Feat/htj2k (RadicalImaging#26)

* feat(htj2k):Write single part and multipart HTJ2K images

* Fix the unit tests and lint changes

* Moved things arounnd so it can be used by test code

Author: wayfarer3130

package.json

@@ -26,6 +26,8 @@
     "prettier-eslint": "^13.0.0"
   },
   "dependencies": {
+    "@cornerstonejs/codec-openjph": "^1.0.3",
+    "@cornerstonejs/dicom-codec": "^0.1.5",
     "husky": "^7.0.4"
   },
   "workspaces": [

packages/s3-deploy/lib/S3Ops.mjs

@@ -7,7 +7,6 @@ import path from "path";
 import copyTo from "./copyTo.mjs";
 
 const compressedRe = /((\.br)|(\.gz))$/;
-const indexRe = /\/index\.[a-zA-Z]*$/;
 
 const octetStream = "application/octet-stream";
 const multipartRelated = "multipart/related";
@@ -50,7 +49,7 @@ class S3Ops {
       fileName = `${this.group.path}${fileName}`;
     }
     const indexPos = fileName.lastIndexOf("/index");
-    if (indexPos!==-1 && fileName.indexOf('/',indexPos+1)==-1) {
+    if (indexPos !== -1 && fileName.indexOf("/", indexPos + 1) == -1) {
       fileName = fileName.substring(0, indexPos);
     }
     if (fileName[0] == "/") {
@@ -137,7 +136,7 @@ class S3Ops {
       console.log("result=", result);
       return result?.Contents;
     } catch (e) {
-      console.log("Error sending", Bucket, Key, e);
+      console.log("Error sending", Bucket, s3Uri, e);
       console.log("e=", e);
       return null;
     }

packages/static-wado-creator/lib/DeleteStudy.js

@@ -1,6 +1,6 @@
 const { JSONReader } = require("@radicalimaging/static-wado-util");
 const { JSONWriter } = require("@radicalimaging/static-wado-util");
-const Tags = require("./dictionary/Tags");
+const { Tags } = require("@radicalimaging/static-wado-util");
 
 module.exports = (options) =>
   async function (studyInstanceUid) {

packages/static-wado-creator/lib/mkdicomwebConfig.js

@@ -25,17 +25,26 @@ const { mkdicomwebConfig } = ConfigPoint.register({
         description: "Clean the outputs before generating/starting to write new values.",
         defaultValue: false,
       },
+      {
+        key: "-d, --deployments <listvalue...>",
+        description: "List of deployments from configuration to deploy to. Separated by space.",
+        defaultValue: undefined,
+      },
       {
         key: "-v, --verbose",
         description: "Write verbose output",
         defaultValue: false,
       },
       {
         key: "-t, --content-type <type>",
-        description: 'Destination type to compress to (choices: "jls", "lei", "jls-lossy" or DICOM Transfer Syntax UID - default: "jls")',
+        description: 'Destination type to compress to (choices: "jls", "lei", "jls-lossy", "jhc", "jxl" or DICOM Transfer Syntax UID - default: "jls")',
         defaultValue: "jls",
         customParser: compressionOptionParser,
       },
+      {
+        key: "-e, --no-encapsulated-image-frame",
+        description: "Avoid encapsulating the image frame.  Writes with the extension and without multipart",
+      },
       {
         key: "-m, --maximum-inline-public-length <value>",
         description: "Maximum length of public binary data",
@@ -50,7 +59,7 @@ const { mkdicomwebConfig } = ConfigPoint.register({
         key: "-r, --recompress <listvalue...>",
         description: "List of types to recompress separated by space",
         defaultValue: ["uncompressed", "jp2"],
-        choices: ["uncompressed", "jp2", "jpeglossless", "rle", "none"],
+        choices: ["uncompressed", "jp2", "jpeglossless", "rle", "jph", "jls", "true", "none"],
       },
       {
         key: "--recompress-thumb <listvalue...>",

packages/static-wado-creator/lib/model/TagLists.js

@@ -1,5 +1,5 @@
 const hashFactory = require("node-object-hash");
-const Tags = require("../dictionary/Tags");
+const { Tags } = require("@radicalimaging/static-wado-util");
 
