larvitar 2.0.5 → 2.0.7

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/waveforms/ecg.ts

@@ -1,191 +0,0 @@
-/** @module waveforms/ecg
- *  @desc This file provides utility functions for
- *        rendering ecg waveforms using plotly.js
- */
-
-// external libraries
-import Plotly, { Datum } from "plotly.js-dist-min";
-
-// internal libraries
-import { Series } from "../types";
-import { NrrdSeries } from "../loaders/nrrdLoader";
-import { updateImage } from "../imageRendering";
-import store from "../imageStore";
-import { getSeriesDataFromLarvitarManager } from "../loaders/commonLoader";
-import { updateStackToolState } from "../imageTools";
-
-/*
- * This module provides the following functions to be exported:
- * renderECG(data, divId, colorMarker, numberOfFrames, frameTime, frameId)
- * syncECGFrame(traceData, seriesId, canvasId, numberOfFrames, divId)
- * updateECGFrame(traceData, frameId, numberOfFrames, divId)
- */
-
-const LAYOUT: Partial<Plotly.Layout> = {
-  xaxis: {
-    rangemode: "tozero",
-    showgrid: true,
-    gridcolor: "rgba(238,135,51,0.5)",
-    dtick: 1,
-    tickwidth: 2,
-    tickcolor: "#f5f5f5",
-    tickformat: ".2f",
-    tickfont: {
-      color: "#f5f5f5"
-    }
-  },
-  yaxis: {
-    rangemode: "nonnegative",
-    showgrid: true,
-    gridcolor: "rgba(238,135,51,0.5)",
-    dtick: 20,
-    tick0: 0,
-    tickwidth: 2,
-    tickcolor: "#f5f5f5",
-    tickfont: {
-      color: "#f5f5f5"
-    }
-  },
-  showlegend: false,
-  paper_bgcolor: "#000000",
-  plot_bgcolor: "#000000"
-};
-
-/**
- * Render ECG waveform in a div
- * @instance
- * @function renderECG
- * @param {number[]} data - ECG waveform data
- * @param {string} divId - DivId to render waveform in
- * @param {string} colorMarker - Color of the marker
- * @param {number} numberOfframes - Number of frames in the image
- * @param {number} frameTime - Time interval of each frame in the image
- * @param {number} frameId - FrameId of the image to be rendered
- * @returns {Object} traceData - Plotly trace data
- */
-export const renderECG = function (
-  data: number[],
-  divId: string,
-  colorMarker: string,
-  numberOfFrames: number,
-  frameTime: number,
-  frameId: number = 0
-): Partial<Plotly.PlotData>[] {
-  // convert info using frameTime and numberOfFrames
-  const totalTime = (numberOfFrames - 1) * (frameTime * 1e-3);
-  const dotX: number = Math.floor((frameId * data.length) / numberOfFrames);
-  // build the trace data
-  const trace: Partial<Plotly.PlotData> = {
-    x: data.map((_, i) => (i * totalTime) / data.length),
-    y: data,
-    mode: "lines",
-    type: "scattergl",
-    line: {
-      width: 1.5,
-      shape: "linear"
-    }
-  };
-
-  // build the marker data
-  const marker: Partial<Plotly.PlotData> = {
-    x: [dotX],
-    y: [data[dotX]],
-    mode: "markers",
-    type: "scattergl",
-    marker: {
-      size: 12,
-      color: colorMarker,
-      symbol: "line-ns-open",
-      line: {
-        width: 3
-      }
-    }
-  };
-  // render data and update ranges
-  const traceData: Partial<Plotly.PlotData>[] = [trace, marker];
-  // fix the range of the x-axis
-  LAYOUT.xaxis!.range = [0, totalTime];
-  // fix the grid of x-axis using a line for each frame
-  LAYOUT.xaxis!.dtick = LAYOUT.xaxis!.dtick = totalTime / (numberOfFrames - 1);
-  Plotly.newPlot(divId, traceData, LAYOUT, {
-    responsive: true,
-    displayModeBar: false
-  });
-  return traceData;
-};
-
-/**
- * Sync ECG waveform with rendered image on click
- * @instance
- * @function syncECGFrame
- * @param {Object} traceData - Plotly trace data
- * @param {string} seriesId - SeriesId of the image
- * @param {string} canvasId - CanvasId of the image
- * @param {number} numberOfFrames - Number of frames in the image
- * @param {string} divId - DivId to render waveform in
- */
-export const syncECGFrame = function (
-  traceData: Partial<Plotly.PlotData>[],
-  seriesId: string,
-  canvasId: string,
-  numberOfFrames: number,
-  divId: string
-) {
-  // document.getElementById('myDiv') return HTMLElement. This type doesn't
-  // contain method 'on' because this method is added within plotly-latest.min.js.
-  const domElement: any = document.getElementById(divId);
-  if (domElement) {
-    domElement.on("plotly_click", function (data: Plotly.PlotMouseEvent) {
-      traceData[1].x = [data.points[0].x];
-      traceData[1].y = [data.points[0].y];
-      Plotly.extendTraces(divId, {}, [0]);
-      const totalTime: number = (traceData[0].x as number[])[
-        (traceData[0].x as number[]).length - 1
-      ];
-      const frameId: number = Math.floor(
-        ((data.points[0].x as number) * numberOfFrames - 1) / totalTime
-      );
-      const series: Series | NrrdSeries | null =
-        getSeriesDataFromLarvitarManager(seriesId);
-      if (series) {
-        updateImage(series as Series, canvasId, frameId, false);
-        updateStackToolState(canvasId, frameId);
-      }
-    });
-  }
-
-  const canvasElement: any = document.getElementById(canvasId);
-  canvasElement.addEventListener("wheel", function (e: WheelEvent) {
-    const viewport = store.get(["viewports", canvasId]);
-    updateECGFrame(traceData, viewport.sliceId, numberOfFrames, divId);
-    updateStackToolState(canvasId, viewport.sliceId);
-  });
-};
-
-/**
- * Sync ECG waveform with rendered image on click
- * @instance
- * @function updateECGFrame
- * @param {Object} traceData - Plotly trace data
- * @param {number} frameId - FrameId of the image
- * @param {number} numberOfFrames - Number of frames in the image
- * @param {string} divId - DivId to render waveform in
- */
-export const updateECGFrame = function (
-  traceData: Partial<Plotly.PlotData>[],
-  frameId: number,
-  numberOfFrames: number,
-  divId: string
-) {
-  const totalTime: number = (traceData[0].x as number[])[
-    (traceData[0].x as number[]).length - 1
-  ];
-  const dotX: number = (frameId * totalTime) / (numberOfFrames - 1);
-  const index: number = (traceData[0].x as number[]).findIndex(
-    (x: number) => x >= dotX
-  );
-  const dotY: Datum | Datum[] = traceData[0].y![index];
-  traceData[1].x = [dotX];
-  traceData[1].y = Array.isArray(dotY) ? dotY : [dotY];
-  Plotly.extendTraces(divId, {}, [0]);
-};