solvematch(1)                                                    solvematch(1)



NAME
       solvematch - Solve for transformation matching one tomogram to another

SYNOPSIS
       solvematch  [options]

DESCRIPTION
       Solvematch will solve for a 3-dimensional linear transformation relat-
       ing the tomogram volumes resulting from tilt series around two differ-
       ent axes.  It can use information from the 3-D coordinates of fiducials
       found by Tiltalign, or from IMOD models of corresponding points in
       the two volumes, or from both of these sources together.  Current ver-
       sions of Tiltalign produce fiducial lists with coordinates correspond-
       ing the coordinates in the tomogram, thus providing all of the informa-
       tion that Solvematch needs to find the transformation.  Older versions
       of Tiltalign produced coordinates centered around zero; this situa-
       tion is discussed below.

   Using Fiducial Coordinates
       When you use fiducial coordinates, the program needs to know how the
       fiducial points correspond between the two tilt series.  There are two
       different ways that this information can be provided.

       If Transferfid was used to produce the seed model for one of the
       axes from the fiducial model for the other, then it can be given an
       option to produce a file with the coordinates of corresponding fiducial
       points from one view in each data set.  This file can be provided to
       Solvematch with the "-transfer" option and the program will be able to
       deduce how the points in the fiducial lists from Tiltalign corre-
       spond.  This capability allows you to add or delete fiducial points in
       either fiducial model after running Transferfid without having to
       keep track of how this affects the correspondence between points.  This
       option requires that both fiducial models be supplied to Solvematch.
       Also, it is essential that Solvematch be informed if the A axis is
       being matched to the B axis, with the -atob option.

       In the absence of a transfer coordinate file, the program needs lists
       of points that correspond between the two data sets.  If it is given a
       small list of points which do correspond, it can find the rest of the
       correspondences and ignore any points from either set that do not have
       a mate.  There are two restrictions in using this capability.  First,
       one must identify at least 4 initial correspondences; in fact, having
       at least 5 is recommended.  Second, if there are fiducials on both sur-
       faces of the section, this initial list must include at least one from
       each surface.

       When you enter point numbers, use the numbers listed on the left in the
       fiducial coordinate file.  These numbers may not correspond to the con-
       tour numbers in the original fiducial model if some contours were not
       included in the solution.  These numbers do not need to be sequential;
       i.e., you can delete points from the coordinate file.  The program will
       refer to points by these numbers.  When you have both fiducial coordi-
       nates and points from matching models, it will refer to the latter
       points by the negative of their point number.

       When using fiducial coordinates, you also need to indicate to Solve-
       match whether the gold fiducials are on one surface or distributed in
       depth (typically but not necessarily on two surfaces).  If there is
       gold on only one surface, you must determine whether the two tomograms
       are inverted in Y (Z in flipped orientation); i.e. whether the gold is
       on the "top" of the section in one tomogram and the "bottom" in the
       other even though they can be superimposed by a rotation.  The program
       needs to know this because there is no reliable information about this
       polarity in the fiducial coordinates.  However, such an inversion
       should be impossible when data are acquired with a CCD camera.

   Using Matching Models
       When fiducial points from Tiltalign are not available, you can use
       models of corresponding points to register the two volumes.  Pick a set
       of points that can be localized well in both tomograms and enter them
       in the same order into a model for each tomogram.  The points can be in
       the same or in different objects or contours, as long as they occur in
       the same order in each model.  The points should be well-distributed in
       all dimensions, and they must not all be in one plane.  At least 8
       points are recommended.  If this is to provide the basis for the final
       alignment of the volumes, they should be relatively near the 8 corners
       of the volume, and more points should be used for greater accuracy; but
       if the alignment is to be refined with correlation, this is not neces-
       sary.

       Using Old, Relative Fiducial Coordinates With fiducial coordinates from
       older versions of Tiltalign, the program can solve for the 3 by 3
       transformation but not for the shifts in X, Y and Z.  There are two
       ways to get these shifts: by cross-correlation of one transformed vol-
       ume with the other, and by giving Solvematch models of corresponding
       points in the two tomograms.  The shell script that does correlations,
       Matchshifts, is generally successful.  If it fails, you have two
       options: rerun Tiltalign to get absolute coordinates; or create match-
       ing models.  If you do this, 3-6 points are recommended.  If fiducials
       are essentially on one surface, then the modeled points are needed to
       find the scaling in Y (Z in flipped orientation) between the two tomo-
       grams.  In this case, be sure to distribute the points in depth (rather
       than all on one surface) and use 5-6 points so as to provide informa-
       tion on this scaling.

   Local Fitting
       Sometimes the fit to the fiducial points gives a high maximum residual
       error because there is a big nonlinear distortion between the two vol-
       umes.  In these cases, fitting to local sets of points can be used to
       determine that the fiducials have been properly identified and that the
       global fit is as good as it is ever going to be.  If the LocalFitting
       option is selected, the program will try local fits when the maximum
       residual is above the specified limit.  It determines the size of the
       area that, on average, would contain the specified minimum number of
       points.  It then sets up local areas of this size, overlapping by 50%,
       and expands an area if necessary to contain the minimum number of
       points.  It performs fits to the points in each area and reports the
       results of the fits.  If the overall maximum residual is less than 1.5
       times the specified limit, and no more than 5% of the areas have maxi-
       mum residuals above this limit, the fit is considered adequate.

