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Refactor on _get_condition_data: minimal commit for speedup #154

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Refactor on _get_condition_data: minimal commit for speedup #154

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12 changes: 8 additions & 4 deletions src/cfp/data/_datamanager.py
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Original file line number Diff line number Diff line change
Expand Up @@ -352,6 +352,10 @@ def _get_condition_data(
else:
perturb_covar_df = perturb_covar_df.reset_index()

orig_index = covariate_data.index
# TODO do something with orig_index
del orig_index
covariate_data.index = np.arange(len(covariate_data))
# get indices of cells belonging to each unique condition
_perturb_covar_df, _covariate_data = (
perturb_covar_df[self._perturb_covar_keys],
Expand Down Expand Up @@ -422,10 +426,10 @@ def _get_condition_data(

# for train/validation, only extract covariate combinations that are present in adata
if adata is not None:
mask = covariate_data.index.isin(perturb_covar_to_cells[i])
mask *= (1 - control_mask) * split_cov_mask
mask = np.array(mask == 1)
if mask.sum() == 0:
mask = np.zeros(len(adata), dtype=bool)
mask[perturb_covar_to_cells[i]] = True
mask &= ~control_mask & split_cov_mask
if not np.any(mask):
continue
# map unique condition id to target id
perturbation_covariates_mask[mask] = tgt_counter # type: ignore[index]
Expand Down