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 ======================================================================-====*/
18 #ifndef clitkBLUTDIRGenericFilter_cxx
19 #define clitkBLUTDIRGenericFilter_cxx
21 /* =================================================
22 * @file clitkBLUTDIRGenericFilter.cxx
28 ===================================================*/
30 #include "clitkBLUTDIRGenericFilter.h"
35 //==============================================================================
36 // Creating an observer class that allows output at each iteration
37 //==============================================================================
38 class CommandIterationUpdate : public itk::Command
41 typedef CommandIterationUpdate Self;
42 typedef itk::Command Superclass;
43 typedef itk::SmartPointer<Self> Pointer;
46 CommandIterationUpdate() {};
48 typedef clitk::GenericOptimizer<args_info_clitkBLUTDIR> OptimizerType;
49 typedef const OptimizerType * OptimizerPointer;
51 // Set the generic optimizer
52 void SetOptimizer(OptimizerPointer o){m_Optimizer=o;}
55 void Execute(itk::Object *caller, const itk::EventObject & event)
57 Execute( (const itk::Object *)caller, event);
60 void Execute(const itk::Object * object, const itk::EventObject & event)
62 if( !(itk::IterationEvent().CheckEvent( &event )) )
67 m_Optimizer->OutputIterationInfo();
70 OptimizerPointer m_Optimizer;
72 //===========================================================================//
74 //==========================================================================//
75 BLUTDIRGenericFilter::BLUTDIRGenericFilter():
76 ImageToImageGenericFilter<Self>("Register DIR")
78 InitializeImageType<2>();
79 InitializeImageType<3>();
82 //=========================================================================//
84 //==========================================================================//
85 void BLUTDIRGenericFilter::SetArgsInfo(const args_info_clitkBLUTDIR & a){
87 if (m_ArgsInfo.reference_given) AddInputFilename(m_ArgsInfo.reference_arg);
89 if (m_ArgsInfo.target_given) {
90 AddInputFilename(m_ArgsInfo.target_arg);
93 if (m_ArgsInfo.output_given) SetOutputFilename(m_ArgsInfo.output_arg);
95 //=========================================================================//
96 //===========================================================================//
97 template<unsigned int Dim>
98 void BLUTDIRGenericFilter::InitializeImageType()
100 ADD_DEFAULT_IMAGE_TYPES(3);
102 //--------------------------------------------------------------------
104 //==============================================================================
105 //Creating an observer class that allows us to change parameters at subsequent levels
106 //==============================================================================
107 template <typename TRegistration,class args_info_clitkBLUTDIR>
108 class RegistrationInterfaceCommand : public itk::Command
111 typedef RegistrationInterfaceCommand Self;
112 typedef itk::Command Superclass;
113 typedef itk::SmartPointer<Self> Pointer;
116 RegistrationInterfaceCommand() { };
120 typedef TRegistration RegistrationType;
121 typedef RegistrationType * RegistrationPointer;
124 typedef typename RegistrationType::FixedImageType FixedImageType;
125 typedef typename FixedImageType::RegionType RegionType;
126 itkStaticConstMacro(ImageDimension, unsigned int,FixedImageType::ImageDimension);
127 typedef clitk::BSplineDeformableTransform<double, ImageDimension, ImageDimension> TransformType;
128 typedef clitk::BSplineDeformableTransformInitializer<TransformType, FixedImageType> InitializerType;
129 typedef typename InitializerType::CoefficientImageType CoefficientImageType;
130 typedef itk::CastImageFilter<CoefficientImageType, CoefficientImageType> CastImageFilterType;
131 typedef typename TransformType::ParametersType ParametersType;
132 typedef typename InitializerType::Pointer InitializerPointer;
133 typedef CommandIterationUpdate::Pointer CommandIterationUpdatePointer;
136 typedef clitk::GenericOptimizer<args_info_clitkBLUTDIR> GenericOptimizerType;
137 typedef typename GenericOptimizerType::Pointer GenericOptimizerPointer;
140 typedef typename RegistrationType::FixedImageType InternalImageType;
141 typedef clitk::GenericMetric<args_info_clitkBLUTDIR, InternalImageType, InternalImageType> GenericMetricType;
142 typedef typename GenericMetricType::Pointer GenericMetricPointer;
144 // Two arguments are passed to the Execute() method: the first
145 // is the pointer to the object which invoked the event and the
146 // second is the event that was invoked.
