larvitar 1.3.0-beta.0 → 1.3.2

package/README.md

@@ -6,11 +6,11 @@
 
 ## Dicom Image Toolkit for CornestoneJS
 
-### Current version: 1.2.6
+### Current version: 1.3.2
 
-### Latest Stable version: 1.2.6
+### Latest Stable version: 1.3.2
 
-### Latest Published Release: 1.2.6
+### Latest Published Release: 1.3.2
 
 This library provides common DICOM functionalities to be used in web-applications: it's wrapper that simplifies the use of cornestone-js environment.
 Orthogonal multiplanar reformat is included as well as custom loader/exporter for nrrd files and [Vuex](https://vuex.vuejs.org/) custom integration.

package/imaging/imageIo.js

@@ -122,18 +122,25 @@ export const buildData = function (series, useSeriesData) {
         data.set(sliceData, offsetData);
         offsetData += sliceData.length;
       });
+      let t1 = performance.now();
+      console.log(`Call to buildData took ${t1 - t0} milliseconds.`);
+      return data;
     } else {
       larvitar_store.addSeriesIds(series.seriesUID, series.imageIds);
+      let image_counter = 0;
       forEach(series.imageIds, function (imageId) {
         getCachedPixelData(imageId).then(sliceData => {
           data.set(sliceData, offsetData);
           offsetData += sliceData.length;
+          image_counter += 1;
+          if (image_counter == series.imageIds.length) {
+            let t1 = performance.now();
+            console.log(`Call to buildData took ${t1 - t0} milliseconds.`);
+            return data;
+          }
         });
       });
     }
-    let t1 = performance.now();
-    console.log(`Call to buildData took ${t1 - t0} milliseconds.`);
-    return data;
   } else {
     throw new Error("Data has not been builded: not enough memory");
   }

package/imaging/imageLoading.js

@@ -139,9 +139,16 @@ export const updateLoadedStack = function (
   let ssid = seriesData.metadata.studyUID;
   let iid = seriesData.metadata.instanceUID;
   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 numberOfTemporalPositions = seriesData.metadata["x00200105"];
+  let acquisitionNumberAttribute = seriesData.metadata["x00200012"];
+  let is4D = seriesData.metadata.is4D;
+
   let color = cornerstoneWADOImageLoader.isColorImage(
     seriesData.metadata["x00280004"]
   );
@@ -157,15 +164,22 @@ export const updateLoadedStack = function (
       larvitarSeriesInstanceUID: sid,
       seriesUID: sid,
       studyUID: ssid,
-      numberOfImages: 0,
+      numberOfImages: is4D ? acquisitionNumberAttribute : 0,
+      numberOfSlices: numberOfSlices,
       numberOfFrames: numberOfFrames,
+      numberOfTemporalPositions: numberOfTemporalPositions,
       isMultiframe: isMultiframe,
+      is4D: is4D,
       modality: modality,
       color: color,
       bytes: 0
     };
   }
 
+  const sortMethods = is4D
+    ? ["imagePosition", "contentTime"]
+    : ["imagePosition"];
+
   // if the parsed file is a new series instance, keep it
   if (isNewInstance(allSeriesStack[id].instances, iid)) {
     // generate an imageId for the file and store it
@@ -176,7 +190,9 @@ export const updateLoadedStack = function (
     );
 
     allSeriesStack[id].imageIds.push(imageId);
-    allSeriesStack[id].numberOfImages += 1;
+    if (is4D === false) {
+      allSeriesStack[id].numberOfImages += 1;
+    }
     allSeriesStack[id].bytes += seriesData.file.size;
     // store needed instance tags
     allSeriesStack[id].instances[imageId] = {
@@ -187,7 +203,7 @@ export const updateLoadedStack = function (
     // order images in stack
     allSeriesStack[id].imageIds = getSortedStack(
       allSeriesStack[id],
-      ["imagePosition"],
+      sortMethods,
       true
     );
     // populate the ordered dictionary of instanceUIDs

package/imaging/imageParsing.js

@@ -5,6 +5,7 @@
 // external libraries
 import { parseDicom } from "dicom-parser";
 import { forEach, each, has, pick } from "lodash";
+import { v4 as uuidv4 } from "uuid";
 
