Add wasm jpegls and j2k/htj2k support

.gitattributes

@@ -0,0 +1,2 @@
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML linguist-generated=true

.gitignore

@@ -18,3 +18,10 @@ dist
 node_modules
 dcm2niix*.js
 dcm2niix*.wasm
+
+# pixi environments
+.pixi
+*.egg-info
+
+*.tar.gz
+openjpeg-2.5.3/

console/makefile

@@ -72,7 +72,7 @@ wasm:
 	emcc -O3 $(UFILES) -lz -s USE_ZLIB -s DEMANGLE_SUPPORT=1 -s EXPORTED_RUNTIME_METHODS='["callMain", "ccall", "cwrap", "FS", "FS_createDataFile", "FS_readFile", "FS_unlink", "allocateUTF8", "getValue", "stringToUTF8", "setValue"]' -s STACK_OVERFLOW_CHECK=2 -s STACK_SIZE=16MB -s ALLOW_MEMORY_GROWTH=1 -s WASM=1 -s EXPORT_ES6=1 -s MODULARIZE=1 -s EXPORTED_FUNCTIONS='["_main", "_malloc", "_free"]' -s FORCE_FILESYSTEM=1 -s INVOKE_RUN=0 -o ../js/src/dcm2niix.js
 	# STACK_SIZE=16MB is the minimum value found to work with the current codebase when targeting WASM
 
-wasm-jpegls:
-	emcc -O3 $(JFLAGS) $(UFILES) -lz -s USE_ZLIB -s DEMANGLE_SUPPORT=1 -s EXPORTED_RUNTIME_METHODS='["callMain", "ccall", "cwrap", "FS", "FS_createDataFile", "FS_readFile", "FS_unlink", "allocateUTF8", "getValue", "stringToUTF8", "setValue"]' -s STACK_OVERFLOW_CHECK=2 -s STACK_SIZE=16MB -s ALLOW_MEMORY_GROWTH=1 -s WASM=1 -s EXPORT_ES6=1 -s MODULARIZE=1 -s EXPORTED_FUNCTIONS='["_main", "_malloc", "_free"]' -s FORCE_FILESYSTEM=1 -s INVOKE_RUN=0 -o ../js/src/dcm2niix.jpegls.js
+wasm-jpeg:
+	emcc -O3 $(JFLAGS) $(CFILES) -DUSE_OPENJPEG -I${PIXI_PROJECT_ROOT}/openjpeg-2.5.3/src/lib/openjp2/ -I${PIXI_PROJECT_ROOT}/openjpeg-2.5.3/build/src/lib/openjp2/ -L${PIXI_PROJECT_ROOT}/openjpeg-2.5.3/build/bin/ -lopenjp2 -lz -s USE_ZLIB -s DEMANGLE_SUPPORT=1 -s EXPORTED_RUNTIME_METHODS='["callMain", "ccall", "cwrap", "FS", "FS_createDataFile", "FS_readFile", "FS_unlink", "allocateUTF8", "getValue", "stringToUTF8", "setValue"]' -s STACK_OVERFLOW_CHECK=2 -s STACK_SIZE=16MB -s ALLOW_MEMORY_GROWTH=1 -s WASM=1 -s EXPORT_ES6=1 -s MODULARIZE=1 -s EXPORTED_FUNCTIONS='["_main", "_malloc", "_free"]' -s FORCE_FILESYSTEM=1 -s INVOKE_RUN=0 -o ../js/src/dcm2niix.jpeg.js
 	# STACK_SIZE=16MB is the minimum value found to work with the current codebase when targeting WASM
 

js/README.md

@@ -15,6 +15,9 @@ The `@niivue/dcm2niix` JavaScript library offers an object oriented API for work
 // <input type="file" id="fileInput" webkitdirectory multiple>
 import { Dcm2niix } from '@niivue/dcm2niix';
 
+// use the jpeg import to load jpegls and j2k build of dcm2niix
+// import { Dcm2niix } from '@niivue/dcm2niix/jpeg';
+
 const dcm2niix = new Dcm2niix();
 // call the init() method to load the wasm before processing any data
 await dcm2niix.init();
@@ -66,6 +69,31 @@ npm install /path/to/niivue-dcm2niix.tgz
 
