@radicalimaging/static-wado-creator 0.6.5 → 1.2.0

package/lib/rejectMain.js

@@ -1,12 +1,12 @@
 const StaticWado = require("./StaticWado");
 const adaptProgramOpts = require("./util/adaptProgramOpts");
 
-module.exports = function rejectMain(options, program) {
+module.exports = function rejectMain(args, options) {
   const finalOptions = adaptProgramOpts(options, {
     ...this,
     isGroup: true,
     isStudyData: true,
   });
   const importer = new StaticWado(finalOptions);
-  return importer.reject(program.args);
+  return importer.reject(args);
 };

package/lib/util/adaptProgramOpts.js

@@ -10,49 +10,30 @@ const assignDefined = (dest, src) => {
 
 module.exports = function adaptProgramOpts(programOpts, defaults) {
   const {
-    maximumInlinePublicLength,
-    maximumInlinePrivateLength,
     group: isGroup,
     instances: isInstanceMetadata,
     deduplicate: isDeduplicate,
     study: isStudyData,
     clean: isClean,
-    recompress,
-    recompressThumb,
-    contentType,
-    colourContentType,
     dir: rootDir,
-    pathDeduplicated,
-    pathInstances,
-    removeDeduplicatedInstances,
-    storeMultipartBulkData,
-    prependBulkDataUri,
-    expandBulkDataUri,
-    verbose,
+    delete: deleteInstances,
+    singlePartImage,
+    encapsulatedImage,
   } = programOpts;
 
   return assignDefined(
     { ...defaults },
     {
-      maximumInlinePublicLength,
-      maximumInlinePrivateLength,
-      isGroup,
-      isInstanceMetadata,
-      isDeduplicate,
+      ...programOpts,
       isStudyData,
       isClean,
-      recompress,
-      recompressThumb,
-      contentType,
-      colourContentType,
+      isInstanceMetadata,
+      isDeduplicate,
+      isGroup,
       rootDir,
-      pathDeduplicated,
-      pathInstances,
-      removeDeduplicatedInstances,
-      storeMultipartBulkData,
-      prependBulkDataUri,
-      expandBulkDataUri,
-      verbose,
+      encapsulatedImage: encapsulatedImage ?? singlePartImage !== true,
+      singlePartImage: singlePartImage ?? encapsulatedImage === false,
+      delete: deleteInstances,
     }
   );
 };

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,
@@ -28,9 +26,12 @@ const CompleteStudyWriter = (options) => {
       } else {
         console.log("Not writing new deduplicated data because it is clean:", studyData.studyInstanceUid);
       }
+      await studyData.deleteInstancesReferenced();
     }
 
     if (!options.isStudyData) {
+      console.verbose("Not configured to write study metadata", studyData.studyInstanceUid);
+      if (options.notifications) this.notificationService.notifyStudy(studyData.studyInstanceUid);
       delete this.studyData;
       Stats.StudyStats.summarize();
       return;
@@ -38,11 +39,12 @@ const CompleteStudyWriter = (options) => {
 
     const isDirtyMetadata = await studyData.dirtyMetadata();
     if (!isDirtyMetadata) {
-      console.log("Study metadata", studyData.studyInstanceUid, "has clean metadata, not writing");
+      console.log("Study metadata", studyData.studyInstanceUid, "is clean.");
       delete this.studyData;
       Stats.StudyStats.summarize(`Study metadata ${studyData.studyInstanceUid} has clean metadata, not writing`);
       return;
     }
+    console.log("Writing study metadata", studyData.studyInstanceUid);
 
     const studyQuery = await studyData.writeMetadata();
 
@@ -59,6 +61,7 @@ const CompleteStudyWriter = (options) => {
       allStudies[studyIndex] = studyQuery;
     }
     await JSONWriter(options.directoryName, "studies", allStudies);
+    if (options.notifications) this.notificationService.notifyStudy(studyData.studyInstanceUid);
     delete this.studyData;
     Stats.StudyStats.summarize(`Wrote study metadata/query files for ${studyData.studyInstanceUid}`);
   }

