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 #if ITK_VERSION_MAJOR == 4
391 extractImageFilter->SetDirectionCollapseToSubmatrix();
393 extractImageFilter->SetInput(fixedImage);
394 extractImageFilter->SetExtractionRegion(transformRegion);
395 extractImageFilter->Update();
396 croppedFixedImage=extractImageFilter->GetOutput();
398 // Update the metric region
399 metricRegion = croppedFixedImage->GetLargestPossibleRegion();
400 metricRegionIndex=metricRegion.GetIndex();
401 croppedFixedImage->TransformIndexToPhysicalPoint(metricRegionIndex, metricRegionOrigin);
403 // Set start index to zero (with respect to croppedFixedImage/transform region)
404 metricRegionIndex.Fill(0);
405 metricRegion.SetIndex(metricRegionIndex);
406 croppedFixedImage->SetRegions(metricRegion);
407 croppedFixedImage->SetOrigin(metricRegionOrigin);
410 typedef itk::ImageMaskSpatialObject< InputImageType::ImageDimension > MaskType;
411 typename MaskType::Pointer movingMask=NULL;
412 if (m_ArgsInfo.targetMask_given)
414 movingMask= MaskType::New();
415 typedef itk::Image< unsigned char, InputImageType::ImageDimension > ImageMaskType;
416 typedef itk::ImageFileReader< ImageMaskType > MaskReaderType;
417 typename MaskReaderType::Pointer maskReader = MaskReaderType::New();
418 maskReader->SetFileName(m_ArgsInfo.targetMask_arg);
421 maskReader->Update();
423 catch( itk::ExceptionObject & err )
425 std::cerr << "ExceptionObject caught !" << std::endl;
426 std::cerr << err << std::endl;
428 if (m_Verbose)std::cout <<"Target image mask was read..." <<std::endl;
430 movingMask->SetImage( maskReader->GetOutput() );
434 //=======================================================
436 //=======================================================
440 // Fixed image region
441 std::cout<<"The fixed image has its origin at "<<fixedImage->GetOrigin()<<std::endl
442 <<"The fixed image region starts at index "<<fixedImageRegion.GetIndex()<<std::endl
443 <<"The fixed image region has size "<< fixedImageRegion.GetSize()<<std::endl;
446 std::cout<<"The transform has its origin at "<<transformRegionOrigin<<std::endl
447 <<"The transform region will start at index "<<transformRegion.GetIndex()<<std::endl
448 <<"The transform region has size "<< transformRegion.GetSize()<<std::endl;
451 std::cout<<"The metric region has its origin at "<<metricRegionOrigin<<std::endl
452 <<"The metric region will start at index "<<metricRegion.GetIndex()<<std::endl
453 <<"The metric region has size "<< metricRegion.GetSize()<<std::endl;
458 //=======================================================
459 // Pyramids (update them for transform initializer)
460 //=======================================================
461 typedef itk::RecursiveMultiResolutionPyramidImageFilter< FixedImageType, FixedImageType> FixedImagePyramidType;
462 typedef itk::RecursiveMultiResolutionPyramidImageFilter< MovingImageType, MovingImageType> MovingImagePyramidType;
463 typename FixedImagePyramidType::Pointer fixedImagePyramid = FixedImagePyramidType::New();
464 typename MovingImagePyramidType::Pointer movingImagePyramid = MovingImagePyramidType::New();
465 fixedImagePyramid->SetUseShrinkImageFilter(false);
466 fixedImagePyramid->SetInput(croppedFixedImage);
467 fixedImagePyramid->SetNumberOfLevels(m_ArgsInfo.levels_arg);
468 movingImagePyramid->SetUseShrinkImageFilter(false);
469 movingImagePyramid->SetInput(movingImage);
470 movingImagePyramid->SetNumberOfLevels(m_ArgsInfo.levels_arg);
471 if (m_Verbose) std::cout<<"Creating the image pyramid..."<<std::endl;
472 fixedImagePyramid->Update();
473 movingImagePyramid->Update();
474 typedef clitk::MultiResolutionPyramidRegionFilter<FixedImageType> FixedImageRegionPyramidType;
475 typename FixedImageRegionPyramidType::Pointer fixedImageRegionPyramid=FixedImageRegionPyramidType::New();
476 fixedImageRegionPyramid->SetRegion(metricRegion);
