larvitar 2.0.5 → 2.0.7

package/imaging/tools/segmentation.ts

@@ -1,532 +0,0 @@
-/** @module imaging/tools/segmentation
- *  @desc  This file provides functionalities
- *         for handling masks and luts
- */
-
-// external libraries
-import cornerstone, { Viewport } from "cornerstone-core";
-import cornerstoneTools from "cornerstone-tools";
-import { cloneDeep, extend, values, sum } from "lodash";
-const segModule = cornerstoneTools.getModule("segmentation");
-const { getters, setters } = segModule;
-
-// internal libraries
-import { setToolActive, setToolDisabled } from "./main";
-import { isElement } from "../imageUtils";
-import store from "../imageStore";
-import { updateStackToolState } from "../imageTools";
-
-// custom code
-import { setLabelmap3DForElement } from "./custom/setLabelMap3D";
-import {
-  BrushProperties,
-  MaskProperties,
-  MaskVisualizations,
-  SegmentationConfig
-} from "./types.d";
-import type { TypedArray } from "../types";
-// override function
-setters.labelmap3DForElement = setLabelmap3DForElement;
-
-// General segmentation cs tools module configuration
-const config: SegmentationConfig = {
-  arrayType: 0,
-  renderOutline: false,
-  renderFill: true,
-  shouldRenderInactiveLabelmaps: true,
-  radius: 10,
-  minRadius: 1,
-  maxRadius: 50,
-  segmentsPerLabelmap: 10,
-  fillAlpha: 0.9,
-  fillAlphaInactive: 0.9,
-  outlineAlpha: 1.0,
-  outlineAlphaInactive: 1.0,
-  outlineWidth: 1,
-  storeHistory: true
-};
-
-// ====================================================
-// utils to convert from hex to rgb and vice-versa ====
-// ====================================================
-
-function componentToHex(c: number) {
-  var hex = c.toString(16);
-  return hex.length == 1 ? "0" + hex : hex;
-}
-
-export function rgbToHex(c: number[]) {
-  let r = componentToHex(c[0]);
-  let g = componentToHex(c[1]);
-  let b = componentToHex(c[2]);
-  return "#" + r + g + b;
-}
-
-export function hexToRgb(hex: string) {
-  var result = /^#?([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})$/i.exec(hex);
-
-  if (!result) {
-    console.error("Error parsing hex color");
-    return [0, 0, 0];
-  }
-
-  return [
-    parseInt(result[1], 16),
-    parseInt(result[2], 16),
-    parseInt(result[3], 16)
-  ];
-}
-
-/**
- * Convert color from hsv to rgb
- * @param {Array} color as [h,s,v] 0-1
- * @returns color as [r,g,b] 0-255
- */
-function HSVtoRGB([h, s, v]: [number, number, number]) {
-  var r, g, b, i, f, p, q, t;
-  i = Math.floor(h * 6);
-  f = h * 6 - i;
-  p = v * (1 - s);
-  q = v * (1 - f * s);
-  t = v * (1 - (1 - f) * s);
-  switch (i % 6) {
-    case 0:
-      (r = v), (g = t), (b = p);
-      break;
-    case 1:
-      (r = q), (g = v), (b = p);
-      break;
-    case 2:
-      (r = p), (g = v), (b = t);
-      break;
-    case 3:
-      (r = p), (g = q), (b = v);
-      break;
-    case 4:
-      (r = t), (g = p), (b = v);
-      break;
-    case 5:
-      (r = v), (g = p), (b = q);
-      break;
-    default:
-      (r = v), (g = t), (b = p);
-      console.error("HSVtoRGB: Input color must be [h,s,v] 0-1");
-  }
-  return [Math.round(r * 255), Math.round(g * 255), Math.round(b * 255)];
-}
-
-/**
- * Force cs tools refresh on all enabled images
- */
-export function forceRender() {
-  let enabledElements = cornerstone.getEnabledElements();
-  enabledElements.forEach(enEl => {
-    cornerstone.updateImage(enEl.element);
-  });
-}
-
-/**
- * Generate the custom LUT - single volume version
- */
-
-function generateLUT(opacity: number) {
-  let lut = new Array(segModule.configuration.segmentsPerLabelmap).fill(0);
-  lut = lut.map((e, i) => {
-    return HSVtoRGB([i / lut.length, 1, 1]).concat(Math.round(opacity * 255));
-  });
-
-  return lut;
-}
-
-/**
- * Generate the custom LUT - multiple volume version
- * @param {String} hex_color - color for LUT in the #RRGGBB form
- * @param {NUmber} opacity - number between 0 and 1
- */
-function generateUniformLUT(hex_color: string, opacity: number) {
-  let lut = new Array(segModule.configuration.segmentsPerLabelmap);
-  let rgb_color = hexToRgb(hex_color);
-  let rgba_color = rgb_color.concat(Math.round(opacity * 255));
-  lut.fill(rgba_color);
-  return lut;
-}
-
-/**
- * Set color for label
- * @param {Number} labelId
- * @param {String} color in hex format
- */
-export function setLabelColor(labelId: string, color: string) {
-  let volumeId = 0; // TODO MULTIVOLUME
-  let rgb = hexToRgb(color);
-  let rgba = [...rgb, 128];
-  setters.colorForSegmentIndexOfColorLUT(volumeId, labelId, rgba);
-  // force render ? depends on image visualization (render all ?)
