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;
73 //===========================================================================//
75 //==========================================================================//
76 BLUTDIRGenericFilter::BLUTDIRGenericFilter():
77 ImageToImageGenericFilter<Self>("Register DIR")
79 InitializeImageType<2>();
80 InitializeImageType<3>();
84 //=========================================================================//
86 //==========================================================================//
87 void BLUTDIRGenericFilter::SetArgsInfo(const args_info_clitkBLUTDIR & a){
89 if (m_ArgsInfo.reference_given) AddInputFilename(m_ArgsInfo.reference_arg);
91 if (m_ArgsInfo.target_given) {
92 AddInputFilename(m_ArgsInfo.target_arg);
95 if (m_ArgsInfo.output_given) SetOutputFilename(m_ArgsInfo.output_arg);
98 //=========================================================================//
99 //===========================================================================//
100 template<unsigned int Dim>
101 void BLUTDIRGenericFilter::InitializeImageType()
103 ADD_DEFAULT_IMAGE_TYPES(3);
105 //--------------------------------------------------------------------
107 //==============================================================================
108 //Creating an observer class that allows us to change parameters at subsequent levels
109 //==============================================================================
110 template <typename TRegistration,class args_info_clitkBLUTDIR>
111 class RegistrationInterfaceCommand : public itk::Command
114 typedef RegistrationInterfaceCommand Self;
115 typedef itk::Command Superclass;
116 typedef itk::SmartPointer<Self> Pointer;
119 RegistrationInterfaceCommand() { };
123 typedef TRegistration RegistrationType;
124 typedef RegistrationType * RegistrationPointer;
127 typedef typename RegistrationType::FixedImageType FixedImageType;
128 typedef typename FixedImageType::RegionType RegionType;
129 itkStaticConstMacro(ImageDimension, unsigned int,FixedImageType::ImageDimension);
130 typedef clitk::BSplineDeformableTransform<double, ImageDimension, ImageDimension> TransformType;
131 typedef clitk::BSplineDeformableTransformInitializer<TransformType, FixedImageType> InitializerType;
132 typedef typename InitializerType::CoefficientImageType CoefficientImageType;
133 typedef itk::CastImageFilter<CoefficientImageType, CoefficientImageType> CastImageFilterType;
134 typedef typename TransformType::ParametersType ParametersType;
135 typedef typename InitializerType::Pointer InitializerPointer;
136 typedef CommandIterationUpdate::Pointer CommandIterationUpdatePointer;
139 typedef clitk::GenericOptimizer<args_info_clitkBLUTDIR> GenericOptimizerType;
140 typedef typename GenericOptimizerType::Pointer GenericOptimizerPointer;
143 typedef typename RegistrationType::FixedImageType InternalImageType;
144 typedef clitk::GenericMetric<args_info_clitkBLUTDIR, InternalImageType, InternalImageType> GenericMetricType;
145 typedef typename GenericMetricType::Pointer GenericMetricPointer;
147 // Two arguments are passed to the Execute() method: the first
148 // is the pointer to the object which invoked the event and the
149 // second is the event that was invoked.