 // internal libraries
 import { getPixelRepresentation, randomId, parseTag } from "./imageUtils.js";
@@ -126,10 +127,17 @@ export const parseDataSet = function (dataSet, metadata, customFilter) {
  * @function parseNextFile
  * @param {Array} parsingQueue - Array of queued files to be parsed
  * @param {Object} allSeriesStack - Series stack object to be populated
+ * @param {string} uuid - Series uuid to be used if series instance uuid is missing
  * @param {Function} resolve - Promise resolve function
  * @param {Function} reject - Promise reject function
  */
-let parseNextFile = function (parsingQueue, allSeriesStack, resolve, reject) {
+let parseNextFile = function (
+  parsingQueue,
+  allSeriesStack,
+  uuid,
+  resolve,
+  reject
+) {
   // initialize t0 on first file of the queue
   if (
     Object.keys(allSeriesStack).length === 0 &&
@@ -155,22 +163,24 @@ let parseNextFile = function (parsingQueue, allSeriesStack, resolve, reject) {
     let t1 = performance.now();
     console.log(`Call to readFiles took ${t1 - t0} milliseconds.`);
     file = null;
-    reject(allSeriesStack, "Available memory is not enough");
+    reject("Available memory is not enough");
     return;
   } else {
     // parse the file and wait for results
     parseFile(file)
       .then(seriesData => {
+        // use generated series uid if not found in dicom file
+        seriesData.metadata.seriesUID = seriesData.metadata.seriesUID || uuid;
         // add file to cornerstoneWADOImageLoader file manager
         updateLoadedStack(seriesData, allSeriesStack);
         // proceed with the next file to parse
-        parseNextFile(parsingQueue, allSeriesStack, resolve, reject);
+        parseNextFile(parsingQueue, allSeriesStack, uuid, resolve, reject);
         seriesData = null;
         file = null;
       })
       .catch(err => {
         console.warn(err);
-        parseNextFile(parsingQueue, allSeriesStack, resolve, reject);
+        parseNextFile(parsingQueue, allSeriesStack, uuid, resolve, reject);
         file = null;
       });
   }
@@ -193,7 +203,8 @@ let parseFiles = function (fileList) {
     }
   });
   return new Promise((resolve, reject) => {
-    parseNextFile(parsingQueue, allSeriesStack, resolve, reject);
+    const uuid = uuidv4();
+    parseNextFile(parsingQueue, allSeriesStack, uuid, resolve, reject);
   });
 };
 
@@ -220,6 +231,14 @@ let parseFile = function (file) {
         let metadata = {};
         parseDataSet(dataSet, metadata);
 
+        let temporalPositionIdentifier = metadata["x00200100"]; // Temporal order of a dynamic or functional set of Images.
+        let numberOfTemporalPositions = metadata["x00200105"]; // Total number of temporal positions prescribed.
+        const is4D =
+          (temporalPositionIdentifier !== undefined) &
+          (numberOfTemporalPositions > 1)
+            ? true
+            : false;
+
         let numberOfFrames = metadata["x00280008"];
         let isMultiframe = numberOfFrames > 1 ? true : false;
         // Overwrite SOPInstanceUID to manage multiframes.
@@ -279,6 +298,14 @@ let parseFile = function (file) {
               imageObject.metadata.frameDelay = metadata["x00181066"];
             }
             imageObject.metadata.isMultiframe = isMultiframe;
+            if (is4D) {
+              imageObject.metadata.temporalPositionIdentifier =
+                metadata["x00200100"];
+              imageObject.metadata.numberOfTemporalPositions =
+                metadata["x00200105"];
+              imageObject.metadata.contentTime = metadata["x00080033"];
+            }
+            imageObject.metadata.is4D = is4D;
             imageObject.metadata.windowCenter = metadata["x00281050"];
             imageObject.metadata.windowWidth = metadata["x00281051"];
             imageObject.metadata.minPixelValue = metadata["x00280106"];
@@ -292,7 +319,7 @@ let parseFile = function (file) {
           }
         }
       } catch (err) {
-        console.error(err);
+        console.warn(err);
         reject("can not read this file");
       }
     };

