@radicalimaging/static-wado-creator 1.3.0 → 1.5.0

package/lib/createPart10.js

@@ -1,6 +1,5 @@
 /* eslint-disable no-param-reassign */
 const { Tags, readBulkData } = require("@radicalimaging/static-wado-util");
-const fs = require("fs");
 const dcmjs = require("dcmjs");
 
 const StaticWado = require("./StaticWado");

package/lib/mkdicomwebConfig.js

@@ -72,7 +72,7 @@ const { mkdicomwebConfig } = ConfigPoint.register({
       {
         key: "-t, --content-type <type>",
         description: 'Destination type to compress to (choices: "jpeg", "jls", "lei", "jls-lossy", "jhc", "jxl" or DICOM Transfer Syntax UID - default: "jls")',
-        defaultValue: "jhc",
+        defaultValue: "jls",
         customParser: compressionOptionParser,
       },
       {
@@ -135,8 +135,8 @@ const { mkdicomwebConfig } = ConfigPoint.register({
         defaultValue: false,
       },
       {
-        key: "--no-thumb",
-        description: "Skip thumbnail generation",
+        key: "--thumb",
+        description: "Generate thumbnails",
       },
       {
         key: "--dcm2jpg",

package/lib/operation/ThumbnailService.js

@@ -110,10 +110,6 @@ class ThumbnailService {
   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];
@@ -133,6 +129,11 @@ class ThumbnailService {
       }
       return null;
     }
+
+    if (!options.thumb) {
+      return null;
+    }
+
     if (options.dcm2jpg) {
       return this.dcm2jpg(id.filename, id.imageFrameRootPath.replace(/frames/, "thumbnail"), {});
     }

package/lib/operation/adapter/transcodeImage.js

@@ -201,14 +201,14 @@ const beforeEncode = (options, encoder) => {
 
 function scale(imageFrame, imageInfo) {
   const { rows, columns, bitsPerPixel, pixelRepresentation, samplesPerPixel } = imageInfo;
-  let arrayConstructor = Float32Array;
+  let ArrayConstructor = Float32Array;
   if (bitsPerPixel === 8) {
-    arrayConstructor = pixelRepresentation ? Int8Array : Uint8Array;
+    ArrayConstructor = pixelRepresentation ? Int8Array : Uint8Array;
   } else if (bitsPerPixel > 8 && bitsPerPixel <= 16) {
-    arrayConstructor = pixelRepresentation ? Int16Array : Uint16Array;
+    ArrayConstructor = pixelRepresentation ? Int16Array : Uint16Array;
   }
   const src = {
-    pixelData: new arrayConstructor(imageFrame.buffer),
+    pixelData: new ArrayConstructor(imageFrame.buffer),
     rows,
     columns,
     samplesPerPixel,
@@ -218,7 +218,7 @@ function scale(imageFrame, imageInfo) {
     columns: Math.round(columns / 4),
     samplesPerPixel,
   };
-  dest.pixelData = new arrayConstructor(dest.rows * dest.columns * samplesPerPixel);
+  dest.pixelData = new ArrayConstructor(dest.rows * dest.columns * samplesPerPixel);
   replicate(src, dest);
 
   return {
@@ -286,6 +286,10 @@ async function generateLossyImage(id, decoded, options) {
   }
 }
 
+function isPalette(dataSet) {
+  return dataSet.string(Tags.RawPhotometricInterpretation) === "PALETTE COLOR";
+}
+
 /**
  * Transcode imageFrame. It uses transcodeMap to define the target encoding based on source encoding.
  *
@@ -302,7 +306,7 @@ async function transcodeImageFrame(id, targetIdSrc, imageFrame, dataSet, options
 
   const samplesPerPixel = dataSet.uint16(Tags.RawSamplesPerPixel);
   const planarConfiguration = dataSet.uint16("x00280006");
-  if (!shouldTranscodeImageFrame(id, options, samplesPerPixel) || planarConfiguration === 1) {
+  if (!shouldTranscodeImageFrame(id, options, samplesPerPixel) || planarConfiguration === 1 || isPalette(dataSet)) {
     console.verbose("Shouldn't transcode");
     return {
       id,

