fix: create transcoded images as stand alone option

.gitignore

@@ -52,5 +52,10 @@ node_modules/
 
 # VS Code
 *.code-workspace
-*~
-*.swp
+
+# Root commands
+*.cmd
+
+# vim files
+**/*~
+**/*.swp

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

@@ -53,14 +53,14 @@ async function cs3dThumbnail(
   dataset,
   metadata,
   transferSyntaxUid,
-  doneCallback
+  doneCallback,
 ) {
   if (!originalImageFrame) {
     throw new Error(`No originalImageFrame data available`);
   }
   if (!dataset && !metadata) {
     throw new Error(
-      `Neither dataset ${!!dataset} nor metadata ${!!metadata} available.`
+      `Neither dataset ${!!dataset} nor metadata ${!!metadata} available.`,
     );
   }
   if (isVideo(transferSyntaxUid)) {
@@ -74,7 +74,7 @@ async function cs3dThumbnail(
       originalImageFrame,
       dataset,
       metadata,
-      transferSyntaxUid
+      transferSyntaxUid,
     );
   } catch (error) {
     console.log("Error while decoding image:", error);
@@ -90,13 +90,13 @@ async function cs3dThumbnail(
   const pixelData = dicomCodec.getPixelData(
     imageFrame,
     imageInfo,
-    transferSyntaxUid
+    transferSyntaxUid,
   );
   return staticCS.getRenderedBuffer(
     transferSyntaxUid,
     pixelData,
     metadata,
-    doneCallback
+    doneCallback,
   );
 }
 
@@ -146,7 +146,7 @@ class StaticWado {
       setStudyData,
       rawDicomWriter: RawDicomWriter(this.options),
       notificationService: new NotificationService(
-        this.options.notificationDir
+        this.options.notificationDir,
       ),
       internalGenerateImage: cs3dThumbnail,
     };
@@ -184,13 +184,13 @@ class StaticWado {
     if (!this.showProgress) return;
     this.processedFiles++;
     const percentage = Math.round(
-      (this.processedFiles / this.totalFiles) * 100
+      (this.processedFiles / this.totalFiles) * 100,
     );
     const progressBar =
       "=".repeat(Math.floor(percentage / 4)) +
       "-".repeat(25 - Math.floor(percentage / 4));
     process.stdout.write(
-      `\r[${progressBar}] ${percentage}% | ${this.processedFiles}/${this.totalFiles} files`
+      `\r[${progressBar}] ${percentage}% | ${this.processedFiles}/${this.totalFiles} files`,
     );
   }
 
@@ -202,7 +202,7 @@ class StaticWado {
           if (fs.statSync(file).isDirectory()) {
             const dirFiles = fs.readdirSync(file, { recursive: true });
             this.totalFiles += dirFiles.filter(
-              (f) => !fs.statSync(path.join(file, f)).isDirectory()
+              (f) => !fs.statSync(path.join(file, f)).isDirectory(),
             ).length;
           } else {
             this.totalFiles++;
@@ -215,7 +215,7 @@ class StaticWado {
                 { FailureReason: 0xd000, TextValue: "File not DICOM" },
               ],
             },
-            file
+            file,
           );
         }
       }
@@ -297,13 +297,13 @@ class StaticWado {
         sopInstanceUid: dataSet.string("x00080018"),
         transferSyntaxUid: dataSet.string("x00020010"),
       },
-      params.file
+      params.file,
     );
 
     const targetId = transcodeId(
       id,
       this.options,
-      dataSet.uint16(Tags.RawSamplesPerPixel)
+      dataSet.uint16(Tags.RawSamplesPerPixel),
     );
 
     let bulkDataIndex = 0;
@@ -323,7 +323,7 @@ class StaticWado {
             {
               gzip: false,
               mkdir: true,
-            }
+            },
           );
           await writeStream.write(bulkData);
           await writeStream.close();
@@ -332,7 +332,7 @@ class StaticWado {
           targetId,
           _bulkDataIndex,
           bulkData,
-          options
+          options,
         );
       },
       imageFrame: async (originalImageFrame) => {
@@ -345,7 +345,7 @@ class StaticWado {
           targetId,
           originalImageFrame,
           dataSet,
-          this.options
+          this.options,
         );
 
         const lossyImage = await generateLossyImage(id, decoded, this.options);
@@ -357,7 +357,7 @@ class StaticWado {
           await this.callback.imageFrame(
             lossyImage.id,
             currentImageFrameIndex,
-            lossyImage.imageFrame
+            lossyImage.imageFrame,
           );
         }
 
