Merge branch 'master' into BumpITKv4.5rc2

.github/workflows/documentation.yml

@@ -0,0 +1,101 @@
+name: Documentation
+
+on:
+  push:
+    branches:
+      - master
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  build-wasm-documentation:
+    runs-on: ubuntu-22.04
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Free Disk Space (Ubuntu)
+      uses: jlumbroso/free-disk-space@main
+
+    - uses: actions/setup-node@v4
+      with:
+        node-version: '20'
+
+    - name: Install
+      uses: pnpm/action-setup@v2
+      with:
+        version: 8
+        run_install: true
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+
+    - name: Build
+      run: |
+        pnpm build
+
+    - name: Build package typescript documentation
+      run: |
+        mkdir -p docs/ts/docs
+        mkdir -p docs//ts/app
+
+        sed "s%      basePath:.*%      basePath: '/ITKMorphologicalContourInterpolation/ts/docs',%" wasm/typescript/index.html > docs/ts/docs/index.html
+        cp wasm/typescript/README.md docs/ts/docs/
+        mkdir -p docs/ts/docs/test/browser/demo-app
+        cp wasm/typescript/test/browser/demo-app/logo.svg docs/ts/docs/test/browser/demo-app/
+
+        pushd wasm/typescript
+        rm -rf demo-app node_modules/.vite
+        export VITE_BASE_URL="/ITKMorphologicalContourInterpolation/ts/app/"
+        pnpm build
+        popd
+        rsync -a wasm/typescript/demo-app/ docs/ts/app/
+
+    - name: Build package python documentation
+      run: |
+        mkdir -p docs/py/docs
+        mkdir -p docs/py/app
+
+        export SPHINX_BASE_URL="/ITKMorphologicalContourInterpolation/py/docs/"
+        pushd wasm/python/itkwasm-morphological-contour-interpolation/docs
+        pip install -r requirements.txt
+        make html
+        popd
+        rsync -a wasm/python/itkwasm-morphological-contour-interpolation/docs/_build/html/ docs/py/docs/
+
+    - name: Upload Pages artifact
+      uses: actions/upload-pages-artifact@v3
+      with:
+        path: docs
+        retention-days: 7
+
+  deploy-gh-pages:
+    needs: build-wasm-documentation
+    runs-on: ubuntu-22.04
+
+    # Grant GITHUB_TOKEN the permissions required to make a Pages deployment
+    permissions:
+      contents: read
+      pages: write      # to deploy to Pages
+      id-token: write   # to verify the deployment originates from an appropriate source
+
+    # Deploy to the github-pages environment
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    steps:
+    - name: Deploy to GitHub Pages
+      id: deployment
+      uses: actions/deploy-pages@v4
+      # with:
+        # preview: true <-> currently not available to the public

.github/workflows/wasm.yml

@@ -0,0 +1,36 @@
+name: WebAssembly
+
+on: [push,pull_request]
+
+jobs:
+  build-wasm:
+    name: "Build WebAssembly"
+    runs-on: ubuntu-22.04
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Free Disk Space (Ubuntu)
+      uses: jlumbroso/free-disk-space@main
+
+    - uses: actions/setup-node@v4
+      with:
+        node-version: '20'
+
+    - name: Install
+      uses: pnpm/action-setup@v2
+      with:
+        version: 8
+        run_install: true
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+
+    - name: Build
+      run: |
+        pnpm build
+
+    - name: Test
+      run: |
+        pnpm test

.gitignore

@@ -26,3 +26,6 @@
 *.exe
 *.out
 *.app
+
+# wasm build
+node_modules/

CMakeLists.txt

@@ -4,12 +4,34 @@ if(POLICY CMP0135)
   cmake_policy(SET CMP0135 NEW)
 endif()
 
