Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells

EXTRACTTILTS(1)							EXTRACTTILTS(1)

NAME
	extracttilts - Extract tilt angles or other info from image file header

SYNOPSIS
	extracttilts  [option] input_image_file [output_file]

DESCRIPTION
  EXTRACTTILTS will extract one kind of information from the header of an
  image file, if it is present, and produce a file with a list of the values.
  The default behavior is to extract tilt angles; these can be extracted from
  headers in the Agard/FEI format or from headers produced by SerialEM.
  Enter an option to extract one of the other kinds of information written by
  SerialEM.

  In addition to extracting data stored in the image file header, the program
  can extract from a metadata file written by SerialEM in the autodoc format.
  A wider range of information can be stored in such a file than in the
  header.  The metadata file must have the same number of sections as the
  image file.

  Extracttilts 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.  If no output file
    is given, the values are printed to standard output.

 -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.

 -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.

 -tilts OR -TiltAngles
    Extract tilt angles from header or metadata file (the default behavior). 
    The angles are in degrees.

 -stage OR -StagePositions
    Extract stage positions from header or metadata file.  The positions are
    in microns.

 -mag OR -Magnifications
    Extract magnifications from header or metadata file.

 -intensities OR -Intensities
    Extract intensities from header or metadata file.  On the Tecnai, these
    are the intensity values reported by Tecnai scripting, which range from 0
    to 1 and differ by a scaling factor from the percent C2 readout in the
    Tecnai user interface.  On the JEOL, they correspond to the percent C3
    readout shown in SerialEM.

 -exp OR -ExposureDose
    Extract incident dose on specimen during camera exposure, referred to as
    exposure dose in SerialEM.  The units are electrons per square Angstrom.

 -camera OR -CameraExposure
    Extract camera exposure time, in seconds, from metadata file.

 -pixel OR -PixelSpacing
    Extract pixel size in Angstroms from metadata file

 -defocus OR -Defocus
    Extract defocus in microns from metadata file.  The value is the focus
    readout of the microscope, not the defocus measured by autofocusing.

 -warn OR -WarnIfTiltsSuspicious
    When extracting tilt angles, warn if more than half of them are near zero
    or any are bigger than 95 degrees.

 -all OR -AllPieces
    Extract the selected item for all pieces of a montage.  The default is to
    output the value for the last piece of the montage at each Z value.

 -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 tilt information
  Output file for tilt angles, or Return to print to standard output


HISTORY
  Written by David Mastronarde, 1999
  Converted for PIP input and to get other information, 3/17/04