fenestra(1)                 General Commands Manual                fenestra(1)

       fenestra - find areas of holes in model objects


       This program will measure the sizes of holes through model objects
       described by a series of contours, such as fenestrations in Golgi cis-
       ternae.  It assumes that the objects have been modeled in Z planes
       while the holes appear when looking at the X or Y face of the model.
       For each model object, you must first create a separate object with
       points specifying the locations of the holes.  In general, each hole
       should be marked by two points, on the first and last Z planes where
       the opening occurs.  These points should be placed fairly carefully
       midway between the two contours and underneath the contour that closes
       off the hole on the adjacent Z place.

       You may place the locator points in separate contours or in the same
       contour, although in the latter case one must be particularly careful
       to enter a pair of points for each hole.  A hole occurring on only one
       Z plane may be specified by either one point or two, but if you use one
       point you MUST place that point in a separate contour.

       The program works by finding points on either side of the hole that are
       closest to the line connecting the two locator points.  Given all of
       these edge points, it then finds the plane that fits these points best.
       The normal to this plane is taken as the best direction for viewing the
       hole.  An initial area is computed from the polygon determined by pro-
       jecting the points into that plane.  Then, the program reexamines the
       contours at the edge of the hole and finds the points that encroach the
       most upon the hole, when viewed from the best direction determined from
       the initial points.  These points are used to compute a "minimized"
       area.  An equivalent diameter is reported, based on this minimized

       The program can read a series of model files and place the output in a
       single text file.

       Entries to the program:

       Name of output file for areas and diameters

       0 for short output of minimized area and equivalent diameter, or 1 for
       long output identifying the locator point contour number and location,
       the projection angles, and tyhe initial area

       For output of the points from which area was computed, as contours
       showing the outline of each hole, enter the number of a new object for
       the initial points, and another number for an object for the refined
       points.  Enter 0,0 for no output, or 0 and an object # for just the
       refined points.  Make sure the same object numbers will work for all of
       the models that will be processed.

       Model file name, or a blank line if there are no more models to

       A list of the numbers of the objects to be analyzed (Ranges may be
       used, e.g., 1-3,6,8)

       A list of the numbers of the corresponding objects with locator points
       (again, ranges may be used)

       An identifier or type number for each object being analyzed.

       IF you selected output of contours, enter the name of the new model

       The program will now loop back and ask for another input model to ana-
       lyze.  Enter a blank line when done.

               Written by David Mastronarde  9/14/97

       Email bug reports to mast at colorado dot edu.

IMOD                                4.10.22                        fenestra(1)