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BUG: Fix ITKImportImageStack image flip operations. Add unit test for flip operations. (BlueQuartzSoftware#815)
Signed-off-by: Michael Jackson <[email protected]> Co-authored-by: nyoungbq <[email protected]>
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‎src/Plugins/ITKImageProcessing/src/ITKImageProcessing/Filters/ITKImportImageStack.cpp

Lines changed: 1 addition & 1 deletion
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@@ -104,7 +104,7 @@ void FlipAboutXAxis(DataArray<T>& dataArray, Vec3<usize>& dims)
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{
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auto& tempDataStore = dataArray.getDataStoreRef();
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usize numComp = tempDataStore.getNumberOfComponents();
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size_t rowLCV = (dims[1] % 2 == 1) ? (dims[1] - 1 / 2) : dims[1] / 2;
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size_t rowLCV = (dims[1] % 2 == 1) ? ((dims[1] - 1) / 2) : dims[1] / 2;
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usize bottomRow = dims[1] - 1;
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for(usize row = 0; row < rowLCV; row++)

‎src/Plugins/ITKImageProcessing/test/CMakeLists.txt

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@@ -113,6 +113,7 @@ if(EXISTS "${DREAM3D_DATA_DIR}" AND SIMPLNX_DOWNLOAD_TEST_FILES)
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file(MAKE_DIRECTORY "${DREAM3D_DATA_DIR}/TestFiles/")
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endif()
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download_test_data(DREAM3D_DATA_DIR ${DREAM3D_DATA_DIR} ARCHIVE_NAME fiji_montage.tar.gz SHA512 70139babc838ce3ab1f5adddfddc86dcc51996e614c6c2d757bcb2e59e8ebdc744dac269233494b1ef8d09397aecb4ccca3384f0a91bb017f2cf6309c4ac40fa)
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download_test_data(DREAM3D_DATA_DIR ${DREAM3D_DATA_DIR} ARCHIVE_NAME image_flip_test_images.tar.gz SHA512 4e282a270251133004bf4b979d0d064631b618fc82f503184c602c40d388b725f81faf8e77654d285852acc3217d51534c9a71240be4a87a91dc46da7871e7d2)
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endif()
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‎src/Plugins/ITKImageProcessing/test/ITKImportImageStackTest.cpp

Lines changed: 228 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,13 @@
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#include <catch2/catch.hpp>
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#include "ITKImageProcessing/Filters/ITKImageReader.hpp"
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#include "ITKImageProcessing/Filters/ITKImportImageStack.hpp"
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#include "ITKImageProcessing/ITKImageProcessing_test_dirs.hpp"
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#include "ITKTestBase.hpp"
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#include "simplnx/DataStructure/DataArray.hpp"
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#include "simplnx/DataStructure/Geometry/ImageGeom.hpp"
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#include "simplnx/Parameters/ChoicesParameter.hpp"
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#include "simplnx/Parameters/GeneratedFileListParameter.hpp"
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#include "simplnx/UnitTest/UnitTestCommon.hpp"
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@@ -20,6 +22,144 @@ namespace
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const std::string k_ImageStackDir = unit_test::k_DataDir.str() + "/ImageStack";
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const DataPath k_ImageGeomPath = {{"ImageGeometry"}};
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const DataPath k_ImageDataPath = k_ImageGeomPath.createChildPath(ImageGeom::k_CellDataName).createChildPath("ImageData");
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const std::string k_FlippedImageStackDirName = "image_flip_test_images";
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const DataPath k_XGeneratedImageGeomPath = DataPath({"xGeneratedImageGeom"});
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const DataPath k_YGeneratedImageGeomPath = DataPath({"yGeneratedImageGeom"});
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const DataPath k_XFlipImageGeomPath = DataPath({"xFlipImageGeom"});
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const DataPath k_YFlipImageGeomPath = DataPath({"yFlipImageGeom"});
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const std::string k_ImageDataName = "ImageData";
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const ChoicesParameter::ValueType k_NoImageTransform = 0;
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const ChoicesParameter::ValueType k_FlipAboutXAxis = 1;
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const ChoicesParameter::ValueType k_FlipAboutYAxis = 2;
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const fs::path k_ImageFlipStackDir = fs::path(fmt::format("{}/{}", unit_test::k_TestFilesDir, k_FlippedImageStackDirName));
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// Exemplar Array Paths
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const DataPath k_XFlippedImageDataPath = k_XFlipImageGeomPath.createChildPath(Constants::k_Cell_Data).createChildPath(::k_ImageDataName);
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const DataPath k_YFlippedImageDataPath = k_YFlipImageGeomPath.createChildPath(Constants::k_Cell_Data).createChildPath(::k_ImageDataName);
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// Make sure we can instantiate the ITK Import Image Stack Filter
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// ITK Image Processing Plugin Uuid
