feat(IO): Use cbor over zip

Author: thewtex

CMakeLists.txt

@@ -26,6 +26,7 @@ endif()
 
 include(FetchContent)
 set(_itk_build_testing ${BUILD_TESTING})
+set(BUILD_TESTING OFF)
 set(_itk_build_shared ${BUILD_SHARED_LIBS})
 
 # Uses newer CMake
@@ -42,27 +43,6 @@ FetchContent_Declare(
   GIT_TAG ${RapidJSON_GIT_TAG}
   )
 
-set(minizip-ng_GIT_REPOSITORY https://github.com/zlib-ng/minizip-ng.git)
-# 3.0.3
-set(minizip-ng_GIT_TAG 0930f1aebebb3554570a94357464f0a67b387c6d)
-option(MZ_COMPAT OFF "Enables compatibility layer")
-option(MZ_ZLIB OFF "Enables ZLIB compression")
-option(MZ_BZIP2 OFF "Enables BZIP2 compression")
-option(MZ_LZMA OFF "Enables LZMA & XZ compression")
-option(MZ_ZSTD OFF "Enables ZSTD compression")
-option(MZ_PKCRYPT OFF "Enables PKWARE traditional encryption")
-option(MZ_WZAES OFF "Enables WinZIP AES encryption")
-option(MZ_OPENSSL OFF "Enables OpenSSL encryption")
-option(MZ_LIBBSD OFF "Build with libbsd for crypto random")
-option(MZ_SIGNING OFF "Enables zip signing support")
-option(MZ_ICONV OFF "Enables iconv string encoding conversion library")
-set(MZ_PROJECT_SUFFIX "-itk" CACHE STRING "Minizip name suffix")
-FetchContent_Declare(
-  minizip-ng
-  GIT_REPOSITORY ${minizip-ng_GIT_REPOSITORY}
-  GIT_TAG ${minizip-ng_GIT_TAG}
-  )
-
 set(CLI11_GIT_REPOSITORY "https://github.com/CLIUtils/CLI11")
 set(CLI11_GIT_REPOSITORY "https://github.com/thewtex/CLI11")
 # v2.1.2 + WASI
@@ -83,12 +63,26 @@ FetchContent_Declare(
   GIT_TAG        ${rang_GIT_TAG}
 )
 
+set(libcbor_GIT_REPOSITORY "https://github.com/PJK/libcbor")
+set(libcbor_GIT_REPOSITORY "https://github.com/thewtex/libcbor")
+set(libcbor_GIT_TAG "de9762657d99ccb4d72c78e49819ea5d2a7a413d")
+FetchContent_Declare(
+  libcbor
+  GIT_REPOSITORY ${libcbor_GIT_REPOSITORY}
+  GIT_TAG        ${libcbor_GIT_TAG}
+)
+set(WITH_TESTS OFF CACHE BOOL "Build libcbor tests")
+set(WITH_EXAMPLES OFF CACHE BOOL "Build libcbor examples")
+
 
-FetchContent_MakeAvailable(rapidjson_lib minizip-ng cli11 rang)
+list(APPEND CMAKE_MODULE_PATH ${libcbor_SOURCE_DIR}/CMakeModules)
+FetchContent_MakeAvailable(rapidjson_lib cli11 rang libcbor)
 set(RapidJSON_INCLUDE_DIR "${rapidjson_lib_SOURCE_DIR}/include")
-set(minizip-ng_INCLUDE_DIR "${minizip-ng_SOURCE_DIR}")
 set(cli11_INCLUDE_DIR "${cli11_SOURCE_DIR}/include")
 set(rang_INCLUDE_DIR "${rang_SOURCE_DIR}/include")
+set(libcbor_INCLUDE_DIR "${libcbor_SOURCE_DIR}/src")
+set(libcbor_EXPORT_DIR "${libcbor_BINARY_DIR}/src")
+set(libcbor_CONFIGURATION_DIR "${libcbor_BINARY_DIR}/")
 
