reflect hs2p change to supress cufile logging

README.md

@@ -45,8 +45,8 @@ from slide2vec import ExecutionOptions, Pipeline, PreprocessingConfig
 pipeline = Pipeline(
     model=model,
     preprocessing=PreprocessingConfig(
-        target_spacing_um=0.5,
-        target_tile_size_px=224,
+        requested_spacing_um=0.5,
+        requested_tile_size_px=224,
         tissue_threshold=0.1,
     ),
     execution=ExecutionOptions(output_dir="outputs/demo"),
@@ -62,8 +62,8 @@ Tile embeddings can be spatially grouped into regions for downstream models that
 
 ```python
 preprocessing = PreprocessingConfig(
-    target_spacing_um=0.5,
-    target_tile_size_px=224,
+    requested_spacing_um=0.5,
+    requested_tile_size_px=224,
     region_tile_multiple=6,  # 6x6 tiles per region
 )
 embedded = model.embed_slide("/path/to/slide.svs", preprocessing=preprocessing)

docs/python-api.md

@@ -49,8 +49,8 @@ from slide2vec import Model, PreprocessingConfig
 model = Model.from_preset("virchow2")
 preprocessing = PreprocessingConfig(
     backend="auto",
-    target_spacing_um=0.5,
-    target_tile_size_px=224,
+    requested_spacing_um=0.5,
+    requested_tile_size_px=224,
     tissue_threshold=0.1,
     segmentation={"downsample": 64},
     filtering={"ref_tile_size": 224},
@@ -65,15 +65,15 @@ embedded = model.embed_slide("/path/to/slide.svs", preprocessing=preprocessing)
 
 Common fields:
 
-- `target_spacing_um`
-- `target_tile_size_px`
+- `requested_spacing_um`
+- `requested_tile_size_px`
 - `tissue_threshold`
-- `backend` — `"auto"`, `"cucim"`, `"openslide"`, `"vips"`, or `"asap"`
-- `on_the_fly` — read tiles directly from WSI during embedding (default `True`)
-- `use_supertiles` — group tiles into spatial blocks to reduce WSI read calls (default `True`)
-- `read_coordinates_from` — reuse pre-extracted coordinates
-- `read_tiles_from` — reuse pre-extracted tile tar archives
-- `resume` — resume from a previous tiling run (default `False`)
+- `backend` - `"auto"`, `"cucim"`, `"openslide"`, `"vips"`, or `"asap"`
+- `on_the_fly` - read tiles directly from WSI during embedding (default `True`)
+- `use_supertiles` - group tiles into spatial blocks to reduce WSI read calls (default `True`)
+- `read_coordinates_from` - reuse pre-extracted coordinates
+- `read_tiles_from` - reuse pre-extracted tile tar archives
+- `resume` - resume from a previous tiling run (default `False`)
 - `preview`
 
 For hierarchical extraction, see the [dedicated section](#hierarchical-feature-extraction) below.
@@ -100,15 +100,15 @@ Common fields:
 
 - `batch_size`
 - `num_gpus`
-- `precision` — `"fp16"`, `"bf16"`, `"fp32"`, or `None` (auto-determined from model)
-- `num_workers` — DataLoader workers (`None` means auto; this resolves to the job CPU budget, capped by SLURM and 64, except cuCIM on-the-fly mode derives `cpu_budget // num_cucim_workers`)
-- `num_preprocessing_workers` — hs2p tiling workers (default: all CPUs available to the job, capped by SLURM when present and limited to 64)
-- `prefetch_factor` — DataLoader prefetch factor (default `4`)
-- `persistent_workers` — keep DataLoader workers alive across batches (default `True`)
+- `precision` - `"fp16"`, `"bf16"`, `"fp32"`, or `None` (auto-determined from model)
+- `num_workers` - DataLoader workers (`None` means auto; this resolves to the job CPU budget, capped by SLURM and 64, except cuCIM on-the-fly mode derives `cpu_budget // num_cucim_workers`)
+- `num_preprocessing_workers` - hs2p tiling workers (default: all CPUs available to the job, capped by SLURM when present and limited to 64)
+- `prefetch_factor` - DataLoader prefetch factor (default `4`)
+- `persistent_workers` - keep DataLoader workers alive across batches (default `True`)
 - `output_dir`
-- `output_format` — `"pt"` (default) or `"npz"`
-- `save_tile_embeddings` — persist tile embeddings for slide-level models (default `False`)
-- `save_latents` — persist latent representations when available (default `False`)
+- `output_format` - `"pt"` (default) or `"npz"`
+- `save_tile_embeddings` - persist tile embeddings for slide-level models (default `False`)
+- `save_latents` - persist latent representations when available (default `False`)
 
 `num_gpus` defaults to all available GPUs. `embed_slide(...)` uses tile sharding for one slide, and `embed_slides(...)` balances whole slides across GPUs while preserving input order.
 
@@ -125,19 +125,19 @@ from slide2vec import Model, PreprocessingConfig
 
 model = Model.from_preset("virchow2")
 preprocessing = PreprocessingConfig(
-    target_spacing_um=0.5,
-    target_tile_size_px=224,
+    requested_spacing_um=0.5,
+    requested_tile_size_px=224,
     region_tile_multiple=6,  # 6x6 tiles per region
 )
 embedded = model.embed_slide("/path/to/slide.svs", preprocessing=preprocessing)
 ```
 
