enhance(1) General Commands Manual enhance(1)
NAME
enhance - to apply gaussian bandpass filter
SYNOPSIS
enhance [input_filename] [output_filename]
DESCRIPTION
This is a two-dimensional gaussian bandpass filter program for image
enhancement purposes. For three-dimensional images, each image in the
stack is separately bandpass filtered. This program is superceded by
Mtffilter, which provides all of the same filtering capabilities
plus padding to avoid edge artifacts.
The filter is specified by four input parameters: Sigma1, Sigma2,
Radius1, and Radius2. Several other IMOD programs take these same 4
parameters, which produce the same effect as described here. The fil-
ter functions produced by these parameters can be visualized with the
program Filterplot. The filter is the product of two gaussian func-
tions, the first one typically controlled by Sigma1 and the second one
by Sigma2, Radius1, and Radius2. If all values are positive or zero,
then the first filter is in the form of a gaussian highpass filter
given by:
(1. - exp(-r**2/(2*Sigma1**2)))
The second filter is a gaussian-edged band-pass filter. This filter is
flat between Radius1 --> Radius2 and decays symmetrically as a gaussian
below Radius1 or above Radius2:
exp(-(r-Radius)**2/(2.*sigma2**2))
If either Sigma = 0, then that part of the filter is removed.
The units are in fractional reciprocal lattice units, that is r goes
from 0-->sqrt(2)/2 (0-->.5 on each axis)
If Sigma1 is negative, the first filter is the second derivative of a
gaussian, Del-squared G, with formula
r**2*exp(-r**2/(2.*Sigma1**2))
This filter alone is bandpass with a peak at 1.414*|Sigma1|, so Sigma2
and the Radii can be set to zero.
If Sigma2 is negative, the second filter is inverted (1 minus the
Gaussian band-pass filter). This filter is then multiplied by the fil-
ter specified by sigma1 (if any).
If Radius1 is negative, then the first filter is 0 out to |Radius1| and
rises as an inverted gaussian from that point:
(1. - exp(-(r-|Radius1|)**2/(2.*Sigma1**2)))
The effective Radius1 for the second filter is then 0, but this filter
can still be used to add lowpass filtering.
Several modes of operation are possible:
Gaussian low-pass filter (temperature factor)
: Sigma1 & Radii = 0, use Sigma2
Gaussian bandpass centered at Radius
: Sigma1=0, use Radius1=Radius2 & Sigma2
Gaussian-edged badpass between Radius1 & Radius2
: Sigma1=0, use Radius1,Radius2 & Sigma2
Gaussian bandpass (low-pass + high-pass)
: Radii = 0, use Sigma1 & Sigma2
For versions of IMOD distributed or built with FFTW, there are no
restrictions on the image dimensions other than that the size in X must
be even.
The program will accept file names either from the command line or as
entries to the program after it is started. If there are two names on
the command line, they will be taken as the input and output file
names; if there is one name, it will be taken as the input file name
and the program will ask for the output file name; if there are no com-
mand line arguments, the program will ask for both input and output
file names.
The output file will have the same mode as the input, and for integer
data modes, each section will be individually scaled to occupy the
range for that mode.
Input parameters are:
SIGMA1,SIGMA2,RADIUS1,RADIUS2
as described above
IORIG if IORIG = 1 then the F(0,0) is
unchanged by filter operation
HISTORY
Version 1.10 27.MAY.82 DAA FOR VAX
Version 1.11 02.JUNE.82 DAA FOR VAX
Version 1.12 10.JUNE.82 DAA FOR VAX
Version 1.13 23.JULY.82 DAA FOR VAX
Update 1.13 18.November.82 DAA FOR VAX
Bug fix 14.July.88 DNM FOR uVAX
Bit mode 09.August.88 DNM FOR uVAX
Del-squared G 01.September.88 DNM FOR uVAX
Inverted filter 26.April.89 DNM FOR uVAX
Ported to unix 07.December.94 DNM FOR SGI
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 5.0.2 enhance(1)