added tile store benchmarking script

hs2p/api.py

@@ -24,7 +24,6 @@
 )
 from hs2p.configs.resolvers import build_default_sampling_spec
 from hs2p.progress import emit_progress, emit_progress_log
-from hs2p.stderr_utils import run_with_filtered_stderr
 from hs2p.wsi import (
     CoordinateOutputMode,
     CoordinateSelectionStrategy,
@@ -33,7 +32,7 @@
     overlay_mask_on_slide as _overlay_mask_on_slide,
     write_coordinate_preview,
 )
-from hs2p.wsi.backend import resolve_backend
+from hs2p.wsi.backend import coerce_wsd_path, resolve_backend
 
 
 @dataclass(frozen=True)
@@ -645,7 +644,7 @@ def _iter_cucim_tile_arrays_for_tar_extraction(
     if result.backend != "cucim":
         return None
     try:
-        cucim = run_with_filtered_stderr(lambda: importlib.import_module("cucim"))
+        cucim = importlib.import_module("cucim")
     except ModuleNotFoundError:
         warnings.warn(
             "CuCIM is unavailable for backend='cucim'; falling back to sequential wholeslidedata tile extraction.",
@@ -695,7 +694,10 @@ def _iter_wsd_tile_arrays_for_tar_extraction(
 ):
     import wholeslidedata as wsd
 
-    wsi = wsd.WholeSlideImage(result.image_path, backend=result.backend)
+    wsi = wsd.WholeSlideImage(
+        coerce_wsd_path(result.image_path, backend=result.backend),
+        backend=result.backend,
+    )
     read_step_px = _resolve_read_step_px(result)
     step_px_lv0 = _resolve_step_px_lv0(result)
     for read_plan in _iter_grouped_read_plans_for_tar_extraction(

hs2p/wsi/backend.py

@@ -24,6 +24,17 @@ def _normalize_path(path: Path | None) -> str | None:
     return str(Path(path))
 
 
+def coerce_wsd_path(path: Path | str, *, backend: str) -> Path | str:
+    """Return a path object compatible with the requested WSD backend.
+
+    CuCIM-backed WSD opens require plain strings, while the other backends
+    accept pathlib objects.
+    """
+    if backend == "cucim":
+        return str(path)
+    return Path(path)
+
+
 def _is_cucim_supported_format(wsi_path: Path) -> bool:
     suffix = wsi_path.suffix.lower()
     return suffix in CUCIM_SUPPORTED_SUFFIXES
@@ -37,9 +48,12 @@ def _backend_can_open_slide(
     backend: str,
 ) -> bool:
     try:
-        wsd.WholeSlideImage(Path(wsi_path), backend=backend)
+        wsd.WholeSlideImage(coerce_wsd_path(wsi_path, backend=backend), backend=backend)
         if mask_path is not None:
-            wsd.WholeSlideImage(Path(mask_path), backend=backend)
+            wsd.WholeSlideImage(
+                coerce_wsd_path(mask_path, backend=backend),
+                backend=backend,
+            )
         return True
     except Exception:
         return False

hs2p/wsi/wsi.py

@@ -11,7 +11,7 @@
 from PIL import Image
 
 from hs2p.configs import FilterConfig, SegmentationConfig, TilingConfig
-from hs2p.wsi.backend import resolve_backend
+from hs2p.wsi.backend import coerce_wsd_path, resolve_backend
 from hs2p.wsi.utils import HasEnoughTissue, ResolvedTileGeometry
 
 # ignore all warnings from wholeslidedata
@@ -78,7 +78,10 @@ def __init__(
         self.requested_backend = backend
         selection = resolve_backend(backend, wsi_path=path, mask_path=mask_path)
         self.backend = selection.backend
-        self.wsi = wsd.WholeSlideImage(path, backend=self.backend)
+        self.wsi = wsd.WholeSlideImage(
+            coerce_wsd_path(path, backend=self.backend),
+            backend=self.backend,
+        )
 
         self._scaled_contours_cache = {}  # add a cache for scaled contours
         self._scaled_holes_cache = {}  # add a cache for scaled holes
@@ -97,7 +100,10 @@ def __init__(
                 raise ValueError(
                     "sampling_spec is required when loading a mask-backed slide"
                 )
-            self.mask = wsd.WholeSlideImage(mask_path, backend=self.backend)
+            self.mask = wsd.WholeSlideImage(
+                coerce_wsd_path(mask_path, backend=self.backend),
+                backend=self.backend,
+            )
             self.seg_level = self.load_segmentation(
                 segment_params,
                 sampling_spec=sampling_spec,

scripts/benchmark_tile_read_strategies.py

@@ -26,7 +26,6 @@
     TimeRemainingColumn,
 )
 
-from hs2p.stderr_utils import run_with_filtered_stderr
 
 MODE_CONFIG = {
     "regular_wsd": {
@@ -380,7 +379,7 @@ def benchmark_wsd_mode(
 
 def _require_cucim():
     try:
-        return run_with_filtered_stderr(lambda: importlib.import_module("cucim"))
+        return importlib.import_module("cucim")
     except ModuleNotFoundError as exc:
         raise RuntimeError(
             "CuCIM is required for the requested benchmark modes but is not installed."
@@ -398,7 +397,7 @@ def benchmark_cucim_batch_mode(
     from hs2p.benchmarking import group_read_plans_by_read_size
 
     cucim = _require_cucim()
-    cu_image = run_with_filtered_stderr(lambda: cucim.CuImage(str(result.image_path)))
+    cu_image = cucim.CuImage(str(result.image_path))
     tile_size_px = int(result.read_tile_size_px)
     checksum = 0
     tile_count = 0