setupcombine(1) General Commands Manual setupcombine(1)
NAME
setupcombine - Create command files for combining dual-axis tomograms
SYNOPSIS
setupcombine [options] -name rootname
DESCRIPTION
Setupcombine generates the command files needed to combine two single-
axis tomograms into one. These files include solvematch.com,
matchvol1.com, patchcorr.com, matchorwarp.com, volcombine.com, and com-
bine.com, which are all used for processing in Etomo. Files
matchvol2.com and warpvol.com 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.
OPTIONS
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
ACorrespondenceList.
-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-
denceList.
-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
"combine.com" will contain a goto statement to run Autopatch-
fit(1) after "matchvol1.com" instead of "patchcorr.com" then
"matchorwarp.com".
-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 solvvematch.com and patchcorr.com 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 combine.com 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
-StandardInput
Read parameter entries from standard input
FILES
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 ~.
AUTHOR
David Mastronarde
BUGS
Email bug reports to mast at colorado dot edu
SEE ALSO
solvematch, corrsearch3d, matchorwarp, combinefft, dens-
match(1), filltomo
HISTORY
Setupcombine was a originally a C-shell script. In December 2010 it
was converted to Python.
IMOD 5.0.2 setupcombine(1)