larvitar 0.20.0 → 1.1.2

package/imaging/tools/{tools.segmentation.js → segmentation.js}

@@ -1,33 +1,18 @@
+/** @module imaging/tools/segmentation
+ *  @desc  This file provides functionalities
+ *         for handling masks and luts
+ */
+
 // external libraries
 import cornerstone from "cornerstone-core";
 import cornerstoneTools from "cornerstone-tools/dist/cornerstoneTools.js";
-// tools
-import { setToolActive, setToolDisabled } from "./tools.main";
-// utils
-import { cloneDeep, extend, values } from "lodash";
-
+import { cloneDeep, extend, values, sum } from "lodash";
 const segModule = cornerstoneTools.getModule("segmentation");
-const setters = segModule.setters;
-const getters = segModule.getters;
-
-/**
- * THIS MODULE IS A WIP
- */
+const { getters, setters } = segModule;
 
-// DEV
-window.segModule = segModule;
-window.cornerstone = cornerstone;
-window.cornerstoneTools = cornerstoneTools;
-
-/**
- * NOTES ON CS TOOLS SEGMENTATION MODULE
- * The value in the mask (binary) define which color will be used from the LUT map
- * The different masks are 'labelmap', while different values in the same mask are 'segments'
- * Segments get the color from the lutmap (up to 2^16 segments) and can be shown/hidden one by one
- * > setters.toggleSegmentVisibility(htmlelement,segmentvalue,labelmapid)
- * > setters.colorForSegmentIndexOfColorLUT(colorLutIndex, segmentValue, colorRGBAarray)
- * Labelmaps are linked to a colormap and can be active / inactive
- * */
+// internal libraries
+import { setToolActive, setToolDisabled } from "./main";
+import { isElement } from "../imageUtils";
 
 // General segmentation cs tools module configuration
 const config = {
@@ -145,53 +130,148 @@ function generateUniformLUT(hex_color, opacity) {
   return lut;
 }
 
+/**
+ * Set color for label
+ * @param {Number} labelId
+ * @param {String} color in hex format
+ */
+export function setLabelColor(labelId, color) {
+  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) {
+  let volumeId = 0; // TODO MULTIVOLUME
+  let rgba = getters.colorForSegmentIndexColorLUT(volumeId, labelId);
+  return rgbToHex(rgba);
+}
+
 /**
  * A function to group all settings to load before masks
- * TODO add a param to override config
+ * @param {Object} customConfig - Object containing override values for segmentation module config
  */
-export function initSegmentationModule() {
+export function initSegmentationModule(customConfig) {
   // set configuration
   segModule.configuration = cloneDeep(config);
+  extend(segModule.configuration, customConfig);
 }
 
 /**
  * Add segmentation mask to segmentation module
- * @param {Number} labelId - The label index (must be unique)
+ * @param {Object} maskProps - 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, data, elementId, cb) {
-  let element = document.getElementById(elementId);
-  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);
-  if (cb) {
-    cb();
+export function addSegmentationMask(props, data, elementId) {
+  let promise = new Promise(resolve => {
+    let element = isElement(elementId)
+      ? elementId
+      : document.getElementById(elementId);
+    if (!element) {
+      console.error("invalid html element: " + elementId);
+      return;
+    }
+    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);
+    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, sliceIndex, pixelData) {
+  // optimization: if pixelData contains no labels, return
+  if (sum(pixelData) === 0) {
+    return;
+  }
+
+  let element = isElement(elementId)
+    ? elementId
+    : document.getElementById(elementId);
+  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
+ * @param {String} elementId - The target html element Id or its DOM HTMLElement
  */
 export function setActiveLabelmap(labelId, elementId) {
-  let element = document.getElementById(elementId);
+  let element = isElement(elementId)
+    ? elementId
+    : document.getElementById(elementId);
+  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) {
+  let element = isElement(elementId)
+    ? elementId
+    : document.getElementById(elementId);
+  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
+ * @param {String} elementId - The target html element Id or its DOM HTMLElement
  */
 export function setActiveSegment(segmentIndex, elementId) {
-  let element = document.getElementById(elementId);
+  let element = isElement(elementId)
+    ? elementId
+    : document.getElementById(elementId);
+  if (!element) {
+    console.error("invalid html element: " + elementId);
+    return;
+  }
   setters.activeSegmentIndex(element, segmentIndex);
 }
 
