larvitar 2.0.4 → 2.0.6

package/imaging/tools/strategies/eraseFreehand.js

@@ -1,76 +0,0 @@
-/** @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");
-
-/**
- * Erase all pixels labeled with the activeSegmentIndex,
- * in the region defined by evt.operationData.points.
- * @param  {} evt The Cornerstone event.
- * @param  {} operationData An object containing the `pixelData` to
- *                          modify, the `segmentIndex` and the `points` array.
- * @returns {null}
- */
-function eraseFreehand(evt, operationData, inside = true) {
-  const { points, segmentationMixinType } = operationData;
-
-  if (segmentationMixinType !== `freehandSegmentationMixin`) {
-    logger.error(
-      `eraseInsideFreehand operation requires freehandSegmentationMixin operationData, recieved ${segmentationMixinType}`
-    );
-
-    return;
-  }
-
-  const { image } = evt.detail;
-  const vertices = points.map(a => [a.x, a.y]);
-  const [topLeft, bottomRight] = getBoundingBoxAroundPolygon(vertices, image);
-
-  inside
-    ? eraseInsideShape(
-        evt,
-        operationData,
-        point => isPointInPolygon([point.x, point.y], vertices),
-        topLeft,
-        bottomRight
-      )
-    : eraseOutsideShape(
-        evt,
-        operationData,
-        point => isPointInPolygon([point.x, point.y], vertices),
-        topLeft,
-        bottomRight
-      );
-}
-
-/**
- * Erase all pixels inside/outside the region defined by `operationData.points`.
- * @param  {} evt The Cornerstone event.
- * @param {}  operationData An object containing the `pixelData` to
- *                          modify, the `segmentIndex` and the `points` array.
- * @returns {null}
- */
-export function eraseInsideFreehand(evt, operationData) {
-  eraseFreehand(evt, operationData, true);
-}
-
-/**
- * Erase all pixels outside the region defined by `operationData.points`.
- * @param  {} evt The Cornerstone event.
- * @param  {} operationData An object containing the `pixelData` to
- *                          modify, the `segmentIndex` and the `points` array.
- * @returns {null}
- */
-export function eraseOutsideFreehand(evt, operationData) {
-  eraseFreehand(evt, operationData, false);
-}

package/imaging/tools/strategies/fillFreehand.js

@@ -1,79 +0,0 @@
-/** @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");
-
-/**
- * Fill all pixels inside/outside the region defined by
- * `operationData.points` with the `activeSegmentIndex` value.
- * @param  {} evt The Cornerstone event.
- * @param  {} operationData An object containing the `pixelData` to
- *                          modify, the `segmentIndex` and the `points` array.
- * @returns {null}
- */
-function fillFreehand(evt, operationData, inside = true) {
-  const { points, segmentationMixinType } = operationData;
-
-  if (segmentationMixinType !== `freehandSegmentationMixin`) {
-    logger.error(
-      `eraseInsideFreehand operation requires freehandSegmentationMixin operationData, recieved ${segmentationMixinType}`
-    );
-
-    return;
-  }
-
-  // Obtain the bounding box of the entire drawing so that
-  // we can subset our search. Outside of the bounding box,
-  // everything is outside of the polygon.
-  const { image } = evt.detail;
-  const vertices = points.map(a => [a.x, a.y]);
-  const [topLeft, bottomRight] = getBoundingBoxAroundPolygon(vertices, image);
-
-  inside
-    ? fillInsideShape(
-        evt,
-        operationData,
-        point => isPointInPolygon([point.x, point.y], vertices),
-        topLeft,
-        bottomRight
-      )
-    : fillOutsideShape(
-        evt,
-        operationData,
-        point => isPointInPolygon([point.x, point.y], vertices),
-        topLeft,
-        bottomRight
-      );
-}
-
-/**
- * Fill all pixels inside/outside the region defined by `operationData.points`.
- * @param  {} evt The Cornerstone event.
- * @param {}  operationData An object containing the `pixelData` to
- *                          modify, the `segmentIndex` and the `points` array.
- * @returns {null}
- */
-export function fillInsideFreehand(evt, operationData) {
-  fillFreehand(evt, operationData, true);
-}
-
-/**
- * Fill all pixels outside the region defined by `operationData.points`.
- * @param  {} evt The Cornerstone event.
- * @param  {} operationData An object containing the `pixelData` to
- *                          modify, the `segmentIndex` and the `points` array.
- * @returns {null}
- */
-export function fillOutsideFreehand(evt, operationData) {
-  fillFreehand(evt, operationData, false);
-}

