filterplot(1)               General Commands Manual              filterplot(1)



NAME
       filterplot - plot filter created by 4 IMOD filter parameters

SYNOPSIS
       filterplot [graph options]

DESCRIPTION
       Filterplot shows a graph of the filter function created by the four
       parameters that are used in many IMOD programs: Sigma1, Sigma2,
       Radius1, and Radius2.  After you start the program, simply enter the
       parameters to see the graph of the filter attenuation factor versus
       spatial frequency.  Frequency is in reciprocal pixels and ranges from 0
       to 0.5 in the graph, although the filter function does extend farther
       than 0.5 to cover the higher frequencies found at oblique angles in 2D
       images and 3D volumes.

       The filter is the product of two gaussian functions, the first one typ-
       ically 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

HISTORY
       Added to package, 6/19/08

       Filterplot takes several standard command-line options about the graph-
       ics window: -s followed by a window size in x and y, -p followed by a
       window position in x and y, -message followed by a message to be shown
       in a message box, -tooltip followed by a tooltip for the graphics win-
       dow, and -nograph to disable the graphics window.

BUGS
       Email bug reports to mast at colorado dot edu.



IMOD                                 5.2.6                       filterplot(1)