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Before converting to STAR, put refined shifts in terms of blob apix #125

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Before converting to STAR, put refined shifts in terms of blob apix #125

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0f86305
Before converting to STAR, put refined shifts in terms of blob apix
PlethoraChutney Nov 4, 2024
86f8376
Sync with DA
PlethoraChutney Jan 29, 2025
d8b9992
Move apix conversion to cryosparc2_model_parameters()
PlethoraChutney Jan 29, 2025
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1 change: 1 addition & 0 deletions pyem/cli/csparc2star.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,7 @@ def main(args):
if args.input[0].endswith(".cs"):
log.info("Detected CryoSPARC 2+ .cs file")
cs = np.load(args.input[0])

if args.first10k:
cs = cs[:10000]

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7 changes: 7 additions & 0 deletions pyem/metadata/cryosparc2.py
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Expand Up @@ -145,6 +145,13 @@ def cryosparc_2_cs_model_parameters(cs, df=None, minphic=0):
if df is None:
df = pd.DataFrame()
phic_names = [n for n in cs.dtype.names if "class_posterior" in n]
# convert shifts from alignment psize to blob psize
for dimension in ["alignments2D", "alignments3D"]:
try:
cs[f"{dimension}/shift"] = cs[f"{dimension}/shift"] * cs[f"{dimension}/psize_A"].reshape(-1, 1) / cs["blob/psize_A"].reshape(-1, 1)
cs[f"{dimension}/psize_A"] = cs["blob/psize_A"]
except ValueError:
pass
if u'alignments3D/class_posterior' in cs.dtype.names:
log.info("Assigning pose from single 3D refinement")
for k in model:
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