package/lib/operation/getValue.js

@@ -8,7 +8,9 @@ function decodeUtf8(s, options) {
 }
 
 /** Gets a value as a UTF-8 string - todo, make UTF-8 decode optional. */
-const getValueInlineString = (dataSet, attr, options) => [decodeUtf8(dataSet.string(attr.tag), options)];
+const getValueInlineString = (dataSet, attr, options) => [
+  decodeUtf8(dataSet.string(attr.tag), options),
+];
 
 const getStrings = (dataSet, attr, options) => {
   const ret = dataSet.string(attr.tag);
@@ -20,21 +22,27 @@ const getStrings = (dataSet, attr, options) => {
 
 const getValuePatientName = (dataSet, attr) => {
   const strings = getStrings(dataSet, attr);
-  return (strings && strings.map((item) => ({ Alphabetic: item }))) || undefined;
+  return (
+    (strings && strings.map((item) => ({ Alphabetic: item }))) || undefined
+  );
 };
 
 /** Gets either InlineBinary or BulkDataURI, if already defined */
 const getValueInlineBinary = (dataSet, attr) => {
   if (attr.BulkDataURI) return { BulkDataURI: attr.BulkDataURI };
-  const binaryValue = dataSet.byteArray.slice(attr.dataOffset, attr.dataOffset + attr.length);
+  const binaryValue = dataSet.byteArray.slice(
+    attr.dataOffset,
+    attr.dataOffset + attr.length
+  );
   return { InlineBinary: binaryValue.toString("base64") };
 };
 
 const getValueInlineSignedShort = (dataSet, attr) => {
-  if (attr.length > 2) {
-    return getValueInlineBinary(dataSet, attr);
+  const ret = [];
+  for (let i = 0; i < attr.length / 2; i++) {
+    ret.push(dataSet.int16(attr.tag, i));
   }
-  return [dataSet.int16(attr.tag)];
+  return ret;
 };
 
 const getValueInlineUnsignedShort = (dataSet, attr) => {
@@ -70,9 +78,11 @@ const getValueInlineFloat = (dataSet, attr) => {
   return ret;
 };
 
-const getValueInlineIntString = (dataSet, attr) => getStrings(dataSet, attr).map((val) => parseInt(val));
+const getValueInlineIntString = (dataSet, attr) =>
+  getStrings(dataSet, attr).map((val) => parseInt(val));
 
-const getValueInlineFloatString = (dataSet, attr) => getStrings(dataSet, attr).map((val) => parseFloat(val));
+const getValueInlineFloatString = (dataSet, attr) =>
+  getStrings(dataSet, attr).map((val) => parseFloat(val));
 
 const getValueInlineFloatDouble = (dataSet, attr) => {
   if (attr.length > 8) {
@@ -177,15 +187,30 @@ const isValueInline = (attr, options) => {
  * @param {*} parentAttr attr's parent. If not present means attr is at root level.
  * @returns
  */
-const getValue = async (dataSet, attr, vr, getDataSet, callback, options, parentAttr) => {
+const getValue = async (
+  dataSet,
+  attr,
+  vr,
+  getDataSet,
+  callback,
+  options,
+  parentAttr
+) => {
   // It will only process pixelData tag if on metadata root. Otherwise it will be skiped.
   if (attr.tag === "x7fe00010" && !parentAttr) {
-    const BulkDataURI = await extractImageFrames(dataSet, attr, vr, callback, options);
+    const BulkDataURI = await extractImageFrames(
+      dataSet,
+      attr,
+      vr,
+      callback,
+      options
+    );
     return { BulkDataURI };
   }
   if (attr.tag === "xfffee00d") return undefined;
   // Group length
-  if (attr.tag.length == 9 && attr.tag.substring(5, 9) === "0000") return undefined;
+  if (attr.tag.length == 9 && attr.tag.substring(5, 9) === "0000")
+    return undefined;
   if (attr.items) {
     // sequences
     const result = [];
@@ -202,7 +227,10 @@ const getValue = async (dataSet, attr, vr, getDataSet, callback, options, parent
   if (isValueInline(attr, options)) {
     return getValueInline(dataSet, attr, vr, options);
   }
-  const binaryValue = dataSet.byteArray.slice(attr.dataOffset, attr.dataOffset + attr.length);
+  const binaryValue = dataSet.byteArray.slice(
+    attr.dataOffset,
+    attr.dataOffset + attr.length
+  );
   const mimeType = attr.tag == "x00420011" && dataSet.string("x00420012");
 
