Aligments values are not generated in .star

[fonsecareyna82]

When I try to convert a .cs file that corresponds to a set of particles and I pass the passthrough file (where the particle alignments are) as an auxiliary file, the values for the rot, tilt, psi, shifts, etc. do not appear in the .star file.....
Line 319 which is commented out in the code in cryosparc2.py is where this data should be collected.

[asarnow]

Can you uncomment that line, and then try 1) your example above where the alignments are in the passthrough and 2) another test where the alignments are in both the main file and the passthrough?

It's already implemented this way and it should be safe to uncomment, I just want to make sure that we are really using the main file values in case the alignments are available in both.

[fonsecareyna82]

Yes, I have debugged the code by uncommenting and commenting line 319 of cryosparc2.py and indeed, with the uncommented code the values of the alignments are written in the .star file. With the commented code they are not written.

We have a CS plugin inside Scipion where we have integrated more than 20 algorithms and so far we have not had this problem. I have never had to pass the passthrough as an auxiliary file.
This problem has occurred in a dataset downloaded from EMPIAR by one of our users and tried to import a .cs file with particles. In the dataset there is also the passthrough file and this is where the alignments come from.
I really don't know what kind of job they came from.
I only know that we import the alignments correctly by uncommenting the code