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Add support for Warp starfiles. #39

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Add support for Warp starfiles. #39

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26 changes: 23 additions & 3 deletions src/io/RELION/RELIONParticleData.py
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Original file line number Diff line number Diff line change
Expand Up @@ -141,6 +141,19 @@ def read_file(self):
if "rlnCoordinateZ" in list(val.keys()):
data_loop = key
break
elif 'wrpCoordinateZ1' in list(val.keys()): # Check whether it's a Warp/M starfile and if so, edit parameter names.
print(f"Changing Warp/M starfile columns to Relion format.")
wrp_to_rln = [('wrpCoordinateX1', 'rlnCoordinateX'),
('wrpCoordinateY1', 'rlnCoordinateY'),
('wrpCoordinateZ1', 'rlnCoordinateZ'),
('wrpAngleRot1', 'rlnAngleRot'),
('wrpAngleTilt1', 'rlnAngleTilt'),
('wrpAnglePsi1', 'rlnAnglePsi'), ]
for old, new in wrp_to_rln:
if old in val.columns:
print(f'renaming {old} to {new}')
val.rename(columns={old: new}, inplace=True)
data_loop = key

# Abort if none found
if data_loop is None:
Expand Down Expand Up @@ -260,14 +273,21 @@ def read_file(self):

# Now make particles
df.reset_index()

_raised_tomoname_parse_error = False
for idx, row in df.iterrows():
p = self.new_particle()

# Name
if names_present:
n = row["rlnTomoName"].split("_")
num = int(n[-1])
p["rlnTomoName"] = num
try:
n = row["rlnTomoName"].split("_")
num = int(n[-1])
p["rlnTomoName"] = num
except Exception as e:
"" if _raised_tomoname_parse_error else print(f'Could not parse rlnTomoName the original way - applying workaround.')
_raised_tomoname_parse_error = True
p["rlnTomoName"] = int(''.join(filter(str.isdigit, row["rlnTomoName"])))

# Position
p["pos_x"] = row["rlnCoordinateX"]
Expand Down