resamplemod(1)                                                  resamplemod(1)



NAME
       resamplemod - Turn a model perpendicular to Z axis and resection

SYNOPSIS
       resamplemod  [options]  input_file  output_file

DESCRIPTION
       Resamplemod can be used to resample or resection a model of fiber tra-
       jectories after rotating it so that the fibers run parallel to the Z
       axis.  The program can find the mean trajectories of the fibers them-
       selves and then rotate the model to bring the mean trajectory parallel
       to the Z axis, or one can supply a special contour to indicate the axis
       that should be rotated to the vertical.  Contours will be resampled at
       single pixel intervals so that the model will have the correct dimen-
       sions when it has the same Z scale factor as the original model.

OPTIONS
       Resamplemod 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-
       theses.


       -input (-i) OR -InputFile      File name
              Input model file.

       -output (-o) OR -OutputFile    File name
              Output model file.

       -exclude (-e) OR -ExcludeObjects    List of integer ranges
              Objects to exclude from resampling; for example, closed contour
              objects.

       -direction (-d) OR -DirectionObjects     List of integer ranges
              Objects to use to determine mean direction of fibers.  The
              default is to use all of the objects; enter a list to use a sub-
              set of objects, or just a single object number if you have cre-
              ated a special object with a contour to indicate the direction.

       -main (-m) OR -MainAxis   Integer
              Dominant axis along which fibers run (1 = X, 2 = Y, or 3 = Z.)
              The default is the Z axis (3), which is appropriate for serial
              section models.  A different axis is generally needed for a
              model from a tomogram.  If the model was built on a tomogram
              loaded into 3dmod with flipping (-Y), enter a number that refers
              to the axis that was seen in 3dmod.

       -skip (-s) OR -SkipInversion
              Do not invert contours that go from high to low along the main
              axis.  The default is the reorder contours if necessary so that
              they go from low Z to high Z in the output model.

       -param (-p) OR -ParameterFile       Parameter file
              Read parameter entries as keyword-value pairs from a parameter
              file.

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

       -StandardInput
              Read parameter entries from standard input.


HISTORY
       Written by David Mastronarde, 2000; incorporated in IMOD 9/5/03


BUGS
       Email bug reports to mast at colorado dot edu.



BL3DEMC                              4.7.3                      resamplemod(1)