larvitar 1.5.2 → 1.5.6

package/.github/workflows/build-docs.yml

@@ -38,6 +38,12 @@ jobs:
           repository: clenemt/docdash
           path: ./template/docdash/
 
+      # Install docdash node modules
+      - name: Install node modules
+        working-directory: ./template/docdash/
+        run: |
+          yarn install
+
       # Generate docs
       - name: Generate docs
         run: |
@@ -50,6 +56,4 @@ jobs:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           message: "Update docs"
           branch: ${{ github.head_ref }}
-          empty: true 
-      
-
+          empty: true

package/README.md

@@ -6,15 +6,16 @@
 
 ## Dicom Image Toolkit for CornerstoneJS
 
-### Current version: 1.5.2
+### Current version: 1.5.6
 
-### Latest Published Release: 1.5.2
+### Latest Published Release: 1.5.6
 
 This library provides common DICOM functionalities to be used in web-applications: it's wrapper that simplifies the use of cornerstone-js environment.
 Orthogonal multiplanar reformat is included as well as custom loader/exporter for nrrd files and [Vuex](https://vuex.vuejs.org/) custom integration.
 
 - `index` main file
 - `dataDictionary` json file for dicom tags
+- `imageAnonymization` provides anonymization functionalities
 - `imageColormaps` provides color maps functionalities
 - `imageContours` using to populate cornerstone tool for segmentation contours on 2D images
 - `imageIo` import a dicom image in .nrrd format and build contiguous array for exporting data as volume

package/imaging/imageAnonymization.js

@@ -4,19 +4,61 @@
  */
 
 // external libraries
-import aes from "crypto-js/aes";
 import sha256 from "crypto-js/sha256";
 import Hex from "crypto-js/enc-hex";
 import { forEach } from "lodash";
 
+const SH = [
+  "x00080050" // Accession Number,
+];
+
+const OPTIONAL = [
+  "x00100030", // Patient's Birth Date
+  "x00080090", // Referring Physician's Name,
+  "x00100020", // Patient ID
+  "x00100040", // Patient's Sex
+  "x00200010" // Study ID
+];
+
+const REMOVE = [
+  "x00080014", // Instance Creator UID
+  "x00080080", // Institution Name
+  "x00080081", // Institution Address
+  "x00080092", // Referring Physician's Address
+  "x00080094", // Referring Physician's Telephone numbers
+  "x00081010", // Station Name
+  "x00081030", // Study Description
+  "x0008103e", // Series Description
+  "x00081040", // Institutional Department name
+  "x00081048", // Physician(s) of Record
+  "x00081050", // Performing Physicians' Name
+  "x00081060", // Name of Physician(s) Reading study
+  "x00081070", // Operator's Name
+  "x00081080", // Admitting Diagnoses Description
+  "x00082111", // Derivation Description
+  "x00100032", // Patient's Birth Time
+  "x00101000", // Other Patient Ids
+  "x00101001", // Other Patient Names
+  "x00101010", // Patient's Age
+  "x00101020", // Patient's Size
+  "x00101030", // Patient's Weight
+  "x00101090", // Medical Record Locator
+  "x00102160", // Ethnic Group
+  "x00102180", // Occupation
+  "x001021b0", // Additional Patient's History
+  "x00104000", // Patient Comments
+  "x00181000", // Device Serial Number
+  "x00181030", // Protocol Name
+  "x00204000", // Image Comments
+  "x00400275" // Request Attributes Sequence
+];
+
 // global vars
 const TAGS = [
   "x00080014", // Instance Creator UID
-  "x00080018", // SOP Instance UID
   "x00080050", // Accession Number
   "x00080080", // Institution Name
   "x00080081", // Institution Address
-  "x00080081", // Institution Address
   "x00080090", // Referring Physician's Name
   "x00080092", // Referring Physician's Address
   "x00080094", // Referring Physician's Telephone numbers
@@ -29,7 +71,6 @@ const TAGS = [
   "x00081060", // Name of Physician(s) Reading study
   "x00081070", // Operator's Name
   "x00081080", // Admitting Diagnoses Description
-  "x00081155", // Referenced SOP Instance UID
   "x00082111", // Derivation Description
   "x00100010", // Patient's Name
   "x00100020", // Patient ID
@@ -48,15 +89,12 @@ const TAGS = [
   "x00104000", // Patient Comments
   "x00181000", // Device Serial Number
   "x00181030", // Protocol Name
-  "x0020000d", // Study Instance UID
-  "x0020000e", // Series Instance UID
   "x00200010", // Study ID
   "x00200052", // Frame of Reference UID
   "x00200200", // Synchronization Frame of Reference UID
   "x00204000", // Image Comments
   "x00400275", // Request Attributes Sequence
   "x0040a124", // UID
-  "x0040a730", // Content Sequence
   "x00880140", // Storage Media File-set UID
   "x30060024", // Referenced Frame of Reference UID
   "x300600c2" // Related Frame of Reference UID
@@ -65,7 +103,6 @@ const TAGS = [
 /*
  * This module provides the following functions to be exported:
  * anonymize(series)
- * encrypt(series, passphrase)
  */
 
