COLIMATE User's Manual

COLIMATE User's manual

Using a Colimate generated menu is VERY EASY. The main concept in a Colimate program is the application. An application is compound of a set of programs divided in groups. Each program has got at least one command line. The idea is that the Colimate menu will help you to fill all parameter values such that you can launch the command line without having to write and remember a tedious command line structure. Thus, an application may have the following appearance

When the application menu bar is highlighted you can exit by pressing CTRL-Q. Here you see that there are several groups: File, SelFiles, Phantoms, ... Each group has got several programs inside, even with several parsing lines or command lines each one, as it is the case of the group Image with the programs Mask and Threshold, and inside mask the command lines: apply_single_mask, apply_multiple_mask, ...

The group File is a common Colimate group to all Colimate menus. There you can find the following options:

Load: Load variable status at this moment. The file must be generated previously by the option save on this same menu
Save: Save variable status at this moment. Internally Colimate mantains a table with all programs, menus, variables, ... The content of this table is dumped to an ASCII readable file
Change Dir: This option is useful if you want to change the work directory from the one where you call the application
System: here you can issue any command to the shell
Quit: Exit the application

Once you are inside a menu you must fill all fields you need to construct the command line. Depending on the specific command line you chose for a program, some fields cannot be filled as they are meaningless in this working mode. When you are finished you must press the button "EXEC", something like pressing ENTER. Then the command is issued in background in a separate subshell. The command issued is printed to screen so you can see always what the computer is doing. Colimate also implements some light previous error checking, so if you leave some parameter out, or the value is not correct (it is not a number or the file should exist and it doesn't, for instance), then an error message is shown and the command is not issued.

Click on the radio buttons to select optional parameters. Click on the default buttons to get the default value for an specific parameter or on the Default All if you want to collect all default values. Lists like the one shown as "Value type" which is actually set to "User defined" are used to select very common values of other parameters, in this case for the substitute value. If you place the mouse over the parameter labels, some help is shown telling some information about the parameter used.

You can also get some information about the program either clicking on the Help button (a new window is open with some program explanation) or the WWW button (which asks the open Netscape to follow the corresponding link where this program is described. If no Netscape is open, a new one is called).

All line editors (where you can edit parameter values) mantain a history of past values (not many, usually 10). Use up and down arrows to move among them, press ESC if you want to write a new one that is not in the list. Furthermore, if the line editor corresponds to a file, by pressing the rightbutton of the mouse you access to another popup menu which allows you to select the file from the directory tree with a graphical interface or perform any other operation on it based on the application action definition for this button. In the example shown, Xmipp, actions like editing the file with nedit, or viewing with xv, ghostview and acroread are defined.

After this, all I can say is Enjoy it!!.