 ## Development
 
+### Environment setup
+
+You will need:
+- NodeJS/NPM
+- Emscripten
+- Pixi
+- Make/Cmake
+
+[Pixi](https://prefix.dev/) is used to create the environment for building the WASM port of `dcm2niix`. To install pixi, follow their instructions. 
+
+> Note: on macos-arm64, you can get emscripten using homebrew since there is not yet a native arm64 version of emscripten on conda-forge (which is where pixi searches for packages).
+
+### Building dcm2niix WASM
+
+```bash
+pixi run wasm
+```
+
+### clean up after build
+
+```bash
+pixi run clean
+```
+
+### If doing things manually
 First `cd` into the `js` directory of the `dcm2niix` repository.
 
 ```bash

js/esbuild.config.jpegls.js → js/esbuild.config.jpeg.js

@@ -2,8 +2,8 @@ const esbuild = require('esbuild');
 const fs = require('fs');
 
 esbuild.build({
-  entryPoints: ['./src/index.jpegls.js'],
-  outfile: './dist/index.jpegls.js',
+  entryPoints: ['./src/index.jpeg.js'],
+  outfile: './dist/index.jpeg.js',
   bundle: true,
   format: 'esm',
   target: ['es2020'],
@@ -17,8 +17,8 @@ esbuild.build({
   // Technically, none of the files in the src folder require processing by esbuild, 
   // but it does allow minification (optional), and ES version target specification if needed.
   // In the future, if we use Typescript, we can use esbuild to transpile the Typescript to JS.
-  fs.copyFileSync('./src/worker.jpegls.js', './dist/worker.jpegls.js');
-  fs.copyFileSync('./src/dcm2niix.jpegls.wasm', './dist/dcm2niix.jpegls.wasm');
-  fs.copyFileSync('./src/dcm2niix.jpegls.js', './dist/dcm2niix.jpegls.js');
+  fs.copyFileSync('./src/worker.jpeg.js', './dist/worker.jpeg.js');
+  fs.copyFileSync('./src/dcm2niix.jpeg.wasm', './dist/dcm2niix.jpeg.wasm');
+  fs.copyFileSync('./src/dcm2niix.jpeg.js', './dist/dcm2niix.jpeg.js');
   console.log('Build completed!');
 }).catch(() => process.exit(1));

js/index.html

@@ -18,9 +18,9 @@ <h1>dcm2niix WASM Demo</h1>
   <a id="downloadLink" style="display: none;">Download Processed Image(s)</a>
 
   <script type="module">
-    import { Dcm2niix } from './dist/index.js';
+    // import { Dcm2niix } from './dist/index.js';
     // use below line for jpegls version
-    // import { Dcm2niix } from './dist/index.jpegls.js';
+    import { Dcm2niix } from './dist/index.jpeg.js';
 
     const fileInput = document.getElementById('fileInput');
     const processButton = document.getElementById('processButton');
@@ -52,7 +52,7 @@ <h1>dcm2niix WASM Demo</h1>
       }
       const dcm2niix = new Dcm2niix();
       await dcm2niix.init()
-      const resultFileList = await dcm2niix.inputFromDropItems(files).run()
+      const resultFileList = await dcm2niix.inputFromDropItems(files).v().run()
 
       resultFileList.forEach((resultFile, index) => {
           let url = URL.createObjectURL(resultFile);

js/package.json

@@ -7,19 +7,20 @@
     ".": {
       "import": "./dist/index.js"
     },
-    "./with-jpegls": {
-      "import": "./dist/index.jpegls.js"
+    "./jpeg": {
+      "import": "./dist/index.jpeg.js"
     }
   },
   "scripts": {
     "test": "echo \"Error: no test specified\" && exit 1",
-    "build": "node esbuild.config.js && node esbuild.config.jpegls.js",
+    "build": "node esbuild.config.js && node esbuild.config.jpeg.js",
     "makeWasm": "make wasm -C ../console",
-    "makeWasmJpegls": "JPEGLS=1 make wasm-jpegls -C ../console",
+    "makeWasmJpeg": "JPEGLS=1 make wasm-jpeg -C ../console",
     "fixWasmJs": "node scripts/pre-build.js -i src/dcm2niix.js -o src/dcm2niix.js",
-    "fixWasmJsJpegls": "node scripts/pre-build.js -i src/dcm2niix.jpegls.js -o src/dcm2niix.jpegls.js",
-    "prebuild": "npm run makeWasm && npm run makeWasmJpegls && npm run fixWasmJs && npm run fixWasmJsJpegls",
+    "fixWasmJsJpeg": "node scripts/pre-build.js -i src/dcm2niix.jpeg.js -o src/dcm2niix.jpeg.js",
+    "prebuild": "npm run makeWasm && npm run makeWasmJpeg && npm run fixWasmJs && npm run fixWasmJsJpeg",
     "demo": "npm run build && npx http-server .",
+    "demo-no-build": "npx http-server .",
     "pub": "npm run build && npm publish --access public"
   },
   "keywords": [

js/src/index.jpegls.js → js/src/index.jpeg.js

@@ -4,7 +4,7 @@ export class Dcm2niix {
   }
 
   init() {
-    this.worker = new Worker(new URL('./worker.jpegls.js', import.meta.url), { type: 'module' });
+    this.worker = new Worker(new URL('./worker.jpeg.js', import.meta.url), { type: 'module' });
     return new Promise((resolve, reject) => {
       // handle worker ready message.
       // This gets reassigned in the run() method, 

js/src/worker.jpegls.js → js/src/worker.jpeg.js

@@ -2,7 +2,7 @@
 // The worker is of type "module" so that it can use ES6 module syntax.
 // Importantly, the emscripten code must be compiled with: -s EXPORT_ES6=1 -s MODULARIZE=1.
 // This allows proper module bundlers to import the worker and wasm properly with code splitting. 
-import Module from './dcm2niix.jpegls.js';
+import Module from './dcm2niix.jpeg.js';
 
 // initialise an instance of the Emscripten Module so that
 // it is ready when the worker receives a message.