package/imaging/imageRendering.js

@@ -369,16 +369,29 @@ export const updateImage = function (
     return;
   }
   let imageId = series.imageIds[imageIndex];
+
   if (imageId) {
+    if (series.is4D) {
+      const timestamp = series.instances[imageId].metadata.contentTime;
+      const timeId =
+        series.instances[imageId].metadata.temporalPositionIdentifier - 1; // timeId from 0 to N
+      larvitar_store.set("timeId", [elementId, timeId]);
+      larvitar_store.set("timestamp", [elementId, timestamp]);
+    }
+
     if (cacheImage) {
       cornerstone.loadAndCacheImage(imageId).then(function (image) {
         cornerstone.displayImage(element, image);
         larvitar_store.set("sliceId", [elementId, imageIndex]);
+        larvitar_store.set("minPixelValue", [elementId, image.minPixelValue]);
+        larvitar_store.set("maxPixelValue", [elementId, image.maxPixelValue]);
       });
     } else {
       cornerstone.loadImage(imageId).then(function (image) {
         cornerstone.displayImage(element, image);
         larvitar_store.set("sliceId", [elementId, imageIndex]);
+        larvitar_store.set("minPixelValue", [elementId, image.minPixelValue]);
+        larvitar_store.set("maxPixelValue", [elementId, image.maxPixelValue]);
       });
     }
   } else {
@@ -512,6 +525,26 @@ export const updateViewportData = function (
     case "Rotate":
       larvitar_store.set("rotation", [elementId, viewportData.rotation]);
       break;
+    case "mouseWheel":
+      const isTimeserie = larvitar_store.get(
+        "viewports",
+        elementId,
+        "isTimeserie"
+      );
+      if (isTimeserie) {
+        const index = viewportData.newImageIdIndex;
+        const timeId = larvitar_store.get("viewports", elementId, "timeIds")[
+          index
+        ];
+        const timestamp = larvitar_store.get(
+          "viewports",
+          elementId,
+          "timestamps"
+        )[index];
+        larvitar_store.set("timeId", [elementId, timeId]);
+        larvitar_store.set("timestamp", [elementId, timestamp]);
+      }
+      break;
     default:
       break;
   }
@@ -536,6 +569,22 @@ export const storeViewportData = function (image, elementId, viewport, data) {
   larvitar_store.set("minSliceId", [elementId, 0]);
   larvitar_store.set("sliceId", [elementId, data.imageIndex]);
   larvitar_store.set("maxSliceId", [elementId, data.numberOfSlices - 1]);
+
+  if (data.isTimeserie) {
+    larvitar_store.set("minTimeId", [elementId, 0]);
+    larvitar_store.set("timeId", [elementId, data.timeIndex]);
+    larvitar_store.set("maxTimeId", [
+      elementId,
+      data.numberOfTemporalPositions - 1
+    ]);
+    let maxSliceId = data.numberOfSlices * data.numberOfTemporalPositions - 1;
+    larvitar_store.set("maxSliceId", [elementId, maxSliceId]);
+
+    larvitar_store.set("timestamp", [elementId, data.timestamp]);
+    larvitar_store.set("timestamps", [elementId, data.timestamps]);
+    larvitar_store.set("timeIds", [elementId, data.timeIds]);
+  }
+
   larvitar_store.set("defaultViewport", [
     elementId,
     viewport.scale,
@@ -674,6 +723,24 @@ let getSeriesData = function (series, defaultProps) {
     data.numberOfSlices = series.imageIds.length;
     data.imageIndex = 0;
     data.imageId = series.imageIds[data.imageIndex];
+  } else if (series.is4D) {
+    data.isMultiframe = false;
+    data.isTimeserie = true;
+    // check with real indices
+    data.numberOfSlices = series.numberOfImages;
+    data.numberOfTemporalPositions = series.numberOfTemporalPositions;
+    data.imageIndex = 0;
+    data.timeIndex = 0;
+    data.timestamp = series.instances[series.imageIds[0]].metadata["x00080033"];
+    data.imageId = series.imageIds[data.imageIndex];
+    data.timestamps = [];
+    data.timeIds = [];
+    each(series.imageIds, function (imageId) {
+      data.timestamps.push(series.instances[imageId].metadata.contentTime);
+      data.timeIds.push(
+        series.instances[imageId].metadata.temporalPositionIdentifier - 1 // timeId from 0 to N
+      );
+    });
   } else {
     data.isMultiframe = false;
     data.numberOfSlices =
@@ -692,7 +759,6 @@ let getSeriesData = function (series, defaultProps) {
     data.imageId = series.imageIds[data.imageIndex];
   }
   data.isColor = series.color;
-  data.isTimeserie = false; // TODO 4D
 
