model2point(1)              General Commands Manual             model2point(1)

       model2point - converts model file to point file

       model2point  [options]  model_file  point_file

       Model2point will convert an IMOD or WIMP model file to a list of points
       with integer or floating point coordinates.  Each point will be written
       on a separate line, and the coordinates may be written either with no
       information about which object or contour the point came from, or with
       contour numbers, or with object numbers.

       Model2point and the companion program, Point2model, provide a more
       simple, but less versatile, way of converting data from and to an IMOD
       model than the Ascii format that can be output by Imodinfo.

       Prior to IMOD 4.10.35, Model2point put out integer coordinates by
       default, but it now puts out floating point values by default. Thus,
       the -float option is no longer needed, unless the environment variable
       MODEL2POINT_INTEGERS is set to revert to the old behavior.

       Model2point uses the PIP package for input (see the manual page for
       pip).  The following options can be specified either as command line
       arguments (with the -) or one per line in a command file or parameter
       file (without the -).  Options can be abbreviated to unique letters;
       the currently valid abbreviations for short names are shown in paren-

       -input (-inp) OR -InputFile    File name
              Input model file.  If this option is not entered, the first non-
              option argument will be used for the input file.

       -output (-ou) OR -OutputFile   File name
              Output text file for points.  If this option is not entered, the
              second non-option argument will be used for the output file.

       -float (-fl) OR -FloatingPoint
              Output model coordinates as floating point; otherwise the near-
              est integer value is output.  Floating point output is the
              default unless the environment variable MODEL2POINT_INTEGERS is
              set to any value.  This entry is still useful for overriding the
              environment variable setting.

       -integer (-int) OR -IntegerOutput
              Output model coordinates by taking the nearest integer instead
              of outputting floating point numbers, which is the default
              behavior.  This option cannot be entered with -float.

       -scaled (-s) OR -ScaledCoordinates
              Output coordinates in the model coordinate system, scaled by the
              original image pixel size in Angstroms and offset by origin val-
              ues.  The default is to output index coordinates corresponding
              to the pixel coordinates in the image.

       -object (-ob) OR -ObjectAndContour
              Output object and contour numbers for each point (numbered from

       -contour (-c) OR -Contour
              Output contour number for each point (numbered from 1)

       -zero (-ze) OR -NumberedFromZero
              Output object and contour numbers starting from 0 instead of 1

       -zcoord (-zc) OR -ZCoordinatesFromZero
              Output Z coordinates that are 0 instead of -0.5 at the bottom of
              the volume.  In IMOD models, integer Z values are defined as
              being located in the middle of a pixel in Z, which makes model
              coordinates range from -0.5 to NZ - 0.5 for a volume of NZ
              slices.  With this option, the point coordinates will be shifted
              so that they range from 0 to NZ, i.e., so that their fractional
              parts actually correspond to their fractional positions within
              the pixels in Z.

       -values (-v) OR -ValuesInLastColumn      Integer
              Enter 1 to output general point values as the last number on
              each line, after the Z coordinate, or -1 to output general con-
              tour values for the first point in each contour.  A point file
              with either format can be read back in by Point2model, pro-
              vided that the -values option is given to that program.  When a
              point or contour has no stored value, a value of 0 will be out-
              put, unless a different value is specified with the -fill

       -fill (-fi) OR -FillValue      Floating point
              Value to output when contour/point has no stored value (default

       -help (-h) OR -usage
              Print help output.

              Read parameter entries from standard input.

       Written by David Mastronarde, 4/23/95
       Converted to PIP, added output options

       Email bug reports to mast at colorado dot edu.

IMOD                                4.11.0                      model2point(1)