Combine recordings

toolbox/process/functions/process_combine_recordings.m

@@ -0,0 +1,202 @@
+function varargout = process_combine_recordings(varargin)
+% process_combine_recordings: Combine multiple synchronized signals into
+% one recording (resampling the signals to the highest sampling frequency)
+
+% @=============================================================================
+% This function is part of the Brainstorm software:
+% https://neuroimage.usc.edu/brainstorm
+% 
+% Copyright (c) University of Southern California & McGill University
+% This software is distributed under the terms of the GNU General Public License
+% as published by the Free Software Foundation. Further details on the GPLv3
+% 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: Edouard Delaire, 2024
+%          Raymundo Cassani, 2024
+
+eval(macro_method);
+end
+
+
+%% ===== GET DESCRIPTION =====
+function sProcess = GetDescription()
+    % Description the process
+    sProcess.Comment     = 'Combine files';
+    sProcess.Category    = 'Custom';
+    sProcess.SubGroup    = 'Synchronize';
+    sProcess.Index       = 682;
+    % Definition of the input accepted by this process
+    sProcess.InputTypes  = { 'raw'};
+    sProcess.OutputTypes = { 'raw'};
+    sProcess.nInputs     = 1;
+    sProcess.nMinFiles   = 2;
+
+    % Option: Condition
+    sProcess.options.condition.Comment = 'Condition name:';
+    sProcess.options.condition.Type    = 'text';
+    sProcess.options.condition.Value   = '';
+end
+
+
+%% ===== FORMAT COMMENT =====
+function Comment = FormatComment(sProcess) %#ok<DEFNU>
+    Comment = sProcess.Comment;
+end
+
+
+%% ===== RUN =====
+function OutputFiles = Run(sProcess, sInputs)
+    OutputFiles = {};
+
+    % === Sync event management === %
+    nInputs        = length(sInputs);
+    fs             = zeros(1, nInputs);
+    sOldTiming     = cell(1, nInputs);
+    sIdxChAn       = cell(1, nInputs);
+
+    bst_progress('start', 'Combining files', 'Loading data...', 0, 3*nInputs);
+
+    % Get Time vector, events and sampling frequency for each file
+    for iInput = 1:nInputs
+
+        sDataRaw = in_bst_data(sInputs(iInput).FileName, 'Time', 'F');
+        sOldTiming{iInput}.Time   = sDataRaw.Time;
+        sOldTiming{iInput}.Events = sDataRaw.F.events;
+
+        fs(iInput) = 1/(sOldTiming{iInput}.Time(2) -  sOldTiming{iInput}.Time(1)); % in Hz
+    end
+
+    bst_progress('inc', nInputs);
+    bst_progress('text', 'Synchronizing...');
+
+    % First Input is the one wiht highest sampling frequency
+    [~, im] = max(fs);
+
+    sInputs([1, im])    = sInputs([im, 1]);
+    sOldTiming([1, im]) = sOldTiming([im, 1]);
+    new_times           = sOldTiming{1}.Time;
+
+    iNewStudy = db_add_condition(sInputs(iInput).SubjectName,  ['@raw' sProcess.options.condition.Value]);
+    sNewStudy = bst_get('Study', iNewStudy);
+
+    % Save channel definition
+    bst_progress('text', 'Combining channels files...');
+
+    NewChannelMat   = in_bst_channel(sInputs(1).ChannelFile);
+    sIdxChAn{1}     = 1:length(NewChannelMat.Channel);
+
+    % Copy videos
+    sOldStudy = bst_get('Study', sInputs(1).iStudy);
+    if isfield(sOldStudy,'Image') && ~isempty(sOldStudy.Image)
+        for iOldVideo = 1 : length(sOldStudy.Image)
+            sOldVideo = load(file_fullpath(sOldStudy.Image(iOldVideo).FileName));
+            if isempty(sOldVideo.VideoStart)
+                sOldVideo.VideoStart = 0;
+            end
+            iNewVideo = import_video(iNewStudy, sOldVideo.LinkTo);
+            sNewStudy = bst_get('Study', iNewStudy);
+            figure_video('SetVideoStart', file_fullpath(sNewStudy.Image(iNewVideo).FileName), sprintf('%.3f', sOldVideo.VideoStart));
+        end
+    end
+
+    % Save sync data to file
+    for iInput = 2:nInputs
+
+        % Copy videos
+        sOldStudy = bst_get('Study', sInputs(iInput).iStudy);
+        if isfield(sOldStudy,'Image') && ~isempty(sOldStudy.Image)
+            for iOldVideo = 1 : length(sOldStudy.Image)
+                sOldVideo = load(file_fullpath(sOldStudy.Image(iOldVideo).FileName));
+                if isempty(sOldVideo.VideoStart)
+                    sOldVideo.VideoStart = 0;
+                end
+                iNewVideo = import_video(iNewStudy, sOldVideo.LinkTo);
+                sNewStudy = bst_get('Study', iNewStudy);
+                figure_video('SetVideoStart', file_fullpath(sNewStudy.Image(iNewVideo).FileName), sprintf('%.3f', sOldVideo.VideoStart));
+            end
+        end
+
+        ChannelMat = in_bst_channel(sInputs(iInput).ChannelFile);
+
+        sIdxChAn{iInput} = length(NewChannelMat.Channel) +  (1:length(ChannelMat.Channel));
+        NewChannelMat.Channel = [ NewChannelMat.Channel , ChannelMat.Channel  ];
+
+
+        if isfield(ChannelMat,'Nirs') && isfield(NewChannelMat,'Nirs')
+            NewChannelMat.Nirs = sort( union(ChannelMat.Nirs, NewChannelMat.Nirs));
+        elseif isfield(ChannelMat,'Nirs')  && ~isfield(NewChannelMat,'Nirs')
+            NewChannelMat.Nirs = ChannelMat.Nirs;
+        end
+    end
+
+    [~, iChannelStudy] = bst_get('ChannelForStudy', iNewStudy);
+    db_set_channel(iChannelStudy, NewChannelMat, 0, 0);
+    newStudyPath = bst_fileparts(file_fullpath(sNewStudy.FileName));
+
+    % Link to raw file
+    OutputFile = bst_process('GetNewFilename', bst_fileparts(sNewStudy.FileName), 'data_0raw_combned');
+
+    % Raw file
+    [~, rawBaseOut, rawBaseExt] = bst_fileparts(newStudyPath);
+    rawBaseOut = strrep([rawBaseOut rawBaseExt], '@raw', '');
+    RawFileOut = bst_fullfile(newStudyPath, [rawBaseOut '.bst']);
+
+    bst_progress('inc', nInputs);
+    bst_progress('text', 'Saving files...');
+
+    % Read channel flags
+    channelflag = [];
+    for iInput = 1:nInputs
+        sDataRawSync = in_bst_data(sInputs(iInput).FileName, 'ChannelFlag');
+        channelflag = [channelflag; sDataRawSync.ChannelFlag];
+    end
+
+    % Set Output sFile structure
+    sDataRawSync = in_bst_data(sInputs(1).FileName, 'F');
+    sFileIn = sDataRawSync.F;
+    sFileIn.header.nsamples = length(new_times);
+    sFileIn.prop.times      = [ new_times(1), new_times(end)];
+    sFileIn.channelflag     = channelflag;
+    sFileOut = out_fopen(RawFileOut, 'BST-BIN', sFileIn, NewChannelMat);
+
+    sDataSync        = in_bst(sInputs(1).FileName, [], 1, 1, 'no');
+    sOutMat          = rmfield(sDataSync, 'F');
+    sOutMat.format   = 'BST-BIN';
+    sOutMat.DataType = 'raw';
+    sOutMat.F        = sFileOut;
+    sOutMat.ChannelFlag = channelflag;
+    sOutMat.Comment     = [sDataSync.Comment ' | Combined'];
+
+    bst_save(OutputFile, sOutMat, 'v6');
+
+    % Save sync data to file
+    for iInput = 1:nInputs
+        % Load raw data
+        sDataSync        = in_bst(sInputs(iInput).FileName, [], 1, 1, 'no');
+
+        % Update raw data
+        if iInput > 1
+            sDataSync.F      = interp1(sDataSync.Time, sDataSync.F', new_times)';
+        end
+        % Write block
+        out_fwrite(sFileOut, NewChannelMat, 1, [], sIdxChAn{iInput}, sDataSync.F);
+
+        bst_progress('inc', 1);
+    end
+
+    % Register in BST database
+    db_add_data(iNewStudy, OutputFile, sOutMat);
+    OutputFiles{iInput} = OutputFile;
+
+    bst_progress('stop');
+end
+

