This program takes unaligned tilt series, performs alignment, and generate a tomogram.
		e2tomogram.py <tilt series stack> --rawtlt <raw tilt file> [options]
		e2tomogram.py <tilt series> <tilt series> <tilt series> ... --rawtlt <folder with .tlt files> [options]
		e2tomogram.py <tilt series stack> --tltstep <angle between tilts> [options]
	Note: Tiltseries must have the correct Apix values in their headers.

Option Type Description
--version None show program's version number and exit
--alltiltseries None Use all tilt series in the folder. Acceptable file extensions include hdf, mrc, mrcs, st.
--zeroid int Index of the center tilt. Ignored when rawtlt is provided.
--tltstep float Step between tilts. Ignored when rawtlt/mdoc is provided. Set to 0 if tilt present in header.
--rawtlt str Specify a text file contains raw tilt angles. Will look for files with the same name as the tilt series if a directory is provided
--mdoc str Specify a SerialEM .mdoc file or a folder containing same-named .mdoc files
--npk int Number of landmarks to use (such as gold fiducials). Default is 20.
--tltax float Angle of the tilt axis. Note the angle stored internally will have an opposite sign. The program will calculate one if this option is not provided.
--tltkeep float Fraction of tilts to keep in the reconstruction.
--tltrange str Include only tilts between 'START' and 'STOP', i.e. -40.0,40.0. Default behavior is to include all tilts.
--outsize str Size of output tomograms. choose from 1k, 2k and 4k. default is 1k
--niter str Number of iterations for bin8, bin4, bin2 images. Default if 2,1,1,1
--bytile None make final tomogram by tiles..
--load None load existing tilt parameters.
--notmp None Do not write temporary files.
--pkkeep float Fraction of landmarks to keep in the tracking.
--compressbits int Number of bits of precision in output tomogram with lossless compression. -1 -> uncompressed float
--clipz int Z thickness of the final tomogram output. default is -1, (5/16 of tomogram length)
--bxsz int Box size of the particles for tracking. Default is 32. Maybe helpful to use a larger one for fiducial-less cases..
--pk_maxval float Maximum Density value of landmarks (n sigma). Default is -5
--pk_mindist float Minimum distance between landmarks, as fraction of micrograph length. Default is 0.125
--correctrot None correct for global rotation and position sample flat in tomogram.
--filterto float filter to abs.
--filterres float filter final tomogram to target resolution (in A). Default is 40
--extrapad None Use extra padding for tilted reconstruction. slower and cost more memory, but reduce boundary artifacts when the sample is thick
--moretile None Sample more tiles during reconstruction. Slower, but reduce boundary artifacts when the sample is thick
--rmbeadthr float Density value threshold (of sigma) for removing beads. high contrast objects beyond this value will be removed. default is -1 for not removing. try 10 for removing fiducials
--threads int Number of threads
--tmppath str Temporary path
--verbose, -v int Verbose
--noali None skip initial alignment
--dryrun None skip final reconstruction
--patchtrack int use patch tracking before landmark based alignment. input 0/1/2 as the number of patch tracking iterations.
--posz None auto positioning along z axis
--xdrift None apply extra correction for drifting along x axis
--ppid int Set the PID of the parent process, used for cross platform PPID
--reconmode str Intepolation mode for reconstruction. default is trilinear. check e2help.py for details. Not recommended to change.
--maxshift float Maximum shift between tilt(/image size). default is 0.35
--highpass int initial highpass filter for alignment in pixels. default if 3
--badone None Remove one bad tilt during coarse alignment. seem to work better with smaller maxshift...
--flip None Flip the tomogram by rotating the tilt axis. need --load existing alignment
--autoclipxy None Optimize the x-y shape of the tomogram to fit in the tilt images. only works in bytile reconstruction. useful for non square cameras.