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Feat(csparc2star): Add support for multi volume groups in CS v4.5+ #1

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Feat(csparc2star): Add support for multi volume groups in CS v4.5+ #1

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15 changes: 15 additions & 0 deletions pyem/metadata/cryosparc2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -151,6 +151,21 @@ def cryosparc_2_cs_model_parameters(cs, df=None, minphic=0):
if model[k] is not None:
name = u'alignments3D/' + k
df[model[k]] = pd.DataFrame(cs[name])
# CryoSPARC v4.5+
elif u'alignments3D_multi/class_posterior' in cs.dtype.names:
log.info("Assigning pose from most likely 3D classes using alignments3D_multi columns")
cls = np.argmax(cs['alignments3D_multi/class_posterior'], axis=1)
cls_prob = cs['alignments3D_multi/class_posterior'][range(cls.shape[0]), cls]
for k in model:
if model[k] is not None:
if k == u'split': # singleton column
df[model[k]] = pd.DataFrame(cs['alignments3D_multi/split'])
else:
df[model[k]] = pd.DataFrame(cs['alignments3D_multi/' + k][range(cls.shape[0]), cls, ...])

if minphic > 0:
df.drop(df.loc[cls_prob < minphic].index, inplace=True)
# CryoSPARC <= v4.4
elif len(phic_names) > 1:
log.info("Assigning pose from most likely 3D classes")
phic = np.array([cs[p] for p in phic_names if u'alignments2D' not in p])
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