copytomocoms(1) copytomocoms(1)
NAME
copytomocoms - Create command files for generating tomograms
SYNOPSIS
copytomocoms [options] -name rootname
DESCRIPTION
Copytomocoms generates the command files needed for nearly all of the
processing involved in generating a tomogram. The program is run by
the setup page of eTomo.
There are several ways in which tilt angles can be entered: as a start-
ing and increment tilt angle, in a file with a list of angles (which
can be extracted from the image file or supplied separately), or
directly as a list of angles. For each axis, one of these option must
be entered for the tilt angle entry, but only one way can be specified.
Options
Copytomocoms 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 data set (omit a or b for dual-axis set)
-dual OR -DualAxis
Dual-axis data set
-montage OR -MontagedImages
Data are montaged
-backup OR -BackupDirectory File name
Directory for backing up small files. Commands to save such
files are placed ina script named "savework", which is run at
end of every command file. The directory need not exist yet.
-pixel OR -PixelSize Floating point
Pixel size of images in nanometers. This entry is required.
-gold OR -GoldBeadSize Unknown argument type
Size of gold beads in nanometers. This entry is required.
Enter an arbitrary number like 1 if you are not going to track
fiducials.
-rotation OR -RotationAngle Floating point
Angle from the vertical to the tilt axis in raw images for the A
axis or only axis. This entry is required.
-brotation OR -BRotationAngle Floating point
Angle from the vertical to the tilt axis for B axis. This entry
is required for a dual-axis set.
-firstinc OR -FirstAndIncAngle Two floats
First tilt angle and tilt angle increment for the A axis or only
axis.
-bfirstinc OR -BFirstAndIncAngle Two floats
First tilt angle and tilt angle increment for B axis
-userawtlt OR -UseRawtltFile
Take tilt angle from a .rawtlt file for the A axis or only axis.
-buserawtlt OR -BUseRawtltFile
Take tilt angle from a .rawtlt file for B axis
-extract OR -ExtractAngles
Extract tilt angles from data file for the A axis or only axis.
This entry implies -userawtlt.
-bextract OR -BExtractAngles
Extract tilt angles from data file for B axis
-angles OR -TiltAngles List of integer ranges
Complete list of tilt angles for the A or only axis, on one line
with no spaces.
-bangles OR -BTiltAngles List of integer ranges
Complete list of tilt angles for the B axis
-skip OR -ViewsToSkip List of integer ranges
List of views to exclude from processing for A or only axis.
This entry and the next are fed into view exclusion lists in
track*.com, align*.com, and tilt*.com.
-bskip OR -BViewsToSkip List of integer ranges
List of views to exclude from processing for B axis
-distort OR -DistortionField File name
Correct image distortion with the given .idf file. The file
will be copied to the current directory.
-binning OR -BinningOfImages Integer
Binning of the raw images; this entry is needed for distortion
correction unless there is no ambiguity about whether they are
binned; i.e., unless the images are not binned and are too large
to be considered binned.
-gradient OR -GradientTable File name
Correct for magnification gradients using the given .mgt file.
Extractmagrad will be run to extract mag gradient files for
each axis.
-focus OR -FocusWasAdjusted
Focus was adjusted between frames when acquiring montage for the
A axis or the only axis
-bfocus OR -BFocusWasAdjusted
Focus was adjusted between montage frames for the B axis
-voltage OR -VoltageInKV Integer
Microscope voltage in kV
-Cs OR -SphericalAberration Floating point
Spherical aberration
-ctfnoise OR -NoiseConfigFile File name
Configuration file listing noise files for ctfplotter
-defocus OR -Defocus Floating point
Defocus in nanometers, with underfocus positive
-CTFfiles OR -CopyCTFfiles Integer
Just copy files for CTF plotting and correction (1 for plotting,
2 for correction, 3 for both)
-xsize OR -XImageSize Integer
X size of image data (needed if data file not present)
-ysize OR -YImageSize Integer
Y size of image data (needed if data file not present)
-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
extracttilts, extractpieces, extractmagrad
HISTORY
Copytomocoms was a original a C-shell script. In February 2011 it was
converted to Python.
BL3DEMC 4.5.6 copytomocoms(1)