findwarp(1) General Commands Manual findwarp(1)NAMEfindwarp - to find a series of 3-D transformations to warp one volume into alignment with anotherSYNOPSISfindwarp [options] input_file [output_file]DESCRIPTIONFindwarp 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-extraoption to indicate the kind of extra column, and the-selectoption 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-desiredoption). 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-legacyoption 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.OPTIONSFindwarp 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-PatchFileFilenameName 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-OutputFileFilenameOptional 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-RegionModelFilenameModel file with contours enclosing the patches to be included in the fits.-volume(-v)OR-VolumeOrSizeXYZFilenameEither the name of the file or the X, Y, and Z dimensions of the volume being matched to.-initial(-i)OR-InitialTransformFileFilenameFile 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-ResidualPatchOutputFilenameOutput 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-TargetMeanResidualMultiplefloatsOne 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-MeasuredRatioMinAndMaxTwofloatsThe minimum and maximum ratio of measurements to unknowns to be allowed in the automatic fits. The defaults are 4 and 20.-legacy(-l)OR-LegacyRatioEvaluationIntegerThis 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-XSkipLeftAndRightTwointegersNumber of columns of patches to exclude on the left and right-yskip(-y)OR-YSkipLowerAndUpperTwointegersNumber 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-ZSkipLowerAndUpperTwointegersNumber 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-ExtraValueSelectionTwointegersSelect 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-selectoption. (Successive entries accumulate)-select(-se)OR-SelectionCriteriaMultiplefloatsOne 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-extraoption and it must have the same number of criteria entered each time. (Successive entries accumulate)-desired(-des)OR-DesiredMaxResidualFloatingpointWhen 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-LocalRowsAndColumnsTwointegersNumber 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-LocalSlabsIntegerBy 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-MinExtentToFitIntegerMinimum 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-MaxFractionToDropFloatingpointMaximum 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-MinResidualToDropFloatingpointThe 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-CriterionProbabilitiesTwofloatsTwo 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-DiscountIfZeroVectorsFloatingpointUse 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-DebugAtXYZThreefloatsCenter location at which to print debug output about fits-param(-par)OR-ParameterFileParameterfileRead parameter entries as keyword-value pairs from a parameter file.-help(-h)OR-usagePrint help output-StandardInputRead parameter entries from standard input.INTERACTIVEINPUTSIf 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.HISTORYWritten 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 outputBUGSEmail bug reports to mast at colorado dot edu. IMOD 4.12.35 findwarp(1)