Merge branch 'feature/analysisresults'

* Display of DICOM Segmentation instances
* Display of DICOM Parametric Map instances
* Display of DICOM Microscopy Bulk Simple Annotations instances
* Styling images using Palette Color Lookup Tables
* Dynamically switching between origin servers (as long as they rely on the same identity provider)
* Decoding of JPEG, JPEG-LS, and JPEG 2000 transfer syntaxes using WebAssembly bindings of the libjpeg-turbo, CharLS, and openjpeg C/C++ libraries
* Color management based on ICC profiles using WebAssembly bindings of the dicomicc C library
* Improved image transformations and rendering using WebGL
* Use of webpack instead of rollup for building
* Use of jest instead of mocha for testing

Co-authored-by Chris Gorman <[email protected]>

Author: hackermd

.github/workflows/run_unit_tests.yml

@@ -0,0 +1,33 @@
+# This workflow will install JavaScript dependencies, run tests and lint.
+
+name: unit tests
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        node-version: ["12.x", "14.x", "16.x"]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Node ${{ matrix.node-version }}
+      uses: actions/setup-node@v2
+      with:
+        node-version: ${{ matrix.node-version }}
+        cache: "npm"
+    - name: Install dependencies
+      run: npm install
+    - name: Build package in production mode
+      run: npm run build:prod
+    - name: Lint with standard
+      run: npm run lint
+    - name: Test with jest
+      run: npm run test

CONTRIBUTING.md

@@ -4,7 +4,7 @@
 
 The library is intended to provide a lightweight and standard-compliant viewer for microscopy images in DICOM format.
 
-The viewer relies on [Openlayers](http://openlayers.org/) for rendering pyramid images and dynamically retrieves pyramid tiles (image frames) via [DICOMweb WADO-RS](https://www.dicomstandard.org/dicomweb/retrieve-wado-rs-and-wado-uri/) using [dicomweb-client](https://github.com/mghcomputationalpathology/dicomweb-client).
+The viewer relies on [Openlayers](http://openlayers.org/) for rendering pyramid images and dynamically retrieves pyramid tiles (image frames) via [DICOMweb WADO-RS](https://www.dicomstandard.org/dicomweb/retrieve-wado-rs-and-wado-uri/) using [dicomweb-client](https://github.com/herrmannlab/dicomweb-client).
 However, the viewer API fully abstracts the underlying rendering library and doesn't expose the lower level Openlayers API directly, such that another rendering library could in principle be used in the future if this would be of advantage.
 
 A central design choice was to not expose any Openlayers objects or functions via the public API, but always provide an abstraction layer.

README.md

@@ -1,33 +1,29 @@
-[![Build Status](https://travis-ci.com/mghcomputationalpathology/dicom-microscopy-viewer.svg?branch=master)](https://travis-ci.com/mghcomputationalpathology/dicom-microscopy-viewer)
+[![Build Status](https://github.com/herrmannlab/dicom-microscopy-viewer/actions/workflows/run_unit_tests.yml/badge.svg)](https://github.com/herrmannlab/dicom-microscopy-viewer/actions)
+[![NPM version](https://badge.fury.io/js/dicom-microscopy-viewer.svg)](http://badge.fury.io/js/dicom-microscopy-viewer)
 
 # DICOM Microscopy Viewer
 
-Vanilla JS library for web-based visualization of [DICOM VL Whole Slide Microscopy Image](http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.32.8.html) datasets.
+Vanilla JS library for web-based visualization of [DICOM VL Whole Slide Microscopy Image](http://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.32.8.html) datasets and derived information.
 
 The viewer allows visualization of slide microscopy images stored in a [DICOMweb](https://www.dicomstandard.org/dicomweb/) compatible archive.
 It leverages the [dicomweb-client](https://github.com/dcmjs-org/dicomweb-client) JavaScript library to retrieve data from the archive.
 
 ## Features
 
-* Display of different image types: `VOLUME`, `OVERVIEW`, `LABEL`
+* Display of different image types: `VOLUME`/`THUMBNAIL`, `OVERVIEW`, `LABEL`
 * Annotation of regions of interest (ROI) as vector graphics based on 3-dimensional spatial coordinates (SCOORD3D): `POINT`, `MULTIPOINT`, `POLYLINE`, `POLYGON`, `ELLIPSE`, `ELLIPSOID`
 * Assembly of concatenations
-* Decoding of compressed pixel data, supporting baseline JPEG, JPEG 2000 and JPEG-LS codecs
+* Decoding of compressed pixel data, supporting baseline JPEG, JPEG 2000, and JPEG-LS codecs
+* Correction of color images using ICC profiles
 * Additive blending and coloring of monochromatic images of multiple optical paths (channels), supporting highly-multiplexed immunofluorescence imaging
-
-## Live demo
-
-Check out the online examples at [microscopy.dcmjs.org](https://microscopy.dcmjs.org/).
+* Overlay of image analysis results in the form of [DICOM Segmentation](https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.51.html), [Parametric Map](https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.75.html), [Comprehensive 3D SR](https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.35.13.html), or [Microscopy Bulk Simple Annotations](https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.87.html)
 
 ## Documentation
 
-The online Application Programming Interface (API) documentation is available at [mghcomputationalpathology.github.io/dicom-microscopy-viewer](https://mghcomputationalpathology.github.io/dicom-microscopy-viewer/).
+Documentation of the JavaScript Application Programming Interface (API) is available online at [mghcomputationalpathology.github.io/dicom-microscopy-viewer](https://mghcomputationalpathology.github.io/dicom-microscopy-viewer/).
 
 ## Getting started
 
-Take a look at the examples in the `/examples` directory.
-They are also available online at [microscopy.dcmjs.org](https://microscopy.dcmjs.org/).
-
 ### Basic usage
 
 ```html
@@ -60,9 +56,11 @@ client.searchForInstances(searchInstanceOptions).then((instances) => {
       sopInstanceUID,
     };
     const promise = client.retrieveInstanceMetadata(retrieveInstanceOptions).then(metadata => {
-      const imageType = metadata[0]["00080008"]["Value"];
-      if (imageType[2] === "VOLUME") {
-        return(metadata[0]);
+      const image = new DICOMMicroscopyViewer.metadata.VLWholeSlideMicroscopyViewer({
+          metadata
+      })
+      if (image.imageType[2] === "VOLUME") {
+        return(image);
       }
     });
     promises.push(promise);
@@ -98,7 +96,6 @@ Please cite the following article when using the viewer for scientific studies:
     Volume={9},
     Number={37}
 }
-
 ```
 
 ## Installation
@@ -111,26 +108,21 @@ npm install dicom-microscopy-viewer
 
 ## Building & Testing
 
-Build code locally:
+We use [webpack](https://webpack.js.org/) for bundling and [Jest](https://github.com/facebook/jest) for testing.
+
+Build:
 
 ```None
-git clone https://github.com/mghcomputationalpathology/dicom-microscopy-viewer ~/dicom-microscopy-viewer
-cd ~/dicom-microscopy-viewer
 npm install
 npm run build
 ```
 
-test code locally:
+Test:
 
 ```None
-git clone https://github.com/mghcomputationalpathology/dicom-microscopy-viewer ~/dicom-microscopy-viewer
-cd ~/dicom-microscopy-viewer
-npm install
-npm test
+npm run test
 ```
 
-We use [rollup](https://rollupjs.org/guide/en) for bundling and [Jest](https://github.com/facebook/jest) for testing.
-
 Build the documentation:
 
 ```None