larvitar 1.5.13 → 2.0.0

package/imaging/{imageLoading.js → imageLoading.ts}

@@ -1,29 +1,32 @@
 /** @module imaging/imageLoading
  *  @desc This file provides functionalities for
- *        initialize, configure and update WadoImageLoader
+ *        initialize, configure and update DICOMImageLoader
  */
 
 // external libraries
 import cornerstone from "cornerstone-core";
 import dicomParser from "dicom-parser";
+// import cornerstoneDICOMImageLoader from "@cornerstonejs/dicom-image-loader/dist/cornerstoneDICOMImageLoader.bundle.min.js";
 import { default as cornerstoneDICOMImageLoader } from "cornerstone-wado-image-loader";
 import cornerstoneWebImageLoader from "cornerstone-web-image-loader";
 import cornerstoneFileImageLoader from "cornerstone-file-image-loader";
 import { forEach } from "lodash";
 
 // internal libraries
-import { larvitar_store } from "./imageStore";
+import store from "./imageStore";
 import { getSortedStack, getSortedUIDs } from "./imageUtils";
 import { loadNrrdImage } from "./loaders/nrrdLoader";
 import { loadReslicedImage } from "./loaders/resliceLoader";
 import { loadMultiFrameImage } from "./loaders/multiframeLoader";
+import { ImageObject, Instance, Series, StagedProtocol } from "./types";
+import { getLarvitarManager } from "./loaders/commonLoader";
 
 /**
  * Global standard configuration
  * @inner
  * @var {Object} globalConfig
  * @property {Number} maxWebWorkers - number of maximum web workers
- * @property {String} webWorkerPath - path to default WADO web worker
+ * @property {String} webWorkerPath - path to default DICOM web worker
  * @property {} - see https://github.com/cornerstonejs/cornerstoneDICOMImageLoader/blob/master/docs/WebWorkers.md
  */
 
@@ -54,12 +57,12 @@ const globalConfig = {
  */
 
 /**
- * Configure cornerstoneDICOMImageLoader
+ * Configure DICOMImageLoader
  * @instance
  * @function initializeImageLoader
  * @param {Object} config - Custom config @default globalConfig
  */
-export const initializeImageLoader = function (config) {
+export const initializeImageLoader = function (config?: typeof globalConfig) {
   let imageLoaderConfig = config ? config : globalConfig;
   cornerstoneDICOMImageLoader.external.cornerstone = cornerstone;
   cornerstoneDICOMImageLoader.external.dicomParser = dicomParser;
@@ -119,28 +122,32 @@ export const registerMultiFrameImageLoader = function () {
 };
 
 /**
- * Update the allSeriesStack object using wadoImageLoader fileManager
+ * Update the allSeriesStack object using DICOMImageLoader fileManager
  * @instance
  * @function updateLoadedStack
  * @param {Object} seriesData - Cornerstone series object
  * @param {Object} allSeriesStack - Dict containing all series objects
  * @param {String} customId - Optional custom id to overwrite seriesUID as default one
+ * @param {number} sliceIndex - Optional custom index to overwrite slice index as default one
  */
 export const updateLoadedStack = function (
-  seriesData,
-  allSeriesStack,
-  customId
+  seriesData: ImageObject,
+  allSeriesStack: ReturnType<typeof getLarvitarManager>,
+  customId?: string,
+  sliceIndex?: number
 ) {
+  let lid = seriesData.metadata.larvitarSeriesInstanceUID;
   let sid = seriesData.metadata.seriesUID;
   let ssid = seriesData.metadata.studyUID;
-  let iid = seriesData.metadata.instanceUID;
+  let iid = seriesData.metadata.instanceUID as string;
   let seriesDescription = seriesData.metadata.seriesDescription;
   let numberOfSlices = seriesData.metadata["x00540081"]
     ? seriesData.metadata["x00540081"]
     : seriesData.metadata["x00201002"];
   let numberOfFrames = seriesData.metadata["x00280008"];
   let modality = seriesData.metadata["x00080060"];
-  let isMultiframe = numberOfFrames > 1 ? true : false;
+  let isMultiframe =
+    numberOfFrames && (numberOfFrames as number) > 1 ? true : false;
   let numberOfTemporalPositions = seriesData.metadata["x00200105"];
   let acquisitionNumberAttribute = seriesData.metadata["x00200012"];
   let is4D = seriesData.metadata.is4D;
@@ -150,50 +157,91 @@ export const updateLoadedStack = function (
 