147 void Execute(itk::Object * object, const itk::EventObject & event)
149 if( !(itk::IterationEvent().CheckEvent( &event )) )
155 RegistrationPointer registration = dynamic_cast<RegistrationPointer>( object );
156 unsigned int numberOfLevels=registration->GetNumberOfLevels();
157 unsigned int currentLevel=registration->GetCurrentLevel()+1;
160 std::cout<<std::endl;
161 std::cout<<"========================================"<<std::endl;
162 std::cout<<"Starting resolution level "<<currentLevel<<" of "<<numberOfLevels<<"..."<<std::endl;
163 std::cout<<"========================================"<<std::endl;
164 std::cout<<std::endl;
169 // fixed image region pyramid
170 typedef clitk::MultiResolutionPyramidRegionFilter<InternalImageType> FixedImageRegionPyramidType;
171 typename FixedImageRegionPyramidType::Pointer fixedImageRegionPyramid=FixedImageRegionPyramidType::New();
172 fixedImageRegionPyramid->SetRegion(m_MetricRegion);
173 fixedImageRegionPyramid->SetSchedule(registration->GetFixedImagePyramid()->GetSchedule());
175 // Reinitialize the metric (!= number of samples)
176 m_GenericMetric= GenericMetricType::New();
177 m_GenericMetric->SetArgsInfo(m_ArgsInfo);
178 m_GenericMetric->SetFixedImage(registration->GetFixedImagePyramid()->GetOutput(registration->GetCurrentLevel()));
179 if (m_ArgsInfo.referenceMask_given) m_GenericMetric->SetFixedImageMask(registration->GetMetric()->GetFixedImageMask());
180 m_GenericMetric->SetFixedImageRegion(fixedImageRegionPyramid->GetOutput(registration->GetCurrentLevel()));
181 typedef itk::ImageToImageMetric< InternalImageType, InternalImageType > MetricType;
182 typename MetricType::Pointer metric=m_GenericMetric->GetMetricPointer();
183 registration->SetMetric(metric);
185 // Get the current coefficient image and make a COPY
186 typename itk::ImageDuplicator<CoefficientImageType>::Pointer caster=itk::ImageDuplicator<CoefficientImageType>::New();
187 caster->SetInputImage(m_Initializer->GetTransform()->GetCoefficientImage());
189 typename CoefficientImageType::Pointer currentCoefficientImage=caster->GetOutput();
191 // Write the intermediate result?
192 if (m_ArgsInfo.intermediate_given>=numberOfLevels)
193 writeImage<CoefficientImageType>(currentCoefficientImage, m_ArgsInfo.intermediate_arg[currentLevel-2], m_ArgsInfo.verbose_flag);
195 // Set the new transform properties
196 m_Initializer->SetImage(registration->GetFixedImagePyramid()->GetOutput(currentLevel-1));
197 if( m_Initializer->m_ControlPointSpacingIsGiven)
198 m_Initializer->SetControlPointSpacing(m_Initializer->m_ControlPointSpacingArray[registration->GetCurrentLevel()]);
199 if( m_Initializer->m_NumberOfControlPointsIsGiven)
200 m_Initializer->SetNumberOfControlPointsInsideTheImage(m_Initializer->m_NumberOfControlPointsInsideTheImageArray[registration->GetCurrentLevel()]);
202 // Reinitialize the transform
203 if (m_ArgsInfo.verbose_flag) std::cout<<"Initializing transform for level "<<currentLevel<<" of "<<numberOfLevels<<"..."<<std::endl;
204 m_Initializer->InitializeTransform();
205 ParametersType* newParameters= new typename TransformType::ParametersType(m_Initializer->GetTransform()->GetNumberOfParameters());
207 // DS : if we want to skip the last pyramid level, force to only 1 iteration
208 DD(m_ArgsInfo.skipLastPyramidLevel_flag);
209 if ((currentLevel == numberOfLevels) && (m_ArgsInfo.skipLastPyramidLevel_flag)) {
210 DD(m_ArgsInfo.maxIt_arg);
211 std::cout << "I skip the last pyramid level : set max iteration to 0" << std::endl;
212 m_ArgsInfo.maxIt_arg = 0;
213 DD(m_ArgsInfo.maxIt_arg);
216 // Reinitialize an Optimizer (!= number of parameters)
217 m_GenericOptimizer = GenericOptimizerType::New();
218 m_GenericOptimizer->SetArgsInfo(m_ArgsInfo);
219 m_GenericOptimizer->SetMaximize(m_Maximize);
220 m_GenericOptimizer->SetNumberOfParameters(m_Initializer->GetTransform()->GetNumberOfParameters());
223 typedef itk::SingleValuedNonLinearOptimizer OptimizerType;
224 OptimizerType::Pointer optimizer = m_GenericOptimizer->GetOptimizerPointer();
225 optimizer->AddObserver( itk::IterationEvent(), m_CommandIterationUpdate);
226 registration->SetOptimizer(optimizer);
227 m_CommandIterationUpdate->SetOptimizer(m_GenericOptimizer);
229 // Set the previous transform parameters to the registration
230 // if(m_Initializer->m_Parameters!=NULL )delete m_Initializer->m_Parameters;
231 m_Initializer->SetInitialParameters(currentCoefficientImage,*newParameters);
