X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=registration%2FclitkDemonsDeformableRegistrationGenericFilter.txx;h=d4b0cb238c55665da8b57e9d9cc52f57bd0e1090;hb=d14e4a0c980c241ba87ba8bce7602028be5d0862;hp=887676e3ddb0a874313a9243e69cb3bc5846d987;hpb=413cf925a4e665aacd68d0a3eb9328818ac3abde;p=clitk.git

diff --git a/registration/clitkDemonsDeformableRegistrationGenericFilter.txx b/registration/clitkDemonsDeformableRegistrationGenericFilter.txx
old mode 100755
new mode 100644
index 887676e..d4b0cb2
--- a/registration/clitkDemonsDeformableRegistrationGenericFilter.txx
+++ b/registration/clitkDemonsDeformableRegistrationGenericFilter.txx
@@ -3,7 +3,7 @@
 
   Authors belong to: 
   - University of LYON              http://www.universite-lyon.fr/
-  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
+  - Léon Bérard cancer center       http://www.centreleonberard.fr
   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
 
   This software is distributed WITHOUT ANY WARRANTY; without even
@@ -14,7 +14,7 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-======================================================================-====*/
+===========================================================================**/
 #ifndef __clitkDemonsDeformableRegistrationGenericFilter_txx
 #define __clitkDemonsDeformableRegistrationGenericFilter_txx
 #include "clitkDemonsDeformableRegistrationGenericFilter.h"
@@ -151,8 +151,8 @@ namespace clitk
     //find the multiresolution filter
     //     typedef typename  RegistrationFilterType::FixedImageType InternalImageType;
     //     typedef typename  RegistrationFilterType::MovingImageType MovingImageType;
-    typedef typename  RegistrationFilterType::DeformationFieldType DeformationFieldType;
-    typedef clitk::MultiResolutionPDEDeformableRegistration<FixedImageType, MovingImageType, DeformationFieldType> MultiResolutionRegistrationType; 
+    typedef typename  RegistrationFilterType::DisplacementFieldType DisplacementFieldType;
+    typedef clitk::MultiResolutionPDEDeformableRegistration<FixedImageType, MovingImageType, DisplacementFieldType> MultiResolutionRegistrationType;
     typedef CommandResolutionLevelUpdate<MultiResolutionRegistrationType> LevelObserver;
     
