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://www.centreleonberard.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 ===========================================================================**/
18 #ifndef clitkBLUTDIRGenericFilter_cxx
19 #define clitkBLUTDIRGenericFilter_cxx
21 /* =================================================
22 * @file clitkBLUTDIRGenericFilter.cxx
28 ===================================================*/
30 #include "clitkBLUTDIRGenericFilter.h"
31 #include "clitkBLUTDIRCommandIterationUpdateDVF.h"
36 //==============================================================================
37 // Creating an observer class that allows output at each iteration
38 //==============================================================================
39 class CommandIterationUpdate : public itk::Command
42 typedef CommandIterationUpdate Self;
43 typedef itk::Command Superclass;
44 typedef itk::SmartPointer<Self> Pointer;
47 CommandIterationUpdate() {};
49 typedef clitk::GenericOptimizer<args_info_clitkBLUTDIR> OptimizerType;
50 typedef const OptimizerType * OptimizerPointer;
52 // Set the generic optimizer
53 void SetOptimizer(OptimizerPointer o){m_Optimizer=o;}
56 void Execute(itk::Object *caller, const itk::EventObject & event)
58 Execute( (const itk::Object *)caller, event);
61 void Execute(const itk::Object * object, const itk::EventObject & event)
63 if( !(itk::IterationEvent().CheckEvent( &event )) )
68 m_Optimizer->OutputIterationInfo();
71 OptimizerPointer m_Optimizer;
74 //===========================================================================//
76 //==========================================================================//
77 BLUTDIRGenericFilter::BLUTDIRGenericFilter():
78 ImageToImageGenericFilter<Self>("Register DIR")
80 InitializeImageType<2>();
81 InitializeImageType<3>();
85 //=========================================================================//
87 //==========================================================================//
88 void BLUTDIRGenericFilter::SetArgsInfo(const args_info_clitkBLUTDIR & a){
90 if (m_ArgsInfo.reference_given) AddInputFilename(m_ArgsInfo.reference_arg);
92 if (m_ArgsInfo.target_given) {
93 AddInputFilename(m_ArgsInfo.target_arg);
96 if (m_ArgsInfo.output_given) SetOutputFilename(m_ArgsInfo.output_arg);
98 if (m_ArgsInfo.verbose_given) m_Verbose=true;
101 //=========================================================================//
102 //===========================================================================//
103 template<unsigned int Dim>
104 void BLUTDIRGenericFilter::InitializeImageType()
106 ADD_DEFAULT_IMAGE_TYPES(3);
108 //--------------------------------------------------------------------
110 //==============================================================================
111 //Creating an observer class that allows us to change parameters at subsequent levels
112 //==============================================================================
113 template <typename TRegistration,class args_info_clitkBLUTDIR>
114 class RegistrationInterfaceCommand : public itk::Command
117 typedef RegistrationInterfaceCommand Self;
118 typedef itk::Command Superclass;
119 typedef itk::SmartPointer<Self> Pointer;
122 RegistrationInterfaceCommand() { };
126 typedef TRegistration RegistrationType;
127 typedef RegistrationType * RegistrationPointer;
130 typedef typename RegistrationType::FixedImageType FixedImageType;
131 typedef typename FixedImageType::RegionType RegionType;
132 itkStaticConstMacro(ImageDimension, unsigned int,FixedImageType::ImageDimension);
133 typedef clitk::MultipleBSplineDeformableTransform<double, ImageDimension, ImageDimension> TransformType;
134 typedef clitk::MultipleBSplineDeformableTransformInitializer<TransformType, FixedImageType> InitializerType;
135 typedef typename InitializerType::CoefficientImageType CoefficientImageType;
136 typedef itk::CastImageFilter<CoefficientImageType, CoefficientImageType> CastImageFilterType;
137 typedef typename TransformType::ParametersType ParametersType;
138 typedef typename InitializerType::Pointer InitializerPointer;
139 typedef CommandIterationUpdate::Pointer CommandIterationUpdatePointer;
142 typedef clitk::GenericOptimizer<args_info_clitkBLUTDIR> GenericOptimizerType;
143 typedef typename GenericOptimizerType::Pointer GenericOptimizerPointer;
146 typedef typename RegistrationType::FixedImageType InternalImageType;
147 typedef clitk::GenericMetric<args_info_clitkBLUTDIR, InternalImageType, InternalImageType> GenericMetricType;
148 typedef typename GenericMetricType::Pointer GenericMetricPointer;
150 // Two arguments are passed to the Execute() method: the first
151 // is the pointer to the object which invoked the event and the
152 // second is the event that was invoked.
