tomocleanup

tomocleanup(1) General Commands Manual tomocleanup(1)
NAME
 tomocleanup - Remove or list intermediate files in a tilt series data
 set
SYNOPSIS
 tomocleanup options directory ...
DESCRIPTION
 Tomocleanup removes intermediate files from a tilt series data set
 directory, similar to the cleanup operation in Etomo. It can also
 provide a list of the files without removing them. Selected kinds of
 files can be retained if desired. If none of the options for keeping
 files are given, all large files will be removed except the raw stack
 and the latest stage of reconstruction: for single axis, either the
 "_full" reconstruction file or the final trimmed reconstruction file;
 for dual-axis, either the single-axis reconstructions, or the combined
 volume, or final trimmed reconstruction file.
OPTIONS
 Tomocleanup uses the PIP package for input (see the manual page for
 pip). Options can be specified either as command line arguments
 (with the -) or one per line in a command file (without the -).
 Options can be abbreviated to unique letters; the currently valid
 abbreviations for short names are shown in parentheses.
 -dir (-d) OR -Directory File name
 Name of directory in which to clean up files (. for current
 directory). At least one directory must be entered either with
 this option or as a non-option argument. (Successive entries
 accumulate)
 -aligned (-al) OR -KeepAlignedStack
 Keep the final aligned stack file (after all modifications)
 -untrimmed (-un) OR -KeepUntrimmedRec
 Keep an untrimmed reconstruction ("_full" file for single axis,
 "sum" file for dual axis); the default is to remove this if the
 final Output from Trimvol exists.
 -axis (-ax) OR -KeepAxisRecs
 Keep the single axis reconstructions of a dual-axis data set;
 the default is to remove these if the combined file or final
 trimmed reconstruction exists.
 -sirt (-s) OR -KeepSIRTRecs
 Keep SIRT reconstructions or ones built with SIRT-like filter;
 the default is to remove these.
 -filter (-f) OR -KeepFilterTrials
 Keep filter trials output from Multifiltsetup
 -trial (-t) OR -TrialRun Integer
 List files to be deleted but do not remove them. Enter 1 to have
 back files ending in "~" summarized on one line, or 2 to have
 them listed individually. In the latter case, and if there is
 only one directory entered, the program will output only file-
 names that can be used directly.
 -help (-h) OR -usage
 Print help output
 -StandardInput
 Read parameter entries from standard input
FILES
 When files are actually removed, the program writes leaves a complete
 list of the files removed in a file "cleanedUpFiles".
AUTHOR
 David Mastronarde
SEE ALSO
 sirtsetup, multifiltsetup
BUGS
 Email bug reports to mast at colorado dot edu.
IMOD 5.2.6 tomocleanup(1)