e2tomo_icongpu 

usage: This program requires ICON-GPU and IMOD. Wrapper to run ICON-GPU reconstructions using fewer parameters. The program automatically crops the tiltseries into a square, runs test alignments
	to make sure a good XY size is picked (some sizes make ICON crash), and picks the correct iteration numbers. 
	The reconstructed tomogram is also automatically rotated around x so that z is the shortest size using IMOD's clip rotx function, and can be optionally binned if --shrink is provided.

	Preprocessing and reconstruction normally happen in separate runs since preprocessing acts on the raw (or ideally, X-ray corrected) tiltseries, the .st file from IMOD after X-ray correction.
	On the other hand, the reconstruction should be performed with the preprocessed tiltseries AFTER it has been aligned with IMOD (the .ali file) and AFTER gold fiducials have been deleted.
	This program automatically backs up the .st and .ali IMOD files while replacing them with the ICONPreProcessed files (gold deletion needs to proceed in IMOD's pipeline) prior to reconstruction.
	An option is provided through --skipgolderasing to streamline the entire pipeline with a single run of this program if the sample has no gold fiducials or the user doesn't want to delete them.

	To preprocess the raw tiltseries, run:

	e2tomo_icongpu.py --tiltseries=<.st file> --iconpreproc --thickness=<value in pixels>

	This MUST be run from the IMOD reconstruction directory, with all alignment files in it, so that the preprocessed tiltseries can be realigned automatically without going through IMOD's ETOMO pipeline again.

	For reconstruction, run:

	e2tomo_icongpu.py --tiltseries=<.ali file> --sizez=<size of output tomogram in z>

	The .tlt file should be located automatically if it has the same name (but with .tlt extension) as the --tiltseries, as should be the case for an intact IMOD directory.
	Otherwise, to supply an alternative .tlt file, add --tltfile=<.tlt file from imod> to the command above.

	(This can be run in any given directory as long as the .ali and .tlt files are there).

	If you don't need or want to delete gold fiducials and want to run BOTH steps at once (ICONPreProcess and reconstruction with ICON-GPU), add --skipgolderasing
Option Type Description
--version None show program's version number and exit
--gpus str default=-1 (all available GPUs will be used). To select specific GPUs to use, provide them as a comma-separated list of integers.
--highpasspixels int Default=4. Number of Fourier pixels to zero out during highpass filtering AFTER reconstruction (postprocessing). Provide 'None' or '0' to disactivate.
--iconpreproc None default=False. If on, this will trigger a call to ICONPreProcess on the .st file supplied through --tiltseries.
--lowpassresolution float Default=100. Resolution in angstroms to lowpass filter the tomogram AFTER reconstruction (postprocessing). Type 'None' or '0' to disactivate.
--path str Default=icongpu. Name of the directory where to store the output results. Only works when reconstructing the .ali file (preprocessing of the .st file will output the preprocessed tiltseries to the current directory). A numbered series of 'icongpu' directories will be created (i.e., if the program is run more than once, results will be stored in iconpu_01, icongpu_02, etc., directories, to avoid overwriting data).
--ppid int Default=-1. Set the PID of the parent process, used for cross platform PPID
--shrink int Default=0 (not used). Shrink factor to provide IMOD's binvol program with to bin/shrink the output tomogram after rotation about the x axis.
--sizez int Default=0 (not used). Output size in Z for the reconstructed tomogram. This should be the same as the --thickness value provided during tiltseries preprocessing, or larger (it's good to make sure the entire reconstruction will fit in the reconstruction volume without being too tight). If running a reconstruction of the .ali file and both --thickness and --sizez are provided, the latter will supersede the former.
--skipgolderasing None default=False. If on, this will call IMOD to generate a new aligned tiltseries after ICONPreProcess, and then ICON-GPU will be automatically called to perform the reconstruction. Typically, one would NOT use this option as it is useful to delete the gold fiducials prior to reconstruction.
--thickness int default=0. Thickness of the specimen as seen in a preliminary weighted back projection reconstruction from IMOD (through how many slices in Z are there specimen densities?).
--tiltseries str default=None. .st file from IMOD if --iconpreproc is turned on. Otherwise, supply the .ali file from IMOD *after* X-ray correction, iconpreprocessing, and alignment with IMOD.
--tltfile str default=None. .tlt file from IMOD.
--verbose, -v int verbose level [0-9], higher number means higher level of verboseness.