usage: prog [options]
This program automates the CTF fitting and structure factor generation process, which normally involves a
sequence of at least 4 different steps. For most projects, this will work correctly with no human intervention.
We strongly recommend running the GUI after it completes to double-check the fitting of a few of the closest
and a few of the furthest from focus images by hand.

If you detect fitting problems on any images, manually adjust those images to a defocus near the correct value,
then rerun this program (without --fromscratch) and the problem should be fixed.

For defocus with astigmatism fitting, whole frame fitting as implemented in e2rawdata.py and
e2evalimage.py generally produce superior fits. If you have run this whole-frame fitting, e2ctf_auto will
take this into account, and only fit the other required parameters.

Important: This program must be run from the project directory, not from within the particles directory

Option Type Description
--version None show program's version number and exit
--hires None Perform CTF processing for projects targeting 2-6 A resolution
--midres None Perform CTF processing for projects targeting 7-15 A resolution
--lores None Perform CTF processing for projects targeting 15-30 A resolution
--apix float Angstroms per pixel for all images
--voltage float Microscope voltage in KV
--cs float Microscope Cs (spherical aberation)
--fromscratch None Force refitting of CTF from scratch, ignoring any previous fits.
--curdefocusfix None Recomputes everything, but maintains the current particle-based defocus/astigmatism, including any manual adjustments
--astigmatism None Includes astigmatism in automatic fitting (use e2rawdata first)
--phaseplate None Include phase/amplitude contrast in CTF estimation. For use with hole-less phase plates.
--extrapad None If particles were boxed more tightly than EMAN requires, this will add some extra padding
--invartype None Which type of invariants to generate: (bispec,harmonic)
--snrfilt None Apply a SNR filter to phase flipped output images
--missingonly None Operates only on images with missing __ctf_flip_invar files, for cases where a previous run failed before completion
--highdensity None If particles are very close together, this will interfere with SSNR estimation. If set uses an alternative strategy, but may over-estimate SSNR.
--invert None Invert the contrast of the particles in output files (default false)
--outputonly None Skips all of the initial steps, and just generates the final output, assuming previous steps completed successfully
--defocusmin float Minimum defocus in autofitting
--defocusmax float Maximum defocus in autofitting
--constbfactor float Set B-factor to fixed specified value, negative value autofits
--ac float Amplitude contrast (percentage, default 10)
--threads int Number of threads to run in parallel on the local computer
--minqual int Files with a quality value lower than specified will be skipped
--ppid int Set the PID of the parent process, used for cross platform PPID
--verbose, -v int verbose level [0-9], higher number means higher level of verboseness