 /* eslint "no-param-reassign": "off" */
 

packages/static-wado-creator/lib/model/uids.js

@@ -12,7 +12,7 @@ const jpeg = "image/jpeg";
 const jls = "image/jls";
 const jll = "image/jll";
 const jxl = "image/x-jxl";
-const htj2k = "image/x-htj2k";
+const htj2k = "image/jphc";
 const jp2 = "image/jp2";
 const rle = "image/dicom-rle";
 
@@ -21,20 +21,19 @@ const uids = {
   "1.2.840.10008.1.2.1": uncompressed,
   "1.2.840.10008.1.2.1.99": uncompressed,
   "1.2.840.10008.1.2.2": uncompressed,
-  "1.2.840.10008.1.2.4.50": { contentType: jpeg, lossy: true },
+  "1.2.840.10008.1.2.4.50": { contentType: jpeg, lossy: true, extension: ".jpeg" },
   "1.2.840.10008.1.2.4.51": { contentType: jpeg, lossy: true },
   "1.2.840.10008.1.2.4.57": { contentType: jpeg },
-  "1.2.840.10008.1.2.4.70": { contentType: jll },
-  "1.2.840.10008.1.2.4.140": { contentType: jxl },
+  "1.2.840.10008.1.2.4.70": { contentType: jll, extension: ".jll" },
+  "1.2.840.10008.1.2.4.140": { contentType: jxl, extension: ".jxl" },
+  // Lossy, original JPEG reconstruction mode
   "1.2.840.10008.1.2.4.141": { contentType: jxl, lossy: true },
-  "1.2.840.10008.1.2.4.80": { contentType: jls },
+  "1.2.840.10008.1.2.4.142": { contentType: jxl, lossy: true },
+  "1.2.840.10008.1.2.4.80": { contentType: jls, extension: ".jls" },
   "1.2.840.10008.1.2.4.81": { contentType: jls, lossy: true },
-  "1.2.840.10008.1.2.4.90": { contentType: jp2 },
+  "1.2.840.10008.1.2.4.90": { contentType: jp2, extension: ".jp2" },
   "1.2.840.10008.1.2.4.91": { contentType: jp2 },
-  // From JPEG original data, lossless to JXL
-  "1.2.840.10008.1.2.4.142": { contentType: jxl, lossy: true },
-  "1.2.840.10008.1.2.4.150": { contentType: htj2k },
-  // **
+  "1.2.840.10008.1.2.4.96": { contentType: htj2k, extension: ".jhc" },
   "1.2.840.10008.1.2.5": { contentType: rle },
   default: {},
 };

packages/static-wado-creator/lib/operation/InstanceDeduplicate.js

@@ -1,7 +1,7 @@
 // TODO review returning type of some methods
 const { JSONWriter } = require("@radicalimaging/static-wado-util");
+const { Tags } = require("@radicalimaging/static-wado-util");
 const TagLists = require("../model/TagLists");
-const Tags = require("../dictionary/Tags");
 
 const { getValue, setValue } = Tags;
 

packages/static-wado-creator/lib/operation/StudyData.js

@@ -2,7 +2,7 @@ const path = require("path");
 const fs = require("fs");
 const hashFactory = require("node-object-hash");
 const { JSONReader, JSONWriter } = require("@radicalimaging/static-wado-util");
-const Tags = require("../dictionary/Tags");
+const { Tags } = require("@radicalimaging/static-wado-util");
 const TagLists = require("../model/TagLists");
 
 const { getValue, setValue, getList, setList } = Tags;

packages/static-wado-creator/lib/operation/ThumbnailService.js

@@ -4,10 +4,10 @@ const dicomCodec = require("@cornerstonejs/dicom-codec");
 const staticCS = require("@radicalimaging/static-cs-lite");
 const fs = require("fs");
 const { exec } = require("child_process");
+const { Tags } = require("@radicalimaging/static-wado-util");
 const decodeImage = require("./adapter/decodeImage");
 const { shouldThumbUseTranscoded } = require("./adapter/transcodeImage");
 const { isVideo } = require("../writer/VideoWriter");
-const Tags = require("../dictionary/Tags");
 
