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2 Parent(s): b55a796 49d8c3b

Merge pull request #1 from andreped/demo

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Implemented simple demo app; docker and nginx configuration; hf space workflows

Files changed (7) hide show
  1. .gitignore +4 -0
  2. Dockerfile +38 -0
  3. README.md +89 -1
  4. index.html +75 -0
  5. nginx.conf +17 -0
  6. package-lock.json +1412 -0
  7. package.json +8 -0
.gitignore ADDED
@@ -0,0 +1,4 @@
 
 
 
 
 
1
+ *.DS_Store
2
+ *node_modules/
3
+ *.jpeg
4
+ *A05_files/
Dockerfile ADDED
@@ -0,0 +1,38 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ FROM nginx:alpine
2
+
3
+ # Install necessary packages
4
+ RUN apk add --no-cache shadow wget unzip nodejs npm
5
+
6
+ # Add a new user
7
+ RUN useradd -m -u 1000 user
8
+
9
+ # Set the working directory
10
+ WORKDIR /app
11
+
12
+ # Copy relevant files from repo for configuration and deployment
13
+ COPY index.html /usr/share/nginx/html
14
+ COPY nginx.conf /etc/nginx/nginx.conf
15
+ COPY package.json /app/package.json
16
+
17
+ # Download and uncompress test data
18
+ RUN wget https://github.com/andreped/wsi-visualization-demo/releases/download/sample-data/test-sample.zip \
19
+ && unzip test-sample.zip -d /usr/share/nginx/html \
20
+ && rm test-sample.zip
21
+
22
+ # Install npm dependencies
23
+ RUN cd /app && npm install
24
+
25
+ # Copy the installed dependencies to the nginx html directory
26
+ RUN cp -r node_modules/ /usr/share/nginx/html
27
+
28
+ # Change ownership of nginx directories to the new user
29
+ RUN chown -R user:user /var/cache/nginx /var/run /var/log/nginx /usr/share/nginx/html
30
+
31
+ # Expose port 7860
32
+ EXPOSE 7860
33
+
34
+ # Switch to the new user
35
+ USER user
36
+
37
+ # Start nginx
38
+ CMD ["nginx", "-g", "daemon off;"]
README.md CHANGED
@@ -1 +1,89 @@
1
- # wsi-annotation-demo
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ ---
2
+ title: wsi-annotation-demo
3
+ emoji: 🔬
4
+ colorFrom: blue
5
+ colorTo: red
6
+ sdk: docker
7
+ sdk_version: "24.0.6"
8
+ app_file: Dockerfile
9
+ pinned: false
10
+ ---
11
+
12
+ # wsi-annotation-demo
13
+
14
+ [![license](https://img.shields.io/github/license/DAVFoundation/captain-n3m0.svg?style=flat-square)](https://github.com/andreped/wsi-annotation-demo/blob/main/LICENSE.md)
15
+ <a target="_blank" href="https://huggingface.co/spaces/andreped/wsi-annotation-demo"><img src="https://img.shields.io/badge/🤗%20Hugging%20Face-Spaces-yellow.svg"></a>
16
+
17
+ ## Why?
18
+
19
+ This repository was developed to demonstrate how to do the following:
20
+ * Creating a simple web application for rendering a whole slide image in real time.
21
+ * Allow annotating a whole slide image in real-time.
22
+ * Containerizing and deploying a web app for deployment on Hugging Face Spaces.
23
+
24
+ To access the live demo, click on the `Hugging Face` badge above. Below is a snapshot of the current state of the demo app.
25
+
26
+ <img width="1400" alt="demo-hf-spaces" src="X">
27
+
28
+ ## Stack
29
+
30
+ For this demonstration, we have used the following:
31
+
32
+ | Component | Description |
33
+ | - | - |
34
+ | **OpenSeadragon** | The actual library for rendering the WSI |
35
+ | **Annotorious** | Library supporting annotation of large images |
36
+ | **Deep Zoom Image (DZI)** | Image file format compatible with OpenSeadragon |
37
+ | **npm** | Installation of frontend dependencies |
38
+ | **nginx** | HTTP web server |
39
+ | **Docker** | Containerization of the web app |
40
+ | **Hugging Face Spaces** | Deployment platform |
41
+
42
+ ## Continuous integration
43
+
44
+ For this project, we continuously update the Hugging Face deployment for each commit to the main branch.
45
+
46
+ | Build Type | Status |
47
+ | - | - |
48
+ | **HF Space Deploy** | [![CI](https://github.com/andreped/wsi-annotation-demo/workflows/Deploy/badge.svg)](https://github.com/andreped/wsi-annotation-demo/actions) |
49
+ | **File Size Check** | [![CI](https://github.com/andreped/wsi-annotation-demo/workflows/Check%20file%20size/badge.svg)](https://github.com/andreped/wsi-annotation-demo/actions) |