 Config fields:
 
-- `region_tile_multiple` — region grid width/height in tiles (e.g., `6` means 6x6 = 36 tiles per region; must be >= 2)
-- `target_region_size_px` — explicit parent region size in pixels; auto-derived from `target_tile_size_px * region_tile_multiple` if omitted
+- `region_tile_multiple` - region grid width/height in tiles (e.g., `6` means 6x6 = 36 tiles per region; must be >= 2)
+- `requested_region_size_px` - explicit parent region size in pixels; auto-derived from `requested_tile_size_px * region_tile_multiple` if omitted
 
-When the selected read spacing differs from `target_spacing_um`, hierarchical extraction resolves effective geometry tile-first: it scales `target_tile_size_px` to the effective read spacing, then derives the effective parent region as `effective_tile_size_px * region_tile_multiple`. This keeps unrolled subtile geometry aligned with the model-facing tile size contract under spacing-driven rounding.
+When the selected read spacing differs from `requested_spacing_um`, hierarchical extraction resolves geometry tile-first: it scales `requested_tile_size_px` to the read spacing, then derives the read parent region as `read_tile_size_px * region_tile_multiple`. This keeps unrolled subtile geometry aligned with the model-facing tile size contract under spacing-driven rounding.
 
 When persisted via `Pipeline`, hierarchical artifacts are written to `hierarchical_embeddings/` and `RunResult` includes a `hierarchical_artifacts` list.
 
@@ -152,8 +152,8 @@ from slide2vec import ExecutionOptions, Model, Pipeline, PreprocessingConfig
 
 model = Model.from_preset("virchow2")
 preprocessing = PreprocessingConfig(
-    target_spacing_um=0.5,
-    target_tile_size_px=224,
+    requested_spacing_um=0.5,
+    requested_tile_size_px=224,
     tissue_threshold=0.1,
 )
 pipeline = Pipeline(

pyproject.toml

@@ -21,7 +21,7 @@ classifiers = [
     "Programming Language :: Python :: 3.13",
 ]
 dependencies = [
-    "hs2p[asap,cucim,openslide,vips]>=3.1.4",
+    "hs2p[asap,cucim,openslide,vips]>=3.2.0",
     "omegaconf",
     "matplotlib",
     "numpy<2",
@@ -85,7 +85,7 @@ fm = [
     "pandas",
     "pillow",
     "rich",
-    "hs2p[asap,cucim,openslide,vips]>=3.1.4",
+    "hs2p[asap,cucim,openslide,vips]>=3.2.0",
     "wandb",
     "torch>=2.3,<2.8",
     "torchvision>=0.18.0",

scripts/benchmark_embedding_throughput.py

@@ -787,8 +787,8 @@ def _build_model_pipeline_from_config(config: dict[str, Any]):
     preview = dict(tiling_cfg.get("preview", {}))
     preprocessing = PreprocessingConfig(
         backend=str(tiling_cfg.get("backend", "asap")),
-        target_spacing_um=float(params.get("target_spacing_um", 0.5)),
-        target_tile_size_px=int(params.get("target_tile_size_px", 224)),
+        requested_spacing_um=float(params.get("requested_spacing_um", 0.5)),
+        requested_tile_size_px=int(params.get("requested_tile_size_px", 224)),
         tolerance=float(params.get("tolerance", 0.05)),
         overlap=float(params.get("overlap", 0.0)),
         tissue_threshold=float(params.get("tissue_threshold", 0.01)),

scripts/benchmark_end_to_end_paths.py

@@ -227,9 +227,9 @@ def _default_base_config(
             "read_coordinates_from": None,
             "read_tiles_from": None,
             "params": {
-                "target_spacing_um": 0.5,
+                "requested_spacing_um": 0.5,
                 "tolerance": 0.05,
-                "target_tile_size_px": 256,
+                "requested_tile_size_px": 256,
                 "overlap": 0.0,
                 "tissue_threshold": 0.01,
                 "drop_holes": False,
@@ -440,8 +440,8 @@ def _build_pipeline_from_config_dict(config: dict[str, Any]):
 
