feat(WASMZstdImageIO): Add support for .iwi.cbor.zstd

Fast, high compression ratio binary storage for Image's.

Author: thewtex

CMakeLists.txt

@@ -73,6 +73,7 @@ FetchContent_Declare(
 )
 set(WITH_TESTS OFF CACHE BOOL "Build libcbor tests")
 set(WITH_EXAMPLES OFF CACHE BOOL "Build libcbor examples")
+set(SANITIZE OFF CACHE BOOL "Enable sanitizers in Debug mode in libcbor")
 
 list(APPEND CMAKE_MODULE_PATH ${libcbor_SOURCE_DIR}/CMakeModules)
 FetchContent_MakeAvailable(rapidjson_lib cli11 rang libcbor)

include/itkWASMImageIO.h

@@ -27,11 +27,13 @@ namespace itk
 {
 /** \class WASMImageIO
  *
- * \brief Read and write the an itk::Image in  format.
+ * \brief Read and write an itk::Image in a web-friendly format.
  *
- * This format is intended to facilitage data exchange in itk-wasm.
- * It reads and writes an itk-wasm Image object where TypedArrays are
- * replaced by binary files on the file system or in a ZIP file.
+ * This format is intended to facilitate data exchange in itk-wasm.
+ * It reads and writes an itk-wasm Image object in a CbOR file on the
+ * filesystem with JSON files and binary files for TypedArrays.
+ * 
+ * The file extensions used are .iwi and .iwi.cbor.
  *
  * \ingroup IOFilters
  * \ingroup WebAssemblyInterface
@@ -94,8 +96,8 @@ class WebAssemblyInterface_EXPORT WASMImageIO: public StreamingImageIOBase
     return 0;
   }
 
-  void ReadCBOR(void * buffer = nullptr);
-  void WriteCBOR(const void * buffer = nullptr);
+  void ReadCBOR(void * buffer = nullptr, unsigned char * cborBuffer = nullptr, size_t cborBufferLength = 0);
+  size_t WriteCBOR(const void * buffer = nullptr, unsigned char ** cborBuffer = nullptr, bool allocateCBORBuffer = false);
 
 private:
   ITK_DISALLOW_COPY_AND_ASSIGN(WASMImageIO);

src/CMakeLists.txt

@@ -29,6 +29,7 @@ if(BUILD_ITK_WASM_IO_MODULES)
 set(common_link_flags " -s ALLOW_MEMORY_GROWTH=1 -s FORCE_FILESYSTEM=1 -s MODULARIZE=1 -s WASM=1 -lnodefs.js -s EXIT_RUNTIME=0 -s INVOKE_RUN=1 --post-js ${CMAKE_CURRENT_SOURCE_DIR}/emscripten-module/itkJSPost.js")
 set(esm_link_flags " -s EXPORT_ES6=1 -s USE_ES6_IMPORT_META=0")
 
+include(${CMAKE_CURRENT_SOURCE_DIR}/io/internal/pipelines/common/CompressStringify/BuildZstd.cmake)
 add_subdirectory(io/internal/pipelines/common/CompressStringify)
 add_subdirectory(io/internal/pipelines/image/ConvertImage)
 add_subdirectory(io/internal/pipelines/image/ReadDICOM)

src/io/getFileExtension.ts

@@ -6,6 +6,10 @@ function getFileExtension (filePath: string): string {
   } else if (extension.toLowerCase() === 'cbor') {
     const index = filePath.slice(0, -5).lastIndexOf('.')
     extension = filePath.slice((index - 1 >>> 0) + 2)
+  } else if (extension.toLowerCase() === 'zstd') {
+    // .iwi.cbor.zstd
+    const index = filePath.slice(0, -10).lastIndexOf('.')
+    extension = filePath.slice((index - 1 >>> 0) + 2)
   } else if (extension.toLowerCase() === 'zip') {
     const index = filePath.slice(0, -4).lastIndexOf('.')
     extension = filePath.slice((index - 1 >>> 0) + 2)

src/io/internal/extensionToImageIO.ts

@@ -17,6 +17,7 @@ const extensionToIO = new Map([
 
   ['iwi', 'itkWASMImageIO'],
   ['iwi.cbor', 'itkWASMImageIO'],
+  ['iwi.cbor.zstd', 'itkWASMZstdImageIO'],
 
