slide2vec 4.6.2__tar.gz → 4.6.4__tar.gz

{slide2vec-4.6.2 → slide2vec-4.6.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: slide2vec
-Version: 4.6.2
+Version: 4.6.4
 Summary: Embedding of whole slide images with Foundation Models
 Author-email: Clément Grisi <clement.grisi@radboudumc.nl>
 License-Expression: Apache-2.0

{slide2vec-4.6.2 → slide2vec-4.6.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "slide2vec"
-version = "4.6.2"
+version = "4.6.4"
 description = "Embedding of whole slide images with Foundation Models"
 readme = "README.md"
 requires-python = ">=3.10"
@@ -164,7 +164,7 @@ no_implicit_reexport = true
 max-line-length = 160
 
 [tool.bumpver]
-current_version = "4.6.2"
+current_version = "4.6.4"
 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-4.6.2 → slide2vec-4.6.4}/slide2vec/__init__.py

@@ -11,7 +11,7 @@ from slide2vec.api import (
 from slide2vec.artifacts import HierarchicalEmbeddingArtifact, SlideEmbeddingArtifact, TileEmbeddingArtifact
 
 
-__version__ = "4.6.2"
+__version__ = "4.6.4"
 
 __all__ = [
     "Model",

{slide2vec-4.6.2 → slide2vec-4.6.4}/slide2vec/encoders/models/conch.py

@@ -141,6 +141,13 @@ class CONCH(TileEncoder):
     def encode_dim(self) -> int:
         return 512
 
+    @property
+    def patch_size(self) -> tuple[int, int]:
+        # The CONCH vision trunk is a timm ViT-B/16; expose its patch size so the
+        # dense path can resolve the token grid. open_clip builds the trunk without
+        # dynamic_img_size, so dense extraction must use the native 448 window.
+        return _patch_size_from_trunk(self._model.visual.trunk)
+
     @property
     def device(self) -> torch.device:
         return self._device
@@ -204,6 +211,11 @@ class CONCHv15(TileEncoder):
     def encode_dim(self) -> int:
         return 768
 
+    @property
+    def patch_size(self) -> tuple[int, int]:
+        # CONCHv15's TITAN trunk is a timm ViT; expose its patch size for the dense path.
+        return _patch_size_from_trunk(self._model.trunk)
+
     @property
     def device(self) -> torch.device:
         return self._device

{slide2vec-4.6.2 → slide2vec-4.6.4}/slide2vec/encoders/models/hibou.py

@@ -123,6 +123,12 @@ class _HibouBase(TileEncoder):
     def encode_dim(self) -> int:
         return self._encode_dim
 
+    @property
+    def patch_size(self) -> tuple[int, int]:
+        # HF Dinov2-style config carries the patch size; expose it for the dense path.
+        patch = int(self._model.config.patch_size)
+        return patch, patch
+
     @property
     def device(self) -> torch.device:
         return self._device

{slide2vec-4.6.2 → slide2vec-4.6.4}/slide2vec/encoders/models/midnight.py

@@ -124,6 +124,12 @@ class Midnight(TileEncoder):
     def encode_dim(self) -> int:
         return 3072
 
+    @property
+    def patch_size(self) -> tuple[int, int]:
+        # HF Dinov2-style config carries the patch size; expose it for the dense path.
+        patch = int(self._model.config.patch_size)
+        return patch, patch
+
     @property
     def device(self) -> torch.device:
         return self._device

{slide2vec-4.6.2 → slide2vec-4.6.4}/slide2vec/encoders/models/musk.py

@@ -114,6 +114,11 @@ class MUSK(TileEncoder):
     def encode_dim(self) -> int:
         return 2048 if self._output_variant == "ms_aug" else 1024  # cls
 
+    @property
+    def patch_size(self) -> tuple[int, int]:
+        # BEiT3 vision embedding carries the patch size; expose it for the dense path.
+        return _as_hw(self._model.beit3.vision_embed.patch_size)
+
     @property
     def device(self) -> torch.device:
         return self._device

