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 4.5.6 point2model(1)