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constexpr AbstractPlugin::IdType k_ITKImageProcessingID = *Uuid::FromString("115b0d10-ab97-5a18-88e8-80d35056a28e");
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const FilterHandle k_ImportImageStackFilterHandle(nx::core::FilterTraits<ITKImportImageStack>::uuid, k_ITKImageProcessingID);
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void ExecuteImportImageStackXY(DataStructure& dataStructure, const std::string& filePrefix)
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{
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// Filter needs RotateSampleRefFrameFilter to run
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Application::GetOrCreateInstance()->loadPlugins(unit_test::k_BuildDir.view(), true);
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auto* filterList = nx::core::Application::Instance()->getFilterList();
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REQUIRE(filterList != nullptr);
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// Define Shared parameters
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std::vector<float32> k_Origin = {0.0f, 0.0f, 0.0f};
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std::vector<float32> k_Spacing = {1.0f, 1.0f, 1.0f};
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GeneratedFileListParameter::ValueType k_FileListInfo;
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// Set File list for reads
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{
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k_FileListInfo.inputPath = k_ImageFlipStackDir.string();
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k_FileListInfo.startIndex = 1;
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k_FileListInfo.endIndex = 1;
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k_FileListInfo.incrementIndex = 1;
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k_FileListInfo.fileExtension = ".tiff";
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k_FileListInfo.filePrefix = filePrefix;
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k_FileListInfo.fileSuffix = "";
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k_FileListInfo.paddingDigits = 1;
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k_FileListInfo.ordering = GeneratedFileListParameter::Ordering::LowToHigh;
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}
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// Run generated X flip
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{
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auto importImageStackFilter = filterList->createFilter(::k_ImportImageStackFilterHandle);
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REQUIRE(nullptr != importImageStackFilter);
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Arguments args;
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args.insertOrAssign(ITKImportImageStack::k_Origin_Key, std::make_any<std::vector<float32>>(k_Origin));
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args.insertOrAssign(ITKImportImageStack::k_Spacing_Key, std::make_any<std::vector<float32>>(k_Spacing));
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args.insertOrAssign(ITKImportImageStack::k_InputFileListInfo_Key, std::make_any<GeneratedFileListParameter::ValueType>(k_FileListInfo));
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args.insertOrAssign(ITKImportImageStack::k_ImageGeometryPath_Key, std::make_any<DataPath>(::k_XGeneratedImageGeomPath));
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args.insertOrAssign(ITKImportImageStack::k_ImageTransformChoice_Key, std::make_any<ChoicesParameter::ValueType>(::k_FlipAboutXAxis));
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auto preflightResult = importImageStackFilter->preflight(dataStructure, args);
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SIMPLNX_RESULT_REQUIRE_VALID(preflightResult.outputActions)
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auto executeResult = importImageStackFilter->execute(dataStructure, args);
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SIMPLNX_RESULT_REQUIRE_VALID(executeResult.result)
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}
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// Run generated Y flip
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{
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auto importImageStackFilter = filterList->createFilter(::k_ImportImageStackFilterHandle);
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REQUIRE(nullptr != importImageStackFilter);
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Arguments args;
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args.insertOrAssign(ITKImportImageStack::k_Origin_Key, std::make_any<std::vector<float32>>(k_Origin));
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args.insertOrAssign(ITKImportImageStack::k_Spacing_Key, std::make_any<std::vector<float32>>(k_Spacing));
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args.insertOrAssign(ITKImportImageStack::k_InputFileListInfo_Key, std::make_any<GeneratedFileListParameter::ValueType>(k_FileListInfo));
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args.insertOrAssign(ITKImportImageStack::k_ImageGeometryPath_Key, std::make_any<DataPath>(::k_YGeneratedImageGeomPath));
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args.insertOrAssign(ITKImportImageStack::k_ImageTransformChoice_Key, std::make_any<ChoicesParameter::ValueType>(::k_FlipAboutYAxis));
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auto preflightResult = importImageStackFilter->preflight(dataStructure, args);
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SIMPLNX_RESULT_REQUIRE_VALID(preflightResult.outputActions)
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auto executeResult = importImageStackFilter->execute(dataStructure, args);
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SIMPLNX_RESULT_REQUIRE_VALID(executeResult.result)
