Export ctf log

[PKirchweger]

Hi Developers and Users,

I would like to access the estimated defocus values for each tilt in the tilt series. Is it exported to somewhere?
I have checked if I can pull it out of the log file, but I didn't find it. Is there a way to export a file similar to the .tlt file, with the estimated defocus per line?

Thanks!

best,
Peter

[abartesaghi]

There is currently no way to do this from the web interface. However, the CTF information is kept internally in *.pkl files (one for each tilt-series) and it can be accessed using Python, as follows:

import pandas as pd
ctf = pd.read_pickle('PROJECT_PATH/pkl/TILT_SERIES_NAME.pkl')['ctf']
print(ctf)

where PROJECT_PATH is the filesystem location of the pre-processing block and TILT_SERIES_NAME is the name of the tilt-series.

The code above should produce something like this:

    tilt_angle           df1           df2        ast        cc     est_res
0       -60.00  34505.320312  32289.714844   0.000000  0.018838  718.200012
1       -57.00  40173.843750  39336.269531 -34.180779  0.016099    9.576000
2       -53.99  40875.519531  38946.929688 -78.535278  0.019217   11.400000
...
39       57.19  39423.015625  38668.175781 -66.243355  0.021899    9.207692
40       60.20  38880.031250  37661.507812  81.736458  0.027622   10.881818

If you don't have a Python installation handy with pandas on it, you can use nextPYP's pyp.sif container as follows:

singularity exec -B PROJECT_PATH PATH_TO_PYP_CONTAINER/pyp.sif python -c "import pandas as pd; print(pd.read_pickle('PROJECT_PATH/pkl/TILT_SERIES_NAME.pkl')['ctf'])"

where PATH_TO_PYP_CONTAINER is the location of the pyp.sif container file (usually in the sharedExec/containers folder under nextPYP's installation folder).

[PKirchweger]

Hi Alberto.
A python script or somthing similar was exectly what I was looking for.
Thank you!