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gene decoder bool #122

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20 changes: 10 additions & 10 deletions src/state/_cli/_tx/_predict.py
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Original file line number Diff line number Diff line change
Expand Up @@ -233,8 +233,8 @@ def load_config(cfg_path: str) -> dict:
all_pert_names = []
all_celltypes = []
all_gem_groups = []
all_pert_barcodes = []
all_ctrl_barcodes = []
# all_pert_barcodes = []
# all_ctrl_barcodes = []

with torch.no_grad():
for batch_idx, batch in enumerate(tqdm(test_loader, desc="Predicting", unit="batch")):
Expand All @@ -251,12 +251,12 @@ def load_config(cfg_path: str) -> dict:
else:
all_pert_names.append(batch_preds["pert_name"])

if isinstance(batch_preds["pert_cell_barcode"], list):
all_pert_barcodes.extend(batch_preds["pert_cell_barcode"])
all_ctrl_barcodes.extend(batch_preds["ctrl_cell_barcode"])
else:
all_pert_barcodes.append(batch_preds["pert_cell_barcode"])
all_ctrl_barcodes.append(batch_preds["ctrl_cell_barcode"])
# if isinstance(batch_preds["pert_cell_barcode"], list):
# all_pert_barcodes.extend(batch_preds["pert_cell_barcode"])
# all_ctrl_barcodes.extend(batch_preds["ctrl_cell_barcode"])
# else:
# all_pert_barcodes.append(batch_preds["pert_cell_barcode"])
# all_ctrl_barcodes.append(batch_preds["ctrl_cell_barcode"])

# Handle celltype_name
if isinstance(batch_preds["celltype_name"], list):
Expand Down Expand Up @@ -297,8 +297,8 @@ def load_config(cfg_path: str) -> dict:
data_module.pert_col: all_pert_names,
data_module.cell_type_key: all_celltypes,
data_module.batch_col: all_gem_groups,
"pert_cell_barcode": all_pert_barcodes,
"ctrl_cell_barcode": all_ctrl_barcodes,
# "pert_cell_barcode": all_pert_barcodes,
# "ctrl_cell_barcode": all_ctrl_barcodes,
}
)

Expand Down
7 changes: 7 additions & 0 deletions src/state/tx/models/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -154,6 +154,7 @@ def __init__(
super().__init__()
self.decoder_cfg = decoder_cfg
self.save_hyperparameters()
self.gene_decoder_bool = kwargs.get("gene_decoder_bool", True)

# Core architecture settings
self.input_dim = input_dim
Expand Down Expand Up @@ -193,6 +194,9 @@ def _build_networks(self):

def _build_decoder(self):
"""Create self.gene_decoder from self.decoder_cfg (or leave None)."""
if self.gene_decoder_bool == False:
self.gene_decoder = None
return
if self.decoder_cfg is None:
self.gene_decoder = None
return
Expand All @@ -204,6 +208,9 @@ def on_load_checkpoint(self, checkpoint: dict[str, tp.Any]) -> None:
Re-create the decoder using the exact hyper-parameters saved in the ckpt,
so that parameter shapes match and load_state_dict succeeds.
"""
if self.gene_decoder_bool == False:
self.gene_decoder = None
return
if "decoder_cfg" in checkpoint["hyper_parameters"]:
self.decoder_cfg = checkpoint["hyper_parameters"]["decoder_cfg"]
self.gene_decoder = LatentToGeneDecoder(**self.decoder_cfg)
Expand Down