153 void Execute(itk::Object * object, const itk::EventObject & event)
155 if( !(itk::IterationEvent().CheckEvent( &event )) )
161 RegistrationPointer registration = dynamic_cast<RegistrationPointer>( object );
162 unsigned int numberOfLevels=registration->GetNumberOfLevels();
163 unsigned int currentLevel=registration->GetCurrentLevel()+1;
166 std::cout<<std::endl;
167 std::cout<<"========================================"<<std::endl;
168 std::cout<<"Starting resolution level "<<currentLevel<<" of "<<numberOfLevels<<"..."<<std::endl;
169 std::cout<<"========================================"<<std::endl;
170 std::cout<<std::endl;
175 // fixed image region pyramid
176 typedef clitk::MultiResolutionPyramidRegionFilter<InternalImageType> FixedImageRegionPyramidType;
177 typename FixedImageRegionPyramidType::Pointer fixedImageRegionPyramid=FixedImageRegionPyramidType::New();
178 fixedImageRegionPyramid->SetRegion(m_MetricRegion);
179 fixedImageRegionPyramid->SetSchedule(registration->GetFixedImagePyramid()->GetSchedule());
181 // Reinitialize the metric (!= number of samples)
182 m_GenericMetric= GenericMetricType::New();
183 m_GenericMetric->SetArgsInfo(m_ArgsInfo);
184 m_GenericMetric->SetFixedImage(registration->GetFixedImagePyramid()->GetOutput(registration->GetCurrentLevel()));
185 if (m_ArgsInfo.referenceMask_given) m_GenericMetric->SetFixedImageMask(registration->GetMetric()->GetFixedImageMask());
186 m_GenericMetric->SetFixedImageRegion(fixedImageRegionPyramid->GetOutput(registration->GetCurrentLevel()));
187 typedef itk::ImageToImageMetric< InternalImageType, InternalImageType > MetricType;
188 typename MetricType::Pointer metric=m_GenericMetric->GetMetricPointer();
189 registration->SetMetric(metric);
191 // Get the current coefficient image and make a COPY
192 typename itk::ImageDuplicator<CoefficientImageType>::Pointer caster = itk::ImageDuplicator<CoefficientImageType>::New();
193 std::vector<typename CoefficientImageType::Pointer> currentCoefficientImages = m_Initializer->GetTransform()->GetCoefficientImages();
194 for (unsigned i = 0; i < currentCoefficientImages.size(); ++i)
196 caster->SetInputImage(currentCoefficientImages[i]);
198 currentCoefficientImages[i] = caster->GetOutput();
202 // Write the intermediate result?
203 if (m_ArgsInfo.intermediate_given>=numberOfLevels)
204 writeImage<CoefficientImageType>(currentCoefficientImage, m_ArgsInfo.intermediate_arg[currentLevel-2], m_ArgsInfo.verbose_flag);
207 // Set the new transform properties
208 m_Initializer->SetImage(registration->GetFixedImagePyramid()->GetOutput(currentLevel-1));
209 if( m_Initializer->m_ControlPointSpacingIsGiven)
210 m_Initializer->SetControlPointSpacing(m_Initializer->m_ControlPointSpacingArray[registration->GetCurrentLevel()]);
211 if( m_Initializer->m_NumberOfControlPointsIsGiven)
212 m_Initializer->SetNumberOfControlPointsInsideTheImage(m_Initializer->m_NumberOfControlPointsInsideTheImageArray[registration->GetCurrentLevel()]);
214 // Reinitialize the transform
215 if (m_ArgsInfo.verbose_flag) std::cout<<"Initializing transform for level "<<currentLevel<<" of "<<numberOfLevels<<"..."<<std::endl;
216 m_Initializer->InitializeTransform();
217 ParametersType* newParameters= new typename TransformType::ParametersType(m_Initializer->GetTransform()->GetNumberOfParameters());
219 // DS : if we want to skip the last pyramid level, force to only 1 iteration
220 DD(m_ArgsInfo.skipLastPyramidLevel_flag);
221 if ((currentLevel == numberOfLevels) && (m_ArgsInfo.skipLastPyramidLevel_flag)) {
222 DD(m_ArgsInfo.maxIt_arg);
223 std::cout << "I skip the last pyramid level : set max iteration to 0" << std::endl;
224 m_ArgsInfo.maxIt_arg = 0;
225 DD(m_ArgsInfo.maxIt_arg);
228 // Reinitialize an Optimizer (!= number of parameters)
229 m_GenericOptimizer = GenericOptimizerType::New();
230 m_GenericOptimizer->SetArgsInfo(m_ArgsInfo);
231 m_GenericOptimizer->SetMaximize(m_Maximize);
232 m_GenericOptimizer->SetNumberOfParameters(m_Initializer->GetTransform()->GetNumberOfParameters());
235 typedef itk::SingleValuedNonLinearOptimizer OptimizerType;
236 OptimizerType::Pointer optimizer = m_GenericOptimizer->GetOptimizerPointer();
237 optimizer->AddObserver( itk::IterationEvent(), m_CommandIterationUpdate);
238 registration->SetOptimizer(optimizer);
239 m_CommandIterationUpdate->SetOptimizer(m_GenericOptimizer);
241 // Set the previous transform parameters to the registration
242 // if(m_Initializer->m_Parameters!=NULL )delete m_Initializer->m_Parameters;
243 m_Initializer->SetInitialParameters(currentCoefficientImages, *newParameters);
244 registration->SetInitialTransformParametersOfNextLevel(*newParameters);
248 void Execute(const itk::Object * , const itk::EventObject & )
