setupcombine(1) 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.
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 -):
-name OR -RootName File name
Root name of dataset, excluding a and b
-atob OR -MatchAtoB
Match A to B instead of B to A
-tolist 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 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 OR -TransferPointFile File name
File of matching fiducial coordinates produced by running trans-
ferfid with the -c option.
-uselist OR -UsePointList List of integer ranges
List of starting points to use from the A axis in Solvematch
-surfaces 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.
-patchsize 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).
-xlimits 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 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 OR -ZLowerAndUpper Two integers
Lower and upper coordinate limits of patches in Z. There is no
default; these limits must be entered.
-regionmod OR -PatchRegionModel File name
Model with contours enclosing regions to do patch correlations
in. The same model will be supplied to Matchorwarp.
-tempdir 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 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.
-help 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.
BL3DEMC 4.5.6 setupcombine(1)