150 void Execute(itk::Object * object, const itk::EventObject & event)
152 if( !(itk::IterationEvent().CheckEvent( &event )) )
158 RegistrationPointer registration = dynamic_cast<RegistrationPointer>( object );
159 unsigned int numberOfLevels=registration->GetNumberOfLevels();
160 unsigned int currentLevel=registration->GetCurrentLevel()+1;
163 std::cout<<std::endl;
164 std::cout<<"========================================"<<std::endl;
165 std::cout<<"Starting resolution level "<<currentLevel<<" of "<<numberOfLevels<<"..."<<std::endl;
166 std::cout<<"========================================"<<std::endl;
167 std::cout<<std::endl;
172 // fixed image region pyramid
173 typedef clitk::MultiResolutionPyramidRegionFilter<InternalImageType> FixedImageRegionPyramidType;
174 typename FixedImageRegionPyramidType::Pointer fixedImageRegionPyramid=FixedImageRegionPyramidType::New();
175 fixedImageRegionPyramid->SetRegion(m_MetricRegion);
176 fixedImageRegionPyramid->SetSchedule(registration->GetFixedImagePyramid()->GetSchedule());
178 // Reinitialize the metric (!= number of samples)
179 m_GenericMetric= GenericMetricType::New();
180 m_GenericMetric->SetArgsInfo(m_ArgsInfo);
181 m_GenericMetric->SetFixedImage(registration->GetFixedImagePyramid()->GetOutput(registration->GetCurrentLevel()));
182 if (m_ArgsInfo.referenceMask_given) m_GenericMetric->SetFixedImageMask(registration->GetMetric()->GetFixedImageMask());
183 m_GenericMetric->SetFixedImageRegion(fixedImageRegionPyramid->GetOutput(registration->GetCurrentLevel()));
184 typedef itk::ImageToImageMetric< InternalImageType, InternalImageType > MetricType;
185 typename MetricType::Pointer metric=m_GenericMetric->GetMetricPointer();
186 registration->SetMetric(metric);
188 // Get the current coefficient image and make a COPY
189 typename itk::ImageDuplicator<CoefficientImageType>::Pointer caster=itk::ImageDuplicator<CoefficientImageType>::New();
190 caster->SetInputImage(m_Initializer->GetTransform()->GetCoefficientImage());
192 typename CoefficientImageType::Pointer currentCoefficientImage=caster->GetOutput();
194 // Write the intermediate result?
195 if (m_ArgsInfo.intermediate_given>=numberOfLevels)
196 writeImage<CoefficientImageType>(currentCoefficientImage, m_ArgsInfo.intermediate_arg[currentLevel-2], m_ArgsInfo.verbose_flag);
198 // Set the new transform properties
199 m_Initializer->SetImage(registration->GetFixedImagePyramid()->GetOutput(currentLevel-1));
200 if( m_Initializer->m_ControlPointSpacingIsGiven)
201 m_Initializer->SetControlPointSpacing(m_Initializer->m_ControlPointSpacingArray[registration->GetCurrentLevel()]);
202 if( m_Initializer->m_NumberOfControlPointsIsGiven)
203 m_Initializer->SetNumberOfControlPointsInsideTheImage(m_Initializer->m_NumberOfControlPointsInsideTheImageArray[registration->GetCurrentLevel()]);
205 // Reinitialize the transform
206 if (m_ArgsInfo.verbose_flag) std::cout<<"Initializing transform for level "<<currentLevel<<" of "<<numberOfLevels<<"..."<<std::endl;
207 m_Initializer->InitializeTransform();
208 ParametersType* newParameters= new typename TransformType::ParametersType(m_Initializer->GetTransform()->GetNumberOfParameters());
210 // DS : if we want to skip the last pyramid level, force to only 1 iteration
211 DD(m_ArgsInfo.skipLastPyramidLevel_flag);
212 if ((currentLevel == numberOfLevels) && (m_ArgsInfo.skipLastPyramidLevel_flag)) {
213 DD(m_ArgsInfo.maxIt_arg);
214 std::cout << "I skip the last pyramid level : set max iteration to 0" << std::endl;
215 m_ArgsInfo.maxIt_arg = 0;
216 DD(m_ArgsInfo.maxIt_arg);
219 // Reinitialize an Optimizer (!= number of parameters)
220 m_GenericOptimizer = GenericOptimizerType::New();
221 m_GenericOptimizer->SetArgsInfo(m_ArgsInfo);
222 m_GenericOptimizer->SetMaximize(m_Maximize);
223 m_GenericOptimizer->SetNumberOfParameters(m_Initializer->GetTransform()->GetNumberOfParameters());
