@radicalimaging/static-wado-creator 0.6.4 → 1.1.0

package/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 = {
@@ -15,7 +15,7 @@ const transcodeOp = {
 const transcodeDestinationMap = {
   lei: {
     transferSyntaxUid: "1.2.840.10008.1.2.1",
-    transcodeOp: transcodeOp.none
+    transcodeOp: transcodeOp.none,
   },
   jls: {
     transferSyntaxUid: "1.2.840.10008.1.2.4.80",
@@ -33,6 +33,10 @@ const transcodeDestinationMap = {
     transferSyntaxUid: "1.2.840.10008.1.2.4.91",
     transcodeOp: transcodeOp.encode,
   },
+  jhc: {
+    transferSyntaxUid: "3.2.840.10008.1.2.4.96",
+    transcodeOp: transcodeOp.encode,
+  },
 };
 
 const transcodeSourceMap = {
@@ -50,11 +54,11 @@ const transcodeSourceMap = {
   },
   "1.2.840.10008.1.2.4.57": {
     transcodeOp: transcodeOp.decode,
-    alias: "jpeglossless",
+    alias: "jls",
   },
   "1.2.840.10008.1.2.4.70": {
     transcodeOp: transcodeOp.decode,
-    alias: "jpeglossless",
+    alias: "jls",
   },
   "1.2.840.10008.1.2.4.90": {
     transcodeOp: transcodeOp.decode,
@@ -64,6 +68,10 @@ const transcodeSourceMap = {
     transcodeOp: transcodeOp.decode,
     alias: "jp2",
   },
+  "3.2.840.10008.1.2.4.96": {
+    transcodeOp: transcodeOp.decode,
+    alias: "jhc",
+  },
   "1.2.840.10008.1.2.5": {
     transcodeOp: transcodeOp.decode,
     alias: "rle",
@@ -71,9 +79,9 @@ const transcodeSourceMap = {
 };
 
 /**
- * Get an existing destination transcoder from destination map. 
+ * Get an existing destination transcoder from destination map.
  *
- * @param {*} id Destination type to compress to 
+ * @param {*} id Destination type to compress to
  * @returns A partial transcoder definition. Otherwise it returns undefined.
  */
 function getDestinationTranscoder(id) {
@@ -92,14 +100,14 @@ function getDestinationTranscoder(id) {
  */
 function getTranscoder(transferSyntaxUid, { contentType, verbose }) {
   if (verbose) {
-    console.log(`getTranscoder for ${transferSyntaxUid}`);
+    console.log('getTranscoder for', transferSyntaxUid, 'source to', contentType);
   }
   const sourceTranscoder = transcodeSourceMap[transferSyntaxUid];
   const destinationTranscoder = getDestinationTranscoder(contentType);
   if (!sourceTranscoder || !destinationTranscoder) {
     return undefined;
   }
-  
+
   return {
     transferSyntaxUid: destinationTranscoder.transferSyntaxUid,
     transcodeOp: sourceTranscoder.transcodeOp | destinationTranscoder.transcodeOp, // eslint-disable-line no-bitwise
@@ -107,24 +115,29 @@ function getTranscoder(transferSyntaxUid, { contentType, verbose }) {
   };
 }
 
-
 /**
  * Tell whether given id contain transferSyntaxUid which can be transcoded or not.
  * @param {*} id object containing transferSyntaxUid
  * @param {*} options runner options
  */
 function shouldTranscodeImageFrame(id, options) {
-  if (!options.recompress) {
+  const { recompress } = options;
+  if (!recompress) {
+    if( options.verbose ) console.log("Not transcoding because recompress not set");
     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();
+  const ret  = isValidTranscoder();
+  if( !ret && options.verbose ) {
+    console.log("Not transcoding");
+  }
+  return ret;
 }
 
 /**
@@ -171,6 +184,7 @@ async function transcodeImageFrame(id, targetIdSrc, imageFrame, dataSet, options
   let result = {};
 
   if (!shouldTranscodeImageFrame(id, options)) {
+    console.log("Shouldn't transcode");
     return {
       id,
       imageFrame,
@@ -182,6 +196,7 @@ async function transcodeImageFrame(id, targetIdSrc, imageFrame, dataSet, options
 
