WARNING: Experimental program. Processing subtiltseries is enabled (Oct/2014),
		but other functionality might be incomplete.
		This program can do the following:
		1) Flip phases of the entire image for all images in a tilt series using the same 
		parameters for all images (approximate solution that will only work for low-tilt
		and/or small images) or
		2) Using different parameters for each image (supply --ctfparamfile or
		--defocilist in that case)
		The same can be done for subtiltseries extracted with e2spt_subtilt.py,
		except that for subtiltseries the correction is tweaked on a per-particle basis and
		is thus as accurate as possible.
		3) The program can also correct frames (in tilt series or subtiltseries) on a 
		strip-by-strip basis.

Option Type Description
--version None show program's version number and exit
--tiltseries str Aligned tilt series. File format must be MRC and must have .mrc or .st or .ali extension.
--exclude str Comma-separated list of image indexes in the --tiltseries to exclude from CTF fitting. For example, --exclude 0,3,4,6,7.
--skipstripping str Default=None. Comma-separated list of image indexes to exclude from strip-based fitting (in this case, only global defocus tiling the entire image wil be measured).
--imagestem str Default=None. If the images to apply ctf correction on are already unstacked and are individual mrc files, supply a common string to all of them.
--invert None Invert the contrast of the output data, compared to the input data.
--excludeedges None Ignore 'excedent' (smaller than the width of a strip) at the edge of micrographs after dividing them into strips.
--mintiles int Minimum number of 'good tiles' in strip to consider it.
--defocusvariationlimit float default=0.1. total variation in defocus (in micrometers) tolerated within a strip and still consider it a region of 'constant defocus'.
--infodir str Folder typically produced by e2evalimage.py or previous runs of this program containing info.json files, one per tilt image in a tilt series. Each .json file should contain the fitted ctf and all associated parameters for each tilt image.
--output str Filename for the output CTF-corrected tilt series.
--subtiltsdir str Provide a directory containing individual stacks, where each stack is a 'mini tilt series' or a 'subtilt series' for single particles. Then, each image for each particle in the dir will be phase-phlipped using the ctf parameters you provide. If each image in the subtilt series is at a different defocus, then the parameters should be provided through --ctfparamsfile, whith a different defocus value per row. (There should be as many rows as images in each subtiltseries).
--path str Directory to store results in. The default is a numbered series of directories containing the prefix 'sptctf'; for example, sptctf_02 will be the directory by default if 'sptctf_01' already exists.
--reconstructor str Default=fourier:mode=gauss_2. The reconstructor to use to reconstruct the tilt series into a tomogram. Type 'e2help.py reconstructors' at the command line to see all options and parameters available. To specify the interpolation scheme for the fourier reconstruction, specify 'mode'. Options are 'nearest_neighbor', 'gauss_2', 'gauss_3', 'gauss_5', 'gauss_5_slow', 'gypergeom_5', 'experimental'. For example --reconstructor=fourier:mode=gauss_5
--verbose, -v int verbose level [0-9], higher number means higher level of verboseness.
--ppid int Set the PID of the parent process, used for cross platform PPID
--pad2d float Padding factor to zero-pad\n\t\tthe 2d images in the tilt series prior to reconstruction.\n\t\t(The final reconstructed subvolumes will be cropped to the original size).
--pad3d float Padding factor to zero-pad\n\t\tthe reconstruction volume. (The final reconstructed subvolumes will be cropped to \n\t\tthe original size).
--save3d None If on, the CTF\n\t\tcorrected subtiltseries will be reconstrcuted into subvolumes and save into a stack.\n\t\tOptions --reconstructor, --pad2d, --pad3d are used if --save3d is on.
--save2d None If on, the CTF\n\t\tcorrected subtiltseries will be saved as 2-D imag stacks [one per particle].
--outputstem str Stem common to all\n\t\toutput image stacks. For example, if --outputstem=myvirus and --save2d is provided, \n\t\tthe phase-flipped images for each subtiltseries wille be saved to myvirus_subtiltptclXXXX.hdf.\n\t\tIf --save3d is provided, the stack of reconstructed subvolumes will be saved to myvirus_stack3d.hdf
--savestriptiles None Saves\n\t\tall tiles for all strips, for all images, in one stack per strip.
--saveffts None Saves\n\t\tffts of each average of tiles per strip, for all images.
--icethickness int This corresponds\n\t\tto the Z dimension in pixels of the reconstructed raw tomogram (uncropped), at the same binning\n\t\t(sampling) as the provided tiltseries, images or subtiltseries.\n\t\tThis value MUST be provided, only if --subtiltsdir is given.\n\t\t
--autofit None Runs automated\n\t\tCTF fitting on the input images, based on tiling.
--firstfitglobal None Default=False.\n\t\tSupplying this option will tile the entire image first (for each tilt angle) and find the average\n\t\tdefocus. Then it will use that value to provide an educated 'guess' during stripe-by-stripe \n\t\tfitting for each image.
--tilesize int Tile size to use for strips\n\t\twhen --autofit is provided.
--defocusmin float If --autofit, minimum autofit defocus. Default=0.0, not used. A value will be estimated based on tilt angle and distance from the tilt axis.
--defocusmax float Default=0.0, not used. If --autofit, maximum autofit defocus. A value will be estimated based on tilt angle and distance from the tilt axis.
--stripstep int This will determine the\n\t\tamount of strips and the overlap between them for defocus estimation. The default \n\t\tis half the tilesize. For example, for a 4000x4000 pixels image, a tile size of\n\t\t400 would yield 20, not 10 strips, by default. If --stripstep=1 were provided, the\n\t\timage would be devided into 4000-400=3600 strips. The first strip would go from pixel\n\t\t0 to pixel 400, the second strip from pixel 1 to pixel 401, the third from pixel 2\n\t\tto 402, etc... up to the las strip going from pixel 3600 to 4000.