     preprocessing = PreprocessingConfig(
         backend=str(tiling_cfg.get("backend", "cucim")),
-        target_spacing_um=float(params.get("target_spacing_um", 0.5)),
-        target_tile_size_px=int(params.get("target_tile_size_px", 256)),
+        requested_spacing_um=float(params.get("requested_spacing_um", 0.5)),
+        requested_tile_size_px=int(params.get("requested_tile_size_px", 256)),
         tolerance=float(params.get("tolerance", 0.05)),
         overlap=float(params.get("overlap", 0.0)),
         tissue_threshold=float(params.get("tissue_threshold", 0.01)),

scripts/benchmark_tile_read_strategies.py

@@ -281,9 +281,9 @@ def _default_base_config(
             "read_coordinates_from": None,
             "read_tiles_from": None,
             "params": {
-                "target_spacing_um": 0.5,
+                "requested_spacing_um": 0.5,
                 "tolerance": 0.05,
-                "target_tile_size_px": 224,
+                "requested_tile_size_px": 224,
                 "overlap": 0.0,
                 "tissue_threshold": 0.1,
                 "drop_holes": False,
@@ -510,8 +510,8 @@ def _build_pipeline_from_config_dict(config: dict[str, Any]):
 
     preprocessing = PreprocessingConfig(
         backend=str(tiling_cfg.get("backend", "cucim")),
-        target_spacing_um=float(params.get("target_spacing_um", 0.5)),
-        target_tile_size_px=int(params.get("target_tile_size_px", 256)),
+        requested_spacing_um=float(params.get("requested_spacing_um", 0.5)),
+        requested_tile_size_px=int(params.get("requested_tile_size_px", 256)),
         tolerance=float(params.get("tolerance", 0.05)),
         overlap=float(params.get("overlap", 0.0)),
         tissue_threshold=float(params.get("tissue_threshold", 0.01)),

scripts/generate_gt.py

@@ -27,9 +27,9 @@
 
 # Must stay in sync with test_output_consistency.py
 TILING_PARAMS = dict(
-    target_spacing_um=0.5,
+    requested_spacing_um=0.5,
     tolerance=0.07,
-    target_tile_size_px=224,
+    requested_tile_size_px=224,
     overlap=0.0,
     tissue_threshold=0.1,
     drop_holes=False,

slide2vec/api.py

@@ -42,9 +42,9 @@ class SlideLike(Protocol):
 @dataclass(frozen=True, kw_only=True)
 class PreprocessingConfig:
     backend: str = "auto"
-    target_spacing_um: float | None = None
-    target_tile_size_px: int | None = None
-    target_region_size_px: int | None = None
+    requested_spacing_um: float | None = None
+    requested_tile_size_px: int | None = None
+    requested_region_size_px: int | None = None
     region_tile_multiple: int | None = None
     tolerance: float = 0.05
     overlap: float = 0.0
@@ -75,11 +75,11 @@ def from_config(cls, cfg: Any) -> "PreprocessingConfig":
         preview_downsample = int(preview_cfg.downsample)
         return cls(
             backend=tiling.backend,
-            target_spacing_um=float(tiling.params.target_spacing_um),
-            target_tile_size_px=int(tiling.params.target_tile_size_px),
-            target_region_size_px=(
+            requested_spacing_um=float(tiling.params.requested_spacing_um),
+            requested_tile_size_px=int(tiling.params.requested_tile_size_px),
+            requested_region_size_px=(
                 int(v)
-                if (v := getattr(tiling.params, "target_region_size_px", None)) is not None
+                if (v := getattr(tiling.params, "requested_region_size_px", None)) is not None
                 else None
             ),
             region_tile_multiple=(
@@ -454,28 +454,28 @@ def ensure_defaults() -> tuple[int, float]:
         return defaults
 
     if preprocessing is None:
-        target_tile_size_px, target_spacing_um = ensure_defaults()
+        requested_tile_size_px, requested_spacing_um = ensure_defaults()
         return _resolve_hierarchical_preprocessing(
             PreprocessingConfig(
                 backend="auto",
-                target_spacing_um=target_spacing_um,
-                target_tile_size_px=target_tile_size_px,
+                requested_spacing_um=requested_spacing_um,
+                requested_tile_size_px=requested_tile_size_px,
             )
         )
 
