larvitar 1.3.3 → 1.4.0

package/README.md

@@ -4,15 +4,13 @@
 
 # Larvitar
 
-## Dicom Image Toolkit for CornestoneJS
+## Dicom Image Toolkit for CornerstoneJS
 
-### Current version: 1.3.3
+### Current version: 1.4.0
 
-### Latest Stable version: 1.3.3
+### Latest Published Release: 1.4.0
 
-### Latest Published Release: 1.3.3
-
-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 +20,7 @@ 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
@@ -90,3 +88,9 @@ Full documentation and examples are available at http://www.dvisionlab.com/Larvi
 # Build package
 
 `yarn build-lib`
+
+# Development
+
+Use `yarn dev-lib` to have `rollup` hot-reload (live recompiling the library).
+In order to test functionalities you can modify the library import path in an example (see the `docs/examples` folder) to use the recompiled bundle in `dist/`, then serve the .html file with VSCode extension [LiveServer](https://marketplace.visualstudio.com/items?itemName=ritwickdey.LiveServer) or other similar tools.
+Once you are done, upgrade the version, build the library and copy it to the `docs/examples` folder. This file must be included into the commit, while docs will be compiled by the Github action.

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/imageTools.js

@@ -1,6 +1,9 @@
 /** @module imaging/imageTools
  *  @desc This file provides functionalities for
  *        interacting with cornerstone tools
+ *        DEPRECATION WARNING: these are legacy functions
+ *        that will be removed soon. Use the corresponding
+ *        functions in /tools/main.js instead.
  */
 
 // external libraries
@@ -277,6 +280,7 @@ export const clearMeasurements = function () {
  * @param {Object} options - The custom options. @default from tools/default.js
  * @param {String} activeViewport - The active viewport (if "all", viewports array will be used)
  * @param {Array} viewports - The hmtl element id to be used for tool initialization.
+ * @deprecated (OBSOLETE)
  */
 export const setToolActive = function (
   toolName,
@@ -304,10 +308,11 @@ export const setToolActive = function (
 
 /**
  * Set Tool "disabled" on all elements (ie, not rendered) & refresh cornerstone elements
- * @function setToolActive
+ * @function setToolDisabled
  * @param {String} toolName - The tool name.
  * @param {String} activeViewport - The active viewport (if "all", viewports array will be used)
  * @param {Array} viewports - The hmtl element id to be used for tool initialization.
+ * @deprecated (OBSOLETE)
  */
 export const setToolDisabled = function (toolName, activeViewport, viewports) {
   cornerstoneTools.setToolDisabled(toolName);
@@ -332,6 +337,7 @@ export const setToolDisabled = function (toolName, activeViewport, viewports) {
  * @param {String} toolName - The tool name.
  * @param {String} activeViewport - The active viewport (if "all", viewports array will be used)
  * @param {Array} viewports - The hmtl element id to be used for tool initialization.
+ * @deprecated (OBSOLETE)
  */
 export const setToolEnabled = function (toolName, activeViewport, viewports) {
   cornerstoneTools.setToolEnabled(toolName);
@@ -356,6 +362,7 @@ export const setToolEnabled = function (toolName, activeViewport, viewports) {
  * @param {String} toolName - The tool name.
  * @param {String} activeViewport - The active viewport (if "all", viewports array will be used)
  * @param {Array} viewports - The hmtl element id to be used for tool initialization.
+ * @deprecated (OBSOLETE)
  */
 export const setToolPassive = function (toolName, activeViewport, viewports) {
   cornerstoneTools.setToolPassive(toolName);

package/imaging/tools/interaction.js

@@ -22,27 +22,42 @@ import { updateViewportData } from "../imageRendering";
  */
 
 /**
- * Setup mouse handler modifiers and keyboard shortcuts
- * NOTE: at the moment only mouse right button is affected
+ * Global event callbacks
+ */
+let onKeyDownFn = null;
+let onKeyUpFn = null;
+
+/**
+ * Setup mouse handler modifiers and keyboard shortcuts:
+ * register a tool on right button and another one
+ * when pressing a modifier (ctrl/shift/alt) + right button
+ * The activation take place on all active viewports
  * Improvements could be:
  * - "restore previous active tool" instead of passed "default" tool
  * - manage left button (an idea could be to cycle over object keys for both buttons)
  * - possibility to change modifier keys
  * @param {Object} config - see tools/default
- * @param {Array} viewports - The hmtl element ids to be used for tool activation.
  */
 
-export function addMouseKeyHandlers(config, viewports) {
+export function addMouseKeyHandlers(config) {
   if (!config) {
     config = DEFAULT_MOUSE_KEYS;
   }
 
