copytomocoms(1) General Commands Manual 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 -).
Options can be abbreviated to unique letters; the currently valid
abbreviations for short names are shown in parentheses.
-name (-n) OR -RootName File name
Root name of data set (omit a or b for dual-axis set)
-stackext (-sta) OR -StackExtension Text string
Extension of raw stack excluding the period. If this is not
specified, the program will assume the extension ".st" unless
the -style option is entered. With a -style option and no spec-
ified stack extension, it will look for ".st", ".mrc", ".hdf",
".tif", and ".tiff" and require that only one of those types is
present. With this entry, which could in principle be arbi-
trary, it will not care if files with other extensions are
present.
-dual (-du) OR -DualAxis
Dual-axis data set
-montage (-m) OR -MontagedImages
Data are montaged
-backup (-bac) 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 (-pi) OR -PixelSize Floating point
Pixel size of images in nanometers. This entry is required.
-gold (-go) OR -GoldBeadSize Floating point
Size of gold beads in nanometers. This entry is required.
Enter 0 if you are not going to track fiducials.
-rotation (-ro) 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 (-bro) OR -BRotationAngle Floating point
Angle from the vertical to the tilt axis for B axis. The
default for a dual-axis set is the angle entered for A.
-firstinc (-fi) OR -FirstAndIncAngle Two floats
First tilt angle and tilt angle increment for the A axis or only
axis.
-bfirstinc (-bfi) OR -BFirstAndIncAngle Two floats
First tilt angle and tilt angle increment for B axis
-userawtlt (-use) OR -UseRawtltFile
Take tilt angle from a .rawtlt file for the A axis or only axis.
-buserawtlt (-bu) OR -BUseRawtltFile
Take tilt angle from a .rawtlt file for B axis
-extract (-e) OR -ExtractAngles
Extract tilt angles from data file for the A axis or only axis.
This entry implies -userawtlt.
-bextract (-be) OR -BExtractAngles
Extract tilt angles from data file for B axis
-angles (-a) OR -TiltAngles List of integer ranges
Complete list of tilt angles for the A or only axis, on one line
with no spaces.
-bangles (-ban) OR -BTiltAngles List of integer ranges
Complete list of tilt angles for the B axis
-twodir (-t) OR -TwoDirectionsAngle Floating point
The tilt series was taken in two directions starting at the
given angle. The first half of the series will be defined as a
separate view group for Tiltalign and Beadtrack, from the
first view through the first occurrence of the given angle.
-btwodir (-bt) OR -BTwoDirectionsAngle Floating point
Tilt series for B axis was bi-directional from given starting
angle
-reversed (-re) OR -ReversedBidirectional
The part of the tilt series acquired first is the second part of
the tilt series stack. Without this option, the program assumes
that the tilt series is in the same order as the file produced
by automated acquisition software, in which the part acquired
first is inverted in order and placed in the beginning of the
stack.
-breversed (-bre) OR -BReversedBidirectional
First acquired part of B axis tilt series is second part of
stack
-skip (-sk) 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 (-bs) OR -BViewsToSkip List of integer ranges
List of views to exclude from processing for B axis
-distort (-di) OR -DistortionField File name
Correct image distortion with the given .idf file. The file
will be copied to the current directory.
-binning (-bi) OR -BinningOfImages Floating point
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 (-gr) 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 (-fo) OR -FocusWasAdjusted
Focus was adjusted between frames when acquiring montage for the
A axis or the only axis
-bfocus (-bfo) OR -BFocusWasAdjusted
Focus was adjusted between montage frames for the B axis
-voltage (-v) OR -VoltageInKV Integer
Microscope voltage in kV
-Cs OR -SphericalAberration Floating point
Spherical aberration
-ctfnoise (-ct) OR -NoiseConfigFile File name
Configuration file listing noise files for ctfplotter
-defocus (-de) OR -Defocus Floating point
Defocus in nanometers, with underfocus positive
-CTFfiles (-CT) OR -CopyCTFfiles Integer
Just copy files for CTF plotting and correction (1 for plotting,
2 for correction, 3 for both)
-fei (-fe) OR -SetFEIPixelSize
Set the standard pixel spacing in the header of each image file
if it comes from FEI software. The pixel size from the extended
header will be multiplied by the binning of the images, if any,
and placed in the standard header location, so that it will
propagate through the processing. If there is already a stan-
dard pixel spacing not equal to 1, 2, 3, or 4, it will not be
modified.
-change (-ch) 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 Copytomocoms, "comfile" is the root name of the command file
with optional "a" or "b", "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 "com-
param.xcorra.tiltxcorr.FilterSigma1=0.02". Files are processed
in order, and a duplicate entry for an option generally over-
rides an earlier one. However, for a dual-axis data set, a
directive specific to a particular axis, such as that example,
will always be preferred over a generic directive with no "a" or
"b" on the command file name. For a single-axis data set,
directives with a "b" are ignored and ones with an "a" or with
no "a" or "b" are treated equivalently, such that later ones
override earlier ones. (Successive entries accumulate)
-one (-o) 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)
-style (-sty) OR -NamingStyle Integer
0 for output image files to have descriptive extensions like
".preali", 1 for extension ".mrc", or 2 for extension ".hdf".
In the latter two cases the usual descriptive text is put before
the extension, and command files will contain an environment
variable setting to make programs generate files of the corre-
sponding type.
-pcm (-pc) OR -MakeComExtensionPcm Integer
0 or 1 to name output command files with extension ".com" or
".pcm". The latter is not yet supported by Etomo.
-xsize (-x) OR -XImageSize Integer
X size of image data (needed if data file not present)
-ysize (-y) OR -YImageSize Integer
Y size of image data (needed if data file not present)
-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
extracttilts, extractpieces, extractmagrad
HISTORY
Copytomocoms was a original a C-shell script. In February 2011 it was
converted to Python.
IMOD 4.11.0 copytomocoms(1)