usage: Program to fit CTF (find defocus and estimate highest resolution conent) in raw images of tiltseries by periodogram averaging of 
	tiles in strips parallel to the tilt axis.

Option Type Description
--version None show program's version number and exit
--ampcont float Default=0.05. Amplitude contrast to use for CTF correction phase flipping.
--apix float Default=whatever is on the header of the images. Sampling of the images in angstroms/pixel.
--bfactor int Default=1000. Bfactor ("temperature factor") to use.
--cs float Default=2.7. Cs of the microscope with which the images were collected.
--defocus float Default=None. Target defocus at the tilt axis. If not provided, a "global defocus" value will be estimated automatially.
--debug None Default=False. Shows plots as they are being produced -requires user feedback to proceed.
--input str Default=None. Single 2D image or image stack to calculate CTF for.
--path str Directory to store results in. The default is a numbered series of directories containing the prefix 'tomoctfraw'; for example, sptctf_02 will be the directory by default if 'sptctf_01' already exists.
--phaseplate None Default=False. Supply this if the data were collected with hole-free phase plate.
--plots None Default=False. Turn this option on to generate plots of the background-subtracted 1D power spectrum overlaid with the best CTF fit. Running on a cluster or via ssh remotely might not support plotting.
--ppid int Set the PID of the parent process, used for cross platform PPID
--savefft None Default=False. Saves the average of the ffts of the tiles for an image or its strips.
--tilesize int Tile size to use for strips when --autofit is provided.
--tiltangle float Default=None. Single 2D image or image stack to calculate CTF for.
--tltfile str File containing a list of tilt angles corresponding to the tilt angles of images 0 to n.
--verbose, -v int verbose level [0-9], higner number means higher level of verboseness.
--voltage int Default=300. Voltage of the microscope with which the images where collected.