 /**
@@ -79,9 +116,30 @@ export const anonymize = function (series) {
     forEach(TAGS, function (tag) {
       if (tag in instance.metadata) {
         let anonymized_value = sha256(instance.metadata[tag]).toString(Hex);
-        instance.metadata[tag] = anonymized_value;
+        // Patient Tag Anonymization
+        if (tag === "x00100010") {
+          instance.metadata[tag] =
+            "Anonymized^" + anonymized_value.substring(0, 6);
+        }
+        // Short string
+        else if (SH.includes(tag) === true) {
+          instance.metadata[tag] = anonymized_value.substring(0, 16);
+        }
+        // Required, empty if unknown
+        else if (OPTIONAL.includes(tag) === true) {
+          instance.metadata[tag] = "";
+        }
+        // Optional
+        else if (REMOVE.includes(tag) === true) {
+          delete instance.metadata[tag];
+        }
+        // Default sha256
+        else {
+          instance.metadata[tag] = anonymized_value;
+        }
       }
     });
+    instance.metadata["x00120062"] = "YES"; // Patient Identity Removed Attribute
     instance.metadata.seriesUID = instance.metadata["x0020000e"];
     instance.metadata.instanceUID = instance.metadata["x00080018"];
     instance.metadata.studyUID = instance.metadata["x0020000d"];
@@ -90,72 +148,11 @@ export const anonymize = function (series) {
     instance.metadata.patientName = instance.metadata["x00100010"];
     instance.metadata.patientBirthdate = instance.metadata["x00100030"];
     instance.metadata.seriesDescription = instance.metadata["x0008103e"];
+    instance.metadata.anonymized = true;
   });
 
-  delete series["instanceUIDs"];
-  series.instanceUIDs = {};
-
-  forEach(series.imageIds, function (imageId) {
-    series.instanceUIDs[series.instances[imageId].metadata.instanceUID] =
-      imageId;
-  });
-
-  series.larvitarSeriesInstanceUID = sha256(
-    series.larvitarSeriesInstanceUID
-  ).toString(Hex);
-  series.seriesUID = sha256(series.seriesUID).toString(Hex);
-  series.seriesDescription = sha256(series.seriesDescription).toString(Hex);
-  series.studyUID = sha256(series.studyUID).toString(Hex);
-
-  return series;
-};
-
-/**
- * Encrypt DICOM series' metadata using AES
- * @function encrypt
- * @param {Object} series - Cornerstone series object
- * @param {String} passphrase - AES passphrase
- * @returns {Object} anonymized_series: Cornerstone encrypted series object
- */
-export const encrypt = function (series, passphrase) {
-  if (!passphrase) {
-    return "Error, provide a valid passphrase";
-  }
-  forEach(series.instances, function (instance) {
-    forEach(TAGS, function (tag) {
-      if (tag in instance.metadata) {
-        let anonymized_value = aes
-          .encrypt(instance.metadata[tag], passphrase)
-          .toString();
-        instance.metadata[tag] = anonymized_value;
-      }
-    });
-    instance.metadata.seriesUID = instance.metadata["x0020000e"];
-    instance.metadata.instanceUID = instance.metadata["x00080018"];
-    instance.metadata.studyUID = instance.metadata["x0020000d"];
-    instance.metadata.accessionNumber = instance.metadata["x00080050"];
-    instance.metadata.studyDescription = instance.metadata["x00081030"];
-    instance.metadata.patientName = instance.metadata["x00100010"];
-    instance.metadata.patientBirthdate = instance.metadata["x00100030"];
-    instance.metadata.seriesDescription = instance.metadata["x0008103e"];
-  });
-
-  delete series["instanceUIDs"];
-  series.instanceUIDs = {};
-
-  forEach(series.imageIds, function (imageId) {
-    series.instanceUIDs[series.instances[imageId].metadata.instanceUID] =
-      imageId;
-  });
-
-  series.larvitarSeriesInstanceUID = aes
-    .encrypt(series.larvitarSeriesInstanceUID, passphrase)
-    .toString();
-  series.seriesUID = aes.encrypt(series.seriesUID, passphrase).toString();
-  series.seriesDescription = aes
-    .encrypt(series.seriesDescription, passphrase)
-    .toString();
-  series.studyUID = aes.encrypt(series.studyUID, passphrase).toString();
+  series.seriesDescription = undefined;
+  series.anonymized = true;
 
