Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells

EXTRACTMAGRAD(1)        					EXTRACTMAGRAD(1)

NAME
	extractmagrad - Extract mag gradients for each image from header

SYNOPSIS
	extractmagrad  [options] input_image_file output_file

DESCRIPTION
  Extractmagrad will extract information needed to correct for magnification
  gradients from the header of an image file.  Intensities and tilt angles
  must be present in the extended header of the image file.  In addition, a
  file must be supplied with a table of mag gradients versus intensity.

  The program can read either version 1 or version 2 of the mag gradient
  table.  In a version 1 table, each line should contain a Tecnai scripting
  intensity value between 0 and 1 (not the scaled percent C2 readout), the
  magnification change in percent per micron of Z height, and the image
  rotation in degrees per micron of Z height.  The lines must be in order by
  increasing intensity.  The program will interpolate between values in this
  table but not extrapolate beyond the first or last intensities.  A version 2
  table starts with a line with the version number (2), followed by a line
  with the Tecnai scripting intensity at crossover.  After this would be the
  lines for the magnification and rotation at each intensity.  Given this kind
  of table, the program will use the crossover intensity to linearize the
  data, which improves the interpolation between measured points and allows it
  to extrapolate reliably.

  The output of the program is a file containing pixel size and tilt axis
  information plus a tilt angle, mag gradient, and rotation for each image
  in the input file.  This is the information needed by Newstack and Xfmodel
  to adjust images and models for the mag gradients.

  Extractmagrad 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 -InputImageFile   File name
    Image file with tilt angles and intensities in header

 -output OR -OutputFile   File name
    Output file for tilt angles and mag gradients.  This file will be in the
    format required for the -gradient entries to Newstack and Xfmodel.

 -gradient OR -GradientTable   File name
    File with table of mag gradients versus intensity (required)

 -rotation OR -RotationAngle   Floating point
    Angle of rotation of the tilt axis in the images; specifically, the angle
    from the vertical to the tilt axis (counterclockwise positive).

 -pixel OR -PixelSize   Floating point
    Pixel size in nanometers (optional if pixel size is in header)

 -dgrad OR -DeltaGradient   Floating point
    Amount to add to all mag gradients, in % per micron of Z height.  This can
    be used to experiment with different gradients.

 -drot OR -DeltaRotation   Floating point
    Amount to add to all rotations, in degrees per micron of Z height

 -help OR -usage
    Print help output

  -StandardInput
     Read parameter entries from standard input.


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