@@ -369,13 +369,13 @@ class StaticWado {
             id,
             frameIndex: currentImageFrameIndex,
           },
-          this.options
+          this.options,
         );
 
         return this.callback.imageFrame(
           transcodedId,
           currentImageFrameIndex,
-          transcodedImageFrame
+          transcodedImageFrame,
         );
       },
       videoWriter: async (_dataSet) => this.callback.videoWriter(id, _dataSet),
@@ -394,14 +394,14 @@ class StaticWado {
       dataSet,
       transcodedMeta,
       this.callback,
-      this.options
+      this.options,
     );
     await thumbnailService.generateRendered(
       id,
       dataSet,
       transcodedMeta,
       this.callback,
-      this.options
+      this.options,
     );
     await this.callback.metadata(targetId, transcodedMeta);
 
@@ -418,14 +418,14 @@ class StaticWado {
     dataSet,
     metadata,
     transferSyntaxUid,
-    doneCallback
+    doneCallback,
   ) {
     return cs3dThumbnail(
       originalImageFrame,
       dataSet,
       metadata,
       transferSyntaxUid,
-      doneCallback
+      doneCallback,
     );
   }
 
@@ -464,7 +464,7 @@ class StaticWado {
       const study = await JSONReader(
         `${studiesDir}/${dir}`,
         "index.json.gz",
-        null
+        null,
       );
       if (study === null) {
         console.log("No study found in", dir);

packages/static-wado-creator/lib/createPart10.js

@@ -18,7 +18,7 @@ const createFmi = (instance) => {
     UncompressedLEIExplicit;
   const MediaStorageSOPClassUID = Tags.getValue(
     instance,
-    Tags.MediaStorageSOPClassUID
+    Tags.MediaStorageSOPClassUID,
   );
   const SOPInstanceUID = Tags.getValue(instance, Tags.SOPInstanceUID);
   const naturalFmi = {

packages/static-wado-creator/lib/createThumbnail.js → packages/static-wado-creator/lib/createThumbnail.mjs

@@ -1,83 +1,23 @@
-const {
+import {
   Tags,
   readBulkData,
   handleHomeRelative,
-} = require("@radicalimaging/static-wado-util");
-const dcmjs = require("dcmjs");
+  readBulkDataValue,
+  readAllBulkData,
+} from "@radicalimaging/static-wado-util";
+import dcmjs from "dcmjs";
 
-const StaticWado = require("./StaticWado");
-const adaptProgramOpts = require("./util/adaptProgramOpts");
-const WriteStream = require("./writer/WriteStream");
+import StaticWado from "./StaticWado";
+import adaptProgramOpts from "./util/adaptProgramOpts";
+import WriteStream from "./writer/WriteStream";
 
 const UncompressedLEIExplicit = "1.2.840.10008.1.2.1";
 const { DicomDict, DicomMetaDictionary } = dcmjs.data;
 
 const fileMetaInformationVersionArray = new Uint8Array(2);
 fileMetaInformationVersionArray[1] = 1;
 
