Merge remote-tracking branch 'origin/fix-zarr-check' into fix-zarr-check

Author: shaneahmed

tests/test_wsireader.py

@@ -34,7 +34,6 @@
 from tiatoolbox.annotation import SQLiteStore
 from tiatoolbox.utils import imread, tiff_to_fsspec
 from tiatoolbox.utils.exceptions import FileNotSupportedError
-from tiatoolbox.utils.magic import is_sqlite3
 from tiatoolbox.utils.transforms import imresize, locsize2bounds
 from tiatoolbox.utils.visualization import AnnotationRenderer
 from tiatoolbox.wsicore import WSIReader, wsireader
@@ -2219,22 +2218,6 @@ def test_is_ngff_regular_zarr(track_tmp_path: Path) -> None:
         WSIReader.open(zarr_path)
 
 
-def test_is_ngff_sqlite3(track_tmp_path: Path, remote_sample: Callable) -> None:
-    """Test is_ngff is false for a sqlite3 file.
-
-    Copies the ngff-1 sample to a sqlite3 file and checks that it is
-    identified as an ngff file.
-
-    """
-    ngff_path = remote_sample("ngff-1")
-    source = zarr.storage.LocalStore(ngff_path)
-    dest = zarr.SQLiteStore(track_tmp_path / "ngff.sqlite3")
-    # Copy the store to a sqlite3 file
-    zarr.copy_store(source, dest)
-
-    assert is_sqlite3(dest.path)
-
-
 def test_store_reader_no_info(track_tmp_path: Path) -> None:
     """Test AnnotationStoreReader with no info."""
     SQLiteStore(track_tmp_path / "store.db")
@@ -2319,16 +2302,6 @@ def test_store_reader_info_from_base(
     assert store_reader.info.mpp[0] == wsi_reader.info.mpp[0]
 
 
-def test_ngff_sqlitestore(track_tmp_path: Path, remote_sample: Callable) -> None:
-    """Test SQLiteStore with an NGFF file."""
-    ngff_path = remote_sample("ngff-1")
-    source = zarr.storage.LocalStore(ngff_path)
-    dest = zarr.SQLiteStore(track_tmp_path / "ngff.sqlite3")
-    # Copy the store to a sqlite3 file
-    zarr.copy_store(source, dest)
-    wsireader.NGFFWSIReader(dest.path)
-
-
 def test_ngff_zattrs_non_micrometer_scale_mpp(
     track_tmp_path: Path,
     remote_sample: Callable,

tiatoolbox/wsicore/__init__.py

@@ -11,6 +11,7 @@
 __all__ = [
     "WSIMeta",
     "WSIReader",
+    "WSIReaderParams",
 ]
 
 
@@ -20,3 +21,4 @@ class WSIReaderParams(TypedDict, total=False):
     meta: WSIMeta | None
     mpp: tuple[Number, Number] | Number
     power: Number
+    storage_options: dict  # For FsspecStore

tiatoolbox/wsicore/wsireader.py

@@ -12,7 +12,7 @@
 from datetime import UTC, datetime
 from numbers import Number
 from pathlib import Path
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Unpack
 
 import cv2
 import fsspec
@@ -31,14 +31,13 @@
 from PIL import Image
 from tifffile import TiffPages
 from zarr.experimental.cache_store import CacheStore
-from zarr.storage import MemoryStore
+from zarr.storage import FsspecStore, MemoryStore
 
 from tiatoolbox import logger, utils
 from tiatoolbox.annotation import AnnotationStore, SQLiteStore
 from tiatoolbox.utils import postproc_defs
 from tiatoolbox.utils.env_detection import pixman_warning
 from tiatoolbox.utils.exceptions import FileNotSupportedError
-from tiatoolbox.utils.magic import is_sqlite3
 from tiatoolbox.utils.visualization import AnnotationRenderer
 from tiatoolbox.wsicore.wsimeta import WSIMeta
 
@@ -55,6 +54,7 @@
         Resolution,
         Units,
     )
+    from tiatoolbox.wsicore import WSIReaderParams
     from tiatoolbox.wsicore.metadata.ngff import Multiscales
 
 pixman_warning()
@@ -146,9 +146,8 @@ def is_ngff(  # noqa: PLR0911
 
     """
     path = Path(path)
-    store = zarr.SQLiteStore(str(path)) if path.is_file() and is_sqlite3(path) else path
     try:
-        zarr_group = zarr.open(store, mode="r")
+        zarr_group = zarr.open(path, mode="r")
     except Exception:  # skipcq: PYL-W0703  # noqa: BLE001
         return False
     if not isinstance(zarr_group, zarr.Group):
@@ -347,7 +346,7 @@ def open(
         mpp: tuple[Number, Number] | None = None,
         power: Number | None = None,
         post_proc: str | callable | None = "auto",
-        **kwargs: dict,
+        **kwargs: Unpack[WSIReaderParams],
     ) -> WSIReader:
         """Return an appropriate :class:`.WSIReader` object.
 
@@ -482,7 +481,7 @@ def _handle_special_cases(
         mpp: tuple[Number, Number] | None = None,
         power: Number | None = None,
         post_proc: str | callable | None = "auto",
-        **kwargs: dict,
+        **kwargs: Unpack[WSIReaderParams],
     ) -> WSIReader | None:
         """Handle special cases for selecting the appropriate WSIReader.
 
@@ -5744,15 +5743,18 @@ class NGFFWSIReader(WSIReader):
 
     """
 
-    def __init__(self: NGFFWSIReader, path: str | Path, **kwargs: dict) -> None:
+    def __init__(
+        self: NGFFWSIReader, path: str | Path, **kwargs: Unpack[WSIReaderParams]
+    ) -> None:
         """Initialize :class:`NGFFWSIReader`."""
         super().__init__(path, **kwargs)
         from imagecodecs import numcodecs  # noqa: PLC0415
 
         from tiatoolbox.wsicore.metadata import ngff  # noqa: PLC0415
 
         numcodecs.register_codecs()
-        store = zarr.SQLiteStore(path) if is_sqlite3(path) else path
+        storage_options = kwargs.get("storage_options", {})
+        store = FsspecStore.from_url(path, storage_options=storage_options)
         self._zarr_group: zarr.Group = zarr.open(store, mode="r")
         attrs = self._zarr_group.attrs
         multiscales = attrs["multiscales"][0]
@@ -5815,7 +5817,7 @@ def _info(self: NGFFWSIReader) -> WSIMeta:
                 array.shape[:2][::-1]
                 for _, array in sorted(self._zarr_group.arrays(), key=lambda x: x[0])
             ],
-            slide_dimensions=self._zarr_group[0].shape[:2][::-1],
+            slide_dimensions=self._zarr_group["0"].shape[:2][::-1],
             vendor=self.zattrs._creator.name,  # skipcq: PYL-W0212  # noqa: SLF001
             raw=self._zarr_group.attrs,
             mpp=mpp,
@@ -6319,7 +6321,7 @@ def __init__(
         renderer: AnnotationRenderer | None = None,
         base_wsi: WSIReader | str | None = None,
         alpha: float = 1.0,
-        **kwargs: dict,
+        **kwargs: Unpack[WSIReaderParams],
     ) -> None:
         """Initialize :class:`AnnotationStoreReader`."""
         super().__init__(store, **kwargs)