smoothsurf(1) General Commands Manual smoothsurf(1)NAMEsmoothsurf - to smooth a surface defined by model contoursSYNOPSISsmoothsurf [options] input_file output_fileDESCRIPTIONThis 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.OPTIONSSmoothsurf 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-InputFileFilenameInput model file.-output(-ou)OR-OutputFileFilenameOutput model file.-objects(-ob)OR-ObjectsToSmoothListofintegerrangesA 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-NumberOfSectionsIntegerNumber of sections or slices in Z to include in the fit. Higher numbers smooth more. The default is 7.-distance(-d)OR-MaximumDistanceFloatingpointMaximum 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-ContourOrderIntegerOrder 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-SurfaceOrderIntegerOrder 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-SortSurfacesIntegerThis 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-RetainMeshesDo 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-usagePrint help output.-StandardInputRead parameter entries from standard input.HISTORYWritten 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 headerBUGSEmail bug reports to mast at colorado dot edu. IMOD 4.12.62 smoothsurf(1)