larvitar 0.18.2 → 1.2.0

package/imaging/tools/setLabelMap3D.js

@@ -0,0 +1,248 @@
+/**
+ * This is a custom version of setLabelMap3D from cs tools source code
+ * This let us implement a non-blocking version of the for loop that loads 3d labelmaps on a volume
+ * @ronzim
+ */
+
+// import getElement from "./getElement";
+// import { getToolState } from "../../../stateManagement/toolState.js";
+// import state from "./state";
+// import getSegmentsOnPixelData from "./getSegmentsOnPixeldata";
+// import { triggerLabelmapModifiedEvent } from "../../../util/segmentation";
+// import ARRAY_TYPES from "./arrayTypes";
+// import { getModule } from "../../index.js";
+
+const ARRAY_TYPES = {
+  UINT_16_ARRAY: 0,
+  FLOAT_32_ARRAY: 1
+};
+const { UINT_16_ARRAY, FLOAT_32_ARRAY } = ARRAY_TYPES;
+
+import cornerstoneTools from "cornerstone-tools/dist/cornerstoneTools.js";
+const { triggerLabelmapModifiedEvent } = cornerstoneTools.importInternal(
+  "util/segmentationUtils"
+);
+const getModule = cornerstoneTools.getModule;
+const getToolState = cornerstoneTools.getToolState;
+const storeGetters = cornerstoneTools.store.getters;
+const state = getModule("segmentation").state;
+
+/**
+ * These function are reported since they are not exposed by cs tools
+ *
+ */
+
+// from getSegmentsOnPixelData.js
+function getSegmentsOnPixelData(pixelData) {
+  return [...new Set(pixelData)];
+}
+
+// from getElement.js
+function getElement(elementOrEnabledElementUID) {
+  if (elementOrEnabledElementUID instanceof HTMLElement) {
+    return elementOrEnabledElementUID;
+  }
+
+  return storeGetters.enabledElementByUID(elementOrEnabledElementUID);
+}
+
+/**
+ * Takes a 16-bit encoded `ArrayBuffer` and stores it as a `Labelmap3D` for the
+ * `BrushStackState` associated with the element.
+ *
+ * @param  {HTMLElement|string} elementOrEnabledElementUID The cornerstone
+ *                                                  enabled element or its UUID.
+ * @param  {ArrayBuffer} buffer
+ * @param  {number} labelmapIndex The index to store the labelmap under.
+ * @param  {Object[]} metadata = [] Any metadata about the segments.
+ * @param  {number[][]} [segmentsOnLabelmapArray] An array of array of segments on each imageIdIndex.
+ *                       If not present, is calculated.
+ * @param  {colorLUTIndex} [colorLUTIndex = 0] The index of the colorLUT to use to render the segmentation.
+ * @returns {null}
+ */
+async function setLabelmap3DForElement(
+  elementOrEnabledElementUID,
+  buffer,
+  labelmapIndex,
+  metadata = [],
+  segmentsOnLabelmapArray,
+  colorLUTIndex = 0
+) {
+  const element = getElement(elementOrEnabledElementUID);
+
+  if (!element) {
+    return;
+  }
+
+  const stackState = getToolState(element, "stack");
+  const numberOfFrames = stackState.data[0].imageIds.length;
+  const firstImageId = stackState.data[0].imageIds[0];
+
+  const res = await setLabelmap3DByFirstImageId(
+    firstImageId,
+    buffer,
+    labelmapIndex,
+    metadata,
+    numberOfFrames,
+    segmentsOnLabelmapArray,
+    colorLUTIndex
+  );
+
+  triggerLabelmapModifiedEvent(element, labelmapIndex);
+
+  return res;
+}
+
+/**
+ * Takes an 16-bit encoded `ArrayBuffer` and stores it as a `Labelmap3D` for
+ * the `BrushStackState` associated with the firstImageId.
+ *
+ * @param  {HTMLElement|string} firstImageId  The firstImageId of the series to
+ *                                            store the segmentation on.
+ * @param  {ArrayBuffer} buffer
+ * @param  {number} labelmapIndex The index to store the labelmap under.
+ * @param  {Object[]} metadata = [] Any metadata about the segments.
+ * @param  {number} numberOfFrames The number of frames, required to set up the