-const readBulkDataValue = async (studyDir, instance, value, options) => {
-  const { BulkDataURI } = value;
-  value.vr = "OB";
-  const seriesUid = Tags.getValue(instance, Tags.SeriesInstanceUID);
-  const numberOfFrames = Tags.getValue(instance, Tags.NumberOfFrames) || 1;
-  if (BulkDataURI.indexOf("/frames") !== -1) {
-    const seriesDir = `${studyDir}/series/${seriesUid}`;
-    if (options?.frame === false) {
-      return;
-    }
-    // Really only support a limited number of frames based on memory size
-    value.Value = [];
-    if (typeof options?.frame === "number") {
-      console.noQuiet("Reading frame", options.frame);
-      const bulk = await readBulkData(seriesDir, BulkDataURI, options.frame);
-      if (!bulk) {
-        return;
-      }
-      value.Value[options.frame - 1] = bulk.binaryData;
-      value.transferSyntaxUid = bulk.transferSyntaxUid;
-      value.contentType = bulk.contentType;
-      return;
-    }
-    console.noQuiet("Reading frames", 1, "...", numberOfFrames);
-    for (let frame = 1; frame <= numberOfFrames; frame++) {
-      const bulk = await readBulkData(seriesDir, BulkDataURI, frame);
-      if (!bulk) break;
-      value.Value.push(bulk.binaryData);
-      value.transferSyntaxUid = bulk.transferSyntaxUid;
-      value.contentType = bulk.contentType;
-    }
-  } else {
-    const bulk = await readBulkData(studyDir, BulkDataURI);
-    value.Value = [new ArrayBuffer(bulk.binaryData)];
-    value.contentType = bulk.contentType;
-  }
-};
-
-const readBinaryData = async (dir, instance, options = { frame: true }) => {
-  for (const tag of Object.keys(instance)) {
-    const v = instance[tag];
-    if (v.BulkDataURI) {
-      await readBulkDataValue(dir, instance, v, options);
-      continue;
-    }
-    if (!v.vr) {
-      const value0 = v.Value?.[0];
-      if (typeof value0 === "string") {
-        v.vr = "LT";
-      } else {
-        console.log("Deleting", tag, v.Value, v);
-        delete instance[tag];
-      }
-      continue;
-    }
-    if (v.vr === "SQ" && v.Values?.length) {
-      await Promise.all(v.Values.map(readBinaryData));
-      continue;
-    }
-  }
-};
-
-module.exports = async function createThumbnail(options, program) {
+export async function createThumbnail(options, program) {
   const finalOptions = adaptProgramOpts(options, {
     ...this,
     // Instance metadata is the instances/<sopUID>/metadata.gz files
@@ -141,7 +81,7 @@ module.exports = async function createThumbnail(options, program) {
       continue;
     }
 
-    await readBinaryData(dir, instance, codecOptions);
+    await readAllBulkData(dir, instance, codecOptions);
 
     const availableTransferSyntaxUID = Tags.getValue(
       instance,
@@ -178,4 +118,6 @@ module.exports = async function createThumbnail(options, program) {
     }
   }
   await Promise.all(promises);
-};
+}
+
+export default createThumbnail;

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

@@ -2,7 +2,8 @@ const ConfigPoint = require("config-point");
 const { staticWadoConfig } = require("@radicalimaging/static-wado-util");
 const createMain = require("./createMain");
 const createPart10 = require("./createPart10");
-const createThumbnail = require("./createThumbnail");
+const { createThumbnail } = require("./createThumbnail");
+const { transcodeImages } = require("./transcodeImages");
 const deleteMain = require("./deleteMain");
 const rejectMain = require("./rejectMain");
 const serverMain = require("./serverMain");
@@ -305,6 +306,12 @@ const { mkdicomwebConfig } = ConfigPoint.register({
           },
         ],
       },
+      {
+        command: "transcode",
+        main: transcodeImages,
+        helpDescription:
+          "Transcode images or create alternate representations for the specified study",
+      },
       {
         command: "instance",
         arguments: ["input"],

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

@@ -44,7 +44,7 @@ async function deduplicateSingleInstance(id, imageFrame, { force }) {
       deduplicated,
       key,
       this.extractors[key],
-      TagLists.RemoveExtract
+      TagLists.RemoveExtract,
     );
     const hashKey = getValue(extracted, Tags.DeduppedHash);
     await studyData.addExtracted(this, hashKey, extracted);
@@ -99,7 +99,7 @@ const InstanceDeduplicate = (options) =>
     const deduppedInstance = await this.deduplicateSingleInstance(
       id,
       imageFrame,
-      options
+      options,
     );
     if (deduppedInstance) {
       // this refers to callee

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

@@ -32,15 +32,15 @@ function ScanStudy(options) {
     const deduplicatedInstancesPath = path.join(
       deduplicatedInstancesRoot,
       // studyInstanceUid,
-      studySubDir
+      studySubDir,
     );
     const deduplicatedPath = path.join(deduplicatedRoot, studySubDir);
     console.verbose(
       "Importing",
       studyInstanceUid,
       studyPath,
       deduplicatedInstancesPath,
-      deduplicatedPath
+      deduplicatedPath,
     );
     return this.completeStudy.getCurrentStudyData(this, {
       studyPath,