   // rows, cols and x y z spacing
   data.rows = series.instances[series.imageIds[0]].metadata["x00280010"];

package/imaging/imageStore.js

@@ -15,6 +15,12 @@ const DEFAULT_VIEWPORT = {
   minSliceId: 0,
   maxSliceId: 0,
   sliceId: 0,
+  minTimeId: 0,
+  maxTimeId: 0,
+  timeId: 0,
+  timestamp: 0,
+  timestamps: [],
+  timeIds: [],
   rows: 0,
   cols: 0,
   spacing_x: 0.0,
@@ -232,6 +238,18 @@ class Larvitar_Store {
         this.state["viewports"][data[0]]["maxSliceId"] = data[1];
       } else if (field == "sliceId") {
         this.state["viewports"][data[0]]["sliceId"] = data[1];
+      } else if (field == "minTimeId") {
+        this.state["viewports"][data[0]]["minTimeId"] = data[1];
+      } else if (field == "maxTimeId") {
+        this.state["viewports"][data[0]]["maxTimeId"] = data[1];
+      } else if (field == "timeId") {
+        this.state["viewports"][data[0]]["timeId"] = data[1];
+      } else if (field == "timestamp") {
+        this.state["viewports"][data[0]]["timestamp"] = data[1];
+      } else if (field == "timestamps") {
+        this.state["viewports"][data[0]]["timestamps"] = data[1];
+      } else if (field == "timeIds") {
+        this.state["viewports"][data[0]]["timeIds"] = data[1];
       } else if (field == "isColor") {
         this.state["viewports"][data[0]]["isColor"] = data[1];
       } else if (field == "isMultiframe") {

package/imaging/imageUtils.js

@@ -205,8 +205,8 @@ export const getPixelTypedArray = function (dataSet, pixelDataElement) {
  * @instance
  * @function getSortedStack
  * @param {Object} seriesData - The dataset
- * @param {Array} sortPriorities - TODO
- * @param {Bool} returnSuccessMethod - TODO ask @SZ
+ * @param {Array} sortPriorities - An array which represents the priority tasks
+ * @param {Bool} returnSuccessMethod - Boolean for returning the success method
  * @return {Object} The sorted stack
  */
 export const getSortedStack = function (
@@ -868,14 +868,7 @@ let sortStackCallback = function (seriesData, imageId, method) {
       return instanceNumber;
 
     case "contentTime":
-      var cardiacNumberOfImages =
-        seriesData.instances[imageId].metadata.x00181090;
-      var contentTime = seriesData.instances[imageId].metadata.x00080033;
-      if (cardiacNumberOfImages && cardiacNumberOfImages > 1 && contentTime) {
-        return contentTime;
-      } else {
-        throw "Not a time series: cardiacNumberOfImages tag not available or <= 1.";
-      }
+      return seriesData.instances[imageId].metadata.x00080033;
 
     case "imagePosition":
       var p = seriesData.instances[imageId].metadata.imagePosition;

package/imaging/loaders/nrrdLoader.js

@@ -62,33 +62,35 @@ export const buildNrrdImage = function (volume, seriesId, custom_header) {
   // need to extract header from nrrd file format
   // sizes, spaceDirections and spaceOrigin
 
