Add FsspecJsonWSIReader class.

[aacic]

The FsspecJsonWSIReader reads fsspec json file which represents SVS or TIFF whole slide image. The images are accessible by HTTP range requests, eg:

https://api.gdc.cancer.gov/data/73c69d24-6f9e-44e2-bfe5-a608d4cf5c27

The whole image can be downloaded like:

curl -C - -o TCGA-22-1017-01Z-00-DX1.9562FE79-A261-42D3-B394-F3E0E2FF7DDA.svs https://api.gdc.cancer.gov/data/73c69d24-6f9e-44e2-bfe5-a608d4cf5c27

The FsspecJsonWSIReader class has a _zarr_store field which is created by reading json file using fsspec:

mapper = fsspec.get_mapper(
            "reference://", fo=str(input_img), target_protocol="file"
        )
self._zarr_array = zarr.open(mapper, mode="r")
self._zarr_store = self._zarr_array.store

self._zarr_lru_cache = zarr.LRUStoreCache(self._zarr_store, max_size=cache_size)
self._zarr_group = zarr.open(self._zarr_lru_cache)

This is equivalent to TIFFWSIReader code:

self._zarr_store = tifffile.imread(
            self.input_path,
            series=self.series_n,
            aszarr=True,
        )
        self._zarr_lru_cache = zarr.LRUStoreCache(self._zarr_store, max_size=cache_size)
        self._zarr_group = zarr.open(self._zarr_lru_cache)

Both FsspecJsonWSIReader and TIFFWSIReader forward calls to read_bounds and read_rect methods of theTIFFWSIReaderDelegate delegate instance.

The method _info of theTIFFWSIReaderDelegate reads SVS metadata which is stored in the root group metadata like:

{
  ".zattrs": {
    "multiscales": [
      {
        "metadata": {
          "objective_power": 40,
          "vendor": "Aperio",
          "mpp": [0.2525, 0.2525]	
        }
      }
    ]
  }
}

To test, execute from the root dir:

pip install -r requirements/requirements_dev.txt
mkdir -p samples/slides
mkdir -p samples/fsspec
cd samples/slides
curl -C - -o TCGA-22-1017-01Z-00-DX1.9562FE79-A261-42D3-B394-F3E0E2FF7DDA.svs   https://api.gdc.cancer.gov/data/73c69d24-6f9e-44e2-bfe5-a608d4cf5c27
cd ../../
cp tiatoolbox/utils/tiff_to_fsspec.py .
python tiff_to_fsspec.py "samples/slides/TCGA-22-1017-01Z-00-DX1.9562FE79-A261-42D3-B394-F3E0E2FF7DDA.svs"  "samples/fsspec/73c69d24-6f9e-44e2-bfe5-a608d4cf5c27_fsspec.json" "https://api.gdc.cancer.gov/data/73c69d24-6f9e-44e2-bfe5-a608d4cf5c27"

Create tileserver.py inside of the project root:

from flask_cors import CORS

from tiatoolbox.visualization import TileServer
from tiatoolbox.wsicore.wsireader import FsspecJsonWSIReader

wsi = FsspecJsonWSIReader.open(
    "./samples/fsspec/73c69d24-6f9e-44e2-bfe5-a608d4cf5c27_fsspec.json"
)


# Initialize and run the TileServer
tile_server = TileServer(
    title="Tiatoolbox TileServer",
    layers={"layer": wsi},
)
CORS(tile_server, send_wildcard=True)


tile_server.run(host="127.0.0.1", port=5000)

Open http://127.0.0.1:5000/ and verify that it works.

[review-notebook-app]

Check out this pull request on 

See visual diffs & provide feedback on Jupyter Notebooks.

---

Powered by ReviewNB

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.93%. Comparing base (2416ba9) to head (3a78386).
Report is 16 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #897      +/-   ##
===========================================
+ Coverage    99.90%   99.93%   +0.02%     
===========================================
  Files           70       71       +1     
  Lines         8736     8834      +98     
  Branches      1149     1152       +3     
===========================================
+ Hits          8728     8828     +100     
  Misses           3        3              
+ Partials         5        3       -2     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[shaneahmed]

Add a link to tiff-fsspec generator file.

[aacic]

The method is migrated to:
FsspecJsonWSIReader.is_valid_zarr_fsspec(file_path: str) -> bool:

I've extended the docs and added a link to tiff-to-fsspec generator file.

[shaneahmed]

Add some documentation / introduction about the fsspec / json files.

[aacic]

Added documentation and the link to tiff_to_fsspec.py.

[shaneahmed]

Thanks @aacic