-}
-
-/**
- * Get color from label
- * @param {Number} labelId
- * @returns {String} Color in hex format
- */
-export function getLabelColor(labelId: string) {
-  let volumeId = 0; // TODO MULTIVOLUME
-  let rgba = getters.colorForSegmentIndexColorLUT(volumeId, labelId);
-  return rgbToHex(rgba);
-}
-
-/**
- * A function to group all settings to load before masks
- * @param {Object} customConfig - Object containing override values for segmentation module config
- */
-export function initSegmentationModule(customConfig: SegmentationConfig) {
-  // set configuration
-  segModule.configuration = cloneDeep(config);
-  extend(segModule.configuration, customConfig);
-}
-
-/**
- * Add segmentation mask to segmentation module
- * @param {Object} props - The mask properties (labelId, color and opacity)
- * @param {TypedArray} - The mask data array
- * @param {String} elementId - The target html element Id or its DOM HTMLElement
- * @returns {Promise} - Return a promise which will resolve when segmentation mask is added
- */
-
-export function addSegmentationMask(
-  props: MaskProperties,
-  data: TypedArray,
-  elementId: string | HTMLElement
-) {
-  let promise = new Promise<void>(async resolve => {
-    let element = isElement(elementId)
-      ? (elementId as HTMLElement)
-      : document.getElementById(elementId as string);
-    if (!element) {
-      console.error("invalid html element: " + elementId);
-      return;
-    }
-
-    const res = await setters.labelmap3DForElement(
-      element,
-      data.buffer,
-      props.labelId
-    );
-    // if user set a color property, use that color for all segments on the labelmap
-    let lut = props.color
-      ? generateUniformLUT(props.color, props.opacity)
-      : generateLUT(props.opacity);
-    setters.colorLUT(props.labelId, lut);
-    // bind labelmap to colorLUT
-    let labelmap3d = getters.labelmap3D(element, props.labelId);
-    setters.colorLUTIndexForLabelmap3D(labelmap3d, props.labelId);
-
-    // set current imageIdIndex in tool state
-    let currentImageIdIndex = store.get(["viewports", element.id, "sliceId"]);
-    if (currentImageIdIndex !== "error" && currentImageIdIndex >= 0) {
-      updateStackToolState(element.id, currentImageIdIndex);
-    } else {
-      console.error("Cannot get currentImageIdIndex");
-    }
-
-    resolve();
-  });
-  return promise;
-}
-
-/**
- * Set a new mask slice into the labelmap buffer
- * @param {String} elementId - The target html element Id or its DOM HTMLElement
- * @param {Number} sliceIndex - the index of the new mask slice
- * @param {ArrayBuffer} pixelData - the pixelData array
- */
-export function loadMaskSlice(
-  elementId: string | HTMLElement,
-  sliceIndex: number,
-  pixelData: TypedArray
-) {
-  // optimization: if pixelData contains no labels, return
-  if (sum(pixelData) === 0) {
-    return;
-  }
-
-  let element = isElement(elementId)
-    ? (elementId as HTMLElement)
-    : document.getElementById(elementId as string);
-  if (!element) {
-    console.error("invalid html element: " + elementId);
-    return;
-  }
-  let volumeId = 0; // TODO for multivolume
-  // get labelmap buffer
-  let labelmaps2D = getters.labelmap3D(element, volumeId).labelmaps2D;
-
-  // add if not alresdy present
-  if (!labelmaps2D[sliceIndex]) {
-    labelmaps2D[sliceIndex] = {};
-  }
-
-  labelmaps2D[sliceIndex].pixelData = pixelData;
-  setters.updateSegmentsOnLabelmap2D(labelmaps2D[sliceIndex]);
-  cornerstone.updateImage(element);
-}
-
-/**
- * Activate a specific labelmap through its labelId
- * @param {Number} labelId - The labelmap id to activate
- * @param {String} elementId - The target html element Id or its DOM HTMLElement
- */
-export function setActiveLabelmap(
-  labelId: number,
-  elementId: string | HTMLElement
-) {
-  let element = isElement(elementId)
-    ? (elementId as HTMLElement)
-    : document.getElementById(elementId as string);
-  if (!element) {
-    console.error("invalid html element: " + elementId);
-    return;
-  }
-  setters.activeLabelmapIndex(element, labelId);
-}
-
-/**
- * Get active labelmap for target element
