tomocleanup(1)              General Commands Manual             tomocleanup(1)

       tomocleanup - Remove or list intermediate files in a tilt series data

       tomocleanup  options  directory ...

       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.

       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

       -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

              Read parameter entries from standard input

       When files are actually removed, the program writes leaves a complete
       list of the files removed in a file "cleanedUpFiles".

       David Mastronarde

       sirtsetup, multifiltsetup

       Email bug reports to mast at colorado dot edu.

IMOD                                4.12.62                     tomocleanup(1)