk::Image< unsigned char, InputImageType::ImageDimension > ImageMaskType;
330 typedef itk::ImageFileReader< ImageMaskType > MaskReaderType;
331 typename MaskReaderType::Pointer maskReader = MaskReaderType::New();
332 maskReader->SetFileName(m_ArgsInfo.referenceMask_arg);
334 maskReader->Update();
335 } catch ( itk::ExceptionObject & err ) {
336 std::cerr << "ExceptionObject caught while reading mask !" << std::endl;
337 std::cerr << err << std::endl;
340 if (m_Verbose)std::cout <<"Reference image mask was read..." <<std::endl;
342 // Set the image to the spatialObject
343 fixedMask->SetImage( maskReader->GetOutput() );
346 typedef itk::ImageMaskSpatialObject< InputImageType::ImageDimension > MaskType;
347 typename MaskType::Pointer movingMask=NULL;
348 if (m_ArgsInfo.targetMask_given) {
349 movingMask= MaskType::New();
350 typedef itk::Image< unsigned char, InputImageType::ImageDimension > ImageMaskType;
351 typedef itk::ImageFileReader< ImageMaskType > MaskReaderType;
352 typename MaskReaderType::Pointer maskReader = MaskReaderType::New();
353 maskReader->SetFileName(m_ArgsInfo.targetMask_arg);
355 maskReader->Update();
356 } catch ( itk::ExceptionObject & err ) {
357 std::cerr << "ExceptionObject caught !" << std::endl;
358 std::cerr << err << std::endl;
360 if (m_Verbose)std::cout <<"Target image mask was read..." <<std::endl;
362 movingMask->SetImage( maskReader->GetOutput() );
366 //============================================================================
367 // The image pyramids
368 //============================================================================
369 typedef itk::RecursiveMultiResolutionPyramidImageFilter<InternalImageType,InternalImageType > FixedImagePyramidType;
370 typedef itk::RecursiveMultiResolutionPyramidImageFilter<InternalImageType,InternalImageType > MovingImagePyramidType;
371 typename FixedImagePyramidType::Pointer fixedImagePyramid = FixedImagePyramidType::New();
372 typename MovingImagePyramidType::Pointer movingImagePyramid = MovingImagePyramidType::New();
373 fixedImagePyramid->SetUseShrinkImageFilter(false);
374 fixedImagePyramid->SetInput(fixedImage);
375 fixedImagePyramid->SetNumberOfLevels(m_ArgsInfo.levels_arg);
376 movingImagePyramid->SetUseShrinkImageFilter(false);
377 movingImagePyramid->SetInput(movingImage);
378 movingImagePyramid->SetNumberOfLevels(m_ArgsInfo.levels_arg);
379 if (m_Verbose) std::cout<<"Creating the image pyramid..."<<std::endl;
380 fixedImagePyramid->Update();
381 movingImagePyramid->Update();
385 //============================================================================
386 // We retrieve the type of metric from the command line
387 //============================================================================
388 typedef clitk::GenericMetric<args_info_clitkAffineRegistration, InternalImageType, InternalImageType> GenericMetricType;
389 typename GenericMetricType::Pointer genericMetric=GenericMetricType::New();
390 genericMetric->SetArgsInfo(m_ArgsInfo);
391 genericMetric->SetFixedImage(fixedImagePyramid->GetOutput(0));
392 if (fixedMask) genericMetric->SetFixedImageMask(fixedMask);
393 typedef itk::ImageToImageMetric< InternalImageType, InternalImageType > MetricType;
394 typename MetricType::Pointer metric=genericMetric->GetMetricPointer();
395 if (movingMask) metric->SetMovingImageMask(movingMask);
397 #ifdef ITK_USE_OPTIMIZED_REGISTRATION_METHODS
398 if (threadsGiven) metric->SetNumberOfThreads( threads );
400 if (m_Verbose) std::cout<<"Not setting the number of threads (not compiled with USE_OPTIMIZED_REGISTRATION_METHODS)..."<<std::endl;
403 //============================================================================
404 // Initialize using image moments.
