slide2vec 4.6.0__tar.gz → 4.6.1__tar.gz

{slide2vec-4.6.0 → slide2vec-4.6.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: slide2vec
-Version: 4.6.0
+Version: 4.6.1
 Summary: Embedding of whole slide images with Foundation Models
 Author-email: Clément Grisi <clement.grisi@radboudumc.nl>
 License-Expression: Apache-2.0
@@ -15,7 +15,7 @@ Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: hs2p[asap,cucim,openslide,sam2,vips]>=4.0.7
+Requires-Dist: hs2p[asap,cucim,openslide,sam2,vips]>=4.0.8
 Requires-Dist: omegaconf
 Requires-Dist: matplotlib
 Requires-Dist: numpy<2
@@ -65,7 +65,7 @@ Requires-Dist: numpy<2; extra == "fm"
 Requires-Dist: pandas; extra == "fm"
 Requires-Dist: pillow; extra == "fm"
 Requires-Dist: rich; extra == "fm"
-Requires-Dist: hs2p[asap,cucim,openslide,sam2,vips]>=4.0.7; extra == "fm"
+Requires-Dist: hs2p[asap,cucim,openslide,sam2,vips]>=4.0.8; extra == "fm"
 Requires-Dist: wandb; extra == "fm"
 Requires-Dist: torch<2.8,>=2.3; extra == "fm"
 Requires-Dist: torchvision>=0.18.0; extra == "fm"

{slide2vec-4.6.0 → slide2vec-4.6.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "slide2vec"
-version = "4.6.0"
+version = "4.6.1"
 description = "Embedding of whole slide images with Foundation Models"
 readme = "README.md"
 requires-python = ">=3.10"
@@ -21,7 +21,7 @@ classifiers = [
     "Programming Language :: Python :: 3.13",
 ]
 dependencies = [
-    "hs2p[asap,cucim,openslide,sam2,vips]>=4.0.7",
+    "hs2p[asap,cucim,openslide,sam2,vips]>=4.0.8",
     "omegaconf",
     "matplotlib",
     "numpy<2",
@@ -88,7 +88,7 @@ fm = [
     "pandas",
     "pillow",
     "rich",
-    "hs2p[asap,cucim,openslide,sam2,vips]>=4.0.7",
+    "hs2p[asap,cucim,openslide,sam2,vips]>=4.0.8",
     "wandb",
     "torch>=2.3,<2.8",
     "torchvision>=0.18.0",
@@ -164,7 +164,7 @@ no_implicit_reexport = true
 max-line-length = 160
 
 [tool.bumpver]
-current_version = "4.6.0"
+current_version = "4.6.1"
 version_pattern = "MAJOR.MINOR.PATCH"
 commit = false       # We do version bumping in CI, not as a commit
 tag = false          # Git tag already exists — we don't auto-tag

{slide2vec-4.6.0 → slide2vec-4.6.1}/slide2vec/__init__.py

@@ -11,7 +11,7 @@ from slide2vec.api import (
 from slide2vec.artifacts import HierarchicalEmbeddingArtifact, SlideEmbeddingArtifact, TileEmbeddingArtifact
 
 
-__version__ = "4.6.0"
+__version__ = "4.6.1"
 
 __all__ = [
     "Model",

{slide2vec-4.6.0 → slide2vec-4.6.1}/slide2vec/runtime/hierarchical.py

@@ -1,4 +1,5 @@
 import numpy as np
+from hs2p.wsi.geometry import plan_spacing_read
 
 from slide2vec.api import PreprocessingConfig
 from slide2vec.utils.coordinates import coordinate_arrays
@@ -17,6 +18,21 @@ def is_hierarchical_preprocessing(preprocessing: PreprocessingConfig | None) ->
     return preprocessing.region_tile_multiple is not None or preprocessing.requested_region_size_px is not None
 
 
+def _level_downsample_pairs(level_downsamples) -> list[tuple[float, float]]:
+    pairs: list[tuple[float, float]] = []
+    for downsample in level_downsamples:
+        if isinstance(downsample, (tuple, list, np.ndarray)):
+            if len(downsample) == 0:
+                raise ValueError("level_downsamples entries must not be empty")
+            x_value = float(downsample[0])
+            y_value = float(downsample[1]) if len(downsample) > 1 else x_value
+            pairs.append((x_value, y_value))
+        else:
+            value = float(downsample)
+            pairs.append((value, value))
+    return pairs
+
+
 def resolve_hierarchical_geometry(preprocessing: PreprocessingConfig, tiling_result) -> dict[str, int]:
     if preprocessing.region_tile_multiple is None:
         raise ValueError("Hierarchical preprocessing requires region_tile_multiple")
@@ -28,14 +44,16 @@ def resolve_hierarchical_geometry(preprocessing: PreprocessingConfig, tiling_res
     multiple = int(preprocessing.region_tile_multiple)
     if requested_region_size_px % multiple != 0:
         raise ValueError("requested_region_size_px must be divisible by region_tile_multiple")
-    read_spacing_um = float(getattr(tiling_result, "read_spacing_um"))
     base_spacing_um = float(getattr(tiling_result, "base_spacing_um"))
-    if abs(read_spacing_um - requested_spacing_um) / requested_spacing_um <= float(preprocessing.tolerance):
-        read_tile_size_px = requested_tile_size_px
-    else:
-        read_tile_size_px = int(
-            round(requested_tile_size_px * requested_spacing_um / read_spacing_um)
-        )
+    read_plan = plan_spacing_read(
+        requested_spacing_um=requested_spacing_um,
+        level0_spacing_um=base_spacing_um,
+        level_downsamples=_level_downsample_pairs(getattr(tiling_result, "level_downsamples")),
+        target_size_px=(requested_tile_size_px, requested_tile_size_px),
+        tolerance=float(preprocessing.tolerance),
+    )
+    read_spacing_um = float(read_plan.read_spacing_um)
+    read_tile_size_px = int(read_plan.read_size_px[0])
     read_region_size_px = read_tile_size_px * multiple
     # Use the actual read geometry that produced the tile crop. When the
     # resolved spacing is considered equivalent to the requested spacing,

