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add ability to read existing coordinate files #34

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Merged
clemsgrs merged 2 commits into from
Jan 5, 2026
Merged

add ability to read existing coordinate files #34

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2533a79
add ability to run existing coordinate files
clemsgrs Jan 5, 2026
4d0ee39
tiny improvement
clemsgrs Jan 5, 2026
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28 changes: 23 additions & 5 deletions hs2p/tiling.py
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Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,21 @@ def process_slide(
Process a single slide: extract tile coordinates and visualize if needed.
"""
wsi_name = wsi_path.stem.replace(" ", "_")
if cfg.tiling.read_coordinates_from is not None:
coordinates_path = Path(cfg.tiling.read_coordinates_from, f"{wsi_name}.npy")
if coordinates_path.is_file() and cfg.visualize and tile_visualize_dir is not None:
coordinates_arr = np.load(coordinates_path, allow_pickle=True)
coordinates = list(zip(coordinates_arr["x"], coordinates_arr["y"]))
tile_size_lv0 = coordinates_arr["tile_size_lv0"][0]
visualize_coordinates(
wsi_path=wsi_path,
coordinates=coordinates,
tile_size_lv0=tile_size_lv0,
save_dir=tile_visualize_dir,
downsample=cfg.tiling.visu_params.downsample,
backend=cfg.tiling.backend,
)
return str(wsi_path), {"status": "success"}
try:
tissue_mask_visu_path = None
if cfg.visualize and mask_visualize_dir is not None:
Expand Down Expand Up @@ -141,15 +156,15 @@ def main(args):
color_mapping = {k: v for e in cfg.tiling.sampling_params.color_mapping for k, v in e.items()}
else:
color_mapping = None

sampling_params = SamplingParameters(
pixel_mapping=pixel_mapping,
color_mapping=color_mapping,
tissue_percentage=tissue_percentage,
)

if not skip_tiling:

mask = process_df["tiling_status"] != "success"
process_stack = process_df[mask]
total = len(process_stack)
Expand All @@ -158,13 +173,16 @@ def main(args):
Path(x) for x in process_stack.wsi_path.values.tolist()
]
mask_paths_to_process = [
Path(x) if x is not None else x
Path(x) if x is not None and not pd.isna(x) else x
for x in process_stack.mask_path.values.tolist()
]

# setup directories for coordinates and visualization
coordinates_dir = output_dir / "coordinates"
coordinates_dir.mkdir(exist_ok=True, parents=True)
if cfg.tiling.read_coordinates_from is not None:
coordinates_dir = Path(cfg.tiling.read_coordinates_from)
else:
coordinates_dir = output_dir / "coordinates"
coordinates_dir.mkdir(exist_ok=True, parents=True)
mask_visualize_dir = None
tile_visualize_dir = None
if cfg.visualize:
Expand Down