ENH: Add Image Reader/Writer that depend on Tiff and Stb libraries.

CMakeLists.txt

@@ -189,6 +189,12 @@ find_package(boost_mp11 CONFIG REQUIRED)
 find_package(nod CONFIG REQUIRED)
 find_package(spdlog CONFIG REQUIRED)
 
+#------------------------------------------------------------------------------
+# Find the Image IO libraries
+#------------------------------------------------------------------------------
+find_package(Stb REQUIRED)
+find_package(TIFF REQUIRED)
+
 # -----------------------------------------------------------------------
 # Find HDF5 and get the path to the DLL libraries and put that into a
 # global property for later install, debugging and packaging
@@ -266,6 +272,7 @@ target_link_libraries(simplnx
     Boost::mp11
     nod::nod
     spdlog::spdlog
+    TIFF::TIFF
 )
 
 if(UNIX)
@@ -573,7 +580,13 @@ set(SIMPLNX_HDRS
   ${SIMPLNX_SOURCE_DIR}/Utilities/MontageUtilities.hpp
   ${SIMPLNX_SOURCE_DIR}/Utilities/SIMPLConversion.hpp
   ${SIMPLNX_SOURCE_DIR}/Utilities/IntersectionUtilities.hpp
-    ${SIMPLNX_SOURCE_DIR}/Utilities/NeighborUtilities.hpp
+  ${SIMPLNX_SOURCE_DIR}/Utilities/NeighborUtilities.hpp
+
+  ${SIMPLNX_SOURCE_DIR}/Utilities/ImageIO/IImageIO.hpp
+  ${SIMPLNX_SOURCE_DIR}/Utilities/ImageIO/ImageMetadata.hpp
+  ${SIMPLNX_SOURCE_DIR}/Utilities/ImageIO/ImageIOFactory.hpp
+  ${SIMPLNX_SOURCE_DIR}/Utilities/ImageIO/StbImageIO.hpp
+  ${SIMPLNX_SOURCE_DIR}/Utilities/ImageIO/TiffImageIO.hpp
 
   ${SIMPLNX_SOURCE_DIR}/Utilities/Math/GeometryMath.hpp
  # ${SIMPLNX_SOURCE_DIR}/Utilities/Math/MatrixMath.hpp
@@ -791,6 +804,10 @@ set(SIMPLNX_SRCS
 
   ${SIMPLNX_SOURCE_DIR}/Utilities/Parsing/Text/CsvParser.cpp
   ${SIMPLNX_SOURCE_DIR}/Utilities/MD5.cpp
+
+  ${SIMPLNX_SOURCE_DIR}/Utilities/ImageIO/ImageIOFactory.cpp
+  ${SIMPLNX_SOURCE_DIR}/Utilities/ImageIO/StbImageIO.cpp
+  ${SIMPLNX_SOURCE_DIR}/Utilities/ImageIO/TiffImageIO.cpp
 )
 
 # Add Core FilterParameters

cmake/Summary.cmake

@@ -58,6 +58,7 @@ message(STATUS "* span-lite (${span-lite_VERSION}) ${span-lite_DIR}")
 message(STATUS "* boost_mp11 (${boost_mp11_VERSION}) ${boost_mp11_DIR}")
 message(STATUS "* nod (${nod_VERSION}) ${nod_DIR}")
 message(STATUS "* reproc++ (${reproc_VERSION}) ${reproc++_DIR}")
+message(STATUS "* stb (${stb_VERSION}) ${stb_DIR}")
 if(SIMPLNX_USE_LOCAL_EBSD_LIB)
     message(STATUS "* EbsdLib: Local repository being used")
 else()

src/Plugins/ITKImageProcessing/src/ITKImageProcessing/Common/ReadImageUtils.hpp

@@ -30,9 +30,16 @@ void ConvertImageToDataStoreAsType(itk::Image<PixelT, Dimension>& image, DataSto
 
   const auto* rawBufferPtr = reinterpret_cast<const T*>(pixelContainer->GetBufferPointer());
 