--subset int Requires --subtiltsdir. Specify how many subtiltseries (or particles) to ctf correct. If you specify 10, the first 10 subtiltseires in --subtiltsdir will be corrected. 0 means "process all" because it makes no sense to process none
--icethicknessauto None \n\t\tIf --subtiltsdir is provided (and if --icethickness is *not* provided), the thickness of the \n\t\tspecimen in Z will be calculated by computing the difference between the largest \n\t\tand the smallest Z coordinate found in the header of the subtiltseries, plus the size of the specimen, calculated from --radius.
--radius int Radius of the particle in pixels.
--framexsize int This correspond to the X\n\t\tsize in pixes of the images/frames in the raw tilt series; that is, the size of the entire frame\n\t\talong the X axis (perpendicular to the direction of the tilt axis in the aligned tilt series).\n\t\tIt is used to calculate the distance of each particle (subtiltseries) to the tilt axis, since\n\t\tthis will induce different shifts in defocus in 3-D for the actual particles. Particles\n\t\tright at the tilt axis don't move "up" or "down" as they are tilted.\n\t\tThis MUST be provided if --subtiltsdir is provided.\n\t\tOthwerwise, it will be read from the header of the images provided.
--phaseflipwhole None This \n\t\twill perform phase flipping on the entire image for each image in an aligned tilt \n\t\tseries using the CTF parameters supplied.
--phaseflipstrips None This will\n\t\tperform phase flipping on images of an aligned tilt series on a strip-by-strip basis,\n\t\tassuming the supplied ctf parameters correspond to the proper values at the tilt axis,\n\t\teither the same values for all images (--defocus,--ampcont,--cs,--apix,--voltage,--bfactor)\n\t\tor a different set for each (--ctfparamsfile), taking into account the tilt angle for \n\t\teach image (--tltfile), which should be supplied through an IMOD-like .tlt file.
--prunetest float Default=0.1.\n\t\tDecimal number that indicates the percentage of --tilesize (in terms of side length) \n\t\tto tolerate of 'bad' values (i.e., empty regions of constant density) at the corners, \n\t\tand still include the tile for CTF fitting. For example, if --tilesize=256, and\n\t\t--prunetest=0.1, a box of ~25-26 pixels each corner of every tile will be analyzed\n\t\tand if the standard deviation of any of the corners is 0, the tile will be excluded.\n\t\tTo turn off this option supply --prunetest=-1.0. The program automatically adjusts \n\t\tthings so that the minimum size of regions at the corners to check will be 4x4 pixels.
--tltfile str File containing a list of \n\t\ttilt angles corresponding to the tilt angles of images 0 to n of an aligned\n\t\ttilt series
--coords str text file containing x y z (or just z) coordinates for the particles, used to calculate icethickness if --icethicknessauto is specified for ctf fitting. NOT needed if --subtiltsdir is provided for ctf correction.
--ctfparamsfile str This should be a text file\n\t\twith ctf parameters in the following format;\n\t\tdefocus=value voltage=value cs=value apix=value bfactor=value ampcont=value\n\t\tA single space should separate each parameter from the next.\n\t\tDo not write any unit symbols for the values; just the numerical value.\n\t\tDefocus should be in microns, voltage in kV, apix in angstroms per pixel, and ampcont (amplitude contrast)\n\t\tshould be a decimal; for example, 0.1 for 10 percent amplitude contrast.\n\t\tIF you want to use DIFFERENT PARAMETERS PER IMAGE, then the file must contain\n\t\tmultiple rows with the different values.\n\t\tThe first row will be used to phase flip the first image,\n\t\tthe second row to phase flip the second, etc.
--defocilist str Text file containing\n\t\ta single column of defocus values in microns. The file should have as many\n\t\tdefocus values as images in the tiltseries or subtiltseries supplied.
--defocus float Default=0. \n\t\tTarget defocus at the tilt axis. In the absence of ctfparamsfile(s)\n\t\tthis value will be assumed to be the defocus at the tilt axis for all tilt images.
--voltage int Default=200. Voltage of\n\t\tthe microscope with which the images where collected. Supply it to replace the value\n\t\tin ctfparamsfile(s), or if ctfparamsfile(s) are lacking altogether.
--cs float Default=2.1. Cs of the microscope\n\t\twith which the images were collected. Supply it to replace the value in ctfparamsfile(s), \n\t\tor if ctfparamsfile(s) are lacking altogether.
--apix float Default=whatever is on the header\n\t\tof the images. Sampling of the images in angstroms/pixel. \n\t\tSupply --apix here to replace the value in ctfparamsfile(s), or if ctfparamsfile(s) \n\t\tare lacking altogether.
--bfactor int Default=1000. Bfactor or\n\t\ttemperature factor to use. Supply it to replace the value\n\t\tin ctfparamsfile(s), or if ctfparamsfile(s) are lacking altogether.
--ampcont float Default=0.05. Amplitude \n\t\tcontrast to use for CTF correction phase flipping. Supply it to replace the value\n\t\tin ctfparamsfile(s), or if ctfparamsfile(s) are lacking altogether.
--nozcorrection None If you \n\t\tturn on this option and --subtiltsdir is provided, the position in Z of each subtomogram\n\t\twill not be considered for CTF correction
--defocustop None Assumes the signal for defocus measurement (e.g., carbon film) is at the top layer of the tomogram.
--defocusbottom None Assumes the signal for defocus measurement (e.g., carbon film) is at the top layer of the tomogram.