 set(BUILD_TESTING ${_itk_build_testing})
 set(BUILD_SHARED_LIBS ${_itk_build_shared})
@@ -98,11 +92,13 @@ find_path(RapidJSON_INCLUDE_DIR
  )
 set(WebAssemblyInterface_INCLUDE_DIRS
   ${RapidJSON_INCLUDE_DIR}
-  ${minizip-ng_INCLUDE_DIR}
   ${cli11_INCLUDE_DIR}
   ${rang_INCLUDE_DIR}
+  ${libcbor_INCLUDE_DIR}
+  ${libcbor_EXPORT_DIR}
+  ${libcbor_CONFIGURATION_DIR}
   )
-list(APPEND WebAssemblyInterface_LIBRARIES minizip-itk)
+list(APPEND WebAssemblyInterface_LIBRARIES cbor)
 
 get_filename_component(_module_dir "${CMAKE_CURRENT_LIST_FILE}" PATH)
 set(CMAKE_MODULE_PATH "${_module_dir}/CMake/" ${CMAKE_MODULE_PATH})
@@ -115,6 +111,6 @@ if(NOT ITK_SOURCE_DIR)
 else()
   itk_module_impl()
 endif()
-itk_module_target_label(minizip-itk)
-itk_module_target_export(minizip-itk)
-itk_module_target_install(minizip-itk)
+itk_module_target_label(cbor)
+itk_module_target_export(cbor)
+itk_module_target_install(cbor)

doc/content/docs/file_formats.md

@@ -3,9 +3,9 @@ title: ITK WASM File Formats
 
 While IO modules are available to work with a number of [scientific image](./image_formats.html) and [mesh](./mesh_formats.html) file formats, itk-wasm execution pipeline WebAssembly modules only support the ITK WASM File Formats by default. This ensures that size of the WebAssembly pipeline binary is minimal.
 
-The itk-wasm file formats provide performant mapping to the [interface types](./interface_types.html) in a simple JSON + binary array buffer format. The formats can be output in a directory or bundled in a single `.zip` file.
+The itk-wasm file formats provide performant mapping to the [interface types](./interface_types.html) in a simple JSON + binary array buffer format. The formats can be output in a directory or bundled in a single `.cbor` file.
 
 <dl>
-  <dt><b>ITK WASM Image (.iwi,.iwi.zip)</b><dt><dd>Serialization of an [Image](../Image.html).</dd>
-  <dt><b>ITK WASM Mesh (.iwm,.iwm.zip)</b><dt><dd>Serialization of a [Mesh](../Mesh.html), or [PolyData](../PolyData.html).</dd>
-</dl>
+  <dt><b>ITK WASM Image (.iwi,.iwi.cbor)</b><dt><dd>Serialization of an [Image](../Image.html).</dd>
+  <dt><b>ITK WASM Mesh (.iwm,.iwm.cbor)</b><dt><dd>Serialization of a [Mesh](../Mesh.html), or [PolyData](../PolyData.html).</dd>
+</dl>

doc/content/docs/itk_js_to_itk_wasm_migration_guide.md

@@ -121,12 +121,12 @@ Addresses an important issue in image orientation support.
 
 ## Image file format
 
-The JSON file format is replaced by a WASM file format with a different layout. A directory ending in `.iwi` or a `.iwi.zip` file is supported for images and a directory ending in `.iwm` and `.iwm.zip` is supported for meshes.
+The JSON file format is replaced by a WASM file format with a different layout. A directory ending in `.iwi` or a `.iwi.cbor` file is supported for images and a directory ending in `.iwm` and `.iwm.cbor` is supported for meshes.
 
 ## Node Sync functions
 
 Node `*Sync` functions have been removed -- use the equivalent async versions instead.
 
