Merge pull request #489 from thewtex/cbor-file

cbor file

Author: thewtex

.github/workflows/toolchains.yml

@@ -109,51 +109,3 @@ jobs:
         name: docker-cache
         path: ./docker-cache
         retention-days: 7
-
-  build-itk-wasm-vtk-io:
-    name: "Build itk-wasm-vtk-io"
-    needs: build-itk-wasm
-    runs-on: ubuntu-20.04
-
-    steps:
-    - uses: actions/checkout@v2
-
-    - name: 'Free up disk space'
-      run: |
-        # Workaround for https://github.com/actions/virtual-environments/issues/709
-        df -h
-        sudo apt-get remove -y '^dotnet-.*'
-        sudo apt-get remove -y '^llvm-.*'
-        sudo apt-get remove -y 'php.*'
-        sudo apt-get autoremove -y
-        sudo apt-get clean
-        sudo rm -rf "/usr/local/share/boost"
-        sudo rm -rf /usr/share/dotnet/
-        sudo rm -rf "$AGENT_TOOLSDIRECTORY"
-        df -h
-
-    - name: Pull latest Docker images
-      run: |
-        ./src/docker/pull.sh
-
-    - uses: actions/download-artifact@v2
-      continue-on-error: true
-      with:
-        name: docker-cache
-        path: ./docker-cache
-
-    - name: Build itk-wasm-vtk-io
-      run: |
-        if [[ -e ./docker-cache/itk-wasm-emscripten-base.tar.xz ]]; then xz -d -k < ./docker-cache/itk-wasm-emscripten-base.tar.xz | docker load ; fi
-        if [[ -e ./docker-cache/itk-wasm-emscripten.tar.xz ]]; then xz -d -k < ./docker-cache/itk-wasm-emscripten.tar.xz | docker load ; fi
-        if [[ -e ./docker-cache/itk-wasm-emscripten-vtk-io.tar.xz ]]; then xz -d -k < ./docker-cache/itk-wasm-emscripten-vtk-io.tar.xz | docker load ; fi
-        ./src/docker/itk-wasm-vtk-io/build.sh
-        mkdir -p ./docker-cache
-        docker save insighttoolkit/itk-wasm-emscripten-vtk-io:latest | xz -e9 -T0 > ./docker-cache/itk-wasm-emscripten-vtk-io.tar.xz
-
-    - name: Cache docker results
-      uses: actions/upload-artifact@v2
-      with:
-        name: docker-cache
-        path: ./docker-cache
-        retention-days: 7

.npmignore

@@ -8,4 +8,3 @@ test
 build.js
 dist/image-io/
 dist/mesh-io/
-dist/polydata-io/

CMakeLists.txt

@@ -22,23 +22,11 @@ if(BUILD_ITK_WASM_IO_MODULES)
   set(meshios_ITKIOMeshOBJ itkOBJMeshIO)
   set(meshios_ITKIOMeshOFF itkOFFMeshIO)
   set(meshios_IOMeshSTL itkSTLMeshIO)
-
-  set(PolyDataIOPipelines
-    "VTKLegacyFileReader"
-    "VTKXMLFileReader"
-    "VTKExodusFileReader"
-    "VTKPLYFileReader"
-    CACHE STRING
-    "String delimited list of VTK PolyData IO pipelines to support.")
-  set(polydataios_VTKExodusFileReader VTK::IOExodus VTK::CommonDataModel
-    VTK::FiltersCore VTK::FiltersGeometry)
-  set(polydataios_VTKLegacyFileReader VTK::IOLegacy VTK::FiltersGeometry)
-  set(polydataios_VTKXMLFileReader VTK::IOXML VTK::FiltersGeometry VTK::IOLegacy)
-  set(polydataios_VTKPLYFileReader VTK::IOPLY)
 endif()
 
 include(FetchContent)
 set(_itk_build_testing ${BUILD_TESTING})
+set(BUILD_TESTING OFF)
 set(_itk_build_shared ${BUILD_SHARED_LIBS})
 
 # Uses newer CMake
@@ -55,27 +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
@@ -96,12 +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})
@@ -111,11 +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})
@@ -128,6 +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)

README.md

@@ -16,8 +16,8 @@ The project provides tools to a) build C/C++ code to
 JavaScript/Typescript data structures, and traditional file formats, c)
 transfer data efficiently in and out of the WebAssembly runtime, and d)
 asynchronous, parallel execution of processing pipelines in a worker pool.
-*itk-wasm* can be used to execute [ITK](https://www.itk.org/),
-[VTK](https://www.vtk.org/) or arbitrary C++ codes in the browser, on a
+*itk-wasm* can be used to execute [ITK](https://www.itk.org/)
+or arbitrary C++ codes in the browser, on a
 workstation / server with [Node.js](https://nodejs.org/), or standalone
 execution and wrapped in [WASI](https://wasi.dev/) runtimes.
 

