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)