Software at CIS : Scripting BrainWorks Functionality

BrainWorks is CIS's image viewing, processing, and analysis software program. It performs a number of complex and powerful tasks on image data. Currently these tasks can only be performed manually by initiating them from the GUI. It would be desirable to add some form of batch mode processing to BrainWorks so that repetitive research tasks can be performed according to a script created by the researcher, and the results of each task saved for verification by the researcher when the processing is complete.

An initial effort in this direction has already been made at CIS, in which a single processing task is isolated, and a separate program is written, compiled, and executed to perform the task. Those efforts reside on the CIS file system under /cis/project/bwwrap.

This approach has provided researchers with the capability to perform BrainWorks functionality outside of the GUI, and, by writing shell scripts, some BrainWorks scripting capability has been effected. A list of the functions that have been encapsulated in this way can be seen here.

The development approach to building these command line programs has been to copy into a separate directory as much of the standard BrainWorks source code as necessary for the desired functionality, create a new main program that loads files into image objects and performs the desired operation, write a new make file, then build all the necessary code into a new module. Needless to say the continued replication of applicable BrainWorks source code is not the most efficient way to develop new scripting capability, not to mention the configuration nightmare created by many copies of the same source.

A more effective means of providing this functionality would be to build scriptability directly into BrainWorks. Two means of scripting should be available to BrainWorks users:

From the menu under File->Script.
From the command line with the -b option (i.e., BrainWorks -b script).

The names of existing command line programs will serve as the names of the operations available from a BW script file. The parameters for each call will be the same. Calls to the shell should be supported.

The following needs to be added to BrainWorks to implement scriptability:

Script command in the main menu under File. (2 days)
A command line argument for batch mode (i.e., -b or --batch). (3 days)
A script reader that can open a file, create an output file to hold task results, then call functions to perform the requested tasks. (10 days)
An API that exposes the functions that can be performed by BW scripts. (5 days)
A library of BW scripting functionality. (15 days)

The total time to complete this task should be 35 work days. This includes creating scripting functionality for the command line tasks that already exist. On average I expect that the functions on the wishlist to take about 5 days each, for a total of 30.

Future enhancements to scripting capability will include

ability to run scripts as background processes from the BrainWorks GUI
the ability to perform the script functions available on image data already loaded into BrainWorks (i.e., operations on images in memory vs. images in files)
the ability to require operator intervention during a script (e.g., to ask the operator to perform point picking during a script).
provide BW scripting as an extension of a standard scripting language such as perl of python