build.js

@@ -22,7 +22,6 @@ program
   .option('-s, --no-copy-build-artifacts', 'Do not copy build artifacts')
   .option('-e, --no-build-emscripten-pipelines', 'Do not build the emscripten test pipelines')
   .option('-w, --no-build-wasi-pipelines', 'Do not build the wasi test pipelines')
-  .option('-v, --no-build-vtk', 'Do not build the VTK-dependent io')
   .option('-d, --debug', 'Create a debug build of the Emscripten modules')
   .parse(process.argv)
 
@@ -56,23 +55,14 @@ if (options.buildIo) {
   if (options.debug) {
     dockcross = 'build/dockcross-debug'
   }
-  if (options.buildVtk) {
-    dockcross = `${dockcross}-with-vtk`
-  }
   try {
     fs.statSync(dockcross)
   } catch (err) {
     if (err.code === 'ENOENT') {
       const output = fs.openSync(dockcross, 'w')
       let buildImage = 'itkwasm/emscripten:latest'
-      if (options.buildVtk) {
-        buildImage = 'itkwasm/emscripten-vtk-io:latest'
-      }
       if (options.debug) {
         buildImage = 'itkwasm/emscripten:latest-debug'
-        if (options.buildVtk) {
-          buildImage = 'itkwasm/emscripten-vtk-io:latest-debug'
-        }
       }
       const dockerCall = spawnSync('docker', ['run', '--rm', buildImage], {
         env: process.env,
@@ -97,7 +87,7 @@ if (options.buildIo) {
       if (options.debug) {
         buildType = '-DCMAKE_BUILD_TYPE:STRING=Debug'
       }
-      const cmakeCall = spawnSync('bash', [dockcross, 'bash', '-c', `cmake ${buildType} -Bbuild -H. -GNinja -DITK_DIR=/ITK-build -DVTK_DIR=/VTK-build -DITK_WASM_NO_INTERFACE_LINK=1 -DBUILD_ITK_WASM_IO_MODULES=ON`], {
+      const cmakeCall = spawnSync('bash', [dockcross, 'bash', '-c', `cmake ${buildType} -Bbuild -H. -GNinja -DITK_DIR=/ITK-build -DITK_WASM_NO_INTERFACE_LINK=1 -DBUILD_ITK_WASM_IO_MODULES=ON`], {
         env: process.env,
         stdio: 'inherit'
       })
@@ -137,11 +127,6 @@ if (options.copyBuildArtifacts) {
   } catch (err) {
     if (err.code !== 'EEXIST') throw err
   }
-  try {
-    fs.mkdirSync(path.join('dist', 'polydata-io'))
-  } catch (err) {
-    if (err.code !== 'EEXIST') throw err
-  }
   try {
     fs.mkdirSync(path.join('dist', 'web-workers'))
   } catch (err) {
@@ -174,24 +159,9 @@ if (options.copyBuildArtifacts) {
     callback(null, result)
   }
 
-  let polyDataIOFiles = glob.sync(path.join('build', 'polydata-io', '*.js'))
-  polyDataIOFiles = polyDataIOFiles.concat(glob.sync(path.join('build', 'polydata-io', '*.wasm')))
-  const copyPolyDataIOModules = function (polyDataIOFile, callback) {
-    const io = path.basename(polyDataIOFile)
-    const output = path.join('dist', 'polydata-io', io)
-    fs.copySync(polyDataIOFile, output)
-    callback(null, io)
-  }
-  const buildPolyDataIOsParallel = function (callback) {
-    console.log('Copying polydata-io modules...')
-    const result = asyncMod.map(polyDataIOFiles, copyPolyDataIOModules)
-    callback(null, result)
-  }
-
   asyncMod.parallel([
     buildImageIOsParallel,
     buildMeshIOsParallel,
-    buildPolyDataIOsParallel,
   ])
 } // options.copySources
 
