slide2vec 7.0.0__tar.gz → 7.1.0__tar.gz

{slide2vec-7.0.0 → slide2vec-7.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: slide2vec
-Version: 7.0.0
+Version: 7.1.0
 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,tifffile,vips]>=6.0.0
+Requires-Dist: hs2p[asap,cucim,openslide,sam2,tifffile,vips]>=6.1.0
 Requires-Dist: omegaconf
 Requires-Dist: matplotlib
 Requires-Dist: numpy<2
@@ -75,7 +75,7 @@ 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,tifffile,vips]>=6.0.0; extra == "fm"
+Requires-Dist: hs2p[asap,cucim,openslide,sam2,tifffile,vips]>=6.1.0; extra == "fm"
 Requires-Dist: wandb; extra == "fm"
 Requires-Dist: torch<2.8,>=2.3; extra == "fm"
 Requires-Dist: torchvision>=0.18.0; extra == "fm"
@@ -136,17 +136,22 @@ For gated models such as Virchow2, request access on the model's Hugging Face pa
 ## Embed a slide
 
 ```python
+from hs2p import TilingConfig
 from slide2vec import Model, PreprocessingConfig
 
 model = Model.from_preset("virchow2")
-preprocessing = PreprocessingConfig(requested_spacing_um=0.5)
+preprocessing = PreprocessingConfig(
+    tiling=TilingConfig(
+        requested_spacing_um=0.5, requested_tile_size_px=224, tolerance=0.05, overlap=0.0
+    ),
+)
 embedded = model.embed_slide("/path/to/slide.svs", preprocessing=preprocessing)
 
 tile_embeddings = embedded.tile_embeddings  # (N, 2560)
 x, y = embedded.x, embedded.y               # level-0 tile coordinates
 ```
 
-The preset supplies tile size and precision defaults. Declare spacing explicitly for models such as Virchow2 that support several scales. Use `list_models()` to list presets, or filter with `list_models("tile")`, `list_models("slide")`, or `list_models("patient")`.
+`tiling` is an hs2p `TilingConfig`. Leave it unset to take spacing and tile size from the preset; Virchow2 supports several scales, so it needs an explicit one. The preset also supplies precision. Use `list_models()` to list presets, or filter with `list_models("tile")`, `list_models("slide")`, or `list_models("patient")`.
 
 See [getting started](https://clemsgrs.github.io/slide2vec/getting-started.html) for preprocessing and execution settings, and the [API guide](https://clemsgrs.github.io/slide2vec/api.html) for patient embeddings, image inputs, and dense grids.
 
@@ -163,11 +168,11 @@ slide-2,/data/slide-2.svs
 Optional `mask_path` and `spacing_at_level_0` columns supply a mask or correct missing or incorrect level-0 spacing. Patient-level models also require `patient_id`; see the [manifest schema](https://clemsgrs.github.io/slide2vec/manifest.html).
 
 ```python
-from slide2vec import ExecutionOptions, Model, Pipeline, PreprocessingConfig
+from slide2vec import ExecutionOptions, Model, Pipeline
 
 pipeline = Pipeline(
     model=Model.from_preset("virchow2"),
-    preprocessing=PreprocessingConfig(requested_spacing_um=0.5),
+    preprocessing=preprocessing,  # from the example above
     execution=ExecutionOptions(output_dir="outputs/run"),
 )
 result = pipeline.run(manifest_path="/path/to/slides.csv")

{slide2vec-7.0.0 → slide2vec-7.1.0}/README.md

@@ -20,17 +20,22 @@ For gated models such as Virchow2, request access on the model's Hugging Face pa
 ## Embed a slide
 
