matchshifts(1) General Commands Manual matchshifts(1)NAMEmatchshifts - Find shift component of transformation between two vol- umesSYNOPSISmatchshifts root_name1 root_name2 NX NY NZ [xf_in] [xf_out]DESCRIPTIONMatchshifts 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.ARGUMENTSroot_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.FILESThe 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.AUTHORDavid Mastronarde <mast at colorado dot edu>SEEALSOsolvematch, xyzproj, matchvol, tiltxcorr, clip, taperv- oledge(1) IMOD 4.9.10 matchshifts(1)