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) {
@@ -24,7 +24,10 @@ const DeduplicateWriter = (options) =>
     const studyData = await this.completeStudy.getCurrentStudyData(this, id);
 
     if (options.isDeduplicate) {
+      if (options.verbose) console.log("Writing single instance", id.studyInstanceUid);
       await perInstanceWriter(id, data);
+    } else if (options.verbose) {
+      console.log("Not writing single instance deduplicated");
     }
     studyData.addDeduplicated(data, id.filename);
   };

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");
@@ -20,7 +20,6 @@ const HashDataWriter =
   (options) =>
   async (id, key, data, additionalOptions = {}) => {
     const isRaw = ArrayBuffer.isView(data);
-    const { storeMultipartBulkData } = options;
     const { mimeType } = additionalOptions;
     // If the file has an extension, it should be directly accessible as that file type.
     const gzip = !isRaw || (data.length > 1024 && !mimeType);
@@ -31,7 +30,7 @@ const HashDataWriter =
       mkdir: true,
       gzip,
     });
-    if (isRaw && storeMultipartBulkData) {
+    if (isRaw) {
       await WriteMultipart(writeStream, [new MultipartHeader("Content-Type", "application/octet-stream")], rawData);
     } else {
       await writeStream.write(rawData);

package/lib/writer/ImageFrameWriter.js

@@ -5,24 +5,40 @@ const ExpandUriPath = require("./ExpandUriPath");
 const { MultipartHeader, MultipartAttribute } = require("./MultipartHeader");
 
 const ImageFrameWriter = (options) => {
-  const { verbose } = options;
-
+  const { encapsulatedImage, singlePartImage } = options;
   return async (id, index, imageFrame) => {
     const { transferSyntaxUid } = id;
     const type = uids[transferSyntaxUid] || uids.default;
-    const writeStream = WriteStream(id.imageFrameRootPath, `${1 + index}`, {
-      gzip: type.gzip,
-      mkdir: true,
-    });
+    const extension = type.extension;
     let content;
     if (imageFrame instanceof Uint8Array) {
       content = imageFrame;
     } else {
       content = Buffer.from(imageFrame.buffer);
     }
-    await WriteMultipart(writeStream, [new MultipartHeader("Content-Type", type.contentType, [new MultipartAttribute("transfer-syntax", transferSyntaxUid)])], content);
-    await writeStream.close();
-    if (verbose) console.log("Wrote image frame", id.sopInstanceUid, index + 1);
+
+    if (encapsulatedImage || !extension) {
+      const writeStream = WriteStream(id.imageFrameRootPath, `${1 + index}`, {
+        gzip: type.gzip,
+        mkdir: true,
+      });
+      await WriteMultipart(
+        writeStream,
+        [new MultipartHeader("Content-Type", type.contentType, [new MultipartAttribute("transfer-syntax", transferSyntaxUid)])],
+        content
+      );
+      await writeStream.close();
+      console.verbose("Wrote encapsulated image frame", id.sopInstanceUid, index + 1, type.contentType);
+    }
+    if (extension && singlePartImage) {
+      const writeStreamSingle = WriteStream(id.imageFrameRootPath, `${1 + index}${extension}`, {
+        gzip: type.gzip,
+        mkdir: true,
+      });
+      await writeStreamSingle.write(content);
+      await writeStreamSingle.close();
+      console.verbose("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/ThumbnailWriter.js

@@ -1,21 +1,14 @@
 const WriteStream = require("./WriteStream");
 
-const ThumbnailWriter = (options) => {
-  const { verbose } = options;
+const ThumbnailWriter = () => async (filePath, fileName, thumbBuffer) => {
+  const writeStream = WriteStream(filePath, fileName, {
+    mkdir: true,
+  });
 
-  return async (filePath, fileName, thumbBuffer) => {
-    const writeStream = WriteStream(filePath, fileName, {
-      mkdir: true,
-    });
+  await writeStream.write(thumbBuffer);
 
-    await writeStream.write(thumbBuffer);
-
-    await writeStream.close();
-
-    if (verbose) {
-      console.log("Wrote thumbnail frame", filePath, fileName);
-    }
-  };
+  console.verbose("Wrote thumbnail frame", filePath, fileName);
+  return writeStream.close();
 };
 
 module.exports = ThumbnailWriter;

