@radicalimaging/static-wado-creator 1.2.2 → 1.2.4

package/lib/StaticWado.js

@@ -198,8 +198,8 @@ class StaticWado {
     await this.callback.rawDicomWriter?.(id, result, buffer);
 
     const transcodedMeta = transcodeMetadata(result.metadata, id, this.options);
-    await thumbnailService.generateThumbnails(id, dataSet, transcodedMeta, this.callback);
-
+    await thumbnailService.generateThumbnails(id, dataSet, transcodedMeta, this.callback, this.options);
+    await thumbnailService.generateRendered(id, dataSet, transcodedMeta, this.callback, this.options);
     await this.callback.metadata(targetId, transcodedMeta);
 
     // resolve promise with statistics

package/lib/mkdicomwebConfig.js

@@ -109,6 +109,20 @@ const { mkdicomwebConfig } = ConfigPoint.register({
         description: "Force no recompression thumbnail",
         defaultValue: false,
       },
+      {
+        key: "--no-thumb",
+        description: "Skip thumbnail generation",
+      },
+      {
+        key: "--dcm2jpg",
+        description: "Use dcm2jpg for thumbnail image generation",
+        defaultValue: false,
+      },
+      {
+        key: "--rendered",
+        description: "Use dcm2jpg to generate a rendered PNG image",
+        defaultValue: false,
+      },
       {
         key: "-T, --color-content-type <value>",
         description: "Colour content type",
@@ -152,9 +166,9 @@ const { mkdicomwebConfig } = ConfigPoint.register({
         arguments: ["input"],
         main: createMain,
         helpDescription:
-          "Make DICOMweb query and metadata from binary Part 10 DICOM files.  Does a full read of\n" +
-          "deduplicated files each time a study instance UID is found, and only updates those studies\n" +
-          "having at least one ",
+          "Make DICOMweb query and metadata from binary Part 10 DICOM files.  Does a full read\n" +
+          "of deduplicated files each time a study instance UID is found, and only updates\n" +
+          "those studies having at least one ",
       },
       {
         command: "index",

package/lib/model/TagLists.js

@@ -3,7 +3,7 @@ const { Tags } = require("@radicalimaging/static-wado-util");
 
 /* eslint "no-param-reassign": "off" */
 
-const hasher = hashFactory();
+const hasher = hashFactory.hasher();
 
 const { PatientID, PatientName, IssuerOfPatientID } = Tags;
 const { StudyDescription, AccessionNumber, StudyInstanceUID, StudyDate, StudyTime } = Tags;

package/lib/operation/StudyData.js

@@ -6,7 +6,7 @@ const { Tags } = require("@radicalimaging/static-wado-util");
 const TagLists = require("../model/TagLists");
 
 const { getValue, setValue, getList, setList } = Tags;
-const hasher = hashFactory();
+const hasher = hashFactory.hasher();
 
 const getSeriesInstanceUid = (seriesInstance) => getValue(seriesInstance, Tags.SeriesInstanceUID);
 

package/lib/operation/ThumbnailService.js

@@ -80,6 +80,26 @@ class ThumbnailService {
     execSpawn(`ffmpeg -i "${input}" -vf  "thumbnail,scale=640:360" -frames:v 1 -f singlejpeg "${output}"`);
   }
 
+  dcm2jpg(input, output, options) {
+    const script = ["dcm2jpg", `"${input}" "${output}"`];
+    if (options?.format) {
+      script.push("-F", options.format);
+    }
+    execSpawn(script.join(" "));
+  }
+
+  /** Generates a rendered copy of this, assuming --rendered is set.
+   * Requires dcm2jpg to be available.
+   */
+  async generateRendered(itemid, dataSet, metadata, callback, options) {
+    if (!options.rendered) {
+      return null;
+    }
+    const { id } = this.favoriteThumbnailObj;
+    const rendered = id.imageFrameRootPath.replace(/frames/, "rendered");
+    return this.dcm2jpg(id.filename, rendered, { format: "png" });
+  }
+
   /**
    * Generates thumbnails for the levels: instances, series, study.  This is asynchronous
    *
@@ -87,9 +107,13 @@ class ThumbnailService {
    * @param {*} metadata
    * @param {*} callback
    */
-  generateThumbnails(itemId, dataSet, metadata, callback) {
+  async generateThumbnails(itemId, dataSet, metadata, callback, options) {
     const { imageFrame, id } = this.favoriteThumbnailObj;
 