- * @param {String} elementId - The target html element Id or its DOM HTMLElement
- * @returns {Object} The active labelmap object that contains the buffer
- */
-export function getActiveLabelmapBuffer(elementId: string | HTMLElement) {
-  let element = isElement(elementId)
-    ? (elementId as HTMLElement)
-    : document.getElementById(elementId as string);
-  if (!element) {
-    console.error("invalid html element: " + elementId);
-    return;
-  }
-  return getters.activeLabelmapBuffer(element);
-}
-
-/**
- * Activate a specific segment through its index
- * @param {Number} segmentIndex - The segment index to activate
- * @param {String} elementId - The target html element Id or its DOM HTMLElement
- */
-export function setActiveSegment(
-  segmentIndex: number,
-  elementId: string | HTMLElement
-) {
-  let element = isElement(elementId)
-    ? (elementId as HTMLElement)
-    : document.getElementById(elementId as string);
-  if (!element) {
-    console.error("invalid html element: " + elementId);
-    return;
-  }
-  setters.activeSegmentIndex(element, segmentIndex);
-}
-
-/**
- * Change opacity for active label
- * @param {Number} opacity - The desired opacity value
- */
-export function setActiveLabelOpacity(opacity: number) {
-  segModule.configuration.fillAlpha = opacity;
-  forceRender();
-}
-
-/**
- * Change opacity for inactive labels
- * @param {Number} opacity - The desired opacity value
- */
-export function setInactiveLabelOpacity(opacity: number) {
-  segModule.configuration.fillAlphaInactive = opacity;
-  forceRender();
-}
-
-/**
- * Toggle mask visibility
- * @param {String} elementId - The target html element Id or its DOM HTMLElement
- * @param {Number} labelId - The id of the mask label
- */
-export function toggleVisibility(
-  elementId: string | HTMLElement,
-  labelId: number
-) {
-  let element = isElement(elementId)
-    ? (elementId as HTMLElement)
-    : document.getElementById(elementId as string);
-  if (!element) {
-    console.error("invalid html element: " + elementId);
-    return;
-  }
-  let volumeId = 0; // TODO MULTIVOLUME
-  setters.toggleSegmentVisibility(element, labelId, volumeId);
-  cornerstone.updateImage(element);
-}
-
-/**
- * Toggle between 'contours mode' and 'filled mode'
- * @param {Bool} toggle - Contour mode enabled if true
- */
-export function toggleContourMode(toggle: boolean) {
-  if (toggle) {
-    segModule.configuration.fillAlpha = 0.0;
-    segModule.configuration.fillAlphaInactive = 0.0;
-    segModule.configuration.outlineAlpha = 1.0;
-    segModule.configuration.outlineAlphaInactive = 1.0;
-    segModule.configuration.outlineWidth = 3;
-  } else {
-    segModule.configuration.fillAlpha = config.fillAlpha;
-    segModule.configuration.fillAlphaInactive = config.fillAlphaInactive;
-    segModule.configuration.outlineAlpha = config.outlineAlpha;
-    segModule.configuration.outlineAlphaInactive = config.outlineAlphaInactive;
-    segModule.configuration.outlineWidth = config.outlineWidth;
-  }
-  forceRender();
-}
-
-/**
- * Set mask appearance props
- * @param {Object} maskProps - The mask appearance props (labelId, visualization [0=filled, 1=contour, 2=hidden], opacity (if mode=0), between 0 and 1)
- */
-
-export function setMaskProps(props: MaskProperties) {
-  // Lut index and segment values are hardcoded because they will depend on design choices:
-  // eg single/multiple volumes for segmentations
-  let lutIndex = props.labelId;
-  let labelIndex = props.labelId;
-  // let segmentValue = MAP_VALUES[props.id];
-  let segmentValue = 1; // binary mask, segment 1 is the only to be affected by color & opacity
-  let currentColor = getters.colorForSegmentIndexColorLUT(
-    props.labelId,
-    segmentValue
-  );
-  let htmlelement = document.getElementById("axial");
-
-  let newColor = currentColor;
-  switch (props.visualization) {
-    // full
-    case MaskVisualizations.FILL:
-      segModule.configuration.renderOutline = true;
-      getters.isSegmentVisible(htmlelement, segmentValue, labelIndex)
-        ? null
-        : setters.toggleSegmentVisibility(
