makegradtable(1) General Commands Manual makegradtable(1)
NAME
makegradtable - make a magnification gradient table
SYNOPSIS
makegradtable [options] output_file
DESCRIPTION
Makegradtable can be used to construct a magnification gradient table
from two kinds of data: gradients based upon analysis of montaged
images at high tilt, and transformations that align images taken at
different Z heights. In the one case it will read a log file from run-
ning Findgradient, and in the other case it will read the transfor-
mation file produced by Xfalign and possibly edited in Midas.
These data can be smoothed and extrapolated as needed. To do this, the
program will transform the beam intensity values into: 1 / (Intensity -
crossover). Gradients are nearly linearly related to this transformed
intensity value, so lines can be fit to the points and used for smooth-
ing and extrapolation.
To run the program, you must have a file of the intensities extracted
from the original image file header, which can be obtained with
extracttilts -int input_file output_file
You must also supply the intensity of beam crossover for the given spot
size.
To derive a gradient table from montages, enter the name of the log
file from Findgradient with the FindgradFile option. This file should
contain program output once for each intensity that is to be included
in the gradient table. The output can be from running each section
separately or from running several sections together (i.e., ones taken
at the same intensity). If more than one run of Findgradient was
needed to analyze the montages, the log files can simply be concate-
nated; just be sure that each intensity is represented only once. The
section numbers given in the log file will be used to look up the
intensities from the intensity file.
To derive a gradient table from images taken at different Z heights,
the original image stack should consist of image pairs where the inten-
sity is kept the same for the two images of a pair, and the stage is
moved by the same amount and in the same direction for each pair.
Transformations can be obtained with Xfalign using the -bpair
option, which will just align the paired images to each other. When
running Makegradtable, enter the name of the transform file with the
TransformFile option and enter the Z height change if it is different
from 10 microns. The program will obtain gradients from every second
transform in the file.
The program will produce a version 2 mag gradient table with the fol-
lowing format, with the last line repeated for each intensity:
Version_number
crossover_intensity
intensity %_mag_change_per_micron degrees_rotation_per_micron
...
The table becomes incorrect when the microscope alignments are updated
in a way that changes the crossover intensity. When this happens, you
can use Fixgradtable to make a new table with the entries adjusted
for the change in crossover.
OPTIONS
Makegradtable uses the PIP package for input exclusively (see the man-
ual page for pip). The following options can be specified either as
command line arguments (with the -) or one per line in a command file
or parameter file (without the -). Options can be abbreviated to
unique letters; the currently valid abbreviations for short names are
shown in parentheses.
-findgrad (-f) OR -FindgradFile File name
Input file with output from Findgradient
-xffile (-x) OR -TransformFile File name
Input file with transforms for image pairs from stage moves in Z
-intensity (-i) OR -IntensityFile File name
File with intensity values from extracttilts -int
-output (-o) OR -OutputTable File name
Output file for mag gradient table. If this option is not
entered, the first non-option argument will be taken as the name
of the output file.
-raw (-ra) OR -RawOutput File name
Output file for raw, smoothed, and extrapolated data. If this
option is not entered, the same data will be printed to standard
output. The columns in this output are: a type identifier (1
for measured and 2 for extrapolated data), intensity, trans-
formed intensity, the raw and smoothed percent magnification
change per micron, and the raw and smoothed degrees of rotation
per micron.
-crossover (-c) OR -CrossoverIntensity Floating point
Underlying intensity value at crossover. For an FEI microscope,
this is not the intensity value that appears in the user inter-
face but the intensity used internally, which is saved in Seri-
alEMcalibrations.txt when crossover is calibrated in SerialEM.
This entry is required.
-microns (-mi) OR -MicronsMoved Floating point
Number of microns of stage movement in Z (default 10)
-msmooth (-ms) OR -SmoothMags
Smooth magnification changes with linear fits
-rsmooth (-rs) OR -SmoothRotations
Smooth rotation changes with linear fits
-sfit (-s) OR -MaxInFitForSmoothing Two integers
Maximum number of points in fits for smoothing mags and rota-
tions. If one of these values is 0, a line will be fit to all
points on one side of crossover and the smoothed values will be
the values in this line. Otherwise, for each point, a line is
fit to the nearest points up to this maximum number, and the
value of the line is used as the smoothed value at that inten-
sity. The default is 5 for magnifications and 0 for rotations.
-efit (-ef) OR -MaxInFitForExtrapolation Two integers
Maximum number of points in fits for extrapolating mags and
rotations. With the default values of 0, a line will be fit to
all points on one side of crossover and the line will be extrap-
olated both toward crossover and to more extreme intensities.
Otherwise, a line will be fit to the given number of points at
the end of the curve, and this line will be used to find the
extrapolated value at that end of the curve.
-extremes (-ex) OR -ExtremesForExtrapolation Two floats
Extreme values to extrapolate to (default 0.2 and 0.8)
-distance (-d) OR -DistanceFromCrossover Floating point
Use this entry to specify how close to crossover to extrapolate
the curves to. The number is expressed as a fraction of the
distance from crossover to the last measured intensity on the
particular side of crossover, where the intensities are trans-
formed as given above. Typically, with the default fraction of
0.5, the extrapolated gradient will be twice what it is at the
last measured intensity.
-param (-p) OR -ParameterFile Parameter file
Read parameter entries as keyword-value pairs from a parameter
file.
-help (-h) OR -usage
Print help output.
-StandardInput
Read parameter entries from standard input.
HISTORY
Written by David Mastronarde, February 2006
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 4.11.0 makegradtable(1)