Brainstorm process: Process a raw file, create new raw file and add it to database

process_something_raw_file.m

function varargout = process_something_raw_file( varargin )
% PROCESS_SOMETHING_RAW_FILE: Do something on a raw file, create new raw file, add it to BST database.
%
% @=============================================================================
% This software is part of the Brainstorm software:
% http://neuroimage.usc.edu/brainstorm
%
% Copyright (c)2000-2023 Brainstorm by the University of Southern California
% This software is distributed under the terms of the GNU General Public License
% as published by the Free Software Foundation. Further details on the GPL
% license can be found at http://www.gnu.org/copyleft/gpl.html.
%
% FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
% UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
% WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
% MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
% LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
%
% For more information type "brainstorm license" at command prompt.
% =============================================================================@
%
% Authors:

eval(macro_method);
end


%% ===== GET DESCRIPTION =====
function sProcess = GetDescription() %#ok<DEFNU>
    % Description the process
    sProcess.Comment     = 'Something on raw file';
    sProcess.Description = '';
    sProcess.Category    = 'Custom';
    sProcess.SubGroup    = 'Example';
    sProcess.Index       = 9999;
    sProcess.Description = '';
    % Definition of the input accepted by this process
    sProcess.InputTypes  = {'raw'};
    sProcess.OutputTypes = {'raw'};
    sProcess.nInputs     = 1;
    sProcess.nMinFiles   = 1;
    % Multiplier
    sProcess.options.multiplier.Comment = 'Multiply raw data by: ';
    sProcess.options.multiplier.Type    = 'value';
    sProcess.options.multiplier.Value   = {1000, 'No units', 0};
end


%% ===== FORMAT COMMENT =====
function Comment = FormatComment(sProcess) %#ok<DEFNU>
    Comment = sProcess.Comment;
end


%% ===== RUN =====
function sOutputFiles = Run(sProcess, sInput) %#ok<DEFNU>
    sOutputFiles = {};
    % Input structure
    [sMat, matName] = in_bst(sInput.FileName, [], 1, 1, 'no');   
    signalsIn  = sMat.(matName);
    % Output structure
    sOutMat = sMat;
    signalsOut = signalsIn * sProcess.options.multiplier.Value{1};
    
    % In sFile structure
    DataMat = in_bst_data(sInput.FileName, 'F');
    sFileIn = DataMat.F;

    % Get channel file
    ChannelMat = in_bst_channel(sInput.ChannelFile);
    % Get input raw path and name
    if ismember(sFileIn.format, {'CTF', 'CTF-CONTINUOUS'})
        [~, rawBaseIn] = bst_fileparts(bst_fileparts(sFileIn.filename));
    else
        [~, rawBaseIn] = bst_fileparts(sFileIn.filename);
    end
    % Make sure that there are not weird characters in the folder names
    rawBaseIn = file_standardize(rawBaseIn);    
    
    % New folder name
    newCondition = ['@raw', rawBaseIn, '_something'];
    % Get new condition name
    ProtocolInfo = bst_get('ProtocolInfo');
    newStudyPath = file_unique(bst_fullfile(ProtocolInfo.STUDIES, sInput.SubjectName, newCondition));
    % Output file name derives from the condition name
    [~, rawBaseOut, rawBaseExt] = bst_fileparts(newStudyPath);
    rawBaseOut = strrep([rawBaseOut rawBaseExt], '@raw', '');
    % Full output filename
    RawFileOut = bst_fullfile(newStudyPath, [rawBaseOut '.bst']);
    % Get input study (to copy the creation date)
    sInputStudy = bst_get('AnyFile', sInput.FileName);
    % Get new condition name
    [~, ConditionName] = bst_fileparts(newStudyPath, 1);
    % Create output condition
    iOutputStudy = db_add_condition(sInput.SubjectName, ConditionName, [], sInputStudy.DateOfStudy);
    % Get output study
    sOutputStudy = bst_get('Study', iOutputStudy);
    % Full file name
    MatFile = bst_fullfile(ProtocolInfo.STUDIES, bst_fileparts(sOutputStudy.FileName), ['data_0raw_' rawBaseOut '.mat']);

    % Create an empty Brainstorm-binary file
    sFileOut = out_fopen(RawFileOut, 'BST-BIN', sFileIn, ChannelMat);

    % Set Output sFile structure
    sOutMat.F = sFileOut;
    % Save new link to raw .mat file
    bst_save(MatFile, sOutMat, 'v6');
    % Create new channel file
    db_set_channel(iOutputStudy, ChannelMat, 2, 0);
    % Write block
    out_fwrite(sFileOut, ChannelMat, 1, [], [], signalsOut);
    
    % Register in BST database
    db_add_data(iOutputStudy, MatFile, sOutMat);
    sOutputFiles{end+1} = MatFile;        
   
end