imodsortsurf(1)             General Commands Manual            imodsortsurf(1)



NAME
       imodsortsurf - Sort contours into surfaces or surfaces into objects

SYNOPSIS
       imodsortsurf  [options]  input_model  output_model

DESCRIPTION
       This program can do three different operations related to surfaces.
         1) It can use the mesh produced by imodmesh to analyze the connec-
       tions between contours, and assign each set of connected contours a
       separate surface number.  If you then want the mesh for these objects
       to have the new surface numbers, it is necessary to remesh the objects
       with "imodmesh -S" or the "Surface" option in the "Meshing" panel of
       the 3dmod Model View Object Edit dialog.
         2) It can analyze a mesh in an object without contours (such as is
       produced by saving an object from the isosurface display in 3dmod
       Model View) and sort it into separate, unconnected surfaces, each with
       a different surface number.
         3) It can place each surface into a separate object.  This operation
       can be done either on existing surfaces or on the surfaces produced by
       analyzing the mesh.  It works by moving the contours themselves for a
       conventional object, or by moving the mesh components for an object
       without contours.  When contours are moved, the objects must all be
       meshed to see the surfaces.

       In conjunction with any of these operations, it is possible to specify
       a threshold volume and remove surfaces whose volume is below the
       threshold, or to specify a number or fraction of surfaces with the
       largest volumes to retain and remove the rest.  A threshold volume
       needs to be specified in the units of the model, typically as cubic
       nanometers or microns, but as cubic voxels if there is no pixel size
       set.  You can use Imodinfo to find out what units to use and the
       range of appropriate values.  This filtering may leave surface numbers
       that have no contours or meshes.  When the object has contours, the
       "cylinder volume" (see Imodinfo) is computed and compared to the
       threshold or used for sorting by volume; when the object has only
       meshes, the volume inside the mesh will be used.  The latter will not
       work well if there are surfaces that have open, cut sides, because
       these may have inappropriately small volume measures.

   OPTIONS
       -o list
              Restrict the sorting to objects in the given list of object num-
              bers, which can consist of a comma-separated set of ranges.  The
              default is to do all objects.

       -s     Split surfaces into new objects.

       -e     Use existing surfaces when splitting them into new objects.  The
              default is to analyze the surfaces from the mesh instead.  With
              this option, no mesh is required.

       -c     Make new objects the same color as the object from which they
              are derived.  Most other display properties are transferred from
              the existing object to the new object.

       -k     Keep the surface numbers when moving contours into new objects.
              The default is to set surface numbers to zero.

       -r vol Remove contours or meshes that form surfaces whose volume is
              less than the given value, specified as described above.

       -R     Retains only the contours or meshes that form surfaces with the
              largest volumes, keeping either the given fraction of surfaces
              (if the value is less than 1) or the given number of surfaces
              (if the value is 1 or higher).


AUTHOR
       David Mastronarde,  mast at colorado dot edu

SEE ALSO
       imodmesh, 3dmod

BUGS
       When surfaces are split into new objects, contour and surface labels
       will be lost.  Also, stored view information will not be copied to the
       new objects.



IMOD                                5.2.15                     imodsortsurf(1)