```solvematch(1)               General Commands Manual              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
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, the best
option for dual-axis tomograms is to use Dualvolmatch instead of
Solvematch.  Otherwise, you can use models of corresponding points to
register the two volumes in Solvematch.  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 dimen-
sions, 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 necessary.

Using Old, Relative Fiducial Coordinates
With fiducial coordinates from older versions of Tiltalign, the pro-
gram can solve for the 3 by 3 transformation but not for the shifts in
X, Y and Z.  There are several ways to get these shifts: by rerunning
Tiltalign to get absolute coordinates; by finding the transformation
with Dualvolmatch, or by giving Solvematch models of corresponding
points in the two tomograms.  If you create matching models, 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 orien-
tation) between the two tomograms.  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 information 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
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 or -1 if fiducials are 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.  When 1 or -1 is entered, the program will
determine whether the tomograms are upside-down from each other
(i.e., inverted in depth) by assuming that the tomograms have
the same handedness.

-inverted (-i) OR -InvertedInDepth       Integer
This option can be used with a -surfaces entry of 1 to prevent
the program from analyzing whether tomograms are inverted by
assuming that they have the same handedness. Enter 1 if tomo-
grams are inverted in the depth dimension, or 0 if they are not.
Tomograms are inverted if features at high Z in one tomogram are
at low Z in the other; this property is independent of whether
they are mirror images of each other.  This entry should be
needed only if tomograms are in fact mirror images.

-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