477 fixedImageRegionPyramid->SetSchedule(fixedImagePyramid->GetSchedule());
480 //=======================================================
481 // Rigid or Affine Transform
482 //=======================================================
483 typedef itk::AffineTransform <double,3> RigidTransformType;
484 RigidTransformType::Pointer rigidTransform=NULL;
485 if (m_ArgsInfo.initMatrix_given)
487 if(m_Verbose) std::cout<<"Reading the prior transform matrix "<< m_ArgsInfo.initMatrix_arg<<"..."<<std::endl;
488 rigidTransform=RigidTransformType::New();
489 itk::Matrix<double,4,4> rigidTransformMatrix=clitk::ReadMatrix3D(m_ArgsInfo.initMatrix_arg);
492 itk::Matrix<double,3,3> finalRotation = clitk::GetRotationalPartMatrix3D(rigidTransformMatrix);
493 rigidTransform->SetMatrix(finalRotation);
495 //Set the translation
496 itk::Vector<double,3> finalTranslation = clitk::GetTranslationPartMatrix3D(rigidTransformMatrix);
497 rigidTransform->SetTranslation(finalTranslation);
501 //=======================================================
502 // B-LUT FFD Transform
503 //=======================================================
504 typedef clitk::MultipleBSplineDeformableTransform<TCoordRep,InputImageType::ImageDimension, SpaceDimension > TransformType;
505 typename TransformType::Pointer transform = TransformType::New();
506 if (labels) transform->SetLabels(labels);
507 if (rigidTransform) transform->SetBulkTransform(rigidTransform);
509 //-------------------------------------------------------------------------
510 // The transform initializer
511 //-------------------------------------------------------------------------
512 typedef clitk::MultipleBSplineDeformableTransformInitializer< TransformType,FixedImageType> InitializerType;
513 typename InitializerType::Pointer initializer = InitializerType::New();
514 initializer->SetVerbose(m_Verbose);
515 initializer->SetImage(fixedImagePyramid->GetOutput(0));
516 initializer->SetTransform(transform);
518 //-------------------------------------------------------------------------
520 //-------------------------------------------------------------------------
521 typename FixedImageType::RegionType::SizeType splineOrders ;
522 splineOrders.Fill(3);
523 if (m_ArgsInfo.order_given)
524 for(unsigned int i=0; i<InputImageType::ImageDimension;i++)
525 splineOrders[i]=m_ArgsInfo.order_arg[i];
526 if (m_Verbose) std::cout<<"Setting the spline orders to "<<splineOrders<<"..."<<std::endl;
527 initializer->SetSplineOrders(splineOrders);
529 //-------------------------------------------------------------------------
531 //-------------------------------------------------------------------------
534 if (m_ArgsInfo.spacing_given)
536 initializer->m_ControlPointSpacingArray.resize(m_ArgsInfo.levels_arg);
537 initializer->SetControlPointSpacing(m_ArgsInfo.spacing_arg);
538 initializer->m_ControlPointSpacingArray[m_ArgsInfo.levels_arg-1]=initializer->m_ControlPointSpacing;
539 if (m_Verbose) std::cout<<"Using a control point spacing of "<<initializer->m_ControlPointSpacingArray[m_ArgsInfo.levels_arg-1]
540 <<" at level "<<m_ArgsInfo.levels_arg<<" of "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;
542 for (int i=1; i<m_ArgsInfo.levels_arg; i++ )
544 initializer->m_ControlPointSpacingArray[m_ArgsInfo.levels_arg-1-i]=initializer->m_ControlPointSpacingArray[m_ArgsInfo.levels_arg-i]*2;
545 if (m_Verbose) std::cout<<"Using a control point spacing of "<<initializer->m_ControlPointSpacingArray[m_ArgsInfo.levels_arg-1-i]
546 <<" at level "<<m_ArgsInfo.levels_arg-i<<" of "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;
552 if (m_ArgsInfo.control_given)
554 initializer->m_NumberOfControlPointsInsideTheImageArray.resize(m_ArgsInfo.levels_arg);
555 initializer->SetNumberOfControlPointsInsideTheImage(m_ArgsInfo.control_arg);
556 initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-1]=initializer->m_NumberOfControlPointsInsideTheImage;
