NEW: Add Simple Zoomify Viewer For WSIReader

[John-P]

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

• Rename class / module?
• Unit tests

Dependencies

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

Demo

ZoomifyViewer.mp4

Update: Added Graticule & Screen Space Graticule (Grids)

ZoomifyViewer.Graticules.mp4

Demo Code

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

[John-P]

As a result this has made some bugs in VirtualWSIReader in combination with ZoomifyGenerator apparent and will be useful for testing and debugging.

[John-P]

@shaneahmed Only a quick draft and simple tool but may be useful to motivate Zoomify tile generation and also as a way of debugging it / showing results in general.

[codecov]

Codecov Report

Merging #212 (3a51b21) into develop (9bb597d) will increase coverage by 0.00%.
The diff coverage is 100.00%.

@@           Coverage Diff            @@
##           develop     #212   +/-   ##
========================================
  Coverage    99.83%   99.83%           
========================================
  Files           52       53    +1     
  Lines         4848     4883   +35     
  Branches       796      798    +2     
========================================
+ Hits          4840     4875   +35     
  Misses           2        2           
  Partials         6        6           

Impacted Files	Coverage Δ
tiatoolbox/visualization/tileserver.py	100.00% <100.00%> (ø)

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[shaneahmed]

Thanks @John-P This will strengthen visualisation part. Can we add tests to fix coverage?