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TileDB-Inc · Jun 20, 2024 · 20479a5 · 20479a5
1 parent e8385e2
commit 20479a5
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Showing 4 changed files with 16 additions and 4 deletions.
diff --git a/tiledb/bioimg/converters/base.py b/tiledb/bioimg/converters/base.py
@@ -58,7 +58,12 @@
 
 class ImageReader(ABC):
     @abstractmethod
-    def __init__(self, input_path: str, logger: logging.Logger, **kwargs: Any):
+    def __init__(self, input_path: str,
+                 *,
+                 logger: Optional[logging.Logger],
+                 config: Optional[tiledb.Config] = None,
+                 ctx: Optional[tiledb.Ctx] = None,
+                 **kwargs: Any):
         """Initialize this ImageReader"""
 
     def __enter__(self) -> ImageReader:
@@ -359,7 +364,7 @@ def to_tiledb(
             reader = source
         elif cls._ImageReaderType is not None:
             reader = cls._ImageReaderType(
-                source, logger, **reader_kwargs if reader_kwargs else {}
+                source, logger=logger, **reader_kwargs if reader_kwargs else {}
             )
         else:
             raise NotImplementedError(f"{cls} does not support importing")

diff --git a/tiledb/bioimg/converters/ome_tiff.py b/tiledb/bioimg/converters/ome_tiff.py
@@ -9,6 +9,7 @@
 
 from tiledb import VFS, Config, Ctx
 from tiledb.cc import WebpInputFormat
+from tiledb.highlevel import _get_ctx
 
 from .. import ATTR_NAME, EXPORT_TILE_SIZE, WHITE_RGBA
 from ..helpers import get_decimal_from_rgba, get_logger_wrapper, get_rgba, iter_color
@@ -21,6 +22,7 @@ class OMETiffReader(ImageReader):
     def __init__(
         self,
         input_path: str,
+        *,
         logger: Optional[logging.Logger] = None,
         config: Optional[Config] = None,
         ctx: Optional[Ctx] = None,
@@ -37,7 +39,9 @@ def __init__(
 
         # Use VFS for all paths local or remote for reading the input image
         self._input_path = input_path
-        self._vfs = VFS(config=config, ctx=ctx)
+        self._ctx = _get_ctx(ctx, config)
+        self._cfg = self._ctx.config()
+        self._vfs = VFS(config=self._cfg, ctx=self._ctx)
         self._vfs_fh = self._vfs.open(input_path, mode="rb")
         self._tiff = tifffile.TiffFile(self._vfs_fh)
         # XXX ignore all but the first series

diff --git a/tiledb/bioimg/converters/ome_zarr.py b/tiledb/bioimg/converters/ome_zarr.py
@@ -25,6 +25,7 @@ class OMEZarrReader(ImageReader):
     def __init__(
         self,
         input_path: str,
+        *,
         logger: Optional[logging.Logger] = None,
         config: Optional[Config] = None,
         ctx: Optional[Ctx] = None,

diff --git a/tiledb/bioimg/converters/openslide.py b/tiledb/bioimg/converters/openslide.py
@@ -27,6 +27,7 @@ class OpenSlideReader(ImageReader):
     def __init__(
         self,
         input_path: str,
+        *,
         logger: Optional[logging.Logger] = None,
         config: Optional[Config] = None,
         ctx: Optional[Ctx] = None,
@@ -40,11 +41,12 @@ def __init__(
         self._ctx = _get_ctx(ctx, config)
         self._cfg = self._ctx.config()
         self._logger = get_logger_wrapper(False) if not logger else logger
-        resolved_path = input_path
         if is_remote_protocol(input_path):
             resolved_path = cache_filepath(
                 input_path, config, ctx, self._logger, scratch_space
             )
+        else:
+            resolved_path = input_path
         self._osd = osd.OpenSlide(resolved_path)
 
     def __exit__(self, exc_type: Any, exc_val: Any, exc_tb: Any) -> None: