Merge pull request #590 from ANTsX/alloc_init

ENH: Bump ITK and ANTs, initialize all memory allocated for images
ANTsX · Mar 22, 2024 · cb70f4a · cb70f4a
2 parents cd1e956 + de4b63b
commit cb70f4a
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Showing 19 changed files with 39 additions and 44 deletions.
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -330,7 +330,7 @@ py::capsule antsImageClone( py::capsule antsImage )
   out_image->SetOrigin( in_image->GetOrigin() ) ;
   out_image->SetDirection( in_image->GetDirection() );
   //out_image->CopyInformation( in_image );
-  out_image->Allocate() ;
+  out_image->AllocateInitialized() ;
 
   itk::ImageRegionConstIterator< InImageType > in_iterator( in_image , in_image->GetLargestPossibleRegion() ) ;
   itk::ImageRegionIterator< OutImageType > out_iterator( out_image , out_image->GetLargestPossibleRegion() ) ;

diff --git a/ants/lib/ANTsVersionConfig.h b/ants/lib/ANTsVersionConfig.h
@@ -17,7 +17,7 @@
 *=========================================================================*/
 
 #define ANTS_VERSION_MAJOR 2
-#define ANTS_VERSION_MINOR 3
-#define ANTS_VERSION_PATCH 5
+#define ANTS_VERSION_MINOR 5
+#define ANTS_VERSION_PATCH 1
 #define ANTS_VERSION_TWEAK 
-#define ANTS_VERSION "v2.3.5.post95-g6f07ac5"
+#define ANTS_VERSION "v2.5.1.post95-g2236a75"
diff --git a/ants/lib/LOCAL_antsImageClone.cxx b/ants/lib/LOCAL_antsImageClone.cxx
@@ -25,7 +25,7 @@ py::capsule antsImageClone( py::capsule antsImage )
   out_image->SetOrigin( in_image->GetOrigin() ) ;
   out_image->SetDirection( in_image->GetDirection() );
   //out_image->CopyInformation( in_image );
-  out_image->Allocate() ;
+  out_image->AllocateInitialized();
 
   itk::ImageRegionConstIterator< InImageType > in_iterator( in_image , in_image->GetLargestPossibleRegion() ) ;
   itk::ImageRegionIterator< OutImageType > out_iterator( out_image , out_image->GetLargestPossibleRegion() ) ;

diff --git a/ants/lib/LOCAL_antsImageToImageMetric.h b/ants/lib/LOCAL_antsImageToImageMetric.h
@@ -359,8 +359,7 @@ ANTsImageToImageMetric< MetricBaseType > create_ants_metric(std::string pixeltyp
     itkField->SetSpacing( moving->GetSpacing() );
     itkField->SetOrigin( moving->GetOrigin() );
     itkField->SetDirection( moving->GetDirection() );
-    itkField->Allocate();
-    //itkField->FillBuffer(0);
+    itkField->AllocateInitialized();
 
     typename TransformType::Pointer idTransform = TransformType::New();
     idTransform->SetDisplacementField( itkField );

diff --git a/ants/lib/LOCAL_antsTransform.cxx b/ants/lib/LOCAL_antsTransform.cxx
@@ -84,7 +84,7 @@ py::capsule antsTransformFromDisplacementField( py::capsule field )
   itkField->SetSpacing( antsrField->GetSpacing() );
   itkField->SetOrigin( antsrField->GetOrigin() );
   itkField->SetDirection( antsrField->GetDirection() );
-  itkField->Allocate();
+  itkField->AllocateInitialized();
 
   typedef itk::ImageRegionIteratorWithIndex<DisplacementFieldType> IteratorType;
   IteratorType it( itkField, itkField->GetLargestPossibleRegion() );
@@ -143,7 +143,7 @@ py::capsule antsTransformToDisplacementField( py::capsule xfrm, py::capsule ref
   antsrField->CopyInformation( domainImage );
   antsrField->SetRegions( domainImage->GetLargestPossibleRegion() );
   antsrField->SetNumberOfComponentsPerPixel( Dimension );
-  antsrField->Allocate();
+  antsrField->AllocateInitialized();
 
