patch2imod(1)                                                    patch2imod(1)



NAME
       patch2imod - makes model from patch displacement or residual file

SYNOPSIS
       patch2imod [options] <patch file> <IMOD model file>

DESCRIPTION
       patch2imod creates an IMOD model from a file containing 3-D displace-
       ments at a series of positions, such as the patch file generated by
       corrsearch3d.  Each displacement will be represented by a vector
       starting at the position of the patch, and whose magnitude and direc-
       tion are determined by the 3-D displacement multiplied by a scale fac-
       tor.  These vectors are simply open contours consisting of two points.
       In addition, if the patch file contains correlation coefficients or
       residual values, these values will be stored in the model.

       The resulting model can be viewed to determine the location of patches
       with aberrant displacements and even edited to remove such patches.
       The easiest way to do this is to start 3dmod with just the model file
       and no image file, open the model view window, and use the right mouse
       button in the model view window to select vectors that differ greatly
       from their neighbors.  The currently selected vector(s) will be high-
       lighted by being thicker.  They may then be deleted with the D hot key.
       The edited model can be converted back to a patch file with
       imod2patch.

       The correlation or residual values can be visualized by opening the
       "Values" panel in the model view Object Edit window and selecting "Show
       stored values".  The color display can be manipulated and subsets of
       vectors can be selected.

       One can also read the model in on top of a tomogram; by default it is
       marked as flipped so that it will display correctly on tomograms in
       their original orientations.

       The scaling is stored as the pixel size in the model header.  Do not
       change this value, or imod2patch will not be able to convert the dis-
       placements back correctly.

       The program will also convert a list of 2-D residuals produced by
       tiltalign.  In this case, the model is not marked as flipped, so
       that it can be displayed on top of the original image file.

   Options
       -s <value>
              Change the vector length scaling to the given value; the default
              is 10.

       -f     Do not flip Y and Z coordinates in the model.  Use this option
              to display the model on a tomogram that has been flipped or
              rotated from its original orientation.

       -c <size>
              Include four clipping planes in the model to enclose a square
              area of the given size in the center of the model.  These planes
              will not be on by default, but can be turned on and manipulated
              together in the model view Object Edit window.  These planes
              could be helpful for seeing a subset of vectors when the model
              is rotated.

       -n <name>
              Give this name to the model object.  The name is useful for
              indicating what kind of values are stored with the vectors.

FILES
       If the model file already exists, it becomes a backup file with ~ added
       to its name.

AUTHOR
       David Mastronarde

SEE ALSO
       imod2patch, patchcrawl3d, patchcorr3d, 3dmod, 3dmodv,
       findwarp, refinematch, tiltalign

BUGS
       Email bug reports to mast at colorado dot edu.



BL3DEMC                             3.13.2                       patch2imod(1)