   const BulkDataURI = await callback.bulkdata(binaryValue, { mimeType });

package/lib/writer/HashDataWriter.js

@@ -16,7 +16,6 @@ const extensions = {
 };
 
 const baseHasher = hashFactory.hasher();
-const MAX_HASH = 1024 * 1024;
 
 const hasher = {
   hash: (v) => {

package/lib/writer/VideoWriter.js

@@ -19,16 +19,23 @@ const VIDEO_TYPES = {
   // TODO - add the new multi-segment MPEG2 and H264 variants
 };
 
-const isVideo = (value) => VIDEO_TYPES[value && value.string ? value.string(Tags.RawTransferSyntaxUID) : value];
+const isVideo = (value) =>
+  VIDEO_TYPES[
+    value && value.string ? value.string(Tags.RawTransferSyntaxUID) : value
+  ];
 
 const VideoWriter = () =>
   async function run(id, dataSet) {
     console.log(`Writing video  ${id.sopInstanceUid}`);
     const extension = VIDEO_TYPES[dataSet.string(Tags.RawTransferSyntaxUID)];
     const filename = `index.${extension}`;
-    const writeStream = WriteStream(`${id.sopInstanceRootPath}/rendered`, filename, {
-      mkdir: true,
-    });
+    const writeStream = WriteStream(
+      `${id.sopInstanceRootPath}/rendered`,
+      filename,
+      {
+        mkdir: true,
+      }
+    );
     let length = 0;
     const { fragments } = dataSet.elements.x7fe00010;
 
@@ -39,13 +46,18 @@ const VideoWriter = () =>
     // The zero position fragment isn't available, even though present in the original data
     for (let i = 0; i < fragments.length; i++) {
       const fragment = fragments[i];
-      const blob = dataSet.byteArray.slice(fragment.position, fragment.position + fragment.length);
+      const blob = dataSet.byteArray.slice(
+        fragment.position,
+        fragment.position + fragment.length
+      );
       length += blob.length;
       await writeStream.write(blob);
     }
     await writeStream.close();
-    console.log(`Done video ${id.sopInstanceRootPath}\\${filename} of length ${length}`);
-    return `series/${id.seriesInstanceUid}/instances/${id.sopInstanceUid}/pixeldata.${extension}?length=${length}&offset=0`;
+    console.log(
+      `Done video ${id.sopInstanceRootPath}\\${filename} of length ${length}`
+    );
+    return `series/${id.seriesInstanceUid}/instances/${id.sopInstanceUid}/rendered?length=${length}&offset=0&accept=video/mp4`;
   };
 
 module.exports = VideoWriter;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@radicalimaging/static-wado-creator",
-  "version": "1.3.0",
+  "version": "1.5.0",
   "description": "Library to convert DICOMP10 to DICOMweb format. Original upstream: https://github.com/chafey/dicomp10-to-dicomweb-js",
   "publishConfig": {
     "access": "public"
@@ -55,15 +55,16 @@
     "verbose": true
   },
   "dependencies": {
-    "@cornerstonejs/dicom-codec": ">=1.0.2",
-    "@radicalimaging/static-cs-lite": ">=1.3.0",
-    "@radicalimaging/static-wado-util": ">=1.3.0",
+    "@cornerstonejs/dicom-codec": ">=1.0.5",
+    "@radicalimaging/static-cs-lite": "^1.5.0",
+    "@radicalimaging/static-wado-util": "^1.5.0",
     "canvas": "^2.11.1",
     "config-point": ">=0.5.1",
     "dcmjs": "^0.29.5",
     "dicom-parser": "^1.8.13",
     "glob": "^7.2.0",
     "node-object-hash": "^3.0.0",
+    "npmjs": "npm publish",
     "uuid": "^8.3.2"
   },
   "devDependencies": {

