Implement aperio svs workloads (wip)

recipes/reading_tifffile.py

@@ -0,0 +1,76 @@
+"""Read an Aperio SVS file via the Tifffile Zarr interface
+as well as via FSStore and the fsspec.ReferenceFileSystem
+
+pip install fsspec[http] tifffile imagecodecs imagecodecs_numcodecs
+"""
+from pathlib import Path
+from typing import Final
+
+import fsspec
+import zarr
+from perfcapture.dataset import Dataset
+from perfcapture.workload import Workload
+from tifffile import TiffFile
+from tifffile.tifffile import tiff2fsspec
+from zarr.storage import FSStore
+
+
+_OUTPUT_TILE_SIZE_X: Final[int] = 1024
+_OUTPUT_TILE_SIZE_Y: Final[int] = 1024
+SVS_TIFF = "https://data.cytomine.coop/open/openslide/aperio-svs/CMU-1.svs"
+SERIES_IDX = 0
+
+
+class TifffileSVSDataset(Dataset):
+    def create(self) -> None:
+        fs, path = fsspec.core.url_to_fs(SVS_TIFF)
+        fn = str(self.path.joinpath("CMU-1.svs").absolute())
+        kc = str(self.path.joinpath("CMU-1.json").absolute())
+        fs.get(path, fn)
+        tiff2fsspec(
+            fn,
+            url=fn,
+            out=kc,
+            series=SERIES_IDX,
+        )
+
+
+class ReadViaTifffileWorkload(Workload):
+    def init_datasets(self) -> tuple[Dataset, ...]:
+        return (TifffileSVSDataset(),)
+
+    def run(self, dataset_path: Path) -> None:
+        """Read Aperio SVS file via tifffile.ZarrTiffStore"""
+        svs = dataset_path.joinpath("CMU-1.svs")
+        store = TiffFile(svs).aszarr(maxworkers=1)
+        array = zarr.open_group(store, mode="r")[str(SERIES_IDX)]
+
+        for idx_x in range(0, array.shape[1], _OUTPUT_TILE_SIZE_X):
+            for idx_y in range(0, array.shape[0], _OUTPUT_TILE_SIZE_Y):
+                _ = array[
+                    idx_y: idx_y + _OUTPUT_TILE_SIZE_Y,
+                    idx_x: idx_x + _OUTPUT_TILE_SIZE_X,
+                    :
+                ]
+
+
+class ReadViaReferenceFileSystemWorkload(Workload):
+    def init_datasets(self) -> tuple[Dataset, ...]:
+        return (TifffileSVSDataset(),)
+
+    def run(self, dataset_path: Path) -> None:
+        """Read Aperio SVS via fsspec.ReferenceFileSystem"""
+        fs = fsspec.filesystem(
+            "reference",
+            fo=str(dataset_path.joinpath("CMU-1.json")),
+        )
+        store = FSStore("", fs=fs)
+        array = zarr.open_group(store, mode="r")[str(SERIES_IDX)]
+
+        for idx_x in range(0, array.shape[1], _OUTPUT_TILE_SIZE_X):
+            for idx_y in range(0, array.shape[0], _OUTPUT_TILE_SIZE_Y):
+                _ = array[
+                    idx_y: idx_y + _OUTPUT_TILE_SIZE_Y,
+                    idx_x: idx_x + _OUTPUT_TILE_SIZE_X,
+                    :
+                ]