@@ -213,6 +293,24 @@ export function setInactiveLabelOpacity(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, labelId) {
+  let element = isElement(elementId)
+    ? elementId
+    : document.getElementById(elementId);
+  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
@@ -236,9 +334,7 @@ export function toggleContourMode(toggle) {
 
 /**
  * Set mask appearance props
- * @param {String} tag - The mask tag
- * @param {Integer} mode - [0=filled, 1=contour, 2=hidden]
- * @param {Float} alpha - Opacity value (if mode=0), between 0 and 1
+ * @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) {
   // Lut index and segment values are hardcoded because they will depend on design choices:
@@ -299,6 +395,7 @@ export function clearSegmentationState() {
 /**
  * Enable brushing
  * @param {Number} dimension - The initial brush radius
+ * @param {Array} thresholds - The threshold values (min and max)
  */
 export function enableBrushTool(dimension, thresholds) {
   segModule.configuration.radius = dimension;
@@ -324,35 +421,41 @@ export function setBrushProps(props) {
   forceRender();
 }
 
-/**
- * Retrieve the buffer that represents the current active mask
- */
-export function getActiveLabelmapBuffer() {
-  let element = document.getElementById("axial");
-  let object = segModule.getters.activeLabelmapBuffer(element);
-  return object.buffer;
-}
-
 /**
  * Undo last brush operation (stroke)
+ * @param {String} elementId - The target html element Id or its DOM HTMLElement
  */
 export function undoLastStroke(elementId) {
-  let element = document.getElementById(elementId);
+  let element = isElement(elementId)
+    ? elementId
+    : document.getElementById(elementId);
+  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) {
-  let element = document.getElementById(elementId);
+  let element = isElement(elementId)
+    ? elementId
+    : document.getElementById(elementId);
+  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 activate
  */
 export function deleteMask(labelId) {
   let masks = values(segModule.state.series)[0].labelmaps3D;

package/imaging/tools/segmentations.md

@@ -0,0 +1,32 @@
+# 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
+
+TODO

package/imaging/tools/{tools.state.js → state.js}

@@ -1,8 +1,14 @@
+/** @module imaging/tools/state
+ *  @desc  This file provides functionalities
+ *         for handling tools' state
+ */
+
 // external libraries
 import cornerstone from "cornerstone-core";
 import cornerstoneTools from "cornerstone-tools";
-
 import { each } from "lodash";
+
+// internal libraries
 import { state_example } from "./cstools_state_example.js";
 
 /**

package/imaging/tools/strategies/eraseFreehand.js

@@ -1,17 +1,16 @@
-import cornerstoneTools from "cornerstone-tools";
-
-const {
-  getBoundingBoxAroundPolygon,
-  eraseInsideShape,
-  eraseOutsideShape
-} = cornerstoneTools.importInternal("util/segmentationUtils");
+/** @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");
 
 /**

package/imaging/tools/strategies/fillFreehand.js

@@ -1,17 +1,16 @@
-import cornerstoneTools from "cornerstone-tools";
-
-const {
-  getBoundingBoxAroundPolygon,
-  fillInsideShape,
-  fillOutsideShape
-} = cornerstoneTools.importInternal("util/segmentationUtils");
+/** @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");
 
