slide2vec 6.3.0__tar.gz → 6.3.1__tar.gz

{slide2vec-6.3.0 → slide2vec-6.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: slide2vec
-Version: 6.3.0
+Version: 6.3.1
 Summary: Embedding of whole slide images with Foundation Models
 Author-email: Clément Grisi <clement.grisi@radboudumc.nl>
 License-Expression: Apache-2.0

{slide2vec-6.3.0 → slide2vec-6.3.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "slide2vec"
-version = "6.3.0"
+version = "6.3.1"
 description = "Embedding of whole slide images with Foundation Models"
 readme = "README.md"
 requires-python = ">=3.10"
@@ -180,7 +180,7 @@ no_implicit_reexport = true
 max-line-length = 160
 
 [tool.bumpver]
-current_version = "6.3.0"
+current_version = "6.3.1"
 version_pattern = "MAJOR.MINOR.PATCH"
 commit = false
 tag = false

{slide2vec-6.3.0 → slide2vec-6.3.1}/slide2vec/__init__.py

@@ -31,7 +31,7 @@ from slide2vec.encoders import (
 )
 
 
-__version__ = "6.3.0"
+__version__ = "6.3.1"
 
 __all__ = [
     "Model",

{slide2vec-6.3.0 → slide2vec-6.3.1}/slide2vec/data/tile_reader.py

@@ -40,31 +40,20 @@ class SuperTileBatchSampler:
 
 
 def _open_wsi_backend(image_path: str, backend: str, gpu_decode: bool):
-    """Open a WSI file with the given backend and return the reader."""
-    if backend == "cucim":
-        from hs2p.wsi.backends.cucim import CuCIMReader
-        return CuCIMReader(image_path, gpu_decode=gpu_decode)
-    elif backend == "openslide":
-        from hs2p.wsi.backends.openslide import OpenSlideReader
-        return OpenSlideReader(image_path)
-    elif backend == "vips":
-        from hs2p.wsi.backends.vips import VIPSReader
-        return VIPSReader(image_path)
-    elif backend == "asap":
-        from hs2p.wsi.backends.asap import ASAPReader
-        with suppress_c_stderr():
-            return ASAPReader(image_path)
-    else:
-        raise ValueError(
-            f"Unknown backend: {backend!r}. "
-            "Choose from: cucim, openslide, vips, asap"
-        )
+    """Open a slide with the backend tiling resolved for it and return the reader.
 
+    hs2p's ``open_slide`` knows every backend tiling can resolve, ``pil`` for flat
+    PNG/JPEG slides included. Reads address pyramid levels and level-0 pixels only, so a
+    slide without spacing metadata opens without it.
+    """
+    from hs2p.wsi.reader import open_slide
 
-class WSITileReader:
-    """Random-access tile reader for WSI files supporting four backends.
+    with suppress_c_stderr() if backend == "asap" else nullcontext():
+        return open_slide(image_path, backend, gpu_decode=gpu_decode, require_spacing=False)
 
-    Backends: ``"cucim"`` (default), ``"openslide"``, ``"vips"``, ``"asap"``.
+
+class WSITileReader:
+    """Random-access tile reader over any slide backend hs2p can open.
 
     When ``use_supertiles=True``, tiles are grouped into 8×8/4×4/2×2 blocks so
     that one region read covers multiple tiles.  ``num_cucim_workers`` and

{slide2vec-6.3.0 → slide2vec-6.3.1}/slide2vec.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: slide2vec
-Version: 6.3.0
+Version: 6.3.1
 Summary: Embedding of whole slide images with Foundation Models
 Author-email: Clément Grisi <clement.grisi@radboudumc.nl>
 License-Expression: Apache-2.0

{slide2vec-6.3.0 → slide2vec-6.3.1}/tests/test_hs2p5_integration.py

@@ -90,6 +90,34 @@ def test_tile_archive_is_written_when_requested_or_not_reading_on_the_fly(
         assert Path(pd.read_csv(process_list).iloc[0]["tiles_tar_path"]) == archive_path
 
 
+@pytest.mark.parametrize("use_supertiles", [True, False], ids=["supertiles", "single-tiles"])
+def test_flat_slide_tiles_are_read_on_the_fly_with_the_backend_tiling_resolved(
+    tmp_path, use_supertiles
+):
+    from slide2vec.data.tile_reader import OnTheFlyBatchTileCollator
+
+    slide = _flat_slide(tmp_path, np.ones((32, 32), dtype=np.uint8))
+    pixels = np.random.default_rng(0).integers(0, 256, (128, 128, 3), dtype=np.uint8)
+    Image.fromarray(pixels).save(slide.image_path)
+
+    _, (result,), _ = prepare_tiled_slides(
+        [slide], _preprocessing(), output_dir=tmp_path / "out", num_workers=1
+    )
+    collator = OnTheFlyBatchTileCollator(
+        image_path=slide.image_path,
+        tiling_result=result,
+        backend=result.backend,
+        use_supertiles=use_supertiles,
+    )
+    indices, tiles, _ = collator(list(range(len(result.x))))
+
+    assert result.backend == "pil"
+    assert tiles.shape == (16, 3, 32, 32)
+    for index, tile in zip(indices.tolist(), tiles):
+        x, y = int(result.x[index]), int(result.y[index])
+        np.testing.assert_array_equal(tile.permute(1, 2, 0).numpy(), pixels[y : y + 32, x : x + 32])
+
+
 @pytest.mark.parametrize("output_mode", ["per_annotation", "merged"])
 def test_spacingless_annotation_mask_groups_values_and_preserves_bag_identity(tmp_path, output_mode):
     labels = np.full((32, 32), 2, dtype=np.uint8)