{slide2vec-4.6.2 → slide2vec-4.6.4}/slide2vec/utils/config.py

@@ -41,6 +41,21 @@ def _encoder_derived_cfg(model_name: str) -> dict:
     }
 
 
+def _fill_null_encoder_defaults(cfg, encoder_defaults: dict) -> None:
+    """Fill null leaves with encoder defaults after user/CLI config merging."""
+    defaults_cfg = OmegaConf.create(encoder_defaults)
+    for path in (
+        "tiling.params.requested_tile_size_px",
+        "tiling.params.requested_spacing_um",
+        "speed.precision",
+    ):
+        if OmegaConf.select(cfg, path) is not None:
+            continue
+        default_value = OmegaConf.select(defaults_cfg, path)
+        if default_value is not None:
+            OmegaConf.update(cfg, path, default_value, merge=False)
+
+
 def validate_model_recommended_settings(cfg, *, run_on_cpu: bool = False) -> None:
     from slide2vec.encoders.registry import encoder_registry
     from slide2vec.encoders.validation import validate_encoder_config
@@ -88,14 +103,17 @@ def get_cfg_from_args(args):
 
     default_cfg = OmegaConf.create(default_config)
     model_name = OmegaConf.select(requested_cfg, "model.name")
-    spacing = OmegaConf.select(requested_cfg, "tiling.params.requested_spacing_um")
-    tile_size = OmegaConf.select(requested_cfg, "tiling.params.requested_tile_size_px")
-    if model_name and (spacing is None or tile_size is None):
-        encoder_defaults = _encoder_derived_cfg(model_name)
-        if encoder_defaults:
-            default_cfg = OmegaConf.merge(default_cfg, OmegaConf.create(encoder_defaults))
-
     cfg = OmegaConf.merge(default_cfg, user_cfg, cli_cfg)
+    if model_name and any(
+        OmegaConf.select(cfg, path) is None
+        for path in (
+            "tiling.params.requested_tile_size_px",
+            "tiling.params.requested_spacing_um",
+            "speed.precision",
+        )
+    ):
+        encoder_defaults = _encoder_derived_cfg(model_name)
+        _fill_null_encoder_defaults(cfg, encoder_defaults)
     OmegaConf.resolve(cfg)
     validate_model_recommended_settings(cfg, run_on_cpu=bool(getattr(args, "run_on_cpu", False)))
     return cfg

{slide2vec-4.6.2 → slide2vec-4.6.4}/slide2vec.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: slide2vec
-Version: 4.6.2
+Version: 4.6.4
 Summary: Embedding of whole slide images with Foundation Models
 Author-email: Clément Grisi <clement.grisi@radboudumc.nl>
 License-Expression: Apache-2.0

{slide2vec-4.6.2 → slide2vec-4.6.4}/tests/test_regression_core.py

@@ -79,6 +79,34 @@ def test_get_cfg_from_args_fills_missing_preprocessing_from_single_spacing_model
     assert cfg.tiling.params.requested_tile_size_px == 448
 
 
+def test_get_cfg_from_args_fills_null_spacing_from_model_default(tmp_path: Path):
+    pytest.importorskip("omegaconf")
+
+    from slide2vec.utils.config import get_cfg_from_args
+
+    cfg_path = tmp_path / "config.yaml"
+    cfg_path.write_text(
+        "\n".join(
+            [
+                "csv: /tmp/slides.csv",
+                "output_dir: /tmp/output",
+                "model:",
+                "  name: conchv15",
+                "tiling:",
+                "  params:",
+                "    requested_spacing_um:",
+                "    requested_tile_size_px: 448",
+            ]
+        )
+    )
+    args = SimpleNamespace(config_file=str(cfg_path), output_dir=None, opts=[], run_on_cpu=False)
+
+    cfg = get_cfg_from_args(args)
+
+    assert cfg.tiling.params.requested_spacing_um == pytest.approx(0.5)
+    assert cfg.tiling.params.requested_tile_size_px == 448
+
+
 def test_get_cfg_from_args_rejects_models_with_ambiguous_spacing_defaults(tmp_path: Path):
     pytest.importorskip("omegaconf")