larvitar 1.4.0 → 1.5.0

package/.github/workflows/build-docs.yml

@@ -1,23 +1,24 @@
 name: CI-docs
 
-# Controls when the action will run. Triggers the workflow on push or pull request
-# events but only for the master branch
 on:
-  push:
-    branches: [master]
+  pull_request:
+    types:
+      - opened
+      - reopened
+      - synchronize
 
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
-  # First job, build package
   build:
-    # The type of runner that the job will run on
     runs-on: ubuntu-latest
 
-    # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
-      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      # CLone repo at current branch
       - name: Clone repo
         uses: actions/checkout@v2
+        with:
+          persist-credentials: false
+          ref: ${{ github.head_ref }}
+          token: ${{ secrets.GIT_TOKEN }}
 
       # Setup node environment
       - name: Setup Node.js environment
@@ -42,10 +43,13 @@ jobs:
         run: |
           yarn generate-docs
 
-      # Commit Package and Docs
+      # Commit docs on current branch (update pull request)
       - name: Commit docs
-        run: |
-          git config --global user.name 'Mattia-gh-action'
-          git config --global user.email 'ronzim@users.noreply.github.com'
-          git commit --allow-empty -am "Automated docs generation"
-          git push
+        uses: actions-js/push@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          message: "Update docs"
+          branch: ${{ github.head_ref }}
+          empty: true 
+      
+

package/README.md

@@ -6,9 +6,9 @@
 
 ## Dicom Image Toolkit for CornerstoneJS
 
-### Current version: 1.4.0
+### Current version: 1.5.0
 
-### Latest Published Release: 1.4.0
+### Latest Published Release: 1.5.0
 
 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.

package/imaging/imageParsing.js

@@ -270,7 +270,7 @@ let parseFile = function (file) {
           reject(dataSet.warnings);
         } else {
           let pixelDataElement = dataSet.elements.x7fe00010;
-
+          let SOPUID = metadata["x00080016"];
           if (pixelDataElement) {
             // done, pixelDataElement found
             let instanceUID = metadata["x00080018"] || randomId();
@@ -323,6 +323,29 @@ let parseFile = function (file) {
             imageObject.metadata.length = pixelDataElement.length;
             imageObject.metadata.repr = getPixelRepresentation(dataSet);
             resolve(imageObject);
+          } else if (SOPUID == "1.2.840.10008.5.1.4.1.1.104.1") {
+            let pdfObject = {
+              // data needed for rendering
+              file: file,
+              dataSet: dataSet
+            };
+            pdfObject.metadata = metadata;
+            pdfObject.metadata.seriesUID = seriesInstanceUID;
+            pdfObject.instanceUID = metadata["x00080018"] || randomId();
+            pdfObject.metadata.studyUID = metadata["x0020000d"];
+            pdfObject.metadata.accessionNumber = metadata["x00080050"];
+            pdfObject.metadata.studyDescription = metadata["x00081030"];
+            pdfObject.metadata.patientName = metadata["x00100010"];
+            pdfObject.metadata.patientBirthdate = metadata["x00100030"];
+            pdfObject.metadata.seriesDate = metadata["x00080021"];
+            pdfObject.metadata.seriesModality =
+              metadata["x00080060"].toLowerCase();
+            pdfObject.metadata.mimeType = metadata["x00420012"];
+            pdfObject.metadata.is4D = false;
+            pdfObject.metadata.numberOfFrames = 0;
+            pdfObject.metadata.numberOfSlices = 0;
+            pdfObject.metadata.numberOfTemporalPositions = 0;
+            resolve(pdfObject);
           } else {
             // done, no pixelData
             reject("no pixelData");

package/imaging/imageRendering.js

@@ -115,6 +115,44 @@ export function loadAndCacheImages(series, callback) {
   });
 }
 
+/**
+ * Render a PDF from a DICOM Encapsulated PDF
+ * @instance
+ * @function renderDICOMPDF
+ * @param {Object} image - The image PDF object
+ * @param {String} elementId - The html div id used for rendering or its DOM HTMLElement
+ * @returns {Promise} - Return a promise which will resolve when image is displayed
+ */
+export const renderDICOMPDF = function (image, elementId) {
+  let element = isElement(elementId)
+    ? elementId
+    : document.getElementById(elementId);
+  if (!element) {
+    console.error("invalid html element: " + elementId);
+    return;
+  }
+  const SOPUID = image.dataSet.string("x00080016");
+  if (SOPUID === "1.2.840.10008.5.1.4.1.1.104.1") {
+    let fileTag = image.dataSet.elements.x00420011;
+    let pdfByteArray = image.dataSet.byteArray.slice(
+      fileTag.dataOffset,
+      fileTag.dataOffset + fileTag.length
+    );
+    let PDF = new Blob([pdfByteArray], { type: "application/pdf" });
+    let fileURL = URL.createObjectURL(PDF);
+    element.innerHTML =
+      '<object data="' +
+      fileURL +
+      '" type="application/pdf" width="100%" height="100%"></object>';
+    fileTag = null;
+    pdfByteArray = null;
+    PDF = null;
+    fileURL = null;
+  } else {
+    throw new Error("This is not a DICOM with a PDF");
+  }
+};
+
 /**
  * Render an image (png or jpg) from File on a html div using cornerstone
  * @instance

package/imaging/tools/interaction.js

@@ -6,6 +6,8 @@
 // external libraries
 import { throttle } from "lodash";
 import * as keyCodes from "keycode-js";
+import cornerstone from "cornerstone-core";
+import cornerstoneTools from "cornerstone-tools/dist/cornerstoneTools.js";
 
