setupcombine(1)             General Commands Manual            setupcombine(1)

       setupcombine - Create command files for combining dual-axis tomograms

       setupcombine  [options]  -name rootname

       Setupcombine generates the command files needed to combine two single-
       axis tomograms into one.  These files include,,,,, and com-, which are all used for processing in Etomo.  Files and are also created and could be used at the
       command line instead of the matchorwarp step.  In all of the parameter
       entries, Z refers to the thickness dimension, although this corresponds
       to the Y dimension of the volumes when running the underlying programs.

       Setupcombine uses the PIP package for input (see the manual page for
       pip).  Options can be specified either as command line arguments
       (with the -) or one per line in a command file (without the -).
       Options can be abbreviated to unique letters; the currently valid
       abbreviations for short names are shown in parentheses.

       -name (-na) OR -RootName       File name
              Root name of dataset, excluding a and b

       -atob (-at) OR -MatchAtoB
              Match A to B instead of B to A

       -tolist (-to) OR -ToVolPointList    List of integer ranges
              List of points in tomogram being matched to that have corre-
              sponding points, used to provide the entry to Solvematch for

       -fromlist (-f) OR -FromVolPointList      List of integer ranges
              List of corresponding points in tomogram being transformed to
              match, used to provide the entry to Solvematch for BCorrespon-

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

       -uselist (-use) OR -UsePointList    List of integer ranges
              List of starting points to use from the A axis in Solvematch

       -surfaces (-su) OR -SurfaceModelType     Integer
              This entry provides the SurfacesOrUseModels entry for Solve-
              match.  Enter 0 to use matching models and fiducials if any, 2
              for fiducials distributed in Z (e.g. on two surfaces), 1 or -1
              for fiducials on one surface (-1 if tomograms are inverted in Z
              with respect to each other), or -2 to use matching models only.

       -initial (-ini) OR -InitialVolumeMatching
              Use Dualvolmatch to find the initial transformation between
              volumes by matching reprojections and correlating patches,
              instead of using Solvematch, which requires fidicial posi-
              tions or matching models.

       -patchsize (-p) OR -PatchTypeOrXYZ       Text string
              Enter a letter to indicate the size of patches, or three numbers
              for the desired size in X, Y, and Z.  The sizes available by
              letter are S for small (64x32x64), M for medium (80x40x80), L
              for large (100x50x100), or E for extra large (120x60x120).

       -autopatch (-au) OR -AutoPatchFinalSize       Text string
              Enter a final patch size for doing automated patch correlation
              and fitting with Autopatchfit.  The size can be either a let-
              ter to indicate the size as for the -patchsize option (S, M, L,
              or E), or three numbers for the desired size in X, Y, and Z.
              The final size may not be smaller than the initial patch size in
              any dimension.  Including this option will cause several
              changes. Corrsearch3d will use kernel filtering with a
              default sigma of 1.45, will analyze local standard deviation and
              output two measures of structure in the patch output file, and
              will eliminate patches with a structure measure of less than
              0.5.  Patches will be more numerous and denser in X and Y, and
              usually in Z as well.  In Findwarp, fitting will be over a
              minimum of 3 patches in X and Y, and thresholds of 0.5,0.57, and
              0.65 in the measure of structure are applied successively to
              eliminate patches at each residual criterion.  The command file
              "" will contain a goto statement to run Autopatch-
              fit(1) after "" instead of "" then

       -extra (-e) OR -ExtraResidualTargets     Text string
              This option can be used to provide extra target residual values
              to be used by Autopatchfit on its final trial.

       -xlimits (-x) OR -XLowerAndUpper    Two integers
              Lower and upper coordinate limits of patches in X.  The default
              limits exclude a border that varies from 24 pixels for the
              shorter tomogram dimension under 1000 pixels to 80 pixels for
              the shorter tomogram dimension above 4000 pixels.

       -ylimits (-y) OR -YLowerAndUpper    Two integers
              Lower and upper coordinate limits of patches in Y.  The default
              limits exclude a border that is the same as for the X limits
              just described.

       -zlimits (-z) OR -ZLowerAndUpper    Two integers
              Lower and upper coordinate limits of patches in Z.  If the
              -autopatch option is entered, the default is the full range in Z
              (which is actually the Y dimension of the tomogram).  If not,
              there is no default and these limits must be entered.

       -regionmod (-r) OR -PatchRegionModel     File name
              Model with contours enclosing regions to do patch correlations
              in.  The same model will be supplied to Matchorwarp.

       -lowradius (-l) OR -LowFromBothRadius    Floating point
              Value for the LowFromBothRadius option to Combinefft

       -wedgefrac (-we) OR -WedgeReductionFraction   Floating point
              Value for the ReductionFraction option to Combinefft

       -change (-cha) OR -ChangeParametersFile       File name
              Name of file with directives for changing parameters.  A direc-
              tive has the form "comparam.comfile.process.option=value" where
              "comparam" is a required prefix for directives to be processed
              by Setupcombine, "comfile" is the name of the command file,
              "process" is the name of a program being run on a line starting
              with "$", "option" is an option to add or modify, and "value" is
              its value.  An example is "comparam.patchcorr.corrsearch3d.Ker-
              nelSigma=2.5".  Files are processed in order, and a duplicate
              entry for an option overrides an earlier one.  Parameters can be
              changed only in and by this mecha-
              nism.  (Successive entries accumulate)

       -one OR -OneParameterChange    Text string
              One directive for changing parameters, in the format just
              described.  Entries with this option are processed after, and
              can override, ones entered from files, and later ones override
              earlier ones.  (Successive entries accumulate)

       -tempdir (-te) OR -TemporaryDirectory    File name
              Location to create a temporary local directory.  This directory
              will be used for the transformed volumes, the temporary files
              created during volume transformations, and the chunks of the
              combined volume.

       -noclean (-no) OR -NoTempCleanup
              Do not clean up the temporary directory when finished.  This
              option allows you to examine the transformed volume after the
              operation is completed.  The default is to remove the temporary
              directory and its contents when the combine operation completes.

       -info (-inf) OR -InfoOnPatchSizes
              List the 4 patch sizes specified by S, M, L, and E and exit.  No
              other options will have any effect.

       -only (-onl) OR -OnlyMakeCombineCom
              Just create a new copy of and exit.  There are no
              required entries in this case and the only relevant entries are
              the -initial, -autopatch, and -extra options.

       -style (-sty) OR -NamingStyle       Integer
              0 if image files have descriptive extensions like ".preali", or
              1 or 2 if descriptive text is before the extension ".mrc" or
              ".hdf".  This entry is needed only if the style cannot be deter-
              mined from files in the dataset.

       -stackext (-sta) OR -StackExtension      Text string
              Extension of raw stack excluding the period. This entry is
              needed only if this extension cannot be determined from files in
              the dataset.

       -chunked (-chu) OR -ChunkedHDFFiles      Integer
              Enter 1 to make the output from multiple Combinefft runs go
              directly into a single chunked HDF file.  Tests on local and
              networked file systems gave slower results with this approach.

       -warnings (-wa) OR -WarningsToStandardOut
              Print warnings to standard out instead of standard error

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

              Read parameter entries from standard input

       All files are modified from the master files in the $IMOD_DIR/com
       directory.  Existing copies of the command files will be made into
       backup files by adding the extension ~.

       David Mastronarde

       Email bug reports to mast at colorado dot edu

       solvematch, corrsearch3d, matchorwarp, combinefft, dens-
       match(1), filltomo

       Setupcombine was a originally a C-shell script.  In December 2010 it
       was converted to Python.

IMOD                                4.11.0                     setupcombine(1)