Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells
FINDWARP(1) FINDWARP(1)
NAME
findwarp - to find a series of 3-D transformations to warp one volume
into alignment with another
SYNOPSIS
findwarp [options] input_file [output_file]
DESCRIPTION
Findwarp will solve for a series of general 3-dimensional linear
transformations that can then be used by Warpvol to align two volumes
to each other. It performs a series of multiple linear regression on
local sets of the displacements between the volumes determined at a matrix
of positions (patches). The displacements must be contained in a file
with the following form:
Number of displacements
One line for each displacement consisting of the X, Y, and Z
coordinates in the first volume, then the displacements in X, Y
and Z involved in moving from the first to the second volume
The program has two basic modes of operation. In one mode, it will
compute a solution for a specified number of patches to be included in
each local fit. In the other mode, it automatically searches for the
largest number of patches that gives local fits with mean residuals less
than a specified criterion. These modes behave differently depending on
whether the program is run with parameter input via the PIP interface or
via interactive input. With parameter input, the program will either
run one set of local fits with a given number of patches, or find the best
warping automatically. If the program is run interactively, it loops on
the specification of the subsets of displacements to use until the user
decides to write out a particular subset. However, at any point it can be
told to find the best warping automatically with the current set of
parameters, in which case it does so then exits.
The program will automatically eliminate "outliers", patch displacements
that are likely to be incorrect because they are so extreme, when compared
to the rest of the displacements. This elimination is conservative, but
if for some reason it operates incorrectly, you can control the parameters
of elimination or stop the elimination from occurring. By default, the
program will eliminate up to 10% of the patches from each local fit.
The program also provides two methods for fitting to only a subset of the
data. One method is to eliminate whole rows or columns of patches. The
other is to use a model file to specify which patches to include in the
fit. This model can be quite simple, consisting of just a single contour
enclosing the region where patches are generally good. This contour can
be drawn in any Z plane of the volume. However, if the good region
changes through the depth of the tomogram, you can draw contours at
several Z levels. If you have two layers of patches, draw two contours,
one near the top and one near the bottom of the tomogram; if you have
three layers, add another contour in the middle, etc. For a given patch,
the program will find the contour at the nearest Z level and use that one
to determine whether to include the patch.
In addition, the program will work with a patch file from which bad
patches have been removed by hand. This may become necessary if bad
patches are too frequent in some location to be eliminated as outliers.
To use this feature, use Patch2imod to convert the patch file to a
model file where displacements are represented by vectors, examine the
file in 3dmod, eliminate aberrant contours, and convert the model file to
a new patch file with Imod2patch.
If there is only one layer of patches in the thin dimension, there is
insufficient information to solve for the full transformation, so the
program will solve for only two of the three columns of each local
transformation matrix, and keep the third column of each matrix fixed.
The same procedure is used if a particular local area does not have
sufficient data on more than one layer in the thin dimension.
For a given arrangement of patches, the program finds a mean and maximum
residual for each of the fits. It first reports how many points have been
eliminated as outliers, in how many fits they appeared to be outliers, and
a summary of the distribution of their residuals. On one line, it next
reports the average and the maximum of the mean residuals. On the next
line, it reports the average and maximum of the maximum residuals. The
goal is to find an arrangement that contains as many patches as possible
in each direction yet has residuals comparable to those found with a
volume that does not need warping (typically 0.1 to 0.2).
Findwarp uses the PIP package for input (see the manual page for pip)
but can still take input interactively for exploring the effect of varying
parameters. 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 -):
-patch OR -PatchFile File name
Name of input file with positions and displacements. If this option is
not entered, the first non-option argument will be used for the input file
name.
-output OR -OutputFile File name
Optional output file for warping transformations. If this option is not
entered, the second non-option argument (if any) will be used for the
output file name.
-region OR -RegionModel File name
Model file with contours enclosing the patches to be included in the fits.
-volume OR -VolumeOrSizeXYZ File name
Either the name of the file or the X, Y, and Z dimensions of the volume
being matched to.
-initial OR -InitialTransformFile File name
File with initial 3D transform used to make the second volume for the
patch correlations. This transform will be incorporated into the warping
transformations written to the output file. The format of such a file is
described in the Matchvol man page.
-residual OR -ResidualPatchOutput File name
Output file for positions, displacements, and mean residual values,
averaged over all the fits that include a position. This value will be
zero for patches excluded from all fits. If the patch input file has
correlation coefficients, they will be replaced by the residuals. After
the residual value, this file will also have a value for the fraction of
fits in which the vector was removed as an outlier.
-target OR -TargetMeanResidual Multiple floats
One or more mean residual values to try to reach in the automatic search
for the best warping. Multiple values should be entered in increasing
order. The program will try to find a warping with the largest number of
included patches that gives a mean residual below the first value; then it
tries again with the second value, etc.
-measured OR -MeasuredRatioMinAndMax Two floats
The minimum and maximum ratio of measurements to unknowns to be allowed in
the automatic fits. The defaults are 4 and 20.
-xskip OR -XSkipLeftAndRight Two integers
Number of columns of patches to exclude on the left and right
-yskip OR -YSkipLowerAndUpper Two integers
Number of patches to exclude on the lower and upper sides in Y. This
entry specifies either rows or slabs of patches to exclude, depending on
whether the volume is oriented so that it is thin in the Z or Y dimension.
-zskip OR -ZSkipLowerAndUpper Two integers
Number of patches to exclude on the lower and upper sides in Z. This
entry specifies either slabs or rows of patches to exclude, depending on
whether the volume is oriented so that it is thin in the Z or Y dimension.
