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Merge pull request #906 from rordenlab/hanayik/enable-zlib-again
Re-add zlib support and enable jpegls support
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| Original file line number | Diff line number | Diff line change |
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@@ -16,5 +16,5 @@ __pycache__/ | |
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| dist | ||
| node_modules | ||
| dcm2niix.js | ||
| dcm2niix.wasm | ||
| dcm2niix*.js | ||
| dcm2niix*.wasm | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| const esbuild = require('esbuild'); | ||
| const fs = require('fs'); | ||
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| esbuild.build({ | ||
| entryPoints: ['./src/index.jpegls.js'], | ||
| outfile: './dist/index.jpegls.js', | ||
| bundle: true, | ||
| format: 'esm', | ||
| target: ['es2020'], | ||
| minify: false, | ||
| define: { | ||
| 'process.env.NODE_ENV': '"production"', | ||
| }, | ||
| }).then(() => { | ||
| // copy worker.js, dcm2niix.wasm, dcm2niix.js to dist folder | ||
| // (they do not require any processing by esbuild). | ||
| // 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'); | ||
| console.log('Build completed!'); | ||
| }).catch(() => process.exit(1)); |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,315 @@ | ||
| export class Dcm2niix { | ||
| constructor() { | ||
| this.worker = null; | ||
| } | ||
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| init() { | ||
| this.worker = new Worker(new URL('./worker.jpegls.js', import.meta.url), { type: 'module' }); | ||
| return new Promise((resolve, reject) => { | ||
| // handle worker ready message. | ||
| // This gets reassigned in the run() method, | ||
| // but we need to handle the ready message before that. | ||
| // Maybe there is a less hacky way to do this? | ||
| this.worker.onmessage = (event) => { | ||
| if (event.data && event.data.type === 'ready') { | ||
| resolve(true); // Resolve the promise when the worker is ready | ||
| } | ||
| } | ||
|
|
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| // Handle worker init errors. | ||
| this.worker.onerror = (error) => { | ||
| reject(new Error(`Worker failed to load: ${error.message}`)); | ||
| } | ||
| }); | ||
| } | ||
|
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| conformFileList(fileObjectOrArray) { | ||
| // prepare files with their relative paths. | ||
| // annoyingly, safari strips the webkitRelativePath property when sending files to the worker. | ||
| // fileList is a FileList object, not an array, so we need to convert it to an array. | ||
| // filesWithRelativePaths is an array of objects with the file and webkitRelativePath properties. | ||
| // Now we can use the webkitRelativePath property in the worker. | ||
| // This is important for dcm2niix to work with nested dicom directories in safari. | ||
| const filesWithRelativePaths = Array.from(fileObjectOrArray).map((file) => ({ | ||
| file, | ||
| // need to check for both webkitRelativePath and _webkitRelativePath. | ||
| // _webkitRelativePath is used in case the file was not from a webkitdirectory file input element (e.g. from a drop event). | ||
| // IMPORTANT: it is up to other developers to ensure that the special _webkitRelativePath property is set correctly when using drop events. | ||
| webkitRelativePath: file.webkitRelativePath || file._webkitRelativePath || '' | ||
| })); | ||
| return filesWithRelativePaths | ||
| } | ||
|
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| input(fileListObject) { | ||
| const conformedFileList = this.conformFileList(fileListObject); | ||
| return new Processor({ worker: this.worker, fileList: conformedFileList }); | ||
| } | ||
|
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| inputFromWebkitDirectory(fileListObject) { | ||
| const conformedFileList = this.conformFileList(fileListObject); | ||
| return new Processor({ worker: this.worker, fileList: conformedFileList }); | ||
| } | ||
|
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| inputFromDropItems(dataTransferItemArray) { | ||
| const conformedFileList = this.conformFileList(dataTransferItemArray); | ||
| return new Processor({ worker: this.worker, fileList: conformedFileList }); | ||
| } | ||
| } | ||
|
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| class Processor { | ||
| constructor({ worker, fileList }) { | ||
| this.worker = worker; | ||