 /**
  * Return the middle index of given list

packages/static-wado-creator/lib/operation/adapter/transcodeImage.js

@@ -1,5 +1,5 @@
 const dicomCodec = require("@cornerstonejs/dicom-codec");
-const Tags = require("../../dictionary/Tags");
+const { Tags } = require("@radicalimaging/static-wado-util");
 const getImageInfo = require("./getImageInfo");
 
 const transcodeOp = {
@@ -33,6 +33,10 @@ const transcodeDestinationMap = {
     transferSyntaxUid: "1.2.840.10008.1.2.4.91",
     transcodeOp: transcodeOp.encode,
   },
+  jhc: {
+    transferSyntaxUid: "1.2.840.10008.1.2.4.96",
+    transcodeOp: transcodeOp.encode,
+  },
 };
 
 const transcodeSourceMap = {
@@ -64,6 +68,10 @@ const transcodeSourceMap = {
     transcodeOp: transcodeOp.decode,
     alias: "jp2",
   },
+  "1.2.840.10008.1.2.4.96": {
+    transcodeOp: transcodeOp.decode,
+    alias: "jhc",
+  },
   "1.2.840.10008.1.2.5": {
     transcodeOp: transcodeOp.decode,
     alias: "rle",
@@ -113,14 +121,15 @@ function getTranscoder(transferSyntaxUid, { contentType, verbose }) {
  * @param {*} options runner options
  */
 function shouldTranscodeImageFrame(id, options) {
-  if (!options.recompress) {
+  const { recompress } = options;
+  if (!recompress) {
     return false;
   }
 
   function isValidTranscoder() {
     const { transferSyntaxUid } = id;
     const transcoder = getTranscoder(transferSyntaxUid, options);
-    return transcoder && transcoder.transferSyntaxUid && options.recompress.includes(transcoder.alias);
+    return transcoder && transcoder.transferSyntaxUid && (recompress.includes("true") || recompress.includes(transcoder.alias));
   }
 
   return isValidTranscoder();

packages/static-wado-creator/lib/operation/getDataSet.js

@@ -1,6 +1,6 @@
+const { Tags } = require("@radicalimaging/static-wado-util");
 const getVR = require("./getVR");
 const getValue = require("./getValue");
-const Tags = require("../dictionary/Tags");
 
 /**
  * Get dataset.

packages/static-wado-creator/lib/operation/getVR.js

@@ -1,4 +1,4 @@
-const dataDictionary = require("../dictionary/dataDictionary");
+const { dataDictionary } = require("@radicalimaging/static-wado-util");
 
 const getVR = (attr) => {
   if (attr.vr) {

packages/static-wado-creator/lib/writer/CompleteStudyWriter.js

@@ -1,6 +1,6 @@
 const { JSONReader, JSONWriter, Stats } = require("@radicalimaging/static-wado-util");
+const { Tags } = require("@radicalimaging/static-wado-util");
 const StudyData = require("../operation/StudyData");
-const Tags = require("../dictionary/Tags");
 
 /**
  * CompleteStudyWriter takes the deduplicated data values, all loaded into the study parameter,

packages/static-wado-creator/lib/writer/DeduplicateWriter.js

@@ -2,7 +2,7 @@ const hashFactory = require("node-object-hash");
 
 const hasher = hashFactory();
 const { JSONWriter } = require("@radicalimaging/static-wado-util");
-const Tags = require("../dictionary/Tags");
+const { Tags } = require("@radicalimaging/static-wado-util");
 const TagLists = require("../model/TagLists");
 
 async function writeDeduplicatedFile(dir, data, hashValueSrc) {

packages/static-wado-creator/lib/writer/HashDataWriter.js

@@ -2,7 +2,7 @@ const hashFactory = require("node-object-hash");
 
