imodfillin(1)               General Commands Manual              imodfillin(1)

       imodfillin - fill in missing contours in IMOD model using mesh data

       imodfillin  [options]  input_model  output_model

       imodfillin will fill in contours in an IMOD model on sections that were
       skipped during modeling.  It interpolates a contour between existing
       ones using information in the object mesh created by imodmesh.  Each
       interpolated contour will fall on the surface connecting existing con-
       tours.  It is thus necessary to run imodmesh before imodfillin.
       Since you need to have a mesh between contours on non-adjacent sec-
       tions, you should use one or more imodmesh options to connect across
       gaps in the data.  If sections have either a complete set of contours
       or no contours at all, then the -s option will suffice.  If the pattern
       is less rigid than this, use the -P option in addition (or exclu-
       sively), where the number of passes that you specify with this option
       equals the maximum number of sections of separation between contours
       that you wish to connect.  Do not use any imodmesh option that would
       set the z increment to greater than 1 (i.e., -l, -i, or -z ), for then
       imodfillin will probably create contours on sections that already have

       By default, the program will attempt to fill in all closed-contour
       objects that have meshes, but will skip open-contour objects.  Use the
       -o option to specify a subset of objects to be done, or to force it to
       do particular open-contour objects.

       The created contours will inherit any surface or time information con-
       tained in the meshes.  If your original contours have surface numbers,
       be sure to mesh with the -S option to preserve this surface information
       in the meshes, so that the interpolated contours will have the same
       surface numbers as the original ones.

       -e     Place new contours in existing objects.  Use this option if you
              do not plan to check and modify the interpolated contours.

       -n     Place new contours in new objects; this is the default, so that
              contours can be checked conveniently.  One new object will be
              created for each object that is being filled in.  These contours
              may be moved into the proper object either one by one or all at
              once via the Edit-Contour-Move dialog and M hotkey in 3dmod.

       -o list
              Do operations only on objects in the list of numbers.  The list
              can consist of comma-separated ranges (e.g., 1,7-11,13-17,19).
              Without this option, all closed contour objects with meshes are
              filled in.

       -i value
              Set the Z increment for filling in contours.  This option has
              two effects: the program will fill in only gaps that are wider
              than the given value, and it will insert new contours at this
              given Z increment instead of on every section.

       -R value
              Resolution or tolerance for point reduction in the generated
              contours.  Points are eliminated if they are within this dis-
              tance of the lines connecting the remaining points, just as with
              the -R option in imodmesh.  Values in the range 0.25 to 0.5
              are often useful.

       If the model file already exists, it becomes a backup file with ~ added
       to its name.

       David Mastronarde

       3dmod, imodmesh

       Email bug reports to mast at colorado dot edu.

IMOD                                4.11.0                       imodfillin(1)