toolbox/tree/tree_callbacks.m

@@ -899,8 +899,8 @@
                                 end
                             end
                         elseif ismember('NIRS', DisplayMod{iType})
-                            gui_component('MenuItem', jMenuDisplay, [], 'NIRS (scalp)', IconLoader.ICON_CHANNEL, [], @(h,ev)DisplayChannels(bstNodes, Device, 'scalp', 0, 0));
-                            gui_component('MenuItem', jMenuDisplay, [], 'NIRS (pairs)', IconLoader.ICON_CHANNEL, [], @(h,ev)DisplayChannels(bstNodes, Device, 'scalp', 0, 1));
+                            gui_component('MenuItem', jMenuDisplay, [], 'NIRS (scalp)', IconLoader.ICON_CHANNEL, [], @(h,ev)DisplayChannels(bstNodes, 'NIRS-BRS', 'scalp', 0, 0));
+                            gui_component('MenuItem', jMenuDisplay, [], 'NIRS (pairs)', IconLoader.ICON_CHANNEL, [], @(h,ev)DisplayChannels(bstNodes, 'NIRS-BRS', 'scalp', 0, 1));
                         else
                             gui_component('MenuItem', jMenuDisplay, [], channelTypeDisplay, IconLoader.ICON_CHANNEL, [], @(h,ev)DisplayChannels(bstNodes, DisplayMod{iType}, 'scalp'));
                         end