 const hasher = hashFactory();
 const path = require("path");
-const Tags = require("../dictionary/Tags");
+const { Tags } = require("@radicalimaging/static-wado-util");
 const WriteStream = require("./WriteStream");
 const WriteMultipart = require("./WriteMultipart");
 const ExpandUriPath = require("./ExpandUriPath");

packages/static-wado-creator/lib/writer/ImageFrameWriter.js

@@ -5,24 +5,41 @@ const ExpandUriPath = require("./ExpandUriPath");
 const { MultipartHeader, MultipartAttribute } = require("./MultipartHeader");
 
 const ImageFrameWriter = (options) => {
-  const { verbose } = options;
+  const { verbose, encapsulatedImageFrame = true } = options;
 
   return async (id, index, imageFrame) => {
     const { transferSyntaxUid } = id;
     const type = uids[transferSyntaxUid] || uids.default;
-    const writeStream = WriteStream(id.imageFrameRootPath, `${1 + index}`, {
-      gzip: type.gzip,
-      mkdir: true,
-    });
+    const extension = type.extension;
     let content;
     if (imageFrame instanceof Uint8Array) {
       content = imageFrame;
     } else {
       content = Buffer.from(imageFrame.buffer);
     }
-    await WriteMultipart(writeStream, [new MultipartHeader("Content-Type", type.contentType, [new MultipartAttribute("transfer-syntax", transferSyntaxUid)])], content);
-    await writeStream.close();
-    if (verbose) console.log("Wrote image frame", id.sopInstanceUid, index + 1);
+
+    if (encapsulatedImageFrame || !extension) {
+      const writeStream = WriteStream(id.imageFrameRootPath, `${1 + index}`, {
+        gzip: type.gzip,
+        mkdir: true,
+      });
+      await WriteMultipart(
+        writeStream,
+        [new MultipartHeader("Content-Type", type.contentType, [new MultipartAttribute("transfer-syntax", transferSyntaxUid)])],
+        content
+      );
+      writeStream.close();
+      if (verbose) console.log("Wrote encapsulated image frame", id.sopInstanceUid, index + 1);
+    }
+    if (extension) {
+      const writeStreamSingle = WriteStream(id.imageFrameRootPath, `${1 + index}${extension}`, {
+        gzip: type.gzip,
+        mkdir: true,
+      });
+      await writeStreamSingle.write(content);
+      writeStreamSingle.close();
+      if (verbose) console.log("Wrote single part image frame", id.sopInstanceUid, index + 1);
+    }
     const includeSeries = true;
     return ExpandUriPath(id, `instances/${id.sopInstanceUid}/frames`, { includeSeries, ...options });
   };

packages/static-wado-creator/lib/writer/RawDicomWriter.js

@@ -1,7 +1,7 @@
+const { Tags } = require("@radicalimaging/static-wado-util");
 const WriteStream = require("./WriteStream");
 const WriteMultipart = require("./WriteMultipart");
 const { MultipartHeader } = require("./MultipartHeader");
-const Tags = require("../dictionary/Tags");
 
 const modalitiesToRawWrite = ["SEG", "SR"];
 

packages/static-wado-creator/lib/writer/VideoWriter.js

@@ -1,5 +1,5 @@
 /** Write raw video file */
-const Tags = require("../dictionary/Tags");
+const { Tags } = require("@radicalimaging/static-wado-util");
 const WriteStream = require("./WriteStream");
 
 const MPEG2 = "mpg";

packages/static-wado-creator/tests/e2e/index.test.js

@@ -1,6 +1,6 @@
 const fs = require("fs");
 const { execSync } = require("child_process");
-const { JSONReader } = require("@radicalimaging/static-wado-util");
+const { JSONReader, Tags } = require("@radicalimaging/static-wado-util");
 const must = require("must");
 
