header(1)                   General Commands Manual                  header(1)



NAME
       header - to read and display the header of an MRC image file.

SYNOPSIS
       header [options] filename(s)

DESCRIPTION
       Header will read and display the information in the header of an MRC
       image file - image size, data type, min, max, etc.  The program will
       accept the file name either from the command line or as an entry to the
       program after it is started.  If there is no file name or other argu-
       ments on the command line, the program asks for an input file name.

       If no options are given, the program will print the complete standard
       header output, which is the same as what other Fortran programs output
       when reading an image file header.  If any of the output options
       describe below are given, then the program prints only the numeric out-
       put for the given options, without any descriptive labels.  If multiple
       options are given, each option will produce one line of numeric output,
       with the output in the order that the options appear below (and that
       the output appears in the standard header output). If multiple file
       names are entered, then all of the header entries will be printed for
       one file, then for the next, etc.

       The origin values are reported with the original IMOD sign convention
       (subareas have more negative origins), which is the way that origins
       are stored internally in IMOD programs.  If they are stored in the file
       with the MRC standard convention instead, then the standard header out-
       put will show the text "..(inverted_in_file).." on the origin line,
       unless the origins are all zero.

       If the program finds that the file has an extended header from Seri-
       alEM, it will report what items are stored there and summarize the com-
       mands needed to extract them.  If the file has an Agard/FEI-style
       extended header, the program will report a pixel size and rotation
       angle from there.  In such a case, if the pixel spacing in the standard
       header is 2, 3, or 4, the program will assume that this represents bin-
       ning that was applied in IMOD, and it will report the original pixel
       size times this binning.  If the file came from the FEI acquisition
       software, the sign of the rotation angle is inverted to conform with
       the conventions used in IMOD.

OPTIONS
       The options are processed by the PIP package (see man page for pip).
       Options can be abbreviated to unique letters; the currently valid
       abbreviations for short names are shown in parentheses.  They are:

       -input (-i) OR -InputFile      File name
              Input image file.  All nonoption arguments will be treated as
              input files.  (Successive entries accumulate)

       -size (-s) OR -Size
              Output image dimensions

       -mode (-mo) OR -Mode
              Output data mode

       -pixel (-p) OR -PixelSize
              Output pixel spacing in angstroms

       -origin (-o) OR -Origin
              Output origin values

       -minimum (-mi) OR -Minimum
              Output minimum value of data

       -maximum (-ma) OR -Maximum
              Output maximum value of data

       -mean (-me) OR -Mean
              Output mean value of data

       -rms (-r) OR -RootMeanSquare
              Output the RMS value (root-mean-square deviation from the mean)
              stored in the header.

       -volume (-v) OR -VolumeNumber       Integer
              For an HDF file with multiple volumes, the program will report
              the number of volumes and output the header of the first.  Use
              this option to specify a different volume number to see the
              header of, numbered from 1.

       -brief (-b) OR -Brief
              Output brief header with dimensions, pixel size, mode, minimum,
              maximum, and mean value, and the first and last title.  This is
              the only way to get a brief header output; the IMOD_BRIEF_HEADER
              environment variable is ignored when running this program.

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

       -StandardInput
              Read parameter entries from standard input.

HISTORY
       Originally written as part of the MRC image processing package.
       Converted to run on SGI by Paul Furcinitti and David Mastronarde, 1994.
       Converted to PIP input with simplified output options, 2/15/06.

BUGS
       Email bug reports to mast at colorado dot edu.



IMOD                                4.10.10                          header(1)