How to Run e2boxer.py using python, without using GUI.

[Aniruth Sundararajan]

I want to do  Particle picking using a reference template, but i want to automate the process,

without having to upload the reference template via GUI, each time.

My Code

subprocess.run(['e2boxer.py', mrc_path, '--boxsize', str(box_size), '--apix', str(pixel_spacing), '--voltage', str(voltage), '--cs', str(cs), '--ptclsize', str(particle_size), '--write_ptcls', '--all' ],check=True)

What should i do, to link the reference template to this.

[Steve Ludtke]

I’m not sure what you mean by “each time”? The GUI is designed to load all of the micrographs in the project at once, adjust the settings interactively so it works well for the project, then autobox the entire set of micrographs with one button press, so not sure what repetition you are trying to avoid.

If you want to run the autopicking via your own Python script, you may be able to make it work with the --autopick option (see --help for command line parameters), but it isn’t a widely used method so, not clear what issues you may have. The available modes are auto_local, auto_ref, auto_gauss and auto_convnet. Look at “aboxmodes” in e2boxer.py for more details.

Alternatively, you could import e2boxer, then call do_autobox_all() yourself from Python, since you’re using Python anyway. The command-line interface will always be more limited than what you can do directly from Python. 

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