+  if (onKeyDownFn) {
+    document.removeEventListener("keydown", onKeyDownFn);
+  }
+  if (onKeyUpFn) {
+    document.removeEventListener("keyup", onKeyUpFn);
+  }
+
   // Prevent context menu on right click
   document.addEventListener("contextmenu", evt => {
     evt.preventDefault();
     return false;
   });
 
+  // Define behaviour on key down: activate registered tool
   function onKeyDown(evt) {
     // keyboard shortcuts (activate on left mouse button)
     let codes = config.keyboard_shortcuts
@@ -56,11 +71,7 @@ export function addMouseKeyHandlers(config, viewports) {
         .filter(key => keyCodes[key] == evt.keyCode)
         .pop();
       if (config.debug) console.log("active", config.keyboard_shortcuts[key]);
-      setToolActive(
-        config.keyboard_shortcuts[key],
-        { mouseButtonMask: 1 },
-        viewports
-      );
+      setToolActive(config.keyboard_shortcuts[key], { mouseButtonMask: 1 });
       document.addEventListener("keydown", onKeyDown, { once: true });
     }
     // right drag + shift
@@ -70,11 +81,7 @@ export function addMouseKeyHandlers(config, viewports) {
       evt.keyCode == keyCodes.KEY_SHIFT
     ) {
       if (config.debug) console.log("active", config.mouse_button_right.shift);
-      setToolActive(
-        config.mouse_button_right.shift,
-        { mouseButtonMask: 2 },
-        viewports
-      );
+      setToolActive(config.mouse_button_right.shift, { mouseButtonMask: 2 });
       document.addEventListener("keyup", onKeyUp, { once: true });
     }
     // right drag + ctrl
@@ -84,11 +91,7 @@ export function addMouseKeyHandlers(config, viewports) {
       evt.keyCode == keyCodes.KEY_CONTROL
     ) {
       if (config.debug) console.log("active", config.mouse_button_right.ctrl);
-      setToolActive(
-        config.mouse_button_right.ctrl,
-        { mouseButtonMask: 2 },
-        viewports
-      );
+      setToolActive(config.mouse_button_right.ctrl, { mouseButtonMask: 2 });
       document.addEventListener("keyup", onKeyUp, { once: true });
     }
     // leave default
@@ -98,36 +101,36 @@ export function addMouseKeyHandlers(config, viewports) {
     }
   }
 
+  // Define behaviour on key up: restore original tool
   function onKeyUp(e) {
     if (config.debug)
       console.log("active default", config.mouse_button_right.default);
-    setToolActive(
-      config.mouse_button_right.default,
-      { mouseButtonMask: 2 },
-      viewports
-    );
+    setToolActive(config.mouse_button_right.default, { mouseButtonMask: 2 });
     document.addEventListener("keydown", onKeyDown, { once: true });
   }
 
   // activate default, if any
-
   if (config.mouse_button_right && config.mouse_button_right.default) {
-    setToolActive(
-      config.mouse_button_right.default,
-      { mouseButtonMask: 2 },
-      viewports
-    );
+    setToolActive(config.mouse_button_right.default, { mouseButtonMask: 2 });
   }
 
   if (config.mouse_button_left && config.mouse_button_left.default) {
-    setToolActive(
-      config.mouse_button_left.default,
-      { mouseButtonMask: 1 },
-      viewports
-    );
+    setToolActive(config.mouse_button_left.default, { mouseButtonMask: 1 });
   }
 
   document.addEventListener("keydown", onKeyDown, { once: true });
+
+  onKeyDownFn = onKeyDown;
+  onKeyUpFn = onKeyUp;
+}
+
+/**
+ *
+ */
+export function removeMouseKeyHandlers() {
+  document.removeEventListener("keydown", onKeyDownFn);
+  onKeyDownFn = null;
+  onKeyUpFn = null;
 }
 
 /**

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);
+  }
 }
 
 /**

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

@@ -205,6 +205,7 @@ import { saveAnnotations, loadAnnotations } from "./imaging/tools/io";
 
 import {
   addMouseKeyHandlers,
+  removeMouseKeyHandlers,
   toggleMouseToolsListeners
 } from "./imaging/tools/interaction";
 
@@ -367,6 +368,7 @@ export {
   loadAnnotations,
   // tools/interaction
   addMouseKeyHandlers,
+  removeMouseKeyHandlers,
   // tools/segmentation
   initSegmentationModule,
   addSegmentationMask,

package/package.json

@@ -6,7 +6,7 @@
     "medical",
     "cornerstone"
   ],
-  "version": "1.3.3",
+  "version": "1.4.0",
   "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"
-}
+}