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deepcopy-layers in preprocess #304

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6 changes: 4 additions & 2 deletions scgpt/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,8 @@
from scanpy.get import _get_obs_rep, _set_obs_rep
from anndata import AnnData

from copy import deepcopy

from scgpt import logger


Expand Down Expand Up @@ -144,7 +146,7 @@ def __call__(self, adata: AnnData, batch_key: Optional[str] = None) -> Dict:
if self.result_log1p_key:
_set_obs_rep(
adata,
_get_obs_rep(adata, layer=key_to_process),
deepcopy(_get_obs_rep(adata, layer=key_to_process)),
layer=self.result_log1p_key,
)
key_to_process = self.result_log1p_key
Expand Down Expand Up @@ -178,7 +180,7 @@ def __call__(self, adata: AnnData, batch_key: Optional[str] = None) -> Dict:
n_bins = self.binning # NOTE: the first bin is always a spectial for zero
binned_rows = []
bin_edges = []
layer_data = _get_obs_rep(adata, layer=key_to_process)
layer_data = deepcopy(_get_obs_rep(adata, layer=key_to_process))
layer_data = layer_data.toarray() if issparse(layer_data) else layer_data
if layer_data.min() < 0:
raise ValueError(
Expand Down