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3dem / relion

Image-processing software for cryo-electron microscopy
https://relion.readthedocs.io/en/latest/
GNU General Public License v2.0
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Rewrite relion_star_printtable #610

Open biochem-fan opened 4 years ago

biochem-fan commented 4 years ago

I was using a bash script relion_star_printtable $1 data_fsc rlnResolution rlnFourierShellCorrelation to extract FSC from relion_image_handler —fsc output.

If I use this on postprocess.star, which does not have the rlnFourierShellCorrelation column but rlnFourierShellCorrelationCorrected, rlnFourierShellCorrelationParticleMaskFraction, rlnFourierShellCorrelationUnmaskedMaps, rlnFourierShellCorrelationMaskedMaps, rlnCorrectedFourierShellCorrelationPhaseRandomizedMaskedMaps, it DOES NOT give an error. Instead, it matches the column name incompletely and take the last one which contains the given label, in this case rlnFourierShellCorrelationMaskedMaps.

This is dangerous.

Another caveat is that it uses a hard-coded temporary file name tmp*.dat. This means if you call it from scripts in parallel, the result gets mixed up.

biochem-fan commented 4 years ago

Most problems are addressed in cfdec26. Nonetheless, we should rewrite this in C++ in future.