226 typedef itk::SingleValuedNonLinearOptimizer OptimizerType;
227 OptimizerType::Pointer optimizer = m_GenericOptimizer->GetOptimizerPointer();
228 optimizer->AddObserver( itk::IterationEvent(), m_CommandIterationUpdate);
229 registration->SetOptimizer(optimizer);
230 m_CommandIterationUpdate->SetOptimizer(m_GenericOptimizer);
232 // Set the previous transform parameters to the registration
233 // if(m_Initializer->m_Parameters!=NULL )delete m_Initializer->m_Parameters;
234 m_Initializer->SetInitialParameters(currentCoefficientImage,*newParameters);
235 registration->SetInitialTransformParametersOfNextLevel(*newParameters);
239 void Execute(const itk::Object * , const itk::EventObject & )
244 void SetInitializer(InitializerPointer i){m_Initializer=i;}
245 InitializerPointer m_Initializer;
247 void SetArgsInfo(args_info_clitkBLUTDIR a){m_ArgsInfo=a;}
248 args_info_clitkBLUTDIR m_ArgsInfo;
250 void SetCommandIterationUpdate(CommandIterationUpdatePointer c){m_CommandIterationUpdate=c;};
251 CommandIterationUpdatePointer m_CommandIterationUpdate;
253 GenericOptimizerPointer m_GenericOptimizer;
254 void SetMaximize(bool b){m_Maximize=b;}
257 GenericMetricPointer m_GenericMetric;
258 void SetMetricRegion(RegionType i){m_MetricRegion=i;}
259 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::LabelGeometryImageFilter<ImageMaskType> GeometryImageFilterType;
348 typename GeometryImageFilterType::Pointer geometryImageFilter=GeometryImageFilterType::New();
349 geometryImageFilter->SetInput(maskReader->GetOutput());
350 geometryImageFilter->Update();
351 typename GeometryImageFilterType::BoundingBoxType boundingBox = geometryImageFilter->GetBoundingBox(1);
353 // Limit the transform region to the mask
354 for (unsigned int i=0; i<InputImageType::ImageDimension; i++)
356 transformRegionIndex[i]=boundingBox[2*i];
357 transformRegionSize[i]=boundingBox[2*i+1]-boundingBox[2*i]+1;
359 transformRegion.SetSize(transformRegionSize);
360 transformRegion.SetIndex(transformRegionIndex);
361 fixedImage->TransformIndexToPhysicalPoint(transformRegion.GetIndex(), transformRegionOrigin);
363 // Crop the fixedImage to the bounding box to facilitate multi-resolution
364 typedef itk::ExtractImageFilter<FixedImageType,FixedImageType> ExtractImageFilterType;
365 typename ExtractImageFilterType::Pointer extractImageFilter=ExtractImageFilterType::New();
366 extractImageFilter->SetInput(fixedImage);
367 extractImageFilter->SetExtractionRegion(transformRegion);
368 extractImageFilter->Update();
369 croppedFixedImage=extractImageFilter->GetOutput();
371 // Update the metric region
372 metricRegion = croppedFixedImage->GetLargestPossibleRegion();
373 metricRegionIndex=metricRegion.GetIndex();
374 croppedFixedImage->TransformIndexToPhysicalPoint(metricRegionIndex, metricRegionOrigin);
376 // Set start index to zero (with respect to croppedFixedImage/transform region)
377 metricRegionIndex.Fill(0);
378 metricRegion.SetIndex(metricRegionIndex);
379 croppedFixedImage->SetRegions(metricRegion);
380 croppedFixedImage->SetOrigin(metricRegionOrigin);
383 typedef itk::ImageMaskSpatialObject< InputImageType::ImageDimension > MaskType;
384 typename MaskType::Pointer movingMask=NULL;
385 if (m_ArgsInfo.targetMask_given)
387 movingMask= MaskType::New();
388 typedef itk::Image< unsigned char, InputImageType::ImageDimension > ImageMaskType;
389 typedef itk::ImageFileReader< ImageMaskType > MaskReaderType;
390 typename MaskReaderType::Pointer maskReader = MaskReaderType::New();
391 maskReader->SetFileName(m_ArgsInfo.targetMask_arg);
394 maskReader->Update();
396 catch( itk::ExceptionObject & err )
398 std::cerr << "ExceptionObject caught !" << std::endl;
399 std::cerr << err << std::endl;
401 if (m_Verbose)std::cout <<"Target image mask was read..." <<std::endl;