       If local fitting is being done, then the program will also compute a
       local fit to points at the center of the volume so as to determine how
       far the global 3D transformation will shift data at the center of the
       volume out of alignment.  If this shift is large enough, then
       corrsearch3d may have trouble starting to find the alignment of the
       data.  Thus, if the program finds that this shift is bigger than a
       specified limit, it recommends initial shifts to be used when running
       corrsearch3d and may also recommend that the initial matching volume
       be made the same size as the volume being transformed.  It will exit
       with an error so that you can adjust these parameters before proceed-
       ing.

   Program Operation
       The program will automatically remove "outliers", pairs of points that
       are likely to be incorrect because their residual errors are so extreme
       relative to the other points.  Up to 10% of points may be removed in
       this way.  If, even after removing such outliers, the maximum residual
       in the linear fit is still higher than a value that you specify, then
       the program will exit with an error.

       The program determines the transformation and computes the deviation
       between each actual point in the first tomogram and the transformation
       of the corresponding point in the second tomogram.  It reports the mean
       and S.D. of these deviations, the number of the point with the highest
       deviation, and the magnitude of its deviation.

OPTIONS
       Solvematch uses the PIP package for input (see the manual page for
       pip) and can also take input interactively to maintain compatibility
       with old command files.  The following options can be specified either
       as command line arguments (with the -) or one per line in a command
       file or parameter file (without the -).  Options can be abbreviated to
       unique letters; the currently valid abbreviations for short names are
       shown in parentheses.


       -output (-o) OR -OutputFile    File name
              Output file for 3D transformation.  This entry may be omitted.

       -afiducials (-af) OR -AFiducialFile      File name
              Name of file with coordinates of fiducials from the first tilt
              series.  To solve for the transformation using matching models
              only, omit this entry.

       -bfiducials (-bf) OR -BFiducialFile      File name
              Name of file with coordinates of fiducials from the second tilt
              series.  This entry is not needed when using matching models
              only.

       -alist (-al) OR -ACorrespondenceList     List of integer ranges
              A list of the points in series 1 for which a corresponding point
              in series 2 is known with confidence.  Ranges may be entered
              (e.g. 1-5,7,6,12).  This entry and the following one are not
              needed when a coordinate file from transferfid is available.
              The default is that all points correspond between the two
              series.

       -blist (-bl) OR -BCorrespondenceList     List of integer ranges
              A list of the corresponding points in the second series.  The
              same number of values must be entered in this list as in the
              preceding list.  Again, the default is that all points corre-
              spond between the two series.

       -transfer (-t) OR -TransferCoordinateFile     File name
              File of matching fiducial coordinates produced by running trans-
              ferfid with the -c option.

       -amodel (-amo) OR -AFiducialModel   File name
              Name of fiducial model file for first tilt series.  This entry
              is needed only when a transfer coordinate file is being used.

       -bmodel (-bmo) OR -BFiducialModel   File name
              Name of fiducial model file for second tilt series.  This entry
              is needed only when a transfer coordinate file is being used.

       -use OR -UsePoints   List of integer ranges
              List of starting points to use from the A axis (the first series
              taken).  The program will start with these correspondences and
              add other pairs of points that appear to correspond.

       -atob OR -MatchingAtoB
              The first series here (referred to as A in these options) is the
              B axis, i.e. the second tilt series taken, and the second series
              is the A axis.

       -xtilts (-x) OR -XAxisTilts    Two floats
              The values of X axis tilt that were used in generating the first
              and second tomograms.  These angles are needed to make the fidu-
              cial coordinates from Tiltalign correspond to the actual posi-
              tions of the particles in the tomograms.  The default values are
              0.

       -angles (-ang) OR -AngleOffsetsToTilt    Two floats
              The values of tilt angle offsets that were used when running
              Tilt to generate the first and second tomograms.  These are dif-
              ferent from the angle offsets used when running Tiltalign, which
              need not be supplied to Solvematch.  The default values are 0.

       -zshifts (-z) OR -ZShiftsToTilt     Two floats
              The values of Z shift that were used when running Tilt to gener-
              ate the first and second tomograms.  These are different from
              the Z shifts used when running Tiltalign, which need not be sup-
              plied to Solvematch.  The default values are 0.

       -surfaces (-su) OR -SurfacesOrUseModels       Integer
              This entry governs the mode of operation of the program.  To
              obtain the transformation from fiducial points only, enter:
                2 if there are fiducials on two surfaces,
                1 if fiducials are on one surface and the tomograms are NOT
              inverted relative to each other,
               -1 if the tomograms are inverted and there are fiducials on
              only one surface,
                0 to use model files of corresponding points; with this entry
              both the matching model points and fiducial points will be used
              if the fiducials are available.
               -2 to use only the matching model points and ignore any entries
              of fiducial point files.
              The default is 2.