-            htmlelement,
-            segmentValue,
-            labelIndex
-          );
-      newColor[3] = Math.round(props.opacity * 255);
-      setters.colorForSegmentIndexOfColorLUT(lutIndex, segmentValue, newColor);
-      break;
-    // contours
-    case MaskVisualizations.CONTOUR:
-      segModule.configuration.renderOutline = true;
-      getters.isSegmentVisible(htmlelement, segmentValue, labelIndex)
-        ? null
-        : setters.toggleSegmentVisibility(
-            htmlelement,
-            segmentValue,
-            labelIndex
-          );
-      newColor[3] = 0;
-      setters.colorForSegmentIndexOfColorLUT(lutIndex, segmentValue, newColor);
-      break;
-    // hidden
-    case MaskVisualizations.HIDDEN:
-      setters.toggleSegmentVisibility(htmlelement, segmentValue, labelIndex);
-      break;
-  }
-  forceRender();
-}
-
-/**
- * Clear state for segmentation module
- */
-export function clearSegmentationState() {
-  segModule.state.series = {};
-}
-
-/**
- * Enable brushing
- * NOTE: if options contains `thresholds`, ThresholdsBrush is activated, otherwise BrushTool is activated.
- * Anyway, the activated tool name is returned
- * @param {Object} options - An object containing configuration values (eg radius, thresholds, etc...)
- */
-export function enableBrushTool(viewports: string[], options: BrushProperties) {
-  setBrushProps(options);
-  const brushType = "thresholds" in options ? "ThresholdsBrush" : "Brush";
-  setToolActive(brushType, undefined, viewports);
-  return brushType;
-}
-
-/**
- * Disable brushing
- * This function disables both brush tools, if found active on `viewports`
- * @param {String} toolToActivate - The name of the tool to activate after removing the brush @optional
- */
-export function disableBrushTool(viewports: string[], toolToActivate?: string) {
-  viewports.forEach((viewport: string) => {
-    const el = document.getElementById(viewport);
-    if (cornerstoneTools.isToolActiveForElement(el, "ThresholdsBrush")) {
-      setToolDisabled("ThresholdsBrush", [viewport]);
-    }
-    if (cornerstoneTools.isToolActiveForElement(el, "Brush")) {
-      setToolDisabled("Brush", [viewport]);
-    }
-  });
-
-  if (toolToActivate) {
-    setToolActive(toolToActivate);
-  }
-}
-
-/**
- * Change the brush props
- * @param {Object} props - The new brush props {radius: number[px], thresholds: array[min,max]}
- */
-export function setBrushProps(props: BrushProperties) {
-  extend(segModule.configuration, props);
-  forceRender();
-}
-
-/**
- * Undo last brush operation (stroke)
- * @param {String} elementId - The target html element Id or its DOM HTMLElement
- */
-export function undoLastStroke(elementId: string | HTMLElement) {
-  let element = isElement(elementId)
-    ? (elementId as HTMLElement)
-    : document.getElementById(elementId as string);
-  if (!element) {
-    console.error("invalid html element: " + elementId);
-    return;
-  }
-  let activeLabelMapIndex = segModule.getters.activeLabelmapIndex(element);
-  setters.undo(element, activeLabelMapIndex);
-}
-
-/**
- * Redo last brush operation (stroke)
- * @param {String} elementId - The target html element Id or its DOM HTMLElement
- */
-export function redoLastStroke(elementId: string | HTMLElement) {
-  let element = isElement(elementId)
-    ? (elementId as HTMLElement)
-    : document.getElementById(elementId as string);
-  if (!element) {
-    console.error("invalid html element: " + elementId);
-    return;
-  }
-  let activeLabelMapIndex = segModule.getters.activeLabelmapIndex(element);
-  setters.redo(element, activeLabelMapIndex);
-}
-
-/**
- * Delete mask from state
- * @param {Number} labelId - The labelmap id to delete
- */
-export function deleteMask(labelId: number) {
-  let masks = values(segModule.state.series)[0].labelmaps3D;
-  delete masks[labelId];
-  forceRender();
-}

package/imaging/tools/segmentations.md

@@ -1,38 +0,0 @@
-# Introduction
-
-This guide explains the key concepts of Larvitar **segmentation masks management**, based on cornerstone tools's **segmentation module**.
