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fix: use configured label names in survival prediction output #170

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Merged
mducducd merged 2 commits into from
Apr 2, 2026
Merged

fix: use configured label names in survival prediction output #170

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4bc6b91
fix: use configured label names in survival prediction output, closes…
mducducd Apr 2, 2026
13cd428
fix: remove pin_memory from DataLoaders to avoid DeprecationWarning
mducducd Apr 2, 2026
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2 changes: 0 additions & 2 deletions src/stamp/modeling/data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -132,7 +132,6 @@ def tile_bag_dataloader(
collate_fn=collate_fn,
worker_init_fn=Seed.get_loader_worker_init() if Seed._is_set() else None,
persistent_workers=(num_workers > 0),
pin_memory=torch.cuda.is_available(),
)

return (
Expand Down Expand Up @@ -416,7 +415,6 @@ def create_dataloader(
num_workers=num_workers,
worker_init_fn=Seed.get_loader_worker_init() if Seed._is_set() else None,
persistent_workers=(num_workers > 0),
pin_memory=torch.cuda.is_available(),
)
return dl, categories or []
else:
Expand Down
10 changes: 8 additions & 2 deletions src/stamp/modeling/deploy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -342,6 +342,8 @@ def deploy_categorical_model_(
patient_label=patient_label,
ground_truth_label=ground_truth_label,
cut_off=cut_off,
time_label=time_label,
status_label=status_label,
).to_csv(output_dir / f"patient-preds-{model_i}.csv", index=False)
else:
df_builder(
Expand All @@ -351,6 +353,8 @@ def deploy_categorical_model_(
patient_label=patient_label,
ground_truth_label=ground_truth_label,
cut_off=cut_off,
time_label=time_label,
status_label=status_label,
).to_csv(output_dir / "patient-preds.csv", index=False)

if task == "classification":
Expand Down Expand Up @@ -641,6 +645,8 @@ def _to_survival_prediction_df(
],
predictions: Mapping[PatientId, torch.Tensor],
patient_label: PandasLabel,
time_label: PandasLabel = "time",
status_label: PandasLabel = "event",
cut_off: float | None = None,
**kwargs,
) -> pd.DataFrame:
Expand Down Expand Up @@ -671,9 +677,9 @@ def _to_survival_prediction_df(
# call .split on ground-truth values — assume structured input. If
# the value is not a 2-tuple/list, treat both fields as unknown.
if isinstance(gt, (tuple, list)) and len(gt) == 2:
row["time"], row["event"] = gt
row[time_label], row[status_label] = gt
else:
row["time"], row["event"] = None, None
row[time_label], row[status_label] = None, None

rows.append(row)

Expand Down
2 changes: 0 additions & 2 deletions src/stamp/preprocessing/__init__.py
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Expand Up @@ -311,14 +311,12 @@ def extract_(
default_slide_mpp=default_slide_mpp,
)
# Parallelism is implemented in the dataset iterator already, so one worker is enough!
# pin_memory speeds up CPU→GPU DMA for tile batches.
# num_workers=1 is intentional: WSI read parallelism is inside _supertiles.
dl = DataLoader(
ds,
batch_size=64,
num_workers=1,
drop_last=False,
pin_memory=torch.cuda.is_available(),
)

feats, xs_um, ys_um = [], [], []
Expand Down
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