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_CXX
20 #define CLITKAFFINEREGISTRATIONGENERICFILTER_CXX
22 #include "clitkAffineRegistrationGenericFilter.h"
26 //==============================================================================
27 //Creating an observer class that allows us to monitor the registration
28 //================================================================================
29 class CommandIterationUpdate : public itk::Command
32 typedef CommandIterationUpdate Self;
33 typedef itk::Command Superclass;
34 typedef itk::SmartPointer<Self> Pointer;
37 CommandIterationUpdate() {};
39 typedef clitk::GenericOptimizer<args_info_clitkAffineRegistration> OptimizerType;
40 typedef const OptimizerType * OptimizerPointer;
42 // Set the generic optimizer
43 void SetOptimizer(OptimizerPointer o) {
48 void Execute(itk::Object *caller, const itk::EventObject & event) {
49 Execute( (const itk::Object *)caller, event);
52 void Execute(const itk::Object * object, const itk::EventObject & event) {
53 if ( !(itk::IterationEvent().CheckEvent( &event )) ) {
57 m_Optimizer->OutputIterationInfo();
60 OptimizerPointer m_Optimizer;
62 //==================================================================================================================================//
64 //===================================================================================================================================//
66 AffineRegistrationGenericFilter::AffineRegistrationGenericFilter():
67 ImageToImageGenericFilter<Self>("Register")
70 InitializeImageType<2>();
71 InitializeImageType<3>();
74 //==========================================================================================================//
75 //============================================================================================================//
76 //--------------------------------------------------------------------
77 template<unsigned int Dim>
78 void AffineRegistrationGenericFilter::InitializeImageType()
80 ADD_DEFAULT_IMAGE_TYPES(Dim);
82 //--------------------------------------------------------------------
85 //==============================================================================
86 //Creating an observer class that allows us to change parameters at subsequent levels
87 //==============================================================================
88 template <typename TRegistration>
89 class RegistrationInterfaceCommand : public itk::Command
92 typedef RegistrationInterfaceCommand Self;
93 typedef itk::Command Superclass;
94 typedef itk::SmartPointer<Self> Pointer;
97 RegistrationInterfaceCommand() {};
101 typedef TRegistration RegistrationType;
102 typedef RegistrationType * RegistrationPointer;
105 typedef typename RegistrationType::FixedImageType InternalImageType;
106 typedef clitk::GenericMetric<args_info_clitkAffineRegistration, InternalImageType, InternalImageType> GenericMetricType;
108 // Two arguments are passed to the Execute() method: the first
109 // is the pointer to the object which invoked the event and the
110 // second is the event that was invoked.
111 void Execute(itk::Object * object, const itk::EventObject & event) {
112 if ( !(itk::IterationEvent().CheckEvent( &event )) ) {
117 RegistrationPointer registration = dynamic_cast<RegistrationPointer>( object );
118 unsigned int numberOfLevels=registration->GetNumberOfLevels();
119 unsigned int currentLevel=registration->GetCurrentLevel()+1;
122 std::cout<<std::endl;
123 std::cout<<"========================================"<<std::endl;
124 std::cout<<"Starting resolution level "<<currentLevel<<" of "<<numberOfLevels<<"..."<<std::endl;
125 std::cout<<"========================================"<<std::endl;
126 std::cout<<std::endl;
129 if (currentLevel>1) {
130 // Reinitialize the metric (!= number of samples)
131 typename GenericMetricType::Pointer genericMetric= GenericMetricType::New();
132 genericMetric->SetArgsInfo(m_ArgsInfo);
133 genericMetric->SetFixedImage(registration->GetFixedImagePyramid()->GetOutput(registration->GetCurrentLevel()));
134 if (m_ArgsInfo.referenceMask_given) genericMetric->SetFixedImageMask(registration->GetMetric()->GetFixedImageMask());
135 typedef itk::ImageToImageMetric< InternalImageType, InternalImageType > MetricType;
136 typename MetricType::Pointer metric=genericMetric->GetMetricPointer();
137 registration->SetMetric(metric);
141 void Execute(const itk::Object * , const itk::EventObject & ) {