   ['lsm', 'itkLSMImageIO'],
 

src/io/internal/pipelines/common/CompressStringify/BuildZstd.cmake

@@ -0,0 +1,25 @@
+include(FetchContent)
+option(ZSTD_BUILD_CONTRIB "BUILD_CONTRIB" OFF)
+option(ZSTD_BUILD_PROGRAMS "BUILD_PROGRAMS" OFF)
+option(ZSTD_BUILD_SHARED "BUILD_SHARED" OFF)
+option(ZSTD_BUILD_STATIC "BUILD_STATIC" ON)
+option(ZSTD_BUILD_TESTS "BUILD_TESTS" OFF)
+option(ZSTD_BUILD_LEGACY_SUPPORT "BUILD_LEGACY_SUPPORT" OFF)
+option(ZSTD_MULTITHREAD_SUPPORT "BUILD_MULTITHREAD_SUPPORT" OFF)
+option(ZSTD_BUILD_PROGRAMS_LINK_SHARED "BUILD_PROGRAMS_LINK_SHARED" OFF)
+option(ZSTD_BUILD_LZ4 "BUILD_LZ4" OFF)
+option(ZSTD_BUILD_LZMA "BUILD_LZMA" OFF)
+option(ZSTD_BUILD_ZLIB "BUILD_ZLIB" OFF)
+set(zstd_GIT_REPOSITORY "https://github.com/facebook/zstd.git")
+# v1.5.2
+set(zstd_GIT_TAG c9c7be85f49f45a581ec00c309afda5c62ba9ef2)
+FetchContent_Declare(
+  zstd_lib
+  GIT_REPOSITORY ${zstd_GIT_REPOSITORY}
+  GIT_TAG        ${zstd_GIT_TAG}
+)
+
+FetchContent_MakeAvailable(zstd_lib)
+set(zstd_lib_INCLUDE_DIR "${zstd_lib_SOURCE_DIR}/lib")
+include_directories(${zstd_lib_INCLUDE_DIR})
+add_subdirectory("${zstd_lib_SOURCE_DIR}/build/cmake" "${zstd_lib_BINARY_DIR}")

src/io/internal/pipelines/common/CompressStringify/CMakeLists.txt

@@ -4,25 +4,9 @@ project(CompressStringify)
 set(CMAKE_CXX_STANDARD 17)
 
 include(FetchContent)
-option(ZSTD_BUILD_CONTRIB "BUILD_CONTRIB" OFF)
-option(ZSTD_BUILD_PROGRAMS "BUILD_PROGRAMS" OFF)
-option(ZSTD_BUILD_SHARED "BUILD_SHARED" OFF)
-option(ZSTD_BUILD_STATIC "BUILD_STATIC" ON)
-option(ZSTD_BUILD_TESTS "BUILD_TESTS" OFF)
-option(ZSTD_BUILD_LEGACY_SUPPORT "BUILD_LEGACY_SUPPORT" OFF)
-option(ZSTD_MULTITHREAD_SUPPORT "BUILD_MULTITHREAD_SUPPORT" OFF)
-option(ZSTD_BUILD_PROGRAMS_LINK_SHARED "BUILD_PROGRAMS_LINK_SHARED" OFF)
-option(ZSTD_BUILD_LZ4 "BUILD_LZ4" OFF)
-option(ZSTD_BUILD_LZMA "BUILD_LZMA" OFF)
-option(ZSTD_BUILD_ZLIB "BUILD_ZLIB" OFF)
-set(zstd_GIT_REPOSITORY "https://github.com/facebook/zstd.git")
-# v1.5.2
-set(zstd_GIT_TAG c9c7be85f49f45a581ec00c309afda5c62ba9ef2)
-FetchContent_Declare(
-  zstd_lib
-  GIT_REPOSITORY ${zstd_GIT_REPOSITORY}
-  GIT_TAG        ${zstd_GIT_TAG}
-)
+if (NOT TARGET libzstd_static)
+  include(${CMAKE_CURRENT_SOURCE_DIR}/BuildZstd.cmake)
+endif()
 
 set(cpp_base64_GIT_REPOSITORY "https://github.com/thewtex/cpp-base64.git")
 set(cpp_base64_GET_TAG 9144cd53be930b37235ae552a92b5d2aa51e9325)
@@ -32,11 +16,7 @@ FetchContent_Declare(
   GIT_TAG        ${cpp_base64_GIT_TAG}
 )
 
-FetchContent_MakeAvailable(zstd_lib cpp_base64)
-set(zstd_lib_INCLUDE_DIR "${zstd_lib_SOURCE_DIR}/lib")
-include_directories(${zstd_lib_INCLUDE_DIR})
-# message(FATAL_ERROR "${zstd_lib_INCLUDE_DIR}")
-add_subdirectory("${zstd_lib_SOURCE_DIR}/build/cmake" "${zstd_lib_BINARY_DIR}")
+FetchContent_MakeAvailable(cpp_base64)
 
 find_package(ITK REQUIRED COMPONENTS WebAssemblyInterface)
 include(${ITK_USE_FILE})

src/io/internal/pipelines/image/ConvertImage/CMakeLists.txt

@@ -3,6 +3,10 @@ project(ConvertImage)
 
 set(CMAKE_CXX_STANDARD 17)
 