253 void SetInitializer(InitializerPointer i){m_Initializer=i;}
254 InitializerPointer m_Initializer;
256 void SetArgsInfo(args_info_clitkBLUTDIR a){m_ArgsInfo=a;}
257 args_info_clitkBLUTDIR m_ArgsInfo;
259 void SetCommandIterationUpdate(CommandIterationUpdatePointer c){m_CommandIterationUpdate=c;};
260 CommandIterationUpdatePointer m_CommandIterationUpdate;
262 GenericOptimizerPointer m_GenericOptimizer;
263 void SetMaximize(bool b){m_Maximize=b;}
266 GenericMetricPointer m_GenericMetric;
267 void SetMetricRegion(RegionType i){m_MetricRegion=i;}
268 RegionType m_MetricRegion;
273 //==============================================================================
274 // Update with the number of dimensions and pixeltype
275 //==============================================================================
276 template<class InputImageType>
277 void BLUTDIRGenericFilter::UpdateWithInputImageType()
279 if (m_Verbose) std::cout << "BLUTDIRGenericFilter::UpdateWithInputImageType()" << std::endl;
281 //=============================================================================
283 //=============================================================================
284 bool threadsGiven=m_ArgsInfo.threads_given;
285 int threads=m_ArgsInfo.threads_arg;
286 typedef typename InputImageType::PixelType PixelType;
288 typedef double TCoordRep;
290 typename InputImageType::Pointer fixedImage = this->template GetInput<InputImageType>(0);
292 typename InputImageType::Pointer inputFixedImage = this->template GetInput<InputImageType>(0);
295 typename InputImageType::Pointer movingImage = this->template GetInput<InputImageType>(1);
297 typename InputImageType::Pointer inputMovingImage = this->template GetInput<InputImageType>(1);
299 typedef itk::Image< PixelType,InputImageType::ImageDimension > FixedImageType;
300 typedef itk::Image< PixelType, InputImageType::ImageDimension> MovingImageType;
301 const unsigned int SpaceDimension = InputImageType::ImageDimension;
302 //Whatever the pixel type, internally we work with an image represented in float
303 //Reading reference image
304 if (m_Verbose) std::cout<<"Reading images..."<<std::endl;
305 //=======================================================
307 //=======================================================
308 typename FixedImageType::Pointer croppedFixedImage=fixedImage;
309 //=======================================================
311 //=======================================================
312 // The original input region
313 typename FixedImageType::RegionType fixedImageRegion = fixedImage->GetLargestPossibleRegion();
315 // The transform region with respect to the input region:
316 // where should the transform be DEFINED (depends on mask)
317 typename FixedImageType::RegionType transformRegion = fixedImage->GetLargestPossibleRegion();
318 typename FixedImageType::RegionType::SizeType transformRegionSize=transformRegion.GetSize();
319 typename FixedImageType::RegionType::IndexType transformRegionIndex=transformRegion.GetIndex();
320 typename FixedImageType::PointType transformRegionOrigin=fixedImage->GetOrigin();
322 // The metric region with respect to the extracted transform region:
323 // where should the metric be CALCULATED (depends on transform)
324 typename FixedImageType::RegionType metricRegion = fixedImage->GetLargestPossibleRegion();
325 typename FixedImageType::RegionType::SizeType metricRegionSize=metricRegion.GetSize();
326 typename FixedImageType::RegionType::IndexType metricRegionIndex=metricRegion.GetIndex();
327 typename FixedImageType::PointType metricRegionOrigin=fixedImage->GetOrigin();
330 //===========================================================================
331 // If given, we connect a mask to reference or target
332 //============================================================================
333 typedef itk::ImageMaskSpatialObject< InputImageType::ImageDimension > MaskType;
334 typedef itk::Image< unsigned char, InputImageType::ImageDimension > ImageLabelType;
335 typename MaskType::Pointer fixedMask = NULL;
336 typename ImageLabelType::Pointer labels = NULL;
337 if (m_ArgsInfo.referenceMask_given)
339 fixedMask = MaskType::New();
340 labels = ImageLabelType::New();
341 typedef itk::ImageFileReader< ImageLabelType > LabelReaderType;
342 typename LabelReaderType::Pointer labelReader = LabelReaderType::New();
343 labelReader->SetFileName(m_ArgsInfo.referenceMask_arg);
346 labelReader->Update();
348 catch( itk::ExceptionObject & err )
350 std::cerr << "ExceptionObject caught while reading mask or labels !" << std::endl;
351 std::cerr << err << std::endl;
354 if (m_Verbose)std::cout <<"Reference image mask was read..." <<std::endl;
357 typedef itk::ResampleImageFilter<ImageLabelType, ImageLabelType> ResamplerType;