   typedef itk::ImageRegionIteratorWithIndex<ImageType> IteratorType;
   IteratorType it( domainImage, domainImage->GetLargestPossibleRegion() );
@@ -213,7 +213,7 @@ PYBIND11_MODULE(antsTransform, m) {
     m.def("transformImageD2UC4", &transformImage<itk::Transform<double,2, 2>, itk::Image<unsigned char, 2>>);
     m.def("transformImageD3UC4", &transformImage<itk::Transform<double,3, 3>, itk::Image<unsigned char, 3>>);
     m.def("transformImageD4UC4", &transformImage<itk::Transform<double,4, 4>, itk::Image<unsigned char, 4>>);
-    
+
     m.def("transformImageF2UI2", &transformImage<itk::Transform<float, 2, 2>, itk::Image<unsigned int, 2>>);
     m.def("transformImageF3UI3", &transformImage<itk::Transform<float, 3, 3>, itk::Image<unsigned int, 3>>);
     m.def("transformImageF4UI4", &transformImage<itk::Transform<float, 4, 4>, itk::Image<unsigned int, 4>>);

diff --git a/ants/lib/LOCAL_composeDisplacementFields.cxx b/ants/lib/LOCAL_composeDisplacementFields.cxx
@@ -57,14 +57,14 @@ py::capsule composeDisplacementFields( py::capsule & antsDisplacementField,
   inputITKDisplacementField->SetRegions( fieldSize );
   inputITKDisplacementField->SetSpacing( fieldSpacing );
   inputITKDisplacementField->SetDirection( fieldDirection );
-  inputITKDisplacementField->Allocate();
+  inputITKDisplacementField->AllocateInitialized();
 
   ITKFieldPointerType inputITKWarpingField = ITKFieldType::New();
   inputITKWarpingField->SetOrigin( fieldOrigin );
   inputITKWarpingField->SetRegions( fieldSize );
   inputITKWarpingField->SetSpacing( fieldSpacing );
   inputITKWarpingField->SetDirection( fieldDirection );
-  inputITKWarpingField->Allocate();
+  inputITKWarpingField->AllocateInitialized();
 
   IteratorType ItF( inputITKDisplacementField, inputITKDisplacementField->GetRequestedRegion() );
   IteratorType ItE( inputITKWarpingField, inputITKWarpingField->GetRequestedRegion() );
@@ -100,7 +100,7 @@ py::capsule composeDisplacementFields( py::capsule & antsDisplacementField,
   antsField->CopyInformation( composer->GetOutput() );
   antsField->SetRegions( composer->GetOutput()->GetRequestedRegion() );
   antsField->SetVectorLength( Dimension );
-  antsField->Allocate();
+  antsField->AllocateInitialized();
 
   ConstIteratorType ItI( composer->GetOutput(),
     composer->GetOutput()->GetRequestedRegion() );

diff --git a/ants/lib/LOCAL_fitBsplineDisplacementField.cxx b/ants/lib/LOCAL_fitBsplineDisplacementField.cxx
@@ -77,7 +77,7 @@ py::capsule fitBsplineVectorImageHelper(
   inputITKField->SetRegions( fieldSize );
   inputITKField->SetSpacing( fieldSpacing );
   inputITKField->SetDirection( fieldDirection );
-  inputITKField->Allocate();
+  inputITKField->AllocateInitialized();
 
   IteratorType It( inputITKField, inputITKField->GetRequestedRegion() );
   for( It.GoToBegin(); !It.IsAtEnd(); ++It )
@@ -190,7 +190,7 @@ py::capsule fitBsplineVectorImageHelper(
   antsField->CopyInformation( bsplineFilter->GetOutput() );
   antsField->SetRegions( bsplineFilter->GetOutput()->GetRequestedRegion() );
   antsField->SetVectorLength( Dimension );
-  antsField->Allocate();
+  antsField->AllocateInitialized();
 
   IteratorType ItB( bsplineFilter->GetOutput(),
     bsplineFilter->GetOutput()->GetRequestedRegion() );

diff --git a/ants/lib/LOCAL_fitBsplineDisplacementFieldToScatteredData.cxx b/ants/lib/LOCAL_fitBsplineDisplacementFieldToScatteredData.cxx
@@ -107,25 +107,21 @@ py::capsule fitBsplineVectorImageToScatteredDataHelper(
     weightImage->SetSpacing( bsplineFilter->GetBSplineDomainSpacing() );
     weightImage->SetDirection( bsplineFilter->GetBSplineDomainDirection() );
     weightImage->SetRegions( bsplineFilter->GetBSplineDomainSize() );
-    weightImage->Allocate();
-    weightImage->FillBuffer( 0.0 );
+    weightImage->AllocateInitialized();
 