@@ -207,14 +177,8 @@ if (options.buildEmscriptenPipelines) {
     console.log('Building ' + pipelinePath + ' with Emscripten...')
     let debugFlags = []
     let buildImage = 'itkwasm/emscripten:latest'
-    if (options.buildVtk) {
-      buildImage = 'itkwasm/emscripten-vtk-io:latest'
-    }
     if (options.debug) {
       buildImage = 'itkwasm/emscripten:latest-debug'
-      if (options.buildVtk) {
-        buildImage = 'itkwasm/emscripten-vtk-io:latest-debug'
-      }
     }
     if (options.debug) {
       debugFlags = ['-DCMAKE_BUILD_TYPE:STRING=Debug', "-DCMAKE_EXE_LINKER_FLAGS_DEBUG='-s DISABLE_EXCEPTION_CATCHING=0'"]

doc/RELEASE.md

@@ -35,9 +35,6 @@ cd -
 cd dist/mesh-io
 npm publish
 cd -
-cd dist/polydata-io
-npm publish
-cd -
 git tag -m "itk-wasm ${version}" -s itk-wasm-v$version HEAD
 git checkout release
 git merge master

doc/content/api/browser_io.md

@@ -11,12 +11,12 @@ These functions return the [WebWorker](https://developer.mozilla.org/en-US/docs/
 
 ---
 
-## readFile(webWorker: Worker | null, file: File): Promise<{ webWorker, [image](./Image.html), [mesh](./Mesh.html), [polyData](https://insightsoftwareconsortium.github.io/itk-wasm/docs/polydata_formats.html) }>
+## readFile(webWorker: Worker | null, file: File): Promise<{ webWorker, [image](./Image.html), [mesh](./Mesh.html) }>
 
 Read an image or mesh or poly data from a [File](https://developer.mozilla.org/en-US/docs/Web/API/File).
 
 
-## readBlob(webWorker: Worker | null, blob: Blob, fileName: string, mimeType: string): Promise<{ webWorker, [image](./Image.html), [mesh](./Mesh.html), [polyData](https://insightsoftwareconsortium.github.io/itk-wasm/docs/polydata_formats.html) }>
+## readBlob(webWorker: Worker | null, blob: Blob, fileName: string, mimeType: string): Promise<{ webWorker, [image](./Image.html), [mesh](./Mesh.html), }>
 
 Read an image or mesh or poly data from a [Blob](https://developer.mozilla.org/en-US/docs/Web/API/Blob). `fileName` is a string with the file name. `mimeType` is an optional mime-type string.
 
@@ -121,17 +121,3 @@ Write an mesh to a an [ArrayBuffer](https://developer.mozilla.org/en-US/docs/Web
 *mesh*:           [Mesh](./Mesh.html) instance to write
 *fileName*:       name that would be used for the resulting file
 *mimeType*:       optional mime-type for the resulting file
-
----
-
-## readPolyDataFile(webWorker: Worker | null, file: File): Promise<{ webWorker, [polyData](https://kitware.github.io/vtk-js/docs/structures_PolyData.html) }>
-
-Read a vtk.js PolyData from a [File](https://developer.mozilla.org/en-US/docs/Web/API/File).
-
-## readPolyDataBlob(webWorker: Worker | null, blob: Blob, fileName: string, mimeType: string): Promise< { webWorker: Worker, [polyData](https://kitware.github.io/vtk-js/docs/structures_PolyData.html) }>
-
-Read a vtk.js PolyData from a [Blob](https://developer.mozilla.org/en-US/docs/Web/API/Blob). `fileName` is a string with the file name. `mimeType` is an optional mime-type string.
-
-## readPolyDataArrayBuffer(webWorker: Worker | null, arrayBuffer: ArrayBuffer, fileName: string, mimeType: string): Promise<{ webWorker: Worker, [polyData](https://kitware.github.io/vtk-js/docs/structures_PolyData.html) }>
-
-Read a vtk.js PolyData from an [ArrayBuffer](https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/ArrayBuffer). `fileName` is a string with the file name. `mimeType` is an optional mime-type string.

doc/content/api/browser_pipelines.md

@@ -30,7 +30,6 @@ Run an itk-wasm Emscripten module with Node.js.
   <dt>`IOTypes.Binary`</dt><dd>A binary [Uint8Array](https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Uint8Array). To write this data type in C++, read the binary file with, e.g.  [std::ofstream](http://www.cplusplus.com/reference/fstream/ofstream/) with the `std::ofstream::binary` flag to [std::ofstream::open](http://www.cplusplus.com/reference/fstream/ofstream/open/).</dd>
   <dt>`IOTypes.Image`</dt><dd>An [itk/Image](./Image.html). To write this data type in C++, use the [itk::ImageFileWriter](https://itk.org/Doxygen/html/classitk_1_1ImageFileWriter.html), add `WebAssemblyInterface` module to the ITK `find_package` `COMPONENTS` in your *CMakeLists.txt*, and use `.json` for the image file name extension.</dd>
   <dt>`IOTypes.Mesh`</dt><dd>An [itk/Mesh](./Mesh.html). To write this data type in C++, use the [itk::MeshFileWriter](https://itk.org/Doxygen/html/classitk_1_1MeshFileWriter.html), add `WebAssemblyInterface` module to the ITK `find_package` `COMPONENTS` in your *CMakeLists.txt*, and use `.json` for the image file name extension.</dd>
-  <dt>`IOTypes.vtkPolyData`</dt><dd>A vtk.js [PolyData](https://kitware.github.io/vtk-js/docs/structures_PolyData.html). To write this data type in C++, use the [vtkJSONDataSetWriter](https://vtk.org/doc/nightly/html/classvtkJSONDataSetWriter.html), and add `vtkIOExport` module to the VTK `find_package` `COMPONENTS` in your *CMakeLists.txt*</dd>
 </dl>
 