358 typename ResamplerType::Pointer resampler = ResamplerType::New();
359 typedef itk::NearestNeighborInterpolateImageFunction<ImageLabelType, TCoordRep> InterpolatorType;
360 typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
361 resampler->SetOutputParametersFromImage(fixedImage);
362 resampler->SetInterpolator(interpolator);
363 resampler->SetInput(labelReader->GetOutput());
365 labels = resampler->GetOutput();
367 // Set the image to the spatialObject
368 fixedMask->SetImage(labels);
370 // Find the bounding box of the "inside" label
371 typedef itk::LabelGeometryImageFilter<ImageLabelType> GeometryImageFilterType;
372 typename GeometryImageFilterType::Pointer geometryImageFilter=GeometryImageFilterType::New();
373 geometryImageFilter->SetInput(labels);
374 geometryImageFilter->Update();
375 typename GeometryImageFilterType::BoundingBoxType boundingBox = geometryImageFilter->GetBoundingBox(1);
377 // Limit the transform region to the mask
378 for (unsigned int i=0; i<InputImageType::ImageDimension; i++)
380 transformRegionIndex[i]=boundingBox[2*i];
381 transformRegionSize[i]=boundingBox[2*i+1]-boundingBox[2*i]+1;
383 transformRegion.SetSize(transformRegionSize);
384 transformRegion.SetIndex(transformRegionIndex);
385 fixedImage->TransformIndexToPhysicalPoint(transformRegion.GetIndex(), transformRegionOrigin);
387 // Crop the fixedImage to the bounding box to facilitate multi-resolution
388 typedef itk::ExtractImageFilter<FixedImageType,FixedImageType> ExtractImageFilterType;
389 typename ExtractImageFilterType::Pointer extractImageFilter=ExtractImageFilterType::New();
390 extractImageFilter->SetInput(fixedImage);
391 extractImageFilter->SetExtractionRegion(transformRegion);
392 extractImageFilter->Update();
393 croppedFixedImage=extractImageFilter->GetOutput();
395 // Update the metric region
396 metricRegion = croppedFixedImage->GetLargestPossibleRegion();
397 metricRegionIndex=metricRegion.GetIndex();
398 croppedFixedImage->TransformIndexToPhysicalPoint(metricRegionIndex, metricRegionOrigin);
400 // Set start index to zero (with respect to croppedFixedImage/transform region)
401 metricRegionIndex.Fill(0);
402 metricRegion.SetIndex(metricRegionIndex);
403 croppedFixedImage->SetRegions(metricRegion);
404 croppedFixedImage->SetOrigin(metricRegionOrigin);
407 typedef itk::ImageMaskSpatialObject< InputImageType::ImageDimension > MaskType;
408 typename MaskType::Pointer movingMask=NULL;
409 if (m_ArgsInfo.targetMask_given)
411 movingMask= MaskType::New();
412 typedef itk::Image< unsigned char, InputImageType::ImageDimension > ImageMaskType;
413 typedef itk::ImageFileReader< ImageMaskType > MaskReaderType;
414 typename MaskReaderType::Pointer maskReader = MaskReaderType::New();
415 maskReader->SetFileName(m_ArgsInfo.targetMask_arg);
418 maskReader->Update();
420 catch( itk::ExceptionObject & err )
422 std::cerr << "ExceptionObject caught !" << std::endl;
423 std::cerr << err << std::endl;
425 if (m_Verbose)std::cout <<"Target image mask was read..." <<std::endl;
427 movingMask->SetImage( maskReader->GetOutput() );
431 //=======================================================
433 //=======================================================
437 // Fixed image region
438 std::cout<<"The fixed image has its origin at "<<fixedImage->GetOrigin()<<std::endl
439 <<"The fixed image region starts at index "<<fixedImageRegion.GetIndex()<<std::endl
440 <<"The fixed image region has size "<< fixedImageRegion.GetSize()<<std::endl;
443 std::cout<<"The transform has its origin at "<<transformRegionOrigin<<std::endl
444 <<"The transform region will start at index "<<transformRegion.GetIndex()<<std::endl
445 <<"The transform region has size "<< transformRegion.GetSize()<<std::endl;
448 std::cout<<"The metric region has its origin at "<<metricRegionOrigin<<std::endl
449 <<"The metric region will start at index "<<metricRegion.GetIndex()<<std::endl
450 <<"The metric region has size "<< metricRegion.GetSize()<<std::endl;
455 //=======================================================
456 // Pyramids (update them for transform initializer)
457 //=======================================================
458 typedef itk::RecursiveMultiResolutionPyramidImageFilter< FixedImageType, FixedImageType> FixedImagePyramidType;
459 typedef itk::RecursiveMultiResolutionPyramidImageFilter< MovingImageType, MovingImageType> MovingImagePyramidType;
460 typename FixedImagePyramidType::Pointer fixedImagePyramid = FixedImagePyramidType::New();
461 typename MovingImagePyramidType::Pointer movingImagePyramid = MovingImagePyramidType::New();
462 fixedImagePyramid->SetUseShrinkImageFilter(false);
463 fixedImagePyramid->SetInput(croppedFixedImage);
464 fixedImagePyramid->SetNumberOfLevels(m_ArgsInfo.levels_arg);