     WeightImagePointerType countImage = WeightImageType::New();
     countImage->SetOrigin( bsplineFilter->GetBSplineDomainOrigin() );
     countImage->SetSpacing( bsplineFilter->GetBSplineDomainSpacing() );
     countImage->SetDirection( bsplineFilter->GetBSplineDomainDirection() );
     countImage->SetRegions( bsplineFilter->GetBSplineDomainSize() );
-    countImage->Allocate();
-    countImage->FillBuffer( 0.0 );
+    countImage->AllocateInitialized();
 
-    VectorType zeroVector( 0.0 );
     ITKFieldPointerType rasterizedField = ITKFieldType::New();
     rasterizedField->SetOrigin( bsplineFilter->GetBSplineDomainOrigin() );
     rasterizedField->SetSpacing( bsplineFilter->GetBSplineDomainSpacing() );
     rasterizedField->SetDirection( bsplineFilter->GetBSplineDomainDirection() );
     rasterizedField->SetRegions( bsplineFilter->GetBSplineDomainSize() );
-    rasterizedField->Allocate();
-    rasterizedField->FillBuffer( zeroVector );
+    rasterizedField->AllocateInitialized();
 
     for( unsigned int n = 0; n < numberOfPoints; n++ )
       {
@@ -214,7 +210,7 @@ py::capsule fitBsplineVectorImageToScatteredDataHelper(
   antsField->CopyInformation( bsplineFilter->GetOutput() );
   antsField->SetRegions( bsplineFilter->GetOutput()->GetRequestedRegion() );
   antsField->SetVectorLength( Dimension );
-  antsField->Allocate();
+  antsField->AllocateInitialized();
 
   IteratorType It( bsplineFilter->GetOutput(),
     bsplineFilter->GetOutput()->GetRequestedRegion() );

diff --git a/ants/lib/LOCAL_fitBsplineObjectToScatteredData.cxx b/ants/lib/LOCAL_fitBsplineObjectToScatteredData.cxx
@@ -313,7 +313,7 @@ py::capsule fitBsplineVectorImageHelper(
   antsField->SetSpacing( spacing );
   antsField->SetVectorLength( DataDimension );
   antsField->SetDirection( direction );
-  antsField->Allocate();
+  antsField->AllocateInitialized();
 
   IteratorType It( bsplineFilter->GetOutput(),
     bsplineFilter->GetOutput()->GetRequestedRegion() );

diff --git a/ants/lib/LOCAL_fitThinPlateSplineDisplacementFieldToScatteredData.cxx b/ants/lib/LOCAL_fitThinPlateSplineDisplacementFieldToScatteredData.cxx
@@ -80,7 +80,7 @@ py::capsule fitThinPlateSplineVectorImageToScatteredDataHelper(
     field->SetOrigin( fieldOrigin );
     field->SetSpacing( fieldSpacing );
     field->SetDirection( fieldDirection );
-    field->Allocate();
+    field->AllocateInitialized();
     }
 
   auto sourceLandmarks = PointSetType::New();
@@ -119,7 +119,7 @@ py::capsule fitThinPlateSplineVectorImageToScatteredDataHelper(
   antsField->CopyInformation( field );
   antsField->SetRegions( field->GetRequestedRegion() );
   antsField->SetVectorLength( Dimension );
-  antsField->Allocate();
+  antsField->AllocateInitialized();
 
   typename TransformType::InputPointType  source;
   typename TransformType::OutputPointType target;

diff --git a/ants/lib/LOCAL_integrateVelocityField.cxx b/ants/lib/LOCAL_integrateVelocityField.cxx
@@ -45,7 +45,7 @@ py::capsule integrateVelocityField( py::capsule & antsVelocityField,
   ITKVelocityFieldPointerType inputITKVelocityField = ITKVelocityFieldType::New();
   inputITKVelocityField->CopyInformation( inputVelocityField );
   inputITKVelocityField->SetRegions( inputVelocityField->GetRequestedRegion() );
-  inputITKVelocityField->Allocate();
+  inputITKVelocityField->AllocateInitialized();
 
   IteratorType It( inputITKVelocityField,
                    inputITKVelocityField->GetRequestedRegion() );
@@ -79,7 +79,7 @@ py::capsule integrateVelocityField( py::capsule & antsVelocityField,
   antsField->CopyInformation( integrator->GetOutput() );
   antsField->SetRegions( integrator->GetOutput()->GetRequestedRegion() );
   antsField->SetVectorLength( Dimension );
-  antsField->Allocate();
+  antsField->AllocateInitialized();
 
