extractpieces(1)            General Commands Manual           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 coordi-
       nates (a piece list file).  In addition, it can extract coordinates
       from an image metadata file produced by SerialEM, and can do so auto-
       matically if the image file itself does not have piece coordinates.
       The program can also extract coordinates stored as attributes in an HDF
       file, or from an ".idoc" file saved by SerialEM.

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.  An image file name is required unless the
              -other option is entered.

       -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.  You do not supply the name of the .mdoc file
              when you use this option.  As of IMOD 4.8.7, the program will
              look for such a file automatically if the requested values are
              not present in the image file header.  Thus, this option is no
              longer necessary except for forcing the program to ignore values
              in the header and access the .mdoc file first.

       -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 if
              you do omit the input file, 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.



IMOD                                 5.2.6                    extractpieces(1)