package/imaging/tools/strategies/index.js

@@ -1,2 +0,0 @@
-export { eraseInsideFreehand, eraseOutsideFreehand } from "./eraseFreehand";
-export { fillInsideFreehand, fillOutsideFreehand } from "./fillFreehand";

package/imaging/tools/types.d.ts

@@ -1,243 +0,0 @@
-type ToolOptions = {
-  mouseButtonMask?: number | number[];
-  supportedInteractionTypes?: string[];
-  loop?: boolean;
-  allowSkipping?: boolean;
-  invert?: boolean;
-} & { [key: string]: unknown };
-
-export type ToolConfig = {
-  name: string;
-  viewports: string | string[];
-  configuration: Object;
-  options: ToolOptions;
-  class: string;
-  sync?: string;
-  cleanable?: boolean;
-  defaultActive?: boolean;
-  shortcut?: string;
-  type?: "utils" | "annotation" | "segmentation" | "overlay";
-  description?: string;
-};
-
-export type ToolStyle = {
-  width: number;
-  color: string; // "#00FF00"
-  activeColor: string; // "#00FF00"
-  fillColor: string; // "#00FF00"
-  fontFamily: string; // "Arial"
-  fontSize: number;
-  backgroundColor: string; // "rgba(1,1,1,0.7)"
-};
-
-export type ToolSettings = {
-  mouseEnabled: boolean;
-  touchEnabled: boolean;
-  showSVGCursors: boolean;
-  globalToolSyncEnabled: boolean;
-  autoResizeViewports: boolean;
-  lineDash: [number, number];
-};
-
-export type ToolMouseKeys = {
-  debug: boolean;
-  mouse_button_left: {
-    shift: string;
-    ctrl: string;
-    default: string;
-  };
-  mouse_button_right: {
-    shift: string;
-    ctrl: string;
-    default: string;
-  };
-  keyboard_shortcuts: {
-    // alt key + letter
-    // key in the form "KEY_A"
-    [key: string]: string;
-  };
-};
-
-type HanldePosition = {
-  active: boolean;
-  allowedOutsideImage?: boolean;
-  drawnIndependently?: boolean;
-  highlight: boolean;
-  index?: number;
-  locked?: boolean;
-  moving?: boolean;
-  x: number;
-  y: number;
-};
-
-type HandleTextBox = {
-  active: boolean;
-  allowedOutsideImage: boolean;
-  boundingBox: { height: number; left: number; top: number; width: number };
-  drawnIndependently: boolean;
-  hasBoundingBox: boolean;
-  hasMoved: boolean;
-  highlight?: boolean;
-  index?: number;
-  movesIndependently: boolean;
-  x: number;
-  y: number;
-};
-
-type BaseToolStateData = {
-  active: boolean;
-  color: string;
-  invalidated: boolean;
-  uuid: string;
-  visible: boolean;
-};
-
-type AngleStateData = BaseToolStateData & {
-  handles: {
-    end: HanldePosition;
-    middle: HanldePosition;
-    start: HanldePosition;
-    textBox: HandleTextBox;
-  };
-  rAngle: number;
-};
-
-type ArrowAnnotateStateData = BaseToolStateData & {
-  handles: {
-    end: HanldePosition;
-    start: HanldePosition;
-    textBox: HandleTextBox;
-  };
-  text: string;
-};
-
-type BidirectionalStateData = BaseToolStateData & {
-  handles: {
-    end: HanldePosition;
-    perpendicularEnd: HanldePosition;