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/lib/writer/WriteStream.js

@@ -2,6 +2,8 @@ const fs = require("fs");
 const zlib = require("zlib");
 const path = require("path");
 
+let writeCount = 0;
+
 /** Create an optionally gzipped stream,
  * where the write operations are performed in order executed,
  * and don't require synchronization, only the 'close' operation
@@ -14,6 +16,14 @@ const WriteStream = (dir, nameSrc, options = {}) => {
 
   const tempName = path.join(dir, `tempFile-${Math.round(Math.random() * 1000000000)}`);
   const finalName = path.join(dir, name);
+  writeCount++;
+  if (writeCount > 10) {
+    console.log("Write count", tempName, finalName, writeCount);
+    if (writeCount > 100) {
+      console.error("Too many open writes", new Error());
+      throw new Error(`Write count too high ${writeCount} destination ${finalName}`);
+    }
+  }
   const rawStream = fs.createWriteStream(tempName);
   const closePromise = new Promise((resolve) => {
     rawStream.on("close", () => {
@@ -33,7 +43,8 @@ const WriteStream = (dir, nameSrc, options = {}) => {
   async function close() {
     await this.writeStream.end();
     await this.closePromise;
-    await fs.rename(tempName, finalName, () => true); // console.log('Renamed', tempName,finalName));
+    await fs.rename(tempName, finalName, () => true);
+    writeCount--;
   }
 
   return {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@radicalimaging/static-wado-creator",
-  "version": "0.6.5",
+  "version": "1.2.0",
   "description": "Library to convert DICOMP10 to DICOMweb format. Original upstream: https://github.com/chafey/dicomp10-to-dicomweb-js",
   "publishConfig": {
     "access": "public"
@@ -42,29 +42,25 @@
     "lib"
   ],
   "bin": {
-    "mkdicomweb": "bin/mkdicomweb.js",
-    "mkdicomwebdeduplicated": "bin/mkdicomwebdeduplicated.js",
-    "mkdicomwebdeduplicatedgroup": "bin/mkdicomwebdeduplicatedgroup.js",
-    "mkdicomwebinstances": "bin/mkdicomwebinstances.js",
-    "mkdicomwebstudy": "bin/mkdicomwebstudy.js"
+    "mkdicomweb": "bin/mkdicomweb.js"
   },
   "scripts": {
     "test": "jest --config ./jest.config.js",
     "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}\""
+    "link:exec": "npm install -g && npm link",
+    "lint": "npx eslint --color \"**/*.{js,mjs,cjs}\"",
+    "lint:fix": "npx eslint --fix --color \"**/*.{js,mjs,cjs}\""
   },
   "jest": {
     "verbose": true
   },
   "dependencies": {
-    "@cornerstonejs/dicom-codec": "^0.1.3",
-    "@radicalimaging/static-cs-lite": "^0.0.2",
-    "@radicalimaging/static-wado-util": "^0.6.2",
-    "canvas": "^2.9.1",
-    "config-point": "0.5.1",
-    "dcmjs": "^0.27.0",
+    "@cornerstonejs/dicom-codec": ">=0.1.6",
+    "@radicalimaging/static-cs-lite": ">=1.2.0",
+    "@radicalimaging/static-wado-util": ">=1.2.0",
+    "canvas": "^2.11.0",
+    "config-point": ">=0.5.1",
+    "dcmjs": "^0.29.5",
     "dicom-parser": "^1.8.13",
     "glob": "^7.2.0",
     "node-object-hash": "^2.3.10",

package/lib/dictionary/Tags.js

@@ -1,119 +0,0 @@
-const dcmjs = require("dcmjs");
-const dataDictionary = require("./dataDictionary");
-
-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",
-  RawSopInstanceUID: "x00080018",
-
-  // 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)) {
-      if (value.length == 1) return value[0];
-      return value.length === 0 ? "" : value;
-    }
-    if (value.Value) {
-      if (value.Value.length == 1) return value.Value[0];
-      return 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;