-rowcol OR -LocalRowsAndColumns Two integers
Number of rows and columns of patches to include in each local fit. The
second value will apply to the longer of the Y and the Z dimension. If
this option is not entered, the program will automatically search for the
best warping.
-slabs OR -LocalSlabs Integer
By default, fits include all slabs of patches in the shorter of the Y and
Z dimensions. This entry allow fits to be done to subsets of patches in
that dimension. If the -rowcol option is used, then this entry specifies
the number of slabs of patches to include in each fit. Otherwise, the
entry sets the minimum number of slabs of patches that will be tried in
the automatic search for the best warping.
-maxfrac OR -MaxFractionToDrop Floating point
Maximum fraction of patches to drop from each fit by outlier elimination.
Enter 0 to for no outlier elimination. The default is 0.1.
-minresid OR -MinResidualToDrop Floating point
The minimum residual for outlier elimination; patches with residuals
smaller than this value will be retained no matter how extreme they are
relative to the other patches. The default is 0.5.
-prob OR -CriterionProbabilities Two floats
Two probabilities controlling outlier elimination: a criterion probability
for a patch to be evaluated as an outlier (default 0.01), and a criterion
probability for a patch to be eliminated regardless of the distribution of
extreme values (default 0.002).
-discount OR -DiscountIfZeroVectors Floating point
Use this option to ignore local fits that have many zero vectors when
computing the average mean residual and the average maximum residual.
This will prevent misleading averages when analyzing the warping fields
used to align adjacent volumes for stitching. Fits with the number of
zero vectors bigger than the given fraction of the total vectors will be
excluded from the averages.
-debug OR -DebugAtXYZ Three floats
Center location at which to print debug output about fits
-param OR -ParameterFile Parameter file
Read parameter entries as keyword-value pairs from a parameter file.
-help OR -usage
Print help output
-StandardInput
Read parameter entries from standard input.
If the program is started with no command line arguments, it takes
interactive input with the following entries:
Name of file with positions and displacements
(At this point the program will report the number of patches in X, Y,
and Z in this file, or complain if the data do not have the
proper form.)
Either the file name, or the X, Y, and Z dimensions of the volume being
matched to.
Name of an Imod model file with contours enclosing the patches to
be included in the fit, or Return to use all patches.
0 to proceed interactively, or 1 to find best warping automatically
IF you enter 1, next enter:
One or more target mean residuals to achieve.
The minimum and maximum ratio of measurements to unknowns to be
allowed in the local fits, or / to use the default values.
0 to use all of the data, or 1 to specify a subset of patches to use
IF you enter 1, next enter three lines:
Number of columns of patches to eliminate from the left and right
sides of the data, 0,0 to use all patches in X, or / to use previous
values.
Number of rows or slabs of patches to eliminate from the lower and
upper extent in Y, 0,0 to use all patches in Y, or / to use previous
values.
Number of slabs or rows of patches to eliminate from the lower and
upper extent in Z, 0,0 to use all patches in Z, or / to use previous
values.
IF you selected automatic warping, the program now proceeds by fitting to
the largest possible area that does not exceed the maximum ratio of
measurements to unknowns, and it tries progressively smaller areas
until the desired mean residual is achieved. It does this using the
parameters (e.g., row or column elimination) that were set on any
previous interactive rounds of fitting. If the target residual is
reached, it requests the names of the initial transformation file and
the output file, as described below, and exits. If the residual is not
reached, it tries the next target residual if any, and if no targets
are met, it exits with an error.
IF you are proceeding interactively, continue with the following:
IF there are more than 2 patches in the thin dimension, the program next
asks whether you always want to do the local fits to all patches in
that dimension. Just enter 0 for the typical situation.
0 to use default parameters for outlier elimination, or 1 to adjust
any of these parameters. Just enter 0 unless you know better.
IF you enter 1, then make four entries, or / to take the default:
Maximum fraction of patches to eliminate from each fit. Set this
to 0 to stop the outlier elimination from occurring.
The minimum residual for elimination; patches with residuals
smaller than this value will be retained no matter how extreme
they are relative to the other patches.
Criterion probability for patches to be considered candidates for
for elimination. A smaller value will eliminate fewer patches.
Criterion probability for patches to be eliminated regardless of
the pattern of outliers. A higher value may force the
elimination of more patches.
Number of local patches in X and Y, X and Z, or X, Y, and Z to include in
each fit. These values must be at least 2 and no larger than the total
number of patches in the respective direction.
The program will loop on the last entry until the same numbers are entered
twice in a row (e.g. with a /). If you enter 0 for the number of patches
in X, it will loop back to the query about whether you want to find
warping automatically. When you do enter a /, it will request:
Name of file with initial 3D transformation that was applied to one of the
volumes before the patch correlation, or Return if there was no such
file. The format of such a file is described in the Matchvol man
page.
Name of output file in which to place the transformations. These will be
inverse transformations, ready for use by Warpvol.
An exception to the above occurs if you specify that all available patches
are to be used in a single fit. You would do this if you just needed to
eliminate a row or column of patches from the fit. In this case, when you
enter a /, the program will simply ask for the name of a file in which to
place the single refining transformation, just as with Refinematch.
HISTORY
Written by David Mastronarde 1/30/97
12/24/98: added outlier elimination, integrated complex options.
6/6/99: added ability to output single refining transformation.
1/1/00: added model exclusion and automatic finding of best warp
6/7/01: rewrote data input to handle data with missing patches
7/20/02: rearranged input to make it easier to run automatically with
rows or columns removed
8/21/06: converted to PIP, made it handle either orientation of volume, made
automatic fitting more flexible in the thin dimension, changed outlier
output to a summary, added option for patch and residual output