   // last chance to prevent transcoding
   if (targetId.transferSyntaxUid !== transcoder.transferSyntaxUid) {
+     console.log("Image is already in", targetId.transferSyntaxUid, "not transcoding");
     return {
       id,
       imageFrame,
@@ -189,9 +204,8 @@ async function transcodeImageFrame(id, targetIdSrc, imageFrame, dataSet, options
     };
   }
 
-  if (options.verbose) {
-    console.log("Transcoding to", transcoder.transferSyntaxUid);
-  }
+  if( options.verbose ) console.log("Transcoding to", transcoder.transferSyntaxUid);
+  
   const imageInfo = getImageInfo(dataSet);
   let done = false;
   let processResultMsg = "";
@@ -289,7 +303,10 @@ function transcodeMetadata(metadata, id, options) {
   const result = { ...metadata };
 
   if (result[Tags.AvailableTransferSyntaxUID]) {
-    Tags.setValue(result,Tags.AvailableTransferSyntaxUID, transcodedId.transferSyntaxUid);
+    Tags.setValue(result, Tags.AvailableTransferSyntaxUID, transcodedId.transferSyntaxUid);
+    if( this.verbose ) {
+      console.log("Apply available tsuid", transcodeId.transferSyntaxUid);
+    }
   }
 
   return result;

package/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.

package/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) {

package/lib/util/adaptProgramOpts.js

@@ -29,6 +29,7 @@ module.exports = function adaptProgramOpts(programOpts, defaults) {
     prependBulkDataUri,
     expandBulkDataUri,
     verbose,
+    scpPort,
   } = programOpts;
 
   return assignDefined(
@@ -50,6 +51,7 @@ module.exports = function adaptProgramOpts(programOpts, defaults) {
       pathInstances,
       removeDeduplicatedInstances,
       storeMultipartBulkData,
+      scpPort,
       prependBulkDataUri,
       expandBulkDataUri,
       verbose,

package/lib/util/compressionOptionParser.js

@@ -1,13 +1,13 @@
 const { program } = require("@radicalimaging/static-wado-util");
 const { getDestinationTranscoder } = require("../operation/adapter/transcodeImage");
 
-module.exports = function compressionOptionParser(value) { 
+module.exports = function compressionOptionParser(value) {
   const destination = getDestinationTranscoder(value);
   if (destination) {
     console.log("Found destination transferSyntax ", destination.transferSyntaxUid, "for ", value);
   } else {
     console.log("No transcoder destination for ", value);
     throw new program.InvalidArgumentError(`No transcoder destination for ${value}`);
-  } 
+  }
   return destination.transferSyntaxUid;
-}
+};

package/lib/writer/CompleteStudyWriter.js

@@ -1,8 +1,6 @@
-const { Stats } = require("@radicalimaging/static-wado-util");
-const { JSONReader } = require("@radicalimaging/static-wado-util");
-const JSONWriter = require("./JSONWriter");
+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,
@@ -47,12 +45,12 @@ const CompleteStudyWriter = (options) => {
     const studyQuery = await studyData.writeMetadata();
 
     const allStudies = await JSONReader(options.directoryName, "studies/index.json.gz", []);
-    const studyUID = Tags.getValue(studyQuery,Tags.StudyInstanceUID);
+    const studyUID = Tags.getValue(studyQuery, Tags.StudyInstanceUID);
     if (!studyUID) {
       console.error("studyQuery=", studyQuery);
       throw new Error("Study query has null studyUID");
     }
-    const studyIndex = allStudies.findIndex((item) => Tags.getValue(item,Tags.StudyInstanceUID) == studyUID);
+    const studyIndex = allStudies.findIndex((item) => Tags.getValue(item, Tags.StudyInstanceUID) == studyUID);
     if (studyIndex == -1) {
       allStudies.push(studyQuery);
     } else {

package/lib/writer/DeduplicateWriter.js

@@ -1,8 +1,8 @@
 const hashFactory = require("node-object-hash");
 
 const hasher = hashFactory();
-const JSONWriter = require("./JSONWriter");
-const Tags = require("../dictionary/Tags");
+const { JSONWriter } = require("@radicalimaging/static-wado-util");
+const { Tags } = require("@radicalimaging/static-wado-util");
 const TagLists = require("../model/TagLists");
 