| this.fileList = fileList; | ||
| this.commands = []; // default to verbose output for testing | ||
| } | ||
|
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| _addCommand(cmd, ...args) { | ||
| this.commands.push(cmd, ...args.map(String)); | ||
| return this; | ||
| } | ||
|
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| // --version | ||
| version() { | ||
| return this._addCommand('--version'); | ||
| } | ||
|
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| // -1..-9 gz compression level (1=fastest..9=smallest, default 6) | ||
| compressionLevel(level) { | ||
| return this._addCommand(`-${level}`); | ||
| } | ||
|
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| // -a adjacent DICOMs (images from same series always in same folder) for faster conversion (n/y, default n) | ||
| a(value) { | ||
| return this._addCommand('-a', value); | ||
| } | ||
| // alias for -a | ||
| adjacent(value) { | ||
| return this.a(value); | ||
| } | ||
|
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| // -b BIDS sidecar (y/n/o [o=only: no NIfTI], default y) | ||
| b(value) { | ||
| return this._addCommand('-b', value); | ||
| } | ||
| // alias for -b | ||
| bids(value) { | ||
| return this.b(value); | ||
| } | ||
|
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| // -ba BIDS anonymize (y/n, default y) | ||
| ba(value) { | ||
| return this._addCommand('-ba', value); | ||
| } | ||
| // alias for -ba | ||
| bidsAnonymize(value) { | ||
| return this.ba(value); | ||
| } | ||
|
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| // -c comment stored as NIfTI aux_file (up to 24 characters) | ||
| c(value) { | ||
| return this._addCommand('-c', value); | ||
| } | ||
| // alias for -c | ||
| comment(value) { | ||
| return this.c(value); | ||
| } | ||
|
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| // -d directory search depth (0..9, default 5) | ||
| // Note: not used in browser/wasm since file list is a flat list | ||
| d(value) { | ||
| return this._addCommand('-d', value); | ||
| } | ||
| // alias for -d | ||
| directorySearchDepth(value) { | ||
| return this.d(value); | ||
| } | ||
|
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| // export as NRRD (y) or MGH (o) or JSON/JNIfTI (j) or BJNIfTI (b) instead of NIfTI (y/n/o/j/b, default n) | ||
| e(value) { | ||
| return this._addCommand('-e', value); | ||
| } | ||
| // alias for -e | ||
| exportFormat(value) { | ||
| return this.e(value); | ||
| } | ||
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| // -f : filename (%a=antenna (coil) name, %b=basename, %c=comments, %d=description, | ||
| // %e=echo number, %f=folder name, %g=accession number, %i=ID of patient, %j=seriesInstanceUID, | ||
| // %k=studyInstanceUID, %m=manufacturer, %n=name of patient, %o=mediaObjectInstanceUID, | ||
| // %p=protocol, %r=instance number, %s=series number, %t=time, %u=acquisition number, | ||
| // %v=vendor, %x=study ID; %z=sequence name; | ||
| // | ||
| // default '%f_%p_%t_%s') | ||
| f(value) { | ||
| return this._addCommand('-f', value); | ||
| } | ||
| // alias for -f | ||
| filenameformat(value) { | ||
| return this.f(value); | ||
| } | ||
|
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| // -i : ignore derived, localizer and 2D images (y/n, default n) | ||
| i(value) { | ||
| return this._addCommand('-i', value); | ||
| } | ||
| // alias for -i | ||
| ignoreDerived(value) { | ||
| return this.i(value); | ||
| } | ||
|
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| // -l : losslessly scale 16-bit integers to use dynamic range (y/n/o [yes=scale, no=no, but uint16->int16, o=original], default o) | ||
| l(value) { | ||
| return this._addCommand('-l', value); | ||
| } | ||
| // alias for -l | ||
| losslessScale(value) { | ||
| return this.l(value); | ||
| } | ||
|
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| // -m : merge 2D slices from same series regardless of echo, exposure, etc. (n/y or 0/1/2, default 2) [no, yes, auto] | ||
| m(value) { | ||
| return this._addCommand('-m', value); | ||
| } | ||
| // alias for -m | ||
| merge2DSlices(value) { | ||
| return this.m(value); | ||
| } | ||
|
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||
| // -n : only convert this series CRC number - can be used up to 16 times (default convert all) | ||
| n(value) { | ||
| return this._addCommand('-n', value); | ||
| } | ||
| // alias for -n | ||
| seriesCRC(value) { | ||
