clonemodel(1)               General Commands Manual              clonemodel(1)



NAME
       clonemodel - clone copies of a model (e.g. an isosurface from a PEET
       average) back to the aligned positions and orientations.

SYNOPSIS
       clonemodel  [options]  -at csv_file  input_model  output_model


DESCRIPTION
       After aligning and averaging a set of subvolumes with PEET and creating
       an isosurface model of the average, it is often useful to create a new
       model containing multple copies of that isosurface reflecting the posi-
       tions and orientations of the individual aligned particles in the orig-
       inal volume. Clonemodel performs this operation, optionally pseudo-col-
       oring each copy according to the corresponding cross-correlation coef-
       ficient or other stored value . The input_model will be cloned at loca-
       tions and orientations specified in summary file csv_file and the out-
       put written to output_model.  The comma-separated value summary file,
       csv_file, will typically have been created by running PEET program cre-
       ateAlignedModel(1).  The output_model will be silently overwritten if
       it already exists. Neither input_model nor csv_file will be modified.

       The PEET alignment and average must have been created with "Align Aver-
       ages Vertically" disabled for proper orientations of the cloned models.

       While clonemodel is designed for use with a csv summary file created by
       PEET and a model containing an isosurface rendering of the PEET aver-
       age, this is not required. Except for the first, header line, which is
       always ignored, each line in the summary file must contain 7 comma-sep-
       arated fields representing contour number, X, Y, and Z center coordi-
       nates 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 model. An optional 8th field, if present, represents a
       value to be mapped to a pseudo-color for that cloned model.  Partially
       missing values will be treated as if they were 0. If no values are
       present, color will be inherited from the input model.


OPTIONS
       Clonemodel 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 (-i) 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 (-o) OR -OutputFile    File name
              Name to give the output file containing cloned copies of the
              input model.  If this option is not entered, the second non-
              option argument will be used.

       -at (-a) OR -AtPoints     File name
              Name of the summary file giving coordinates and orientations, at
              which clones are to be inserted, and, optionally, a value to be
              mapped to a pseudo-color.

       -reference (-r) OR -ReferenceImage       File name
              Image file from which to set image coordinate reference informa-
              tion.  Using this option attaches this information to the model
              just as loading the model into 3dmod along with this image and
              resaving the model does.  The model should then display cor-
              rectly on subsets or supersets of this volume, or on volumes
              with more or less binning.

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

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

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

       -v OR -VRange   Two floats
              The min and max values for psuedo-coloring cloned models accord-
              ing to the optional 8th field of the summary file. If ommitted,
              values present will be mapped to use the full range of psuedo-
              colors.

       -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.


AUTHOR
       John Heumann  <heumannj at colorado dot edu>

SEE ALSO
       createAlignedModel(1), clonevolume



IMOD                                 5.2.0                       clonemodel(1)