Add process to merge adjacent event into a continious event

toolbox/process/functions/process_evt_merge_continious.m

@@ -0,0 +1,218 @@
+function varargout = process_evt_merge_continious( varargin )
+% process_evt_merge_continious:  Merge continious, uninterrupted events
+% into one event. 
+%
+% USAGE:  OutputFiles = process_evt_merge_continious('Run', sProcess, sInputs)
+
+% @=============================================================================
+% 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, 2026
+
+eval(macro_method);
+end
+
+
+%% ===== GET DESCRIPTION =====
+function sProcess = GetDescription() 
+    % Description the process
+    sProcess.Comment     = 'Generate continuous events';
+    sProcess.Category    = 'File';
+    sProcess.SubGroup    = 'Events';
+    sProcess.Index       = 55;
+    sProcess.Description = '';
+    % Definition of the input accepted by this process
+    sProcess.InputTypes  = {'data', 'raw', 'matrix'};
+    sProcess.OutputTypes = {'data', 'raw', 'matrix'};
+    sProcess.nInputs     = 1;
+    sProcess.nMinFiles   = 1;
+
+    % Event name
+    sProcess.options.combine.Comment = 'Event Names (seperated by comma)';
+    sProcess.options.combine.Type    = 'text';
+    sProcess.options.combine.Value   = '';
+
+    % Ignore bad segment
+    sProcess.options.ignore_bad.Comment = 'Remove bad segments';
+    sProcess.options.ignore_bad.Type    = 'checkbox';
+    sProcess.options.ignore_bad.Value   = 1;
+
+    % Event name
+    sProcess.options.evt_sufix.Comment = 'Event suffix';
+    sProcess.options.evt_sufix.Type    = 'text';
+    sProcess.options.evt_sufix.Value   = 'continuous';
+
+    % Minimum events durations
+    sProcess.options.min_duration.Comment = 'Minimum event duration: ';
+    sProcess.options.min_duration.Type    = 'value';
+    sProcess.options.min_duration.Value   = {30, 's', 0};
+
+
+end
+
+
+%% ===== FORMAT COMMENT =====
+function Comment = FormatComment(sProcess)
+    Comment = sProcess.Comment;
+end
+
+
+%% ===== RUN =====
+function OutputFiles = Run(sProcess, sInput)
+    % Return all the input files
+    OutputFiles = {};   
+
+
+    % ===== GET OPTIONS =====
+    % Combination string
+    eventNames = cellfun(@(x) strtrim(x),  strsplit(sProcess.options.combine.Value, ','),  'UniformOutput',  false);
+    if isempty(eventNames)
+        bst_report('Error', sProcess, [], 'Missing event names.');
+        return;
+    end
+    % Output suffix
+    evt_sufix = sProcess.options.evt_sufix.Value;
+    if isempty(evt_sufix)
+        evt_sufix = 'continuous';
+    end
+
+    % Ignore bad segmens 
+    ignore_bad = sProcess.options.ignore_bad.Value;
+    min_duration = sProcess.options.min_duration.Value{1};
+
+
+    % ===== GET FILE DESCRIPTOR =====
+    isRaw = strcmpi(sInput.FileType, 'raw');
+    % Load the raw file descriptor
+    if isRaw
+        DataMat = in_bst_data(sInput.FileName, {'Time', 'F'});
+        sFile = DataMat.F;
+        sFile.Time = DataMat.Time;
+    else
+        DataMat = in_bst_data(sInput.FileName, {'TIme', 'Events'});
+        sFile.events = DataMat.Events;
+        sFile.epochs = [];
+    end
+
+    % Process only continuous files
+    if ~isempty(sFile.epochs)
+        bst_report('Error', sProcess, sInput, 'This function can only process continuous recordings (no epochs). Skipping File...');
+        return;
+    end
+
+    % If no markers are present in this file
+    if isempty(sFile.events)
+        bst_report('Warning', sProcess, sInput, 'This file does not contain any event. Skipping File...');
+        return;
+    end
+
+    event_idx = zeros(1, length(eventNames));
+    for iEvt = 1:length(eventNames)
+        idx = find(strcmp({sFile.events.label}, eventNames{iEvt}));
+        if isempty(idx)
+            bst_report('Warning', sProcess, sInput, sprintf('Unable to find event %s',  eventNames{iEvt}));
+            continue;
+        end
+
+        event_idx(iEvt) = idx;
+    end
+
+    event_idx = event_idx(event_idx > 0);
+    sEvents = sFile.events(event_idx);
+
+    % Create binary mask
+    mask = event2mask(sFile.Time, sEvents);
+
+    % Remove bad period
+    if ignore_bad
+        bad_events = find(cellfun(@(x)contains(x, 'bad') , {sFile.events.label}));
+        if ~isempty(bad_events)
+            sBadEvents = sFile.events(bad_events);
+            bad_mask = ~event2mask(sFile.Time, sBadEvents);
+
+            mask = mask .* bad_mask;
+        end
+    end
+
+    % Recreate continuous events
+    newEvents = mask2events(sFile.Time, mask, sEvents, min_duration, evt_sufix);
+
+    sFile.events = [sFile.events , newEvents];
+
+    % ===== SAVE RESULT =====
+    % Report results
+    if isRaw
+        DataMat.F = sFile;
+    else
+        DataMat.Events = sFile.events;
+    end
+    bst_save(file_fullpath(sInput.FileName), DataMat, 'v6', 1);
+
+
+
+    % Return all the input files
+    OutputFiles{end+1} = sInput.FileName;
+end
+
+
+function mask = event2mask(Time, sEvents)
+
+    mask = false(length(sEvents), length(Time));
+    for iEvt = 1:length(sEvents)
+
+        for iTime = 1:size(sEvents(iEvt).times, 2)
+            idx_time = panel_time('GetTimeIndices', Time, sEvents(iEvt).times(:, iTime));
+            mask(iEvt, idx_time) = 1;
+        end
+    end
+
+end
+
+function newEvents = mask2events(Time, mask, sEvents, min_duration, evt_sufix)
+
+    newEvents = sEvents;
+    isIncluded = true(1, length(sEvents));
+
+    for iEvt = 1:length(sEvents)
+
+        newEvents(iEvt).label = sprintf('%s/%s', newEvents(iEvt).label, evt_sufix);
+
+        tmp = diff(mask(iEvt,:)); 
+        start_segment = find(tmp == 1) + 1; 
+        end_segment   = find(tmp == -1);
+
+        if length(start_segment) ==  length(end_segment) -1
+            start_segment = [1 start_segment];
+        end     
+        if length(start_segment) ==  length(end_segment) +1
+            end_segment = [ end_segment length(sData.Time)];
+        end  
+
+        new_times  = [ Time(start_segment) ;  Time(end_segment)  ];
+
+        evt_durations = new_times(2,:) - new_times(1,:);
+
+        isIncluded(iEvt) = any(evt_durations >= min_duration);
+
+        newEvents(iEvt).times  = new_times(:, evt_durations >= min_duration);
+        newEvents(iEvt).epochs = ones(1, size(newEvents(iEvt).times, 2));
+    end
+
+    newEvents = newEvents(isIncluded);
+end
+