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ENH: Check for initialization after image allocation. #1702

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Mar 19, 2024
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ENH: Check for initialization after image allocation. #1702

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2 changes: 1 addition & 1 deletion Examples/ComputeSimilarityMetric.cxx
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Expand Up @@ -74,7 +74,7 @@ ComputeSimilarityMetric(int argc, char * argv[])
field->SetLargestPossibleRegion( image1->GetLargestPossibleRegion() );
field->SetBufferedRegion( image1->GetLargestPossibleRegion() );
field->SetLargestPossibleRegion( image1->GetLargestPossibleRegion() );
field->Allocate();
field->AllocateInitialized();
field->SetSpacing(image1->GetSpacing());
field->SetOrigin(image1->GetOrigin());
VectorType zero;
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2 changes: 1 addition & 1 deletion Examples/ConformalMapping.cxx
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Expand Up @@ -835,7 +835,7 @@ typename ImageType::Pointer outimage = ImageType::New();
outimage->SetSpacing( bspliner->GetOutput()->GetSpacing() );
outimage->SetOrigin( bspliner->GetOutput()->GetOrigin() );
outimage->SetRegions( bspliner->GetOutput()->GetLargestPossibleRegion() );
outimage->Allocate();
outimage->AllocateInitialized();

*/
/*
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7 changes: 1 addition & 6 deletions Examples/ConvertImage.cxx
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Expand Up @@ -49,12 +49,7 @@ ConvertImage(int argc, char * argv[])
{
displacementField->CopyInformation(inputImage);
displacementField->SetRegions(inputImage->GetRequestedRegion());
displacementField->Allocate();

VectorType V;
V.Fill(0.0);

displacementField->FillBuffer(V);
displacementField->AllocateInitialized();
}

itk::ImageRegionConstIterator<ComponentImageType> It(inputImage, inputImage->GetLargestPossibleRegion());
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2 changes: 1 addition & 1 deletion Examples/CreateTiledMosaic.cxx
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Expand Up @@ -135,7 +135,7 @@ CreateMosaic(itk::ants::CommandLineParser * parser)
maskImage->CopyInformation(rgbImage);
maskImage->SetRegions(rgbImage->GetRequestedRegion());
maskImage->Allocate();
maskImage->FillBuffer(1);
maskImage->FillBuffer(itk::NumericTraits<typename ImageType::PixelType>::OneValue());

using ShortImageType = itk::Image<unsigned short, ImageDimension>;
using CasterType = itk::CastImageFilter<ImageType, ShortImageType>;
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2 changes: 1 addition & 1 deletion Examples/DeNrrd.cxx
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Expand Up @@ -188,7 +188,7 @@ DeNrrd(std::vector<std::string> args, std::ostream * /*out_stream = nullptr */)
OutputImageType::RegionType outRegion;
outRegion.SetSize( outSize );
outImage->SetRegions( outRegion );
outImage->Allocate();
outImage->AllocateInitialized();

OutputImageType::SpacingType spacing;
spacing[0] = reader->GetOutput()->GetSpacing()[0];
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3 changes: 1 addition & 2 deletions Examples/ExtractSliceFromImage.cxx
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Expand Up @@ -81,8 +81,7 @@ ExtractSliceFromImage(int argc, char * argv[])
typename ImageType::Pointer outImage = ImageType::New();
outImage->CopyInformation(inputImage);
outImage->SetRegions(inputImage->GetLargestPossibleRegion());
outImage->Allocate();
outImage->FillBuffer(0);
outImage->AllocateInitialized();

// paste image slice to higher dimensionl image
using PasteFilterType = itk::PasteImageFilter<ImageType>;
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3 changes: 1 addition & 2 deletions Examples/GetConnectedComponentsFeatureImages.cxx
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Expand Up @@ -41,8 +41,7 @@ GetConnectedComponentsFeatureImages(int itkNotUsed(argc), char * argv[])
typename RealImageType::Pointer output = RealImageType::New();
output->CopyInformation(inputImage);
output->SetRegions(inputImage->GetRequestedRegion());
output->Allocate();
output->FillBuffer(0.0);
output->AllocateInitialized();