-    perpendicularStart: HanldePosition;
-    start: HanldePosition;
-    textBox: HandleTextBox;
-  };
-  isCreating: boolean;
-  longestDiameter: number;
-  shortestDiameter: number;
-  toolName: "Bidirectional";
-  toolType: "Bidirectional";
-};
-
-type EllipticalRoiStateData = BaseToolStateData & {
-  cachedStats: {
-    area: number;
-    count: number;
-    max: number;
-    mean: number;
-    meanStdDevSUV?: number;
-    min: number;
-    stdDev: number;
-    variance: number;
-  };
-  handles: {
-    end: HanldePosition;
-    initialRotation: number;
-    start: HanldePosition;
-    textBox: HandleTextBox;
-  };
-  unit: string;
-};
-
-type FreehandRoiStateData = ToolStateData & {
-  area: number;
-  canComplete: boolean;
-  handles: {
-    points: FreehandHandleData[];
-    textBox: any;
-    invalidHandlePlacement: boolean;
-  };
-  highlight: boolean;
-  meanStdDev: { count: number; mean: number; variance: number; stdDev: number };
-  meanStdDevSUV: undefined;
-  polyBoundingBox: { left: number; top: number; width: number; height: number };
-  unit: string;
-};
-
-type LengthStateData = BaseToolStateData & {
-  handles: {
-    end: HanldePosition;
-    start: HanldePosition;
-    textBox: HandleTextBox;
-  };
-  length: number;
-  unit: string;
-};
-
-type ProbeStateData = BaseToolStateData;
-
-type RectangleRoiStateData = BaseToolStateData & {
-  cachedStats: {
-    area: number;
-    count: number;
-    max: number;
-    mean: number;
-    meanStdDevSUV?: number;
-    min: number;
-    perimeter: number;
-    stdDev: number;
-    variance: number;
-  };
-  handles: {
-    end: HanldePosition;
-    initialRotation: number;
-    start: HanldePosition;
-    textBox: HandleTextBox;
-  };
-  unit: string;
-};
-
-export type ToolState = {
-  [imageId: string]: {
-    Angle: AngleStateData;
-    ArrowAnnotate: ArrowAnnotateStateData;
-    Bidirectional: BidirectionalStateData;
-    EllipticalRoi: EllipticalRoiStateData;
-    FreehandRoi: FreehandRoiStateData;
-    Length: LengthStateData;
-    Probe: ProbeStateData;
-    RectangleRoi: RectangleRoiStateData;
-  };
-};
-
-export type SegmentationConfig = {
-  arrayType: number;
-  renderOutline: boolean;
-  renderFill: boolean;
-  shouldRenderInactiveLabelmaps: boolean;
-  radius: number;
-  minRadius: number;
-  maxRadius: number;
-  segmentsPerLabelmap: number;
-  fillAlpha: number;
-  fillAlphaInactive: number;
-  outlineAlpha: number;
-  outlineAlphaInactive: number;
-  outlineWidth: number;
-  storeHistory: boolean;
-};
-
-export const enum MaskVisualizations {
-  FILL,
-  CONTOUR,
-  HIDDEN
-}
-
-export type MaskProperties = {
-  color: string;
-  labelId: number;
-  opacity: number;
-  visualization: MaskVisualizations;
-};
-
-export type BrushProperties = {
-  radius: number; // px
-  thresholds: [number, number]; // [min, max] in px
-};

