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Data loaders: prefer nuclei_seg, fall back to nuclear_seg #15

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Data loaders: prefer nuclei_seg, fall back to nuclear_seg #15

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9 changes: 8 additions & 1 deletion src/ops_model/data/data_loader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -463,7 +463,14 @@ def __getitem__(self, index):
fov = self.stores[ci.store_key][well]["0"]
mask_label = getattr(ci, "mask_label", "cell_seg")
cell_mask_fov = self.stores[ci.store_key][well]["labels"][mask_label]["0"]
nuc_mask_fov = self.stores[ci.store_key][well]["labels"]["nuclear_seg"]["0"]
# Nuclear mask: prefer native-20x `nuclei_seg` (from the
# `submit_nuclei_segmentation_jobs` step), fall back to legacy
# `nuclear_seg` (5x-upscaled, from `segment_and_stitch_pheno`).
# Both labels are 20x-shaped at level 0 so bbox slicing is unchanged.
# See ops_process PR #113.
_labels_group = self.stores[ci.store_key][well]["labels"]
_nuc_label = "nuclei_seg" if "nuclei_seg" in _labels_group else "nuclear_seg"
nuc_mask_fov = _labels_group[_nuc_label]["0"]
bbox = ast.literal_eval(ci.bbox)
gene_label = self.label_int_lut[ci.gene_name]
total_index = ci.total_index
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9 changes: 8 additions & 1 deletion src/ops_model/features/cp_extraction.py
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Expand Up @@ -1016,7 +1016,14 @@ def extract_cp_features_bulk_read(
img_arr = stores[store_key][well]["0"]
mask_label = getattr(first_row, "mask_label", "cell_seg")
cell_seg_arr = stores[store_key][well]["labels"][mask_label]["0"]
nuc_seg_arr = stores[store_key][well]["labels"]["nuclear_seg"]["0"]
# Nuclear mask: prefer native-20x `nuclei_seg` (from the
# `submit_nuclei_segmentation_jobs` step), fall back to legacy
# `nuclear_seg` (5x-upscaled, from `segment_and_stitch_pheno`).
# Both labels are 20x-shaped at level 0; bbox slicing unchanged.
# See ops_process PR #113.
_labels_group = stores[store_key][well]["labels"]
_nuc_label = "nuclei_seg" if "nuclei_seg" in _labels_group else "nuclear_seg"
nuc_seg_arr = _labels_group[_nuc_label]["0"]
chunk_size = img_arr.chunks[-1] # 512

# Phase 1: Identify unique chunks from bounding boxes
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