232 registration->SetInitialTransformParametersOfNextLevel(*newParameters);
236 void Execute(const itk::Object * , const itk::EventObject & )
241 void SetInitializer(InitializerPointer i){m_Initializer=i;}
242 InitializerPointer m_Initializer;
244 void SetArgsInfo(args_info_clitkBLUTDIR a){m_ArgsInfo=a;}
245 args_info_clitkBLUTDIR m_ArgsInfo;
247 void SetCommandIterationUpdate(CommandIterationUpdatePointer c){m_CommandIterationUpdate=c;};
248 CommandIterationUpdatePointer m_CommandIterationUpdate;
250 GenericOptimizerPointer m_GenericOptimizer;
251 void SetMaximize(bool b){m_Maximize=b;}
254 GenericMetricPointer m_GenericMetric;
255 void SetMetricRegion(RegionType i){m_MetricRegion=i;}
256 RegionType m_MetricRegion;
264 //==============================================================================
265 // Update with the number of dimensions and pixeltype
266 //==============================================================================
267 template<class InputImageType>
268 void BLUTDIRGenericFilter::UpdateWithInputImageType()
270 //=============================================================================
272 //=============================================================================
273 bool threadsGiven=m_ArgsInfo.threads_given;
274 int threads=m_ArgsInfo.threads_arg;
275 typedef typename InputImageType::PixelType PixelType;
277 typedef double TCoordRep;
279 typename InputImageType::Pointer fixedImage = this->template GetInput<InputImageType>(0);
281 typename InputImageType::Pointer inputFixedImage = this->template GetInput<InputImageType>(0);
284 typename InputImageType::Pointer movingImage = this->template GetInput<InputImageType>(1);
286 typename InputImageType::Pointer inputMovingImage = this->template GetInput<InputImageType>(1);
288 typedef itk::Image< PixelType,InputImageType::ImageDimension > FixedImageType;
289 typedef itk::Image< PixelType, InputImageType::ImageDimension> MovingImageType;
290 const unsigned int SpaceDimension = InputImageType::ImageDimension;
291 //Whatever the pixel type, internally we work with an image represented in float
292 //Reading reference image
293 if (m_Verbose) std::cout<<"Reading images..."<<std::endl;
294 //=======================================================
296 //=======================================================
297 typename FixedImageType::Pointer croppedFixedImage=fixedImage;
298 //=======================================================
300 //=======================================================
301 // The original input region
302 typename FixedImageType::RegionType fixedImageRegion = fixedImage->GetLargestPossibleRegion();
304 // The transform region with respect to the input region:
305 // where should the transform be DEFINED (depends on mask)
306 typename FixedImageType::RegionType transformRegion = fixedImage->GetLargestPossibleRegion();
307 typename FixedImageType::RegionType::SizeType transformRegionSize=transformRegion.GetSize();
308 typename FixedImageType::RegionType::IndexType transformRegionIndex=transformRegion.GetIndex();
309 typename FixedImageType::PointType transformRegionOrigin=fixedImage->GetOrigin();
311 // The metric region with respect to the extracted transform region:
312 // where should the metric be CALCULATED (depends on transform)
313 typename FixedImageType::RegionType metricRegion = fixedImage->GetLargestPossibleRegion();
314 typename FixedImageType::RegionType::SizeType metricRegionSize=metricRegion.GetSize();
315 typename FixedImageType::RegionType::IndexType metricRegionIndex=metricRegion.GetIndex();
316 typename FixedImageType::PointType metricRegionOrigin=fixedImage->GetOrigin();
319 //===========================================================================
320 // If given, we connect a mask to reference or target
321 //============================================================================
322 typedef itk::ImageMaskSpatialObject< InputImageType::ImageDimension > MaskType;
323 typename MaskType::Pointer fixedMask=NULL;
324 if (m_ArgsInfo.referenceMask_given)
326 fixedMask= MaskType::New();
327 typedef itk::Image< unsigned char,InputImageType::ImageDimension > ImageMaskType;
328 typedef itk::ImageFileReader< ImageMaskType > MaskReaderType;
329 typename MaskReaderType::Pointer maskReader = MaskReaderType::New();
330 maskReader->SetFileName(m_ArgsInfo.referenceMask_arg);
333 maskReader->Update();
335 catch( itk::ExceptionObject & err )