   return series;
 };

package/imaging/imageLoading.js

@@ -34,10 +34,6 @@ const globalConfig = {
     1
   ),
   startWebWorkersOnDemand: true,
-  webWorkerTaskPaths: [
-    "https://unpkg.com/cornerstone-wado-image-loader@4.1.0/dist/610.bundle.min.worker.js",
-    "https://unpkg.com/cornerstone-wado-image-loader@4.1.0/dist/888.bundle.min.worker.js"
-  ],
   taskConfiguration: {
     decodeTask: {
       loadCodecsOnStartup: true,
@@ -150,6 +146,7 @@ export const updateLoadedStack = function (
   let is4D = seriesData.metadata.is4D;
   let SOPUID = seriesData.metadata["x00080016"];
   let isPDF = SOPUID == "1.2.840.10008.5.1.4.1.1.104.1" ? true : false;
+  let anonymized = seriesData.metadata.anonymized;
 
   let color = cornerstoneWADOImageLoader.isColorImage(
     seriesData.metadata["x00280004"]
@@ -173,6 +170,7 @@ export const updateLoadedStack = function (
       isMultiframe: isMultiframe,
       is4D: is4D,
       isPDF: isPDF,
+      anonymized: anonymized,
       modality: modality,
       color: color,
       bytes: 0

package/imaging/imageParsing.js

@@ -280,6 +280,7 @@ let parseFile = function (file) {
               dataSet: dataSet
             };
             imageObject.metadata = metadata;
+            imageObject.metadata.anonymized = false;
             imageObject.metadata.seriesUID = seriesInstanceUID;
             imageObject.metadata.instanceUID = instanceUID;
             imageObject.metadata.studyUID = metadata["x0020000d"];

package/imaging/imageUtils.js

@@ -9,6 +9,8 @@ import {
   sortBy,
   clone,
   find,
+  filter,
+  keys,
   has,
   max,
   map,
@@ -24,6 +26,7 @@ import { convertBytes } from "dicom-character-set";
 // internal libraries
 import { getDicomImageId } from "./loaders/dicomLoader";
 import TAG_DICT from "./dataDictionary.json";
+import { getSeriesDataFromLarvitarManager } from "./loaders/commonLoader";
 
 // global module variables
 // variables used to manage the reslice functionality
@@ -51,6 +54,7 @@ const resliceTable = {
  * getDistanceBetweenSlices(seriesData, sliceIndex1, sliceIndex2)
  * parseTag(dataSet, propertyName, element)
  * isElement(o)
+ * getImageMetadata(dataSet, imageId)
  */
 
 /**
@@ -848,6 +852,43 @@ export const parseTag = function (dataSet, propertyName, element) {
   return value;
 };
 