145 void SetArgsInfo(args_info_clitkAffineRegistration a) {
148 args_info_clitkAffineRegistration m_ArgsInfo;
151 //==============================================================================================//
153 //==============================================================================================//
154 void AffineRegistrationGenericFilter::SetArgsInfo(const args_info_clitkAffineRegistration & a)
157 if (m_ArgsInfo.reference_given) AddInputFilename(m_ArgsInfo.reference_arg);
159 if (m_ArgsInfo.target_given) {
160 AddInputFilename(m_ArgsInfo.target_arg);
163 if (m_ArgsInfo.output_given) SetOutputFilename(m_ArgsInfo.output_arg);
165 //==============================================================================
166 // Update with the number of dimensions and pixeltype
167 //==============================================================================
168 template<class InputImageType>
169 void AffineRegistrationGenericFilter::UpdateWithInputImageType()
171 //=============================================================================
173 //=============================================================================
175 typedef typename InputImageType::PixelType PixelType;
176 //typedef typename InputImageType::ImageDimension Dimension;
179 bool threadsGiven=m_ArgsInfo.threads_given;
180 int threads=m_ArgsInfo.threads_arg;
182 //Coordinate Representation
183 typedef double TCoordRep;
186 typename InputImageType::Pointer fixedImage = this->template GetInput<InputImageType>(0);
188 typename InputImageType::Pointer inputFixedImage = this->template GetInput<InputImageType>(0);
191 typename InputImageType::Pointer movingImage = this->template GetInput<InputImageType>(1);
193 typename InputImageType::Pointer inputMovingImage = this->template GetInput<InputImageType>(1);
197 //The pixeltype of the fixed image will be used for output
198 typedef itk::Image< PixelType, InputImageType::ImageDimension > FixedImageType;
200 //Whatever the pixel type, internally we work with an image represented in float
201 typedef typename InputImageType::PixelType InternalPixelType;
202 typedef itk::Image< PixelType, InputImageType::ImageDimension > InternalImageType;
205 //Read in the reference/fixed image
206 // typedef itk::ImageFileReader< InternalImageType > ReaderType;
207 // typename ReaderType::Pointer fixedImageReader = ReaderType::New();
208 // fixedImageReader->SetFileName( m_ArgsInfo.reference_arg);
211 //Read in the object/moving image
212 // typename ReaderType::Pointer movingImageReader = ReaderType::New();
213 // movingImageReader->SetFileName( m_ArgsInfo.target_arg );
214 if (m_Verbose) std::cout<<"Reading images..."<<std::endl;
215 // fixedImageReader->Update();
216 // movingImageReader->Update();
218 if (m_Verbose) std::cout << "Reading images... " << std::endl;
220 //we connect pointers to these internal images
221 // typedef typename fixedImageReader fixedImage;
222 // typedef typename movingImageReader movingImage;
224 //We keep the images used for input for possible output
225 // typedef typename fixedImageReader inputFixedImage;
226 // typedef typename movingImageReader inputMovingImage;
229 //============================================================================
231 //============================================================================
233 //If given, the intensities of both images are first normalized to a zero mean and SD of 1
234 // (usefull for MI, not necessary for Mattes' MI but performed anyway for the ouput)
235 if ( m_ArgsInfo.normalize_flag ) {
236 typedef itk::NormalizeImageFilter< InternalImageType,InternalImageType > NormalizeFilterType;
238 typename NormalizeFilterType::Pointer fixedNormalizeFilter = NormalizeFilterType::New();
239 typename NormalizeFilterType::Pointer movingNormalizeFilter = NormalizeFilterType::New();
241 fixedNormalizeFilter->SetInput( fixedImage );
242 movingNormalizeFilter->SetInput( movingImage );
244 fixedNormalizeFilter->Update();
245 movingNormalizeFilter->Update();
247 //We keep the images used for input for possible output
248 inputFixedImage= fixedNormalizeFilter->GetOutput();
249 inputMovingImage= movingNormalizeFilter->GetOutput();
251 //the pointers are reconnected for further output
252 fixedImage=fixedNormalizeFilter->GetOutput();
253 movingImage=movingNormalizeFilter->GetOutput();
255 if (m_Verbose) std::cout << "Normalizing image intensities to zero mean and SD of 1..." << std::endl;
259 //If given, the images are blurred before processing