557 if (m_Verbose) std::cout<<"Using "<< initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-1]<<"control points inside the image"
558 <<" at level "<<m_ArgsInfo.levels_arg<<" of "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;
560 for (int i=1; i<m_ArgsInfo.levels_arg; i++ )
562 for(unsigned int j=0;j<InputImageType::ImageDimension;j++)
563 initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-1-i][j]=ceil ((double)initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-i][j]/2.);
564 // initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-1-i]=ceil ((double)initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-i]/2.);
565 if (m_Verbose) std::cout<<"Using "<< initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-1-i]<<"control points inside the image"
566 <<" at level "<<m_ArgsInfo.levels_arg<<" of "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;
571 // Inialize on the first level
572 if (m_ArgsInfo.verbose_flag) std::cout<<"Initializing transform for level 1 of "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;
573 if (m_ArgsInfo.spacing_given) initializer->SetControlPointSpacing( initializer->m_ControlPointSpacingArray[0]);
574 if (m_ArgsInfo.control_given) initializer->SetNumberOfControlPointsInsideTheImage(initializer->m_NumberOfControlPointsInsideTheImageArray[0]);
575 if (m_ArgsInfo.samplingFactor_given) initializer->SetSamplingFactors(m_ArgsInfo.samplingFactor_arg);
578 initializer->InitializeTransform();
580 //-------------------------------------------------------------------------
581 // Initial parameters (passed by reference)
582 //-------------------------------------------------------------------------
583 typedef typename TransformType::ParametersType ParametersType;
584 const unsigned int numberOfParameters = transform->GetNumberOfParameters();
585 ParametersType parameters(numberOfParameters);
586 parameters.Fill( 0.0 );
587 transform->SetParameters( parameters );
588 if (m_ArgsInfo.initCoeff_given) initializer->SetInitialParameters(m_ArgsInfo.initCoeff_arg, parameters);
590 //-------------------------------------------------------------------------
591 // DEBUG: use an itk BSpline instead of multilabel BLUTs
592 //-------------------------------------------------------------------------
593 typedef itk::Transform< TCoordRep, 3, 3 > RegistrationTransformType;
594 RegistrationTransformType::Pointer regTransform(transform);
595 typedef itk::BSplineDeformableTransform<TCoordRep,SpaceDimension, 3> SingleBSplineTransformType;
596 typename SingleBSplineTransformType::Pointer sTransform;
597 if(m_ArgsInfo.itkbspline_flag) {
598 if( transform->GetTransforms().size()>1)
599 itkExceptionMacro(<< "invalid --itkbspline option if there is more than 1 label")
600 sTransform = SingleBSplineTransformType::New();
601 sTransform->SetBulkTransform( transform->GetTransforms()[0]->GetBulkTransform() );
602 sTransform->SetGridSpacing( transform->GetTransforms()[0]->GetGridSpacing() );
603 sTransform->SetGridOrigin( transform->GetTransforms()[0]->GetGridOrigin() );
604 sTransform->SetGridRegion( transform->GetTransforms()[0]->GetGridRegion() );
605 sTransform->SetParameters( transform->GetTransforms()[0]->GetParameters() );
606 regTransform = sTransform;
607 transform = NULL; // free memory
610 //=======================================================
612 //=======================================================
613 typedef clitk::GenericInterpolator<args_info_clitkBLUTDIR, FixedImageType, TCoordRep > GenericInterpolatorType;
614 typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
615 genericInterpolator->SetArgsInfo(m_ArgsInfo);
616 typedef itk::InterpolateImageFunction< FixedImageType, TCoordRep > InterpolatorType;
617 typename InterpolatorType::Pointer interpolator=genericInterpolator->GetInterpolatorPointer();
620 //=======================================================
