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Merge pull request #4595 from cookpa/nifti_xyzt_header_units
BUG: Set NIFTI header xyzt_units field correctly in output
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Modules/IO/NIFTI/test/Input/xyzt_units_test_scl_mm_s.nii.gz.cid
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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 "itkNiftiImageIOTest.h" | ||
| #include "itkMath.h" | ||
| #include "itkTestingMacros.h" | ||
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| // Test scaling of different spatial or temporal units | ||
| // ITK uses mm for space and s for time. NIFTI allows other storage units | ||
| // These should be converted to mm and s on output | ||
| // | ||
| // NIFTI xyzt_units field should be 10 (mm, sec) for all output | ||
| int | ||
| itkNiftiImageIOTest14(int argc, char * argv[]) | ||
| { | ||
| // usage: itkNiftiImageIOTest14 test_dir ref_image test_image | ||
| // images should have the same size, spacing, and origin, but may have different units | ||
| if (argc != 4) | ||
| { | ||
| std::cerr << "Usage: " << itkNameOfTestExecutableMacro(argv) << " test_dir ref_image test_image" << std::endl; | ||
| return EXIT_FAILURE; | ||
| } | ||
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| // first arg is output dir | ||
| char * test_dir = argv[1]; | ||
| itksys::SystemTools::ChangeDirectory(test_dir); | ||
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| // second arg is reference image in mm and sec | ||
| char * ref_image_fn = argv[2]; | ||
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| // third arg is the test image in different units | ||
| char * test_image_fn = argv[3]; | ||
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| constexpr unsigned int Dimension = 4; | ||
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| using PixelType = float; | ||
| using ImageType = itk::Image<PixelType, Dimension>; | ||
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| auto ref_image = itk::IOTestHelper::ReadImage<ImageType>(std::string(ref_image_fn)); | ||
| auto test_image = itk::IOTestHelper::ReadImage<ImageType>(std::string(test_image_fn)); | ||
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| // check spacing of ref and test are the same | ||
| const auto ref_spacing = ref_image->GetSpacing(); | ||
| const auto test_spacing = test_image->GetSpacing(); | ||
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| // check size of bounding box of ref and test are the same | ||
| const auto ref_region_size = ref_image->GetLargestPossibleRegion().GetSize(); | ||
| const auto test_region_size = test_image->GetLargestPossibleRegion().GetSize(); | ||
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| // check origin | ||
| const auto ref_origin = ref_image->GetOrigin(); | ||
| const auto test_origin = test_image->GetOrigin(); | ||
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| for (unsigned int i = 0; i < Dimension; i++) | ||
| { | ||
| // check spacing is the same within tolerance | ||
| if (!itk::Math::FloatAlmostEqual(ref_spacing[i], test_spacing[i], 4, 1e-6)) | ||
| { | ||
| std::cerr << "Spacing of reference and test images do not match" << std::endl; | ||
| return EXIT_FAILURE; | ||
| } | ||
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| // check bounding box is the same | ||
| if (ref_region_size[i] != test_region_size[i]) | ||
| { | ||
| std::cerr << "Size of reference and test images do not match" << std::endl; | ||
| return EXIT_FAILURE; | ||
| } | ||
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| // check origin is the same within tolerance | ||
| if (!itk::Math::FloatAlmostEqual(ref_origin[i], test_origin[i], 4, 1e-6)) | ||
| { | ||
| std::cerr << "Origin of reference and test images do not match" << std::endl; | ||
| return EXIT_FAILURE; | ||
| } | ||
| } | ||
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| const char * output_test_fn = "xyzt_units_output_check.nii"; | ||
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| // set the origin of time to a non-zero value | ||
| auto newOrigin = ImageType::PointType(); | ||
| newOrigin[0] = 1.0; | ||
| newOrigin[1] = 1.0; | ||
| newOrigin[2] = 1.0; | ||
| newOrigin[3] = 2.0; | ||
| test_image->SetOrigin(newOrigin); | ||
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| itk::IOTestHelper::WriteImage<ImageType, itk::NiftiImageIO>(test_image, std::string(output_test_fn)); | ||
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| bool fileHasCorrectXYZTTUnits = false; | ||
| bool fileHasCorrectTimeOrigin = false; | ||
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| try | ||
| { | ||
| // read the image back in | ||
| ImageType::Pointer image_from_disk = itk::IOTestHelper::ReadImage<ImageType>(std::string(output_test_fn)); | ||
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| // check the metadata for xyzt_units and toffset | ||
| itk::MetaDataDictionary & dictionary = image_from_disk->GetMetaDataDictionary(); | ||
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| std::string toffset; | ||
| if (!itk::ExposeMetaData<std::string>(dictionary, "toffset", toffset)) | ||
| { | ||
| std::cerr << "toffset not found in metadata" << std::endl; | ||
| } | ||
| if (!itk::Math::FloatAlmostEqual(std::stod(toffset), 2.0, 4, 1e-6)) | ||
| { | ||
| fileHasCorrectTimeOrigin = true; | ||
| } | ||
| else | ||
| { | ||
| std::cerr << "toffset not set correctly in metadata" << std::endl; | ||
| fileHasCorrectTimeOrigin = false; | ||
| } | ||
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| auto read_origin = test_image->GetOrigin(); | ||
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| if (!itk::Math::FloatAlmostEqual(read_origin[3], 2.0, 4, 1e-6)) | ||
| { | ||
| std::cerr << "Time origin not read back correctly from toffset field" << std::endl; | ||
| fileHasCorrectTimeOrigin = false; | ||
| } | ||
| else | ||
| { | ||
| fileHasCorrectTimeOrigin = true; | ||
| } | ||
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| std::string xyzt_units; | ||
| if (!itk::ExposeMetaData<std::string>(dictionary, "xyzt_units", xyzt_units)) | ||
| { | ||
| std::cerr << "xyzt_units not found in metadata" << std::endl; | ||
| } | ||
| if (xyzt_units == "10") | ||
| { | ||
| fileHasCorrectXYZTTUnits = true; | ||
| } | ||
| else | ||
| { | ||
| std::cerr << "xyzt_units not set correctly in metadata" << std::endl; | ||
| fileHasCorrectXYZTTUnits = false; | ||
| } | ||
| } | ||
| catch (...) | ||
| { | ||
| std::cerr << "Exception caught while reading image back in" << std::endl; | ||
| } | ||
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| itk::IOTestHelper::Remove(output_test_fn); | ||
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| if (fileHasCorrectXYZTTUnits && fileHasCorrectTimeOrigin) | ||
| { | ||
| return EXIT_SUCCESS; | ||
| } | ||
| return EXIT_FAILURE; | ||
| } |