260 if ( m_ArgsInfo.blur_arg!= 0) {
261 typedef itk::DiscreteGaussianImageFilter<InternalImageType,InternalImageType> GaussianFilterType;
262 typename GaussianFilterType::Pointer fixedSmoother = GaussianFilterType::New();
263 typename GaussianFilterType::Pointer movingSmoother = GaussianFilterType::New();
264 fixedSmoother->SetVariance( m_ArgsInfo.blur_arg );
265 movingSmoother->SetVariance(m_ArgsInfo.blur_arg );
267 fixedSmoother->SetInput( fixedImage );
268 movingSmoother->SetInput( movingImage );
270 fixedSmoother->Update();
271 movingSmoother->Update();
273 fixedImage=fixedSmoother->GetOutput();
274 movingImage=movingSmoother->GetOutput();
276 if (m_Verbose) std::cout << "Blurring images with a Gaussian with standard deviation of " << m_ArgsInfo.blur_arg <<"..." << std::endl;
280 //============================================================================
281 // Setting up the moving image in a reference system
282 //============================================================================
283 const itk::Vector<double, InputImageType::ImageDimension> movingResolution = movingImage->GetSpacing();
284 typename InternalImageType::RegionType movingRegion = movingImage->GetLargestPossibleRegion();
285 typename InternalImageType::RegionType::SizeType movingSize = movingRegion.GetSize();
287 // Print the parameters of the moving image
289 std::cout << "Object or Moving image:"<<std::endl;
290 std::cout << "Size: " << movingSize[0] << ", " << movingSize[1];
291 if (InputImageType::ImageDimension==3) std::cout<<", " << movingSize[2];
292 std::cout << std::endl;
294 std::cout<< "Resolution: "<< movingResolution[0] << ", " << movingResolution[1];
295 if (InputImageType::ImageDimension==3) std::cout<< ", " << movingResolution[2];
296 std::cout << std::endl;
300 //============================================================================
301 // Setting up the fixed image in a reference system
302 //============================================================================
303 const itk::Vector<double, InputImageType::ImageDimension> fixedResolution = fixedImage->GetSpacing();
304 typename InternalImageType::RegionType fixedRegion = fixedImage->GetLargestPossibleRegion();
305 typename InternalImageType::RegionType::SizeType fixedSize = fixedRegion.GetSize();
307 // Print the parameters of the moving image and the transform
309 std::cout << "Target or Moving image:"<<std::endl;
310 std::cout << "Size: " << fixedSize[0] << ", " << fixedSize[1];
311 if (InputImageType::ImageDimension==3) std::cout<<", " << fixedSize[2];
312 std::cout << std::endl;
314 std::cout<< "Resolution: "<< fixedResolution[0] << ", " << fixedResolution[1];
315 if (InputImageType::ImageDimension==3) std::cout<< ", " << fixedResolution[2];
316 std::cout << std::endl;
321 //===========================================================================
322 // If given, we connect a mask to reference or target
323 //============================================================================
324 typedef itk::ImageMaskSpatialObject< InputImageType::ImageDimension > MaskType;
325 typename MaskType::Pointer fixedMask=NULL;
326 if (m_ArgsInfo.referenceMask_given) {
327 fixedMask= MaskType::New();
328 typedef itk::Image< unsigned char, InputImageType::ImageDimension > ImageMaskType;
329 typedef itk::ImageFileReader< ImageMaskType > MaskReaderType;
330 typename MaskReaderType::Pointer maskReader = MaskReaderType::New();
331 maskReader->SetFileName(m_ArgsInfo.referenceMask_arg);
333 maskReader->Update();
334 } catch ( itk::ExceptionObject & err ) {
335 std::cerr << "ExceptionObject caught while reading mask !" << std::endl;
336 std::cerr << err << std::endl;
339 if (m_Verbose)std::cout <<"Reference image mask was read..." <<std::endl;
341 // Set the image to the spatialObject
342 fixedMask->SetImage( maskReader->GetOutput() );
345 typedef itk::ImageMaskSpatialObject< InputImageType::ImageDimension > MaskType;
346 typename MaskType::Pointer movingMask=NULL;
347 if (m_ArgsInfo.targetMask_given) {
348 movingMask= MaskType::New();
349 typedef itk::Image< unsigned char, InputImageType::ImageDimension > ImageMaskType;
350 typedef itk::ImageFileReader< ImageMaskType > MaskReaderType;
351 typename MaskReaderType::Pointer maskReader = MaskReaderType::New();
352 maskReader->SetFileName(m_ArgsInfo.targetMask_arg);
354 maskReader->Update();
355 } catch ( itk::ExceptionObject & err ) {
356 std::cerr << "ExceptionObject caught !" << std::endl;
357 std::cerr << err << std::endl;