+ *                                 relevant labelmap2D views.
+ * @param  {number[][]} [segmentsOnLabelmapArray] An array of array of segments on each imageIdIndex.
+ *                       If not present, is calculated.
+ * @param  {colorLUTIndex} [colorLUTIndex = 0] The index of the colorLUT to use to render the segmentation.
+ * @returns {null}
+ */
+function setLabelmap3DByFirstImageId(
+  firstImageId,
+  buffer,
+  labelmapIndex,
+  metadata = [],
+  numberOfFrames,
+  segmentsOnLabelmapArray,
+  colorLUTIndex = 0
+) {
+  const { configuration } = getModule("segmentation");
+
+  let brushStackState = state.series[firstImageId];
+
+  if (!brushStackState) {
+    state.series[firstImageId] = {
+      activeLabelmapIndex: labelmapIndex,
+      labelmaps3D: []
+    };
+
+    brushStackState = state.series[firstImageId];
+  }
+
+  brushStackState.labelmaps3D[labelmapIndex] = {
+    buffer,
+    labelmaps2D: [],
+    metadata,
+    activeSegmentIndex: 1,
+    colorLUTIndex,
+    segmentsHidden: [],
+    undo: [],
+    redo: []
+  };
+
+  const labelmaps2D = brushStackState.labelmaps3D[labelmapIndex].labelmaps2D;
+  const slicelengthInBytes = buffer.byteLength / numberOfFrames;
+
+  /* non-blocking implementation by @ronzim */
+
+  return new Promise(resolve => {
+    function setSingleSlice(i, numberOfFrames) {
+      var pixelData = void 0;
+
+      switch (configuration.arrayType) {
+        case UINT_16_ARRAY:
+          pixelData = new Uint16Array(
+            buffer,
+            slicelengthInBytes * i, // 2 bytes/voxel
+            slicelengthInBytes / 2
+          );
+          break;
+
+        case FLOAT_32_ARRAY:
+          pixelData = new Float32Array(
+            buffer,
+            slicelengthInBytes * i,
+            slicelengthInBytes / 4
+          );
+          break;
+
+        default:
+          throw new Error(
+            "Unsupported Array Type ".concat(configuration.arrayType)
+          );
+      }
+
+      var segmentsOnLabelmap = segmentsOnLabelmapArray
+        ? segmentsOnLabelmapArray[i]
+        : getSegmentsOnPixelData(pixelData);
+
+      if (
+        segmentsOnLabelmap &&
+        segmentsOnLabelmap.some(function (segment) {
+          return segment;
+        })
+      ) {
+        labelmaps2D[i] = {
+          pixelData: pixelData,
+          segmentsOnLabelmap: segmentsOnLabelmap
+        };
+      }
+
+      ++i;
+
+      if (i < numberOfFrames) {
+        setTimeout(() => {
+          setSingleSlice(i, numberOfFrames);
+        }, 0);
+      } else {
+        resolve("OK");
+      }
+    }
+
+    setSingleSlice(0, numberOfFrames);
+  });
+
+  /* original implementation 
+
+  for (let i = 0; i < numberOfFrames; i++) {
+    let pixelData;
+
+    switch (configuration.arrayType) {
+      case UINT_16_ARRAY:
+        pixelData = new Uint16Array(
+          buffer,
+          slicelengthInBytes * i, // 2 bytes/voxel
+          slicelengthInBytes / 2
+        );
+
+        break;
+
+      case FLOAT_32_ARRAY:
+        pixelData = new Float32Array(
+          buffer,
+          slicelengthInBytes * i,
+          slicelengthInBytes / 4
+        );
+        break;
+
+      default:
+        throw new Error(`Unsupported Array Type ${configuration.arrayType}`);
+    }
+
+    const segmentsOnLabelmap = segmentsOnLabelmapArray
+      ? segmentsOnLabelmapArray[i]
+      : getSegmentsOnPixelData(pixelData);
+
+    if (segmentsOnLabelmap && segmentsOnLabelmap.some(segment => segment)) {
+      labelmaps2D[i] = {
+        pixelData,
+        segmentsOnLabelmap
+      };
+    }
+  }
+  */
+}
+
+export { setLabelmap3DByFirstImageId, setLabelmap3DForElement };

