NEW: Add Simple Zoomify Viewer For WSIReader (#212)

Adds a  simple Zoomify viewer class.

Key Features
========

- Take a dictionary of `WSIReader` objects
- Display then as layers in the web browser (`localhost:5000`) by serving Zoomify tiles
- Togglable layers
- Adjustable opacity
- Layer re-ordering
- Mini-map
- Fullscreen
- Rotation (shift + alt) with reset button
- Mouse coordinates in baseline pixels (bottom right)
- Scale bar in microns
- Works with JP2 images but can be very slow and a little glitchy sometimes.

To Do
====

- [x] Rename class / module?
- [x] Unit tests

Dependencies
=========

- OpenLayers (BSD) and ol-ext (BSD-like, French version) Javascript for the frontend.
- Flask (BSD) for the server.

Demo
====



https://user-images.githubusercontent.com/4615004/144947393-aa492644-6012-48d9-b73b-5109e67393bd.mp4

Update: Added Graticule & Screen Space Graticule (Grids)
------------------------------------------------------------------------------

https://user-images.githubusercontent.com/4615004/145240617-57f21e9a-faa8-4f9e-896b-b89c41c0df0b.mp4

Demo Code
-------------

```python
from tiatoolbox.wsiscore.wsireader import WSIReader
from tiatoolbox.visualization.tileserver import TileServer

wsi = WSIReader.open("/home/john/Downloads/CMU-1.svs")
wsi2 = WSIReader.open("/home/john/Downloads/JP2K-33003-1.svs")
app = TileServer(
    title="Testing TileServer",
    layers={
        "JPEG SVS": wsi,
        "JP2 SVS": wsi2,
    },
)
app.run()
```

 # Future Extensions

- Allow annotation store as layer to display vector polygons / rendered as tiles
- IPython support for embedding in notebooks
- Make the layers UI a bit prettier

Co-authored-by: John Pocock <[email protected]>
Co-authored-by: Shan E Ahmed Raza <[email protected]>
Co-authored-by: George Hadjigeorgiou <[email protected]>

Author: 3 people

requirements.conda.yml

@@ -9,6 +9,7 @@ dependencies:
   - Click
   - cython
   - defusedxml
+  - flask
   - glymur
   - h5py
   - imagecodecs

requirements.dev.conda.yml

@@ -12,6 +12,7 @@ dependencies:
   - defusedxml
   - flake8
   - flake8-bugbear
+  - flask
   - glymur
   - h5py
   - imagecodecs

requirements.txt

@@ -1,6 +1,7 @@
 albumentations>0.5.0
 Click>=7.0
 defusedxml
+flask
 glymur
 imagecodecs
 jupyterlab

requirements.win64.conda.yml

@@ -9,6 +9,7 @@ dependencies:
   - Click
   - cython
   - defusedxml
+  - flask
   - glymur
   - h5py
   - imagecodecs

requirements_dev.txt

@@ -5,6 +5,7 @@ Click>=7.0
 coverage==5.1
 flake8-bugbear
 flake8==3.7.8
+flask
 glymur
 imagecodecs
 jupyterlab

tests/test_tileserver.py

@@ -0,0 +1,46 @@
+"""Tests for tileserver."""
+import pytest
+
+from tiatoolbox.visualization.tileserver import TileServer
+from tiatoolbox.wsicore.wsireader import WSIReader
+
+
+@pytest.fixture()
+def app(remote_sample) -> TileServer:
+    """Create a testing TileServer WSGI app."""
+    wsi = WSIReader.open(remote_sample("ndpi-1"))
+    app = TileServer(title="test", layers={"ndpi": wsi})
+    app.config.from_mapping({"TESTING": True})
+    return app
+
+
+def test_get_tile(app) -> None:
+    """Get a single tile and check the status code and content type."""
+    with app.test_client() as client:
+        response = client.get("/layer/ndpi/zoomify/TileGroup0/0-0-0.jpg")
+        assert response.status_code == 200
+        assert response.content_type == "image/jpeg"
+
+
+def test_get_tile_404(app) -> None:
+    """Request a tile with an index."""
+    with app.test_client() as client:
+        response = client.get("/layer/ndpi/zoomify/TileGroup0/10-0-0.jpg")
+        assert response.status_code == 404
+        assert response.get_data(as_text=True) == "Tile not found"
+
+
+def test_get_tile_layer_key_error(app) -> None:
+    """Request a tile with an invalid layer key."""
+    with app.test_client() as client:
+        response = client.get("/layer/foo/zoomify/TileGroup0/0-0-0.jpg")
+        assert response.status_code == 404
+        assert response.get_data(as_text=True) == "Layer not found"
+
+
+def test_get_index(app) -> None:
+    """Get the index page and check that it is HTML."""
+    with app.test_client() as client:
+        response = client.get("/")
+        assert response.status_code == 200
+        assert response.content_type == "text/html; charset=utf-8"