e2import

usage: prog [options] files
	This program performs a variety of tasks for getting data or metadata from other programs into an EMAN2 project.

	import_movies - imports DDD movie data for a cryoEM project (--importation copy recommended)

	import_particles - will simply copy a set of per-micrograph particle files into EMAN2.1's preferred HDF format in particles/
	import_boxes - will read EMAN1 '.box' files (text files containing coordinates) into appropriate info/*json files (see --box_type)
	import_eman1 - will convert a typical EMAN1 phase-flipped start.hed/img file into an EMAN2 project (converting files, fixing CTF, splitting, ...)

	import_tomos - flag to handle imported files as subtomogams for a SPT project (see also --importation)
	import_serialem - flag to handle imported files as SerialEM mdoc files
	import_fei - flag to handle imported files as FEI tomography metadata files
	import_ucsftomo - flag to handle imported files as UCSF tomo metadata files
	import_tiltseries - imports tilt series for a tomography project (--importation copy recommended)

Option	Type	Description
--version	None	show program's version number and exit
--import_movies	None	Import DDD movies
--darkrefs	None	Specify a comma separated list of dark refereence stacks/images to import. Files will be placed in movierefs_raw. See --importation for additional options.
--gainrefs	None	Specify a comma separated list of gain refereence stacks/images to import. Files will be placed in movierefs_raw. See --importation for additional options.
--apix	float	Specify the apix of the tiltseries you are importing. If -1 (default), the apix in the header will not be changed.
--import_tiltseries	None	Import tiltseries
--mdoc	str	Specify a SerialEM .mdoc file or a folder containing same-named .mdoc files, or 'auto' to try and find .mdoc files automatically
--rawtlt	None	Specify an imod/serialem rawtlt file, and imported tilt series will be sorted in tilt sequence instead of collection sequence, 'auto' will attempt to find a .tlt file automatically
--import_tomos	None	Import tomograms for segmentation and/or subtomogram averaging
--compressbits	int	Bits to keep for compression. default is 8 bits. Use 0 for lossless compression. Currently used only on tiltseries, eman1 and particles
--removesub	str	If set will exclude the specified string from imported filenames
--import_particles	None	Import particles
--import_eman1	None	This will import a phase-flipped particle stack from EMAN1
--importation	None	Specify import mode: move, copy or link
--invert	None	Invert the contrast before importing tomograms
--shrink	int	Shrink tomograms before importing. Does not work while not copying.
--import_boxes	None	Import boxes
--extension	str	Extension of the micrographs that the boxes match
--box_type	None	Type of boxes to import, normally boxes, but for tilted data use tiltedboxes, and untiltedboxes for the tilted particle partner
--boxsize	int	Specify the boxsize for each particle.
--curdefocushint	None	Used with import_eman1, will use EMAN1 defocus as starting point
--curdefocusfix	None	Used with import_eman1, will use EMAN1 defocus unchanged (+-.001 um)
--threads	int	Number of threads to run in parallel on a single computer when multi-computer parallelism isn't useful
--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