header

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). When they are stored in the
 file with the MRC standard convention (as is currently the case), then
 the standard header output 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.
 The program will look for an ".mdoc" file corresponding to the image
 file (i.e., named as the full image file name with ".mdoc" appended) if
 either: 1) the pixel spacing is 1.0 in the main header and there is no
 pixel size from the extended header; or 2) there is no title line with
 "Tilt axis angle" and no rotation angle from the extended header. If
 there is no pixel size information, a PixelSpacing entry in the global
 section of such an ".mdoc" file will be used to output the size in
 nanometers in a line near the end. If there is no rotation angle
 information, the value from a title line (section named "T" in the
 ".mdoc" file) with "Tilt axis angle" will be printed near the end of
 the output. If a title with "TiltAxisAngle" is found instead, the pro-
 gram will also look for a RotationAngle entry in the first image sec-
 tion of an ".mdoc" file. The latter value is defined relative to the X
 axis and should be 90 degrees higher than the value from a title line,
 which is relative to the Y axis. With these two values, it can recog-
 nize that it is a faulty ".mdoc" file from 2024 ThermoFisher software
 and print a correct value.
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, the first and last title, and a one-
 line summary of items in a SerialEM extended header if any.
 This is the only way to get a brief header output; the
 IMOD_BRIEF_HEADER environment variable is ignored when running
 this program.
 -eer (-e) OR -FullSizeOfEERFile
 Output the full super-resolution size and the number of frames
 in an EER file, overriding settings of the environment variables
 IMOD_READ_EER_SUPER_RES and IMOD_READ_EER_Z_SUMMING. By
 default, the program will output whatever size these variable
 settings produce.
 -tag (-t) OR -TiffStringTagToPrint Integer
 Number of a TIFF tag for which a string should be retrieved and
 printed if the field with that tag is present in the file. This
 value overrides a value in the environment variable
 TIFF_STRING_TAG_TO_PRINT. The tag for metadata in EER files is
 65001, and the tag for defects in a Falcon gain reference file
 is 65100.
 -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 5.2.0 header(1)