465 movingImagePyramid->SetUseShrinkImageFilter(false);
466 movingImagePyramid->SetInput(movingImage);
467 movingImagePyramid->SetNumberOfLevels(m_ArgsInfo.levels_arg);
468 if (m_Verbose) std::cout<<"Creating the image pyramid..."<<std::endl;
469 fixedImagePyramid->Update();
470 movingImagePyramid->Update();
471 typedef clitk::MultiResolutionPyramidRegionFilter<FixedImageType> FixedImageRegionPyramidType;
472 typename FixedImageRegionPyramidType::Pointer fixedImageRegionPyramid=FixedImageRegionPyramidType::New();
473 fixedImageRegionPyramid->SetRegion(metricRegion);
474 fixedImageRegionPyramid->SetSchedule(fixedImagePyramid->GetSchedule());
477 //=======================================================
478 // Rigid or Affine Transform
479 //=======================================================
480 typedef itk::AffineTransform <double,3> RigidTransformType;
481 RigidTransformType::Pointer rigidTransform=NULL;
482 if (m_ArgsInfo.initMatrix_given)
484 if(m_Verbose) std::cout<<"Reading the prior transform matrix "<< m_ArgsInfo.initMatrix_arg<<"..."<<std::endl;
485 rigidTransform=RigidTransformType::New();
486 itk::Matrix<double,4,4> rigidTransformMatrix=clitk::ReadMatrix3D(m_ArgsInfo.initMatrix_arg);
489 itk::Matrix<double,3,3> finalRotation = clitk::GetRotationalPartMatrix3D(rigidTransformMatrix);
490 rigidTransform->SetMatrix(finalRotation);
492 //Set the translation
493 itk::Vector<double,3> finalTranslation = clitk::GetTranslationPartMatrix3D(rigidTransformMatrix);
494 rigidTransform->SetTranslation(finalTranslation);
498 //=======================================================
499 // B-LUT FFD Transform
500 //=======================================================
501 typedef clitk::MultipleBSplineDeformableTransform<TCoordRep,InputImageType::ImageDimension, SpaceDimension > TransformType;
502 typename TransformType::Pointer transform = TransformType::New();
503 if (labels) transform->SetLabels(labels);
504 if (rigidTransform) transform->SetBulkTransform(rigidTransform);
506 //-------------------------------------------------------------------------
507 // The transform initializer
508 //-------------------------------------------------------------------------
509 typedef clitk::MultipleBSplineDeformableTransformInitializer< TransformType,FixedImageType> InitializerType;
510 typename InitializerType::Pointer initializer = InitializerType::New();
511 initializer->SetVerbose(m_Verbose);
512 initializer->SetImage(fixedImagePyramid->GetOutput(0));
513 initializer->SetTransform(transform);
515 //-------------------------------------------------------------------------
517 //-------------------------------------------------------------------------
518 typename FixedImageType::RegionType::SizeType splineOrders ;
519 splineOrders.Fill(3);
520 if (m_ArgsInfo.order_given)
521 for(unsigned int i=0; i<InputImageType::ImageDimension;i++)
522 splineOrders[i]=m_ArgsInfo.order_arg[i];
523 if (m_Verbose) std::cout<<"Setting the spline orders to "<<splineOrders<<"..."<<std::endl;
524 initializer->SetSplineOrders(splineOrders);
526 //-------------------------------------------------------------------------
528 //-------------------------------------------------------------------------
531 if (m_ArgsInfo.spacing_given)
533 initializer->m_ControlPointSpacingArray.resize(m_ArgsInfo.levels_arg);
534 initializer->SetControlPointSpacing(m_ArgsInfo.spacing_arg);
535 initializer->m_ControlPointSpacingArray[m_ArgsInfo.levels_arg-1]=initializer->m_ControlPointSpacing;
536 if (m_Verbose) std::cout<<"Using a control point spacing of "<<initializer->m_ControlPointSpacingArray[m_ArgsInfo.levels_arg-1]
537 <<" at level "<<m_ArgsInfo.levels_arg<<" of "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;
539 for (int i=1; i<m_ArgsInfo.levels_arg; i++ )
541 initializer->m_ControlPointSpacingArray[m_ArgsInfo.levels_arg-1-i]=initializer->m_ControlPointSpacingArray[m_ArgsInfo.levels_arg-i]*2;
542 if (m_Verbose) std::cout<<"Using a control point spacing of "<<initializer->m_ControlPointSpacingArray[m_ArgsInfo.levels_arg-1-i]
543 <<" at level "<<m_ArgsInfo.levels_arg-i<<" of "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;
549 if (m_ArgsInfo.control_given)
551 initializer->m_NumberOfControlPointsInsideTheImageArray.resize(m_ArgsInfo.levels_arg);
552 initializer->SetNumberOfControlPointsInsideTheImage(m_ArgsInfo.control_arg);
553 initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-1]=initializer->m_NumberOfControlPointsInsideTheImage;
554 if (m_Verbose) std::cout<<"Using "<< initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-1]<<"control points inside the image"
555 <<" at level "<<m_ArgsInfo.levels_arg<<" of "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;
557 for (int i=1; i<m_ArgsInfo.levels_arg; i++ )