+  const index = volume.header.kinds[0] == "domain" ? 0 : 1;
+
   let spacing_x = Math.sqrt(
-    volume.header["space directions"][0][0] *
-      volume.header["space directions"][0][0] +
-      volume.header["space directions"][0][1] *
-        volume.header["space directions"][0][1] +
-      volume.header["space directions"][0][2] *
-        volume.header["space directions"][0][2]
+    volume.header["space directions"][index + 0][0] *
+      volume.header["space directions"][index + 0][0] +
+      volume.header["space directions"][index + 0][1] *
+        volume.header["space directions"][index + 0][1] +
+      volume.header["space directions"][index + 0][2] *
+        volume.header["space directions"][index + 0][2]
   );
   let spacing_y = Math.sqrt(
-    volume.header["space directions"][1][0] *
-      volume.header["space directions"][1][0] +
-      volume.header["space directions"][1][1] *
-        volume.header["space directions"][1][1] +
-      volume.header["space directions"][1][2] *
-        volume.header["space directions"][1][2]
+    volume.header["space directions"][index + 1][0] *
+      volume.header["space directions"][index + 1][0] +
+      volume.header["space directions"][index + 1][1] *
+        volume.header["space directions"][index + 1][1] +
+      volume.header["space directions"][index + 1][2] *
+        volume.header["space directions"][index + 1][2]
   );
   let spacing_z = Math.sqrt(
-    volume.header["space directions"][2][0] *
-      volume.header["space directions"][2][0] +
-      volume.header["space directions"][2][1] *
-        volume.header["space directions"][2][1] +
-      volume.header["space directions"][2][2] *
-        volume.header["space directions"][2][2]
+    volume.header["space directions"][index + 2][0] *
+      volume.header["space directions"][index + 2][0] +
+      volume.header["space directions"][index + 2][1] *
+        volume.header["space directions"][index + 2][1] +
+      volume.header["space directions"][index + 2][2] *
+        volume.header["space directions"][index + 2][2]
   );
-  header.volume.rows = volume.header.sizes[1];
-  header.volume.cols = volume.header.sizes[0];
-  header.volume.numberOfSlices = volume.header.sizes[2];
+  header.volume.rows = volume.header.sizes[index + 1];
+  header.volume.cols = volume.header.sizes[index + 0];
+  header.volume.numberOfSlices = volume.header.sizes[index + 2];
   header.volume.imagePosition = volume.header["space origin"];
   header.volume.pixelSpacing = [spacing_x, spacing_y];
   header.volume.sliceThickness = spacing_z;
@@ -107,11 +109,11 @@ export const buildNrrdImage = function (volume, seriesId, custom_header) {
     ? custom_header.acquisition_date
     : "";
 
-  let rows = volume.header.sizes[1];
-  let cols = volume.header.sizes[0];
-  let frames = volume.header.sizes[2];
-  let iop = volume.header["space directions"][0].concat(
-    volume.header["space directions"][1]
+  let rows = volume.header.sizes[index + 1];
+  let cols = volume.header.sizes[index + 0];
+  let frames = volume.header.sizes[index + 2];
+  let iop = volume.header["space directions"][index + 0].concat(
+    volume.header["space directions"][index + 1]
   );
   let firstIpp = header.volume.imagePosition;
   let w = getNormalOrientation(iop);

package/imaging/tools/interaction.js

@@ -158,6 +158,7 @@ export const toggleMouseToolsListeners = function (elementId, disable) {
   // mouse wheel handler
   function mouseWheelHandler(evt) {
     larvitar_store.set("sliceId", [evt.target.id, evt.detail.newImageIdIndex]);
+    updateViewportData(evt.srcElement.id, evt.detail, "mouseWheel");
   }
 
   if (disable) {

package/imaging/tools/segmentation.js

@@ -13,6 +13,8 @@ const { getters, setters } = segModule;
 // internal libraries
 import { setToolActive, setToolDisabled } from "./main";
 import { isElement } from "../imageUtils";
+import { larvitar_store } from "../imageStore";
+import { updateStackToolState } from "../imageTools";
 
