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 trans-
       formations 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 at least the following form:

       Number of displacements [optional ID values]
       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 displacement file can have additional columns of values after the
       displacements in X, Y, and Z.  These extra columns are numbered from 1,
       and they may also have ID values on the first line of the file indicat-
       ing their type.

       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 pro-
       gram 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 dis-
       placements to use until the user decides to write out a particular sub-
       set.  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 displace-
       ments that are likely to be incorrect because they are so extreme, when
       compared to the rest of the displacements.  This elimination is conser-
       vative, 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.

       In addition to the outlier removal, the program provides several meth-
       ods for fitting to only a subset of the data; two involving manual
       steps and one automatic.  One manual 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 con-
       tour at the nearest Z level and use that one to determine whether to
       include the patch.

       Automatic removal of some data is also possible if Corrsearch3d com-
       puted some measures of structure for each patch and stored these as
       extra columns in the patch vector file.  Selection of patches based on
       these values is done by entering the -extra option to indicate the kind
       of extra column, and the -select option with one or more threshold val-
       ues for the values in that column.  For example, to select based on the
       fraction of analyzed boxes in each patch that have a high amount of
       structure, which has ID number 5, one might enter "-extra 5,1" and
       "-select 0.5,0.6,0.7".  If multiple criteria are entered, as in this
       example, the entire autofitting process will be repeated with each
       selection criterion to try to satisfy the first residual criterion,
       then higher residual criteria will be considered.  Even if a criterion
       for mean residual is satisfied with a given selection threshold, it may
       go on to a higher threshold to try to reduce the maximum residual (see
       the -desired option).

       The program will also 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 maxi-
       mum 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 residu-
       als.  On the next line, it reports the average and maximum of the maxi-
       mum 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 0.2
       to 0.3).

       The program decides which arrangements of patches are acceptable for
       fitting by determining whether the ratio of measurements to unknown
       values falls within a given range.  Originally, this ratio was evalu-
       ated based on the nominal number of patches in each dimension.  In IMOD
       4.8.14, the maximum number of patches actually available in each dimen-
       sion, and the mean number of patches, is evaluated for each potential
       local fitting size.  Ratios are based on these two values and used to
       determine if a fitting size is acceptable.  This is a more reliable
       method for curved sections, especially when there are relatively many
       patch positions in the thickness dimension.  The default is to use the
       new method for new patch data that have extra column ID values, other-
       wise to use the old method.  There are two ways to override this behav-
       ior: either enter -1 or 1 for the -legacy option to force the use of
       the new or old method, respectively; or set the environment variable
       FINDWARP_LEGACY_RATIOS to -1 or 1.

       If you want to regenerate the combined volume in an older data set,
       where there are no IDs for the extra columns, you can use existing
       patches and get the same result from Findwarp as before.  To get a new
       fitting result (which might be preferable), either make a new set of
       patch vectors or set the environment variable to -1.

OPTIONS
       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 -).  Options can be abbreviated to
       unique letters; the currently valid abbreviations for short names are
       shown in parentheses.


       -patch (-pat) 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 (-o) 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 (-reg) OR -RegionModel      File name
              Model file with contours enclosing the patches to be included in
              the fits.

       -volume (-v) OR -VolumeOrSizeXYZ    File name
              Either the name of the file or the X, Y, and Z dimensions of the
              volume being matched to.

       -initial (-i) 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 (-res) OR -ResidualPatchOutput      File name
              Output file for positions, displacements, and mean residual val-
              ues, 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 (-t) OR -TargetMeanResidual      Multiple floats
              One or more mean residual values to try to reach in the auto-
              matic 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 (-me) 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.

       -legacy (-l) OR -LegacyRatioEvaluation   Integer
              This entry controls the evaluation of the ratio of measurements
              to unknowns, as described above.  The default is 0 to use the
              new method only when there are ID values for the extra columns.
              Enter -1 or 1 to force the use of the new or old method, respec-
              tively.  This entry overrides a setting of the FIND-
              WARP_LEGACY_RATIOS environment variable.

       -xskip (-x) OR -XSkipLeftAndRight   Two integers
              Number of columns of patches to exclude on the left and right

       -yskip (-y) 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 (-z) 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.

       -extra (-extr) OR -ExtraValueSelection   Two integers
              Select only patches with extra value on one side of a criterion.
              To include patches based on values in an extra column, enter two
              numbers for this option: the ID value or the negative of the
              extra column number (numbered from 1); and 1 to select patches
              above the criterion or -1 to select ones below it.  You must
              also enter one or more threshold values with the -select option.
              (Successive entries accumulate)

       -select (-se) OR -SelectionCriteria      Multiple floats
              One or more criteria for selecting patches based on extra val-
              ues.  Multiple criteria should be entered in order of greater
              selectivity.  If there are multiple values being selected on,
              this option must be entered the same number of times as the
              -extra option and it must have the same number of criteria
              entered each time.  (Successive entries accumulate)

       -desired (-des) OR -DesiredMaxResidual   Floating point
              When patches are selected based on extra values and the mean
              residual is acceptable but the maximum of the maximum residuals
              in the fits is above this value, the program will go on to apply
              the next criterion, if there is one.  It will still accept the
              result if the last maximum residual is above this target on the
              last criterion.  The default is 8 times the last residual target
              entered with -target.  Enter 0 to disable this feature.

       -rowcol (-ro) 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 (-sl) 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.

       -extent (-exte) OR -MinExtentToFit       Integer
              Minimum number of rows and columns of patches to include in each
              local fit.   When there are many (~10 or more) overlapping
              patches in the thickness dimension, an entry of 3 will keep the
              program from doing 2 by 2 or 2 by 3 fits in the other dimen-
              sions, which would only have a single patch of overlap between
              laterally adjacent fits.  Such an entry would also be appropri-
              ate when the spacing between patches is unusually small, to keep
              the transformation from being solved over too small an extent.

       -maxfrac (-ma) 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 (-mi) 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 (-pr) 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 (-di) 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 frac-
              tion of the total vectors will be excluded from the averages.

       -debug (-deb) OR -DebugAtXYZ   Three floats
              Center location at which to print debug output about fits

       -param (-par) 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 INPUTS
       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

BUGS
       Email bug reports to mast at colorado dot edu.



IMOD                                 4.9.3                         findwarp(1)