archiveorig(1)              General Commands Manual             archiveorig(1)



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

SYNOPSIS
       archiveorig  [options]  setname.st

DESCRIPTION
       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
       setname.st, the original stack is assumed to be named setname_orig.st.
       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 setname_xray.st.gz.  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-
       name_orig.st, 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 setname.st to setname_orig.st also
       rename an existing setname_xray.st.gz 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.

OPTIONS
       -d     Delete setname_orig.st after successfully producing set-
              name_xray.st.gz.  By default, the file is left for the user to
              delete.

       -r     Restore setname_orig.st from setname_xray.st.gz and setname.st.
              The X-ray removed stack (setname.st) must be present to perform
              this operation.  The file setname_xray.st.gz is renamed to set-
              name_xray.st.gz.old.

       -n #   Restore the given number of levels of archives, not just the
              last level that created setname_xray.st.gz.  For example, if ar-
              chiving has been done 3 times, there will be files set-
              name_xray.st.gz, setname_xray.st.gz.1, and setname_xray.st.gz.2.
              Entering "-n 3" will use all three files to recreate the origi-
              nal stack.  Entering "-n 2" will use files setname_xray.st.gz
              and setname_xray.st.gz.2 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 setname.st by renaming it, rename setname_orig.st
              to setname.st, and run this program just with "-r".  2) Rename
              setname_xray.st.gz.2.old to setname_xray.st.gz.2 and set-
              name_xray.st.gz.old to setname_xray.st.gz, 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.

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

AUTHOR
       David Mastronarde  <mast at colorado dot edu>

SEE ALSO
       ccderaser, subimage



IMOD                                4.10.10                     archiveorig(1)