   protected:
@@ -369,7 +369,7 @@ namespace clitk
     //------------------------------------
     //Set the max RMS error for the field update
     //------------------------------------
-    itk::Array<double> maxRMSError(nLevels);
+    std::vector<double> maxRMSError(nLevels);
     for (unsigned int i=0 ; i<nLevels; i++)
       {
 	if (m_ArgsInfo.maxRMSError_given==nLevels)	
@@ -387,7 +387,7 @@ namespace clitk
     //------------------------------------
     //Get the stop criterion
     //------------------------------------
-    itk::Array<int> stop(nLevels);
+    std::vector<int> stop(nLevels);
     for (unsigned int i=0; i<nLevels; i++)
       if (m_ArgsInfo.stop_given==nLevels)
 	stop[i]=m_ArgsInfo.stop_arg[i];
@@ -442,7 +442,7 @@ namespace clitk
     typename CommandResolutionLevelUpdate<MultiResolutionRegistrationFilterType>::Pointer levelObserver = 
       CommandResolutionLevelUpdate<MultiResolutionRegistrationFilterType>::New();
     multiResolutionFilter->AddObserver( itk::IterationEvent(), levelObserver );
-    levelObserver->SetMaxRMSError(maxRMSError);
+    levelObserver->SetMaxRMSError(&(maxRMSError[0]));
     levelObserver->SetMaxStep(m_ArgsInfo.maxStep_arg);
     levelObserver->SetSD(sd);
     levelObserver->SetScaleStep(m_ArgsInfo.scaleStep_flag);
@@ -464,7 +464,7 @@ namespace clitk
 	m->SetIntensityDifferenceThreshold( m_ArgsInfo.intThreshold_arg);
 	m->SetUseMovingImageGradient( m_ArgsInfo.movGrad_flag);
 	typename CommandIterationUpdate<DemonsFilterType, FixedImageType, MovingImageType>::Pointer observer = CommandIterationUpdate<DemonsFilterType, FixedImageType, MovingImageType>::New();
-	observer->SetStop(stop);
+	observer->SetStop(&(stop[0]));
 	observer->SetLevelObserver(levelObserver);
 	m->AddObserver( itk::IterationEvent(), observer );
 	if (m_Verbose)  std::cout<<"Using the demons registration filter..."<<std::endl;
@@ -480,7 +480,7 @@ namespace clitk
 	//Set Parameters for this filter
 	m->SetIntensityDifferenceThreshold( m_ArgsInfo.intThreshold_arg);
 	typename CommandIterationUpdate<DemonsFilterType, FixedImageType, MovingImageType>::Pointer observer = CommandIterationUpdate<DemonsFilterType, FixedImageType, MovingImageType>::New();
-	observer->SetStop(stop);
+	observer->SetStop(&(stop[0]));
 	observer->SetLevelObserver(levelObserver);
 	m->AddObserver( itk::IterationEvent(), observer );
 	if (m_Verbose) std::cout<<"Using the symmetric forces demons registration filter..."<<std::endl;
@@ -498,7 +498,7 @@ namespace clitk
 	m->SetMaximumUpdateStepLength( m_ArgsInfo.maxStep_arg);
 	m->SetUseGradientType(grad);
 	typename CommandIterationUpdate<DemonsFilterType, FixedImageType, MovingImageType>::Pointer observer = CommandIterationUpdate<DemonsFilterType, FixedImageType, MovingImageType>::New();
-	observer->SetStop(stop);
+	observer->SetStop(&(stop[0]));
 	observer->SetLevelObserver(levelObserver);
 	m->AddObserver( itk::IterationEvent(), observer );
   	if (m_Verbose) std::cout<<"Using the fast symmetric forces demons registration filter..."<<std::endl;
@@ -516,7 +516,7 @@ namespace clitk
 	m->SetUseFirstOrderExp(m_ArgsInfo.firstOrder_flag);
 	m->SetUseGradientType(grad);
 	typename CommandIterationUpdate<DemonsFilterType, FixedImageType, MovingImageType>::Pointer observer = CommandIterationUpdate<DemonsFilterType, FixedImageType, MovingImageType>::New();
-	observer->SetStop(stop);
+	observer->SetStop(&(stop[0]));
 	observer->SetLevelObserver(levelObserver);
 	m->AddObserver( itk::IterationEvent(), observer );
 	if (m_Verbose) std::cout<<"Using the diffeomorphic demons registration filter..."<<std::endl;
@@ -533,7 +533,7 @@ namespace clitk
     //JV TODO
     // pdeFilter->SetMaximumError(m_ArgsInfo.maxError_arg);
     // pdeFilter->SetMaximumKernelWidth(m_ArgsInfo.maxError_arg);
-    pdeFilter->SetSmoothDeformationField(!m_ArgsInfo.fluid_flag);
+    pdeFilter->SetSmoothDisplacementField(!m_ArgsInfo.fluid_flag);
     pdeFilter->SetSmoothUpdateField(m_ArgsInfo.fluid_flag);
     pdeFilter->SetUseImageSpacing( m_ArgsInfo.spacing_flag );
 
@@ -599,7 +599,7 @@ namespace clitk
     typedef itk::WarpImageFilter< MovingImageType, FixedImageType, DeformationFieldType >    WarpFilterType;
     typename WarpFilterType::Pointer warp = WarpFilterType::New();
 
-    warp->SetDeformationField( deformationField );
+    warp->SetDisplacementField( deformationField );
     warp->SetInput( movingImageReader->GetOutput() );
     warp->SetOutputOrigin(  fixedImage->GetOrigin() );
     warp->SetOutputSpacing( fixedImage->GetSpacing() );