larvitar 1.4.1 → 1.5.1

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: 1.4.1
+### Current version: 1.5.1
 
-### Latest Published Release: 1.4.1
+### Latest Published Release: 1.5.1
 
 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/imageLoading.js

@@ -148,6 +148,8 @@ export const updateLoadedStack = function (
   let numberOfTemporalPositions = seriesData.metadata["x00200105"];
   let acquisitionNumberAttribute = seriesData.metadata["x00200012"];
   let is4D = seriesData.metadata.is4D;
+  let SOPUID = seriesData.metadata["x00080016"];
+  let isPDF = SOPUID == "1.2.840.10008.5.1.4.1.1.104.1" ? true : false;
 
   let color = cornerstoneWADOImageLoader.isColorImage(
     seriesData.metadata["x00280004"]
@@ -170,6 +172,7 @@ export const updateLoadedStack = function (
       numberOfTemporalPositions: numberOfTemporalPositions,
       isMultiframe: isMultiframe,
       is4D: is4D,
+      isPDF: isPDF,
       modality: modality,
       color: color,
       bytes: 0

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 +115,53 @@ export function loadAndCacheImages(series, callback) {
   });
 }
 
+/**
+ * Render a PDF from a DICOM Encapsulated PDF
+ * @instance
+ * @function renderDICOMPDF
+ * @param {Object} seriesStack - The original series data object
+ * @param {String} elementId - The html div id used for rendering or its DOM HTMLElement
+ * @returns {Promise} - Return a promise which will resolve when pdf is displayed
+ */
+export const renderDICOMPDF = function (seriesStack, elementId) {
+  let t0 = performance.now();
+  let element = isElement(elementId)
+    ? elementId
+    : document.getElementById(elementId);
+  if (!element) {
+    console.error("invalid html element: " + elementId);
+    return;
+  }
+  let renderPromise = new Promise((resolve, reject) => {
+    let image = seriesStack.instances[seriesStack.imageIds[0]];
+    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>';
+      let t1 = performance.now();
+      console.log(`Call to renderDICOMPDF took ${t1 - t0} milliseconds.`);
+      image = null;
+      fileTag = null;
+      pdfByteArray = null;
+      PDF = null;
+      fileURL = null;
+      resolve();
+    } else {
+      reject("This is not a DICOM with a PDF");
+    }
+  });
+  return renderPromise;
+};
+
 /**
  * Render an image (png or jpg) from File on a html div using cornerstone
  * @instance

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": "1.4.1",
+  "version": "1.5.1",
   "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"
-}
+}