 // internal libraries
 import { DEFAULT_MOUSE_KEYS } from "./default";
@@ -31,7 +33,8 @@ 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
+ * The activation take place on all active viewports (we added a check to activate only on viewports
+ * in which the tool has been added previously)
  * 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)
@@ -57,6 +60,9 @@ export function addMouseKeyHandlers(config) {
     return false;
   });
 
+  // get all enabled viewports. Then, filter only viewport in which the target tool had been added previously.
+  let allViewports = cornerstone.getEnabledElements().map(enel => enel.element);
+
   // Define behaviour on key down: activate registered tool
   function onKeyDown(evt) {
     // keyboard shortcuts (activate on left mouse button)
@@ -71,7 +77,17 @@ export function addMouseKeyHandlers(config) {
         .filter(key => keyCodes[key] == evt.keyCode)
         .pop();
       if (config.debug) console.log("active", config.keyboard_shortcuts[key]);
-      setToolActive(config.keyboard_shortcuts[key], { mouseButtonMask: 1 });
+      const viewports = allViewports.filter(viewport =>
+        cornerstoneTools.getToolForElement(
+          viewport,
+          config.keyboard_shortcuts[key]
+        )
+      );
+      setToolActive(
+        config.keyboard_shortcuts[key],
+        { mouseButtonMask: 1 },
+        viewports.map(v => v.id)
+      );
       document.addEventListener("keydown", onKeyDown, { once: true });
     }
     // right drag + shift
@@ -81,7 +97,18 @@ export function addMouseKeyHandlers(config) {
       evt.keyCode == keyCodes.KEY_SHIFT
     ) {
       if (config.debug) console.log("active", config.mouse_button_right.shift);
-      setToolActive(config.mouse_button_right.shift, { mouseButtonMask: 2 });
+      const viewports = allViewports.filter(viewport =>
+        cornerstoneTools.getToolForElement(
+          viewport,
+          config.mouse_button_right.shift
+        )
+      );
+
+      setToolActive(
+        config.mouse_button_right.shift,
+        { mouseButtonMask: 2 },
+        viewports.map(v => v.id)
+      );
       document.addEventListener("keyup", onKeyUp, { once: true });
     }
     // right drag + ctrl
@@ -91,7 +118,18 @@ export function addMouseKeyHandlers(config) {
       evt.keyCode == keyCodes.KEY_CONTROL
     ) {
       if (config.debug) console.log("active", config.mouse_button_right.ctrl);
-      setToolActive(config.mouse_button_right.ctrl, { mouseButtonMask: 2 });
+      const viewports = allViewports.filter(viewport =>
+        cornerstoneTools.getToolForElement(
+          viewport,
+          config.mouse_button_right.ctrl
+        )
+      );
+
+      setToolActive(
+        config.mouse_button_right.ctrl,
+        { mouseButtonMask: 2 },
+        viewports.map(v => v.id)
+      );
       document.addEventListener("keyup", onKeyUp, { once: true });
     }
     // leave default
@@ -105,17 +143,48 @@ export function addMouseKeyHandlers(config) {
   function onKeyUp(e) {
     if (config.debug)
       console.log("active default", config.mouse_button_right.default);
-    setToolActive(config.mouse_button_right.default, { mouseButtonMask: 2 });
+    const viewports = allViewports.filter(viewport =>
+      cornerstoneTools.getToolForElement(
+        viewport,
+        config.mouse_button_right.default
+      )
+    );
+    setToolActive(
+      config.mouse_button_right.default,
+      { mouseButtonMask: 2 },
+      viewports.map(v => v.id)
+    );
     document.addEventListener("keydown", onKeyDown, { once: true });
   }
 
-  // activate default, if any
+  // activate default on mouse right, if any
   if (config.mouse_button_right && config.mouse_button_right.default) {
-    setToolActive(config.mouse_button_right.default, { mouseButtonMask: 2 });
+    const viewports = allViewports.filter(viewport =>
+      cornerstoneTools.getToolForElement(
+        viewport,
+        config.mouse_button_right.default
+      )
+    );
+    setToolActive(
+      config.mouse_button_right.default,
+      { mouseButtonMask: 2 },
+      viewports.map(v => v.id)
+    );
   }
 
+  // activate default on mouse left, if any
   if (config.mouse_button_left && config.mouse_button_left.default) {
-    setToolActive(config.mouse_button_left.default, { mouseButtonMask: 1 });
+    const viewports = allViewports.filter(viewport =>
+      cornerstoneTools.getToolForElement(
+        viewport,
+        config.mouse_button_left.default
+      )
+    );
+    setToolActive(
+      config.mouse_button_left.default,
+      { mouseButtonMask: 1 },
+      viewports.map(v => v.id)
+    );
   }
 
   document.addEventListener("keydown", onKeyDown, { once: true });

package/index.js

@@ -78,6 +78,7 @@ import {
   clearImageCache,
   loadAndCacheImages,
   renderFileImage,
+  renderDICOMPDF,
   renderWebImage,
   disableViewport,
   unloadViewport,
@@ -273,6 +274,7 @@ export {
   clearImageCache,
   loadAndCacheImages,
   renderFileImage,
+  renderDICOMPDF,
   renderWebImage,
   disableViewport,
   unloadViewport,

package/package.json

@@ -6,7 +6,7 @@
     "medical",
     "cornerstone"
   ],
-  "version": "1.4.0",
+  "version": "1.5.0",
   "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"
-}
+}