larvitar 1.1.2 → 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/package.json

@@ -6,7 +6,7 @@
     "medical",
     "cornerstone"
   ],
-  "version": "1.1.2",
+  "version": "1.2.0",
   "description": "javascript library for parsing, loading, rendering and interacting with DICOM images",
   "repository": {
     "url": "https://github.com/dvisionlab/Larvitar.git",