etomo(1) General Commands Manual etomo(1)
NAME
etomo - A GUI program to run IMOD and PEET batch programs
SYNOPSIS
etomo [option ...] [data_file ...]
DESCRIPTION
ETomo is an interface for running a subset of IMOD and PEET commands.
It can be run interactively, with automation, or with a combination of
the two. ETomo contains interfaces for a variety of projects:
tomographic reconstructions, joining tomograms, subvolume averaging,
aligning serial sections, blending montages, nonlinear anisotropic
diffusion, running processes using IMOD's parallel processing
capabilies, flattening tomograms, and testing a GPU.
Automation
Automating Etomo functionality can be done with Etomo parameters and/or
directives. For more information on directives, run imodhelp and choose
"Directives for batch processing and Etomo templates" on the IMOD Help
Index page.
OPTIONS
--h OR --help
Output usage message.
--listen
Forces all 3dmods to be run with the -L option. This only has
an effect on Windows computers because -L is always used on
Linux and Mac.
--moveb
Moves the B axis window to the left of the A axis window when a
major resizing event occurs.
--namingstyle 0|1|2
Sets the file name style for a new dataset. Overrides the
IMOD_OUTPUT_FORMAT environment variable for file name style
only. This does not affect the file format - just the file
names. 0: the old non-standard file name. 1:the standard mrc
extension. 2:The standard hdf extension.
--timestamp
Send timestamps to standard error before and after processes are
run.
--userTemplateLoc "directory_path"
Adds a second User Template directory, in addition to one set in
the Settings dialog.
AUTOMATION OPTIONS - DIRECTIVE FILE
--directive "directive_file.adoc"
Causes automation to be performed based on a file called
directive_file.adoc. No interface will come up and some
command-line automation options will have no effect.
Command-line automation options that can be used with these
options:
--axis
--cpus
--dataset
--fiducial
--frame
--gpus
These options are automatically set to true when --directive is
used:
--fg
--headless
--create
--exit
The directive file must end in ".adoc" and conform to autodoc
syntax.
--fromBRT
Used when batchruntomo calls Etomo. Prevents Etomo from calling
batchruntomo for validation. Not used for calling Etomo from
the command line. When this option is used values from
batchDefaults.adoc will be used in addition to any templates
that are set.
AUTOMATION OPTIONS - COMMAND LINE
--axis single|dual
Sets the Axis Type in the Setup Tomogram dialog during
automation.
--cpus [ignored]
Turns on the Parallel Processing checkbox in the Setup Tomogram
dialog.
--create
Runs Create Com Scripts in the Setup Tomogram dialog during
automation.
--dataset tilt_series_file
Deprecated. Same as rawimagestack.
--rawimagestack tilt_series_file
Sets Raw Image Stack in the Setup Tomogram dialog during
automation. The value should be set to a file containing a tilt
series. The file must be in the local directory unless a file
path is included or the --dir option is used.
--dir "directory_path"
For automation. The absolute or relative directory containing
the file or dataset specified with the --dataset option.
--exit During automation, exit after the Setup Tomogram dialog has
completed.
--fg Causes Etomo to be run in the foreground rather then in the
background. This is useful when running Etomo with automation
from a script because a script will not wait until a background
command has completed.
--fiducial Floating point
Sets the Fiducial Diameter in the Setup Tomogram dialog during
automation.
--frame single|montage
Sets the Frame Type in the Setup Tomogram dialog during
automation.
--gpus [ignored]
Selects the Graphics Card Processing checkbox in the Setup
Tomogram dialog.
--scan Runs Scan Header in the Setup Tomogram dialog during automation.
EXTENSIONS
--plugin
For loading built-in plugins. Will be expanded as necessary.
Currently causes the etomo.plugin.demo package to be loaded in
preference to external plugins implementing the same interface.
DIAGNOSTIC OPTIONS
--actions
Send actions and file name to Etomo's _err.log. File names
which do not contain an extension or are entirely numeric will
be excluded.
--debug [-1|0|1|2|3|4]
Send extra information to Etomo's _err.log.
The optional parameter has the following meaning:
-1 - limited output
0 - no debug output
1 - default debug output
2 - more information
3 - extensive information - log will be very large
4 - may degrade performance
--grabit [c|p]
Grabit causes etomo to run as a command line program. The
purpose of grabit is to allow specific elements of etomo
functionality to be tried out. Currently it can only try out
message processing so its possible that the parameters will
change in the future. When grabit is used the file names at the
end of the command line will be assumed to contain program
output file(s) to be processed by etomo's message processor.
The result will be printed out. Etomo will exit after doing
this. The parameter is optional. Without a parameter it will
create a generic message processor default settings.
Optional Parameter:
b - batchruntomo but with logging off - has a special error
tag
c - copytomocoms - multi-line warning and info messages
p - parallel processing with no multi-line messages
--ignoresettings
ETomo will not load from or save to the .etomo configuration
file.
--memory [interval_in_minutes]
Send memory usage statements to Etomo's _err.log before and
after processes are run. nterval_in_minutes is the interval at
which to send additional memory usage statements.
--selftest
Causes Etomo to do some internal testing. ETomo may run more
slowly.
DEVELOPMENT AND TESTING OPTIONS
--autoclose3dmod
Instead of popping up a message asking to close an open 3dmod
instance, Etomo automatically closes it. Used for automated
user interface testing.
--headless
No interface will come up. Used for unit testing.
--ignoreloc
The interface will come up in the default location rather then
the location saved in .etomo. Used for automated user interface
testing.
--names
The names of screen elements are sent to Etomo's _out.log. Used
for automated user interface testing.
--newstuff
May cause Etomo to run with unreleased functionality.
--test Used for unit testing and automated user interface testing.
DEPRECATED OPTIONS
--demo Deprecated
FILES
Data Files
dataset.edf
Tomographic reconstruction data file.
dataset.ejf
Data file for joining tomograms.
dataset.epe
Subvolume averaging (PEET) data file.
dataset.epp
Data file for generic parallel process and nonlinear anisotropic
diffusion interfaces.
dataset.ess
Data file for aligning serial sections and blending montages.
Log Files
$HOME/.etomologs/etomo_err_timestamp.log
Contains the log. The location is configurable (see man
imodenv).
etomo_err.log
Contains the location of the log. Placed in the directory from
which Etomo is run.
etomo_out.log
Contains the output of the --names parameter. May also contain
diagnostic messages. Placed in the directory from which Etomo
is run.
AUTHOR
Sue Held
SEE ALSO
imodenv, uitest, 3dmod, imodhelp(1).
IMOD 2/12/2009 etomo(1)