package/imaging/tools/{tools.state.js → state.js}

@@ -1,8 +1,14 @@
+/** @module imaging/tools/state
+ *  @desc  This file provides functionalities
+ *         for handling tools' state
+ */
+
 // external libraries
 import cornerstone from "cornerstone-core";
 import cornerstoneTools from "cornerstone-tools";
-
 import { each } from "lodash";
+
+// internal libraries
 import { state_example } from "./cstools_state_example.js";
 
 /**

package/imaging/tools/strategies/eraseFreehand.js

@@ -1,17 +1,16 @@
-import cornerstoneTools from "cornerstone-tools";
-
-const {
-  getBoundingBoxAroundPolygon,
-  eraseInsideShape,
-  eraseOutsideShape
-} = cornerstoneTools.importInternal("util/segmentationUtils");
+/** @module imaging/strategies/eraseFreehand
+ *  @desc  This file provides functionalities for
+ *         erasing pixels
+ */
 
+// external libraries
+import cornerstoneTools from "cornerstone-tools";
+const { getBoundingBoxAroundPolygon, eraseInsideShape, eraseOutsideShape } =
+  cornerstoneTools.importInternal("util/segmentationUtils");
 const isPointInPolygon = cornerstoneTools.importInternal(
   "util/isPointInPolygon"
 );
-
 const getLogger = cornerstoneTools.importInternal("util/getLogger");
-
 const logger = getLogger("util:segmentation:operations:eraseInsideFreehand");
 
 /**

package/imaging/tools/strategies/fillFreehand.js

@@ -1,17 +1,16 @@
-import cornerstoneTools from "cornerstone-tools";
-
-const {
-  getBoundingBoxAroundPolygon,
-  fillInsideShape,
-  fillOutsideShape
-} = cornerstoneTools.importInternal("util/segmentationUtils");
+/** @module imaging/strategies/fillFreehand
+ *  @desc  This file provides functionalities for
+ *         filling pixels
+ */
 
+// external libraries
+import cornerstoneTools from "cornerstone-tools";
+const { getBoundingBoxAroundPolygon, fillInsideShape, fillOutsideShape } =
+  cornerstoneTools.importInternal("util/segmentationUtils");
 const isPointInPolygon = cornerstoneTools.importInternal(
   "util/isPointInPolygon"
 );
-
 const getLogger = cornerstoneTools.importInternal("util/getLogger");
-
 const logger = getLogger("util:segmentation:operations:fillInsideFreehand");
 
 /**

package/index.js

@@ -5,6 +5,7 @@ console.log(`LARVITAR v${VERSION}`);
 import cornerstone from "cornerstone-core";
 import cornerstoneTools from "cornerstone-tools";
 import cornerstoneWADOImageLoader from "cornerstone-wado-image-loader";
+const segModule = cornerstoneTools.getModule("segmentation");
 
 import larvitarModule from "./modules/vuex/larvitar";
 
@@ -14,15 +15,15 @@ import {
   getAvailableMemory
 } from "./imaging/monitors/memory";
 
-import { initLarvitarStore, larvitar_store } from "./imaging/image_store";
+import { initLarvitarStore, larvitar_store } from "./imaging/imageStore";
 
-import { parseContours } from "./imaging/image_contours";
+import { parseContours } from "./imaging/imageContours";
 
 import {
   getImagePresets,
   setImagePreset,
   setImageCustomPreset
-} from "./imaging/image_presets";
+} from "./imaging/imagePresets";
 
 import {
   getNormalOrientation,
@@ -37,7 +38,7 @@ import {
   getReslicedMetadata,
   getReslicedPixeldata,
   getDistanceBetweenSlices
-} from "./imaging/image_utils";
+} from "./imaging/imageUtils";
 
 import {
   buildHeader,
@@ -45,14 +46,16 @@ import {
   buildData,
   buildDataAsync,
   importNRRDImage
-} from "./imaging/image_io";
+} from "./imaging/imageIo";
+
+import { anonymize, encrypt } from "./imaging/imageAnonymization";
 
 import {
   buildLayer,
   updateLayer,
   getActiveLayer,
   setActiveLayer
-} from "./imaging/image_layers";
+} from "./imaging/imageLayers";
 
 import {
   initializeImageLoader,
@@ -62,14 +65,14 @@ import {
   registerResliceLoader,
   registerMultiFrameImageLoader,
   updateLoadedStack
-} from "./imaging/image_loading";
+} from "./imaging/imageLoading";
 
 import {
   readFile,
   readFiles,
-  dumpDataSet,
+  parseDataSet,
   clearImageParsing
-} from "./imaging/image_parsing";
+} from "./imaging/imageParsing";
 
 import {
   clearImageCache,
@@ -83,16 +86,15 @@ import {
   updateImage,
   resetViewports,
   updateViewportData,
-  // toggleMouseHandlers,
   storeViewportData,
   invertImage,
   flipImageHorizontal,
   flipImageVertical,
   rotateImageLeft,
   rotateImageRight
-} from "./imaging/image_rendering";
+} from "./imaging/imageRendering";
 
