splitcorrection(1)          General Commands Manual         splitcorrection(1)

       splitcorrection - Produce multiple command files for running ctfphase-
       flip in parallel

       splitcorrection  [options]  ctfphaseflip_command_file

       splitcorrection is a Python script that will take a command file for
       running the ctfphaseflip program and produce multiple command files
       that can be run in parallel by Processchunks.

       The only argument that the typical user needs to give is -m to specify
       the number of views to be processed by each chunk.  The default value
       is printed out by the program's usage statement.  Thus, a typical com-
       mand might be
          splitcorrection -m 6 correction.com
       After giving this command, there will be a series of command files cor-
       rection-nnn.com to compute the chunks, a file correction-start.com, and
       a file correction-finish.com to finish the task and clean up intermedi-
       ate files. One can then enter
          processchunks machine_list correction
       where "machine_list" is the comma-separated list of machines to use, or
       the number of processors to use on a single machine.

       Splitcorrection 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.

       -m    Integer
              Set the number of views to be processed per chunk to the given
              value (the default is 5 ).

       -b    Integer
              Number of pixels at each boundary between chunks to save in sep-
              arate boundary files (named setname-nnn.cbound) and rewrite to
              the output file in the -finish.com file.  The default is 2048.

       -i OR -InitialComNumber   Integer
              Initial command file number to use, instead of starting with a
              "-start.com" file then files numbered from 1.

       -o OR -OpenForMoreComs
              Leave the command file collection open for more files by finish-
              ing with a "-sync.com" file instead of a "-finish.com" file and
              not removing command and log files.

       -r OR -RootNameOfOutput   File name
              Root name for command files, instead of using the name of the
              input command file.

       -dir (-d) OR -DirectoryForOutput    File name
              Directory in which to place output command files; log files will
              be created there as well.  The command files must still be run
              from the data set directory.

       -unique (-un) OR -UniqueInfoFile
              Give unique numbers to boundary info files by attaching the
              first command file number to the boundary info file.

       -size (-s) OR -InputDimensions      Three integers
              Size the input image file in X, Y, and Z.  Provide this if the
              file does not exist yet, to prevent the program from trying to
              access it.

       -help (-h) OR -usage
              Print help output

              Read parameter entries from standard input

       The finishing command file deletes all the command and log files for
       the chunks after collecting minimum, maximum, and mean density informa-
       tion from the log files.

       David Mastronarde  <mast at colorado dot edu>

       processchunks, ctfphaseflip