337 std::cerr << "ExceptionObject caught while reading mask !" << std::endl;
338 std::cerr << err << std::endl;
341 if (m_Verbose)std::cout <<"Reference image mask was read..." <<std::endl;
343 // Set the image to the spatialObject
344 fixedMask->SetImage( maskReader->GetOutput() );
346 // Find the bounding box of the "inside" label
347 typedef itk::LabelStatisticsImageFilter<ImageMaskType, ImageMaskType> StatisticsImageFilterType;
348 typename StatisticsImageFilterType::Pointer statisticsImageFilter=StatisticsImageFilterType::New();
349 statisticsImageFilter->SetInput(maskReader->GetOutput());
350 statisticsImageFilter->SetLabelInput(maskReader->GetOutput());
351 statisticsImageFilter->Update();
352 typename StatisticsImageFilterType::BoundingBoxType boundingBox = statisticsImageFilter->GetBoundingBox(1);
354 // Limit the transform region to the mask
355 for (unsigned int i=0; i<InputImageType::ImageDimension; i++)
357 transformRegionIndex[i]=boundingBox[2*i];
358 transformRegionSize[i]=boundingBox[2*i+1]-boundingBox[2*i]+1;
360 transformRegion.SetSize(transformRegionSize);
361 transformRegion.SetIndex(transformRegionIndex);
362 fixedImage->TransformIndexToPhysicalPoint(transformRegion.GetIndex(), transformRegionOrigin);
364 // Crop the fixedImage to the bounding box to facilitate multi-resolution
365 typedef itk::ExtractImageFilter<FixedImageType,FixedImageType> ExtractImageFilterType;
366 typename ExtractImageFilterType::Pointer extractImageFilter=ExtractImageFilterType::New();
367 extractImageFilter->SetInput(fixedImage);
368 extractImageFilter->SetExtractionRegion(transformRegion);
369 extractImageFilter->Update();
370 croppedFixedImage=extractImageFilter->GetOutput();
372 // Update the metric region
373 metricRegion = croppedFixedImage->GetLargestPossibleRegion();
374 metricRegionIndex=metricRegion.GetIndex();
375 croppedFixedImage->TransformIndexToPhysicalPoint(metricRegionIndex, metricRegionOrigin);
377 // Set start index to zero (with respect to croppedFixedImage/transform region)
378 metricRegionIndex.Fill(0);
379 metricRegion.SetIndex(metricRegionIndex);
380 croppedFixedImage->SetRegions(metricRegion);
381 croppedFixedImage->SetOrigin(metricRegionOrigin);
384 typedef itk::ImageMaskSpatialObject< InputImageType::ImageDimension > MaskType;
385 typename MaskType::Pointer movingMask=NULL;
386 if (m_ArgsInfo.targetMask_given)
388 movingMask= MaskType::New();
389 typedef itk::Image< unsigned char, InputImageType::ImageDimension > ImageMaskType;
390 typedef itk::ImageFileReader< ImageMaskType > MaskReaderType;
391 typename MaskReaderType::Pointer maskReader = MaskReaderType::New();
392 maskReader->SetFileName(m_ArgsInfo.targetMask_arg);
395 maskReader->Update();
397 catch( itk::ExceptionObject & err )
399 std::cerr << "ExceptionObject caught !" << std::endl;
400 std::cerr << err << std::endl;
402 if (m_Verbose)std::cout <<"Target image mask was read..." <<std::endl;
404 movingMask->SetImage( maskReader->GetOutput() );
408 //=======================================================
410 //=======================================================
414 // Fixed image region
415 std::cout<<"The fixed image has its origin at "<<fixedImage->GetOrigin()<<std::endl
416 <<"The fixed image region starts at index "<<fixedImageRegion.GetIndex()<<std::endl
417 <<"The fixed image region has size "<< fixedImageRegion.GetSize()<<std::endl;
420 std::cout<<"The transform has its origin at "<<transformRegionOrigin<<std::endl
421 <<"The transform region will start at index "<<transformRegion.GetIndex()<<std::endl
422 <<"The transform region has size "<< transformRegion.GetSize()<<std::endl;
425 std::cout<<"The metric region has its origin at "<<metricRegionOrigin<<std::endl
426 <<"The metric region will start at index "<<metricRegion.GetIndex()<<std::endl
427 <<"The metric region has size "<< metricRegion.GetSize()<<std::endl;
432 //=======================================================
433 // Pyramids (update them for transform initializer)
434 //=======================================================
435 typedef itk::RecursiveMultiResolutionPyramidImageFilter< FixedImageType, FixedImageType> FixedImagePyramidType;
436 typedef itk::RecursiveMultiResolutionPyramidImageFilter< MovingImageType, MovingImageType> MovingImagePyramidType;
437 typename FixedImagePyramidType::Pointer fixedImagePyramid = FixedImagePyramidType::New();