405 //============================================================================
406 if (m_ArgsInfo.moment_flag) {
407 typedef itk::ImageMomentsCalculator< InternalImageType > CalculatorType;
408 typename CalculatorType::Pointer fixedCalculator= CalculatorType::New();
410 typename InternalImageType::Pointer fixedThresh;
411 if (m_ArgsInfo.intThreshold_given) {
412 typedef itk::ThresholdImageFilter<InternalImageType> ThresholdImageFilterType;
413 typename ThresholdImageFilterType::Pointer thresholder = ThresholdImageFilterType::New();
414 thresholder->SetInput(fixedImage);
415 thresholder->SetLower(m_ArgsInfo.intThreshold_arg);
416 thresholder->Update();
417 fixedThresh=thresholder->GetOutput();
418 } else fixedThresh=fixedImage;
420 fixedCalculator->SetImage(fixedThresh);
421 fixedCalculator->Compute();
422 Vector<double, InputImageType::ImageDimension> fixedCenter=fixedCalculator->GetCenterOfGravity();
423 if (m_Verbose)std::cout<<"The fixed center of gravity is "<<fixedCenter<<"..."<<std::endl;
425 typedef itk::ImageMomentsCalculator< InternalImageType > CalculatorType;
426 typename CalculatorType::Pointer movingCalculator= CalculatorType::New();
428 typename InternalImageType::Pointer movingThresh;
429 if (m_ArgsInfo.intThreshold_given) {
430 typedef itk::ThresholdImageFilter<InternalImageType> ThresholdImageFilterType;
431 typename ThresholdImageFilterType::Pointer thresholder = ThresholdImageFilterType::New();
432 thresholder->SetInput(movingImage);
433 thresholder->SetLower(m_ArgsInfo.intThreshold_arg);
434 thresholder->Update();
435 movingThresh=thresholder->GetOutput();
436 } else movingThresh=movingImage;
438 movingCalculator->SetImage(movingThresh);
439 movingCalculator->Compute();
440 Vector<double, InputImageType::ImageDimension> movingCenter=movingCalculator->GetCenterOfGravity();
441 if (m_Verbose)std::cout<<"The moving center of gravity is "<<movingCenter<<"..."<<std::endl;
443 Vector<double, InputImageType::ImageDimension> shift= movingCenter-fixedCenter;
444 if (m_Verbose)std::cout<<"The initial shift applied is "<<shift<<"..."<<std::endl;
446 m_ArgsInfo.transX_arg= shift [0];
447 m_ArgsInfo.transY_arg= shift [1];
448 if (InputImageType::ImageDimension==3) m_ArgsInfo.transZ_arg=shift [2];
451 //============================================================================
453 //============================================================================
454 typedef clitk::GenericAffineTransform<args_info_clitkAffineRegistration, TCoordRep, InputImageType::ImageDimension > GenericAffineTransformType;
455 typename GenericAffineTransformType::Pointer genericAffineTransform = GenericAffineTransformType::New();
456 genericAffineTransform->SetArgsInfo(m_ArgsInfo);
457 typedef itk::Transform< double, InputImageType::ImageDimension, InputImageType::ImageDimension > TransformType;
458 typename TransformType::Pointer transform = genericAffineTransform->GetTransform();
461 //=======================================================
463 //=======================================================
464 typedef clitk::GenericInterpolator<args_info_clitkAffineRegistration, InternalImageType,TCoordRep > GenericInterpolatorType;
465 typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
466 genericInterpolator->SetArgsInfo(m_ArgsInfo);
467 typedef itk::InterpolateImageFunction< InternalImageType, TCoordRep > InterpolatorType;
468 typename InterpolatorType::Pointer interpolator=genericInterpolator->GetInterpolatorPointer();
471 //============================================================================
473 //============================================================================
474 typedef clitk::GenericOptimizer<args_info_clitkAffineRegistration> GenericOptimizerType;
475 unsigned int nParam = transform->GetNumberOfParameters();
476 typename GenericOptimizerType::Pointer genericOptimizer=GenericOptimizerType::New();
477 genericOptimizer->SetArgsInfo(m_ArgsInfo);
478 genericOptimizer->SetOutputIteration(m_Verbose);
479 genericOptimizer->SetOutputPosition(m_Verbose);
480 genericOptimizer->SetOutputValue(m_Verbose);
481 genericOptimizer->SetOutputGradient(m_ArgsInfo.gradient_flag);
482 genericOptimizer->SetMaximize(genericMetric->GetMaximize());
483 genericOptimizer->SetNumberOfParameters(nParam);
484 typedef itk::SingleValuedNonLinearOptimizer OptimizerType;
485 OptimizerType::Pointer optimizer=genericOptimizer->GetOptimizerPointer();