50
+
51
+ ## Local development
52
+
53
+ This example is for macOS development, so `brew` is required.
54
+
55
+ 1. Install `node`:
56
+ ```
57
+ brew install node
58
+ ```
59
+
60
+ 2. Install deps:
61
+ ```
62
+ npm install
63
+ ```
64
+
65
+ 3. Open in browser:
66
+ ```
67
+ open index.html
68
+ ```
69
+
70
+ ## Docker
71
+
72
+ 1. Build image:
73
+ ```
74
+ docker build -t wsi-annotation .
75
+ ```
76
+
77
+ 2. Run image:
78
+ ```
79
+ docker run -p 7860:7860 wsi-annotation
80
+ ```
81
+
82
+ 3. Open in browser:
83
+ ```
84
+ open http://localhost:7860
85
+ ```
86
+
87
+ ## License
88
+
89
+ This project has MIT License.
index.html ADDED
@@ -0,0 +1,75 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ <html>
2
+ <head>
3
+ <title>Whole Slide Image Annotation</title>
4
+
5
+ <link rel="stylesheet" href="node_modules/@recogito/annotorious/dist/annotorious.min.css">
6
+ <link rel="stylesheet" href="node_modules/@recogito/annotorious-selector-pack/dist/annotorious-selector-pack.min.css">
7
+
8
+ <!-- Dependencies -->
9
+ <script src="node_modules/openseadragon/build/openseadragon/openseadragon.min.js"></script>
10
+ <script src="node_modules/@recogito/annotorious-openseadragon/dist/openseadragon-annotorious.min.js"></script>
11
+ <script src="https://cdn.jsdelivr.net/npm/@recogito/[email protected]/dist/annotorious-toolbar.min.js"></script>
12
+ <script src="https://cdn.jsdelivr.net/npm/@recogito/[email protected]/dist/annotorious-selector-pack.min.js"></script>
13
+ </head>
14
+ <body>
15
+ <div style="padding: 0 0em; height: 95%; background: #303030">
16
+ <div class="sidebar-left" style="float: left; width: 10%;">
17
+ <h1 style="color: white; font-size: 16; padding: 0 1.5em;">Whole Slide Image Annotation Demo</h1>
18
+
19
+ <hr style="border: 1px solid white;">
20
+
21
+ <div class="position"></div>
22
+ <div class="zoom" style="margin-top: 3em;"></div>
23
+ </div>
24
+ <div id="wsi-canvas" style="float: left; width: 80%; height: 100%; background: white;"></div>
25
+ <div id="annotation-toolbar"></div>
26
+
27
+ <div class="sidebar-right" style="float: right; width: 10%;">
28
+ <div class="position"></div>
29
+ <div class="zoom" style="margin-top: 3em;"></div>
30
+ </div>
31
+
32
+ <div id="annotation_list" style="display: none;"></div>
33
+ </div>
34
+ <link rel="stylesheet" href="annotorious.min.css">
35
+ <script type="text/javascript">
36
+ var viewer = OpenSeadragon({
37
+ id: "wsi-canvas",
38
+ prefixUrl: "node_modules/openseadragon/build/openseadragon/images/",
39
+ zoomPerScroll: 2,
40
+ zoomPerClick: 1,
41
+ showNavigator: true,
42
+ showHomeControl: false,
43
+ showFullPageControl: false,
44
+ showZoomControl: false,
45
+ minZoomLevel: 0.25,
46
+ maxZoomLevel: 40,
47
+ tileSources: {
48
+ Image: {
49
+ xmlns: "http://schemas.microsoft.com/deepzoom/2008",
50
+ Url: "A05_files/",
51
+ Format: "jpeg",
52
+ Overlap: "0",
53
+ TileSize: "256",
54
+ Size: {
55
+ Height: 42625,
56
+ Width: 51553
57
+ }
58
+ },
59
+ overlays: [],
60
+ },
61
+ });
62
+ viewer.innerTracker.keyHandler = null;
63
+
64
+ var anno = OpenSeadragon.Annotorious(viewer);
65
+ Annotorious.SelectorPack(anno);
66
+
67
+ const toolbar = new Annotorious.Toolbar(anno, document.getElementById('annotation-toolbar'));
68
+ viewer.addControl(document.getElementById("annotation-toolbar"), {anchor: OpenSeadragon.ControlAnchor.TOP_LEFT});
69
+
70
+ document.getElementById('annotation-toolbar').addEventListener('click', function(event) {
71
+ event.preventDefault();
72
+ });
73
+ </script>
74
+ </body>
75
+ </html>
nginx.conf ADDED
@@ -0,0 +1,17 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ pid /tmp/nginx.pid;
2
+
3
+ events {
4
+ worker_connections 1024;
5
+ }
6
+
7
+ http {
8
+ server {
9
+ listen 7860;
10
+ server_name localhost;
11
+
12
+ location / {
13
+ root /usr/share/nginx/html;
14
+ index index.html;
15
+ }
16
+ }
17
+ }
package-lock.json ADDED
@@ -0,0 +1,1412 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ {
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package.json ADDED
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