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}
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}
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void ReadInFlippedXYExemplars(DataStructure& dataStructure, const std::string& filePrefix)
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{
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{
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ITKImageReader filter;
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Arguments args;
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fs::path filePath = k_ImageFlipStackDir / (filePrefix + "flip_x.tiff");
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args.insertOrAssign(ITKImageReader::k_FileName_Key, filePath);
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args.insertOrAssign(ITKImageReader::k_ImageGeometryPath_Key, ::k_XFlipImageGeomPath);
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args.insertOrAssign(ITKImageReader::k_ImageDataArrayPath_Key, ::k_XFlippedImageDataPath);
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auto preflightResult = filter.preflight(dataStructure, args);
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SIMPLNX_RESULT_REQUIRE_VALID(preflightResult.outputActions)
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auto executeResult = filter.execute(dataStructure, args);
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SIMPLNX_RESULT_REQUIRE_VALID(executeResult.result)
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}
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{
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ITKImageReader filter;
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Arguments args;
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fs::path filePath = k_ImageFlipStackDir / (filePrefix + "flip_y.tiff");
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args.insertOrAssign(ITKImageReader::k_FileName_Key, filePath);
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args.insertOrAssign(ITKImageReader::k_ImageGeometryPath_Key, ::k_YFlipImageGeomPath);
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args.insertOrAssign(ITKImageReader::k_ImageDataArrayPath_Key, ::k_YFlippedImageDataPath);
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auto preflightResult = filter.preflight(dataStructure, args);
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SIMPLNX_RESULT_REQUIRE_VALID(preflightResult.outputActions)
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auto executeResult = filter.execute(dataStructure, args);
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SIMPLNX_RESULT_REQUIRE_VALID(executeResult.result)
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}
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}
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void CompareXYFlippedGeometries(DataStructure& dataStructure)
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{
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UnitTest::CompareImageGeometry(dataStructure, ::k_XFlipImageGeomPath, k_XGeneratedImageGeomPath);
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UnitTest::CompareImageGeometry(dataStructure, ::k_YFlipImageGeomPath, k_YGeneratedImageGeomPath);
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// Processed
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DataPath k_XGeneratedImageDataPath = k_XGeneratedImageGeomPath.createChildPath(Constants::k_Cell_Data).createChildPath(::k_ImageDataName);
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DataPath k_YGeneratedImageDataPath = k_YGeneratedImageGeomPath.createChildPath(Constants::k_Cell_Data).createChildPath(::k_ImageDataName);
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const auto& xGeneratedImageData = dataStructure.getDataRefAs<UInt8Array>(k_XGeneratedImageDataPath);
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const auto& yGeneratedImageData = dataStructure.getDataRefAs<UInt8Array>(k_YGeneratedImageDataPath);
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// Exemplar
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const auto& xFlippedImageData = dataStructure.getDataRefAs<UInt8Array>(k_XFlippedImageDataPath);
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const auto& yFlippedImageData = dataStructure.getDataRefAs<UInt8Array>(k_YFlippedImageDataPath);
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UnitTest::CompareDataArrays<uint8>(xGeneratedImageData, xFlippedImageData);
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UnitTest::CompareDataArrays<uint8>(yGeneratedImageData, yFlippedImageData);
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}
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} // namespace
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TEST_CASE("ITKImageProcessing::ITKImportImageStack: NoInput", "[ITKImageProcessing][ITKImportImageStack]")
@@ -154,3 +294,91 @@ TEST_CASE("ITKImageProcessing::ITKImportImageStack: CompareImage", "[ITKImagePro
154294
const std::string md5Hash = ITKTestBase::ComputeMd5Hash(dataStructure, k_ImageDataPath);
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REQUIRE(md5Hash == "2620b39f0dcaa866602c2591353116a4");
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}
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TEST_CASE("ITKImageProcessing::ITKImportImageStack: Flipped Image Even-Even X/Y", "[ITKImageProcessing][ITKImportImageStack]")
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{
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const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_CMakeExecutable, nx::core::unit_test::k_TestFilesDir, "image_flip_test_images.tar.gz", k_FlippedImageStackDirName);
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const std::string k_FilePrefix = "image_flip_even_even_";
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DataStructure dataStructure;