403 movingMask->SetImage( maskReader->GetOutput() );
407 //=======================================================
409 //=======================================================
413 // Fixed image region
414 std::cout<<"The fixed image has its origin at "<<fixedImage->GetOrigin()<<std::endl
415 <<"The fixed image region starts at index "<<fixedImageRegion.GetIndex()<<std::endl
416 <<"The fixed image region has size "<< fixedImageRegion.GetSize()<<std::endl;
419 std::cout<<"The transform has its origin at "<<transformRegionOrigin<<std::endl
420 <<"The transform region will start at index "<<transformRegion.GetIndex()<<std::endl
421 <<"The transform region has size "<< transformRegion.GetSize()<<std::endl;
424 std::cout<<"The metric region has its origin at "<<metricRegionOrigin<<std::endl
425 <<"The metric region will start at index "<<metricRegion.GetIndex()<<std::endl
426 <<"The metric region has size "<< metricRegion.GetSize()<<std::endl;
431 //=======================================================
432 // Pyramids (update them for transform initializer)
433 //=======================================================
434 typedef itk::RecursiveMultiResolutionPyramidImageFilter< FixedImageType, FixedImageType> FixedImagePyramidType;
435 typedef itk::RecursiveMultiResolutionPyramidImageFilter< MovingImageType, MovingImageType> MovingImagePyramidType;
436 typename FixedImagePyramidType::Pointer fixedImagePyramid = FixedImagePyramidType::New();
437 typename MovingImagePyramidType::Pointer movingImagePyramid = MovingImagePyramidType::New();
438 fixedImagePyramid->SetUseShrinkImageFilter(false);
439 fixedImagePyramid->SetInput(croppedFixedImage);
440 fixedImagePyramid->SetNumberOfLevels(m_ArgsInfo.levels_arg);
441 movingImagePyramid->SetUseShrinkImageFilter(false);
442 movingImagePyramid->SetInput(movingImage);
443 movingImagePyramid->SetNumberOfLevels(m_ArgsInfo.levels_arg);
444 if (m_Verbose) std::cout<<"Creating the image pyramid..."<<std::endl;
445 fixedImagePyramid->Update();
446 movingImagePyramid->Update();
447 typedef clitk::MultiResolutionPyramidRegionFilter<FixedImageType> FixedImageRegionPyramidType;
448 typename FixedImageRegionPyramidType::Pointer fixedImageRegionPyramid=FixedImageRegionPyramidType::New();
449 fixedImageRegionPyramid->SetRegion(metricRegion);
450 fixedImageRegionPyramid->SetSchedule(fixedImagePyramid->GetSchedule());
453 //=======================================================
454 // Rigid or Affine Transform
455 //=======================================================
456 typedef itk::AffineTransform <double,3> RigidTransformType;
457 RigidTransformType::Pointer rigidTransform=NULL;
458 if (m_ArgsInfo.initMatrix_given)
460 if(m_Verbose) std::cout<<"Reading the prior transform matrix "<< m_ArgsInfo.initMatrix_arg<<"..."<<std::endl;
461 rigidTransform=RigidTransformType::New();
462 itk::Matrix<double,4,4> rigidTransformMatrix=clitk::ReadMatrix3D(m_ArgsInfo.initMatrix_arg);
465 itk::Matrix<double,3,3> finalRotation = clitk::GetRotationalPartMatrix3D(rigidTransformMatrix);
466 rigidTransform->SetMatrix(finalRotation);
468 //Set the translation
469 itk::Vector<double,3> finalTranslation = clitk::GetTranslationPartMatrix3D(rigidTransformMatrix);
470 rigidTransform->SetTranslation(finalTranslation);
474 //=======================================================
475 // B-LUT FFD Transform
476 //=======================================================
477 typedef clitk::BSplineDeformableTransform<TCoordRep,InputImageType::ImageDimension, SpaceDimension > TransformType;
478 typename TransformType::Pointer transform= TransformType::New();
479 if (fixedMask) transform->SetMask( fixedMask );
480 if (rigidTransform) transform->SetBulkTransform( rigidTransform );
482 //-------------------------------------------------------------------------
483 // The transform initializer
