archiveorig(1)              General Commands Manual             archiveorig(1)

       archiveorig - Archive/restore original data after X-ray removal

       archiveorig  [options]

       archiveorig is a Python script that allows one to create a small file
       to archive original data after removing X-rays with Ccderaser.  This
       eliminates the huge redundancy in archiving the both original and X-ray
       removed data.  The script assumes that files are named with the conven-
       tions that Etomo uses.  Specifically, when the input file is given as, the original stack is assumed to be named
       The program then computes the difference between the original and X-ray
       removed stack and uses gzip compression of the difference file, which
       is named  The resulting file should be ~2 MB for a
       1 GB data stack.

       The entire process of removing X-rays, renaming a stack as set-, and archiving the difference can be repeated several
       times.  To allow all changes to be retained and reversed if desired,
       programs that do the renaming of to also
       rename an existing by adding a number to the end.
       The first time, 1 is added; after than, a number 1 higher than the
       highest existing number is added.  The programs that do this are Etomo
       and Batchruntomo.

       -d     Delete after successfully producing set-
      By default, the file is left for the user to

       -r     Restore from and
              The X-ray removed stack ( must be present to perform
              this operation.  The file is renamed to set-

       -n #   Restore the given number of levels of archives, not just the
              last level that created  For example, if ar-
              chiving has been done 3 times, there will be files set-
    ,, and
              Entering "-n 3" will use all three files to recreate the origi-
              nal stack.  Entering "-n 2" will use files
              and to recreate the stack that existed
              after the first round of X-ray removal.  In order to get back to
              the original stack at that point, there are three methods avail-
              able: 1) save by renaming it, rename
              to, and run this program just with "-r".  2) Rename
     to and set-
     to, and run this program
              with "-r -n 3".  3) Run this program with "-d" then run it again
              with "-r -n 2".

       -P     Output process ID.

       If the final output file already exists a backup image of the original
       is created with the ~ extension.

       David Mastronarde  <mast at colorado dot edu>

       ccderaser, subimage

IMOD                                4.10.12                     archiveorig(1)