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Command is thing running the instruction of the computer on Eos. Eos is operated by Character User Interface(CUI) basically.

Example of executing the Command on Eos

Eos's Command is used by standard input (from keyboard) to CUI.

$ Display2 -i MicroscopeImage.roi

The above command Display2 has the ability to display the image as mrcImage, roi ... . In addition it can perform cut out the Particles. Eos's Command can check help of option by using option -h.

$ Display2 -h

The following is example of help at Display2.

Usage: /home/people/keita1023/Eos/bin/X86LINUX64/Display2
   [-i[nput]            In                  (NULL      )] :Optional  :InputDataFile
   [-t[epmlate]         Template            (85.roi    )] :Optional  :Template for InputFile 
   [-H[ighForThres]     ThresHigh           (0.0       )] :Optional  :Template for InputFile 
   [-L[owForThres]      ThresLow            (0.0       )] :Optional  :Template for InputFile 
   [-Zoom               Zoom                (1.0       )] :Optional  :Zoom for InputFile 
   [-Inverse            ] :Optional  :Inverse (HighValue(dark)<->LowValue(bright)) for InputFile 
   [-o[utput]           Out                 (.EosLog   )] :Optional  :OutputLogFile
   [-display            geometry            (:0.0      )] :Optional  :OutputLogFile
   [-geometry           display             (1024x1024+0+0)] :Optional  :OutputLogFile
   [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
   [-m[ode]             mode                (0         )] :Optional  :Mode
New wish commands of Display2
mrcInfoSet [z|min|max] value
mrcInfoSet [log|pow] 
mrcInfoGet [Nx|Ny|Nz|Max|Min|Mean|Hist]

There are about 400 commands (List of command, Functional Order of Commands) of Eos in 2012, and you can perform many image processing by these commands.

Commands in PIONE

Most of the commands in PIONE are for either the administrator of PIONE Webclient or the experts who write the program packages or the PIONE protocols. The usual users do not need the PIONE commands, as they only have to use the PIONE protocols or packages (both of which are prepared beforehand in the PIONE system) through GUI on the Web page.

For summary of the commands, see either overview of the PIONE commands or overview from functions of the PIONE commands.

Commands on Linux

Ubuntu (Linux such as Windows) has become widespread rapidly in recent years, but Linux is difficult OS for the people who is not familiar with the CUI to approach still. There are minimum necessary commands for Eos in the following, but it is also recommended that you refer to the specialized books and sites.

ls Command on CUI is like when open the folder on GUI. pwd is the position(address on the image), and cd is like into and out by clicking.


It is command that displays files or directories in current directory.

$ ls
aaa.txt    bbb.txt


It is command that checks place of current directory.

$ pwd


It is command that returns to home directory, or moves to another directory.

$ pwd
$ cd ./aaa
$ cd


It is command that copies a file to another directory.

$ cp before.txt ./aaa/after.txt


It is command that moves a file at another directory.

$ mv before.txt ./aaa/after.txt

It can also rename filename or directory name.

$ ls
$ mv before.txt after.txt
$ ls