package/imaging/types.d.ts

@@ -1,200 +0,0 @@
-import { vec2 } from "cornerstone-core";
-import { DataSet } from "dicom-parser";
-import { DEFAULT_VIEWPORT } from "./imageStore";
-import { NrrdSeries } from "./loaders/nrrdLoader";
-import { MetaDataTypes } from "./MetaDataTypes";
-import { MetaDataReadable } from "./MetaDataReadable";
-
-// TODO-ts: differentiate each single metadata @szanchi
-/*export type MetadataValue =
-  | string
-  | number
-  | string[]
-  | number[]
-  | boolean
-  | null
-  | Array
-  | undefined; // null or undefined is only for nrrd*/
-
-export type MetaData = MetaDataTypes & MetaDataReadable;
-export interface Image extends cornerstone.Image {
-  render?: Function;
-  decodeTimeInMS?: number;
-  loadTimeInMS?: number;
-  webWorkerTimeInMS?: number;
-  metadata: MetaData;
-  data?: DataSet;
-  floatPixelData?: Float32Array;
-}
-
-export type Instance = {
-  metadata: MetaData;
-  pixelData?: TypedArray | null;
-  dataSet?: DataSet | null;
-  file?: File | null;
-  instanceId?: string;
-  frame?: number;
-};
-
-export type ReslicedInstance = {
-  metadata: MetaData;
-  instanceId?: string;
-  permuteTable?: [number, number, number];
-};
-
-export type StagedProtocol = {
-  numberOfStages: number; // Number of stages
-  numberOfViews: number; // Number of views in stage
-  stageName?: string; // Name of the stage
-  stageNumber?: number; // Number of the stage
-  viewName?: string; // Name of the view
-  viewNumber?: number; // Number of the view
-};
-
-export type Series = {
-  imageIds: string[];
-  instances: { [key: string]: Instance };
-  seriesDescription?: string;
-  anonymized?: boolean;
-  bytes: number;
-  seriesUID: string;
-  currentImageIdIndex: number;
-  numberOfImages?: number;
-  isMultiframe: boolean;
-  color?: boolean;
-  dataSet: DataSet | null;
-  metadata?: MetaData;
-  frameDelay?: number;
-  frameTime?: number;
-  rWaveTimeVector?: number[];
-  instanceUIDs: { [key: string]: string };
-  is4D: boolean;
-  waveform: boolean;
-  ecgData?: number[];
-  traceData?: Partial<Plotly.PlotData>[];
-  isPDF: boolean;
-  stagedProtocol?: StagedProtocol;
-  modality: string;
-  numberOfFrames: number;
-  numberOfSlices: number;
-  numberOfTemporalPositions: number;
-  studyUID: string;
-  larvitarSeriesInstanceUID: string;
-  elements?: { [key: string]: any } | null;
-  layer: Layer;
-  orientation?: "axial" | "coronal" | "sagittal"; // this is needed for legacy reslice
-};
-
-export interface Layer extends cornerstone.EnabledElementLayer {
-  id: string;
-}
-
-export interface Viewport extends cornerstone.Viewport {
-  newImageIdIndex: number;
-  displayedArea: {
-    brhc: {
-      x: number;
-      y: number;
-    };
-  };
-}
-
-export type Contours = {
-  [key: string]: {
-    [key: string]: Array<{
-      x?: number;
-      y?: number;
-      lines: vec2[][];
-    }>;
-  };
-};
-
-export type Header = {
-  volume: Volume;
-  [imageId: string]: Instance.metadata;
-};
-
-export type Volume = {
-  imageIds: string[];
-  seriesId: string;
-  rows: number;
-  cols: number;
-  slope: number;
-  repr: string;
-  intercept: number;
-  imagePosition: [number, number];
-  numberOfSlices: number;
-  imageOrientation: [number, number, number];
-  pixelSpacing: [number, number];
-  sliceThickness: number;
-  phase?: string;
-  study_description?: string;
-  series_description?: string;
-  acquisition_date?: string;
-};
-
-export type LarvitarManager = {
-  [key: string]: NrrdSeries | Series;
-} | null;
-
-export type ImageFrame = {
-  pixelData?: Uint8ClampedArray | Uint16Array | Int16Array | Uint8Array;
-  bitsAllocated: number;
-  rows: number;
-  columns: number;
-  photometricInterpretation: string;
-  samplesPerPixel: number;
-  smallestPixelValue: number;
-  largestPixelValue: number;
-  imageData?: ImageData;
-  pixelRepresentation: number;
-};
-
-export type ImageTracker = {
-  [key: string]: string;
-} | null;
-
-// the result of readFile
-export type ImageObject = {
-  file: File;
-  instanceUID: string;
-  metadata: MetaData;
-  dataSet: DataSet;
-};
-
-export type CachingResponse = {
-  seriesId: string;
-  loading: number;
-  series: Partial<Series>;
-};
-
-export interface CustomDataSet extends DataSet {
-  repr?: string;
-}
-
-type Orientation = "axial" | "coronal" | "sagittal";
-
-type TypedArray =
-  | Float64Array
-  | Uint8Array
-  | Int8Array
-  | Uint16Array
-  | Int16Array
-  | Int32Array
-  | Uint32Array
-  | Float32Array;
-
-type StoreViewport = typeof DEFAULT_VIEWPORT;
-
-type StoreViewportOptions = {
-  numberOfSlices?: number;
-  sliceNumber?: number;
-  wc?: number;
-  ww?: number;
-  defaultWC?: number;
-  defaultWW?: number;
-  scale?: number;
-  colormap?: string;
-  tr_x?: number;
-  tr_y?: number;
-};