438 typename MovingImagePyramidType::Pointer movingImagePyramid = MovingImagePyramidType::New();
439 fixedImagePyramid->SetUseShrinkImageFilter(false);
440 fixedImagePyramid->SetInput(croppedFixedImage);
441 fixedImagePyramid->SetNumberOfLevels(m_ArgsInfo.levels_arg);
442 movingImagePyramid->SetUseShrinkImageFilter(false);
443 movingImagePyramid->SetInput(movingImage);
444 movingImagePyramid->SetNumberOfLevels(m_ArgsInfo.levels_arg);
445 if (m_Verbose) std::cout<<"Creating the image pyramid..."<<std::endl;
446 fixedImagePyramid->Update();
447 movingImagePyramid->Update();
448 typedef clitk::MultiResolutionPyramidRegionFilter<FixedImageType> FixedImageRegionPyramidType;
449 typename FixedImageRegionPyramidType::Pointer fixedImageRegionPyramid=FixedImageRegionPyramidType::New();
450 fixedImageRegionPyramid->SetRegion(metricRegion);
451 fixedImageRegionPyramid->SetSchedule(fixedImagePyramid->GetSchedule());
454 //=======================================================
455 // Rigid or Affine Transform
456 //=======================================================
457 typedef itk::AffineTransform <double,3> RigidTransformType;
458 RigidTransformType::Pointer rigidTransform=NULL;
459 if (m_ArgsInfo.initMatrix_given)
461 if(m_Verbose) std::cout<<"Reading the prior transform matrix "<< m_ArgsInfo.initMatrix_arg<<"..."<<std::endl;
462 rigidTransform=RigidTransformType::New();
463 itk::Matrix<double,4,4> rigidTransformMatrix=clitk::ReadMatrix3D(m_ArgsInfo.initMatrix_arg);
466 itk::Matrix<double,3,3> finalRotation = clitk::GetRotationalPartMatrix3D(rigidTransformMatrix);
467 rigidTransform->SetMatrix(finalRotation);
469 //Set the translation
470 itk::Vector<double,3> finalTranslation = clitk::GetTranslationPartMatrix3D(rigidTransformMatrix);
471 rigidTransform->SetTranslation(finalTranslation);
475 //=======================================================
476 // B-LUT FFD Transform
477 //=======================================================
478 typedef clitk::BSplineDeformableTransform<TCoordRep,InputImageType::ImageDimension, SpaceDimension > TransformType;
479 typename TransformType::Pointer transform= TransformType::New();
480 if (fixedMask) transform->SetMask( fixedMask );
481 if (rigidTransform) transform->SetBulkTransform( rigidTransform );
483 //-------------------------------------------------------------------------
484 // The transform initializer
485 //-------------------------------------------------------------------------
486 typedef clitk::BSplineDeformableTransformInitializer< TransformType,FixedImageType> InitializerType;
487 typename InitializerType::Pointer initializer = InitializerType::New();
488 initializer->SetVerbose(m_Verbose);
489 initializer->SetImage(fixedImagePyramid->GetOutput(0));
490 initializer->SetTransform(transform);
492 //-------------------------------------------------------------------------
494 //-------------------------------------------------------------------------
495 typename FixedImageType::RegionType::SizeType splineOrders ;
496 splineOrders.Fill(3);
497 if (m_ArgsInfo.order_given)
498 for(unsigned int i=0; i<InputImageType::ImageDimension;i++)
499 splineOrders[i]=m_ArgsInfo.order_arg[i];
500 if (m_Verbose) std::cout<<"Setting the spline orders to "<<splineOrders<<"..."<<std::endl;
501 initializer->SetSplineOrders(splineOrders);
503 //-------------------------------------------------------------------------
505 //-------------------------------------------------------------------------
508 if (m_ArgsInfo.spacing_given)
510 initializer->m_ControlPointSpacingArray.resize(m_ArgsInfo.levels_arg);
511 initializer->SetControlPointSpacing(m_ArgsInfo.spacing_arg);
512 initializer->m_ControlPointSpacingArray[m_ArgsInfo.levels_arg-1]=initializer->m_ControlPointSpacing;
513 if (m_Verbose) std::cout<<"Using a control point spacing of "<<initializer->m_ControlPointSpacingArray[m_ArgsInfo.levels_arg-1]
514 <<" at level "<<m_ArgsInfo.levels_arg<<" of "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;
516 for (int i=1; i<m_ArgsInfo.levels_arg; i++ )
518 initializer->m_ControlPointSpacingArray[m_ArgsInfo.levels_arg-1-i]=initializer->m_ControlPointSpacingArray[m_ArgsInfo.levels_arg-i]*2;
519 if (m_Verbose) std::cout<<"Using a control point spacing of "<<initializer->m_ControlPointSpacingArray[m_ArgsInfo.levels_arg-1-i]
520 <<" at level "<<m_ArgsInfo.levels_arg-i<<" of "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;