   let color = cornerstoneDICOMImageLoader.isColorImage(
     seriesData.metadata["x00280004"]
-  );
-  let id = customId || sid;
+  ) as boolean;
+  let id = customId || lid?.toString();
+
+  if (!id) {
+    throw new Error("Unique UID is not defined");
+  }
+
+  // Staged Protocol
+  // https://dicom.nema.org/dicom/2013/output/chtml/part17/sect_K.5.html
+  const numberOfStages = seriesData.metadata["x00082124"]; // Number of stages
+  const numberOfViews = seriesData.metadata["x0008212a"]; // Number of views in stage
+  const isStagedProtocol = numberOfStages ? true : false;
+
   // initialize series stack
   if (!allSeriesStack[id]) {
-    allSeriesStack[id] = {
+    let series: Partial<Series> = {
       currentImageIdIndex: 0,
       imageIds: [], // (ordered)
       instanceUIDs: {}, // instanceUID: imageId (ordered)
       instances: {},
-      seriesDescription: seriesDescription,
-      larvitarSeriesInstanceUID: sid,
-      seriesUID: sid,
-      studyUID: ssid,
-      numberOfImages: is4D ? acquisitionNumberAttribute : 0,
-      numberOfSlices: numberOfSlices,
-      numberOfFrames: numberOfFrames,
-      numberOfTemporalPositions: numberOfTemporalPositions,
+      seriesDescription: seriesDescription as string,
+      larvitarSeriesInstanceUID: lid as string,
+      seriesUID: sid as string,
+      studyUID: ssid as string,
+      numberOfImages: is4D ? (acquisitionNumberAttribute as number) : 0,
+      numberOfSlices: numberOfSlices as number,
+      numberOfFrames: numberOfFrames as number,
+      numberOfTemporalPositions: numberOfTemporalPositions as number,
       isMultiframe: isMultiframe,
-      is4D: is4D,
-      isPDF: isPDF,
-      anonymized: anonymized,
-      modality: modality,
+      is4D: is4D as boolean,
+      isPDF: isPDF as boolean,
+      anonymized: anonymized as boolean,
+      modality: modality as string,
       color: color,
       bytes: 0
     };
+    if (isStagedProtocol) {
+      const stageName = seriesData.metadata["x00082120"];
+      const stageNumber = seriesData.metadata["x00082122"];
+      const viewName = seriesData.metadata["x00082127"];
+      const viewNumber = seriesData.metadata["x00082128"];
+      const stagedProtocol: StagedProtocol = {
+        numberOfStages: numberOfStages as number,
+        numberOfViews: numberOfViews as number,
+        stageName: stageName ? (stageName as string).trim() : undefined,
+        stageNumber: stageNumber as number,
+        viewName: viewName ? (viewName as string).trim() : undefined,
+        viewNumber: viewNumber as number
+      };
+      series.stagedProtocol = stagedProtocol;
+    }
+    allSeriesStack[id] = series as Series;
   }
 
-  const sortMethods = is4D
-    ? ["imagePosition", "contentTime"]
-    : ["imagePosition"];
+  // get instance number from metadata
+  const instanceNumber = seriesData.metadata["x00200013"];
+  const defaultMethod = instanceNumber ? "instanceNumber" : "imagePosition";
+  const sortMethods: Array<"imagePosition" | "contentTime" | "instanceNumber"> =
+    is4D ? [defaultMethod, "contentTime"] : [defaultMethod];
 
   // if the parsed file is a new series instance, keep it
-  if (isNewInstance(allSeriesStack[id].instances, iid)) {
+
+  if (isMultiframe) {
+    allSeriesStack[id].bytes += seriesData.file.size;
+    allSeriesStack[id].dataSet = seriesData.dataSet;
+    allSeriesStack[id].metadata = seriesData.metadata;
+  } else if (isNewInstance(allSeriesStack[id].instances, iid!)) {
     // generate an imageId for the file and store it
     // in allSeriesStack imageIds array, used by
-    // cornerstoneDICOMImageLoader to display the stack of images
+    // DICOMImageLoader to display the stack of images
     let imageId = cornerstoneDICOMImageLoader.wadouri.fileManager.add(
       seriesData.file
-    );
+    ) as string;
+
+    if (sliceIndex !== undefined) {
+      allSeriesStack[id].imageIds[sliceIndex] = imageId;
+    } else {
+      allSeriesStack[id].imageIds.push(imageId);
+    }
 
-    allSeriesStack[id].imageIds.push(imageId);
     if (is4D === false) {
-      allSeriesStack[id].numberOfImages += 1;
+      allSeriesStack[id].numberOfImages =
+        (allSeriesStack[id].numberOfImages || 0) + 1;
     }
+
     allSeriesStack[id].bytes += seriesData.file.size;
     // store needed instance tags
     allSeriesStack[id].instances[imageId] = {
@@ -201,15 +249,27 @@ export const updateLoadedStack = function (
       file: seriesData.file,
       dataSet: seriesData.dataSet
     };
-    // order images in stack
-    allSeriesStack[id].imageIds = getSortedStack(
-      allSeriesStack[id],
-      sortMethods,
-      true
-    );
-    // populate the ordered dictionary of instanceUIDs
-    allSeriesStack[id].instanceUIDs = getSortedUIDs(allSeriesStack[id]);
-    larvitar_store.addSeriesIds(id, allSeriesStack[id].imageIds);
+
+    if (isPDF === false) {
+      if (sliceIndex === undefined) {
+        // order images in stack
+        allSeriesStack[id].imageIds = getSortedStack(
+          allSeriesStack[id] as Series,
+          sortMethods,
+          true
+        );
+        // populate the ordered dictionary of instanceUIDs
+        allSeriesStack[id].instanceUIDs = getSortedUIDs(
+          allSeriesStack[id] as Series
+        );
+      } else {
+        allSeriesStack[id].instanceUIDs[iid] = imageId;
+      }
+      store.addSeriesId(id, allSeriesStack[id].imageIds);
+    } else {
+      allSeriesStack[id].instanceUIDs[iid] = imageId;
+      store.addSeriesId(id, allSeriesStack[id].imageIds);
+    }
   }
 };
 
@@ -223,9 +283,12 @@ export const updateLoadedStack = function (
  * @param {String} iid - instance uid to check
  * @return {Bool} True if is new instance, false if already present
  */
-let isNewInstance = function (instances, iid) {
+let isNewInstance = function (
+  instances: { [key: string]: Instance },
+  iid: string
+) {
   let isNewInstance = true;
-  forEach(instances, function (instance) {
+  forEach(instances, function (instance: Instance) {
     if (instance.metadata.instanceUID === iid) {
       isNewInstance = false;
     }