   ConstIteratorType ItI( integrator->GetOutput(),
     integrator->GetOutput()->GetRequestedRegion() );

diff --git a/ants/lib/LOCAL_invertDisplacementField.cxx b/ants/lib/LOCAL_invertDisplacementField.cxx
@@ -61,14 +61,14 @@ py::capsule invertDisplacementField( py::capsule & antsDisplacementField,
   inputITKDisplacementField->SetRegions( fieldSize );
   inputITKDisplacementField->SetSpacing( fieldSpacing );
   inputITKDisplacementField->SetDirection( fieldDirection );
-  inputITKDisplacementField->Allocate();
+  inputITKDisplacementField->AllocateInitialized();
 
   ITKFieldPointerType inputITKInverseFieldInitialEstimate = ITKFieldType::New();
   inputITKInverseFieldInitialEstimate->SetOrigin( fieldOrigin );
   inputITKInverseFieldInitialEstimate->SetRegions( fieldSize );
   inputITKInverseFieldInitialEstimate->SetSpacing( fieldSpacing );
   inputITKInverseFieldInitialEstimate->SetDirection( fieldDirection );
-  inputITKInverseFieldInitialEstimate->Allocate();
+  inputITKInverseFieldInitialEstimate->AllocateInitialized();
 
   IteratorType ItF( inputITKDisplacementField, inputITKDisplacementField->GetRequestedRegion() );
   IteratorType ItE( inputITKInverseFieldInitialEstimate, inputITKInverseFieldInitialEstimate->GetRequestedRegion() );
@@ -108,7 +108,7 @@ py::capsule invertDisplacementField( py::capsule & antsDisplacementField,
   antsField->CopyInformation( inverter->GetOutput() );
   antsField->SetRegions( inverter->GetOutput()->GetRequestedRegion() );
   antsField->SetVectorLength( Dimension );
-  antsField->Allocate();
+  antsField->AllocateInitialized();
 
   ConstIteratorType ItI( inverter->GetOutput(),
     inverter->GetOutput()->GetRequestedRegion() );

diff --git a/ants/lib/LOCAL_mergeChannels.cxx b/ants/lib/LOCAL_mergeChannels.cxx
@@ -34,7 +34,7 @@ py::capsule mergeChannels( std::vector<void *> imageList )
   vectorImage->SetOrigin( images[0]->GetOrigin() );
   vectorImage->SetDirection( images[0]->GetDirection() );
   vectorImage->SetNumberOfComponentsPerPixel( nImages );
-  vectorImage->Allocate();
+  vectorImage->AllocateInitialized();
 
   // Fill image data
   itk::ImageRegionIteratorWithIndex<VectorImageType> it( vectorImage,
@@ -75,7 +75,7 @@ py::capsule mergeChannels2( std::vector<py::capsule> imageList )
   vectorImage->SetOrigin( images[0]->GetOrigin() );
   vectorImage->SetDirection( images[0]->GetDirection() );
   vectorImage->SetNumberOfComponentsPerPixel( nImages );
-  vectorImage->Allocate();
+  vectorImage->AllocateInitialized();
 
   // Fill image data
   itk::ImageRegionIteratorWithIndex<VectorImageType> it( vectorImage,
@@ -116,7 +116,7 @@ py::capsule mergeChannels3( std::vector<py::capsule> imageList )
   vectorImage->SetOrigin( images[0]->GetOrigin() );
   vectorImage->SetDirection( images[0]->GetDirection() );
   //vectorImage->SetNumberOfComponentsPerPixel( nImages );
-  vectorImage->Allocate();
+  vectorImage->AllocateInitialized();
 
   // Fill image data
   itk::ImageRegionIteratorWithIndex<VectorImageType> it( vectorImage,
@@ -156,7 +156,7 @@ std::vector<py::capsule > splitChannels( py::capsule & antsimage )
     image->SetSpacing( input->GetSpacing() );
     image->SetOrigin( input->GetOrigin() );
     image->SetDirection( input->GetDirection() );
-    image->Allocate();
+    image->AllocateInitialized();
     images.push_back( image );
     }
 

diff --git a/ants/lib/LOCAL_simulateDisplacementField.cxx b/ants/lib/LOCAL_simulateDisplacementField.cxx
@@ -60,9 +60,9 @@ py::capsule simulateBsplineDisplacementField(py::capsule & antsDomainImage,
   antsField->CopyInformation( domainImage );
   antsField->SetRegions( domainImage->GetRequestedRegion() );
   antsField->SetVectorLength( Dimension );
-  antsField->Allocate();
+  antsField->AllocateInitialized();
 
