clonevolume(1)              General Commands Manual             clonevolume(1)



NAME
       clonevolume - clone copies of a volume (typically a PEET averaged sub-
       volume) back to the aligned positions and orientations in a starting
       volume.

SYNOPSIS
       clonevolume  [options]  -at csv_file  -into into_vol  inVol  outVol


DESCRIPTION
       After aligning and averaging a set of subvolumes with PEET, it is often
       useful to copy the averaged subvolume back into a copy of an input vol-
       ume at the positions and orientations of the individual aligned parti-
       cles.  Clonevolume performs this operation. The in_vol will be cloned
       into into_vol at locations and orientations specified by csv_file, and
       the output written to out_vol. The comma-separated value location/ori-
       entation file csv_file will typically have been created by PEET program
       createAlignedModel(1). The out_vol will be silently overwritten if it
       already exists. Neither in_vol, into_vol nor csv_file will be modified.

       The PEET alignment and corresponding average must have beem created
       with "Align Averages Vertically" disabled for proper orientations of
       the cloned subvolumes.

       While clonevolume is designed for use with a csv location file and an
       input volume created by PEET, this is not required. Except for the
       first, header line, which is always ignored, each line in the location
       file must contain 7 comma-separated fields representing contour number,
       X, Y, and Z center coordinates in pixels, and Z-Y-X Slicer angles in
       degrees, (stored in the order X, Y, Z), respectively, representing the
       rotation to be applied to the input volume.


OPTIONS
       Clonevolume 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 -).
       Options can be abbreviated to unique letters; the currently valid
       abbreviations for short names are shown in parentheses.

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

       -output (-o) OR -OutputFile    File name
              Name to give the output volume. If this option is not entered,
              the second non-option argument will be used.

       -at OR -AtPoints     File name
              Name of the summary file giving coordinates and orientations at
              which clones are to be inserted.

       -into (-int) OR -IntoFile      File name
              The volume to which the output should be initialized prior to
              inserting any clones of the input. (Required).

       -x OR -XRange   Two integers
              The input volume will not be cloned at points outside this
              range.

       -y OR -YRange   Two integers
              The input volume will not be cloned at points outside this
              range.

       -z OR -ZRange   Two integers
              The input volume will not be cloned at points outside this
              range.

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

       -contours (-c) OR -ContourNumbers   List of integer ranges
              A comma and dash separated list of contour numbers. If entered,
              clones will be created only at points belonging to one of the
              specified contours in the model of the original volume.

       -alpha (-al) OR -AlphaTransparency       Floating point
              A floating point number between 0 and 1 specifying the trans-
              parency to be used when cloning volumes  (default  0). If 0,
              cloned voxels will simply replace the originals. More generally,
              the output voxels will be alpha times the cloned voxel plus (1 -
              alpha) times the previous value.

       -mask (-m) OR -MaskFile   File name
              The name of a byte (mode 0) file which will be used to mask the
              input volume. Non-zero values in this file indicate voxel loca-
              tions in the input volume which should be cloned.

       -rmin (-rmi) OR -rMin     Integer
              The input volume will not be cloned at radii smaller than this.

       -rmax (-rma) OR -rMax     Integer
              The input volume will not be cloned at radii larger than this.


AUTHOR
       John Heumann  <heumannj at colorado dot edu>

SEE ALSO
       createAlignedModel(1), clonemodel



IMOD                                4.10.10                     clonevolume(1)