larvitar 2.0.4 → 2.0.6

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]);
-};

package/index.ts

@@ -1,431 +0,0 @@
-import pkg from "./package.json";
-const VERSION: string = pkg.version;
-console.groupCollapsed(
-  `%cLARVITAR %cv${VERSION}`,
-  "color: #404888; background: #209A71; font-weight: 900;",
-  "color: #BED730; background: #209A71; font-weight: 900;"
-);
-
-import cornerstone from "cornerstone-core";
-import cornerstoneTools from "cornerstone-tools";
-import { parseDicom } from "dicom-parser";
-
-import { default as cornerstoneDICOMImageLoader } from "cornerstone-wado-image-loader";
-const segModule = cornerstoneTools.getModule("segmentation");
-
-import {
-  checkAndClearMemory,
-  checkMemoryAllocation,
-  getUsedMemory,
-  getAvailableMemory
-} from "./imaging/monitors/memory";
-
-import {
-  getPerformanceMonitor,
-  activatePerformanceMonitor,
-  deactivatePerformanceMonitor
-} from "./imaging/monitors/performance";
-
-import store from "./imaging/imageStore";
-console.log(store);
-console.groupEnd();
-
-import { parseContours } from "./imaging/imageContours";
-
-import { parseECG } from "./imaging/parsers/ecg";
-
-import {
-  renderECG,
-  syncECGFrame,
-  updateECGFrame
-} from "./imaging/waveforms/ecg";
-
-import {
-  getImagePresets,
-  setImagePreset,
-  setImageCustomPreset
-} from "./imaging/imagePresets";
-
-import {
-  getNormalOrientation,
-  getMinPixelValue,
-  getMaxPixelValue,
-  getPixelRepresentation,
-  getTypedArrayFromDataType,
-  getSortedStack,
-  randomId,
-  getMeanValue,
-  getReslicedMetadata,
-  getReslicedPixeldata,
-  getDistanceBetweenSlices,
-  getImageMetadata
-} from "./imaging/imageUtils";
-
-import {
-  buildHeader,
-  getCachedPixelData,
-  buildData,
-  buildDataAsync,
-  importNRRDImage
-} from "./imaging/imageIo";
-
-import { anonymize } from "./imaging/imageAnonymization";
-
-import {
-  buildLayer,
-  updateLayer,
-  getActiveLayer,
-  setActiveLayer
-} from "./imaging/imageLayers";
-
-import {
-  initializeImageLoader,
-  initializeWebImageLoader,
-  initializeFileImageLoader,
-  registerNRRDImageLoader,
-  registerResliceLoader,
-  registerMultiFrameImageLoader,
-  updateLoadedStack
-} from "./imaging/imageLoading";
-
-import {
-  readFile,
-  readFiles,
-  parseDataSet,
-  clearImageParsing
-} from "./imaging/imageParsing";
-
-import {
-  clearImageCache,
-  loadAndCacheImages,
-  renderFileImage,
-  renderDICOMPDF,
-  renderWebImage,
-  disableViewport,
-  unloadViewport,
-  resizeViewport,
-  renderImage,
-  updateImage,
-  resetViewports,
-  updateViewportData,
-  storeViewportData,
-  invertImage,
-  flipImageHorizontal,
-  flipImageVertical,
-  rotateImageLeft,
-  rotateImageRight
-} from "./imaging/imageRendering";
-
-import { resliceSeries } from "./imaging/imageReslice";
-
-import {
-  addDiameterTool,
-  addContoursTool,
-  addMaskEditingTool,
-  getCurrentMaskData,
-  addStackStateToElement,
-  addSeedsTool,
-  clearMeasurements,
-  getToolState,
-  clearToolStateByName,
-  updateDiameterTool,
-  addToolStateSingleSlice,
-  clearCornerstoneElements,
-  syncToolStack,
-  updateStackToolState,
-  setSegmentationConfig
-} from "./imaging/imageTools";
-
-import {
-  csToolsCreateStack,
-  csToolsUpdateImageIds,
-  csToolsUpdateImageIndex,
-  initializeCSTools,
-  setToolsStyle,
-  addDefaultTools,
-  addTool,
-  setToolActive,
-  setToolDisabled,
-  setToolEnabled,
-  setToolPassive,
-  exportAnnotations
-} from "./imaging/tools/main";
-
-import {
-  DEFAULT_TOOLS,
-  dvTools,
-  getDefaultToolsByType,
-  setDefaultToolsProps,
-  registerExternalTool
-} from "./imaging/tools/default";
-
-import {
-  initSegmentationModule,
-  addSegmentationMask,
-  clearSegmentationState,
-  deleteMask,
-  setActiveLabelmap,
-  setActiveSegment,
-  enableBrushTool,
-  disableBrushTool,
-  undoLastStroke,
-  redoLastStroke,
-  setBrushProps,
-  toggleContourMode,
-  toggleVisibility,
-  hexToRgb,
-  rgbToHex,
-  getActiveLabelmapBuffer
-} from "./imaging/tools/segmentation";
-
-import {
-  updateLarvitarManager,
-  populateLarvitarManager,
-  getLarvitarManager,
-  getLarvitarImageTracker,
-  resetLarvitarManager,
-  removeSeriesFromLarvitarManager,
-  getSeriesDataFromLarvitarManager,
-  getImageFrame,
-  getSopInstanceUIDFromLarvitarManager
-} from "./imaging/loaders/commonLoader";
-
-import {
-  buildNrrdImage,
-  getNrrdImageId,
-  loadNrrdImage,
-  getImageIdFromSlice,
-  getSliceNumberFromImageId,
-  getNrrdSerieDimensions
-} from "./imaging/loaders/nrrdLoader";
-
-import {
-  getDicomImageId,
-  cacheImage,
-  cacheImages
-} from "./imaging/loaders/dicomLoader";
-
-import { loadReslicedImage } from "./imaging/loaders/resliceLoader";
-
-import {