-  IteratorType It( bsplineSimulator->GetOutput(), 
+  IteratorType It( bsplineSimulator->GetOutput(),
     bsplineSimulator->GetOutput()->GetRequestedRegion() );
   for( It.GoToBegin(); !It.IsAtEnd(); ++It )
     {
@@ -116,9 +116,9 @@ py::capsule simulateExponentialDisplacementField(py::capsule & antsDomainImage,
   antsField->CopyInformation( domainImage );
   antsField->SetRegions( domainImage->GetRequestedRegion() );
   antsField->SetVectorLength( Dimension );
-  antsField->Allocate();
+  antsField->AllocateInitialized();
 
-  IteratorType It( exponentialSimulator->GetOutput(), 
+  IteratorType It( exponentialSimulator->GetOutput(),
     exponentialSimulator->GetOutput()->GetRequestedRegion() );
   for( It.GoToBegin(); !It.IsAtEnd(); ++It )
     {

diff --git a/ants/lib/ReadWriteData.h b/ants/lib/ReadWriteData.h
@@ -754,7 +754,7 @@ ConvertTimeSeriesImageToMultiChannelImage( TTimeSeriesImageType *timeSeriesImage
   multiChannelImage->SetOrigin( origin );
   multiChannelImage->SetDirection( direction );
   multiChannelImage->SetVectorLength( timeSeriesSize[ImageDimension] );
-  multiChannelImage->Allocate();
+  multiChannelImage->AllocateInitialized();
 
   itk::ImageRegionIteratorWithIndex<MultiChannelImageType> It(
     multiChannelImage, multiChannelImage->GetRequestedRegion() );

diff --git a/scripts/configure_ANTsPy.bat b/scripts/configure_ANTsPy.bat
@@ -18,7 +18,7 @@ COPY data\* %USERPROFILE%\.antspy
 
 :: clone ANTs and move all files into library directory
 SET antsgit=https://github.com/ANTsX/ANTs.git
-SET antstag=6c29d9d1d62f158ca324d5fc8786fffc469998e7
+SET antstag=2236a7589c73bbaf88c8bf34a821ba54e0e545d8
 echo "ANTS;%antstag%" REM UNKNOWN: {"type":"Redirect","op":{"text":">>","type":"dgreat"},"file":{"text":"./data/softwareVersions.csv","type":"Word"}}
 cd ants\lib
 echo "123"

diff --git a/scripts/configure_ANTsPy.sh b/scripts/configure_ANTsPy.sh
@@ -23,7 +23,7 @@ cp data/* ~/.antspy/
 # clone ANTs and move all files into library directory
 
 antsgit=https://github.com/ANTsX/ANTs.git
-antstag=6c29d9d1d62f158ca324d5fc8786fffc469998e7 # 3-15-24
+antstag=2236a7589c73bbaf88c8bf34a821ba54e0e545d8 # 3-20-2024
 echo "ANTS;${antstag}" >> ./data/softwareVersions.csv
 
 cd ants/lib # go to lib dir

diff --git a/scripts/configure_ITK.bat b/scripts/configure_ITK.bat
@@ -4,7 +4,7 @@
 SET CMAKE_BUILD_TYPE=Release
 
 SET itkgit=https://github.com/InsightSoftwareConsortium/ITK.git
-SET itktag=be79ceb0a9343c02dba310f5faee371941f6fa40
+SET itktag=4535548a8539757c5fe9d81f8de5d804cd0a384f
 
 :: if there is a directory but no git, remove it
 if exist itksource\ (

diff --git a/scripts/configure_ITK.sh b/scripts/configure_ITK.sh
@@ -15,7 +15,7 @@ fi
 
 #cd ./src
 itkgit=https://github.com/InsightSoftwareConsortium/ITK.git
-itktag=be79ceb0a9343c02dba310f5faee371941f6fa40 # 3-15-24
+itktag=4535548a8539757c5fe9d81f8de5d804cd0a384f # 2024-03-12
 # if there is a directory but no git, remove it
 if [[ -d itksource ]]; then
     if [[ ! -d itksource/.git ]]; then