| return this.n(value); | ||
| } | ||
|
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| // -o : output directory (omit to save to input folder) | ||
| // o(value){ | ||
| // return this._addCommand('-o', value); | ||
| // } | ||
| // alias for -o | ||
| // outputDirectory(value){ | ||
| // return this.o(value); | ||
| // } | ||
|
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||
| // -p : Philips precise float (not display) scaling (y/n, default y) | ||
| p(value) { | ||
| return this._addCommand('-p', value); | ||
| } | ||
| // alias for -p | ||
| philipsPreciseFloat(value) { | ||
| return this.p(value); | ||
| } | ||
|
|
||
| // -q : only search directory for DICOMs (y/l/n, default y) [y=show number of DICOMs found, l=additionally list DICOMs found, n=no] | ||
| q(value) { | ||
| return this._addCommand('-q', value); | ||
| } | ||
| // alias for -q | ||
| searchDirectory(value) { | ||
| return this.q(value); | ||
| } | ||
|
|
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| // -r : rename instead of convert DICOMs (y/n, default n) | ||
| r(value) { | ||
| return this._addCommand('-r', value); | ||
| } | ||
| // alias for -r | ||
| renameOnly(value) { | ||
| return this.r(value); | ||
| } | ||
|
|
||
| // -s : single file mode, do not convert other images in folder (y/n, default n) | ||
| s(value) { | ||
| return this._addCommand('-s', value); | ||
| } | ||
| // alias for -s | ||
| singleFileMode(value) { | ||
| return this.s(value); | ||
| } | ||
|
|
||
| // -v : verbose (n/y or 0/1/2, default 0) [no, yes, logorrheic] | ||
| v(value) { | ||
| return this._addCommand('-v', value); | ||
| } | ||
| // alias for -v | ||
| verbose(value) { | ||
| return this.v(value); | ||
| } | ||
|
|
||
| // -w : write behavior for name conflicts (0,1,2, default 2: 0=skip duplicates, 1=overwrite, 2=add suffix) | ||
| w(value) { | ||
| return this._addCommand('-w', value); | ||
| } | ||
| // alias for -w | ||
| writeBehavior(value) { | ||
| return this.w(value); | ||
| } | ||
|
|
||
| // -x : crop 3D acquisitions (y/n/i, default n, use 'i'gnore to neither crop nor rotate 3D acquisitions) | ||
| x(value) { | ||
| return this._addCommand('-x', value); | ||
| } | ||
| // alias for -x | ||
| crop(value) { | ||
| return this.x(value); | ||
| } | ||
|
|
||
| // -z : gz compress images (y/o/i/n/3, default n) [y=pigz, o=optimal pigz, i=internal:miniz, n=no, 3=no,3D] | ||
| z(value) { | ||
| return this._addCommand('-z', value); | ||
| } | ||
| // alias for -z | ||
| gzip(value) { | ||
| return this.z(value); | ||
| } | ||
|
|
||
| // --big-endian : byte order (y/n/o, default o) [y=big-end, n=little-end, o=optimal/native] | ||
| bigEndian(value) { | ||
| return this._addCommand('--big-endian', value); | ||
| } | ||
|
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||
| // --ignore_trigger_times : disregard values in 0018,1060 and 0020,9153 | ||
| ignoreTriggerTimes() { | ||
| return this._addCommand('--ignore_trigger_times'); | ||
| } | ||
|
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| // --terse : omit filename post-fixes (can cause overwrites) | ||
| terse() { | ||
| return this._addCommand('--terse'); | ||
| } | ||
|
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||
| // --xml : Slicer format features | ||
| xml() { | ||
| return this._addCommand('--xml'); | ||
| } | ||
|
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| async run() { | ||
| return new Promise((resolve, reject) => { | ||
| this.worker.onmessage = (e) => { | ||
| if (e.data.type === 'error') { | ||
| reject(new Error(e.data.message)); | ||
| } else { | ||
| // get the output file and the exit code from niimath wasm | ||
| const { convertedFiles, exitCode } = e.data; | ||
| // --version gives exit code 3 in dcm2niix CLI and wasm | ||
| if (exitCode === 0 || exitCode === 3) { | ||
| // success | ||
| resolve(convertedFiles); | ||
| } else { | ||
| // error | ||
| reject(new Error(`dcm2niix processing failed with exit code ${exitCode}`)); | ||
| } | ||
| } | ||
| }; | ||
|
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| const args = [...this.commands]; | ||
| if (this.worker === null) { | ||
| reject(new Error('Worker not initialized. Did you await the init() method?')); | ||
| } | ||
| // send files and commands to the worker | ||
| this.worker.postMessage({ fileList: this.fileList, cmd: args }); | ||
| }); | ||
| } | ||
| } |
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