359 if (m_Verbose)std::cout <<"Target image mask was read..." <<std::endl;
361 movingMask->SetImage( maskReader->GetOutput() );
365 //============================================================================
366 // The image pyramids
367 //============================================================================
368 typedef itk::RecursiveMultiResolutionPyramidImageFilter<InternalImageType,InternalImageType > FixedImagePyramidType;
369 typedef itk::RecursiveMultiResolutionPyramidImageFilter<InternalImageType,InternalImageType > MovingImagePyramidType;
370 typename FixedImagePyramidType::Pointer fixedImagePyramid = FixedImagePyramidType::New();
371 typename MovingImagePyramidType::Pointer movingImagePyramid = MovingImagePyramidType::New();
372 fixedImagePyramid->SetUseShrinkImageFilter(false);
373 fixedImagePyramid->SetInput(fixedImage);
374 fixedImagePyramid->SetNumberOfLevels(m_ArgsInfo.levels_arg);
375 movingImagePyramid->SetUseShrinkImageFilter(false);
376 movingImagePyramid->SetInput(movingImage);
377 movingImagePyramid->SetNumberOfLevels(m_ArgsInfo.levels_arg);
378 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();
459 std::cout<<m_ArgsInfo.transform_arg<<std::endl;
462 //=======================================================
464 //=======================================================
465 std::cout<<"setting Interpolator..."<<std::endl;
466 typedef clitk::GenericInterpolator<args_info_clitkAffineRegistration, InternalImageType,TCoordRep > GenericInterpolatorType;
467 typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
468 genericInterpolator->SetArgsInfo(m_ArgsInfo);
469 typedef itk::InterpolateImageFunction< InternalImageType, TCoordRep > InterpolatorType;
470 typename InterpolatorType::Pointer interpolator=genericInterpolator->GetInterpolatorPointer();
471 std::cout<<"end of interpolator"<<std::endl;
473 //============================================================================
475 //============================================================================
476 typedef clitk::GenericOptimizer<args_info_clitkAffineRegistration> GenericOptimizerType;
477 unsigned int nParam = transform->GetNumberOfParameters();
478 typename GenericOptimizerType::Pointer genericOptimizer=GenericOptimizerType::New();
479 genericOptimizer->SetArgsInfo(m_ArgsInfo);
480 genericOptimizer->SetOutputIteration(m_Verbose);
481 genericOptimizer->SetOutputPosition(m_Verbose);
482 genericOptimizer->SetOutputValue(m_Verbose);
483 genericOptimizer->SetOutputGradient(m_ArgsInfo.gradient_flag);
484 genericOptimizer->SetMaximize(genericMetric->GetMaximize());
485 genericOptimizer->SetNumberOfParameters(nParam);
486 typedef itk::SingleValuedNonLinearOptimizer OptimizerType;
487 OptimizerType::Pointer optimizer=genericOptimizer->GetOptimizerPointer();
490 itk::Optimizer::ScalesType scales( nParam );
491 for (unsigned int i=nParam-InputImageType::ImageDimension; i<nParam; i++) //Translations
492 scales[i] = m_ArgsInfo.tWeight_arg;
493 for (unsigned int i=0; i<nParam-InputImageType::ImageDimension; i++) //Rest
494 scales[i] = m_ArgsInfo.rWeight_arg*180./M_PI;
495 optimizer->SetScales(scales);
496 //============================================================================
497 // Multiresolution registration
498 //============================================================================
499 std::cout<<"start MultiResolution..."<<std::endl;
500 typedef itk::MultiResolutionImageRegistrationMethod< InternalImageType,InternalImageType > RegistrationType;
501 typename RegistrationType::Pointer registration = RegistrationType::New();
502 registration->SetFixedImage( fixedImage );
503 registration->SetFixedImageRegion(fixedImage->GetLargestPossibleRegion());
504 registration->SetMovingImage( movingImage );
505 registration->SetFixedImagePyramid( fixedImagePyramid );
506 registration->SetMovingImagePyramid( movingImagePyramid );
507 registration->SetTransform( transform );
508 registration->SetInitialTransformParameters( transform->GetParameters() );
509 registration->SetInterpolator( interpolator );
510 registration->SetMetric(metric);
511 registration->SetOptimizer(optimizer);
512 registration->SetNumberOfLevels( m_ArgsInfo.levels_arg );
513 if (m_Verbose) std::cout << "Setting "<< m_ArgsInfo.levels_arg <<" resolution levels..." << std::endl;
514 if (m_Verbose) std::cout << "Initial Transform: "<< registration->GetInitialTransformParameters()<<std::endl;
516 //============================================================================
