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Fix relion5 compat #220

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merged 3 commits into from
Aug 14, 2024
Merged

Fix relion5 compat #220

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e0c57a8
fix: starfile write as dict so blocks are saved with _data_particles
McHaillet Aug 14, 2024
ddd53af
fix: change rlnDetectorPixelSize to rlnTomoTiltSeriesPixelSize for re…
McHaillet Aug 14, 2024
2beb502
add: make sure new column name is also checked in tests
McHaillet Aug 14, 2024
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8 changes: 6 additions & 2 deletions src/pytom_tm/entry_points.py
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Original file line number Diff line number Diff line change
Expand Up @@ -548,7 +548,9 @@ def extract_candidates(argv=None):

# write out as a RELION type starfile
starfile.write(
df, job.output_dir.joinpath(f"{job.tomo_id}_particles.star"), overwrite=True
{"particles": df},
job.output_dir.joinpath(f"{job.tomo_id}_particles.star"),
overwrite=True,
)


Expand Down Expand Up @@ -1007,5 +1009,7 @@ def merge_stars(argv=None):
dataframes = [starfile.read(f) for f in files]

starfile.write(
pd.concat(dataframes, ignore_index=True), args.output_file, overwrite=True
{"particles": pd.concat(dataframes, ignore_index=True)},
args.output_file,
overwrite=True,
)
1 change: 1 addition & 0 deletions src/pytom_tm/extract.py
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Original file line number Diff line number Diff line change
Expand Up @@ -346,6 +346,7 @@ def extract_particles(
"rlnCoordinateY": "rlnCenteredCoordinateYAngst",
"rlnCoordinateZ": "rlnCenteredCoordinateZAngst",
"rlnMicrographName": "rlnTomoName",
"rlnDetectorPixelSize": "rlnTomoTiltSeriesPixelSize",
}
output = output.rename(columns=column_change)

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1 change: 1 addition & 0 deletions tests/test_tmjob.py
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Expand Up @@ -631,6 +631,7 @@ def test_extraction(self):
"rlnCenteredCoordinateYAngst",
"rlnCenteredCoordinateZAngst",
"rlnTomoName",
"rlnTomoTiltSeriesPixelSize",
):
self.assertTrue(
column in df_rel5.columns,
Expand Down