+/**
+ * @instance
+ * @function getImageMetadata
+ * @param {String} seriesId - The seriesUID
+ * @param {String} instanceUID - The SOPInstanceUID
+ * @return {Array} - List of metadata objects: tag, name and value
+ */
+export const getImageMetadata = function (seriesId, instanceUID) {
+  const seriesData = getSeriesDataFromLarvitarManager(seriesId);
+  const imageId = seriesData.instanceUIDs[instanceUID];
+  let metadata = seriesData.instances[imageId].metadata;
+  // get elements from metadata where the key starts with x and is length 7
+  let metadata_keys = filter(keys(metadata), function (key) {
+    return key.length === 9 && key[0] === "x";
+  });
+  // loop metadata using metadata_keys and return list of key value pairs
+  let metadata_list = map(metadata_keys, function (key) {
+    // if value is a dictionary return empty string
+    const value = metadata[key].constructor == Object ? "" : metadata[key];
+    // convert key removing x and adding comma at position 4
+    const tagKey = (
+      "(" +
+      key.slice(1, 5) +
+      "," +
+      key.slice(5) +
+      ")"
+    ).toUpperCase();
+    const name = TAG_DICT[tagKey] ? TAG_DICT[tagKey].name : "";
+    return {
+      tag: tagKey,
+      name: name,
+      value: value
+    };
+  });
+  return metadata_list;
+};
+
 /* Internal module functions */
 
 /**

package/imaging/loaders/multiframeLoader.js

@@ -175,6 +175,15 @@ export const clearMultiFrameCache = function (seriesId) {
  * @returns {Object} custom image object
  */
 let createCustomImage = function (id, imageId, frameIndex, metadata) {
+  let options = {};
+  // always preScale the pixel array unless it is asked not to
+  options.preScale = {
+    enabled:
+      options.preScale && options.preScale.enabled !== undefined
+        ? options.preScale.enabled
+        : false
+  };
+
   let dataSet = multiframeDatasetCache[id].dataSet;
   let pixelDataElement = dataSet.elements.x7fe00010;
   // Extract pixelData of the required frame
@@ -203,11 +212,27 @@ let createCustomImage = function (id, imageId, frameIndex, metadata) {
       ? window.document.getElementsByTagName("canvas")[0]
       : window.document.createElement("canvas");
 
+  // Get the scaling parameters from the metadata
+  if (options.preScale.enabled) {
+    const scalingParameters = cornerstoneWADOImageLoader.getScalingParameters(
+      cornerstone.metaData,
+      imageId
+    );
+
+    if (scalingParameters) {
+      options.preScale = {
+        ...options.preScale,
+        scalingParameters
+      };
+    }
+  }
+
   const decodePromise = cornerstoneWADOImageLoader.decodeImageFrame(
     imageFrame,
     transferSyntax,
     pixelData,
-    canvas
+    canvas,
+    options
   );
 
   let promise = new Promise((resolve, reject) => {

package/index.js

@@ -37,7 +37,8 @@ import {
   getMeanValue,
   getReslicedMetadata,
   getReslicedPixeldata,
-  getDistanceBetweenSlices
+  getDistanceBetweenSlices,
+  getImageMetadata
 } from "./imaging/imageUtils";
 
 import {
@@ -48,7 +49,7 @@ import {
   importNRRDImage
 } from "./imaging/imageIo";
 
-import { anonymize, encrypt } from "./imaging/imageAnonymization";
+import { anonymize } from "./imaging/imageAnonymization";
 
 import {
   buildLayer,
@@ -243,6 +244,7 @@ export {
   getReslicedMetadata,
   getReslicedPixeldata,
   getDistanceBetweenSlices,
+  getImageMetadata,
   // imageIo
   buildHeader,
   getCachedPixelData,
@@ -251,7 +253,6 @@ export {
   importNRRDImage,
   // imageAnonymization
   anonymize,
-  encrypt,
   // imageLayers
   buildLayer,
   updateLayer,

package/package.json

@@ -6,7 +6,7 @@
     "medical",
     "cornerstone"
   ],
-  "version": "1.5.2",
+  "version": "1.5.6",
   "description": "javascript library for parsing, loading, rendering and interacting with DICOM images",
   "repository": {
     "url": "https://github.com/dvisionlab/Larvitar.git",
@@ -29,7 +29,7 @@
     "cornerstone-core": "^2.6.1",
     "cornerstone-file-image-loader": "^0.3.0",
     "cornerstone-tools": "^6.0.7",
-    "cornerstone-wado-image-loader": "^4.1.3",
+    "cornerstone-wado-image-loader": "^4.10.2",
     "cornerstone-web-image-loader": "^2.1.1",
     "crypto-js": "^4.1.1",
     "dicom-character-set": "^1.0.3",