 ## VTK support
 
-The VTK Docker images, VTK PolyData IO, `readPolyDataFile`, `readPolyDataBlob`, `readPolyDataArrayBuffer`, based on VTK were removed.
+The VTK Docker images, VTK PolyData IO, `readPolyDataFile`, `readPolyDataBlob`, `readPolyDataArrayBuffer`, based on VTK were removed.

include/itkWASMImageIO.h

@@ -94,6 +94,9 @@ class WebAssemblyInterface_EXPORT WASMImageIO: public StreamingImageIOBase
     return 0;
   }
 
+  void ReadCBOR(void * buffer = nullptr);
+  void WriteCBOR(const void * buffer = nullptr);
+
 private:
   ITK_DISALLOW_COPY_AND_ASSIGN(WASMImageIO);
 };

include/itkWASMMeshIO.h

@@ -19,10 +19,11 @@
 #define itkWASMMeshIO_h
 #include "WebAssemblyInterfaceExport.h"
 
-
 #include "itkMeshIOBase.h"
 #include <fstream>
 
+#include "cbor.h"
+
 namespace itk
 {
 /** \class WASMMeshIO
@@ -127,8 +128,19 @@ class WebAssemblyInterface_EXPORT WASMMeshIO: public MeshIOBase
   /** Convenient method to read a buffer as binary. Return true on success. */
   bool ReadBufferAsBinary(std::istream & os, void *buffer, SizeValueType numberOfBytesToBeRead);
 
+  bool FileNameIsCBOR();
+  void ReadCBORBuffer(const char * dataName, void * buffer, SizeValueType numberOfBytesToBeRead);
+  void WriteCBORBuffer(const char * dataName, void * buffer, SizeValueType numberOfBytesToWrite, IOComponentEnum ioComponent);
+
+  /** Reads in the mesh information and populates the related buffers. */
+  void ReadCBOR();
+  /** Writes the buffers into the CBOR item and the buffer out to disk. */
+  void WriteCBOR();
+
 private:
   ITK_DISALLOW_COPY_AND_ASSIGN(WASMMeshIO);
+
+  cbor_item_t * m_CBORRoot{ nullptr };
 };
 } // end namespace itk
 

src/docker/itk-wasm-base/Dockerfile

@@ -1,5 +1,5 @@
 ARG BASE_IMAGE=dockcross/web-wasm
-FROM $BASE_IMAGE:20220127-ce9c068
+FROM $BASE_IMAGE:20220222-c383c8e
 ARG BASE_IMAGE
 
 LABEL maintainer="Matt McCormick <[email protected]>"

src/docker/itk-wasm/Dockerfile

@@ -24,7 +24,9 @@ RUN cd / && \
   cmake \
     -G Ninja \
     -DITK_DIR=/ITK-build \
-    -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE} \
+    -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE_DOCKCROSS} \
+    -DBUILD_TESTING:BOOL=OFF \
+    -DSANITIZE:BOOL=OFF \
     -DITK_WASM_NO_INTERFACE_LINK:BOOL=1 \
     -DCMAKE_BUILD_TYPE:STRING=$CMAKE_BUILD_TYPE \
       ../ITKWebAssemblyInterface && \

src/io/getFileExtension.ts

@@ -3,6 +3,9 @@ function getFileExtension (filePath: string): string {
   if (extension.toLowerCase() === 'gz') {
     const index = filePath.slice(0, -3).lastIndexOf('.')
     extension = filePath.slice((index - 1 >>> 0) + 2)
+  } else if (extension.toLowerCase() === 'cbor') {
+    const index = filePath.slice(0, -5).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

@@ -16,7 +16,7 @@ const extensionToIO = new Map([
   ['JPEG', 'itkJPEGImageIO'],
 
   ['iwi', 'itkWASMImageIO'],
-  ['iwi.zip', 'itkWASMImageIO'],
+  ['iwi.cbor', 'itkWASMImageIO'],
 
   ['lsm', 'itkLSMImageIO'],