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Drop removed .A1 for asarray(...).ravel() #161

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Merged
adamgayoso merged 3 commits into from
Feb 6, 2025
Merged

Drop removed .A1 for asarray(...).ravel() #161

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1a960fb
drop .A1 for asarray(...).ravel()
adamgayoso Jan 11, 2025
ddf28b9
toarray from .A
adamgayoso Jan 11, 2025
1a32916
Merge branch 'master' into toarray
adamgayoso Feb 6, 2025
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6 changes: 3 additions & 3 deletions doubletdetection/doubletdetection.py
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Original file line number Diff line number Diff line change
Expand Up @@ -192,7 +192,7 @@ def fit(self, raw_counts):
(self._num_cells, self._num_genes) = self._raw_counts.shape
if self.normalizer is None:
# Memoize these; default normalizer treats these invariant for all synths
self._lib_size = np.sum(raw_counts, axis=1).A1
self._lib_size = np.asarray(np.sum(raw_counts, axis=1)).ravel()
self._normed_raw_counts = self._raw_counts.copy()
inplace_csr_row_normalize_l1(self._normed_raw_counts)

Expand Down Expand Up @@ -298,14 +298,14 @@ def _one_fit(self):
)
else:
# Follows doubletdetection.plot.normalize_counts, but uses memoized normed raw_counts
synth_lib_size = np.sum(self._raw_synthetics, axis=1).A1
synth_lib_size = np.asarray(np.sum(self._raw_synthetics, axis=1)).ravel()
aug_lib_size = np.concatenate([self._lib_size, synth_lib_size])
normed_synths = self._raw_synthetics.copy()
inplace_csr_row_normalize_l1(normed_synths)
aug_counts = sp_sparse.vstack((self._normed_raw_counts, normed_synths))
scaled_aug_counts = aug_counts * np.median(aug_lib_size)
if self.pseudocount != 1:
aug_counts = np.log(scaled_aug_counts.A + 0.1)
aug_counts = np.log(scaled_aug_counts.toarray() + 0.1)
else:
aug_counts = np.log1p(scaled_aug_counts)
del scaled_aug_counts
Expand Down
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