+    if (!options.thumb) {
+      return null;
+    }
+
     // There are various reasons no thumbnails might be generated, so just return
     if (!id) {
       const pixelData = metadata[Tags.PixelData];
@@ -101,16 +125,20 @@ class ThumbnailService {
           const thumbPath = path.join(itemId.sopInstanceRootPath, "rendered");
           console.log("MP4 - converting video format", mp4Path);
           this.ffmpeg(mp4Path, thumbPath);
-        } else {
-          console.log("pixelData = ", pixelData, Tags.PixelData);
+          return thumbPath;
         }
       } else {
         console.log("Series is of other type...", metadata[Tags.Modality]);
       }
       return null;
     }
-    return new Promise((resolve, reject) => {
-      callback.internalGenerateImage(imageFrame, dataSet, metadata, id.transferSyntaxUid, async (thumbBuffer) => {
+    if( options.dcm2jpg ) {
+      return this.dcm2jpg(id.filename, id.imageFrameRootPath.replace(/frames/,"thumbnail"), {});
+    }
+
+    console.log("Using CS2 to generate thumbnails", id, options);
+
+    await callback.internalGenerateImage(imageFrame, dataSet, metadata, id.transferSyntaxUid, async (thumbBuffer) => {
         try {
           if (thumbBuffer) {
             await callback.thumbWriter(id.sopInstanceRootPath, this.thumbFileName, thumbBuffer);
@@ -119,11 +147,11 @@ class ThumbnailService {
             this.copySyncThumbnail(id.seriesRootPath, id.studyPath);
             Stats.StudyStats.add("Thumbnail Write", `Write thumbnail ${this.thumbFileName}`, 100);
           }
-          resolve(this.thumbFileName);
-        } catch (e) {
-          reject(e);
+          return this.thumbFileName;
+        } catch(e) {
+          console.log("Couldn't generate thumbnail", this.thumbFileName, e);
         }
-      });
+
     });
   }
 

package/lib/operation/adapter/transcodeImage.js

@@ -194,7 +194,8 @@ async function transcodeImageFrame(id, targetIdSrc, imageFrame, dataSet, options
   let result = {};
 
   const samplesPerPixel = dataSet.uint16(Tags.RawSamplesPerPixel);
-  if (!shouldTranscodeImageFrame(id, options, samplesPerPixel)) {
+  const planarConfiguration = dataSet.uint16("x00280006");
+  if (!shouldTranscodeImageFrame(id, options, samplesPerPixel) || planarConfiguration === 1) {
     console.verbose("Shouldn't transcode");
     return {
       id,

package/lib/writer/DeduplicateWriter.js

@@ -1,6 +1,6 @@
 const hashFactory = require("node-object-hash");
 
-const hasher = hashFactory();
+const hasher = hashFactory.hasher();
 const { JSONWriter } = require("@radicalimaging/static-wado-util");
 const { Tags } = require("@radicalimaging/static-wado-util");
 const TagLists = require("../model/TagLists");

package/lib/writer/HashDataWriter.js

@@ -1,6 +1,6 @@
 const hashFactory = require("node-object-hash");
+const { createHash } = require("crypto");
 
-const hasher = hashFactory();
 const path = require("path");
 const { Tags } = require("@radicalimaging/static-wado-util");
 const WriteStream = require("./WriteStream");
@@ -15,6 +15,20 @@ const extensions = {
   "application/xml+cda": ".cda.xml",
 };
 
+const baseHasher = hashFactory.hasher();
+const MAX_HASH = 1024*1024;
+
+const hasher = {
+  hash: (v) => {
+    const type = v.constructor?.name;
+    if (type === "Buffer") {
+      return createHash('sha256').update(v).digest('hex');
+    }
+    return baseHasher.hash(v);
+  },
+};
+
+
 /** Writes out JSON files to the given file name.  Automatically GZips them, and adds the extension */
 const HashDataWriter =
   (options) =>

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@radicalimaging/static-wado-creator",
-  "version": "1.2.2",
+  "version": "1.2.4",
   "description": "Library to convert DICOMP10 to DICOMweb format. Original upstream: https://github.com/chafey/dicomp10-to-dicomweb-js",
   "publishConfig": {
     "access": "public"
@@ -63,7 +63,7 @@
     "dcmjs": "^0.29.5",
     "dicom-parser": "^1.8.13",
     "glob": "^7.2.0",
-    "node-object-hash": "^2.3.10",
+    "node-object-hash": "^3.0.0",
     "uuid": "^8.3.2"
   },
   "devDependencies": {