-
-# Definitions
-
-- _segmentation mask_ or just _mask_: the set of pixels that belongs to a specific structure
-- _volume_: a buffer containing one or more segmentations
-- _label_: the value inside a volume that identifies a specific segmentation
-
-# CS tools
-
-## Segmentation module structure
-
-In cs tools world, the different volumes are defined _labelmaps_, while the different labels in a volume are _segments_. Labelmaps can support up to 2^16 segments.
-The values in the volume (ie, labels) define which color will be used from the LUT map: in fact, segments get the color from the lutmap and can be shown/hidden one by one.
-Each labelmaps can be linked to a different colormap and has a active / inactive property that affects the rendering style (see configuration).
-
-> setters.toggleSegmentVisibility(htmlelement,segmentvalue,labelmapid)  
-> setters.colorForSegmentIndexOfColorLUT(colorLutIndex, segmentValue, colorRGBAarray)
-
-## Configuration
-
-TODO
-
-# Larvitar segmentation management
-
-TODO
-
-# Larvitar segmentation API
-
-To enable brush tools, user can call directly the `setToolActive` / `setToolDisabled` api, in this case he has to handle brush type (thresholds or not), props (radius etc) and tool switching. Otherwise, Larvitar implements the utility functions `enableBrushTool` and `disableBrushTool` that internally handle brush type and props with a single call.
-
-# Customization
-
-Some function in larvitar overrides the default behaviour of cornerstone tools, here is a list of them:
-
-- `setters.labelmap3DForElement` is overridden to have a non-blocking behaviour, the custom code is in ./setLabelMap3D.js, same as original code in cs tools repo.

package/imaging/tools/state.ts

@@ -1,74 +0,0 @@
-/** @module imaging/tools/state
- *  @desc  This file provides functionalities
- *         for handling tools' state
- */
-
-// external libraries
-import cornerstoneTools from "cornerstone-tools";
-import { each } from "lodash";
-
-import type { ToolState } from "./types";
-
-/**
- *
- * @param {*} elementId
- */
-const saveToolState = function (elementId: string) {
-  const elementToolStateManager = cornerstoneTools.getElementToolStateManager(
-    document.getElementById(elementId)
-  );
-
-  const currentState = elementToolStateManager.saveToolState();
-
-  return currentState;
-};
-
-/**
- *
- * @param {*} elementId
- * @param {*} allToolState
- */
-const restoreToolState = function (elementId: string, allToolState: ToolState) {
-  const elementToolStateManager = cornerstoneTools.getElementToolStateManager(
-    document.getElementById(elementId)
-  );
-
-  each(allToolState, (imageState, imageId) => {
-    each(imageState, (toolState, toolName) => {
-      elementToolStateManager.restoreImageIdToolState(imageId, {
-        [toolName]: toolState
-      });
-    });
-  });
-};
-
-// EXAMPLE OF CORRECT USE OF TOOL STATE MANAGER
-
-/*
-  // Declare state manager
-  const stateManager = cornerstoneTools.newImageIdSpecificToolStateManager();
-
-  // Get enabled element (cornerstone.getEnabledElement)
-  const imageId = "imagefile:0";
-  const testElement = cornerstone.getEnabledElements().slice().pop();
-  testElement.image = { imageId };
-  // const testElement = {
-  //   image: {
-  //     imageId
-  //   }
-  // };
-
-  // Setup with some initial data
-  const toolType = "EllipticalRoi";
-  stateManager.restoreImageIdToolState(imageId, {
-    [toolType]: { data: state_to_load[imageId] }
-  });
-
-  // Add more data
-  stateManager.add(testElement, toolType, "addedData");
-
-  // Check the results
-  const allToolState = stateManager.saveToolState();
-}
-*/
-export { saveToolState, restoreToolState };