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 5.2.0 archiveorig(1)