{slide2vec-4.6.0 → slide2vec-4.6.1}/slide2vec.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: slide2vec
-Version: 4.6.0
+Version: 4.6.1
 Summary: Embedding of whole slide images with Foundation Models
 Author-email: Clément Grisi <clement.grisi@radboudumc.nl>
 License-Expression: Apache-2.0
@@ -15,7 +15,7 @@ Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: hs2p[asap,cucim,openslide,sam2,vips]>=4.0.7
+Requires-Dist: hs2p[asap,cucim,openslide,sam2,vips]>=4.0.8
 Requires-Dist: omegaconf
 Requires-Dist: matplotlib
 Requires-Dist: numpy<2
@@ -65,7 +65,7 @@ Requires-Dist: numpy<2; extra == "fm"
 Requires-Dist: pandas; extra == "fm"
 Requires-Dist: pillow; extra == "fm"
 Requires-Dist: rich; extra == "fm"
-Requires-Dist: hs2p[asap,cucim,openslide,sam2,vips]>=4.0.7; extra == "fm"
+Requires-Dist: hs2p[asap,cucim,openslide,sam2,vips]>=4.0.8; extra == "fm"
 Requires-Dist: wandb; extra == "fm"
 Requires-Dist: torch<2.8,>=2.3; extra == "fm"
 Requires-Dist: torchvision>=0.18.0; extra == "fm"

{slide2vec-4.6.0 → slide2vec-4.6.1}/slide2vec.egg-info/requires.txt

@@ -1,4 +1,4 @@
-hs2p[asap,cucim,openslide,sam2,vips]>=4.0.7
+hs2p[asap,cucim,openslide,sam2,vips]>=4.0.8
 omegaconf
 matplotlib
 numpy<2
@@ -27,7 +27,7 @@ numpy<2
 pandas
 pillow
 rich
-hs2p[asap,cucim,openslide,sam2,vips]>=4.0.7
+hs2p[asap,cucim,openslide,sam2,vips]>=4.0.8
 wandb
 torch<2.8,>=2.3
 torchvision>=0.18.0

{slide2vec-4.6.0 → slide2vec-4.6.1}/tests/test_regression_inference.py

@@ -3892,6 +3892,7 @@ def test_resolve_hierarchical_geometry_scales_tile_first_under_spacing_mismatch(
         read_spacing_um=0.27,
         tile_size_lv0=3319,
         base_spacing_um=0.27,
+        level_downsamples=[1.0],
     )
 
     geometry = hierarchical.resolve_hierarchical_geometry(preprocessing, tiling_result)
@@ -3902,6 +3903,44 @@ def test_resolve_hierarchical_geometry_scales_tile_first_under_spacing_mismatch(
     assert geometry["tiles_per_region"] == 64
 
 
+def test_resolve_hierarchical_geometry_uses_hs2p_spacing_plan_for_tile_size(monkeypatch):
+    calls = []
+
+    def fake_plan_spacing_read(**kwargs):
+        calls.append(kwargs)
+        return SimpleNamespace(read_size_px=(415, 415), read_spacing_um=0.27)
+
+    monkeypatch.setattr(hierarchical, "plan_spacing_read", fake_plan_spacing_read)
+    preprocessing = PreprocessingConfig(
+        requested_spacing_um=0.5,
+        requested_tile_size_px=224,
+        requested_region_size_px=1792,
+        region_tile_multiple=8,
+    )
+    tiling_result = SimpleNamespace(
+        read_tile_size_px=3319,
+        read_spacing_um=0.27,
+        tile_size_lv0=3319,
+        base_spacing_um=0.27,
+        level_downsamples=[1.0, 2.0, 4.0],
+    )
+
+    geometry = hierarchical.resolve_hierarchical_geometry(preprocessing, tiling_result)
+
+    assert calls == [
+        {
+            "requested_spacing_um": 0.5,
+            "level0_spacing_um": 0.27,
+            "level_downsamples": [(1.0, 1.0), (2.0, 2.0), (4.0, 4.0)],
+            "target_size_px": (224, 224),
+            "tolerance": 0.05,
+        }
+    ]
+    assert geometry["read_tile_size_px"] == 415
+    assert geometry["read_region_size_px"] == 3320
+    assert geometry["tile_size_lv0"] == 415
+
+
 def test_resolve_hierarchical_geometry_keeps_level0_footprint_when_spacing_matches_base():
     import slide2vec.inference as inference
 
@@ -3916,6 +3955,7 @@ def test_resolve_hierarchical_geometry_keeps_level0_footprint_when_spacing_match
         read_spacing_um=0.486187607049942,
         tile_size_lv0=224,
         base_spacing_um=0.486187607049942,
+        level_downsamples=[1.0],
     )
 
     geometry = hierarchical.resolve_hierarchical_geometry(preprocessing, tiling_result)
@@ -4067,6 +4107,7 @@ def test_compute_hierarchical_embeddings_for_slide_encodes_flat_tile_batches_and
         requested_spacing_um=0.5,
         read_spacing_um=0.5,
         base_spacing_um=0.5,
+        level_downsamples=[1.0],
         read_level=0,
     )