 ```python
+from hs2p import TilingConfig
 from slide2vec import Model, PreprocessingConfig
 
 model = Model.from_preset("virchow2")
-preprocessing = PreprocessingConfig(requested_spacing_um=0.5)
+preprocessing = PreprocessingConfig(
+    tiling=TilingConfig(
+        requested_spacing_um=0.5, requested_tile_size_px=224, tolerance=0.05, overlap=0.0
+    ),
+)
 embedded = model.embed_slide("/path/to/slide.svs", preprocessing=preprocessing)
 
 tile_embeddings = embedded.tile_embeddings  # (N, 2560)
 x, y = embedded.x, embedded.y               # level-0 tile coordinates
 ```
 
-The preset supplies tile size and precision defaults. Declare spacing explicitly for models such as Virchow2 that support several scales. Use `list_models()` to list presets, or filter with `list_models("tile")`, `list_models("slide")`, or `list_models("patient")`.
+`tiling` is an hs2p `TilingConfig`. Leave it unset to take spacing and tile size from the preset; Virchow2 supports several scales, so it needs an explicit one. The preset also supplies precision. Use `list_models()` to list presets, or filter with `list_models("tile")`, `list_models("slide")`, or `list_models("patient")`.
 
 See [getting started](https://clemsgrs.github.io/slide2vec/getting-started.html) for preprocessing and execution settings, and the [API guide](https://clemsgrs.github.io/slide2vec/api.html) for patient embeddings, image inputs, and dense grids.
 
@@ -47,11 +52,11 @@ slide-2,/data/slide-2.svs
 Optional `mask_path` and `spacing_at_level_0` columns supply a mask or correct missing or incorrect level-0 spacing. Patient-level models also require `patient_id`; see the [manifest schema](https://clemsgrs.github.io/slide2vec/manifest.html).
 
 ```python
-from slide2vec import ExecutionOptions, Model, Pipeline, PreprocessingConfig
+from slide2vec import ExecutionOptions, Model, Pipeline
 
 pipeline = Pipeline(
     model=Model.from_preset("virchow2"),
-    preprocessing=PreprocessingConfig(requested_spacing_um=0.5),
+    preprocessing=preprocessing,  # from the example above
     execution=ExecutionOptions(output_dir="outputs/run"),
 )
 result = pipeline.run(manifest_path="/path/to/slides.csv")

{slide2vec-7.0.0 → slide2vec-7.1.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "slide2vec"
-version = "7.0.0"
+version = "7.1.0"
 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,tifffile,vips]>=6.0.0",
+    "hs2p[asap,cucim,openslide,sam2,tifffile,vips]>=6.1.0",
     "omegaconf",
     "matplotlib",
     "numpy<2",
@@ -100,7 +100,7 @@ fm = [
     "pandas",
     "pillow",
     "rich",
-    "hs2p[asap,cucim,openslide,sam2,tifffile,vips]>=6.0.0",
+    "hs2p[asap,cucim,openslide,sam2,tifffile,vips]>=6.1.0",
     "wandb",
     "torch>=2.3,<2.8",
     "torchvision>=0.18.0",
@@ -180,7 +180,7 @@ no_implicit_reexport = true
 max-line-length = 160
 
 [tool.bumpver]
-current_version = "7.0.0"
+current_version = "7.1.0"
 version_pattern = "MAJOR.MINOR.PATCH"
 commit = false
 tag = false

{slide2vec-7.0.0 → slide2vec-7.1.0}/slide2vec/__init__.py

@@ -28,17 +28,25 @@ from slide2vec.runtime.dense_encode import DenseEncodeGeometry, DenseEncodeKit
 from slide2vec.runtime.feature_identity import MISSING_FIELD
 from slide2vec.encoders import (
     EncoderProviderDiagnostic,
+    TileEncoder,
+    TimmTileEncoder,
+    TorchTileEncoder,
     list_encoder_provider_diagnostics,
+    register_encoder,
 )
 
 
-__version__ = "7.0.0"
+__version__ = "7.1.0"
 
 __all__ = [
     "Model",
     "list_models",
     "EncoderProviderDiagnostic",
     "list_encoder_provider_diagnostics",
+    "register_encoder",
+    "TileEncoder",
+    "TimmTileEncoder",
+    "TorchTileEncoder",
     "Pipeline",
     "PreprocessingConfig",
     "DenseOptions",