point2model(1)                                                  point2model(1)



NAME
       point2model - Convert point listing to IMOD model file

SYNOPSIS
       point2model [options] <point_file> <model_file>

DESCRIPTION
       Point2model will convert a text file with a simple list of 3D point
       coordinates, one per line, to an IMOD model.  The file can be in one of
       three forms: each line consisting of X, Y, and Z coordinates; each line
       having a contour number followed by the coordinates; or each line hav-
       ing an object number and a contour number followed by the coordinates.
       The objects and contours can be numbered from either 1 or 0.  These
       forms correspond to the different forms that can be output by the com-
       panion program, Model2point.  When contour numbers are not contained
       in the file, there are options to place points into different contours
       based on the number of points or their Z values.

       In addition to options for processing the coordinates, there are sev-
       eral options for setting properties of the model or objects.  These are
       provided to save having to edit a model in 3dmod, a convenience that
       becomes significant when models are produced repeatedly at the command
       line or by a script.  Other such options could be added easily.

   Options
       Point2model uses the PIP package for input (see the manual page for
       pip).  Options can be specified either as command line arguments
       (with the -) or one per line in a command file (without the -):

       -input OR -InputFile      File name
              Input text file with points.  If this option is not entered, the
              first non-option argument will be used for the input file.

       -output OR -OutputFile    File name
              Output file for model.  If this option is not entered, the sec-
              ond non-option argument will be used for the output file.

       -open OR -OpenContours
              The default is to make all objects be closed contour type.  This
              option and -scat can be used to make all objects be open or
              scattered, respectively.

       -scat OR -ScatteredPoints
              Make objects be scattered point type

       -number OR -PointsPerContour   Integer
              Maximum number of points per contour.  The default is to put all
              points into one contour.  This option is not allowed if the
              point file has contour numbers.

       -planar OR -PlanarContours
              Start a new contour at each new Z value encountered when reading
              sequentially through the lines of input.  This option is not
              allowed if the point file has contour numbers.

       -zero OR -NumberedFromZero
              Objects and contours are numbered from 0 instead of 1

       -circle OR -CircleSize    Integer
              Turn on display of circles of this size (radius) at each point.
              If the points form open contours that progress through Z, this
              option will let you see them in the Zap window of 3dmod without
              having to edit the object.

       -sphere OR -SphereRadius       Integer
              Turn on display of spheres of this radius at each point.  Use
              this option to see scattered points in 3dmod without having to
              edit the object.

       -color OR -ColorOfObject       Three integers
              Color to make an object; enter red, green, and blue values rang-
              ing from 0 to 255.  To assign colors to multiple objects, enter
              this option multiple times.  (Successive entries accumulate)

       -name OR -NameOfObject    Text string
              Name to give an object; enter a text string, enclosed in quotes
              if it contains spaces.  To assign names to multiple objects,
              enter this option multiple times.  (Successive entries accumu-
              late)

       -image OR -ImageForCoordinates      File name
              Make the model's coordinate system match this image file.  This
              is not needed for loading the model onto this image in 3dmod,
              but will allow the model to be used together with this image
              file in various programs (e.g., Beadtrack) without having to
              load it into 3dmod and save it.

       -StandardInput
              Read parameter entries from standard input


AUTHOR
       David Mastronarde  (mast at colorado dot edu)

SEE ALSO
       model2point



BL3DEMC                              4.3.7                      point2model(1)