 /**

package/index.js

@@ -5,6 +5,7 @@ console.log(`LARVITAR v${VERSION}`);
 import cornerstone from "cornerstone-core";
 import cornerstoneTools from "cornerstone-tools";
 import cornerstoneWADOImageLoader from "cornerstone-wado-image-loader";
+const segModule = cornerstoneTools.getModule("segmentation");
 
 import larvitarModule from "./modules/vuex/larvitar";
 
@@ -14,15 +15,15 @@ import {
   getAvailableMemory
 } from "./imaging/monitors/memory";
 
-import { initLarvitarStore, larvitar_store } from "./imaging/image_store";
+import { initLarvitarStore, larvitar_store } from "./imaging/imageStore";
 
-import { parseContours } from "./imaging/image_contours";
+import { parseContours } from "./imaging/imageContours";
 
 import {
   getImagePresets,
   setImagePreset,
   setImageCustomPreset
-} from "./imaging/image_presets";
+} from "./imaging/imagePresets";
 
 import {
   getNormalOrientation,
@@ -37,7 +38,7 @@ import {
   getReslicedMetadata,
   getReslicedPixeldata,
   getDistanceBetweenSlices
-} from "./imaging/image_utils";
+} from "./imaging/imageUtils";
 
 import {
   buildHeader,
@@ -45,16 +46,16 @@ import {
   buildData,
   buildDataAsync,
   importNRRDImage
-} from "./imaging/image_io";
+} from "./imaging/imageIo";
 
-import { anonymize, encrypt } from "./imaging/image_anonymization";
+import { anonymize, encrypt } from "./imaging/imageAnonymization";
 
 import {
   buildLayer,
   updateLayer,
   getActiveLayer,
   setActiveLayer
-} from "./imaging/image_layers";
+} from "./imaging/imageLayers";
 
 import {
   initializeImageLoader,
@@ -64,14 +65,14 @@ import {
   registerResliceLoader,
   registerMultiFrameImageLoader,
   updateLoadedStack
-} from "./imaging/image_loading";
+} from "./imaging/imageLoading";
 
 import {
   readFile,
   readFiles,
-  dumpDataSet,
+  parseDataSet,
   clearImageParsing
-} from "./imaging/image_parsing";
+} from "./imaging/imageParsing";
 
 import {
   clearImageCache,
@@ -91,9 +92,9 @@ import {
   flipImageVertical,
   rotateImageLeft,
   rotateImageRight
-} from "./imaging/image_rendering";
+} from "./imaging/imageRendering";
 
-import { resliceSeries } from "./imaging/image_reslice";
+import { resliceSeries } from "./imaging/imageReslice";
 
 import {
   addDiameterTool,
@@ -111,7 +112,7 @@ import {
   syncToolStack,
   updateStackToolState,
   setSegmentationConfig
-} from "./imaging/image_tools";
+} from "./imaging/imageTools";
 
 import {
   csToolsCreateStack,
@@ -126,13 +127,13 @@ import {
   setToolEnabled,
   setToolPassive,
   exportAnnotations
-} from "./imaging/tools/tools.main";
+} from "./imaging/tools/main";
 
 import {
   DEFAULT_TOOLS,
   getDefaultToolsByType,
   setDefaultToolsProps
-} from "./imaging/tools/tools.default";
+} from "./imaging/tools/default";
 
 import {
   initSegmentationModule,
@@ -142,7 +143,7 @@ import {
   undoLastStroke,
   redoLastStroke,
   setBrushProps
-} from "./imaging/tools/tools.segmentation";
+} from "./imaging/tools/segmentation";
 
 import {
   updateLarvitarManager,
@@ -189,20 +190,21 @@ import {
   addColorMap,
   fillPixelData,
   HSVToRGB
-} from "./imaging/image_colormaps";
+} from "./imaging/imageColormaps";
 