-import { resliceSeries } from "./imaging/image_reslice";
+import { resliceSeries } from "./imaging/imageReslice";
 
 import {
   addDiameterTool,
@@ -110,7 +112,7 @@ import {
   syncToolStack,
   updateStackToolState,
   setSegmentationConfig
-} from "./imaging/image_tools";
+} from "./imaging/imageTools";
 
 import {
   csToolsCreateStack,
@@ -125,13 +127,13 @@ import {
   setToolEnabled,
   setToolPassive,
   exportAnnotations
-} from "./imaging/tools/tools.main";
+} from "./imaging/tools/main";
 
 import {
   DEFAULT_TOOLS,
   getDefaultToolsByType,
   setDefaultToolsProps
-} from "./imaging/tools/tools.default";
+} from "./imaging/tools/default";
 
 import {
   initSegmentationModule,
@@ -141,7 +143,7 @@ import {
   undoLastStroke,
   redoLastStroke,
   setBrushProps
-} from "./imaging/tools/tools.segmentation";
+} from "./imaging/tools/segmentation";
 
 import {
   updateLarvitarManager,
@@ -188,20 +190,21 @@ import {
   addColorMap,
   fillPixelData,
   HSVToRGB
-} from "./imaging/image_colormaps";
+} from "./imaging/imageColormaps";
 
-import { saveAnnotations, loadAnnotations } from "./imaging/tools/tools.io";
+import { saveAnnotations, loadAnnotations } from "./imaging/tools/io";
 
 import {
   addMouseKeyHandlers,
   toggleMouseToolsListeners
-} from "./imaging/tools/tools.interaction";
+} from "./imaging/tools/interaction";
 
 export {
   VERSION,
   // global cornerstone variables
   cornerstone,
   cornerstoneTools,
+  segModule,
   cornerstoneWADOImageLoader,
   // vuex module
   larvitarModule,
@@ -209,14 +212,14 @@ export {
   checkMemoryAllocation,
   getUsedMemory,
   getAvailableMemory,
-  // larvitar store
+  // larvitarStore
   initLarvitarStore,
   larvitar_store,
-  // image_presets
+  // imagePresets
   getImagePresets,
   setImagePreset,
   setImageCustomPreset,
-  // image_utils
+  // imageUtils
   getNormalOrientation,
   getMinPixelValue,
   getMaxPixelValue,
@@ -229,18 +232,21 @@ export {
   getReslicedMetadata,
   getReslicedPixeldata,
   getDistanceBetweenSlices,
-  // image_io
+  // imageIo
   buildHeader,
   getCachedPixelData,
   buildData,
   buildDataAsync,
   importNRRDImage,
-  // image_layers
+  // imageAnonymization
+  anonymize,
+  encrypt,
+  // imageLayers
   buildLayer,
   updateLayer,
   getActiveLayer,
   setActiveLayer,
-  // image_loading
+  // imageLoading
   initializeImageLoader,
   initializeWebImageLoader,
   initializeFileImageLoader,
@@ -248,12 +254,12 @@ export {
   registerResliceLoader,
   registerMultiFrameImageLoader,
   updateLoadedStack,
-  // image_parsing
+  // imageParsing
   readFile,
   readFiles,
-  dumpDataSet,
+  parseDataSet,
   clearImageParsing,
-  // image_rendering
+  // imageRendering
   clearImageCache,
   loadAndCacheImages,
   renderFileImage,
@@ -265,7 +271,6 @@ export {
   updateImage,
   resetViewports,
   updateViewportData,
-  // toggleMouseHandlers,
   toggleMouseToolsListeners,
   storeViewportData,
   invertImage,
@@ -273,15 +278,15 @@ export {
   flipImageVertical,
   rotateImageLeft,
   rotateImageRight,
-  // image_reslice
+  // imageReslice
   resliceSeries,
-  // image_colormaps
+  // imageColormaps
   getColormapsList,
   applyColorMap,
   addColorMap,
   fillPixelData,
   HSVToRGB,
-  // image_contours
+  // imageContours
   parseContours,
   // loaders/commonLoader
   updateLarvitarManager,
@@ -304,7 +309,7 @@ export {
   // loaders/dicomLoader
   getDicomImageId,
   cacheImages,
-  // loaders/multiFrameLoader
+  // loaders/multiframeLoader
   loadMultiFrameImage,
   buildMultiFrameImage,
   getMultiFrameImageId,
@@ -315,7 +320,7 @@ export {
   resetFileManager,
   populateFileManager,
   getFileImageId,
-  // image_tools
+  // imageTools
   addDiameterTool,
   addContoursTool,
   addMaskEditingTool,
@@ -331,7 +336,7 @@ export {
   syncToolStack,
   updateStackToolState,
   setSegmentationConfig,
-  // tools.main
+  // tools/main
   csToolsCreateStack,
   csToolsUpdateImageIds,
   csToolsUpdateImageIndex,
@@ -344,16 +349,16 @@ export {
   setToolEnabled,
   setToolPassive,
   exportAnnotations,
-  // tools.default
+  // tools/default
   DEFAULT_TOOLS,
   getDefaultToolsByType,
   setDefaultToolsProps,
-  // tools.io
+  // tools/io
   saveAnnotations,
   loadAnnotations,
-  // tools.interaction
+  // tools/interaction
   addMouseKeyHandlers,
-  // tools.segmentation
+  // tools/segmentation
   initSegmentationModule,
   addSegmentationMask,
   setActiveLabelmap,

