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