1 function varargout = process_example_customavg( varargin )
   2 % PROCESS_EXAMPLE_CUSTOMAVG: Example file that reads all the data files in input, and saves the average.
   3 
   4 % @=============================================================================
   5 % This software is part of the Brainstorm software:
   6 % http://neuroimage.usc.edu/brainstorm
   7 % 
   8 % Copyright (c)2000-2013 Brainstorm by the University of Southern California
   9 % This software is distributed under the terms of the GNU General Public License
  10 % as published by the Free Software Foundation. Further details on the GPL
  11 % license can be found at http://www.gnu.org/copyleft/gpl.html.
  12 % 
  13 % FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
  14 % UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
  15 % WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
  16 % MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
  17 % LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
  18 %
  19 % For more information type "brainstorm license" at command prompt.
  20 % =============================================================================@
  21 %
  22 % Authors: Francois Tadel, 2013
  23 
  24 macro_methodcall;
  25 end
  26 
  27 
  28 %% ===== GET DESCRIPTION =====
  29 function sProcess = GetDescription() %#ok<DEFNU>
  30     % Description the process
  31     sProcess.Comment     = 'Process example: Custom average';
  32     sProcess.FileTag     = '';
  33     sProcess.Category    = 'Custom';
  34     sProcess.SubGroup    = 'Examples';
  35     sProcess.Index       = 1000;
  36     % Definition of the input accepted by this process
  37     sProcess.InputTypes  = {'data'};
  38     sProcess.OutputTypes = {'data'};
  39     sProcess.nInputs     = 1;
  40     sProcess.nMinFiles   = 2;
  41     % Definition of the options
  42     % === OPTION EXAMPLE
  43     sProcess.options.example1.Comment = {'Choice 1', 'Choice 2', 'Choice 3'};
  44     sProcess.options.example1.Type    = 'radio';
  45     sProcess.options.example1.Value   = 1;
  46     % === OPTION EXAMPLE
  47     sProcess.options.example2.Comment = 'Example option 2';
  48     sProcess.options.example2.Type    = 'checkbox';
  49     sProcess.options.example2.Value   = 1;
  50     % === OPTION EXAMPLE
  51     sProcess.options.example3.Comment = 'Example option 3: ';
  52     sProcess.options.example3.Type    = 'value';
  53     sProcess.options.example3.Value   = {5, 'units', 2};
  54 end
  55 
  56 
  57 %% ===== FORMAT COMMENT =====
  58 function Comment = FormatComment(sProcess) %#ok<DEFNU>
  59     Comment = sProcess.Comment;
  60 end
  61 
  62 
  63 %% ===== RUN =====
  64 function OutputFiles = Run(sProcess, sInputs) %#ok<DEFNU>
  65     % Initialize returned list of files
  66     OutputFiles = {};
  67     % Get option values
  68     example1 = sProcess.options.example1.Value;
  69     example2 = sProcess.options.example2.Value;
  70     example3 = sProcess.options.example3.Value{1};
  71     
  72     % ===== LOAD THE DATA =====
  73     % Read the first file in the list, to initialize the loop
  74     DataMat = in_bst(sInputs(1).FileName, [], 0);
  75     epochSize = size(DataMat.F);
  76     Time = DataMat.Time;
  77     % Initialize the load matrix: [Nchannels x Ntime x Nepochs]
  78     AllMat = zeros(epochSize(1), epochSize(2), length(sInputs));
  79     % Reading all the input files in a big matrix
  80     for i = 1:length(sInputs)
  81         % Read the file #i
  82         DataMat = in_bst(sInputs(i).FileName, [], 0);
  83         % Check the dimensions of the recordings matrix in this file
  84         if ~isequal(size(DataMat.F), epochSize)
  85             % Add an error message to the report
  86             bst_report('Error', sProcess, sInputs, 'One file has a different number of channels or a different number of time samples.');
  87             % Stop the process
  88             return;
  89         end
  90         % Add the current file in the big load matrix
  91         AllMat(:,:,i) = DataMat.F;
  92     end
  93     
  94     % ===== PROCESS =====
  95     % Just doing a simple average of the trials, can be replaced with anything
  96     AllMat = mean(AllMat, 3);
  97     
  98     % ===== SAVE THE RESULTS =====
  99     % Get the output study (pick the one from the first file)
 100     iStudy = sInputs(1).iStudy;
 101     % Create a new data file structure
 102     DataMat = db_template('datamat');
 103     DataMat.F           = AllMat;
 104     DataMat.Comment     = 'Custom comment';
 105     DataMat.ChannelFlag = ones(epochSize(1), 1);   % List of good/bad channels (1=good, -1=bad)
 106     DataMat.Time        = Time;
 107     DataMat.DataType    = 'recordings';
 108     DataMat.nAvg        = length(sInputs);         % Number of epochs that were averaged to get this file
 109     % Create a default output filename 
 110     OutputFiles{1} = bst_process('GetNewFilename', fileparts(sInputs(1).FileName), 'data_custom_');
 111     % Save on disk
 112     save(OutputFiles{1}, '-struct', 'DataMat');
 113     % Register in database
 114     db_add_data(iStudy, OutputFiles{1}, DataMat);
 115 end