517 // Connecting the commander to the registration to monitor it
518 //============================================================================
521 // Output iteration info
522 CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New();
523 observer->SetOptimizer(genericOptimizer);
524 optimizer->AddObserver( itk::IterationEvent(), observer );
528 typedef RegistrationInterfaceCommand<RegistrationType> CommandType;
529 typename CommandType::Pointer command = CommandType::New();
530 command->SetArgsInfo(m_ArgsInfo);
531 registration->AddObserver( itk::IterationEvent(), command );
536 //============================================================================
537 // Finally we can start the registration with the given amount of multiresolution levels
538 //============================================================================
539 if (m_Verbose) std::cout << "Starting the registration now..." << std::endl;
542 registration->StartRegistration();
543 } catch ( itk::ExceptionObject & err ) {
544 std::cerr << "ExceptionObject caught !" << std::endl;
545 std::cerr << err << std::endl;
549 //============================================================================
550 // Processing the result of the registration
551 //============================================================================
552 OptimizerType::ParametersType finalParameters = registration->GetLastTransformParameters();
553 std::cout<< "Result : " <<std::setprecision(12)<<std::endl;
555 for (unsigned int i=nParam-InputImageType::ImageDimension; i<nParam; i++) //Translations
556 std::cout << " Translation " << i << " = " << finalParameters[i];
557 for (unsigned int i=0; i<nParam-InputImageType::ImageDimension; i++) //Rest
558 std::cout << " Other parameter " << i << " = " << finalParameters[i];
560 itk::Matrix<double,InputImageType::ImageDimension+1,InputImageType::ImageDimension+1> matrix;
561 if (m_ArgsInfo.transform_arg == 3) {
562 for (unsigned int i=0; i<InputImageType::ImageDimension; i++) {
563 matrix[i][3] = finalParameters[nParam-InputImageType::ImageDimension+i];
564 for (unsigned int j=0; j<InputImageType::ImageDimension; j++) {
565 matrix[i][j] = finalParameters[i*3+j];
570 matrix = clitk::GetBackwardAffineMatrix<InputImageType::ImageDimension>(finalParameters);
571 std::cout<<"outside GetBackWardAffineMatrix...."<<std::endl;
574 std::cout << " Affine transform matrix =" << std::endl;
575 std::cout << matrix <<std::setprecision(6)<< std::endl;
576 std::cout << " End of Registration" << std::endl;
577 // Write matrix to a file
578 if (m_ArgsInfo.matrix_given) {
580 mFile.open(m_ArgsInfo.matrix_arg);
581 mFile<<std::setprecision(12)<<matrix<< std::setprecision(6)<<std::endl;
585 //============================================================================
586 // Prepare the resampling filter in order to transform the moving image.
587 //============================================================================
588 // if (m_ArgsInfo.output_given || m_ArgsInfo.checker_after_given || m_ArgsInfo.after_given ) {
589 transform->SetParameters( finalParameters );
590 typedef itk::ResampleImageFilter< InternalImageType,InternalImageType > ResampleFilterType;
591 typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
593 resampler->SetTransform( transform );
594 resampler->SetInput( movingImage );
595 resampler->SetSize( fixedImage->GetLargestPossibleRegion().GetSize() );
596 resampler->SetOutputOrigin( fixedImage->GetOrigin() );
597 resampler->SetOutputSpacing( fixedImage->GetSpacing() );
598 resampler->SetDefaultPixelValue( 0 );
601 // if (m_ArgsInfo.output_given) {
602 //We write an output in the same pixeltype then the input
603 /*typedef itk::ImageFileWriter< FixedImageType > WriterType;
604 typename WriterType::Pointer outputWriter = WriterType::New();
605 outputWriter->SetFileName(m_ArgsInfo.output_arg );
606 outputWriter->SetInput( resampler->GetOutput() );
607 outputWriter->Update();*/
608 typedef InternalImageType OutputImageType;
609 typename OutputImageType::Pointer outputImage = resampler->GetOutput();
610 std::cout<<"Writing Output....."<<std::endl;
611 this->template SetNextOutput<OutputImageType>(outputImage);
615 //============================================================================
617 //============================================================================
618 if (m_ArgsInfo.checker_after_given) {
619 //To display correctly the checkerboard image, the intensities must lie in the same range (normalized)