622 //=======================================================
623 typedef clitk::GenericMetric<args_info_clitkBLUTDIR, FixedImageType,MovingImageType > GenericMetricType;
624 typename GenericMetricType::Pointer genericMetric=GenericMetricType::New();
625 genericMetric->SetArgsInfo(m_ArgsInfo);
626 genericMetric->SetFixedImage(fixedImagePyramid->GetOutput(0));
627 if (fixedMask) genericMetric->SetFixedImageMask(fixedMask);
628 genericMetric->SetFixedImageRegion(fixedImageRegionPyramid->GetOutput(0));
629 typedef itk::ImageToImageMetric< FixedImageType, MovingImageType > MetricType;
630 typename MetricType::Pointer metric=genericMetric->GetMetricPointer();
631 if (movingMask) metric->SetMovingImageMask(movingMask);
633 #if defined(ITK_USE_OPTIMIZED_REGISTRATION_METHODS) || ITK_VERSION_MAJOR >= 4
635 metric->SetNumberOfThreads( threads );
636 if (m_Verbose) std::cout<< "Using " << threads << " threads." << std::endl;
639 if (m_Verbose) std::cout<<"Not setting the number of threads (not compiled with USE_OPTIMIZED_REGISTRATION_METHODS)..."<<std::endl;
643 //=======================================================
645 //=======================================================
646 typedef clitk::GenericOptimizer<args_info_clitkBLUTDIR> GenericOptimizerType;
647 GenericOptimizerType::Pointer genericOptimizer = GenericOptimizerType::New();
648 genericOptimizer->SetArgsInfo(m_ArgsInfo);
649 genericOptimizer->SetMaximize(genericMetric->GetMaximize());
650 genericOptimizer->SetNumberOfParameters(regTransform->GetNumberOfParameters());
651 typedef itk::SingleValuedNonLinearOptimizer OptimizerType;
652 OptimizerType::Pointer optimizer = genericOptimizer->GetOptimizerPointer();
655 //=======================================================
657 //=======================================================
658 typedef itk::MultiResolutionImageRegistrationMethod< FixedImageType, MovingImageType > RegistrationType;
659 typename RegistrationType::Pointer registration = RegistrationType::New();
660 registration->SetMetric( metric );
661 registration->SetOptimizer( optimizer );
662 registration->SetInterpolator( interpolator );
663 registration->SetTransform (regTransform );
665 registration->SetNumberOfThreads(threads);
666 if (m_Verbose) std::cout<< "Using " << threads << " threads." << std::endl;
668 registration->SetFixedImage( croppedFixedImage );
669 registration->SetMovingImage( movingImage );
670 registration->SetFixedImageRegion( metricRegion );
671 registration->SetFixedImagePyramid( fixedImagePyramid );
672 registration->SetMovingImagePyramid( movingImagePyramid );
673 registration->SetInitialTransformParameters( regTransform->GetParameters() );
674 registration->SetNumberOfLevels( m_ArgsInfo.levels_arg );
675 if (m_Verbose) std::cout<<"Setting the number of resolution levels to "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;
678 //================================================================================================
680 //================================================================================================
683 // Output iteration info
684 CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New();
685 observer->SetOptimizer(genericOptimizer);
686 optimizer->AddObserver( itk::IterationEvent(), observer );
689 typedef RegistrationInterfaceCommand<RegistrationType,args_info_clitkBLUTDIR> CommandType;
690 typename CommandType::Pointer command = CommandType::New();
691 command->SetInitializer(initializer);
692 command->SetArgsInfo(m_ArgsInfo);
693 command->SetCommandIterationUpdate(observer);
694 command->SetMaximize(genericMetric->GetMaximize());
695 command->SetMetricRegion(metricRegion);
696 registration->AddObserver( itk::IterationEvent(), command );
698 if (m_ArgsInfo.coeff_given)
700 if(m_ArgsInfo.itkbspline_flag) {
701 itkExceptionMacro("--coeff and --itkbpline are incompatible");