-    target_spacing_um = preprocessing.target_spacing_um
-    target_tile_size_px = preprocessing.target_tile_size_px
-    if target_spacing_um is None or target_tile_size_px is None:
+    requested_spacing_um = preprocessing.requested_spacing_um
+    requested_tile_size_px = preprocessing.requested_tile_size_px
+    if requested_spacing_um is None or requested_tile_size_px is None:
         default_tile_size_px, default_spacing_um = ensure_defaults()
-        if target_spacing_um is None:
-            target_spacing_um = default_spacing_um
-        if target_tile_size_px is None:
-            target_tile_size_px = default_tile_size_px
+        if requested_spacing_um is None:
+            requested_spacing_um = default_spacing_um
+        if requested_tile_size_px is None:
+            requested_tile_size_px = default_tile_size_px
     return _resolve_hierarchical_preprocessing(
         replace(
             preprocessing,
-            target_spacing_um=target_spacing_um,
-            target_tile_size_px=target_tile_size_px,
+            requested_spacing_um=requested_spacing_um,
+            requested_tile_size_px=requested_tile_size_px,
         )
     )
 
@@ -484,7 +484,7 @@ def _default_preprocessing_from_registry(name: str | None) -> tuple[int, float]:
     if not name or name not in encoder_registry:
         raise ValueError(
             "Cannot infer preprocessing defaults without a registered model. "
-            "Pass preprocessing.target_spacing_um and preprocessing.target_tile_size_px explicitly."
+            "Pass preprocessing.requested_spacing_um and preprocessing.requested_tile_size_px explicitly."
         )
 
     defaults = resolve_preprocessing_defaults(name)
@@ -499,7 +499,7 @@ def _validate_model_config(
     name = model.name
     if name not in encoder_registry:
         return
-    if preprocessing.region_tile_multiple is not None or preprocessing.target_region_size_px is not None:
+    if preprocessing.region_tile_multiple is not None or preprocessing.requested_region_size_px is not None:
         info = encoder_registry.info(name)
         if info["level"] != "tile":
             raise ValueError("Hierarchical preprocessing is only supported for tile encoders")
@@ -508,8 +508,8 @@ def _validate_model_config(
     precision = None if on_cpu or execution is None else execution.precision
     validate_encoder_config(
         name,
-        target_tile_size_px=preprocessing.target_tile_size_px,
-        target_spacing_um=preprocessing.target_spacing_um,
+        requested_tile_size_px=preprocessing.requested_tile_size_px,
+        requested_spacing_um=preprocessing.requested_spacing_um,
         precision=precision,
         output_variant=model._output_variant,
         allow_non_recommended=bool(model.allow_non_recommended_settings),
@@ -518,32 +518,32 @@ def _validate_model_config(
 
 def _resolve_hierarchical_preprocessing(preprocessing: PreprocessingConfig) -> PreprocessingConfig:
     multiple = preprocessing.region_tile_multiple
-    target_region_size_px = preprocessing.target_region_size_px
+    requested_region_size_px = preprocessing.requested_region_size_px
     if multiple is not None:
         multiple = int(multiple)
         if multiple < 2:
             raise ValueError("region_tile_multiple must be at least 2")
-    if multiple is None and target_region_size_px is None:
+    if multiple is None and requested_region_size_px is None:
         return preprocessing
-    if preprocessing.target_tile_size_px is None:
+    if preprocessing.requested_tile_size_px is None:
         raise ValueError(
-            "target_tile_size_px must be resolved before deriving hierarchical region geometry"
+            "requested_tile_size_px must be resolved before deriving hierarchical region geometry"
         )
-    if target_region_size_px is None:
-        target_region_size_px = int(preprocessing.target_tile_size_px) * int(multiple)
+    if requested_region_size_px is None:
+        requested_region_size_px = int(preprocessing.requested_tile_size_px) * int(multiple)
     elif multiple is None:
-        if int(target_region_size_px) % int(preprocessing.target_tile_size_px) != 0:
+        if int(requested_region_size_px) % int(preprocessing.requested_tile_size_px) != 0:
             raise ValueError(
-                "target_region_size_px must be an exact multiple of target_tile_size_px"
+                "requested_region_size_px must be an exact multiple of requested_tile_size_px"
             )
-        multiple = int(target_region_size_px) // int(preprocessing.target_tile_size_px)
-    elif int(target_region_size_px) != int(preprocessing.target_tile_size_px) * int(multiple):
+        multiple = int(requested_region_size_px) // int(preprocessing.requested_tile_size_px)
+    elif int(requested_region_size_px) != int(preprocessing.requested_tile_size_px) * int(multiple):
         raise ValueError(
-            "target_region_size_px must match target_tile_size_px * region_tile_multiple"
+            "requested_region_size_px must match requested_tile_size_px * region_tile_multiple"
         )
     return replace(
         preprocessing,
-        target_region_size_px=int(target_region_size_px),
+        requested_region_size_px=int(requested_region_size_px),
         region_tile_multiple=int(multiple),
     )