etomo(1)                                                              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 contain four interfaces:  one for doing tomographic
       reconstructions, one for joining tomograms,  one for particle
       averaging, and one for running a process using IMOD's parallel
       processing capabilies.  Etomo's standard error goes to a dated log
       file.  The name location of the logs are placed in a file called
       etomo_err.log, which is placed the current directory.  When in use,
       standard out is send to etomo_out.log.




OPTIONS
       --axis single|dual
              For automation.  Sets the Axis Type field in the Setup Tomogram
              dialog.  See USAGE.


       --create
              For automation.  Pressed the  Create Com Scripts button in the
              Setup Tomogram dialog.  See USAGE.


       --dataset tilt_series_file|dataset_name
              For automation.  Sets the Dataset Name field in the Setup
              Tomogram dialog.  Can be set to a file containing a tilt series
              or to the dataset name.  A dataset name is the root name of the
              tilt series file, excluding the extension (and the axis
              extension - "a" or "b" - in the case of dual axis).  Must be in
              the local directory unless the --dir option is used.  See USAGE.


       --debug
              Send extra information to standard error.  The --debug option
              turns on the following options:  --memory and --timestamp.


       --demo Deprecated.


       --dir "directory_path"
              For automation.  The absolute or relative directory containing
              the file or dataset specified with the --dataset option.


       --exit For automation.  Causes etomo to exit after the Setup Tomogram
              dialog is completed.  See USAGE.


       --fg   Used with automation.  Must be the first option.  Causes etomo
              to be run in the foreground rather then in the background.  This
              is useful when running etomo with automation from a script; a
              script will not wait until etomo is done unless etomo is running
              in the foreground.  See USAGE.


       --fiducial fiducial_diameter
              For automation.  Sets the Fiducial Diameter field in the Setup
              Tomogram dialog.  Fiducial_diameter is a double.  See USAGE.


       --frame single|montage
              For automation.  Selects the Frame Type radio buttons in the
              Setup Tomogram dialog.  See USAGE.


       --headless
              For testing.  No window is created.  Used for unit testing.


       -h, --help
              Send a usage message to standard out (goes to the command line
              not to a file) and exit.


       --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.  When --listen is used in Windows, messages to
              3dmod will be sent through stdin rather then imodsendevent.


       --memory [interval]
              Log memory usage statements before and after processes are run.
              The interval is an integer which denotes the interval in minutes
              at which to send additional memory usage statements.


       --names
              Used with testing.  Send the names of screen elements to
              standard out.  For writing automated regression tests.


       --newstuff
              May cause Etomo to run with unreleased functionality.


       --scan For automation.  Runs Scan Header in the Setup Tomogram dialog.
              See USAGE.


       --selftest
              Causes etomo to do some internal testing.  Etomo may run more
              slowly.


       --test For testing.  Test mode used for unit testing and automated
              regression testing.


       --timestamp
              Send timestamps to standard error before and after processes are
              run.




USAGE
   Automation
       Automation will be completed before handing control over to the user.
       Automation parameters all affect the Reconstruction Setup dialog and
       should be used without a data file.  All automation parameters are
       optional.  The automation parameters will always be executed in the
       same order.  The order in which they appear is ignored, except for
       --fg, which must be first.  Automation parameters are executed in the
       following order:  --fg --dir --dataset --axis --frame --fiducial --scan
       --create --exit




FILES
   Data Files
       *.edf  Tomographic reconstruction data file.


       *.ejf  Data file for joining tomograms.


       *.epe  PEET data file (particle averaging).


       *.epp  Parallel process data file.



   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.



BL3DEMC                            2/12/2009                          etomo(1)