704 std::cout << std::endl << "Output coefficient images every " << m_ArgsInfo.coeffEveryN_arg << " iterations." << std::endl;
705 typedef CommandIterationUpdateDVF<FixedImageType, OptimizerType, TransformType> DVFCommandType;
706 typename DVFCommandType::Pointer observerdvf = DVFCommandType::New();
707 observerdvf->SetFixedImage(fixedImage);
708 observerdvf->SetTransform(transform);
709 observerdvf->SetArgsInfo(m_ArgsInfo);
710 optimizer->AddObserver( itk::IterationEvent(), observerdvf );
715 //=======================================================
717 //=======================================================
718 if (m_Verbose) std::cout << std::endl << "Starting Registration" << std::endl;
722 registration->StartRegistration();
724 catch( itk::ExceptionObject & err )
726 std::cerr << "ExceptionObject caught while registering!" << std::endl;
727 std::cerr << err << std::endl;
732 //=======================================================
734 //=======================================================
735 OptimizerType::ParametersType finalParameters = registration->GetLastTransformParameters();
736 regTransform->SetParameters( finalParameters );
739 std::cout<<"Stop condition description: "
740 <<registration->GetOptimizer()->GetStopConditionDescription()<<std::endl;
744 //=======================================================
745 // Get the BSpline coefficient images and write them
746 //=======================================================
747 if (m_ArgsInfo.coeff_given)
749 typedef typename TransformType::CoefficientImageType CoefficientImageType;
750 std::vector<typename CoefficientImageType::Pointer> coefficientImages = transform->GetCoefficientImages();
751 typedef itk::ImageFileWriter<CoefficientImageType> CoeffWriterType;
752 typename CoeffWriterType::Pointer coeffWriter = CoeffWriterType::New();
753 unsigned nLabels = transform->GetnLabels();
755 std::string fname(m_ArgsInfo.coeff_arg);
756 int dotpos = fname.length() - 1;
757 while (dotpos >= 0 && fname[dotpos] != '.')
760 for (unsigned i = 0; i < nLabels; ++i)
762 std::ostringstream osfname;
763 osfname << fname.substr(0, dotpos) << '_' << i << fname.substr(dotpos);
764 coeffWriter->SetInput(coefficientImages[i]);
765 coeffWriter->SetFileName(osfname.str());
766 coeffWriter->Update();
772 //=======================================================
773 // Compute the DVF (only deformable transform)
774 //=======================================================
775 typedef itk::Vector< float, SpaceDimension > DisplacementType;
776 typedef itk::Image< DisplacementType, InputImageType::ImageDimension > DisplacementFieldType;
777 #if ITK_VERSION_MAJOR >= 4
778 typedef itk::TransformToDisplacementFieldSource<DisplacementFieldType, double> ConvertorType;
780 typedef itk::TransformToDeformationFieldSource<DisplacementFieldType, double> ConvertorType;
782 typename ConvertorType::Pointer filter= ConvertorType::New();
783 filter->SetNumberOfThreads(1);
784 if(m_ArgsInfo.itkbspline_flag)
785 sTransform->SetBulkTransform(NULL);
787 transform->SetBulkTransform(NULL);
788 filter->SetTransform(regTransform);
789 filter->SetOutputParametersFromImage(fixedImage);
791 typename DisplacementFieldType::Pointer field = filter->GetOutput();
794 //=======================================================
796 //=======================================================
797 typedef itk::ImageFileWriter< DisplacementFieldType > FieldWriterType;
798 typename FieldWriterType::Pointer fieldWriter = FieldWriterType::New();
799 fieldWriter->SetFileName( m_ArgsInfo.vf_arg );
800 fieldWriter->SetInput( field );
803 fieldWriter->Update();
805 catch( itk::ExceptionObject & excp )
807 std::cerr << "Exception thrown writing the DVF" << std::endl;
808 std::cerr << excp << std::endl;
813 //=======================================================
814 // Resample the moving image