-  loadMultiFrameImage,
-  buildMultiFrameImage,
-  getMultiFrameImageId,
-  clearMultiFrameCache
-} from "./imaging/loaders/multiframeLoader";
-
-import {
-  fileManager,
-  resetFileLoader,
-  resetFileManager,
-  populateFileManager,
-  getFileImageId
-} from "./imaging/loaders/fileLoader";
-
-import {
-  getColormapsList,
-  applyColorMap,
-  addColorMap,
-  fillPixelData,
-  HSVToRGB
-} from "./imaging/imageColormaps";
-
-import { saveAnnotations, loadAnnotations } from "./imaging/tools/io";
-
-import {
-  addMouseKeyHandlers,
-  removeMouseKeyHandlers,
-  toggleMouseToolsListeners
-} from "./imaging/tools/interaction";
-
-export {
-  VERSION,
-  // global cornerstone variables
-  cornerstone,
-  cornerstoneTools,
-  parseDicom,
-  segModule,
-  cornerstoneDICOMImageLoader,
-  // memory module
-  checkAndClearMemory,
-  checkMemoryAllocation,
-  getUsedMemory,
-  getAvailableMemory,
-  // performance module
-  getPerformanceMonitor,
-  activatePerformanceMonitor,
-  deactivatePerformanceMonitor,
-  // larvitarStore
-  store,
-  // parsers
-  parseECG,
-  syncECGFrame,
-  updateECGFrame,
-  // waveforms
-  renderECG,
-  // imagePresets
-  getImagePresets,
-  setImagePreset,
-  setImageCustomPreset,
-  // imageUtils
-  getNormalOrientation,
-  getMinPixelValue,
-  getMaxPixelValue,
-  getPixelRepresentation,
-  getTypedArrayFromDataType,
-  getSortedStack,
-  randomId,
-  getMeanValue,
-  getReslicedMetadata,
-  getReslicedPixeldata,
-  getDistanceBetweenSlices,
-  getImageMetadata,
-  // imageIo
-  buildHeader,
-  getCachedPixelData,
-  buildData,
-  buildDataAsync,
-  importNRRDImage,
-  // imageAnonymization
-  anonymize,
-  // imageLayers
-  buildLayer,
-  updateLayer,
-  getActiveLayer,
-  setActiveLayer,
-  // imageLoading
-  initializeImageLoader,
-  initializeWebImageLoader,
-  initializeFileImageLoader,
-  registerNRRDImageLoader,
-  registerResliceLoader,
-  registerMultiFrameImageLoader,
-  updateLoadedStack,
-  // imageParsing
-  readFile,
-  readFiles,
-  parseDataSet,
-  clearImageParsing,
-  // imageRendering
-  clearImageCache,
-  loadAndCacheImages,
-  renderFileImage,
-  renderDICOMPDF,
-  renderWebImage,
-  disableViewport,
-  unloadViewport,
-  resizeViewport,
-  renderImage,
-  updateImage,
-  resetViewports,
-  updateViewportData,
-  toggleMouseToolsListeners,
-  storeViewportData,
-  invertImage,
-  flipImageHorizontal,
-  flipImageVertical,
-  rotateImageLeft,
-  rotateImageRight,
-  // imageReslice
-  resliceSeries,
-  // imageColormaps
-  getColormapsList,
-  applyColorMap,
-  addColorMap,
-  fillPixelData,
-  HSVToRGB,
-  // imageContours
-  parseContours,
-  // loaders/commonLoader
-  updateLarvitarManager,
-  populateLarvitarManager,
-  getLarvitarManager,
-  getLarvitarImageTracker,
-  resetLarvitarManager,
-  removeSeriesFromLarvitarManager,
-  getSeriesDataFromLarvitarManager,
-  getImageFrame,
-  getSopInstanceUIDFromLarvitarManager,
-  // loaders/nrrdLoader
-  buildNrrdImage,
-  getNrrdImageId,
-  loadNrrdImage,
-  getImageIdFromSlice,
-  getSliceNumberFromImageId,
-  getNrrdSerieDimensions,
-  // loaders/resliceLoader
-  loadReslicedImage,
-  // loaders/dicomLoader
-  getDicomImageId,
-  cacheImage,
-  cacheImages,
-  // loaders/multiframeLoader
-  loadMultiFrameImage,
-  buildMultiFrameImage,
-  getMultiFrameImageId,
-  clearMultiFrameCache,
-  // loaders/fileLoader
-  fileManager,
-  resetFileLoader,
-  resetFileManager,
-  populateFileManager,
-  getFileImageId,
-  // imageTools
-  addDiameterTool,
-  addContoursTool,
-  addMaskEditingTool,
-  getCurrentMaskData,
-  addStackStateToElement,
-  addSeedsTool,
-  clearMeasurements,
-  getToolState,
-  clearToolStateByName,
-  updateDiameterTool,
-  addToolStateSingleSlice,
-  clearCornerstoneElements,
-  syncToolStack,
-  updateStackToolState,
-  setSegmentationConfig,
-  // tools/main
-  csToolsCreateStack,
-  csToolsUpdateImageIds,
-  csToolsUpdateImageIndex,
-  initializeCSTools,
-  setToolsStyle,
-  addDefaultTools,
-  addTool,
-  setToolActive,
-  setToolDisabled,
-  setToolEnabled,
-  setToolPassive,
-  exportAnnotations,
-  // tools/default
-  DEFAULT_TOOLS,
-  dvTools,
-  getDefaultToolsByType,
-  setDefaultToolsProps,
-  registerExternalTool,
-  // tools/io
-  saveAnnotations,
-  loadAnnotations,
-  // tools/interaction
-  addMouseKeyHandlers,
-  removeMouseKeyHandlers,
-  // tools/segmentation
-  initSegmentationModule,
-  addSegmentationMask,
-  setActiveLabelmap,
-  setActiveSegment,
-  undoLastStroke,
-  redoLastStroke,
-  setBrushProps,
-  hexToRgb,
-  rgbToHex,
-  clearSegmentationState,
-  deleteMask,
-  enableBrushTool,
-  disableBrushTool,
-  toggleContourMode,
-  toggleVisibility,
-  getActiveLabelmapBuffer
-};