526 if (m_ArgsInfo.control_given)
528 initializer->m_NumberOfControlPointsInsideTheImageArray.resize(m_ArgsInfo.levels_arg);
529 initializer->SetNumberOfControlPointsInsideTheImage(m_ArgsInfo.control_arg);
530 initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-1]=initializer->m_NumberOfControlPointsInsideTheImage;
531 if (m_Verbose) std::cout<<"Using "<< initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-1]<<"control points inside the image"
532 <<" at level "<<m_ArgsInfo.levels_arg<<" of "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;
534 for (int i=1; i<m_ArgsInfo.levels_arg; i++ )
536 for(unsigned int j=0;j<InputImageType::ImageDimension;j++)
537 initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-1-i][j]=ceil ((double)initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-i][j]/2.);
538 // initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-1-i]=ceil ((double)initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-i]/2.);
539 if (m_Verbose) std::cout<<"Using "<< initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-1-i]<<"control points inside the image"
540 <<" at level "<<m_ArgsInfo.levels_arg<<" of "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;
545 // Inialize on the first level
546 if (m_ArgsInfo.verbose_flag) std::cout<<"Initializing transform for level 1 of "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;
547 if (m_ArgsInfo.spacing_given) initializer->SetControlPointSpacing( initializer->m_ControlPointSpacingArray[0]);
548 if (m_ArgsInfo.control_given) initializer->SetNumberOfControlPointsInsideTheImage(initializer->m_NumberOfControlPointsInsideTheImageArray[0]);
549 if (m_ArgsInfo.samplingFactor_given) initializer->SetSamplingFactors(m_ArgsInfo.samplingFactor_arg);
552 initializer->InitializeTransform();
554 //-------------------------------------------------------------------------
555 // Initial parameters (passed by reference)
556 //-------------------------------------------------------------------------
557 typedef typename TransformType::ParametersType ParametersType;
558 const unsigned int numberOfParameters = transform->GetNumberOfParameters();
559 ParametersType parameters(numberOfParameters);
560 parameters.Fill( 0.0 );
561 transform->SetParameters( parameters );
562 if (m_ArgsInfo.initCoeff_given) initializer->SetInitialParameters(m_ArgsInfo.initCoeff_arg, parameters);
565 //=======================================================
567 //=======================================================
568 typedef clitk::GenericInterpolator<args_info_clitkBLUTDIR, FixedImageType, TCoordRep > GenericInterpolatorType;
569 typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
570 genericInterpolator->SetArgsInfo(m_ArgsInfo);
571 typedef itk::InterpolateImageFunction< FixedImageType, TCoordRep > InterpolatorType;
572 typename InterpolatorType::Pointer interpolator=genericInterpolator->GetInterpolatorPointer();
575 //=======================================================
577 //=======================================================
578 typedef clitk::GenericMetric<args_info_clitkBLUTDIR, FixedImageType,MovingImageType > GenericMetricType;
579 typename GenericMetricType::Pointer genericMetric=GenericMetricType::New();
580 genericMetric->SetArgsInfo(m_ArgsInfo);
581 genericMetric->SetFixedImage(fixedImagePyramid->GetOutput(0));
582 if (fixedMask) genericMetric->SetFixedImageMask(fixedMask);
583 genericMetric->SetFixedImageRegion(fixedImageRegionPyramid->GetOutput(0));
584 typedef itk::ImageToImageMetric< FixedImageType, MovingImageType > MetricType;
585 typename MetricType::Pointer metric=genericMetric->GetMetricPointer();
586 if (movingMask) metric->SetMovingImageMask(movingMask);
588 #ifdef ITK_USE_OPTIMIZED_REGISTRATION_METHODS
590 metric->SetNumberOfThreads( threads );
591 if (m_Verbose) std::cout<< "Using " << threads << " threads." << std::endl;
594 if (m_Verbose) std::cout<<"Not setting the number of threads (not compiled with USE_OPTIMIZED_REGISTRATION_METHODS)..."<<std::endl;
598 //=======================================================
600 //=======================================================
601 typedef clitk::GenericOptimizer<args_info_clitkBLUTDIR> GenericOptimizerType;
602 GenericOptimizerType::Pointer genericOptimizer = GenericOptimizerType::New();
603 genericOptimizer->SetArgsInfo(m_ArgsInfo);
604 genericOptimizer->SetMaximize(genericMetric->GetMaximize());
