transferfid(1)                                                  transferfid(1)



NAME
       transferfid - make seed model for second axis from fiducials for first
       axis

SYNOPSIS
       transferfid  [options]  setname

DESCRIPTION
       transferfid will make a seed model for tracking fiducials in one axis
       of a dual-axis tilt series, using the fiducial model for the other
       axis.  It first finds a pair of views from the two axes that match up
       well after an appropriate translation, rotation, and stretching of the
       view from the first axis.  It then transforms the corresponding section
       of the fiducial model from the first axis by the same amount, and uses
       Beadtrack to find each bead on the view from the second axis.  This
       collection of new positions then forms the seed model for tracking the
       second axis.

       The program will do all of these operations without any arguments
       except the name of the data set if all files are named appropriately;
       specifically, if the command files for beadtrack are named tracka.com
       and trackb.com, and the tilt angles are in files with extension
       .rawtlt.  By default, the program will transfer fiducials from the "a"
       axis to the "b" axis, in which case it assumes the first fiducial model
       is named setnamea.fid.  However, you can use the -b option to transfer
       from the "b" axis to the "a" axis, in which case the existing fiducial
       model is assumed to be named setnameb.fid.  By default, the program
       will search for the best matching pair of views using the 5 views near-
       est to zero tilt from each data set.  It will consider rotations by
       both -90 and +90 degrees, and it will set the bead radius for Beadtrack
       using the value in tracka.com.

       If the program fails to find the proper alignment between the two axes,
       this is probably because the rotation is too far from 90 degrees,
       and/or the translations are too large.  You can solve this problem by
       using the -m option to run midas and set the initial rotational and
       translational alignment manually.  When you get into Midas, you may
       need to rotate the image by 180 degrees, unless you specify the angle
       in advance with the -a option, but this large rotation will not cause
       problems.  If you find that the images are mirror images of each other,
       then you can either mirror one around the X axis in Midas using the
       entry in the Edit menu, or go back to running Transferfid without Midas
       but with the -x option.

       Once the seed model is created, the program analyzes contours in the
       fiducial model from the first axis to provide information that is
       needed when running solvematch.  If the -c option is used, then cor-
       responding coordinates of the transferred beads in the two data sets
       will be placed into the specified output file.  This information is
       sufficient for solvematch to identify the corresponding fiducials in
       the final alignment, regardless of whether some seed points fail to
       track or some contours are deleted from either fiducial model.  If this
       option is not used, the program indicates what the correspondence
       between points should be when running solvematch.  The list of
       points in A could be in error in some cases unless a fiducial coordi-
       nate file (setnameafid.xyz) is also available.  For this reason, it is
       advisable to run tiltalign at least once on the first fiducial model
       before running transferfid.  The lists could also become erroneous if
       one of the points in the new seed model fails to track, or if fiducials
       are deleted from either model after running transferfid.  If such
       changes occur, just enter a small starting subset of points and let
       solvematch come up with the rest of the correspondences.

       Finding the best pair of views is somewhat time-consuming.  Two ways to
       reduce this time are to reduce the number of views in the search with
       the -n option and to specify the direction of rotation between the axes
       with the -a option.  The latter option alone will save only 15% of the
       time, because the program will abandon one rotation direction if it is
       clearly worse after considering four pairs of views, or only two if the
       difference between directions is very large.


OPTIONS
       Transferfid 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.

       -s OR -Setname       Text string
              Root name of dataset (omit the a or b)

       -b OR -TransferBtoA
              Transfer backwards, from the "b" axis to the "a" axis.  You will
              generally not need to specify any filenames with this option.

       -ia OR -AImageFile   File name
              Set the name of the image file upon which the fiducial model for
              the "a" axis tilt series was built; the default is to take the
              name from the tracka.com command file.

       -ib OR -BImageFile   File name
              Set the name of the image file for tracking beads in the "b"
              axis tilt series; the default is to take the name from the
              trackb.com command file.

       -f OR -FiducialModel      File name
              Set the name of the fiducial model file for the first, already
              tracked tilt series; the default is setnamea.fid (or set-
              nameb.fid with the "-b" option.)

       -o OR -SeedModel     File name
              Set the name of the output file for the seed model; the default
              is setnameb.seed (or setnamea.fid with the "-b" option.)

       -n OR -ViewsToSearch      Integer
              Set the number of views from each data set to include in the
              search for the best matching pair of views; the default is 5.

       -za OR -ACenterView       Integer
              Set the number of the view from the "a" axis tilt series around
              which to search for the best match; the default is the view
              nearest to zero tilt, using tilt angles in the file set-
              namea.rawtlt or tilt angles implied by FirstTiltAngle and Tilt-
              Increment entries in tracka.com.

       -zb OR -BCenterView       Integer
              Set the number of the view from the "b" axis tilt series around
              which to search for the best match; the default is the view
              nearest to zero tilt, using tilt angles in the file set-
              nameb.rawtlt or tilt angles implied by FirstTiltAngle and Tilt-
              Increment entries in trackb.com.

       -a OR -AngleOfRotation    Integer
              Use this option to specify the direction of rotation from the
              first to the second axis.  Only the sign of this number matters,
              so you can enter -1 or -90 for clockwise rotations, or 1 or 90
              for counterclockwise rotations.  In the absence of this option,
              the program will consider both directions of rotation.

       -x OR -MirrorXaxis
              Mirror one image around the X axis before rotating by 90
              degrees.

       -m OR -RunMidas
              Run Midas on the first pair of views, and use the alignment that
              you set in Midas as the initial alignment for all pairs of views
              that are considered.

       -c OR -CorrespondingCoordFile       File name
              Use this option to have corresponding fiducial coordinates on
              the best matching views placed into an output file.  This file
              will also record the section numbers in the two sets and whether
              the transfer was from "b" to "a".

       -lowest (-l) OR -LowestTiltTransformFile      File name
              File in which to save transform for lowest tilt pair of views

       -t OR -LeaveTempFiles
              For diagnosing problems, leave temporary files in the standard
              temporary directory (/usr/tmp, /tmp, or defined by IMOD_TMPDIR)
              or in the current directory if there is no temporary directory.

       -PID   Print process ID

       -StandardInput
              Read parameter entries from standard input


FILES
       Whether or not they fit the default naming conventions, the image files
       for fiducial tracking for each tilt series and the first fiducial model
       must be present in the current directory.  If the output file already
       exists, a backup image of the original is created with the ~ extension.

AUTHOR
       David Mastronarde  <mast at colorado dot edu>

SEE ALSO
       beadtrack, tiltxcorr, remapmodel, clipmodel, xfsimplex,
       xfmodel, midas, solvematch, tiltalign



BL3DEMC                              4.7.3                      transferfid(1)