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)