 *inputs*:       A JavaScript Array containing JavaScript objects with three properties: `path`, `type`, and `data`.

doc/content/api/node_io.md

@@ -7,9 +7,9 @@ Similar to the [web browser API](./browser_io.html), most of these functions ret
 
 ---
 
-## readLocalFile(filePath: string): Promise<[Image](./Image.html) | [Mesh](./Mesh.html) | [PolyData](https://insightsoftwareconsortium.github.io/itk-wasm/docs/polydata_formats.html)>
+## readLocalFile(filePath: string): Promise<[Image](./Image.html) | [Mesh](./Mesh.html) >
 
-Read an image or mesh or polyData from a file on the local filesystem.
+Read an image or mesh from a file on the local filesystem.
 
 ## writeLocalFile(useCompression: boolean, imageOrMesh: [Image](./Image.html) | [Mesh](./Mesh.html), filePath: string): Promise<null>
 
@@ -62,9 +62,3 @@ Write a mesh to a file on the local filesystem with Node.js.
 *binaryFileType*: write in an binary as opposed to a ascii format, if possible
 *mesh*:           [Mesh](./Mesh.html) instance to write
 *filePath*:       path to the file on the local filesystem
-
----
-
-## readPolyDataLocalFile(filePath: string): [vtk.js PolyData](https://kitware.github.io/vtk-js/docs/structures_PolyData.html)
-
-Read a vtk.js PolyData from a file on the local filesystem.

doc/content/api/node_pipelines.md

@@ -25,7 +25,6 @@ Run an itk-wasm Emscripten module with Node.js.
   <dt><b>IOTypes.Binary</b><dt><dd>A binary <a href="https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Uint8Array">Uint8Array</a>. To write this data type in C++, read the binary file with, e.g.  <a href="http://www.cplusplus.com/reference/fstream/ofstream/">std::ofstream</a> with the `std::ofstream::binary` flag to <a href="http://www.cplusplus.com/reference/fstream/ofstream/open/">std::ofstream::open</a>.</dd>
   <dt><b>IOTypes.Image</b></dt><dd>An <a href="./Image.html">Image</a>. To write this data type in C++, use the <href a="https://itk.org/Doxygen/html/classitk_1_1ImageFileWriter.html">itk::ImageFileWriter</a>, add `WebAssemblyInterface` module to the ITK `find_package` `COMPONENTS` in your *CMakeLists.txt*, and use `.iwi` for the image file name extension.</dd>
   <dt><b>IOTypes.Mesh</b></dt><dd>An <a href="Mesh.html">Mesh</a>. To write this data type in C++, use the <a href="https://itk.org/Doxygen/html/classitk_1_1MeshFileWriter.html">itk::MeshFileWriter</a>, add `WebAssemblyInterface` module to the ITK `find_package` `COMPONENTS` in your *CMakeLists.txt*, and use `.json` for the image file name extension.</dd>
-  <dt><b>IOTypes.vtkPolyData</b><dt><dd>A vtk.js <a href="https://kitware.github.io/vtk-js/docs/structures_PolyData.html">PolyData</a> To write this data type in C++, use the <a href="https://vtk.org/doc/nightly/html/classvtkJSONDataSetWriter.html">vtkJSONDataSetWriter</a>, and add `vtkIOExport` module to the VTK `find_package` `COMPONENTS` in your *CMakeLists.txt*</dd>
 </dl>
 
 *inputs*:       A JavaScript Array containing JavaScript objects with three properties: `path`, `type`, and `data`.

doc/content/docs/file_formats.md

@@ -1,11 +1,11 @@
 title: ITK WASM File Formats
 ---
 
-While IO modules are available to work with a number of [scientific image](./image_formats.html), [mesh](./mesh_formats.html), and [polydata](./polydata_formats.html), 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.
+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>