620 //We write the image in the internal image type
621 typedef itk::ResampleImageFilter< InternalImageType,InternalImageType > ResampleFilterType;
622 typename ResampleFilterType::Pointer internalResampler = ResampleFilterType::New();
623 internalResampler->SetTransform( transform );
624 internalResampler->SetInput( inputMovingImage );
625 internalResampler->SetSize( fixedImage->GetLargestPossibleRegion().GetSize() );
626 internalResampler->SetOutputOrigin( fixedImage->GetOrigin() );
627 internalResampler->SetOutputSpacing( fixedImage->GetSpacing() );
628 internalResampler->SetDefaultPixelValue( 0 );
630 //We pass the normalized images to the checker filter
631 typedef itk::CheckerBoardImageFilter< InternalImageType > CheckerBoardFilterType;
632 typename CheckerBoardFilterType::Pointer checkerFilter= CheckerBoardFilterType::New();
634 checkerFilter->SetInput1(inputFixedImage);
635 checkerFilter->SetInput2(internalResampler->GetOutput());
636 typedef itk::ImageFileWriter< InternalImageType > InternalWriterType;
637 typename InternalWriterType::Pointer checkerWriter = InternalWriterType::New();
638 checkerWriter->SetFileName(m_ArgsInfo.checker_after_arg);
639 checkerWriter->SetInput( checkerFilter->GetOutput() );
640 checkerWriter->Update();
644 //============================================================================
646 //============================================================================
647 if (m_ArgsInfo.checker_before_given) {
648 //To display correctly the checkerboard image, the intensities must lie in the same range (normalized)
649 //We write the image in the internal image type
650 //We pass the normalized images to the checker filter
651 typedef itk::CheckerBoardImageFilter< InternalImageType > CheckerBoardFilterType;
652 typename CheckerBoardFilterType::Pointer checkerFilter= CheckerBoardFilterType::New();
654 checkerFilter->SetInput1(inputFixedImage);
655 checkerFilter->SetInput2(inputMovingImage);
656 typedef itk::ImageFileWriter< InternalImageType > InternalWriterType;
657 typename InternalWriterType::Pointer checkerWriter = InternalWriterType::New();
658 checkerWriter->SetFileName(m_ArgsInfo.checker_before_arg);
659 checkerWriter->SetInput( checkerFilter->GetOutput() );
660 checkerWriter->Update();
664 //============================================================================
666 //============================================================================
667 if (m_ArgsInfo.after_given) {
668 typedef itk::SubtractImageFilter< InternalImageType, FixedImageType,FixedImageType > DifferenceImageFilterType;
669 typename DifferenceImageFilterType::Pointer differenceAfterFilter= DifferenceImageFilterType::New();
671 differenceAfterFilter->SetInput1(fixedImage);
672 differenceAfterFilter->SetInput2(resampler->GetOutput());
674 // Prepare a writer to write the difference image
675 typedef itk::ImageFileWriter< FixedImageType > WriterType;
676 typename WriterType::Pointer differenceAfterWriter = WriterType::New();
677 differenceAfterWriter->SetFileName(m_ArgsInfo.after_arg );
678 differenceAfterWriter->SetInput( differenceAfterFilter->GetOutput() );
679 differenceAfterWriter->Update();
683 //============================================================================
684 // Difference Before?
685 //============================================================================
686 if (m_ArgsInfo.before_given) {
687 typedef itk::CastImageFilter< InternalImageType,FixedImageType > CastFilterType;
688 typename CastFilterType::Pointer caster = CastFilterType::New();
689 caster->SetInput( movingImage );
691 typedef itk::SubtractImageFilter< InternalImageType, FixedImageType, FixedImageType > DifferenceImageFilterType;
692 typename DifferenceImageFilterType::Pointer differenceBeforeFilter= DifferenceImageFilterType::New();
695 differenceBeforeFilter->SetInput1(fixedImage);
696 differenceBeforeFilter->SetInput2(caster->GetOutput());
698 // Prepare a writer to write the difference image
699 typedef itk::ImageFileWriter< FixedImageType > WriterType;
700 typename WriterType::Pointer differenceBeforeWriter = WriterType::New();
701 differenceBeforeWriter->SetFileName(m_ArgsInfo.before_arg);
702 differenceBeforeWriter->SetInput( differenceBeforeFilter->GetOutput() );
703 differenceBeforeWriter->Update();
709 //====================================================================
711 #endif //#define CLITKAFFINEREGISTRATIONCGENERICFILTER_CXX