605 genericOptimizer->SetNumberOfParameters(transform->GetNumberOfParameters());
606 typedef itk::SingleValuedNonLinearOptimizer OptimizerType;
607 OptimizerType::Pointer optimizer = genericOptimizer->GetOptimizerPointer();
610 //=======================================================
612 //=======================================================
613 typedef itk::MultiResolutionImageRegistrationMethod< FixedImageType, MovingImageType > RegistrationType;
614 typename RegistrationType::Pointer registration = RegistrationType::New();
615 registration->SetMetric( metric );
616 registration->SetOptimizer( optimizer );
617 registration->SetInterpolator( interpolator );
618 registration->SetTransform (transform);
620 registration->SetNumberOfThreads(threads);
621 if (m_Verbose) std::cout<< "Using " << threads << " threads." << std::endl;
623 registration->SetFixedImage( croppedFixedImage );
624 registration->SetMovingImage( movingImage );
625 registration->SetFixedImageRegion( metricRegion );
626 registration->SetFixedImagePyramid( fixedImagePyramid );
627 registration->SetMovingImagePyramid( movingImagePyramid );
628 registration->SetInitialTransformParameters( transform->GetParameters() );
629 registration->SetNumberOfLevels( m_ArgsInfo.levels_arg );
630 if (m_Verbose) std::cout<<"Setting the number of resolution levels to "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;
633 //================================================================================================
635 //================================================================================================
638 // Output iteration info
639 CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New();
640 observer->SetOptimizer(genericOptimizer);
641 optimizer->AddObserver( itk::IterationEvent(), observer );
644 typedef RegistrationInterfaceCommand<RegistrationType,args_info_clitkBLUTDIR> CommandType;
645 typename CommandType::Pointer command = CommandType::New();
646 command->SetInitializer(initializer);
647 command->SetArgsInfo(m_ArgsInfo);
648 command->SetCommandIterationUpdate(observer);
649 command->SetMaximize(genericMetric->GetMaximize());
650 command->SetMetricRegion(metricRegion);
651 registration->AddObserver( itk::IterationEvent(), command );
655 //=======================================================
657 //=======================================================
658 if (m_Verbose) std::cout << std::endl << "Starting Registration" << std::endl;
662 registration->StartRegistration();
664 catch( itk::ExceptionObject & err )
666 std::cerr << "ExceptionObject caught while registering!" << std::endl;
667 std::cerr << err << std::endl;
672 //=======================================================
674 //=======================================================
675 OptimizerType::ParametersType finalParameters = registration->GetLastTransformParameters();
676 transform->SetParameters( finalParameters );
679 std::cout<<"Stop condition description: "
680 <<registration->GetOptimizer()->GetStopConditionDescription()<<std::endl;
684 //=======================================================
685 // Get the BSpline coefficient images and write them
686 //=======================================================
687 if (m_ArgsInfo.coeff_given)
689 typedef typename TransformType::CoefficientImageType CoefficientImageType;
690 typename CoefficientImageType::Pointer coefficientImage =transform->GetCoefficientImage();
691 typedef itk::ImageFileWriter<CoefficientImageType> CoeffWriterType;
692 typename CoeffWriterType::Pointer coeffWriter=CoeffWriterType::New();
693 coeffWriter->SetInput(coefficientImage);
694 coeffWriter->SetFileName(m_ArgsInfo.coeff_arg);
695 coeffWriter->Update();
700 //=======================================================
701 // Compute the DVF (only deformable transform)
702 //=======================================================
703 typedef itk::Vector< float, SpaceDimension > DisplacementType;
704 typedef itk::Image< DisplacementType, InputImageType::ImageDimension > DeformationFieldType;
705 typedef itk::TransformToDeformationFieldSource<DeformationFieldType, double> ConvertorType;
706 typename ConvertorType::Pointer filter= ConvertorType::New();
707 filter->SetNumberOfThreads(1);
708 transform->SetBulkTransform(NULL);
709 filter->SetTransform(transform);
710 filter->SetOutputParametersFromImage(fixedImage);
712 typename DeformationFieldType::Pointer field = filter->GetOutput();