outputImages.push_back(output);
}
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2 changes: 1 addition & 1 deletion Examples/ImageIntensityStatistics.cxx
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Expand Up @@ -35,7 +35,7 @@ ImageIntensityStatistics(int argc, char * argv[])
labelImage->CopyInformation(intensityImage);
labelImage->SetRegions(intensityImage->GetLargestPossibleRegion());
labelImage->Allocate();
labelImage->FillBuffer(1);
labelImage->FillBuffer(itk::NumericTraits<LabelType>::One);
}

std::vector<LabelType> labels;
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67 changes: 25 additions & 42 deletions Examples/ImageMath_Templates.hxx
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Expand Up @@ -2125,7 +2125,7 @@ CoordinateComponentImages(int argc, char * argv[])
coordinateImages[d] = ImageType::New();
coordinateImages[d]->CopyInformation(domainImage);
coordinateImages[d]->SetRegions(domainImage->GetRequestedRegion());
coordinateImages[d]->Allocate();
coordinateImages[d]->AllocateInitialized();
}

itk::ImageRegionIteratorWithIndex<ImageType> It(domainImage, domainImage->GetRequestedRegion());
Expand Down Expand Up @@ -2541,7 +2541,7 @@ TimeSeriesAssemble(int argc, char * argv[])
outimage->SetSpacing(outSpacing);
outimage->SetOrigin(outOrigin);
outimage->SetDirection(outDirection);
outimage->Allocate();
outimage->AllocateInitialized();
}

ImageIt it(image1, image1->GetLargestPossibleRegion());
Expand Down Expand Up @@ -3082,8 +3082,7 @@ TimeSeriesRegionSCCA(int argc, char * argv[])
region.SetSize(0, nLabels);
region.SetSize(1, nLabels);
connmat->SetRegions(region);
connmat->Allocate();
connmat->FillBuffer(0);
connmat->AllocateInitialized();

// Coorelation parameters
bool robust = false;
Expand Down Expand Up @@ -3251,7 +3250,7 @@ TimeSeriesRegionCorr(int argc, char * argv[])
region.SetSize(1, nLabels);
connmat->SetRegions(region);
connmat->Allocate();
connmat->FillBuffer(-1);
connmat->FillBuffer(-itk::NumericTraits<typename InputImageType::PixelType>::OneValue());

MatrixType timeSig(nLabels, nTimes, 0.0);
for (unsigned int i = 0; i < nLabels; i++)
Expand Down Expand Up @@ -5035,7 +5034,7 @@ StackImage(int argc, char * argv[])
stackImage->SetDirection(refDirection);
stackImage->SetOrigin(refOrigin);
stackImage->SetSpacing(refSpacing);
stackImage->Allocate();
stackImage->AllocateInitialized();

