larvitar 1.3.2 → 1.3.5

package/README.md

@@ -4,15 +4,15 @@
 
 # Larvitar
 
-## Dicom Image Toolkit for CornestoneJS
+## Dicom Image Toolkit for CornerstoneJS
 
-### Current version: 1.3.2
+### Current version: 1.3.5
 
-### Latest Stable version: 1.3.2
+### Latest Stable version: 1.3.5
 
-### Latest Published Release: 1.3.2
+### Latest Published Release: 1.3.5
 
-This library provides common DICOM functionalities to be used in web-applications: it's wrapper that simplifies the use of cornestone-js environment.
+This library provides common DICOM functionalities to be used in web-applications: it's wrapper that simplifies the use of cornerstone-js environment.
 Orthogonal multiplanar reformat is included as well as custom loader/exporter for nrrd files and [Vuex](https://vuex.vuejs.org/) custom integration.
 
 - `index` main file
@@ -22,7 +22,7 @@ Orthogonal multiplanar reformat is included as well as custom loader/exporter fo
 - `imageIo` import a dicom image in .nrrd format and build contiguous array for exporting data as volume
 - `imageLayers` provide support for multi-layer cornerstone fusion renderer
 - `imageLoading` initialize loader and custom loaders
-- `imageParsing` parse dicom files and return a cornestone data structure ready to be used for rendering
+- `imageParsing` parse dicom files and return a cornerstone data structure ready to be used for rendering
 - `imagePresets` provides default image CT presets and set functionality
 - `imageRendering` provides rendering functionalities
 - `imageReslice` provides reslice functionalities

package/imaging/imageParsing.js

@@ -78,11 +78,10 @@ export const readFile = function (entry) {
  * @instance
  * @function parseDataSet
  * @param {Object} dataSet - dicom parser dataSet object
- * @param {Array} metadata - Initialized metadata object
+ * @param {Object} metadata - Initialized metadata object
  * @param {Array} customFilter - Optional filter: {tags:[], frameId: 0}
  */
-// This function iterates through dataSet recursively and adds new HTML strings
-// to the output array passed into it
+// This function iterates through dataSet recursively and store tag values into metadata object
 export const parseDataSet = function (dataSet, metadata, customFilter) {
   // customFilter= {tags:[], frameId:xxx}
   // the dataSet.elements object contains properties for each element parsed.  The name of the property
@@ -113,7 +112,18 @@ export const parseDataSet = function (dataSet, metadata, customFilter) {
         }
       } else {
         let tagValue = parseTag(dataSet, propertyName, element);
-        metadata[propertyName] = tagValue;
+
+        // identify duplicated tags (keep the first occurency and store the others in another tag eg x00280010_uuid)
+        if (metadata[propertyName] !== undefined) {
+          console.debug(
+            `Identified duplicated tag "${propertyName}", values are:`,
+            metadata[propertyName],
+            tagValue
+          );
+          metadata[propertyName + "_" + uuidv4()] = tagValue;
+        } else {
+          metadata[propertyName] = tagValue;
+        }
       }
     }
   } catch (err) {

package/imaging/tools/segmentation.js

@@ -18,6 +18,7 @@ import { updateStackToolState } from "../imageTools";
 
 // custom code
 import { setLabelmap3DForElement } from "./setLabelMap3D";
+import { each } from "hammerjs";
 // override function
 setters.labelmap3DForElement = setLabelmap3DForElement;
 
@@ -419,22 +420,37 @@ export function clearSegmentationState() {
 
 /**
  * Enable brushing
- * @param {Number} dimension - The initial brush radius
- * @param {Array} thresholds - The threshold values (min and max)
+ * 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(dimension, thresholds) {
-  segModule.configuration.radius = dimension;
-  segModule.configuration.thresholds = thresholds;
-  setToolActive("ThresholdsBrush");
+export function enableBrushTool(viewports, options) {
+  console.log("enable", options);
+  setBrushProps(options);
+  const brushType = "thresholds" in options ? "ThresholdsBrush" : "Brush";
+  setToolActive(brushType, viewports);
+  return brushType;
 }
 
 /**
  * Disable brushing
- * @param {String} toolToActivate - The name of the tool to activate after removing the brush
+ * 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(toolToActivate) {
-  setToolDisabled("Brush");
-  setToolActive(toolToActivate);
+export function disableBrushTool(viewports, toolToActivate) {
+  each(viewports, viewport => {
+    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);
+  }
 }
 
 /**
@@ -480,7 +496,7 @@ export function redoLastStroke(elementId) {
 
 /**
  * Delete mask from state
- * @param {Number} labelId - The labelmap id to activate
+ * @param {Number} labelId - The labelmap id to delete
  */
 export function deleteMask(labelId) {
   let masks = values(segModule.state.series)[0].labelmaps3D;

package/imaging/tools/segmentations.md

@@ -29,7 +29,7 @@ TODO
 
 # Larvitar segmentation API
 
-TODO
+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
 

package/index.js

@@ -138,13 +138,20 @@ import {
 import {
   initSegmentationModule,
   addSegmentationMask,
+  clearSegmentationState,
+  deleteMask,
   setActiveLabelmap,
   setActiveSegment,
+  enableBrushTool,
+  disableBrushTool,
   undoLastStroke,
   redoLastStroke,
   setBrushProps,
+  toggleContourMode,
+  toggleVisibility,
   hexToRgb,
-  rgbToHex
+  rgbToHex,
+  getActiveLabelmapBuffer
 } from "./imaging/tools/segmentation";
 
 import {
@@ -369,5 +376,12 @@ export {
   redoLastStroke,
   setBrushProps,
   hexToRgb,
-  rgbToHex
+  rgbToHex,
+  clearSegmentationState,
+  deleteMask,
+  enableBrushTool,
+  disableBrushTool,
+  toggleContourMode,
+  toggleVisibility,
+  getActiveLabelmapBuffer
 };

package/package.json

@@ -6,7 +6,7 @@
     "medical",
     "cornerstone"
   ],
-  "version": "1.3.2",
+  "version": "1.3.5",
   "description": "javascript library for parsing, loading, rendering and interacting with DICOM images",
   "repository": {
     "url": "https://github.com/dvisionlab/Larvitar.git",
@@ -54,4 +54,4 @@
   "module": "dist/larvitar.js",
   "browser": "dist/larvitar.js",
   "type": "module"
-}
+}