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/*=========================================================================
*
* Copyright NumFOCUS
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* https://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
#include "itkImageFileReader.h"
#include "itkImageRegionIteratorWithIndex.h"
#include "itkTestingComparisonImageFilter.h"
#include "itkMath.h"
#include "itkNumericTraits.h"
#include "itkTestingMacros.h"
#include "metaImage.h"
int
itkImageFileReaderPositiveSpacingTest(int argc, char * argv[])
{
if (argc < 1)
{
std::cout << "Usage: " << itkNameOfTestExecutableMacro(argv) << std::endl;
return EXIT_FAILURE;
}
using ImageNDType = itk::Image<short, 2>;
using ReaderType = itk::ImageFileReader<ImageNDType>;
auto reader = ReaderType::New();
reader->SetFileName(argv[1]);
reader->Update();
ImageNDType::Pointer image = reader->GetOutput();
image->DisconnectPipeline();
ImageNDType::SpacingType spacing = image->GetSpacing();
for (unsigned int ii = 0; ii < image->GetImageDimension(); ++ii)
{
if (spacing[ii] < 0)
{
std::cerr << "Spacing should be a positive value. Found " << spacing[ii] << std::endl;
return EXIT_FAILURE;
}
}
std::cout << "Spacing: " << spacing << std::endl;
ImageNDType::DirectionType direction = image->GetDirection();
std::cout << "Direction: " << '\n' << direction << std::endl;
MetaImage metaImage;
if (!metaImage.Read(argv[1], false))
{
std::cerr << "File cannot be opened " << argv[1] << " for reading." << std::endl
<< "Reason: " << itksys::SystemTools::GetLastSystemError();
return EXIT_FAILURE;
}
ImageNDType::DirectionType ioDirection;
ImageNDType::SpacingType ioSpacing;
ImageNDType::PointType ioOrigin;
ImageNDType::SizeType ioSize;
const double * transformMatrix = metaImage.TransformMatrix();
for (unsigned int ii = 0; ii < ImageNDType::ImageDimension; ++ii)
{
ioSize[ii] = metaImage.DimSize(ii);
ioSpacing[ii] = metaImage.ElementSpacing(ii);
ioOrigin[ii] = metaImage.Position(ii);
// Please note: direction cosines are stored as columns of the
// direction matrix
for (unsigned int jj = 0; jj < ImageNDType::ImageDimension; ++jj)
{
ioDirection[jj][ii] = transformMatrix[ii * ImageNDType::ImageDimension + jj];
}
}
std::cout << "Spacing baseline: " << ioSpacing << std::endl;
std::cout << "Direction baseline: " << '\n' << ioDirection << std::endl;
// Go through entire image and make sure that at each physical pixel location, the value of the images, with negative
// spacing and positive spacing, are the same.
// itk::Testing::ComparisonImageFilter does not take into account spacing and orientation.
// We manually go through all pixels in the input image and compare their value without
// their value in the image loaded without ensuring positive spacing.
ImageNDType::DirectionType scale;
ImageNDType::DirectionType indexToPhysicalPoint;
ImageNDType::DirectionType physicalPointToIndex;
for (unsigned int ii = 0; ii < ImageNDType::ImageDimension; ++ii)
{
scale[ii][ii] = ioSpacing[ii];
}
indexToPhysicalPoint = ioDirection * scale;
physicalPointToIndex = indexToPhysicalPoint.GetInverse();
using IteratorType = itk::ImageRegionIteratorWithIndex<ImageNDType>;
IteratorType it(image, image->GetLargestPossibleRegion());
for (it.GoToBegin(); !it.IsAtEnd(); ++it)
{
ImageNDType::IndexType index = it.GetIndex();
ImageNDType::PointType point;
image->TransformIndexToPhysicalPoint(index, point);
// Compute index from physical point in baseline
ImageNDType::IndexType baselineIndex;
for (unsigned int ii = 0; ii < ImageNDType::ImageDimension; ++ii)
{
double sum = 0.0;
for (unsigned int jj = 0; jj < ImageNDType::ImageDimension; ++jj)
{
sum += physicalPointToIndex[ii][jj] * (point[jj] - ioOrigin[jj]);
}
baselineIndex[ii] = itk::Math::RoundHalfIntegerUp<ImageNDType::IndexType::IndexValueType>(sum);
}
if (index != baselineIndex)
{
std::cerr << "Difference found between original image and flipped spacing image: "
<< "Indices do not correspond." << '\n'
<< "Flipped image: " << index << '\n'
<< "Baseline image:" << baselineIndex << std::endl;
return EXIT_FAILURE;
}
}
return EXIT_SUCCESS;
}
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