unsigned int offset = 0;
while (argc > argct)
Expand Down Expand Up @@ -6884,7 +6883,7 @@ CompareHeadersAndImages(int argc, char * argv[])
// varimage->SetLargestPossibleRegion( image->GetLargestPossibleRegion() );
// varimage->SetBufferedRegion( image->GetLargestPossibleRegion() );
// varimage->SetLargestPossibleRegion( image->GetLargestPossibleRegion() );
// varimage->Allocate();
// varimage->AllocateInitialized();
// varimage->SetSpacing(image->GetSpacing());
// varimage->SetOrigin(image->GetOrigin());
// varimage->SetDirection(image->GetDirection());
Expand Down Expand Up @@ -6981,7 +6980,7 @@ CompareHeadersAndImages(int argc, char * argv[])
// varimage->SetSpacing(image->GetSpacing());
// varimage->SetOrigin(image->GetOrigin());
// varimage->SetDirection(image->GetDirection());
// varimage->Allocate();
// varimage->AllocateInitialized();
//
// std::vector<double> estimatedVar(nclasses,0);
// std::vector<double> estimatedCounts(nclasses,0);
Expand Down Expand Up @@ -7026,13 +7025,13 @@ CompareHeadersAndImages(int argc, char * argv[])
// InputImageType,LabelType,
// PosteriorType,PriorType > ClassifierFilterType;
//
// typename InputImageType::Pointer vecImage = InputImageType::New();
// typename InputImageType::Pointer vecImage = InputImageType::New();A
// typedef typename InputImageType::PixelType VecPixelType;
// vecImage->SetSpacing(image->GetSpacing());
// vecImage->SetOrigin(image->GetOrigin());
// vecImage->SetRegions( image->GetLargestPossibleRegion() );
// vecImage->SetVectorLength(nclasses);
// vecImage->Allocate();
// vecImage->AllocateInitialized();
// VecPixelType vvv(nclasses);
// vvv.Fill(0);
// vecImage->FillBuffer(vvv);
Expand Down Expand Up @@ -7107,7 +7106,7 @@ CompareHeadersAndImages(int argc, char * argv[])
// priors->SetDirection(image->GetDirection());
// priors->SetRegions( image->GetLargestPossibleRegion() );
// priors->SetVectorLength(nclasses);
// priors->Allocate();
// priors->AllocateInitialized();
// // std::cout <<" Allocated " << std::endl;
//
// for( vfIter2.GoToBegin(); !vfIter2.IsAtEnd(); ++vfIter2 )
Expand Down Expand Up @@ -7312,10 +7311,7 @@ NegativeImage(int /*argc */, char * argv[])
// vecImage->SetOrigin(image->GetOrigin());
// vecImage->SetLargestPossibleRegion( image->GetLargestPossibleRegion() );
// vecImage->SetBufferedRegion( image->GetLargestPossibleRegion() );
// vecImage->Allocate();
// VecPixelType vvv;
// vvv.Fill(0);
// vecImage->FillBuffer(vvv);
// vecImage->AllocateInitialized();
//
// // setup the iterators
// // typedef VecImageType::PixelType::VectorType VecPixelType;
Expand Down Expand Up @@ -7657,10 +7653,7 @@ itkMRIBiasFieldCorrectionFilter(typename TImage::Pointer image,
// vecImage->SetOrigin(image->GetOrigin());
// vecImage->SetLargestPossibleRegion( image->GetLargestPossibleRegion() );
// vecImage->SetBufferedRegion( image->GetLargestPossibleRegion() );
// vecImage->Allocate();
// VecPixelType vvv;
// vvv.Fill(0);
// vecImage->FillBuffer(vvv);
// vecImage->AllocateInitialized();
//
// // setup the iterators
// // typedef VecImageType::PixelType::VectorType VecPixelType;
Expand Down Expand Up @@ -9324,8 +9317,7 @@ ReplaceVoxelValue(int argc, char * argv[])
typename ImageType::Pointer outputImage = ImageType::New();
outputImage->CopyInformation(inputImage);
outputImage->SetRegions(inputImage->GetRequestedRegion());
outputImage->Allocate();
outputImage->FillBuffer(0);
outputImage->AllocateInitialized();

typename itk::ImageRegionIterator<ImageType> ItI(inputImage, inputImage->GetRequestedRegion());
typename itk::ImageRegionIterator<ImageType> ItO(outputImage, outputImage->GetRequestedRegion());
Expand Down Expand Up @@ -10353,14 +10345,12 @@ ReplicateDisplacement(int argc, char * argv[])
outputImage->SetSpacing(outSpacing);
outputImage->SetOrigin(outOrigin);
outputImage->SetDirection(outDirection);
outputImage->Allocate();
VectorRType vec;
vec.Fill(0);
outputImage->FillBuffer(vec);
outputImage->AllocateInitialized();
// perform the replication
typename VectorImageType::IndexType ind;
typename VectorRImageType::IndexType indp1;
Iterator It1(vecimage1, vecimage1->GetLargestPossibleRegion());
typename VectorRImageType::PixelType vec;
for (It1.GoToBegin(); !It1.IsAtEnd(); ++It1)
{
ind = It1.GetIndex();
Expand Down Expand Up @@ -10487,8 +10477,7 @@ ReplicateImage(int argc, char * argv[])
outputImage->SetSpacing(outSpacing);
outputImage->SetOrigin(outOrigin);
outputImage->SetDirection(outDirection);
outputImage->Allocate();
outputImage->FillBuffer(0);
outputImage->AllocateInitialized();
// perform the replication
typename ImageType::IndexType ind;
typename RImageType::IndexType indp1;
Expand Down Expand Up @@ -10856,8 +10845,7 @@ LabelThickness2(int argc, char * argv[])
typename RealImageType::Pointer thicknessPriorImage = RealImageType::New();
thicknessPriorImage->CopyInformation(labelImage);
thicknessPriorImage->SetRegions(labelImage->GetLargestPossibleRegion());
thicknessPriorImage->Allocate();
thicknessPriorImage->FillBuffer(0);
thicknessPriorImage->AllocateInitialized();