559 for(unsigned int j=0;j<InputImageType::ImageDimension;j++)
560 initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-1-i][j]=ceil ((double)initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-i][j]/2.);
561 // initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-1-i]=ceil ((double)initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-i]/2.);
562 if (m_Verbose) std::cout<<"Using "<< initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-1-i]<<"control points inside the image"
563 <<" at level "<<m_ArgsInfo.levels_arg<<" of "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;
568 // Inialize on the first level
569 if (m_ArgsInfo.verbose_flag) std::cout<<"Initializing transform for level 1 of "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;
570 if (m_ArgsInfo.spacing_given) initializer->SetControlPointSpacing( initializer->m_ControlPointSpacingArray[0]);
571 if (m_ArgsInfo.control_given) initializer->SetNumberOfControlPointsInsideTheImage(initializer->m_NumberOfControlPointsInsideTheImageArray[0]);
572 if (m_ArgsInfo.samplingFactor_given) initializer->SetSamplingFactors(m_ArgsInfo.samplingFactor_arg);
575 initializer->InitializeTransform();
577 //-------------------------------------------------------------------------
578 // Initial parameters (passed by reference)
579 //-------------------------------------------------------------------------
580 typedef typename TransformType::ParametersType ParametersType;
581 const unsigned int numberOfParameters = transform->GetNumberOfParameters();
582 ParametersType parameters(numberOfParameters);
583 parameters.Fill( 0.0 );
584 transform->SetParameters( parameters );
585 if (m_ArgsInfo.initCoeff_given) initializer->SetInitialParameters(m_ArgsInfo.initCoeff_arg, parameters);
587 //-------------------------------------------------------------------------
588 // DEBUG: use an itk BSpline instead of multilabel BLUTs
589 //-------------------------------------------------------------------------
590 typedef itk::Transform< TCoordRep, 3, 3 > RegistrationTransformType;
591 RegistrationTransformType::Pointer regTransform(transform);
592 typedef itk::BSplineDeformableTransform<TCoordRep,SpaceDimension, 3> SingleBSplineTransformType;
593 typename SingleBSplineTransformType::Pointer sTransform;
594 if(m_ArgsInfo.itkbspline_flag) {
595 if( transform->GetTransforms().size()>1)
596 itkExceptionMacro(<< "invalid --itkbspline option if there is more than 1 label")
597 sTransform = SingleBSplineTransformType::New();
598 sTransform->SetBulkTransform( transform->GetTransforms()[0]->GetBulkTransform() );
599 sTransform->SetGridSpacing( transform->GetTransforms()[0]->GetGridSpacing() );
600 sTransform->SetGridOrigin( transform->GetTransforms()[0]->GetGridOrigin() );
601 sTransform->SetGridRegion( transform->GetTransforms()[0]->GetGridRegion() );
602 sTransform->SetParameters( transform->GetTransforms()[0]->GetParameters() );
603 regTransform = sTransform;
604 transform = NULL; // free memory
607 //=======================================================
609 //=======================================================
610 typedef clitk::GenericInterpolator<args_info_clitkBLUTDIR, FixedImageType, TCoordRep > GenericInterpolatorType;
611 typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
612 genericInterpolator->SetArgsInfo(m_ArgsInfo);
613 typedef itk::InterpolateImageFunction< FixedImageType, TCoordRep > InterpolatorType;
614 typename InterpolatorType::Pointer interpolator=genericInterpolator->GetInterpolatorPointer();
617 //=======================================================
619 //=======================================================
620 typedef clitk::GenericMetric<args_info_clitkBLUTDIR, FixedImageType,MovingImageType > GenericMetricType;
621 typename GenericMetricType::Pointer genericMetric=GenericMetricType::New();
622 genericMetric->SetArgsInfo(m_ArgsInfo);
623 genericMetric->SetFixedImage(fixedImagePyramid->GetOutput(0));
624 if (fixedMask) genericMetric->SetFixedImageMask(fixedMask);
625 genericMetric->SetFixedImageRegion(fixedImageRegionPyramid->GetOutput(0));
626 typedef itk::ImageToImageMetric< FixedImageType, MovingImageType > MetricType;
627 typename MetricType::Pointer metric=genericMetric->GetMetricPointer();
628 if (movingMask) metric->SetMovingImageMask(movingMask);
630 #if defined(ITK_USE_OPTIMIZED_REGISTRATION_METHODS) || ITK_VERSION_MAJOR >= 4
632 metric->SetNumberOfThreads( threads );
633 if (m_Verbose) std::cout<< "Using " << threads << " threads." << std::endl;
636 if (m_Verbose) std::cout<<"Not setting the number of threads (not compiled with USE_OPTIMIZED_REGISTRATION_METHODS)..."<<std::endl;
640 //=======================================================
