extractpieces(1)                                              extractpieces(1)



NAME
       extractpieces - Extract piece coordinates from header of image file

SYNOPSIS
       extractpieces  [options]  input_image_file  output_piece_list_file

DESCRIPTION
        EXTRACTPIECES will extract piece coordinates from the header of
        an image file, if they are present, and produce a file with those
        coordinates (a piece list file).  In addition, it can extract coordi-
       nates
        from an image metadata file produced by SerialEM.  The metadata file
        must have the same number of sections as the Z size of the image file.

OPTIONS
       Extractpieces uses the PIP package for input (see the manual page for
       pip). Thus, the following options can be specified either as command
       line arguments (with the -) or one per line in a command file (without
       the -):

       -input OR -InputFile      File name
              Image file with header information to extract.  If this option
              is not entered, the first non-option argument will be taken as
              the input file.

       -output OR -OutputFile    File name
              Output file for header values.  If this option is not entered,
              the second non-option argument will be taken as the output file.

       -mdoc OR -MdocMetadataFile
              Obtain values from a metadata file named with the name of the
              input file plus '.mdoc', instead of from the extended header of
              the image file.  A file with this name is generated by SerialEM
              when an option is selected to save extra information in a meta-
              data file, or when the coordinates are too large to fit in the
              extended header.

       -other OR -OtherMetadataFile   File name
              Obtain values from the metadata file with the given name,
              instead of from the extended header of the image file.  With
              this option, no input image file needs to be supplied; but in
              this case you must specify the output file with "-output"
              instead of as a non-option argument.

       -help OR -usage
              Print help output

       -StandardInput
              Read parameter entries from standard input.

       If the program is started with no command line arguments, it reverts to
       interactive input with the following entries:

         Image file with piece list information in header
         Output file for piece coordinates


HISTORY
         Written by David Mastronarde, October 1999

BUGS
       Email bug reports to mast at colorado dot edu.



BL3DEMC                              4.7.3                    extractpieces(1)