+if(CMAKE_CXX_STANDARD EQUAL "11" )
+   message(FATAL_ERROR "CMAKE_CXX_STANDARD:STRING=11 is not supported in ITK version 5.3 and greater.")
+endif()
+
+if(NOT CMAKE_CXX_STANDARD)
+  if (WASI OR EMSCRIPTEN)
+    set(CMAKE_CXX_STANDARD 20) # Supported values are ``14``, ``17``, and ``20``.
+  else()
+    set(CMAKE_CXX_STANDARD 17) # Supported values are ``14``, ``17``, and ``20``.
+  endif()
+endif()
+if(NOT CMAKE_CXX_STANDARD_REQUIRED)
+  set(CMAKE_CXX_STANDARD_REQUIRED ON)
+endif()
+if(NOT CMAKE_CXX_EXTENSIONS)
+  set(CMAKE_CXX_EXTENSIONS OFF)
+endif()
+
 project(MorphologicalContourInterpolation)
 
 if(NOT ITK_SOURCE_DIR)
   find_package(ITK REQUIRED)
   list(APPEND CMAKE_MODULE_PATH ${ITK_CMAKE_DIR})
   include(ITKModuleExternal)
+  if(WASI OR EMSCRIPTEN)
+    set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+    add_subdirectory(wasm)
+  endif()
 else()
   set(ITK_DIR ${CMAKE_BINARY_DIR})
   itk_module_impl()

README.md

@@ -0,0 +1,77 @@
+# ITKMorphologicalContourInterpolation
+
+![Build, test, package](https://github.com/KitwareMedical/ITKMorphologicalContourInterpolation/workflows/Build,%20test,%20package/badge.svg)
+
+[![PyPI](https://img.shields.io/pypi/v/itk-morphologicalcontourinterpolation.svg)](https://pypi.python.org/pypi/itk-morphologicalcontourinterpolation)
+
+[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://github.com/KitwareMedical/ITKMorphologicalContourInterpolation/blob/master/LICENSE)
+
+## Overview
+
+An [ITK](https://itk.org)-based implementation of morphological contour interpolation based off the paper:
+
+Albu AB1, Beugeling T, Laurendeau D.
+"A morphology-based approach for interslice interpolation of anatomical slices from volumetric images."
+IEEE Trans Biomed Eng.
+2008 Aug;55(8):2022-38.
+doi: 10.1109/TBME.2008.921158.
+
+👨‍💻 [`Live API Demo`] ✨
+
+Documentation can be found in the [Insight Journal article](https://www.insight-journal.org/browse/publication/977):
+
+Zukić D., Vicory J., McCormick M., Wisse L., Gerig G., Yushkevich P., Aylward S.
+"ND Morphological Contour Interpolation",
+The Insight Journal. January-December, 2016.
+https://hdl.handle.net/10380/3563
+https://insight-journal.org/browse/publication/977
+
+- 🕮 [`Wasm Python Documentation`] 📚
+- 🕮 [`JavaScript Documentation`] 📚
+
+## Installation
+
+### Python
+
+To install the wasm Python packages:
+
+```sh
+pip install itkwasm-morphological-contour-interpolation
+```
+
+To install the native Python packages:
+
+```sh
+python -m pip install --upgrade pip
+python -m pip install itk-morphologicalcontourinterpolation
+```
+
+### JavaScript
+
+Install the JavaScript/TypeScript package:
+
+```sh
+npm install @itk-wasm/morphological-contour-interpolation
+```
+
+### C++
+
+Since ITK 4.11.0, this module is available in the ITK source tree as a remote module. To enable it, set:
+
+```
+Module_MorphologicalContourInterpolation:BOOL=ON
+```
+
+in ITK's CMake build configuration.
+
+## License
+
+This software is distributed under the Apache 2.0 license. Please see the *LICENSE* file for details.
+
+## Acknowledgements
+
+This work is supported by NIH grant R01 EB014346, "Continued development and maintenance of the ITK-SNAP 3D image segmentation software."
+
+[`Live API Demo`]: https://kitwaremedical.github.io/ITKMorphologicalContourInterpolation/ts/app/
+[`Wasm Python Documentation`]: https://kitwaremedical.github.io/ITKMorphologicalContourInterpolation/py/docs/
+[`JavaScript Documentation`]: https://kitwaremedical.github.io/ITKMorphologicalContourInterpolation/ts/docs/

environment.yml

@@ -0,0 +1,10 @@
+name: morphological-contour-interpolation
+channels:
+  - conda-forge
+dependencies:
+  - pytest
+  - python=3.11
+  - pip
+  - pip:
+    - hatch
+    - itkwasm-image-io

include/itkMorphologicalContourInterpolator.hxx

@@ -713,13 +713,17 @@ MorphologicalContourInterpolator< TImage >::Interpolate1to1( int axis, TImage* o
         }
     }
 