+  // pixelContainer->Size() returns the number of pixels, not the number of scalar
+  // elements. For multi-component pixel types (e.g. itk::Vector<uint8, 3>), the
+  // underlying scalar buffer contains pixelCount * componentsPerPixel elements.
+  // Multiply by the component count so std::transform iterates over every scalar.
+  const std::size_t componentsPerPixel = itk::NumericTraits<PixelT>::GetLength();
+  const std::size_t totalElements = pixelContainer->Size() * componentsPerPixel;
+
   constexpr auto destMaxV = static_cast<float64>(std::numeric_limits<NewStoreT>::max());
   constexpr auto originMaxV = std::numeric_limits<T>::max();
-  std::transform(rawBufferPtr, rawBufferPtr + pixelContainer->Size(), dataStore.data(), [](auto value) {
+  std::transform(rawBufferPtr, rawBufferPtr + totalElements, dataStore.data(), [](auto value) {
     float64 ratio = static_cast<float64>(value) / static_cast<float64>(originMaxV);
     return static_cast<NewStoreT>(ratio * destMaxV);
   });

src/Plugins/ITKImageProcessing/src/ITKImageProcessing/Filters/ITKImageReaderFilter.cpp

@@ -61,7 +61,7 @@ std::string ITKImageReaderFilter::humanName() const
 //------------------------------------------------------------------------------
 std::vector<std::string> ITKImageReaderFilter::defaultTags() const
 {
-  return {className(), "io", "input", "read", "import"};
+  return {className(), "io", "input", "read", "import", "image", "jpg", "tiff", "bmp", "png"};
 }
 
 //------------------------------------------------------------------------------

src/Plugins/ITKImageProcessing/src/ITKImageProcessing/Filters/ITKImageWriterFilter.cpp

@@ -28,11 +28,10 @@
 #include <cmath>
 #include <filesystem>
 #include <iomanip>
+#include <sstream>
 
 #include "simplnx/Utilities/SIMPLConversion.hpp"
 
-#include <sstream>
-
 namespace fs = std::filesystem;
 
 using namespace nx::core;

src/Plugins/ITKImageProcessing/test/CMakeLists.txt

@@ -132,10 +132,6 @@ if(EXISTS "${DREAM3D_DATA_DIR}" AND SIMPLNX_DOWNLOAD_TEST_FILES)
     file(MAKE_DIRECTORY "${DREAM3D_DATA_DIR}/TestFiles/")
   endif()
   download_test_data(DREAM3D_DATA_DIR ${DREAM3D_DATA_DIR} ARCHIVE_NAME fiji_montage.tar.gz SHA512 70139babc838ce3ab1f5adddfddc86dcc51996e614c6c2d757bcb2e59e8ebdc744dac269233494b1ef8d09397aecb4ccca3384f0a91bb017f2cf6309c4ac40fa)
-  download_test_data(DREAM3D_DATA_DIR ${DREAM3D_DATA_DIR} ARCHIVE_NAME image_flip_test_images.tar.gz SHA512 4e282a270251133004bf4b979d0d064631b618fc82f503184c602c40d388b725f81faf8e77654d285852acc3217d51534c9a71240be4a87a91dc46da7871e7d2)
-  download_test_data(DREAM3D_DATA_DIR ${DREAM3D_DATA_DIR} ARCHIVE_NAME import_image_stack_test.tar.gz SHA512 bec92d655d0d96928f616612d46b52cd51ffa5dbc1d16a64bb79040bbdd3c50f8193350771b177bb64aa68fc0ff7e459745265818c1ea34eb27431426ff15083)
-  download_test_data(DREAM3D_DATA_DIR ${DREAM3D_DATA_DIR} ARCHIVE_NAME import_image_stack_test_v2.tar.gz SHA512 b3600c072ecbdb27ed3ed7298dac88708aa94d1eed21e6b0581b772311d1e3c2c6693713026ae512c86729079b41c629067fb1a7df75697d08dbdf2dfad0f553)
-  download_test_data(DREAM3D_DATA_DIR ${DREAM3D_DATA_DIR} ARCHIVE_NAME itk_image_reader_test.tar.gz SHA512 15c42c913df8e0aebfc4196ea96ed5fdc2fab71daacbaf27287d6aee08483acb37f2f38d88af6c549084bae892b07c7aca8537b2511920d18248c8bc18aab92f)
 endif()
 