 // custom code
 import { setLabelmap3DForElement } from "./setLabelMap3D";
@@ -199,6 +201,19 @@ export function addSegmentationMask(props, data, elementId) {
     // bind labelmap to colorLUT
     let labelmap3d = getters.labelmap3D(element, props.labelId);
     setters.colorLUTIndexForLabelmap3D(labelmap3d, props.labelId);
+
+    // set current imageIdIndex in tool state
+    let currentImageIdIndex = larvitar_store.get(
+      "viewports",
+      elementId,
+      "sliceId"
+    );
+    if (currentImageIdIndex !== "error" && currentImageIdIndex >= 0) {
+      updateStackToolState(elementId, currentImageIdIndex);
+    } else {
+      console.error("Cannot get currentImageIdIndex");
+    }
+
     resolve();
   });
   return promise;

package/index.js

@@ -5,7 +5,6 @@ console.log(`LARVITAR v${VERSION}`);
 import cornerstone from "cornerstone-core";
 import cornerstoneTools from "cornerstone-tools";
 import cornerstoneWADOImageLoader from "cornerstone-wado-image-loader";
-console.log(`WADO v${cornerstoneWADOImageLoader.version}`);
 const segModule = cornerstoneTools.getModule("segmentation");
 
 import larvitarModule from "./modules/vuex/larvitar";
@@ -143,7 +142,9 @@ import {
   setActiveSegment,
   undoLastStroke,
   redoLastStroke,
-  setBrushProps
+  setBrushProps,
+  hexToRgb,
+  rgbToHex
 } from "./imaging/tools/segmentation";
 
 import {
@@ -366,5 +367,7 @@ export {
   setActiveSegment,
   undoLastStroke,
   redoLastStroke,
-  setBrushProps
+  setBrushProps,
+  hexToRgb,
+  rgbToHex
 };

package/modules/vuex/larvitar.js

@@ -8,6 +8,12 @@ const DEFAULT_VIEWPORT = {
   minSliceId: 0,
   maxSliceId: 0,
   sliceId: 0,
+  minTimeId: 0,
+  maxTimeId: 0,
+  timeId: 0,
+  timestamp: 0,
+  timestamps: [],
+  timeIds: [],
   rows: 0,
   cols: 0,
   spacing_x: 0.0,
@@ -128,6 +134,18 @@ export default {
       commit("viewport", { id, d: { maxSliceId } }),
     setSliceId: ({ commit }, [id, sliceId]) =>
       commit("viewport", { id, d: { sliceId } }),
+    setMinTimeId: ({ commit }, [id, minTimeId]) =>
+      commit("viewport", { id, d: { minTimeId } }),
+    setMaxTimeId: ({ commit }, [id, maxTimeId]) =>
+      commit("viewport", { id, d: { maxTimeId } }),
+    setTimeId: ({ commit }, [id, timeId]) =>
+      commit("viewport", { id, d: { timeId } }),
+    setTimestamp: ({ commit }, [id, timestamp]) =>
+      commit("viewport", { id, d: { timestamp } }),
+    setTimestamps: ({ commit }, [id, timestamps]) =>
+      commit("viewport", { id, d: { timestamps } }),
+    setTimeIds: ({ commit }, [id, timeIds]) =>
+      commit("viewport", { id, d: { timeIds } }),
     setIsColor: ({ commit }, [id, isColor]) =>
       commit("viewport", { id, d: { isColor } }),
     setIsMultiframe: ({ commit }, [id, isMultiframe]) =>

package/package.json

@@ -6,7 +6,7 @@
     "medical",
     "cornerstone"
   ],
-  "version": "1.3.0-beta.0",
+  "version": "1.3.2",
   "description": "javascript library for parsing, loading, rendering and interacting with DICOM images",
   "repository": {
     "url": "https://github.com/dvisionlab/Larvitar.git",
@@ -28,8 +28,8 @@
     "@rollup/plugin-commonjs": "^17.1.0",
     "cornerstone-core": "^2.6.1",
     "cornerstone-file-image-loader": "^0.3.0",
-    "cornerstone-tools": "^6.0.6",
-    "cornerstone-wado-image-loader": "3.3.2",
+    "cornerstone-tools": "^6.0.7",
+    "cornerstone-wado-image-loader": "^4.1.3",
     "cornerstone-web-image-loader": "^2.1.1",
     "crypto-js": "^4.1.1",
     "dicom-character-set": "^1.0.3",