Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells

CLIPMODEL(1)							   CLIPMODEL(1)

NAME
	clipmodel - to clip a MT model by location or object number

SYNOPSIS
	clipmodel

DESCRIPTION
  CLIPMODEL will clip out a portion of a model and output either a
  new model file, or a simple list of point coordinates.  It can either
  include only points within a defined rectangular block of 3-
  dimensional coordinate space, or exclude points within such a block.
  This process of inclusion or exclusion may be invoked repeatedly.
  The program can also eliminate an entire IMOD object (or all WIMP
  objects of specified colors).
  
  To specify a rectangular block of coordinate space, one enters the
  minimum and maximum X, Y and Z coordinates of the block.  The
  default values for the minimum and maximum X and Y coordinates are
  very large numbers, so one can select the default if one wants no
  limitation on either the X, the Y, or both coordinates.  A point on
  the edge of the block (i.e. with one coordinate exactly equal to one
  of the lower or upper limits) is treated as if it is inside the
  block.
  
  The coordinates that you enter should correspond to the index 
  coordinates in the image display from which the model was last saved.
  If you last saved the model from an 3dmod display of a subset of the
  image stack, then you need to refer to coordinates within that
  subset.  If this is a problem, reload the model onto the full image
  stack (or a subset starting at 0,0,0) and save it again. Index
  coordinates are numbered from zero, so your Z values should be 1
  less than the section number shown in 3dmod.

  The program does not create new contours.  This limitation means that
  if there is more than one segment of a contour inside a block being
  included (or more than one segment outside a block being excluded),
  you have two options.  The program either can truncate the contour
  to be the longest such segment, discarding any other segments, or
  it can clip all of the points out of the contour that are in the
  region being excluded, connecting the remaining segments with
  straight lines.
  
  If an object consists of scattered points, then all points in the
  region being included will be included, regardless of which clipping
  option you choose for clipping contours.
  
  When you choose to retain all segments in the region being included,
  the program will sum and report the total length of cut edges, so
  that the cut surface can be subtracted from a computed surface area.
  For objects consisting of closed contours, this total will include
  an edge between the starting and ending points of a clipped
  contour, if points were clipped off at those ends of the contour.
  For open contour objects, this edge will not be included.

  Entries:
  
  Name of input model file

  Name of output file for clipped model
  
  0 to output a model file, 1 to output a file with a simple list of
     integer point coordinates, or -1 to output such a point list with
     two additional corner points preceding the points on any given
     section.  Such a file could be used as a set of teaching points
     for MTTEACH and MTDETECT; but beware of the need for each "zone"
     to be contained within a single piece in a montaged image file.
  
  0 to retain only the longest segment of a contour included in a
     volume (if the contour passes through the volume more than once),
     or 1 to retain all segments included in the volume.

  0 to include points in the rectangular coordinate block to be
     specified next, or 1 to exclude points in such a block, or -1 to
     exclude whole IMOD objects, or -2 to clip points off of one end
     of all contours in selected IMOD objects.
  
  IF you entered 0 or 1, next specify the coordinates as follows:

     Minimum and maximum X, minimum and maximum Y coordinates of the
       block.  / selects the defaults of no limits
  
     Minimum and maximum Z of the block
  
  BUT IF you entered -1, enter instead a list of the numbers of the
     objects to be excluded.  For data from a WIMP model file, use
     256 minus the WIMP object color (e.g. 1 for color 255), or the
     negative of this value to refer to WIMP objects that are turned
     off.  Ranges may be entered (e.g. 1-3,6).
  
  OR IF you entered -2, enter the number of points to clip off of the
     start, and the number of points to clip off of the end, of
     contours in selected objects.  Next enter a list of the numbers of
     the objects to be clipped in this fashion, where WIMP objects may
     again be referred to by 256 minus their color, or the negative of
     this value if they are turned off.  Ranges may be entered.

  0 to store the current result, or 1 to loop back and specify a new
     block to include or exclude (or objects to exclude or clip)
  
HISTORY
  Written by David Mastronarde, 1/11/90; modified for IMOD 4/24/97; compute cut
  edges and handle coordinates better, 10/24/00.