larvitar 2.0.4 → 2.0.6

package/imaging/tools/custom/seedTool.js

@@ -1,342 +0,0 @@
-// // external libraries
-// import csTools from "cornerstone-tools";
-// import { each, cloneDeep } from "lodash";
-
-// // internal libraries
-// import { remapVoxel } from "../../imageUtils";
-// import { addToolStateSingleSlice, setToolEnabled } from "../../imageTools";
-// import { getSliceNumberFromImageId } from "../../loaders/nrrdLoader";
-
-// // cornerstone tools imports
-// const BaseAnnotationTool = csTools.importInternal("base/BaseAnnotationTool");
-// // State
-// const getToolState = csTools.getToolState;
-// // Drawing
-// const getNewContext = csTools.importInternal("drawing/getNewContext");
-// const draw = csTools.importInternal("drawing/draw");
-// const drawTextBox = csTools.importInternal("drawing/drawTextBox");
-// const drawCircle = csTools.importInternal("drawing/drawCircle");
-// // Utilities
-// const getRGBPixels = csTools.importInternal("util/getRGBPixels");
-// const calculateSUV = csTools.importInternal("util/calculateSUV");
-// const probeCursor = csTools.importInternal("util/probeCursor");
-// const getLogger = csTools.importInternal("util/getLogger");
-// const throttle = csTools.importInternal("util/throttle");
-
-// const logger = getLogger("tools:annotation:ProbeTool");
-
-// // internal constants
-// const seedLabels = {
-//   segmentation_01: "Aorta",
-//   segmentation_02: "Aneurysm",
-//   segmentation_03: "Carrefour",
-//   regionGrowing: "regionGrowing"
-// };
-
-// /**
-//  * @public
-//  * @class SeedsTool
-//  * @memberof Tools.Annotation
-//  * @classdesc Tool which provides cohordinates of the picked poin
-//  * @extends Tools.Base.BaseAnnotationTool
-//  */
-// export class SeedsTool extends BaseAnnotationTool {
-//   constructor(props = {}) {
-//     const defaultProps = {
-//       name: "Seeds",
-//       supportedInteractionTypes: ["Mouse"],
-//       svgCursor: probeCursor
-//     };
-
-//     super(props, defaultProps);
-
-//     if (props.initialize) {
-//       this.initializeTool(props.preLoadSeeds, props.initViewport);
-//     }
-
-//     this.throttledUpdateCachedStats = throttle(this.updateCachedStats, 110);
-//   }
-
-//   initializeTool(seeds, elementId) {
-//     let element = document.getElementById(elementId);
-
-//     each(seeds, seed => {
-//       let change = {
-//         visible: true,
-//         active: true,
-//         invalidated: true,
-//         color: seed.color,
-//         name: seed.tag,
-//         slice: seed.native_k,
-//         handles: {
-//           end: {
-//             x: seed.native_i,
-//             y: seed.native_j,
-//             highlight: true,
-//             active: true
-//           }
-//         }
-//       };
-
-//       let sliceNumber = seed.native_k;
-
-//       // add to master viewport
-//       addToolStateSingleSlice(element, this.name, change, sliceNumber);
-
-//       // sync remaining viewports
-//       this.syncViewports(elementId, change, sliceNumber);
-//     });
-
-//     csTools.external.cornerstone.updateImage(element);
-//   }
-
-//   createNewMeasurement(eventData) {
-//     if (eventData.event.srcElement.localName != "canvas") {
-//       return;
-//     }
-//     const goodEventData =
-//       eventData && eventData.currentPoints && eventData.currentPoints.image;
-
-//     if (!goodEventData) {
-//       logger.error(
-//         `required eventData not supplied to tool ${this.name}'s createNewMeasurement`
-//       );
-
-//       return;
-//     }
-
-//     var res = {
-//       visible: true,
-//       active: true,
-//       invalidated: true,
-//       color: this.options.color,
-//       name: this.options.seed_name,
-//       slice: getSliceNumberFromImageId(
-//         eventData.image.imageId,
-//         eventData.element.id
-//       ),
-//       handles: {
-//         end: {
-//           x: eventData.currentPoints.image.x,
-//           y: eventData.currentPoints.image.y,
-//           highlight: true,
-//           active: true
-//         }
-//       },
-//       native_i: 0,
-//       native_j: 0,
-//       native_k: 0
-//     };
-
-//     let sliceNumber = getSliceNumberFromImageId(
-//       eventData.image.imageId,
-//       eventData.element.id
-//     );
-
-//     // store native coordinates
-//     this.storeNativeCoordinates(res, eventData.element.id, sliceNumber);
-
-//     // sync all the viewports
-//     this.syncViewports(eventData.element.id, res, sliceNumber);
-
-//     // optionally set data in store
-
-//     // set mode to "enabled"
-//     setToolEnabled(this.name);
-
-//     return res;
-//   }
-
-//   /**
-//    *
-//    *
-//    * @param {*} element
-//    * @param {*} data
-//    * @param {*} coords
-//    * @returns {Boolean}
-//    */
-//   pointNearTool(element, data, coords) {
-//     const hasEndHandle = data && data.handles && data.handles.end;
-//     const validParameters = hasEndHandle;
-
-//     if (!validParameters) {
-//       logger.warn(
-//         `invalid parameters supplied to tool ${this.name}'s pointNearTool`
-//       );
-//     }
-
-//     if (!validParameters || data.visible === false) {
-//       return false;
-//     }
-
-//     const probeCoords = csTools.external.cornerstone.pixelToCanvas(
-//       element,
-//       data.handles.end
-//     );
-
-//     return (
-//       csTools.external.cornerstoneMath.point.distance(probeCoords, coords) < 5
-//     );
-//   }
-
-//   updateCachedStats(image, element, data) {
-//     const x = Math.round(data.handles.end.x);
-//     const y = Math.round(data.handles.end.y);