484 //-------------------------------------------------------------------------
485 typedef clitk::BSplineDeformableTransformInitializer< TransformType,FixedImageType> InitializerType;
486 typename InitializerType::Pointer initializer = InitializerType::New();
487 initializer->SetVerbose(m_Verbose);
488 initializer->SetImage(fixedImagePyramid->GetOutput(0));
489 initializer->SetTransform(transform);
491 //-------------------------------------------------------------------------
493 //-------------------------------------------------------------------------
494 typename FixedImageType::RegionType::SizeType splineOrders ;
495 splineOrders.Fill(3);
496 if (m_ArgsInfo.order_given)
497 for(unsigned int i=0; i<InputImageType::ImageDimension;i++)
498 splineOrders[i]=m_ArgsInfo.order_arg[i];
499 if (m_Verbose) std::cout<<"Setting the spline orders to "<<splineOrders<<"..."<<std::endl;
500 initializer->SetSplineOrders(splineOrders);
502 //-------------------------------------------------------------------------
504 //-------------------------------------------------------------------------
507 if (m_ArgsInfo.spacing_given)
509 initializer->m_ControlPointSpacingArray.resize(m_ArgsInfo.levels_arg);
510 initializer->SetControlPointSpacing(m_ArgsInfo.spacing_arg);
511 initializer->m_ControlPointSpacingArray[m_ArgsInfo.levels_arg-1]=initializer->m_ControlPointSpacing;
512 if (m_Verbose) std::cout<<"Using a control point spacing of "<<initializer->m_ControlPointSpacingArray[m_ArgsInfo.levels_arg-1]
513 <<" at level "<<m_ArgsInfo.levels_arg<<" of "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;
515 for (int i=1; i<m_ArgsInfo.levels_arg; i++ )
517 initializer->m_ControlPointSpacingArray[m_ArgsInfo.levels_arg-1-i]=initializer->m_ControlPointSpacingArray[m_ArgsInfo.levels_arg-i]*2;
518 if (m_Verbose) std::cout<<"Using a control point spacing of "<<initializer->m_ControlPointSpacingArray[m_ArgsInfo.levels_arg-1-i]
519 <<" at level "<<m_ArgsInfo.levels_arg-i<<" of "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;
525 if (m_ArgsInfo.control_given)
527 initializer->m_NumberOfControlPointsInsideTheImageArray.resize(m_ArgsInfo.levels_arg);
528 initializer->SetNumberOfControlPointsInsideTheImage(m_ArgsInfo.control_arg);
529 initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-1]=initializer->m_NumberOfControlPointsInsideTheImage;
530 if (m_Verbose) std::cout<<"Using "<< initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-1]<<"control points inside the image"
531 <<" at level "<<m_ArgsInfo.levels_arg<<" of "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;
533 for (int i=1; i<m_ArgsInfo.levels_arg; i++ )
535 for(unsigned int j=0;j<InputImageType::ImageDimension;j++)
536 initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-1-i][j]=ceil ((double)initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-i][j]/2.);
537 // initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-1-i]=ceil ((double)initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-i]/2.);
538 if (m_Verbose) std::cout<<"Using "<< initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-1-i]<<"control points inside the image"
539 <<" at level "<<m_ArgsInfo.levels_arg<<" of "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;
544 // Inialize on the first level
545 if (m_ArgsInfo.verbose_flag) std::cout<<"Initializing transform for level 1 of "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;
546 if (m_ArgsInfo.spacing_given) initializer->SetControlPointSpacing( initializer->m_ControlPointSpacingArray[0]);
547 if (m_ArgsInfo.control_given) initializer->SetNumberOfControlPointsInsideTheImage(initializer->m_NumberOfControlPointsInsideTheImageArray[0]);
548 if (m_ArgsInfo.samplingFactor_given) initializer->SetSamplingFactors(m_ArgsInfo.samplingFactor_arg);
551 initializer->InitializeTransform();
