Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells

EXTRACTPIECES(1)					       EXTRACTPIECES(1)

NAME
	extractpieces - Extract piece coordinates from header of image file

SYNOPSIS
	extractpieces  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 coordinates 
  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.

  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 metadata 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