smoothsurf(1) General Commands Manual smoothsurf(1)
NAME
smoothsurf - to smooth a surface defined by model contours
SYNOPSIS
smoothsurf [options] input_file output_file
DESCRIPTION
This program will smooth a surface defined by model contours, adjusting
the positions of points in each contour as needed. At each point on
the surface, it fits a 3-D polynomial to all points within a defined
range of Z-levels and within a specified distance of the central point.
That point's position is then replaced by the fitted position from the
polynomial. After this surface smoothing operation, each contour is
independently smoothed by local fitting to 2-D (ordinary) polynomials.
The default values for the number of Z levels (sections or slices) and
for the maximum distance in 3D should give a good starting point for
smoothing models drawn on tomographic reconstructions. Increase or
decrease these two numbers together to increase or decrease the smooth-
ing. Because the default values give a big disparity between the total
extent in Z versus X and Y (7 versus 30), the Z range should be
increased more than the distance. For example, try "-nz 11 -dist 20"
and "-nz 15 -dist 25" for progressively more smoothing. If you want to
experiment more broadly with the parameters, you can try changing the
balance between these two numbers, as well as omitting the independent
contour smoothing with "-cont 0".
For serial section reconstructions, note that the Z scaling is NOT
taken into account in computing 3D distances, so the maximum distance
corresponds more closely to distance in the X/Y planes than to true 3D
distance. The default parameters may be a good starting point, but
here it may be appropriate to increase the maximum distance more rela-
tive to the number of sections (e.g., start with "-dist 25").
Smoothsurf moves only the contours, not the points in any existing
meshes. To see the resulting surface, you need to rerun imodmesh.
OPTIONS
Smoothsurf uses the PIP package for input (see the manual 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 paren-
theses.
-input (-i) OR -InputFile File name
Input model file.
-output (-ou) OR -OutputFile File name
Output model file.
-objects (-ob) OR -ObjectsToSmooth List of integer ranges
A list of the objects to smooth (ranges are allowed, e.g.
1,2,5-7). The default is to do all closed-contour objects, and
open contours that lie in one plane.
-nz (-n) OR -NumberOfSections Integer
Number of sections or slices in Z to include in the fit. Higher
numbers smooth more. The default is 7.
-distance (-d) OR -MaximumDistance Floating point
Maximum distance from the central point being smoothed, for
points to be included in fits. Higher distances smooth more.
The default is 15 pixels.
-contorder (-c) OR -ContourOrder Integer
Order of the polynomials fit to contours to smooth them after
smoothing the surface, or 0 to omit this smoothing. Higher
orders smooth less. The default is order 2; order 1 (linear)
will probably oversmooth and contract the contours.
-surforder (-su) OR -SurfaceOrder Integer
Order of the polynomials fit to the surface. Higher orders
smooth less. The default is order 3. Note that a second-order
polynomial has 5 terms and a third-order has 9 terms.
-sort (-so) OR -SortSurfaces Integer
This option controls whether the program uses surface assign-
ments of contours to keep from including points from contours
that belong to different surfaces in a surface fit. With the
default value of 1, the program will analyze the object mesh, if
any, to sort contours into surfaces (see ImodSortSurf(1)).
Enter -1 to have the program use existing surface values of the
contours, or 0 to ignore surface information.
-retain (-r) OR -RetainMeshes
Do not delete the meshes for the objects being smoothed. These
meshes will not reflect the smoothing and the objects need to be
remeshed, so they are deleted by default unless this option is
entered.
-help (-h) OR -usage
Print help output.
-StandardInput
Read parameter entries from standard input.
HISTORY
Written by David Mastronarde, 9/9/97
6/17/04: Converted to PIP input with default values, fixed bug in contour
smoothing, made it work properly with pixel sizes in image file header
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 4.11.0 smoothsurf(1)