def main(args):
log = logging.getLogger('root')
hdlr = logging.StreamHandler(sys.stdout)
log.addHandler(hdlr)
log.setLevel(logging.getLevelName(args.loglevel.upper()))
if args.input[0].endswith(".cs"):
log.debug("Detected CryoSPARC 2+ .cs file")
cs = np.load(args.input[0])
try:
df = metadata.parse_cryosparc_2_cs(cs, passthroughs=args.input[1:], minphic=args.minphic,
boxsize=args.boxsize, swapxy=args.swapxy,
invertx=args.invertx, inverty=args.inverty)
except (KeyError, ValueError) as e:
log.error(e, exc_info=True)
log.error("Required fields could not be mapped. Are you using the right input file(s)?")
return 1
else:
log.debug("Detected CryoSPARC 0.6.5 .csv file")
if len(args.input) > 1:
log.error("Only one file at a time supported for CryoSPARC 0.6.5 .csv format")
return 1
meta = metadata.parse_cryosparc_065_csv(args.input[0]) # Read cryosparc metadata file.
df = metadata.cryosparc_065_csv2star(meta, args.minphic)
if args.cls is not None:
df = star.select_classes(df, args.cls)
if args.copy_micrograph_coordinates is not None:
df = star.augment_star_ucsf(df, inplace=True)
coord_star = pd.concat(
(star.parse_star(inp, keep_index=False, augment=True) for inp in
glob(args.copy_micrograph_coordinates)), join="inner")
key = star.merge_key(df, coord_star)
log.debug("Coordinates merge key: %s" % key)
if args.cached or key == star.Relion.IMAGE_NAME:
fields = star.Relion.MICROGRAPH_COORDS
else:
fields = star.Relion.MICROGRAPH_COORDS + [star.UCSF.IMAGE_INDEX, star.UCSF.IMAGE_PATH]
df = star.smart_merge(df, coord_star, fields=fields, key=key)
star.simplify_star_ucsf(df)
if args.micrograph_path is not None:
df = star.replace_micrograph_path(df, args.micrograph_path, inplace=True)
if args.transform is not None:
r = np.array(json.loads(args.transform))
df = star.transform_star(df, r, inplace=True)
df = star.check_defaults(df, inplace=True)
if args.relion2:
df = star.remove_new_relion31(df, inplace=True)
star.write_star(args.output, df, resort_records=True, optics=False)
else:
df = star.remove_deprecated_relion2(df, inplace=True)
star.write_star(args.output, df, resort_records=True, optics=True)
log.info("Output fields: %s" % ", ".join(df.columns))
return 0
def main(args):
log = logging.getLogger('root')
hdlr = logging.StreamHandler(sys.stdout)
log.addHandler(hdlr)
log.setLevel(logging.getLevelName(args.loglevel.upper()))
if args.input.endswith(".cs"):
log.debug("Detected CryoSPARC 2+ .cs file")
cs = np.load(args.input)
try:
df = metadata.parse_cryosparc_2_cs(cs,
passthrough=args.passthrough,
minphic=args.minphic)
except (KeyError, ValueError) as e:
log.error(e.message)
log.error(
"A passthrough file may be required (check inside the cryoSPARC 2+ job directory)"
)
log.debug(e, exc_info=True)
return 1
else:
log.debug("Detected CryoSPARC 0.6.5 .csv file")
meta = metadata.parse_cryosparc_065_csv(
args.input) # Read cryosparc metadata file.
df = metadata.cryosparc_065_csv2star(meta, args.minphic)
if args.cls is not None:
df = star.select_classes(df, args.cls)
if args.copy_micrograph_coordinates is not None:
coord_star = pd.concat(
(star.parse_star(inp, keep_index=False)
for inp in glob(args.copy_micrograph_coordinates)),
join="inner")
star.augment_star_ucsf(coord_star)
star.augment_star_ucsf(df)
key = star.merge_key(df, coord_star)
log.debug("Coordinates merge key: %s" % key)
if args.cached or key == star.Relion.IMAGE_NAME:
fields = star.Relion.MICROGRAPH_COORDS
else:
fields = star.Relion.MICROGRAPH_COORDS + [
star.UCSF.IMAGE_INDEX, star.UCSF.IMAGE_PATH
]
df = star.smart_merge(df, coord_star, fields=fields, key=key)
star.simplify_star_ucsf(df)
if args.micrograph_path is not None:
df = star.replace_micrograph_path(df,
args.micrograph_path,
inplace=True)
if args.transform is not None:
r = np.array(json.loads(args.transform))
df = star.transform_star(df, r, inplace=True)
# Write Relion .star file with correct headers.
star.write_star(args.output, df, reindex=True)
log.info("Output fields: %s" % ", ".join(df.columns))
return 0
def main(args):
if args.input.endswith(".cs"):
cs = np.load(args.input)
if args.passthrough is None:
if u"blob/path" not in cs.dtype.names:
print(
"A passthrough file is required (found inside the cryoSPARC 2+ job directory)"
)
return 1
df = metadata.parse_cryosparc_2_cs(cs,
passthrough=args.passthrough,
minphic=args.minphic)
else:
meta = metadata.parse_cryosparc_065_csv(
args.input) # Read cryosparc metadata file.
df = metadata.cryosparc_065_csv2star(meta, args.minphic)
if args.cls is not None:
df = star.select_classes(df, args.cls)
if args.copy_micrograph_coordinates is not None:
coord_star = pd.concat(
(star.parse_star(inp, keep_index=False)
for inp in glob(args.copy_micrograph_coordinates)),
join="inner")
df = star.smart_merge(df,
coord_star,
fields=star.Relion.MICROGRAPH_COORDS)
if args.transform is not None:
r = np.array(json.loads(args.transform))
df = star.transform_star(df, r, inplace=True)
# Write Relion .star file with correct headers.
star.write_star(args.output, df, reindex=True)
return 0
