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Fix for issue #21 - dose was not properly sorted in chlamydataset2relion5.py #22

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Fix for issue #21 - dose was not properly sorted in chlamydataset2relion5.py #22

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cf9d12a
The dose was not properly sorted in chlamydataset2relion.py. Fixes #21
rdrighetto Jan 14, 2026
9ffd00d
Removed print statement
rdrighetto Jan 14, 2026
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2 changes: 1 addition & 1 deletion chlamydataset2relion5/README.md
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Expand Up @@ -46,7 +46,7 @@ wget -r -N -np -nH --cut-dirs=4 --reject "*.eer,*.rawtlt,*_dose-filt.st,*_EVN.st
```bash
cd ChlamyAnnotations/chlamydataset2relion5/

python chlamydataset2relion5.py --tomos_dir /path/to/chlamy_visual_proteomics/ --output_dir /path/to/relion5/project/ --correspondence_star tomolist_num_dir.star --ctf3d /path/to/bin4_ctf3d/ --cryocare /path/to/bin4_cryocare/`
python chlamydataset2relion5.py --tomos_dir /path/to/chlamy_visual_proteomics/ --output_dir /path/to/relion5/project/ --correspondence_star tomolist_num_dir.star --ctf3d /path/to/bin4_ctf3d/ --cryocare /path/to/bin4_cryocare/
```

**Tip:** the `tomolist_num_dir.star` file is provided in this repo for convenience. Alternatively, it can also be [downloaded](https://ftp.ebi.ac.uk/empiar/world_availability/11830/data/chlamy_visual_proteomics/tomolist_num_dir.star) from EMPIAR.
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2 changes: 2 additions & 0 deletions chlamydataset2relion5/chlamydataset2relion5.py
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Expand Up @@ -255,6 +255,8 @@ def collect_tomogram_data(tomos_dir, tomo_prefix, tomolist, ctf3d_path, cryocare
acquisition_order = read_acquisition_order_dose_star(tomos_dir, tomo_prefix)
print(f"Found acquisition order data with {len(acquisition_order)} entries.")
# exposures = calculate_cumulative_exposure(tilt_angles, acquisition_order, dose_per_tilt)
# Sort by tilt angle to match the .tlt file:
acquisition_order = acquisition_order[acquisition_order[:,1].argsort()]
exposures = acquisition_order[:,2]
except FileNotFoundError:
print("Warning: Acquisition order CSV file not found. Using default incremental exposure.")
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