715 //=======================================================
717 //=======================================================
718 typedef itk::ImageFileWriter< DeformationFieldType > FieldWriterType;
719 typename FieldWriterType::Pointer fieldWriter = FieldWriterType::New();
720 fieldWriter->SetFileName( m_ArgsInfo.vf_arg );
721 fieldWriter->SetInput( field );
724 fieldWriter->Update();
726 catch( itk::ExceptionObject & excp )
728 std::cerr << "Exception thrown writing the DVF" << std::endl;
729 std::cerr << excp << std::endl;
734 //=======================================================
735 // Resample the moving image
736 //=======================================================
737 typedef itk::ResampleImageFilter< MovingImageType, FixedImageType > ResampleFilterType;
738 typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
739 if (rigidTransform) transform->SetBulkTransform(rigidTransform);
740 resampler->SetTransform( transform );
741 resampler->SetInput( movingImage);
742 resampler->SetOutputParametersFromImage(fixedImage);
744 typename FixedImageType::Pointer result=resampler->GetOutput();
746 // typedef itk::WarpImageFilter< MovingImageType, FixedImageType, DeformationFieldType > WarpFilterType;
747 // typename WarpFilterType::Pointer warp = WarpFilterType::New();
749 // warp->SetDeformationField( field );
750 // warp->SetInput( movingImageReader->GetOutput() );
751 // warp->SetOutputOrigin( fixedImage->GetOrigin() );
752 // warp->SetOutputSpacing( fixedImage->GetSpacing() );
753 // warp->SetOutputDirection( fixedImage->GetDirection() );
754 // warp->SetEdgePaddingValue( 0.0 );
758 //=======================================================
759 // Write the warped image
760 //=======================================================
761 typedef itk::ImageFileWriter< FixedImageType > WriterType;
762 typename WriterType::Pointer writer = WriterType::New();
763 writer->SetFileName( m_ArgsInfo.output_arg );
764 writer->SetInput( result );
770 catch( itk::ExceptionObject & err )
772 std::cerr << "ExceptionObject caught !" << std::endl;
773 std::cerr << err << std::endl;
778 //=======================================================
779 // Calculate the difference after the deformable transform
780 //=======================================================
781 typedef clitk::DifferenceImageFilter< FixedImageType, FixedImageType> DifferenceFilterType;
782 if (m_ArgsInfo.after_given)
784 typename DifferenceFilterType::Pointer difference = DifferenceFilterType::New();
785 difference->SetValidInput( fixedImage );
786 difference->SetTestInput( result );
790 difference->Update();
792 catch( itk::ExceptionObject & err )
794 std::cerr << "ExceptionObject caught calculating the difference !" << std::endl;
795 std::cerr << err << std::endl;
799 typename WriterType::Pointer differenceWriter=WriterType::New();
800 differenceWriter->SetInput(difference->GetOutput());
801 differenceWriter->SetFileName(m_ArgsInfo.after_arg);
802 differenceWriter->Update();
807 //=======================================================
808 // Calculate the difference before the deformable transform
809 //=======================================================
810 if( m_ArgsInfo.before_given )
813 typename FixedImageType::Pointer moving=FixedImageType::New();
814 if (m_ArgsInfo.initMatrix_given)
816 typedef itk::ResampleImageFilter<MovingImageType, FixedImageType> ResamplerType;
817 typename ResamplerType::Pointer resampler=ResamplerType::New();
818 resampler->SetInput(movingImage);
819 resampler->SetOutputOrigin(fixedImage->GetOrigin());
820 resampler->SetSize(fixedImage->GetLargestPossibleRegion().GetSize());
821 resampler->SetOutputSpacing(fixedImage->GetSpacing());
822 resampler->SetDefaultPixelValue( 0. );
823 if (rigidTransform ) resampler->SetTransform(rigidTransform);
825 moving=resampler->GetOutput();
830 typename DifferenceFilterType::Pointer difference = DifferenceFilterType::New();
831 difference->SetValidInput( fixedImage );
832 difference->SetTestInput( moving );
836 difference->Update();
838 catch( itk::ExceptionObject & err )
840 std::cerr << "ExceptionObject caught calculating the difference !" << std::endl;
841 std::cerr << err << std::endl;
845 typename WriterType::Pointer differenceWriter=WriterType::New();
846 writer->SetFileName( m_ArgsInfo.before_arg );
847 writer->SetInput( difference->GetOutput() );
856 #endif // #define clitkBLUTDIRGenericFilter_txx