 async function writeDeduplicatedFile(dir, data, hashValueSrc) {

package/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");
@@ -47,7 +47,7 @@ HashDataWriter.createHashPath = (data, options = {}) => {
   const { mimeType } = options;
   const isRaw = ArrayBuffer.isView(data);
   const extension = isRaw ? (mimeType && extensions[mimeType]) || "" : ".json";
-  const hashValue = Tags.getValue(data,Tags.DeduppedHash) || hasher.hash(data);
+  const hashValue = Tags.getValue(data, Tags.DeduppedHash) || hasher.hash(data);
 
   return {
     // Use string concat as this value is used for the BulkDataURI which needs forward slashes

package/lib/writer/ImageFrameWriter.js

@@ -5,24 +5,43 @@ 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, type.contentType);
+      }
+    }
+    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, extension);
+    }
     const includeSeries = true;
     return ExpandUriPath(id, `instances/${id.sopInstanceUid}/frames`, { includeSeries, ...options });
   };

package/lib/writer/RawDicomWriter.js

@@ -0,0 +1,36 @@
+const { Tags } = require("@radicalimaging/static-wado-util");
+const WriteStream = require("./WriteStream");
+const WriteMultipart = require("./WriteMultipart");
+const { MultipartHeader } = require("./MultipartHeader");
+
+const modalitiesToRawWrite = ["SEG", "SR"];
+
+const defaultSelector = (instance) => {
+  const modality = instance.metadata[Tags.Modality]?.Value?.[0];
+  return modalitiesToRawWrite.indexOf(modality) !== -1;
+};
+
+/** Writes out raw DICOM files, encapsulated in multipart and gzipped - currently just DICOM SR and SEG */
+const RawDicomWriter =
+  () =>
+  async (id, instance, content, options = { gzip: true }) => {
+    if (!instance) {
+      return undefined;
+    }
+    const selector = options.selector || defaultSelector;
+    if (!selector(instance)) {
+      return undefined;
+    }
+    const contentType = options.contentType || "application/dicom";
+    const writeStream = WriteStream(id.sopInstanceRootPath, "index.mht", {
+      gzip: options.gzip,
+      mkdir: true,
+    });
+    const { length } = content;
+    const buffer = content.slice(0, length);
+    await WriteMultipart(writeStream, [new MultipartHeader("Content-Type", contentType, [])], buffer);
+    await writeStream.close();
+  };
+RawDicomWriter.defaultSelector = defaultSelector;
+
+module.exports = RawDicomWriter;

package/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";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@radicalimaging/static-wado-creator",
-  "version": "0.6.4",
+  "version": "1.1.0",
   "description": "Library to convert DICOMP10 to DICOMweb format. Original upstream: https://github.com/chafey/dicomp10-to-dicomweb-js",
   "publishConfig": {
     "access": "public"
@@ -53,21 +53,22 @@
     "build": "echo \"No build yet\" && exit 0",
     "link:exec": "npm link",
     "lint": "npx eslint --color \"*(bin|lib)/**/*.{js,mjs}\"",
-      "lint:fix": "npx eslint --fix --color \"*(bin|lib)/**/*.{js,mjs}\""
-    },
+    "lint:fix": "npx eslint --fix --color \"*(bin|lib)/**/*.{js,mjs}\""
+  },
   "jest": {
     "verbose": true
   },
   "dependencies": {
     "@cornerstonejs/dicom-codec": "^0.1.3",
-    "@radicalimaging/static-cs-lite": "^0.0.2",
+    "@radicalimaging/static-cs-lite": "^0.0.3",
     "@radicalimaging/static-wado-util": "^0.6.2",
     "canvas": "^2.9.1",
-    "config-point": "^0.5.0",
+    "config-point": "^0.5.1",
+    "dcmjs": "^0.28.0",
     "dicom-parser": "^1.8.13",
     "glob": "^7.2.0",
-    "uuid": "^8.3.2",
-    "node-object-hash": "^2.3.10"
+    "node-object-hash": "^2.3.10",
+    "uuid": "^8.3.2"
   },
   "devDependencies": {
     "must": "^0.13.4"