       -maxresid (-m) OR -MaximumResidual       Floating point
              The limiting value for the maximum residual, so that the program
              will exit with an error if this value is exceeded.

       -local (-l) OR -LocalFitting   Integer
              Minimum number of points required in each local area if local
              fitting is desired.  The default is 0, which disables local
              fits.  Non-zero values must be at least 6.

       -center (-c) OR -CenterShiftLimit   Floating point
              Maximum shift between central local fit and global fit.  This
              shift is computed and tested against this limit only when local
              fitting occurs, namely when the -local option is selected and
              the global maximum residual is greater than the -maxresid entry.
              If the shift is greater than the limit, the program will exit
              with an error, but if the solution is adequate there is no need
              to rerun the program.  The default value is 10.  A value of 0
              disables the test.

       -amatch (-ama) OR -AMatchingModel   File name
              Name of model of points from the first tomogram

       -bmatch (-bma) OR -BMatchingModel   File name
              Name of model of corresponding points from the second tomogram

       -atomogram (-atom) OR -ATomogramOrSizeXYZ     Text string
              Either the file name or the X, Y and Z dimensions of the first
              tomogram.

       -btomogram (-bt) OR -BTomogramOrSizeXYZ       Text string
              Either the file name or the X, Y and Z dimensions of the second
              tomogram.

       -scales (-sc) OR -ScaleFactors      Two floats
              Amounts by which the fiducial coordinates need to be scaled to
              match the coordinates of the first and second tomograms, respec-
              tively.  Each factor should be the binning of the images on
              which the fiducials were modeled divided by the binning of the
              aligned stack.  The entry should not be needed in ordinary cir-
              cumstances.  It overrides the scaling that is computed from a
              pixel size in the fiducial file and the pixel spacing from the
              tomogram header.  The entry can be used as a substitute for pro-
              viding the image file name in the -atomogram and -btomogram
              options.

       -aniso (-ani) OR -AnisotropicLimit       Floating point
              The maximum percentage difference between the scaling along the
              three axes; a percentage difference greater than this limit will
              cause a warning to be issued.  If the difference is in the Y
              direction and points were specified as being on two surfaces,
              the program will also advise that it be run with "-surfaces 1"
              instead.  Enter 0 to disable these warnings.  The default is
              10%.

       -param (-p) OR -ParameterFile       Parameter file
              Read parameter entries as keyword-value pairs from a parameter
              file.

       -help (-h) OR -usage
              Print help output

       -StandardInput
              Read parameter entries from standard input.


INTERACTIVE INPUT
       If the program is started with no command line arguments, it reverts to
       interactive input and is restricted to older modes of operation.  The
       input takes different forms depending on what data are available.  The
       inputs to the program when fiducials from Tiltalign are available are:

       Name of file with coordinates of fiducials from the first tilt series

       Name of file with coordinates of fiducials from the second series

       A list of the points in series 1 for which a corresponding point in
          series 2 is known with confidence, or / if all points correspond
          between the two series.

       A list of the corresponding points in the second series, or / if all
          points correspond between the two series.

       The values of X axis tilt that were used in generating the first and
          second tomograms.

       The limiting value for the maximum residual, so that the program will
          exit with an error if this value is exceeded.

       Enter either 0 to determine shifts from model files of corresponding
          points, or -1, 1, or 2 to determine just the 3 by 3 transformation
          and not the shifts.  Enter 2 if there are fiducials on two
          surfaces, 1 if fiducials are on one surface and the tomograms are
          NOT inverted relative to each other, or -1 if the tomograms are
          inverted and there are fiducials on only one surface.

       IF you entered 0, make the following four entries:

          Either the file name or the X, Y and Z dimensions of the first
            tomogram

          Name of model of points from the first tomogram

          Either the file name or the X, Y and Z dimensions of the second
            tomogram

          Name of model of points from the second tomogram

       Finally, enter name of file for output of the transformation, or
          Return for none


       Inputs to the program when matching models alone are being used:

       A blank line (Return) in place of the name of the first fiducial file

       The limiting value for the maximum residual

       Either the file name or the X, Y and Z size of the first tomogram

       Name of model of points from the first tomogram

       Either the file name or the X, Y and Z size of the second tomogram

       Name of model of points from the second tomogram

       Name of file for output of the transformation, or Return for none


HISTORY
       Written by David Mastronarde, 1995; modified for zero shifts, 7/4/97
       Added outlier elimination and error exit, 6/5/99
       Added ability to start with small initial set of matches, 3/20/00
       Added ability to use matching models only, 7/21/02
       Fixed treatment of single-surface case and converted to PIP, 12/24/03
       Added ability to deal with absolute fiducial coordinates, 6/9/04

BUGS
       Email bug reports to mast at colorado dot edu.



BL3DEMC                              4.7.3                       solvematch(1)