 create_pipeline_tests(PLUGIN_NAME ${PLUGIN_NAME} PIPELINE_LIST ${PREBUILT_PIPELINE_NAMES})

src/Plugins/ITKImageProcessing/test/ITKImageReaderTest.cpp

@@ -14,16 +14,16 @@ using namespace nx::core;
 
 namespace
 {
-const std::string k_TestDataDirName = "itk_image_reader_test";
+const std::string k_TestDataDirName = "itk_image_reader_test_v3";
 const fs::path k_TestDataDir = fs::path(unit_test::k_TestFilesDir.view()) / k_TestDataDirName;
-const fs::path k_ExemplarFile = k_TestDataDir / "itk_image_reader_test.dream3d";
+const fs::path k_ExemplarFile = k_TestDataDir / "itk_image_reader_test_v3.dream3d";
 const fs::path k_InputImageFile = k_TestDataDir / "200x200_0.tif";
 const std::string k_ImageDataName = "ImageData";
 } // namespace
 
 TEST_CASE("ITKImageProcessing::ITKImageReaderFilter: Read_Basic", "[ITKImageProcessing][ITKImageReaderFilter]")
 {
-  const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_TestFilesDir, "itk_image_reader_test.tar.gz", k_TestDataDirName);
+  const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_TestFilesDir, "itk_image_reader_test_v3.tar.gz", k_TestDataDirName, true, true);
 
   UnitTest::LoadPlugins();
   ITKImageReaderFilter filter;
@@ -66,7 +66,7 @@ TEST_CASE("ITKImageProcessing::ITKImageReaderFilter: Read_Basic", "[ITKImageProc
 
 TEST_CASE("ITKImageProcessing::ITKImageReaderFilter: Override_Origin", "[ITKImageProcessing][ITKImageReaderFilter]")
 {
-  const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_TestFilesDir, "itk_image_reader_test.tar.gz", k_TestDataDirName);
+  const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_TestFilesDir, "itk_image_reader_test_v3.tar.gz", k_TestDataDirName, true, true);
 
   UnitTest::LoadPlugins();
   ITKImageReaderFilter filter;
@@ -112,7 +112,7 @@ TEST_CASE("ITKImageProcessing::ITKImageReaderFilter: Override_Origin", "[ITKImag
 
 TEST_CASE("ITKImageProcessing::ITKImageReaderFilter: Centering_Origin", "[ITKImageProcessing][ITKImageReaderFilter]")
 {
-  const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_TestFilesDir, "itk_image_reader_test.tar.gz", k_TestDataDirName);
+  const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_TestFilesDir, "itk_image_reader_test_v3.tar.gz", k_TestDataDirName, true, true);
 
   UnitTest::LoadPlugins();
   ITKImageReaderFilter filter;
@@ -156,7 +156,7 @@ TEST_CASE("ITKImageProcessing::ITKImageReaderFilter: Centering_Origin", "[ITKIma
 
 TEST_CASE("ITKImageProcessing::ITKImageReaderFilter: Cropping", "[ITKImageProcessing][ITKImageReaderFilter]")
 {
-  const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_TestFilesDir, "itk_image_reader_test.tar.gz", k_TestDataDirName);
+  const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_TestFilesDir, "itk_image_reader_test_v3.tar.gz", k_TestDataDirName, true, true);
 
   // This block generates every combination of croppingOptions, changeOrigin, and changeSpacing and then the entire test executes for each combination
   std::vector<float64> spacing = {2.0, 2.0, 1.0};
@@ -233,7 +233,7 @@ TEST_CASE("ITKImageProcessing::ITKImageReaderFilter: Cropping", "[ITKImageProces
 