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// Generate XY Image Geometries with ITKImportImageStack
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::ExecuteImportImageStackXY(dataStructure, k_FilePrefix);
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// Read in exemplars
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::ReadInFlippedXYExemplars(dataStructure, k_FilePrefix);
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#ifdef SIMPLNX_WRITE_TEST_OUTPUT
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UnitTest::WriteTestDataStructure(dataStructure, fmt::format("{}/even_even_import_image_stack_test.dream3d", unit_test::k_BinaryTestOutputDir));
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#endif
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// Compare against exemplars
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::CompareXYFlippedGeometries(dataStructure);
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}
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TEST_CASE("ITKImageProcessing::ITKImportImageStack: Flipped Image Even-Odd X/Y", "[ITKImageProcessing][ITKImportImageStack]")
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{
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const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_CMakeExecutable, nx::core::unit_test::k_TestFilesDir, "image_flip_test_images.tar.gz", k_FlippedImageStackDirName);
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const std::string k_FilePrefix = "image_flip_even_odd_";
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DataStructure dataStructure;
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// Generate XY Image Geometries with ITKImportImageStack
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::ExecuteImportImageStackXY(dataStructure, k_FilePrefix);
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// Read in exemplars
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::ReadInFlippedXYExemplars(dataStructure, k_FilePrefix);
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#ifdef SIMPLNX_WRITE_TEST_OUTPUT
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UnitTest::WriteTestDataStructure(dataStructure, fmt::format("{}/even_odd_import_image_stack_test.dream3d", unit_test::k_BinaryTestOutputDir));
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#endif
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// Compare against exemplars
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::CompareXYFlippedGeometries(dataStructure);
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}
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TEST_CASE("ITKImageProcessing::ITKImportImageStack: Flipped Image Odd-Even X/Y", "[ITKImageProcessing][ITKImportImageStack]")
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{
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const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_CMakeExecutable, nx::core::unit_test::k_TestFilesDir, "image_flip_test_images.tar.gz", k_FlippedImageStackDirName);
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const std::string k_FilePrefix = "image_flip_odd_even_";
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DataStructure dataStructure;
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// Generate XY Image Geometries with ITKImportImageStack
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::ExecuteImportImageStackXY(dataStructure, k_FilePrefix);
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// Read in exemplars
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::ReadInFlippedXYExemplars(dataStructure, k_FilePrefix);
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#ifdef SIMPLNX_WRITE_TEST_OUTPUT
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UnitTest::WriteTestDataStructure(dataStructure, fmt::format("{}/odd_even_import_image_stack_test.dream3d", unit_test::k_BinaryTestOutputDir));
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#endif
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// Compare against exemplars
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::CompareXYFlippedGeometries(dataStructure);
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}
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TEST_CASE("ITKImageProcessing::ITKImportImageStack: Flipped Image Odd-Odd X/Y", "[ITKImageProcessing][ITKImportImageStack]")
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{
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const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_CMakeExecutable, nx::core::unit_test::k_TestFilesDir, "image_flip_test_images.tar.gz", k_FlippedImageStackDirName);
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const std::string k_FilePrefix = "image_flip_odd_odd_";
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DataStructure dataStructure;
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// Generate XY Image Geometries with ITKImportImageStack
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::ExecuteImportImageStackXY(dataStructure, k_FilePrefix);
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// Read in exemplars
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::ReadInFlippedXYExemplars(dataStructure, k_FilePrefix);
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#ifdef SIMPLNX_WRITE_TEST_OUTPUT
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UnitTest::WriteTestDataStructure(dataStructure, fmt::format("{}/odd_odd_import_image_stack_test.dream3d", unit_test::k_BinaryTestOutputDir));
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#endif
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// Compare against exemplars
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::CompareXYFlippedGeometries(dataStructure);
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}

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