642 //=======================================================
643 typedef clitk::GenericOptimizer<args_info_clitkBLUTDIR> GenericOptimizerType;
644 GenericOptimizerType::Pointer genericOptimizer = GenericOptimizerType::New();
645 genericOptimizer->SetArgsInfo(m_ArgsInfo);
646 genericOptimizer->SetMaximize(genericMetric->GetMaximize());
647 genericOptimizer->SetNumberOfParameters(regTransform->GetNumberOfParameters());
648 typedef itk::SingleValuedNonLinearOptimizer OptimizerType;
649 OptimizerType::Pointer optimizer = genericOptimizer->GetOptimizerPointer();
652 //=======================================================
654 //=======================================================
655 typedef itk::MultiResolutionImageRegistrationMethod< FixedImageType, MovingImageType > RegistrationType;
656 typename RegistrationType::Pointer registration = RegistrationType::New();
657 registration->SetMetric( metric );
658 registration->SetOptimizer( optimizer );
659 registration->SetInterpolator( interpolator );
660 registration->SetTransform (regTransform );
662 registration->SetNumberOfThreads(threads);
663 if (m_Verbose) std::cout<< "Using " << threads << " threads." << std::endl;
665 registration->SetFixedImage( croppedFixedImage );
666 registration->SetMovingImage( movingImage );
667 registration->SetFixedImageRegion( metricRegion );
668 registration->SetFixedImagePyramid( fixedImagePyramid );
669 registration->SetMovingImagePyramid( movingImagePyramid );
670 registration->SetInitialTransformParameters( regTransform->GetParameters() );
671 registration->SetNumberOfLevels( m_ArgsInfo.levels_arg );
672 if (m_Verbose) std::cout<<"Setting the number of resolution levels to "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;
675 //================================================================================================
677 //================================================================================================
680 // Output iteration info
681 CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New();
682 observer->SetOptimizer(genericOptimizer);
683 optimizer->AddObserver( itk::IterationEvent(), observer );
686 typedef RegistrationInterfaceCommand<RegistrationType,args_info_clitkBLUTDIR> CommandType;
687 typename CommandType::Pointer command = CommandType::New();
688 command->SetInitializer(initializer);
689 command->SetArgsInfo(m_ArgsInfo);
690 command->SetCommandIterationUpdate(observer);
691 command->SetMaximize(genericMetric->GetMaximize());
692 command->SetMetricRegion(metricRegion);
693 registration->AddObserver( itk::IterationEvent(), command );
695 if (m_ArgsInfo.coeff_given)
697 if(m_ArgsInfo.itkbspline_flag) {
698 itkExceptionMacro("--coeff and --itkbpline are incompatible");
701 std::cout << std::endl << "Output coefficient images every " << m_ArgsInfo.coeffEveryN_arg << " iterations." << std::endl;
702 typedef CommandIterationUpdateDVF<FixedImageType, OptimizerType, TransformType> DVFCommandType;
703 typename DVFCommandType::Pointer observerdvf = DVFCommandType::New();
704 observerdvf->SetFixedImage(fixedImage);
705 observerdvf->SetTransform(transform);
706 observerdvf->SetArgsInfo(m_ArgsInfo);
707 optimizer->AddObserver( itk::IterationEvent(), observerdvf );
712 //=======================================================
714 //=======================================================
715 if (m_Verbose) std::cout << std::endl << "Starting Registration" << std::endl;
719 registration->StartRegistration();
721 catch( itk::ExceptionObject & err )
723 std::cerr << "ExceptionObject caught while registering!" << std::endl;
724 std::cerr << err << std::endl;
729 //=======================================================
731 //=======================================================
732 OptimizerType::ParametersType finalParameters = registration->GetLastTransformParameters();
733 regTransform->SetParameters( finalParameters );
736 std::cout<<"Stop condition description: "
737 <<registration->GetOptimizer()->GetStopConditionDescription()<<std::endl;
741 //=======================================================
742 // Get the BSpline coefficient images and write them
743 //=======================================================
744 if (m_ArgsInfo.coeff_given)
746 typedef typename TransformType::CoefficientImageType CoefficientImageType;
747 std::vector<typename CoefficientImageType::Pointer> coefficientImages = transform->GetCoefficientImages();
748 typedef itk::ImageFileWriter<CoefficientImageType> CoeffWriterType;
749 typename CoeffWriterType::Pointer coeffWriter = CoeffWriterType::New();
750 unsigned nLabels = transform->GetnLabels();
752 std::string fname(m_ArgsInfo.coeff_arg);
753 int dotpos = fname.length() - 1;
754 while (dotpos >= 0 && fname[dotpos] != '.')