 // same level at package folder

packages/static-wado-deploy/lib/DeployGroup.mjs

@@ -38,7 +38,6 @@ class DeployGroup {
    */
   async store(parentDir = "", name = "") {
     const fileName = path.join(this.baseDir, parentDir, name);
-    // console.log('Doing lstat', fileName);
     const lstat = await fs.promises.lstat(fileName);
     const relativeName = (name && `${parentDir}/${name}`) || parentDir || "";
     console.log("relativeName", relativeName);

packages/static-wado-scp/lib/DcmjsDimseScp.js

@@ -2,6 +2,7 @@ const { Stats } = require("@radicalimaging/static-wado-util");
 const StaticWado = require("@radicalimaging/static-wado-creator");
 const dcmjsDimse = require("dcmjs-dimse");
 const dcmjs = require("dcmjs");
+const { loadedPlugins } = require("./loadPlugins");
 
 const { Scp, Dataset } = dcmjsDimse;
 const { CEchoResponse, CStoreResponse, CFindResponse } = dcmjsDimse.responses;
@@ -103,6 +104,7 @@ class DcmjsDimseScp extends Scp {
     const dataset = request.getDataset();
     const { QueryRetrieveLevel } = dataset.elements;
     console.log("QueryRetrieveLevel", QueryRetrieveLevel);
+    // TODO - call loadPlugins pon the given level to see if they can be loaded
     const queryFunc = loadedPlugins[QueryRetrieveLevel];
 
     if (queryFunc && !this.cfindDisabled) {

packages/static-wado-scp/lib/loadPlugins.js

@@ -17,4 +17,6 @@ const loadPlugins = (options) => {
     });
 };
 
+loadPlugins.loadedPlugins = loadedPlugins;
+
 module.exports = loadPlugins;

packages/static-wado-creator/lib/dictionary/Tags.js renamed to packages/static-wado-util/lib/dictionary/Tags.js

@@ -14,6 +14,8 @@ exports.configDiff = require("./update/configDiff");
 exports.configGroup = require("./configGroup.js");
 exports.updateConfiguration = require("./update/updateConfiguration");
 exports.asyncIterableToBuffer = require("./asyncIterableToBuffer");
+exports.Tags = require("./dictionary/Tags");
+exports.dataDictionary = require("./dictionary/dataDictionary");
 
 exports.configureProgram = configureProgram;
 exports.configureCommands = configureCommands;

packages/static-wado-creator/lib/dictionary/dataDictionary.js renamed to packages/static-wado-util/lib/dictionary/dataDictionary.js

@@ -5,7 +5,7 @@ const handleHomeRelative = require("../handleHomeRelative");
 
 const NDJSONReader = async (dirSrc, name, def) => {
   const dir = handleHomeRelative(dirSrc);
-  return new Promise((resolve, reject) => {
+  return new Promise((resolve) => {
     try {
       const ret = [];
       const stream = fs.createReadStream(path.join(dir, name)).pipe(ndjson.parse());
@@ -14,8 +14,7 @@ const NDJSONReader = async (dirSrc, name, def) => {
     } catch (err) {
       if (def === undefined) {
         console.log("Couldn't read", dir, name, err);
-        reject("Couldn't read");
-        return;
+        throw new Error(`Couldn't read ${dir} ${name} ${err}`);
       }
       resolve(def);
     }

packages/static-wado-util/lib/index.js

@@ -38,6 +38,7 @@
   "dependencies": {
     "commander": "^9.0.0",
     "config-point": "^0.5.1",
+    "dcmjs": "^0.29.0",
     "json5": "^2.2.1",
     "json5-writer": "^0.2.0",
     "must": "^0.13.4",

packages/static-wado-util/lib/reader/NDJSONReader.js

@@ -1,5 +1,5 @@
 const fs = require("fs");
-const asyncIteratorToBuffer = require("../../lib/operation/adapter/asyncIterableToBuffer");
+const asyncIteratorToBuffer = require("../../lib/asyncIterableToBuffer");
 
 describe("asyncIterableToBuffer", () => {
   let dicomp10stream;