```matchshifts(1)              General Commands Manual             matchshifts(1)

NAME
matchshifts - Find shift component of transformation between two vol-
umes

SYNOPSIS
matchshifts root_name1 root_name2 NX NY NZ [xf_in] [xf_out]

DESCRIPTION
Matchshifts uses cross correlation to complete the process of finding
an initial transformation between two volumes.  It is now obsolete but
was needed because older versions of Tiltalign produces relative fidu-
cial coordinates, from which the shifts in X, Y, and Z could not be
deduced by Solvematch.  It will now take the output of Solvematch,
assumed to be solvezero.xf, and determine whether the transformation
already contains shifts.  If it does, the solvezero.xf is simply copied
to solve.xf.

If Matchshifts finds a 3x3 transformation matrix with zero shifts in
solvezero.xf, it projects each volume into the X-Z plane, or the cen-
tral 1024 by 1024 pixels if the volumes are larger than that.  It
rotates the projection of the second volume using appropriate terms
from the transformation matrix, then cross-correlates this rotated pro-
jection with the projection of the first volume to obtain an initial
estimate of shifts in X and Z.  In this way, quite large shifts between
the volumes can be determined.  Next, it extracts a subset from the
center of the first volume and uses matchvol to extract and transform
the approximately corresponding subset of the second volume.  The two
subsets are cross-correlated in 3-D to estimate the shifts in X, Y, and
Z.  With these final shifts, it then extracts a subset volume just
adjacent to the central subsets and uses 3-D correlation to check
whether the shifts are correct.  If the displacement between these two
volumes is too large, matchshifts exits with an error message and a
non-zero status.

ARGUMENTS
root_name1 and root_name2 are the root names (without extension .rec)
of the first and second volumes.

NX, NY, NZ are the X, Y, and Z dimensions of the small volume that will
be extracted for 3-D cross-correlation.

An optional sixth argument (xf_in) can be used to specify the name of
the file with the initial 3x3 transformation and zero shifts; otherwise
the file is assumed to be solvezero.xf.

An optional seventh argument (xf_out) can be used to specify the output
file for the completed transformation; otherwise this file will be
solve.xf.

FILES
The program leaves the subset volumes used for checking the alignments.
These files are matchcheck.rec and matchcheck.mat.  The program assumes
that volumes have the extension ".rec" and, unless there is a sixth
argument, it assumes that the 3x3 transformation is in solvezero.xf.

AUTHOR
David Mastronarde  <mast at colorado dot edu>