View source for AnyWave:MATLAB Batch GUI

=Introduction=
AnyWave can run plugin code using the command line as mentioned here:<br/>
[[File:Menu_cli.png|400px|link=AnyWave:CommandLine|'''The Command Line Interface of AnyWave''']]<br>
That implies the user has to write his own shell scripts to accomplish that.<br/>
One alternative is to use the AnyWave built-in Batch GUI that allows to program your batch operations using a user friendly interface.<br/>
This features allows to run your batching operations within AnyWave, in the background with a monitoring of what it is done.<br/>
If we want our plugin to be processed using this feature we must make it compatible with AnyWave Batch GUI system.<br/>

=Make my plugin GUI compatible=
First, the plugin must be callable using the command line.<br/>
Reminder on how to do that:
[[File:Menu_matlab_batch.png|400px|link=AnyWave:Plugin_Batch|'''Make your plugin batchable''']]

==args.json==
Remember, we have defined an arg.json file to describe the command line arguments we would like AnyWave to parse for us:<br/>

==ui.json==
There are some important things to setup in ui.json file:<br/>
There is a key describing the input parameters of the plugin. Suppose that you want to compute something on several files, you must then set several input_keys in the json file.<br/>
This is done by creating the '''input_keys''' key.<br/>
This key will hold the names of all the other keys that must be considered as files that AnyWave will provide to our plugin when running it.<br/>
In our example below, there is only ONE file key, that we called input_file which is the default key name for the file argument.<br/>
Hence, AnyWave will bring a GUI to pick up all the files we want, and run our plugin on all those files.<br/>
Once you setup the FILES entries keys, you must also describe them in the file by setting two values to the corresponding key.<br/>
The first value is always the decorated readable name of the key that will be used to create the GUI.<br/>
The second value is a string. If you set "check" as the value, that will tell AnyWave to check that the file setup is a data file and not a side car file.<br/>
If you don't want a data file to be set, just set an empty string as the value.<br/>

Let's setup an example using one input file and two parameters:<br/>
<syntaxhighlight lang="java">
{
"input_keys" : [ "input_file"],
"input_file" : ["Input File", "check"],
"hp" : ["High Pass Filter", "double"],
"lp" : ["Low Pass Filter", "double"],
"fields_ordering" : ["hp", "lp"]
}
</syntaxhighlight>
'''input_keys''' : mandatory key. Here, we setup only one input file, and the key is called "input_file".<br/>
Then we must describe that key: 
* "Input File" is the name used in the GUI to describe the parameter.
* "check" indicates that the file MUST be a data file that AnyWave can read.
'''fields_ordering''': mandatory key. Describe the GUI fields order. Here we set up HP before LP in the GUI.<br/>
<br/>
Between the mandatory keys, you have the other parameters:<br/>
* hp described as High Pass Filter, and "double" indicates this parameter is a double value.
* lp described as Low Pass Filter, and "double" indicates this parameter is a double value.

Others possible parameter values:<br/>

{| class="wikitable"
|-
! value !! description 
|-
| "double"|| double precision value
|-
| "int" || integer value
|-
| "list" || indicates we want a combo list selection among predefined item.
|-
| "string" || string value
|-
| "stringList" || an array of strings.
|-
| "boolean" || a boolean value.
|}

==default.json==
This file comes to se the default values for parameters described in ui.json.<br/>
So you need to define the same keys and set a default value for them.<br/>
In our skeleton that will be:<br/>
<syntaxhighlight lang="java">
{
"input_file" : "", 
"hp" : 0.,
"lp" : 0.
}
</syntaxhighlight>

=GUI representation of ui.json=
See below the GUI representation of keys inserted in the ui.json:<br/>
{| class="wikitable"
|-
! key !! GUI
|-
| "hp" : ["High Pass", "double"] || [[File:Json_ui_key_double.png]]
|-
| "n_iter" : ["#Iterations", "int"] || [[File:Json_ui_key_int.png]]
|-
| "modality" : ["Modality", "list"] || [[File:Json_ui_key_list.png]]
|-
| "output_prefix" : ["Output Prefix", "string"] || [[File:Json_ui_key_string.png]]
|}

'''Note''': The list type will make a combobox list selection of items. Define the possible items in default.json file:<br/>
"modality" : ["MEG", "EEG", "SEEG"]<br/>

=Example=
A small test plugin that takes TWO files as input:<br/>
* a MEG file
* an EEG file
==desc.txt==
<syntaxhighlight lang="text">
name = MAT_BATCH
description = TEST_BATCH
category = Process:TEST:MAT_BATCHING
flags = CanRunFromCommandLine:NoDataRequired
</syntaxhighlight> 
==ui.json==
<syntaxhighlight lang="java">
{
"input_keys" : [ "meg_file", "eeg_file"],
"meg_file" : ["MEG File", "check"],
"eeg_file" : ["EEG File", "check"],
"output_file_prefix" : ["Output File Prefix", "string"],
 "fields_ordering": [ "output_file_prefix" ]
}
</syntaxhighlight> 
We set up two files as input (eeg_file, meg_file).<br/>
output_file_prefix is a string variable we will use to prefix our output filename.<br/>
There is only one '''field''' because meg_file and eeg_file are input files keys, so they won't appear in the left part of the GUI but in the input file part.<br/>
==default.json==
<syntaxhighlight lang="java">
{
"meg_file" : "",
"eeg_file" : "",
"output_file_prefix" : "resampled"
}
</syntaxhighlight>
==main.m==
<syntaxhighlight lang="matlab">
function main(varargin)
global args;
if isdeployed
% STANDALONE AnyWave Plugin code
   global host;
   global port;
   global pid;

   if (nargin < 3)
       error('missing arguments.');
  end
  host = varargin{1};
  port = str2num(varargin{2});
  pid = str2num(varargin{3});
  if (nargin > 3)
    args = varargin{4};
  end
   
  assignin('base', 'host',  host);
  assignin('base', 'port', port);
  assignin('base', 'pid', pid);
  assignin('base', 'args', args);
% end of STANDALONE AnyWave Plugin code
end

% we assume here that the code will always run in batch mode.
% To check if the plugin was called in batch mode, just check if args variable is empty or not.
if isempty(args)
   error('this plugin will only run in batch mode');
end


pathMEG = args.meg_file;
pathEEG = args.eeg_file;
infosMEG = aw_getfileinfo(pathMEG);
if isempty(infosMEG)
    error('Could not open MEG file');
end
infosEEG = aw_getfileinfo(pathEEG);
if isempty(infosEEG)
   error('Could not open EEG file');
end

cfg=[];
cfg.file = pathEEG;
markersEEG = aw_getmarkers(cfg);
cfg.file = pathMEG;
cfg.channels = { 'Trigger' };
markersMEG = aw_gettriggers(cfg);

cfg = [];
cfg.file = pathEEG;
cfg.filtering = 'yes';
cfg.start = 0;
cfg.duration = -1;
cfg.eeg_lp = infosEEG.max_sr / 3;

eegdata = aw_getdata(cfg);
assert(~isempty(eegdata));
disp(eegdata);
end
</syntaxhighlight>