itk::ImageRegionIteratorWithIndex<LabelImageType> It(labelImage, labelImage->GetLargestPossibleRegion());
for (It.GoToBegin(); !It.IsAtEnd(); ++It)
Expand Down Expand Up @@ -12127,15 +12115,13 @@ MostLikely(int argc, char * argv[])
output->SetSpacing(iLabel->GetSpacing());
output->SetOrigin(iLabel->GetOrigin());
output->SetDirection(iLabel->GetDirection());
output->Allocate();
output->FillBuffer(0);
output->AllocateInitialized();

prob->SetRegions(iLabel->GetLargestPossibleRegion());
prob->SetSpacing(iLabel->GetSpacing());
prob->SetOrigin(iLabel->GetOrigin());
prob->SetDirection(iLabel->GetDirection());
prob->Allocate();
prob->FillBuffer(0);
prob->AllocateInitialized();
}

IteratorType it(output, output->GetLargestPossibleRegion());
Expand Down Expand Up @@ -12273,8 +12259,7 @@ AverageLabels(int argc, char * argv[])
img->SetDirection(images[0]->GetDirection());
img->SetOrigin(images[0]->GetOrigin());
img->SetSpacing(images[0]->GetSpacing());
img->Allocate();
outimages.push_back(img);
img->AllocateInitialized();
}
for (unsigned int i = 0; i < images.size(); i++)
{
Expand Down Expand Up @@ -13048,8 +13033,7 @@ PureTissueN4WeightMask(int argc, char * argv[])
typename ImageType::Pointer output = ImageType::New();
output->CopyInformation(images[0]);
output->SetRegions(images[0]->GetLargestPossibleRegion());
output->Allocate();
output->FillBuffer(0);
output->AllocateInitialized();

itk::ImageRegionIteratorWithIndex<ImageType> ItO(output, output->GetLargestPossibleRegion());
for (ItO.GoToBegin(); !ItO.IsAtEnd(); ++ItO)
Expand Down Expand Up @@ -13217,7 +13201,7 @@ InPaint(int argc, char * argv[])
region.SetSize(size);
region.SetIndex(start);
kernel->SetRegions(region);
kernel->Allocate();
kernel->AllocateInitialized();
kernel->SetSpacing(image1->GetSpacing());
unsigned long kernelsize = region.GetNumberOfPixels();
itk::ImageRegionIterator<ImageType> imageIterator(kernel, region);
Expand Down Expand Up @@ -13341,7 +13325,7 @@ InPaint2(int argc, char * argv[])
region.SetSize(size);
region.SetIndex(start);
kernel->SetRegions(region);
kernel->Allocate();
kernel->AllocateInitialized();
kernel->SetSpacing(image1->GetSpacing());
unsigned long kernelsize = region.GetNumberOfPixels();
itk::ImageRegionIterator<ImageType> imageIterator(kernel, region);
Expand Down Expand Up @@ -13457,8 +13441,7 @@ Check3TissueLabeling(int argc, char * argv[])
typename LabelImageType::Pointer maxPriorLabelImage = LabelImageType::New();
maxPriorLabelImage->CopyInformation(labelImage);
maxPriorLabelImage->SetRegions(labelImage->GetRequestedRegion());
maxPriorLabelImage->Allocate();
maxPriorLabelImage->FillBuffer(0);
maxPriorLabelImage->AllocateInitialized();

itk::ImageRegionIteratorWithIndex<LabelImageType> ItL(labelImage, labelImage->GetRequestedRegion());
itk::ImageRegionIterator<LabelImageType> ItM(maxPriorLabelImage, maxPriorLabelImage->GetRequestedRegion());
Expand Down Expand Up @@ -14366,7 +14349,7 @@ KinematicTensor(int argc, char * argv[])
typename TensorImageType::Pointer strain = TensorImageType::New();
strain->CopyInformation(reader->GetOutput());
strain->SetRegions(reader->GetOutput()->GetLargestPossibleRegion());
strain->Allocate();
strain->AllocateInitialized();

itk::ImageRegionIteratorWithIndex<TensorImageType> It(strain, strain->GetLargestPossibleRegion());