 TEST_CASE("ITKImageProcessing::ITKImageReaderFilter: Override_Spacing", "[ITKImageProcessing][ITKImageReaderFilter]")
 {
-  const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_TestFilesDir, "itk_image_reader_test.tar.gz", k_TestDataDirName);
+  const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_TestFilesDir, "itk_image_reader_test_v3.tar.gz", k_TestDataDirName, true, true);
 
   UnitTest::LoadPlugins();
   ITKImageReaderFilter filter;
@@ -279,7 +279,7 @@ TEST_CASE("ITKImageProcessing::ITKImageReaderFilter: Override_Spacing", "[ITKIma
 
 TEST_CASE("ITKImageProcessing::ITKImageReaderFilter: OriginSpacing_Preprocessed", "[ITKImageProcessing][ITKImageReaderFilter]")
 {
-  const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_TestFilesDir, "itk_image_reader_test.tar.gz", k_TestDataDirName);
+  const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_TestFilesDir, "itk_image_reader_test_v3.tar.gz", k_TestDataDirName, true, true);
 
   UnitTest::LoadPlugins();
   ITKImageReaderFilter filter;
@@ -337,7 +337,7 @@ TEST_CASE("ITKImageProcessing::ITKImageReaderFilter: OriginSpacing_Preprocessed"
 
 TEST_CASE("ITKImageProcessing::ITKImageReaderFilter: OriginSpacing_Postprocessed", "[ITKImageProcessing][ITKImageReaderFilter]")
 {
-  const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_TestFilesDir, "itk_image_reader_test.tar.gz", k_TestDataDirName);
+  const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_TestFilesDir, "itk_image_reader_test_v3.tar.gz", k_TestDataDirName, true, true);
 
   UnitTest::LoadPlugins();
   ITKImageReaderFilter filter;
@@ -396,7 +396,7 @@ TEST_CASE("ITKImageProcessing::ITKImageReaderFilter: OriginSpacing_Postprocessed
 
 TEST_CASE("ITKImageProcessing::ITKImageReaderFilter: DataType_Conversion", "[ITKImageProcessing][ITKImageReaderFilter]")
 {
-  const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_TestFilesDir, "itk_image_reader_test.tar.gz", k_TestDataDirName);
+  const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_TestFilesDir, "itk_image_reader_test_v3.tar.gz", k_TestDataDirName, true, true);
 
   UnitTest::LoadPlugins();
   ITKImageReaderFilter filter;
@@ -443,7 +443,7 @@ TEST_CASE("ITKImageProcessing::ITKImageReaderFilter: DataType_Conversion", "[ITK
 
 TEST_CASE("ITKImageProcessing::ITKImageReaderFilter: Interaction_Crop_DataType", "[ITKImageProcessing][ITKImageReaderFilter]")
 {
-  const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_TestFilesDir, "itk_image_reader_test.tar.gz", k_TestDataDirName);
+  const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_TestFilesDir, "itk_image_reader_test_v3.tar.gz", k_TestDataDirName, true, true);
 
   UnitTest::LoadPlugins();
   ITKImageReaderFilter filter;
@@ -499,7 +499,7 @@ TEST_CASE("ITKImageProcessing::ITKImageReaderFilter: Interaction_Crop_DataType",
 
 TEST_CASE("ITKImageProcessing::ITKImageReaderFilter: Interaction_All", "[ITKImageProcessing][ITKImageReaderFilter]")
 {
-  const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_TestFilesDir, "itk_image_reader_test.tar.gz", k_TestDataDirName);
+  const nx::core::UnitTest::TestFileSentinel testDataSentinel(nx::core::unit_test::k_TestFilesDir, "itk_image_reader_test_v3.tar.gz", k_TestDataDirName, true, true);
 
   UnitTest::LoadPlugins();
   ITKImageReaderFilter filter;