488 itk::Optimizer::ScalesType scales( nParam );
489 for (unsigned int i=nParam-InputImageType::ImageDimension; i<nParam; i++) //Translations
490 scales[i] = m_ArgsInfo.tWeight_arg;
491 for (unsigned int i=0; i<nParam-InputImageType::ImageDimension; i++) //Rest
492 scales[i] = m_ArgsInfo.rWeight_arg*180./M_PI;
493 optimizer->SetScales(scales);
494 //============================================================================
495 // Multiresolution registration
496 //============================================================================
497 typedef itk::MultiResolutionImageRegistrationMethod< InternalImageType,InternalImageType > RegistrationType;
498 typename RegistrationType::Pointer registration = RegistrationType::New();
499 registration->SetFixedImage( fixedImage );
500 registration->SetFixedImageRegion(fixedImage->GetLargestPossibleRegion());
501 registration->SetMovingImage( movingImage );
502 registration->SetFixedImagePyramid( fixedImagePyramid );
503 registration->SetMovingImagePyramid( movingImagePyramid );
504 registration->SetTransform( transform );
505 registration->SetInitialTransformParameters( transform->GetParameters() );
506 registration->SetInterpolator( interpolator );
507 registration->SetMetric(metric);
508 registration->SetOptimizer(optimizer);
509 registration->SetNumberOfLevels( m_ArgsInfo.levels_arg );
510 if (m_Verbose) std::cout << "Setting "<< m_ArgsInfo.levels_arg <<" resolution levels..." << std::endl;
511 if (m_Verbose) std::cout << "Initial Transform: "<< registration->GetInitialTransformParameters()<<std::endl;
513 //============================================================================
514 // Connecting the commander to the registration to monitor it
515 //============================================================================
518 // Output iteration info
519 CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New();
520 observer->SetOptimizer(genericOptimizer);
521 optimizer->AddObserver( itk::IterationEvent(), observer );
525 typedef RegistrationInterfaceCommand<RegistrationType, args_info_clitkAffineRegistration> CommandType;
526 typename CommandType::Pointer command = CommandType::New();
527 command->SetArgsInfo(m_ArgsInfo);
528 registration->AddObserver( itk::IterationEvent(), command );
533 //============================================================================
534 // Finally we can start the registration with the given amount of multiresolution levels
535 //============================================================================
536 if (m_Verbose) std::cout << "Starting the registration now..." << std::endl;
539 registration->StartRegistration();
540 } catch ( itk::ExceptionObject & err ) {
541 std::cerr << "ExceptionObject caught !" << std::endl;
542 std::cerr << err << std::endl;
546 //============================================================================
547 // Processing the result of the registration
548 //============================================================================
549 OptimizerType::ParametersType finalParameters = registration->GetLastTransformParameters();
550 std::cout<< "Result : " <<std::setprecision(12)<<std::endl;
552 for (unsigned int i=nParam-InputImageType::ImageDimension; i<nParam; i++) //Translations
553 std::cout << " Translation " << i << " = " << finalParameters[i];
554 for (unsigned int i=0; i<nParam-InputImageType::ImageDimension; i++) //Rest
555 std::cout << " Other parameter " << i << " = " << finalParameters[i];
558 itk::Matrix<double,InputImageType::ImageDimension+1,InputImageType::ImageDimension+1> matrix;
559 if (m_ArgsInfo.transform_arg == 3) {
560 for (unsigned int i=0; i<InputImageType::ImageDimension; i++) {
561 matrix[i][3] = finalParameters[nParam-InputImageType::ImageDimension+i];
562 for (unsigned int j=0; j<InputImageType::ImageDimension; j++) {
563 matrix[i][j] = finalParameters[i*3+j];
568 matrix = clitk::GetBackwardAffineMatrix<InputImageType::ImageDimension>(finalParameters);
571 std::cout << " Affine transform matrix =" << std::endl;
572 std::cout << matrix <<std::setprecision(6)<< std::endl;
574 // Write matrix to a file
575 if (m_ArgsInfo.matrix_given) {
577 mFile.open(m_ArgsInfo.matrix_arg);
578 mFile<<std::setprecision(12)<<matrix<< std::setprecision(6)<<std::endl;
582 //============================================================================
583 // Prepare the resampling filter in order to transform the moving image.
