extractmagrad(1) General Commands Manual 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 magnifica- tion 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 script- ing intensity value between 0 and 1 (not the scaled percent C2 read- out), 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 ver- sion 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. OPTIONS 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 -). Options can be abbreviated to unique letters; the currently valid abbreviations for short names are shown in parentheses. -input (-i) OR -InputImageFile File name Image file with tilt angles and intensities in header -output (-o) 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 (-g) OR -GradientTable File name File with table of mag gradients versus intensity (required) -rotation (-r) 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 (-p) OR -PixelSize Floating point Pixel size in nanometers (optional if pixel size is in header) -dgrad (-dg) 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 (-dr) OR -DeltaRotation Floating point Amount to add to all rotations, in degrees per micron of Z height -help (-h) 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 BUGS Email bug reports to mast at colorado dot edu. IMOD 5.2.1 extractmagrad(1)