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 4.11.0 clonevolume(1)