How to write your own process

Brainstorm features a flexible plug-in structure. All the operations available when using the Process1 and Process2 tabs, which means most of the Brainstorm features, are in fact written as plug-ins. A Brainstorm plug-in, or "process", is a single Matlab .m script that is automatically identified and added to the menus in the pipeline editor. Two folders are parsed for plug-ins:

• brainstorm3/toolbox/process/functions:
  Brainstorm "official" processes, included in the main distribution of the software

• $HOME/.brainstorm/process:
  User processes folder, to develop new processes or overwrite some default function

Process structure

Sub-functions

A process function must be named "process_...m" and located in one of the two process folders in order to be recognized by the software. Let's call our example function "process_test.m". It contains at least 4 functions:

• process_test(): The first line of the script must contain a function with the same name as the .m script. It contains only a call to the Brainstorm script macro_methodcall. This allows us to call subfunction in the process_test.m script from outside, using the syntax: process_test('FunctionName', arguments)

• GetDescription(): Returns a structure that describes the process: name, category, accepted inputs, options, etc. This function is called when Brainstorm parses the process folders to find all the valid processes. It informs the pipeline editor on how the process has to be integrated in the interface.

• FormatComment(): Returns a string that identifies the process in the interface. In the pipeline editor window, when the process is selected or when its options are modified, this function is called to update the process description line. Most processes would return simply the field sProcess.Comment, some other would add some options in the description (example: Pre-process > Band-pass filter, or Average > Average files).

• Run(): Function called when the process is executed, either from the interface (after clicking on the Run button of the pipeline editor) or from a Matlab script (call to bst_process('CallProcess', 'process_test', ...)). While the three first functions are descriptive, this one really does something. It receives the files placed in the Process1 or Process2 boxes, does its job and returns the output of the computation to Brainstorm.

You are free to add as many subfunctions as needed to the process file. If your process needs some sub-functions to run, it is preferable to copy the full code directly into the "process_test.m" code, rather than leaving it in separate functions. This way it prevents from spreading subfunctions everywhere, which get later lost or forgotten in the distribution when the process is deleted. It might be incomfortable at the beginning if you are not used to work with scripts with over 100 lines, but you'll get used to it, the Matlab code editor offers many solution to make long scripts easy to edit (cells, code folding...). It makes your process easier to maintain and to exchange with other users, which is important in the long run.

Additional functions

Alternative

Run Matlab command