553 //-------------------------------------------------------------------------
554 // Initial parameters (passed by reference)
555 //-------------------------------------------------------------------------
556 typedef typename TransformType::ParametersType ParametersType;
557 const unsigned int numberOfParameters = transform->GetNumberOfParameters();
558 ParametersType parameters(numberOfParameters);
559 parameters.Fill( 0.0 );
560 transform->SetParameters( parameters );
561 if (m_ArgsInfo.initCoeff_given) initializer->SetInitialParameters(m_ArgsInfo.initCoeff_arg, parameters);
564 //=======================================================
566 //=======================================================
567 typedef clitk::GenericInterpolator<args_info_clitkBLUTDIR, FixedImageType, TCoordRep > GenericInterpolatorType;
568 typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
569 genericInterpolator->SetArgsInfo(m_ArgsInfo);
570 typedef itk::InterpolateImageFunction< FixedImageType, TCoordRep > InterpolatorType;
571 typename InterpolatorType::Pointer interpolator=genericInterpolator->GetInterpolatorPointer();
574 //=======================================================
576 //=======================================================
577 typedef clitk::GenericMetric<args_info_clitkBLUTDIR, FixedImageType,MovingImageType > GenericMetricType;
578 typename GenericMetricType::Pointer genericMetric=GenericMetricType::New();
579 genericMetric->SetArgsInfo(m_ArgsInfo);
580 genericMetric->SetFixedImage(fixedImagePyramid->GetOutput(0));
581 if (fixedMask) genericMetric->SetFixedImageMask(fixedMask);
582 genericMetric->SetFixedImageRegion(fixedImageRegionPyramid->GetOutput(0));
583 typedef itk::ImageToImageMetric< FixedImageType, MovingImageType > MetricType;
584 typename MetricType::Pointer metric=genericMetric->GetMetricPointer();
585 if (movingMask) metric->SetMovingImageMask(movingMask);
587 #ifdef ITK_USE_OPTIMIZED_REGISTRATION_METHODS
589 metric->SetNumberOfThreads( threads );
590 if (m_Verbose) std::cout<< "Using " << threads << " threads." << std::endl;
593 if (m_Verbose) std::cout<<"Not setting the number of threads (not compiled with USE_OPTIMIZED_REGISTRATION_METHODS)..."<<std::endl;
597 //=======================================================
599 //=======================================================
600 typedef clitk::GenericOptimizer<args_info_clitkBLUTDIR> GenericOptimizerType;
601 GenericOptimizerType::Pointer genericOptimizer = GenericOptimizerType::New();
602 genericOptimizer->SetArgsInfo(m_ArgsInfo);
603 genericOptimizer->SetMaximize(genericMetric->GetMaximize());
604 genericOptimizer->SetNumberOfParameters(transform->GetNumberOfParameters());
605 typedef itk::SingleValuedNonLinearOptimizer OptimizerType;
606 OptimizerType::Pointer optimizer = genericOptimizer->GetOptimizerPointer();
609 //=======================================================
611 //=======================================================
612 typedef itk::MultiResolutionImageRegistrationMethod< FixedImageType, MovingImageType > RegistrationType;
613 typename RegistrationType::Pointer registration = RegistrationType::New();
614 registration->SetMetric( metric );
615 registration->SetOptimizer( optimizer );
616 registration->SetInterpolator( interpolator );
617 registration->SetTransform (transform);
619 registration->SetNumberOfThreads(threads);
620 if (m_Verbose) std::cout<< "Using " << threads << " threads." << std::endl;
622 registration->SetFixedImage( croppedFixedImage );
623 registration->SetMovingImage( movingImage );
624 registration->SetFixedImageRegion( metricRegion );
625 registration->SetFixedImagePyramid( fixedImagePyramid );
626 registration->SetMovingImagePyramid( movingImagePyramid );
627 registration->SetInitialTransformParameters( transform->GetParameters() );