package/lib/dictionary/Tags.js

@@ -1,111 +0,0 @@
-const dataDictionary = require("./dataDictionary");
-const dcmjs = require("dcmjs");
-
-const { naturalizeDataset, denaturalizeDataset} = dcmjs.data.DicomMetaDictionary
-
-/** Find the actual tag for a private value */
-const findPrivate = (item, tagObject, create) => {
-    if( typeof tagObject === "string" ) return tagObject;
-    if( typeof tagObject === "number" ) return `00000000${tagObject.toString(16)}`.slice(-8);
-    const {creator,tag} = tagObject;
-    if( !creator ) return tag;
-    const start = tag.substring(0,4);
-    const end = tag.substring(6,8);
-    // Should technically go all the way up, but for now only test 0x30 items
-    let assignPosition;
-    for(let offset = 0x10; offset < 0x40; offset++) {
-      const testTag = `${start}00${offset.toString(16)}`
-      const testCreator = item[testTag];
-      if( testCreator===undefined && assignPosition===undefined ) assignPosition = offset;
-      if( testCreator && testCreator.Value && testCreator.Value[0]===creator ) {
-        return `${start}${offset.toString(16)}${end}`
-      }
-    }
-    if( create ) {
-      if( !assignPosition ) throw new Error(`Couldn't find any assign positions for ${creator} ${tag} in ${item}`);
-      const creatorTag = `${start}00${assignPosition.toString(16)}`
-      item[creatorTag] = { Value: [creator], vr: 'CS' };
-      return `${start}${assignPosition.toString(16)}${end}`
-    }
-  };
-
-const DeduppedCreator = "dedupped";
-  
-const Tags = {
-  // Raw tags have the x before them, not parsed yet
-  RawMinTag: "x00000000",
-  RawFirstBodyTag: "x00080000",
-  RawTransferSyntaxUID: "x00020010",
-
-  // This one isn't defined in the dataDictionary
-  AvailableTransferSyntaxUID: "00083002",
-
-  DeduppedCreator,
-
-  // The references to extract data included in this object, 1..n values
-  DeduppedRef: { creator: DeduppedCreator, tag: "00091010"},
-
-  // The hash value of THIS object
-  DeduppedHash: {creator: DeduppedCreator, tag: "00091011"},
-
-  // Type of hash instance
-  DeduppedType: {creator: DeduppedCreator, tag: "00091012"},
-  InstanceType: "instance",
-  InfoType: "info",
-
-  naturalizeDataset, denaturalizeDataset,
-  
-  setValue: (item, tag, value) => {
-    const actualTag = findPrivate(item,tag,true);
-    item[actualTag] = { Value: Array.isArray(value) ? value : [value] };
-    return actualTag;
-  },
-
-  setList: (item, tag, value) => {
-    const actualTag = findPrivate(item,tag,true);
-    item[actualTag] =  {Value: Array.isArray(value) ? value : [value]};
-    return actualTag;
-  },
-
-  pushList: (item, tag, value) => {
-    const actualTag = findPrivate(item,tag,true);
-    if( !item[actualTag] ) item[actualTag] = { Value: [] };
-    item[actualTag].Value.push(value);
-    return actualTag;
-  },
-
-  getValue: (item, tag) => {
-    const actualTag = findPrivate(item,tag);
-    if( !actualTag ) return undefined;
-    const value = item[actualTag];
-    if( value===undefined ) return undefined;
-    if( Array.isArray(value) ) return value.length==1 ? value[0] : (value.length===0 ? "" : value);
-    if( value.Value ) return value.Value.length==1 ? value.Value[0] : (value.Value.length===0 ? "" : value.Value);
-    return value;
-  },
-
-  getList: (item, tag) => {
-    const actualTag = findPrivate(item,tag);
-    if( !actualTag ) return undefined;
-    const value = item[actualTag];
-    if( value===undefined ) return undefined;
-    if( Array.isArray(value) ) return value;
-    if( value.Value ) return value.Value;
-    return [value];
-  },
-
-  removeValue: (item,tag) => {
-    const actualTag = findPrivate(item,tag);
-    if( actualTag ) delete item[actualTag];
-    // TODO, remove creator tag if not used any longer
-  },
-
-  findPrivate,
-};
-
-Object.keys(dataDictionary).forEach((key) => {
-  const value = dataDictionary[key];
-  Tags[value.name] = key;
-});
-
-module.exports = Tags;