-
-//     const stats = {};
-
-//     if (x >= 0 && y >= 0 && x < image.columns && y < image.rows) {
-//       stats.x = x;
-//       stats.y = y;
-
-//       if (image.color) {
-//         stats.storedPixels = getRGBPixels(element, x, y, 1, 1);
-//       } else {
-//         stats.storedPixels = csTools.external.cornerstone.getStoredPixels(
-//           element,
-//           x,
-//           y,
-//           1,
-//           1
-//         );
-//         stats.sp = stats.storedPixels[0];
-//         stats.mo = stats.sp * image.slope + image.intercept;
-//         stats.suv = calculateSUV(image, stats.sp);
-//         stats.color = data.color || this.options.color;
-//         stats.name = data.name || this.options.seed_name;
-//       }
-//     }
-
-//     data.cachedStats = stats;
-//     data.invalidated = false;
-//   }
-
-//   renderToolData(evt) {
-//     const eventData = evt.detail;
-//     const toolData = getToolState(evt.currentTarget, this.name);
-
-//     if (!toolData) {
-//       return;
-//     }
-
-//     // We have tool data for this element - iterate over each one and draw it
-//     const context = getNewContext(eventData.canvasContext.canvas);
-//     const { image, element } = eventData;
-
-//     for (let i = 0; i < toolData.data.length; i++) {
-//       const data = toolData.data[i];
-
-//       if (data.visible === false) {
-//         continue;
-//       }
-
-//       draw(context, context => {
-//         const center = data.handles.end;
-
-//         // Update textbox stats
-//         if (data.invalidated === true) {
-//           if (data.cachedStats) {
-//             this.throttledUpdateCachedStats(image, element, data);
-//           } else {
-//             this.updateCachedStats(image, element, data);
-//           }
-//         }
-
-//         const { x, y, color, name } = data.cachedStats;
-
-//         let text;
-
-//         if (x >= 0 && y >= 0 && x < image.columns && y < image.rows) {
-//           text = this.getLabelText(name);
-
-//           // Coords for text
-//           const coords = {
-//             // Translate the x/y away from the cursor
-//             x: data.handles.end.x + 3,
-//             y: data.handles.end.y - 3
-//           };
-//           const textCoords = csTools.external.cornerstone.pixelToCanvas(
-//             eventData.element,
-//             coords
-//           );
-
-//           drawTextBox(context, text, textCoords.x, textCoords.y, color);
-
-//           drawCircle(context, element, center, this.options.radius || 3, {
-//             color: color,
-//             fillStyle: color
-//           });
-//         }
-//       });
-//     }
-//   }
-
-//   getLabelText(name) {
-//     // let text = (text = ` ${name}`);
-//     let text = seedLabels[name];
-//     return text;
-//   }
-
-//   storeNativeCoordinates(input, inputViewportId, frame) {
-//     let native = remapVoxel(
-//       [
-//         Math.floor(input.handles.end.x),
-//         Math.floor(input.handles.end.y),
-//         parseInt(frame)
-//       ],
-//       inputViewportId,
-//       "axial"
-//     );
-//     input.native_i = native[0];
-//     input.native_j = native[1];
-//     input.native_k = native[2];
-//   }
-
-//   syncViewports(pickingViewportId, change, sliceNumber) {
-//     let enabledElements = csTools.external.cornerstone.getEnabledElements();
-//     var from = pickingViewportId;
-
-//     each(enabledElements, el => {
-//       if (el.element.id == pickingViewportId) {
-//         return;
-//       }
-
-//       let remapped = this.getRemappedChange(
-//         change,
-//         sliceNumber,
-//         from,
-//         el.element.id
-//       );
-
-//       addToolStateSingleSlice(
-//         el.element,
-//         this.name,
-//         remapped.change,
-//         remapped.sliceNumber
-//       );
-//       csTools.external.cornerstone.updateImage(el.element);
-//     });
-//   }
-
-//   getRemappedChange(input, frame, fromOrientation, toOrientation) {
-//     let ijk = remapVoxel(
-//       [
-//         Math.floor(input.handles.end.x),
-//         Math.floor(input.handles.end.y),
-//         parseInt(frame)
-//       ],
-//       fromOrientation,
-//       toOrientation
-//     );
-
-//     let output = cloneDeep(input);
-
-//     output.handles.end.x = ijk[0];
-//     output.handles.end.y = ijk[1];
-
-//     return {
-//       change: output,
-//       sliceNumber: ijk[2]
-//     };
-//   }
-// }

package/imaging/tools/custom/setLabelMap3D.ts

@@ -1,242 +0,0 @@
-/**
- * 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
- */
-
-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";
-import type { TypedArray } from "../../types";
-import { EnabledElement } from "cornerstone-core";
-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: TypedArray) {
-  return [...new Set(pixelData)];
-}
-
-// from getElement.js
-function getElement(elementOrEnabledElementUID: EnabledElement | string) {
-  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: EnabledElement | string,
-  buffer: ArrayBuffer,
-  labelmapIndex: number,
-  metadata: Object[] = [],
-  segmentsOnLabelmapArray: number[][],
-  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: string,
-  buffer: ArrayBuffer,
-  labelmapIndex: number,
-  metadata: Object[] = [],
-  numberOfFrames: number,
-  segmentsOnLabelmapArray: number[][],
-  colorLUTIndex: number = 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: number, numberOfFrames: number) {
-      var pixelData: TypedArray | undefined = 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 };