628 registration->SetNumberOfLevels( m_ArgsInfo.levels_arg );
629 if (m_Verbose) std::cout<<"Setting the number of resolution levels to "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;
632 //================================================================================================
634 //================================================================================================
637 // Output iteration info
638 CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New();
639 observer->SetOptimizer(genericOptimizer);
640 optimizer->AddObserver( itk::IterationEvent(), observer );
643 typedef RegistrationInterfaceCommand<RegistrationType,args_info_clitkBLUTDIR> CommandType;
644 typename CommandType::Pointer command = CommandType::New();
645 command->SetInitializer(initializer);
646 command->SetArgsInfo(m_ArgsInfo);
647 command->SetCommandIterationUpdate(observer);
648 command->SetMaximize(genericMetric->GetMaximize());
649 command->SetMetricRegion(metricRegion);
650 registration->AddObserver( itk::IterationEvent(), command );
654 //=======================================================
656 //=======================================================
657 if (m_Verbose) std::cout << std::endl << "Starting Registration" << std::endl;
661 registration->StartRegistration();
663 catch( itk::ExceptionObject & err )
665 std::cerr << "ExceptionObject caught while registering!" << std::endl;
666 std::cerr << err << std::endl;
671 //=======================================================
673 //=======================================================
674 OptimizerType::ParametersType finalParameters = registration->GetLastTransformParameters();
675 transform->SetParameters( finalParameters );
678 std::cout<<"Stop condition description: "
679 <<registration->GetOptimizer()->GetStopConditionDescription()<<std::endl;
683 //=======================================================
684 // Get the BSpline coefficient images and write them
685 //=======================================================
686 if (m_ArgsInfo.coeff_given)
688 typedef typename TransformType::CoefficientImageType CoefficientImageType;
689 typename CoefficientImageType::Pointer coefficientImage =transform->GetCoefficientImage();
690 typedef itk::ImageFileWriter<CoefficientImageType> CoeffWriterType;
691 typename CoeffWriterType::Pointer coeffWriter=CoeffWriterType::New();
692 coeffWriter->SetInput(coefficientImage);
693 coeffWriter->SetFileName(m_ArgsInfo.coeff_arg);
694 coeffWriter->Update();
699 //=======================================================
700 // Compute the DVF (only deformable transform)
701 //=======================================================
702 typedef itk::Vector< float, SpaceDimension > DisplacementType;
703 typedef itk::Image< DisplacementType, InputImageType::ImageDimension > DeformationFieldType;
704 typedef itk::TransformToDeformationFieldSource<DeformationFieldType, double> ConvertorType;
705 typename ConvertorType::Pointer filter= ConvertorType::New();
706 filter->SetNumberOfThreads(1);
707 transform->SetBulkTransform(NULL);
708 filter->SetTransform(transform);
709 filter->SetOutputParametersFromImage(fixedImage);
711 typename DeformationFieldType::Pointer field = filter->GetOutput();
714 //=======================================================
716 //=======================================================
717 typedef itk::ImageFileWriter< DeformationFieldType > FieldWriterType;
718 typename FieldWriterType::Pointer fieldWriter = FieldWriterType::New();
719 fieldWriter->SetFileName( m_ArgsInfo.vf_arg );
720 fieldWriter->SetInput( field );
723 fieldWriter->Update();
725 catch( itk::ExceptionObject & excp )
727 std::cerr << "Exception thrown writing the DVF" << std::endl;
728 std::cerr << excp << std::endl;
733 //=======================================================
