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API: proposal to rename tissue_exclude kwarg to tissue in predict fn #26

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API: proposal to rename tissue_exclude kwarg to tissue in predict fn #26

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4c0be00
Minor touchups to formatting and text, fix links.
rossbar Jun 10, 2025
3aa0d12
Merge remote-tracking branch 'upstream/master'
rossbar Jun 10, 2025
8787a33
Merge remote-tracking branch 'upstream/master'
rossbar Jun 10, 2025
4956947
API: rename tissue_exclude -> tissue in predict.
rossbar Jun 10, 2025
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6 changes: 3 additions & 3 deletions deepcell_types/predict.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ def get_result(self):
return cell_type_str_pred, top_probs, cell_index


def predict(raw, mask, channel_names, mpp, model_name, device_num, batch_size=256, num_workers=24, tissue_exclude=None):
def predict(raw, mask, channel_names, mpp, model_name, device_num, batch_size=256, num_workers=24, tissue=None):
device = torch.device(device_num)

embedding_model_name = "deepseek-r1-70b-llama-distill-q4_K_M"
Expand Down Expand Up @@ -95,8 +95,8 @@ def predict(raw, mask, channel_names, mpp, model_name, device_num, batch_size=25
with torch.no_grad():
for sample, ch_idx, attn_mask, cell_index in tqdm(data_loader, desc=f"(inference)"):
ct_exclude = None
if tissue_exclude:
ct_exclude = [[i for i in range(len(ct_embeddings)) if i not in [dct_config.ct2idx[i] for i in tct[tissue_exclude]]] for _ in range(len(sample))]
if tissue:
ct_exclude = [[i for i in range(len(ct_embeddings)) if i not in [dct_config.ct2idx[i] for i in tct[tissue]]] for _ in range(len(sample))]
_, _, _, _, probs, _ = model(
sample.to(device),
ch_idx.to(device),
Expand Down