package/jsdoc.json

@@ -1,52 +0,0 @@
-{
-  "tags": {
-    "allowUnknownTags": true
-  },
-  "source": {
-    "include": ["dist/", "./README.md"]
-  },
-  "plugins": ["plugins/markdown"],
-  "opts": {
-    "encoding": "utf8",
-    "template": "./template/docdash",
-    "destination": "./docs/documentation/",
-    "recurse": true,
-    "verbose": true
-  },
-  "markdown": {
-    "parser": "gfm",
-    "hardwrap": true,
-    "idInHeadings": true
-  },
-  "templates": {
-    "cleverLinks": false,
-    "monospaceLinks": false,
-    "default": {
-      "outputSourceFiles": true,
-      "includeDate": false,
-      "useLongnameInNav": true
-    }
-  },
-  "docdash": {
-    "static": true,
-    "sort": true,
-    "meta": {
-      "title": "Larvitar",
-      "description": "Dicom Image Toolkit for CornestoneJS",
-      "keyword": "imaging, dataviz, medical, cornerstone"
-    },
-    "search": true,
-    "collapse": true,
-    "typedefs": true,
-    "removeQuotes": "none",
-    "scripts": [],
-    "menu": {
-      "Github repo": {
-        "href": "https://github.com/dvisionlab/Larvitar",
-        "target": "_blank",
-        "class": "menu-item",
-        "id": "repository"
-      }
-    }
-  }
-}

package/rollup.config.js

@@ -1,51 +0,0 @@
-import resolve from "@rollup/plugin-node-resolve";
-import json from "@rollup/plugin-json";
-import commonjs from "@rollup/plugin-commonjs";
-import pkg from "./package.json";
-
-export default [
-  // browser-friendly UMD build
-  {
-    input: "index.js",
-    output: {
-      name: "larvitar",
-      file: pkg.browser,
-      format: "umd",
-      globals: {
-        fs: "fs",
-        path: "path"
-      }
-    },
-    plugins: [
-      resolve(),
-      {
-        jsnext: true,
-        main: true,
-        browser: true,
-        extensions: [".js", ".json"]
-        // preferBuiltins: true
-      }, // so Rollup can find node_modules
-      commonjs({
-        // requireReturnsDefault: "auto",
-        // esmExternals: true
-      }), // so Rollup can convert node_modules to an ES module,
-      json()
-    ]
-  }
-
-  // CommonJS (for Node) and ES module (for bundlers) build.
-  // (We could have three entries in the configuration array
-  // instead of two, but it's quicker to generate multiple
-  // builds from a single configuration where possible, using
-  // an array for the `output` option, where we can specify
-  // `file` and `format` for each target)
-  // {
-  //   input: "index.js",
-  //   // external: ["cornerstone-core"],
-  //   output: [
-  //     { file: pkg.common, format: "cjs" },
-  //     { file: pkg.module, format: "es" }
-  //   ],
-  //   plugins: [resolve(), commonjs(), json()]
-  // }
-];