Exposing attr in open api (#80)

* Exposing attr in open api

Author: ktsitsi

tests/integration/converters/test_ome_tiff.py

@@ -22,7 +22,6 @@ def test_ome_tiff_converter(tmp_path, open_fileobj):
         with open(input_path, "rb") as f:
             OMETiffConverter.to_tiledb(f, output_path)
     else:
-        print(output_path)
         OMETiffConverter.to_tiledb(input_path, output_path)
 
     with TileDBOpenSlide(output_path) as t:

tests/unit/test_openslide.py

@@ -1,10 +1,14 @@
 import random
 
+import pytest
+
 import tiledb
 from tests import get_schema
 from tiledb.bioimg.helpers import open_bioimg
 from tiledb.bioimg.openslide import TileDBOpenSlide
 
+from .. import ATTR_NAME
+
 
 class TestTileDBOpenSlide:
     def test(self, tmp_path):
@@ -26,3 +30,11 @@ def r():
         with TileDBOpenSlide(group_path) as t:
             assert t.level_count == len(level_dimensions)
             assert t.level_dimensions == tuple(level_dimensions)
+
+        with TileDBOpenSlide(group_path, attr=ATTR_NAME) as t:
+            assert t.level_count == len(level_dimensions)
+            assert t.level_dimensions == tuple(level_dimensions)
+
+        with pytest.raises(KeyError) as e_info:
+            _ = TileDBOpenSlide(group_path, attr="test_attr_name")
+            assert "No attribute matching 'test_attr_name'" in str(e_info.value)

tiledb/bioimg/converters/base.py

@@ -18,6 +18,7 @@
 import tiledb
 from tiledb.cc import WebpInputFormat
 
+from .. import ATTR_NAME
 from ..helpers import (
     ReadWriteGroup,
     create_image_pyramid,
@@ -135,7 +136,12 @@ class ImageConverter:
 
     @classmethod
     def from_tiledb(
-        cls, input_path: str, output_path: str, *, level_min: int = 0
+        cls,
+        input_path: str,
+        output_path: str,
+        *,
+        level_min: int = 0,
+        attr: str = ATTR_NAME,
     ) -> None:
         """
         Convert a TileDB Group of Arrays back to other format images, one per level.
@@ -144,11 +150,12 @@ def from_tiledb(
         :param output_path: path to the image
         :param level_min: minimum level of the image to be converted. By default set to 0
             to convert all levels.
+        :param attr: attribute name for backwards compatiblity support
         """
         if cls._ImageWriterType is None:
             raise NotImplementedError(f"{cls} does not support exporting")
 
-        slide = TileDBOpenSlide(input_path)
+        slide = TileDBOpenSlide(input_path, attr=attr)
         writer = cls._ImageWriterType(output_path)
         with slide, writer:
             writer.write_group_metadata(slide.properties)

tiledb/bioimg/helpers.py

@@ -73,8 +73,8 @@ def get_or_create(self, name: str, schema: tiledb.ArraySchema) -> Tuple[str, boo
         return uri, create
 
 
-def open_bioimg(uri: str, mode: str = "r") -> tiledb.Array:
-    return tiledb.open(uri, mode=mode, attr=ATTR_NAME if mode == "r" else None)
+def open_bioimg(uri: str, mode: str = "r", attr: str = ATTR_NAME) -> tiledb.Array:
+    return tiledb.open(uri, mode=mode, attr=attr if mode == "r" else None)
 
 
 def get_schema(

tiledb/bioimg/openslide.py

@@ -13,29 +13,30 @@
 
 import tiledb
 
+from . import ATTR_NAME
 from .converters.axes import Axes
 from .helpers import open_bioimg
 
 
 class TileDBOpenSlide:
     @classmethod
-    def from_group_uri(cls, uri: str) -> TileDBOpenSlide:
+    def from_group_uri(cls, uri: str, attr: str = ATTR_NAME) -> TileDBOpenSlide:
         warnings.warn(
             "This method is deprecated, please use TileDBOpenSlide() instead",
             DeprecationWarning,
             stacklevel=2,
         )
-        return cls(uri)
+        return cls(uri, attr=attr)
 
-    def __init__(self, uri: str):
+    def __init__(self, uri: str, *, attr: str = ATTR_NAME):
         """Open this TileDBOpenSlide.
 
         :param uri: uri of a tiledb.Group containing the image
         """
         self._group = tiledb.Group(uri)
         pixel_depth = self._group.meta.get("pixel_depth", 1)
         self._levels = sorted(
-            (TileDBOpenSlideLevel(o.uri, pixel_depth) for o in self._group),
+            (TileDBOpenSlideLevel(o.uri, pixel_depth, attr=attr) for o in self._group),
             key=attrgetter("level"),
         )
 
@@ -154,8 +155,8 @@ def _read_image(
 
 
 class TileDBOpenSlideLevel:
-    def __init__(self, uri: str, pixel_depth: int):
-        self._tdb = open_bioimg(uri)
+    def __init__(self, uri: str, pixel_depth: int, *, attr: str):
+        self._tdb = open_bioimg(uri, attr=attr)
         self._pixel_depth = pixel_depth
 
     @property