Expand Down
5 changes: 2 additions & 3 deletions Examples/MeasureImageSimilarity.cxx
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Expand Up @@ -421,8 +421,7 @@ MeasureImageSimilarity(itk::ants::CommandLineParser * parser)
typename DisplacementFieldType::Pointer identityField = DisplacementFieldType::New();
identityField->CopyInformation(fixedImage);
identityField->SetRegions(fixedImage->GetLargestPossibleRegion());
identityField->Allocate();
identityField->FillBuffer(zeroVector);
identityField->AllocateInitialized();

typename DisplacementFieldTransformType::Pointer identityDisplacementFieldTransform =
DisplacementFieldTransformType::New();
Expand All @@ -446,7 +445,7 @@ MeasureImageSimilarity(itk::ants::CommandLineParser * parser)
typename DisplacementFieldType::Pointer gradientField = DisplacementFieldType::New();
gradientField->CopyInformation(fixedImage);
gradientField->SetRegions(fixedImage->GetLargestPossibleRegion());
gradientField->Allocate();
gradientField->AllocateInitialized();

itk::ImageRegionIterator<DisplacementFieldType> ItG(gradientField, gradientField->GetRequestedRegion());

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3 changes: 1 addition & 2 deletions Examples/SmoothDisplacementField.cxx
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Expand Up @@ -192,8 +192,7 @@ SmoothDisplacementField(int argc, char * argv[])
rmseImage->SetDirection(field->GetDirection());
rmseImage->SetSpacing(field->GetSpacing());
rmseImage->SetRegions(field->GetLargestPossibleRegion());
rmseImage->Allocate();
rmseImage->FillBuffer(0.0);
rmseImage->AllocateInitialized();

itk::ImageRegionConstIterator<DisplacementFieldType> fieldIt(field, field->GetLargestPossibleRegion());
itk::ImageRegionConstIterator<DisplacementFieldType> smoothedFieldIt(smoothField,
Expand Down
3 changes: 1 addition & 2 deletions Examples/ThresholdImage.cxx
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Expand Up @@ -219,8 +219,7 @@ OtsuThreshold(int NumberOfThresholds, typename TImage::Pointer input, typename T
typename ImageType::Pointer output = ImageType::New();
output->CopyInformation(maskImage);
output->SetRegions(maskImage->GetLargestPossibleRegion());
output->Allocate();
output->FillBuffer(0);
output->AllocateInitialized();

itk::ImageRegionIterator<ImageType> ItO(output, output->GetLargestPossibleRegion());
for (unsigned int i = 0; i < thresholds.size(); i++)
Expand Down
6 changes: 2 additions & 4 deletions Examples/TimeSCCAN.cxx
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Expand Up @@ -105,8 +105,7 @@ RegionSCCA(typename NetworkType::Pointer network,
size[1] = N;
region.SetSize(size);
network->SetRegions(region);
network->Allocate();
network->FillBuffer(0.0);
network->AllocateInitialized();

unsigned int nVoxels = labels->GetLargestPossibleRegion().GetSize()[0];
unsigned int nTimes = time->GetLargestPossibleRegion().GetSize()[0];
Expand Down Expand Up @@ -311,8 +310,7 @@ RegionAveraging(typename NetworkType::Pointer network,
size[1] = N;
region.SetSize(size);
network->SetRegions(region);
network->Allocate();
network->FillBuffer(0.0);
network->AllocateInitialized();

unsigned int nVoxels = labels->GetLargestPossibleRegion().GetSize()[0];
unsigned int nTimes = time->GetLargestPossibleRegion().GetSize()[0];
Expand Down
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