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 either with Etomo parameters
       or with 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.

       --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 most
              command-line automation options will have no effect.
              Command-line automation options that can be used with these
              options:
                 --cpus
                 --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 useful for calling Etomo from
              the command line.

   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|dataset_name
              Sets Dataset Name in the Setup Tomogram dialog during
              automation.  The value can be a file containing a tilt series,
              or the name of a dataset.  A dataset name is the root name of
              the tilt series file - the extension (and the trailing "a" or
              "b" in the dual axis case) is removed.  The file must be in the
              local directory unless 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

       --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)