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BUG: itkDCMTKFileReader Philips multi-frame MRI Z spacing
Addresses #4131, Z spacing on an Philips MRI volume saved as MRExtendedStorage.
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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. | ||
| * | ||
| *=========================================================================*/ | ||
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| #include "itkImageFileReader.h" | ||
| #include "itkDCMTKImageIO.h" | ||
| #include "itkImageRegionConstIterator.h" | ||
| #include "itkMultiplyImageFilter.h" | ||
| #include "itkAddImageFilter.h" | ||
| #include "itkSubtractImageFilter.h" | ||
| #include "itkStatisticsImageFilter.h" | ||
| #include "itkMath.h" | ||
| #include "itkTestingMacros.h" | ||
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| using PixelType = short; | ||
| using ImageType = itk::Image<PixelType, 3>; | ||
| using DirectionType = ImageType::DirectionType; | ||
| using SpacingType = ImageType::SpacingType; | ||
| using PointType = ImageType::PointType; | ||
| using ReaderType = itk::ImageFileReader<ImageType>; | ||
| using ImageIOType = itk::DCMTKImageIO; | ||
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| namespace | ||
| { | ||
| // | ||
| // if the difference is < average/10000, close enough | ||
| bool | ||
| CloseEnough(double a, double b) | ||
| { | ||
| double diff = itk::Math::abs(a - b); | ||
| double avg = (itk::Math::abs(a) + itk::Math::abs(b)) / 2.0; | ||
| if (diff == 0.0 || diff < avg / 10000.00) | ||
| { | ||
| return true; | ||
| } | ||
| return false; | ||
| } | ||
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| bool | ||
| Equal(DirectionType dir1, DirectionType dir2) | ||
| { | ||
| for (unsigned int i = 0; i < 3; ++i) | ||
| { | ||
| for (unsigned int j = 0; j < 3; ++j) | ||
| { | ||
| if (!CloseEnough(dir1(i, j), dir2(i, j))) | ||
| { | ||
| return false; | ||
| } | ||
| } | ||
| } | ||
| return true; | ||
| } | ||
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| bool | ||
| Equal(SpacingType spacing1, SpacingType spacing2) | ||
| { | ||
| for (unsigned int i = 0; i < 3; ++i) | ||
| { | ||
| if (!CloseEnough(spacing1[i], spacing2[i])) | ||
| { | ||
| return false; | ||
| } | ||
| } | ||
| return true; | ||
| } | ||
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| bool | ||
| Equal(PointType p1, PointType p2) | ||
| { | ||
| for (unsigned int i = 0; i < 3; ++i) | ||
| { | ||
| if (!CloseEnough(p1[i], p2[i])) | ||
| { | ||
| return false; | ||
| } | ||
| } | ||
| return true; | ||
| } | ||
| } // namespace | ||
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| // This tests if slice spacing is correctly read from a Philips MRI where | ||
| // SpacingBetweenSlices is stored as a global tag. | ||
| // | ||
| int | ||
| itkDCMTKImageIOSpacingTest(int argc, char * argv[]) | ||
| { | ||
| if (argc < 2) | ||
| { | ||
| std::cerr << "Missing Parameters." << std::endl; | ||
| std::cerr << "Usage: " << itkNameOfTestExecutableMacro(argv) << " multiframeImage" << std::endl; | ||
| return EXIT_FAILURE; | ||
| } | ||
|
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| auto dcmImageIO = ImageIOType::New(); | ||
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| auto reader = ReaderType::New(); | ||
| reader->SetFileName(argv[1]); | ||
| reader->SetImageIO(dcmImageIO); | ||
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| ITK_TRY_EXPECT_NO_EXCEPTION(reader->Update()); | ||
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| const ImageType::Pointer im = reader->GetOutput(); | ||
| const DirectionType dir = im->GetDirection(); | ||
| const SpacingType spacing = im->GetSpacing(); | ||
| const PointType origin = im->GetOrigin(); | ||
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| std::cerr << "Direction " << dir << std::endl | ||
| << "Spacing " << spacing << std::endl | ||
| << "Origin " << origin << std::endl; | ||
| DirectionType expectedDirection; | ||
| expectedDirection(0, 0) = 0.999894; | ||
| expectedDirection(0, 1) = 0.0145622; | ||
| expectedDirection(0, 2) = -0.000350456; | ||
| expectedDirection(1, 0) = 0.000350419; | ||
| expectedDirection(1, 1) = 5.1034e-06; | ||
| expectedDirection(1, 2) = 1.0; | ||
| expectedDirection(2, 0) = 0.0145622; | ||
| expectedDirection(2, 1) = -0.999894; | ||
| expectedDirection(2, 2) = -1.33323e-11; | ||
| if (!Equal(dir, expectedDirection)) | ||
| { | ||
| std::cerr << "Expected directions" << std::endl | ||
| << expectedDirection << std::endl | ||
| << "Actual directions" << std::endl | ||
| << dir << std::endl; | ||
| return EXIT_FAILURE; | ||
| } | ||
| SpacingType expectedSpacing; | ||
| expectedSpacing[0] = 0.55; | ||
| expectedSpacing[1] = 0.55; | ||
| expectedSpacing[2] = 1.3; | ||
| if (!Equal(spacing, expectedSpacing)) | ||
| { | ||
| std::cerr << "Expected spacing" << std::endl | ||
| << expectedSpacing << std::endl | ||
| << "Actual spacing" << std::endl | ||
| << spacing << std::endl; | ||
| return EXIT_FAILURE; | ||
| } | ||
| PointType expectedOrigin; | ||
| expectedOrigin[0] = -112.767; | ||
| expectedOrigin[1] = -41.4828; | ||
| expectedOrigin[2] = 117.567; | ||
| if (!Equal(origin, expectedOrigin)) | ||
| { | ||
| std::cerr << "Expected origin" << std::endl | ||
| << expectedOrigin << std::endl | ||
| << "Actual origin" << std::endl | ||
| << origin << std::endl; | ||
| return EXIT_FAILURE; | ||
| } | ||
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| std::cout << "Test finished" << std::endl; | ||
| return EXIT_SUCCESS; | ||
| } |