+#if !defined( __wasi__ ) && !defined( __EMSCRIPTEN__ )
   static std::mutex mutexLock;
+#endif
   if ( withinReq ) // else we should not write it
     {
       seqIt.GoToBegin();
       // writing through one RLEImage iterator invalidates all the others
       // so this whole writing loop needs to be serialized
+#if !defined( __wasi__ ) && !defined( __EMSCRIPTEN__ )
       std::lock_guard< std::mutex > mutexHolder( mutexLock );
+#endif
       ImageRegionIterator< TImage > outIt( out, outRegion );
       while ( !outIt.IsAtEnd() )
         {

package.json

@@ -0,0 +1,45 @@
+{
+  "name": "@itk-wasm/morphological-contour-interpolation-build",
+  "version": "1.0.0",
+  "description": "npm scripts to generate itk-wasm artifacts.",
+  "private": true,
+  "type": "module",
+  "itk-wasm": {
+    "typescript-package-name": "@itk-wasm/morphological-contour-interpolation",
+    "typescript-output-dir": "wasm/typescript",
+    "python-package-name": "itkwasm-morphological-contour-interpolation",
+    "python-output-dir": "wasm/python",
+    "package-description": "Morphology-based approach for interslice interpolation of anatomical slices from volumetric images.",
+    "repository": "https://github.com/KitwareMedical/ITKMorphologicalContourInterpolation"
+  },
+  "scripts": {
+    "build": "pnpm build:gen:typescript && pnpm -r build && pnpm build:gen:python",
+    "build:emscripten": "itk-wasm pnpm-script build:emscripten",
+    "build:emscripten:debug": "itk-wasm pnpm-script build:emscripten:debug",
+    "build:wasi": "itk-wasm pnpm-script build:wasi",
+    "build:wasi:debug": "itk-wasm pnpm-script build:wasi:debug",
+    "build:python:wasi": "itk-wasm pnpm-script build:python:wasi",
+    "bindgen:typescript": "itk-wasm pnpm-script bindgen:typescript",
+    "bindgen:python": "itk-wasm pnpm-script bindgen:python",
+    "build:gen:typescript": "itk-wasm pnpm-script build:gen:typescript",
+    "build:gen:python": "itk-wasm pnpm-script build:gen:python",
+    "build:micromamba": "itk-wasm pnpm-script build:micromamba",
+    "build:python:versionSync": "itk-wasm pnpm-script build:python:versionSync",
+    "publish:python": "itk-wasm pnpm-script publish:python",
+    "test": "pnpm test:data:download && pnpm -r test && pnpm test:python",
+    "test:data:download": "echo \"not needed\"",
+    "test:data:pack": "dam pack test/data test/data.tar.gz",
+    "test:python:wasi": "itk-wasm pnpm-script test:python:wasi",
+    "test:python:emscripten": "itk-wasm pnpm-script test:python:emscripten",
+    "test:python:dispatch": "itk-wasm pnpm-script test:python:dispatch",
+    "test:python": "itk-wasm pnpm-script test:python",
+    "test:wasi": "itk-wasm pnpm-script test:wasi -- -V",
+    "clean": "git clean -fdx -e node_modules"
+  },
+  "license": "Apache-2.0",
+  "devDependencies": {
+    "@itk-wasm/dam": "^1.1.0",
+    "@thewtex/setup-micromamba": "^1.9.7",
+    "itk-wasm": "^1.0.0-b.166"
+  }
+}