package/CHANGELOG.md

@@ -1,67 +0,0 @@
-# Change Log
-
-All notable changes to this project will be documented in this file.
-See [Conventional Commits](https://conventionalcommits.org) for commit guidelines.
-
-## [0.6.4](https://github.com/OHIF/static-wado/compare/@radicalimaging/static-wado-creator@0.6.3...@radicalimaging/static-wado-creator@0.6.4) (2022-04-04)
-
-**Note:** Version bump only for package @radicalimaging/static-wado-creator
-
-
-
-
-
-## [0.6.3](https://github.com/OHIF/static-wado/compare/@radicalimaging/static-wado-creator@0.6.2...@radicalimaging/static-wado-creator@0.6.3) (2022-03-14)
-
-**Note:** Version bump only for package @radicalimaging/static-wado-creator
-
-
-
-
-
-## [0.6.2](https://github.com/OHIF/static-wado/compare/@radicalimaging/static-wado-creator@0.6.1...@radicalimaging/static-wado-creator@0.6.2) (2022-03-04)
-
-**Note:** Version bump only for package @radicalimaging/static-wado-creator
-
-
-
-
-
-## [0.6.1](https://github.com/OHIF/static-wado/compare/@radicalimaging/static-wado-creator@0.6.0...@radicalimaging/static-wado-creator@0.6.1) (2022-03-04)
-
-**Note:** Version bump only for package @radicalimaging/static-wado-creator
-
-
-
-
-
-# [0.6.0](https://github.com/OHIF/static-wado/compare/@radicalimaging/static-wado-creator@0.5.1...@radicalimaging/static-wado-creator@0.6.0) (2022-03-03)
-
-
-### Bug Fixes
-
-* **static-wado:** make the various constructors use a straight configuration without using the program data ([1997d9f](https://github.com/OHIF/static-wado/commit/1997d9f0fe2e0a084d31edeb475494bcec78fd77))
-
-
-### Features
-
-* **static-wado:** qido series fallback to retrieve from proxyAe ([#8](https://github.com/OHIF/static-wado/issues/8)) ([47b5550](https://github.com/OHIF/static-wado/commit/47b55503732e25be08b215bdc201593f64de52e6))
-
-
-
-
-
-## 0.5.1 (2022-02-16)
-
-
-### Bug Fixes
-
-* **pencil:** add more files to lint, increase test config and README ([89b667c](https://github.com/OHIF/static-wado/commit/89b667c83d324ab9fa540cda0c037af8fe088f72))
-* **pencil:** adding must package and minor test changes ([9194f3f](https://github.com/OHIF/static-wado/commit/9194f3f1bb52da57e20bb8bb9f07262bcebdffbf))
-* **pencil:** code review.lint ([fa1a58a](https://github.com/OHIF/static-wado/commit/fa1a58a0c62015503575fbeb172b71810c6833de))
-* **pencil:** fix format ([68fbc9b](https://github.com/OHIF/static-wado/commit/68fbc9bf5a3e9bf85e3fbcddfb3e0759e79b769d))
-* **pencil:** fix lint and add pre-commit restr ([deec345](https://github.com/OHIF/static-wado/commit/deec34524531d5a8595a775bac414f63f60e9f23))
-* **pencil:** lint/prettier ([d6ecbc6](https://github.com/OHIF/static-wado/commit/d6ecbc6b5961e03e8a557f4fcc78af53549132cd))
-* **pencil:** moving from wado-js to wado repo ([5916aec](https://github.com/OHIF/static-wado/commit/5916aecd7c77dbc4882681877e2b51210976427f))
-* **pencil:** readme link name ([40408ab](https://github.com/OHIF/static-wado/commit/40408ab6b4e97c8656e30b1dd2c30b92440b9f90))
-* **pencil:** unit tests migration ([d9d56dd](https://github.com/OHIF/static-wado/commit/d9d56dd619fb1f41ed1d5ad85f7f804e013c6527))