734 // Resample the moving image
735 //=======================================================
736 typedef itk::ResampleImageFilter< MovingImageType, FixedImageType > ResampleFilterType;
737 typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
738 if (rigidTransform) transform->SetBulkTransform(rigidTransform);
739 resampler->SetTransform( transform );
740 resampler->SetInput( movingImage);
741 resampler->SetOutputParametersFromImage(fixedImage);
743 typename FixedImageType::Pointer result=resampler->GetOutput();
745 // typedef itk::WarpImageFilter< MovingImageType, FixedImageType, DeformationFieldType > WarpFilterType;
746 // typename WarpFilterType::Pointer warp = WarpFilterType::New();
748 // warp->SetDeformationField( field );
749 // warp->SetInput( movingImageReader->GetOutput() );
750 // warp->SetOutputOrigin( fixedImage->GetOrigin() );
751 // warp->SetOutputSpacing( fixedImage->GetSpacing() );
752 // warp->SetOutputDirection( fixedImage->GetDirection() );
753 // warp->SetEdgePaddingValue( 0.0 );
757 //=======================================================
758 // Write the warped image
759 //=======================================================
760 typedef itk::ImageFileWriter< FixedImageType > WriterType;
761 typename WriterType::Pointer writer = WriterType::New();
762 writer->SetFileName( m_ArgsInfo.output_arg );
763 writer->SetInput( result );
769 catch( itk::ExceptionObject & err )
771 std::cerr << "ExceptionObject caught !" << std::endl;
772 std::cerr << err << std::endl;
777 //=======================================================
778 // Calculate the difference after the deformable transform
779 //=======================================================
780 typedef clitk::DifferenceImageFilter< FixedImageType, FixedImageType> DifferenceFilterType;
781 if (m_ArgsInfo.after_given)
783 typename DifferenceFilterType::Pointer difference = DifferenceFilterType::New();
784 difference->SetValidInput( fixedImage );
785 difference->SetTestInput( result );
789 difference->Update();
791 catch( itk::ExceptionObject & err )
793 std::cerr << "ExceptionObject caught calculating the difference !" << std::endl;
794 std::cerr << err << std::endl;
798 typename WriterType::Pointer differenceWriter=WriterType::New();
799 differenceWriter->SetInput(difference->GetOutput());
800 differenceWriter->SetFileName(m_ArgsInfo.after_arg);
801 differenceWriter->Update();
806 //=======================================================
807 // Calculate the difference before the deformable transform
808 //=======================================================
809 if( m_ArgsInfo.before_given )
812 typename FixedImageType::Pointer moving=FixedImageType::New();
813 if (m_ArgsInfo.initMatrix_given)
815 typedef itk::ResampleImageFilter<MovingImageType, FixedImageType> ResamplerType;
816 typename ResamplerType::Pointer resampler=ResamplerType::New();
817 resampler->SetInput(movingImage);
818 resampler->SetOutputOrigin(fixedImage->GetOrigin());
819 resampler->SetSize(fixedImage->GetLargestPossibleRegion().GetSize());
820 resampler->SetOutputSpacing(fixedImage->GetSpacing());
821 resampler->SetDefaultPixelValue( 0. );
822 if (rigidTransform ) resampler->SetTransform(rigidTransform);
824 moving=resampler->GetOutput();
829 typename DifferenceFilterType::Pointer difference = DifferenceFilterType::New();
830 difference->SetValidInput( fixedImage );
831 difference->SetTestInput( moving );
835 difference->Update();
837 catch( itk::ExceptionObject & err )
839 std::cerr << "ExceptionObject caught calculating the difference !" << std::endl;
840 std::cerr << err << std::endl;
844 typename WriterType::Pointer differenceWriter=WriterType::New();
845 writer->SetFileName( m_ArgsInfo.before_arg );
846 writer->SetInput( difference->GetOutput() );
855 #endif // #define clitkBLUTDIRGenericFilter_txx