On Eos, image processing is basically performed by executing commands using CUI. The results are saved as files, and the file content can be confirmed.
II-1. Command usage on Eos
For the usage of individual commands, refer to the overall or functional command list. This section describes the usage of general Eos commands.
First, type the following, and also confirm if the environment setup of Eos has succeeded:
$ mrcInfo -h
Usage: /Applications/Eos.app/Eos/bin/XXXXXX/mrcInfo Options: [-i[nput] In (NULL )] :Essential :InputDataFile [-o[output] Out (stdout )] :Optional :OutputDataFile [-c[onfig] configFile (NULL )] :Optional :ConfigurationFile [-m[ode] mode (0 )] :Optional :Mode
A character string is put on XXXXXX, which differs depending on the execution environment. This example shows the usage of the mrcInfo command. Usage of each Eos command can be reminded easily after you understand what commands are available. On Eos, almost 400 types of such commands are available currently. They are called Small Tools. In addition to the above options, -c, -m, and -html are usable as reserved ones. “-c” is specified to use a file when inputting information by specifying an argument, “-m” shows the mode of program operation, and “html” means the HTML format usable on the Web. If there is nothing other than Small Tools, they must be executed one by one on the console. This is really troublesome. So, on Eos, commands are put together using Makefile called by the make command, which is used for program development on UNIX. The make command has a function by which the relation between input and output is described and update of the relation is judged. This is useful for many types of image processing. For details, refer to the description of Makefile.
- Since there seem to be limited memory of the make command, and there is nothing supporting the distributed environment, a new integrated environment (PIONE) is currently created. To overcome the former problem, quite tricky definitions have been used in Makefile. For the latter problem, each user logged in the host, and used the process definition function which uses input/output update relation usable by the Make command. However, such effort led to the development of PIONE because the definition book is too difficult to read and understand, and process management is troublesome. For details, refer to the description of PIONE.
Use the command actually. First, download data from example-000.mrc. Then, confirm the content of the file. Execute like below in the directory where downloaded files are saved.
$ mrcInfo -i example-000.mrc N : ( 1784, 1814, 1) Mode : 2 mrcFloatImage StartN : ( 0, 0, 0) M : ( 1, 1, 1) Length : ( 1.250, 1.250, 1.250) A,B,G : ( 90.00, 90.00, 90.00) C,R,S : ( 1, 2, 3) Min,Max,Mean : ( 0.999, 2.28, 1.64) ISPG : 0 NSYMBT : 0 EXTRA : 0: 0 1: 0 2: 0 3: 0 4: 0 5: 0 6: 0 7: 0 8: 0 9: 0 10: 0 11: 0 12: 0 13: 0 14: 0 15: 0 16: 0 17: 0 18: 0 19: 0 20: 0 21: 0 22: 0 23: 0 24: 0 25: 0 26: 0 27: 0 28: 0 XORIGIN : ( 0, 0) LABEL : 0 Tailer Number : 0
If output is like above, the command has succeeded. This shows that the image has a size of 1784 x 1814 and the float type. This also shows that pixel interval is 1.25.
- Some parameters are defined by a format different from the MRC one. The system will not operate well in some cases.
II-2. Why command line is used? On Eos, various commands are available as Small Tools, and executed using CUI. On the other hand, the software often used for image processing is called from the integrated GUI environment such as ImageJ or Photoshop as a plug-in. Even on Eos, Display2 is the software aiming at being usable in the integrated GUI environment. This has not been created completely yet. There are two major reasons why command line is used. One reason is to design execution of integrated large-scale image processing flexibly by combining Eos commands with each other as mentioned above. If plug-in programs are used from the integrated GUI environment, more than one plug-in programs are arranged by designing plug-in programs, describing a macro command arranging more than one plug-in programs, or drawing a manual describing the execution sequence. If command line is used, such plug-in programs can be executed together with a shell script. The other reason is that command line makes it easy to execute the same work on more than one files a large number of times. If executing the same work using GUI only, it is necessary to execute the same work every time using a mouse and so on. For example, although it is tough to change suffixes of 1000 files using GUI, only necessary files can be updated easily using command line together with a shell script or the Make command.