package/modules/vuex/larvitar.js

@@ -1,4 +1,4 @@
-// Larvitare storage
+// Larvitar Vuex storage
 
 import Vue from "vue";
 
@@ -74,6 +74,12 @@ export default {
       }
 
       Vue.set(state.viewports, id, { ...state.viewports[id], ...d });
+    },
+    leftActiveTool: (state, { d }) => {
+      state.leftActiveTool = d.value;
+    },
+    rightActiveTool: (state, { d }) => {
+      state.rightActiveTool = d.value;
     }
   },
   actions: {
@@ -85,8 +91,12 @@ export default {
     deleteViewport: ({ state }, viewportId) =>
       Vue.delete(state.viewports, viewportId),
     setManager: ({ state }, value) => (state.manager = value),
-    setLeftActiveTool: ({ state }, value) => (state.leftActiveTool = value),
-    setRightActiveTool: ({ state }, value) => (state.rightActiveTool = value),
+    setLeftActiveTool: ({ commit }, value) => {
+      commit("leftActiveTool", { d: { value } });
+    },
+    setRightActiveTool: ({ commit }, value) => {
+      commit("rightActiveTool", { d: { value } });
+    },
     removeSeriesIds: ({ state }, seriesId) =>
       Vue.delete(state.series, seriesId),
     setErrorLog: () => {}, // TODO LT pass elementId

package/package.json

@@ -1,11 +1,13 @@
 {
   "name": "larvitar",
   "keywords": [
-    "dicom",
-    "imaging"
+    "DICOM",
+    "imaging",
+    "medical",
+    "cornerstone"
   ],
-  "version": "0.18.2",
-  "description": "javascript library for loading, rendering and interact with DICOM images",
+  "version": "1.2.0",
+  "description": "javascript library for parsing, loading, rendering and interacting with DICOM images",
   "repository": {
     "url": "https://github.com/dvisionlab/Larvitar.git",
     "type": "git"
@@ -18,25 +20,26 @@
   "author": "Simone Manini <simone.manini@dvisionlab.com> (https://www.dvisionlab.com)",
   "contributors": [
     "Mattia Ronzoni <mattia.ronzoni@dvisionlab.com> (https://www.dvisionlab.com)",
-    "Sara Zanchi <sara.zanchi@dvisionlab.com> (https://www.dvisionlab.com)"
+    "Sara Zanchi <sara.zanchi@dvisionlab.com> (https://www.dvisionlab.com)",
+    "Ale Re <ale.re@dvisionlab.com> (https://www.dvisionlab.com)"
   ],
   "license": "MIT",
   "dependencies": {
     "@rollup/plugin-commonjs": "^17.1.0",
-    "cornerstone-core": "^2.3.0",
+    "cornerstone-core": "^2.6.1",
     "cornerstone-file-image-loader": "^0.3.0",
-    "cornerstone-tools": "^5.1.4",
-    "cornerstone-wado-image-loader": "^3.0.6",
+    "cornerstone-tools": "^6.0.6",
+    "cornerstone-wado-image-loader": "^4.0.1",
     "cornerstone-web-image-loader": "^2.1.1",
+    "crypto-js": "^4.1.1",
     "dicom-character-set": "^1.0.3",
-    "dicom-parser": "^1.8.4",
+    "dicom-parser": "^1.8.11",
     "docdash": "^1.2.0",
     "hammerjs": "^2.0.8",
     "keycode-js": "^3.1.0",
     "lodash": "^4.17.15",
     "pako": "^1.0.10",
     "papaparse": "^5.3.0",
-    "serialize-javascript": "^3.1.0",
     "uuid": "^8.3.2"
   },
   "devDependencies": {