815 //=======================================================
816 typedef itk::ResampleImageFilter< MovingImageType, FixedImageType > ResampleFilterType;
817 typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
818 if (rigidTransform) {
819 if(m_ArgsInfo.itkbspline_flag)
820 sTransform->SetBulkTransform(rigidTransform);
822 transform->SetBulkTransform(rigidTransform);
824 resampler->SetTransform( regTransform );
825 resampler->SetInput( movingImage);
826 resampler->SetOutputParametersFromImage(fixedImage);
828 typename FixedImageType::Pointer result=resampler->GetOutput();
830 // typedef itk::WarpImageFilter< MovingImageType, FixedImageType, DeformationFieldType > WarpFilterType;
831 // typename WarpFilterType::Pointer warp = WarpFilterType::New();
833 // warp->SetDeformationField( field );
834 // warp->SetInput( movingImageReader->GetOutput() );
835 // warp->SetOutputOrigin( fixedImage->GetOrigin() );
836 // warp->SetOutputSpacing( fixedImage->GetSpacing() );
837 // warp->SetOutputDirection( fixedImage->GetDirection() );
838 // warp->SetEdgePaddingValue( 0.0 );
842 //=======================================================
843 // Write the warped image
844 //=======================================================
845 typedef itk::ImageFileWriter< FixedImageType > WriterType;
846 typename WriterType::Pointer writer = WriterType::New();
847 writer->SetFileName( m_ArgsInfo.output_arg );
848 writer->SetInput( result );
854 catch( itk::ExceptionObject & err )
856 std::cerr << "ExceptionObject caught !" << std::endl;
857 std::cerr << err << std::endl;
862 //=======================================================
863 // Calculate the difference after the deformable transform
864 //=======================================================
865 typedef clitk::DifferenceImageFilter< FixedImageType, FixedImageType> DifferenceFilterType;
866 if (m_ArgsInfo.after_given)
868 typename DifferenceFilterType::Pointer difference = DifferenceFilterType::New();
869 difference->SetValidInput( fixedImage );
870 difference->SetTestInput( result );
874 difference->Update();
876 catch( itk::ExceptionObject & err )
878 std::cerr << "ExceptionObject caught calculating the difference !" << std::endl;
879 std::cerr << err << std::endl;
883 typename WriterType::Pointer differenceWriter=WriterType::New();
884 differenceWriter->SetInput(difference->GetOutput());
885 differenceWriter->SetFileName(m_ArgsInfo.after_arg);
886 differenceWriter->Update();
891 //=======================================================
892 // Calculate the difference before the deformable transform
893 //=======================================================
894 if( m_ArgsInfo.before_given )
897 typename FixedImageType::Pointer moving=FixedImageType::New();
898 if (m_ArgsInfo.initMatrix_given)
900 typedef itk::ResampleImageFilter<MovingImageType, FixedImageType> ResamplerType;
901 typename ResamplerType::Pointer resampler=ResamplerType::New();
902 resampler->SetInput(movingImage);
903 resampler->SetOutputOrigin(fixedImage->GetOrigin());
904 resampler->SetSize(fixedImage->GetLargestPossibleRegion().GetSize());
905 resampler->SetOutputSpacing(fixedImage->GetSpacing());
906 resampler->SetDefaultPixelValue( 0. );
907 if (rigidTransform ) resampler->SetTransform(rigidTransform);
909 moving=resampler->GetOutput();
914 typename DifferenceFilterType::Pointer difference = DifferenceFilterType::New();
915 difference->SetValidInput( fixedImage );
916 difference->SetTestInput( moving );
920 difference->Update();
922 catch( itk::ExceptionObject & err )
924 std::cerr << "ExceptionObject caught calculating the difference !" << std::endl;
925 std::cerr << err << std::endl;
929 typename WriterType::Pointer differenceWriter=WriterType::New();
930 writer->SetFileName( m_ArgsInfo.before_arg );
931 writer->SetInput( difference->GetOutput() );
940 #endif // #define clitkBLUTDIRGenericFilter_txx