-import { saveAnnotations, loadAnnotations } from "./imaging/tools/tools.io";
+import { saveAnnotations, loadAnnotations } from "./imaging/tools/io";
 
 import {
   addMouseKeyHandlers,
   toggleMouseToolsListeners
-} from "./imaging/tools/tools.interaction";
+} from "./imaging/tools/interaction";
 
 export {
   VERSION,
   // global cornerstone variables
   cornerstone,
   cornerstoneTools,
+  segModule,
   cornerstoneWADOImageLoader,
   // vuex module
   larvitarModule,
@@ -210,14 +212,14 @@ export {
   checkMemoryAllocation,
   getUsedMemory,
   getAvailableMemory,
-  // larvitar store
+  // larvitarStore
   initLarvitarStore,
   larvitar_store,
-  // image_presets
+  // imagePresets
   getImagePresets,
   setImagePreset,
   setImageCustomPreset,
-  // image_utils
+  // imageUtils
   getNormalOrientation,
   getMinPixelValue,
   getMaxPixelValue,
@@ -230,21 +232,21 @@ export {
   getReslicedMetadata,
   getReslicedPixeldata,
   getDistanceBetweenSlices,
-  // image_io
+  // imageIo
   buildHeader,
   getCachedPixelData,
   buildData,
   buildDataAsync,
   importNRRDImage,
-  // image_anonymization
+  // imageAnonymization
   anonymize,
   encrypt,
-  // image_layers
+  // imageLayers
   buildLayer,
   updateLayer,
   getActiveLayer,
   setActiveLayer,
-  // image_loading
+  // imageLoading
   initializeImageLoader,
   initializeWebImageLoader,
   initializeFileImageLoader,
@@ -252,12 +254,12 @@ export {
   registerResliceLoader,
   registerMultiFrameImageLoader,
   updateLoadedStack,
-  // image_parsing
+  // imageParsing
   readFile,
   readFiles,
-  dumpDataSet,
+  parseDataSet,
   clearImageParsing,
-  // image_rendering
+  // imageRendering
   clearImageCache,
   loadAndCacheImages,
   renderFileImage,
@@ -276,15 +278,15 @@ export {
   flipImageVertical,
   rotateImageLeft,
   rotateImageRight,
-  // image_reslice
+  // imageReslice
   resliceSeries,
-  // image_colormaps
+  // imageColormaps
   getColormapsList,
   applyColorMap,
   addColorMap,
   fillPixelData,
   HSVToRGB,
-  // image_contours
+  // imageContours
   parseContours,
   // loaders/commonLoader
   updateLarvitarManager,
@@ -307,7 +309,7 @@ export {
   // loaders/dicomLoader
   getDicomImageId,
   cacheImages,
-  // loaders/multiFrameLoader
+  // loaders/multiframeLoader
   loadMultiFrameImage,
   buildMultiFrameImage,
   getMultiFrameImageId,
@@ -318,7 +320,7 @@ export {
   resetFileManager,
   populateFileManager,
   getFileImageId,
-  // image_tools
+  // imageTools
   addDiameterTool,
   addContoursTool,
   addMaskEditingTool,
@@ -334,7 +336,7 @@ export {
   syncToolStack,
   updateStackToolState,
   setSegmentationConfig,
-  // tools.main
+  // tools/main
   csToolsCreateStack,
   csToolsUpdateImageIds,
   csToolsUpdateImageIndex,
@@ -347,16 +349,16 @@ export {
   setToolEnabled,
   setToolPassive,
   exportAnnotations,
-  // tools.default
+  // tools/default
   DEFAULT_TOOLS,
   getDefaultToolsByType,
   setDefaultToolsProps,
-  // tools.io
+  // tools/io
   saveAnnotations,
   loadAnnotations,
-  // tools.interaction
+  // tools/interaction
   addMouseKeyHandlers,
-  // tools.segmentation
+  // tools/segmentation
   initSegmentationModule,
   addSegmentationMask,
   setActiveLabelmap,

package/modules/vuex/larvitar.js

@@ -1,4 +1,4 @@
-// Larvitare storage
+// Larvitar Vuex storage
 
 import Vue from "vue";