+if (NOT TARGET libzstd_static)
+  include(${CMAKE_CURRENT_SOURCE_DIR}/../../common/CompressStringify/BuildZstd.cmake)
+endif()
+
 # This list should be ordered from approximately most commonly to least
 # commonly used modules.
 set(WebAssemblyInterface_ImageIOModules
@@ -86,8 +90,9 @@ set(imageio_id_itkScancoImageIO 19)
 set(imageios_IOFDF itkFDFImageIO)
 set(imageio_id_itkFDFImageIO 20)
 
-set(imageios_WebAssemblyInterface itkWASMImageIO)
+set(imageios_WebAssemblyInterface itkWASMImageIO itkWASMZstdImageIO)
 set(imageio_id_itkWASMImageIO 21)
+set(imageio_id_itkWASMZstdImageIO 22)
 
 set(ITK_NO_IO_FACTORY_REGISTER_MANAGER 1)
 set(ImageIOIndex_ARRAY "")
@@ -97,6 +102,7 @@ foreach(io_module ${WebAssemblyInterface_ImageIOModules} WebAssemblyInterface)
       find_package(ITK REQUIRED COMPONENTS ITKIOImageBase)
       include(${ITK_USE_FILE})
       include_directories(${WebAssemblyInterface_INCLUDE_DIRS})
+      include_directories(${CMAKE_CURRENT_SOURCE_DIR})
       list(APPEND ITK_LIBRARIES ${WebAssemblyInterface_LIBRARIES})
     else()
       find_package(ITK REQUIRED COMPONENTS ${io_module} WebAssemblyInterface)
@@ -112,11 +118,16 @@ foreach(io_module ${WebAssemblyInterface_ImageIOModules} WebAssemblyInterface)
   endif()
   foreach(imageio ${imageios_${io_module}})
     set(ImageIOIndex_ARRAY "${ImageIOIndex_ARRAY}'${imageio}', ")
+    set(extra_srcs)
+    if(${imageio} STREQUAL "itkWASMZstdImageIO")
+      list(APPEND ITK_LIBRARIES libzstd_static)
+      list(APPEND extra_srcs itkWASMZstdImageIO.cxx)
+    endif()
 
-    add_executable(${imageio}ReadImage ReadImage.cxx)
+    add_executable(${imageio}ReadImage ReadImage.cxx ${extra_srcs})
     target_link_libraries(${imageio}ReadImage PUBLIC ${ITK_LIBRARIES})
     target_compile_definitions(${imageio}ReadImage PUBLIC -DIMAGE_IO_CLASS=${imageio_id_${imageio}})
-    add_executable(${imageio}WriteImage WriteImage.cxx)
+    add_executable(${imageio}WriteImage WriteImage.cxx ${extra_srcs})
     target_link_libraries(${imageio}WriteImage PUBLIC ${ITK_LIBRARIES})
     target_compile_definitions(${imageio}WriteImage PUBLIC -DIMAGE_IO_CLASS=${imageio_id_${imageio}})
     if (EMSCRIPTEN AND DEFINED WebAssemblyInterface_BINARY_DIR)

src/io/internal/pipelines/image/ConvertImage/ReadImage.cxx

@@ -87,6 +87,8 @@
 #elif IMAGE_IO_CLASS == 20
 #include "itkFDFImageIO.h"
 #elif IMAGE_IO_CLASS == 21
+#elif IMAGE_IO_CLASS == 22
+#include "itkWASMZstdImageIO.h"
 #else
 #error "Unsupported IMAGE_IO_CLASS"
 #endif
@@ -176,6 +178,8 @@ int main (int argc, char * argv[])
   return readImage<itk::FDFImageIO>(inputFileName, outputImageIO, quiet);
 #elif IMAGE_IO_CLASS == 21
   return readImage<itk::WASMImageIO>(inputFileName, outputImageIO, quiet);
+#elif IMAGE_IO_CLASS == 22
+  return readImage<itk::WASMZstdImageIO>(inputFileName, outputImageIO, quiet);
 #else
 #error "Unsupported IMAGE_IO_CLASS"
 #endif

src/io/internal/pipelines/image/ConvertImage/WriteImage.cxx

@@ -87,6 +87,8 @@
 #elif IMAGE_IO_CLASS == 20
 #include "itkFDFImageIO.h"
 #elif IMAGE_IO_CLASS == 21
+#elif IMAGE_IO_CLASS == 22
+#include "itkWASMZstdImageIO.h"
 #else
 #error "Unsupported IMAGE_IO_CLASS"
 #endif
@@ -212,6 +214,8 @@ int main (int argc, char * argv[])
   return writeImage<itk::FDFImageIO>(inputImageIO, outputFileName, quiet, useCompression);
 #elif IMAGE_IO_CLASS == 21
   return writeImage<itk::WASMImageIO>(inputImageIO, outputFileName, quiet, useCompression);
+#elif IMAGE_IO_CLASS == 22
+  return writeImage<itk::WASMZstdImageIO>(inputImageIO, outputFileName, quiet, useCompression);
 #else
 #error "Unsupported IMAGE_IO_CLASS"
 #endif