584 //============================================================================
585 if (m_ArgsInfo.output_given || m_ArgsInfo.checker_after_given || m_ArgsInfo.after_given ) {
586 transform->SetParameters( finalParameters );
587 typedef itk::ResampleImageFilter< InternalImageType,InternalImageType > ResampleFilterType;
588 typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
590 resampler->SetTransform( transform );
591 resampler->SetInput( movingImage );
592 resampler->SetSize( fixedImage->GetLargestPossibleRegion().GetSize() );
593 resampler->SetOutputOrigin( fixedImage->GetOrigin() );
594 resampler->SetOutputSpacing( fixedImage->GetSpacing() );
595 resampler->SetDefaultPixelValue( 0 );
598 if (m_ArgsInfo.output_given) {
599 //We write an output in the same pixeltype then the input
600 typedef itk::ImageFileWriter< FixedImageType > WriterType;
601 typename WriterType::Pointer outputWriter = WriterType::New();
602 outputWriter->SetFileName(m_ArgsInfo.output_arg );
603 outputWriter->SetInput( resampler->GetOutput() );
604 outputWriter->Update();
608 //============================================================================
610 //============================================================================
611 if (m_ArgsInfo.checker_after_given) {
612 //To display correctly the checkerboard image, the intensities must lie in the same range (normalized)
613 //We write the image in the internal image type
614 typedef itk::ResampleImageFilter< InternalImageType,InternalImageType > ResampleFilterType;
615 typename ResampleFilterType::Pointer internalResampler = ResampleFilterType::New();
616 internalResampler->SetTransform( transform );
617 internalResampler->SetInput( inputMovingImage );
618 internalResampler->SetSize( fixedImage->GetLargestPossibleRegion().GetSize() );
619 internalResampler->SetOutputOrigin( fixedImage->GetOrigin() );
620 internalResampler->SetOutputSpacing( fixedImage->GetSpacing() );
621 internalResampler->SetDefaultPixelValue( 0 );
623 //We pass the normalized images to the checker filter
624 typedef itk::CheckerBoardImageFilter< InternalImageType > CheckerBoardFilterType;
625 typename CheckerBoardFilterType::Pointer checkerFilter= CheckerBoardFilterType::New();
627 checkerFilter->SetInput1(inputFixedImage);
628 checkerFilter->SetInput2(internalResampler->GetOutput());
629 typedef itk::ImageFileWriter< InternalImageType > InternalWriterType;
630 typename InternalWriterType::Pointer checkerWriter = InternalWriterType::New();
631 checkerWriter->SetFileName(m_ArgsInfo.checker_after_arg);
632 checkerWriter->SetInput( checkerFilter->GetOutput() );
633 checkerWriter->Update();
637 //============================================================================
639 //============================================================================
640 if (m_ArgsInfo.checker_before_given) {
641 //To display correctly the checkerboard image, the intensities must lie in the same range (normalized)
642 //We write the image in the internal image type
643 //We pass the normalized images to the checker filter
644 typedef itk::CheckerBoardImageFilter< InternalImageType > CheckerBoardFilterType;
645 typename CheckerBoardFilterType::Pointer checkerFilter= CheckerBoardFilterType::New();
647 checkerFilter->SetInput1(inputFixedImage);
648 checkerFilter->SetInput2(inputMovingImage);
649 typedef itk::ImageFileWriter< InternalImageType > InternalWriterType;
650 typename InternalWriterType::Pointer checkerWriter = InternalWriterType::New();
651 checkerWriter->SetFileName(m_ArgsInfo.checker_before_arg);
652 checkerWriter->SetInput( checkerFilter->GetOutput() );
653 checkerWriter->Update();
657 //============================================================================
659 //============================================================================
660 if (m_ArgsInfo.after_given) {
661 typedef itk::SubtractImageFilter< InternalImageType, FixedImageType,FixedImageType > DifferenceImageFilterType;
662 typename DifferenceImageFilterType::Pointer differenceAfterFilter= DifferenceImageFilterType::New();
664 differenceAfterFilter->SetInput1(fixedImage);
665 differenceAfterFilter->SetInput2(resampler->GetOutput());
667 // Prepare a writer to write the difference image
668 typedef itk::ImageFileWriter< FixedImageType > WriterType;
669 typename WriterType::Pointer differenceAfterWriter = WriterType::New();
670 differenceAfterWriter->SetFileName(m_ArgsInfo.after_arg );
671 differenceAfterWriter->SetInput( differenceAfterFilter->GetOutput() );
672 differenceAfterWriter->Update();
676 //============================================================================
677 // Difference Before?
678 //============================================================================
679 if (m_ArgsInfo.before_given) {
680 typedef itk::CastImageFilter< InternalImageType,FixedImageType > CastFilterType;
681 typename CastFilterType::Pointer caster = CastFilterType::New();
682 caster->SetInput( movingImage );
684 typedef itk::SubtractImageFilter< InternalImageType, FixedImageType, FixedImageType > DifferenceImageFilterType;
685 typename DifferenceImageFilterType::Pointer differenceBeforeFilter= DifferenceImageFilterType::New();
688 differenceBeforeFilter->SetInput1(fixedImage);
689 differenceBeforeFilter->SetInput2(caster->GetOutput());
691 // Prepare a writer to write the difference image
692 typedef itk::ImageFileWriter< FixedImageType > WriterType;
693 typename WriterType::Pointer differenceBeforeWriter = WriterType::New();
694 differenceBeforeWriter->SetFileName(m_ArgsInfo.before_arg);
695 differenceBeforeWriter->SetInput( differenceBeforeFilter->GetOutput() );
696 differenceBeforeWriter->Update();
701 #endif //#define CLITKAFFINEREGISTRATIONGENERICFILTER_TXX