757 for (unsigned i = 0; i < nLabels; ++i)
759 std::ostringstream osfname;
760 osfname << fname.substr(0, dotpos) << '_' << i << fname.substr(dotpos);
761 coeffWriter->SetInput(coefficientImages[i]);
762 coeffWriter->SetFileName(osfname.str());
763 coeffWriter->Update();
769 //=======================================================
770 // Compute the DVF (only deformable transform)
771 //=======================================================
772 typedef itk::Vector< float, SpaceDimension > DisplacementType;
773 typedef itk::Image< DisplacementType, InputImageType::ImageDimension > DisplacementFieldType;
774 #if ITK_VERSION_MAJOR >= 4
775 typedef itk::TransformToDisplacementFieldSource<DisplacementFieldType, double> ConvertorType;
777 typedef itk::TransformToDeformationFieldSource<DisplacementFieldType, double> ConvertorType;
779 typename ConvertorType::Pointer filter= ConvertorType::New();
780 filter->SetNumberOfThreads(1);
781 if(m_ArgsInfo.itkbspline_flag)
782 sTransform->SetBulkTransform(NULL);
784 transform->SetBulkTransform(NULL);
785 filter->SetTransform(regTransform);
786 filter->SetOutputParametersFromImage(fixedImage);
788 typename DisplacementFieldType::Pointer field = filter->GetOutput();
791 //=======================================================
793 //=======================================================
794 typedef itk::ImageFileWriter< DisplacementFieldType > FieldWriterType;
795 typename FieldWriterType::Pointer fieldWriter = FieldWriterType::New();
796 fieldWriter->SetFileName( m_ArgsInfo.vf_arg );
797 fieldWriter->SetInput( field );
800 fieldWriter->Update();
802 catch( itk::ExceptionObject & excp )
804 std::cerr << "Exception thrown writing the DVF" << std::endl;
805 std::cerr << excp << std::endl;
810 //=======================================================
811 // Resample the moving image
812 //=======================================================
813 typedef itk::ResampleImageFilter< MovingImageType, FixedImageType > ResampleFilterType;
814 typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
815 if (rigidTransform) {
816 if(m_ArgsInfo.itkbspline_flag)
817 sTransform->SetBulkTransform(rigidTransform);
819 transform->SetBulkTransform(rigidTransform);
821 resampler->SetTransform( regTransform );
822 resampler->SetInput( movingImage);
823 resampler->SetOutputParametersFromImage(fixedImage);
825 typename FixedImageType::Pointer result=resampler->GetOutput();
827 // typedef itk::WarpImageFilter< MovingImageType, FixedImageType, DeformationFieldType > WarpFilterType;
828 // typename WarpFilterType::Pointer warp = WarpFilterType::New();
830 // warp->SetDeformationField( field );
831 // warp->SetInput( movingImageReader->GetOutput() );
832 // warp->SetOutputOrigin( fixedImage->GetOrigin() );
833 // warp->SetOutputSpacing( fixedImage->GetSpacing() );
834 // warp->SetOutputDirection( fixedImage->GetDirection() );
835 // warp->SetEdgePaddingValue( 0.0 );
839 //=======================================================
840 // Write the warped image
841 //=======================================================
842 typedef itk::ImageFileWriter< FixedImageType > WriterType;
843 typename WriterType::Pointer writer = WriterType::New();
844 writer->SetFileName( m_ArgsInfo.output_arg );
845 writer->SetInput( result );
851 catch( itk::ExceptionObject & err )
853 std::cerr << "ExceptionObject caught !" << std::endl;
854 std::cerr << err << std::endl;
859 //=======================================================
860 // Calculate the difference after the deformable transform
861 //=======================================================
862 typedef clitk::DifferenceImageFilter< FixedImageType, FixedImageType> DifferenceFilterType;
863 if (m_ArgsInfo.after_given)
865 typename DifferenceFilterType::Pointer difference = DifferenceFilterType::New();
866 difference->SetValidInput( fixedImage );
867 difference->SetTestInput( result );
871 difference->Update();
873 catch( itk::ExceptionObject & err )
875 std::cerr << "ExceptionObject caught calculating the difference !" << std::endl;
876 std::cerr << err << std::endl;
880 typename WriterType::Pointer differenceWriter=WriterType::New();
881 differenceWriter->SetInput(difference->GetOutput());
882 differenceWriter->SetFileName(m_ArgsInfo.after_arg);
883 differenceWriter->Update();
888 //=======================================================
889 // Calculate the difference before the deformable transform
890 //=======================================================
891 if( m_ArgsInfo.before_given )
894 typename FixedImageType::Pointer moving=FixedImageType::New();
895 if (m_ArgsInfo.initMatrix_given)
897 typedef itk::ResampleImageFilter<MovingImageType, FixedImageType> ResamplerType;
898 typename ResamplerType::Pointer resampler=ResamplerType::New();
899 resampler->SetInput(movingImage);
900 resampler->SetOutputOrigin(fixedImage->GetOrigin());
901 resampler->SetSize(fixedImage->GetLargestPossibleRegion().GetSize());
902 resampler->SetOutputSpacing(fixedImage->GetSpacing());
903 resampler->SetDefaultPixelValue( 0. );
904 if (rigidTransform ) resampler->SetTransform(rigidTransform);
906 moving=resampler->GetOutput();
911 typename DifferenceFilterType::Pointer difference = DifferenceFilterType::New();
912 difference->SetValidInput( fixedImage );
913 difference->SetTestInput( moving );
917 difference->Update();
919 catch( itk::ExceptionObject & err )
921 std::cerr << "ExceptionObject caught calculating the difference !" << std::endl;
922 std::cerr << err << std::endl;
926 typename WriterType::Pointer differenceWriter=WriterType::New();
927 writer->SetFileName( m_ArgsInfo.before_arg );
928 writer->SetInput( difference->GetOutput() );
937 #endif // #define clitkBLUTDIRGenericFilter_txx