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# bst_extractmarkersctf

## (Toolbox/bst_extractmarkersctf.m in BrainStorm 2.0 (Alpha))

### Function Synopsis

    DATA = bst_extractmarkersctf(DS_FOLDER, MARKER_RANGE, CHANNELS, MARKERS, MARKERPARAM, VERBOSE);

### Help Text

    BST_EXTRACTMARKERSCTF - Extract signal block from a .ds CTF data set
     function DATA = bst_extractmarkersctf(DS_FOLDER, MARKER_RANGE, CHANNELS, MARKERS, MARKERPARAM, VERBOSE);

     EXTRACT_MARKERS
     Extract signal block from a .ds CTF data set based on the Markers information in the Markerfile

### Cross-Reference Information

This function calls

    ds2brainstorm                      C:\BrainStorm_2001\Toolbox\ds2brainstorm.m

### Listing of function C:\BrainStorm_2001\Toolbox\bst_extractmarkersctf.m

    function DATA = bst_extractmarkersctf(DS_FOLDER, MARKER_RANGE, CHANNELS, MARKERS, MARKERPARAM, VERBOSE);
    %BST_EXTRACTMARKERSCTF - Extract signal block from a .ds CTF data set
    % function DATA = bst_extractmarkersctf(DS_FOLDER, MARKER_RANGE, CHANNELS, MARKERS, MARKERPARAM, VERBOSE);
    %
    % EXTRACT_MARKERS
    % Extract signal block from a .ds CTF data set based on the Markers information in the Markerfile

    %<autobegin> ---------------------- 14-Jun-2004 17:09:51 -----------------------
    % --------- Automatically Generated Comments Block Using AUTO_COMMENTS ---------
    %
    % CATEGORY: Data Processing
    %
    % Alphabetical list of external functions (non-Matlab):
    %   toolbox\ds2brainstorm.m
    %
    % At Check-in: $Author: Mosher $  $Revision: 17 $  $Date: 6/14/04 3:37p $
    %
    % This software is part of BrainStorm Toolbox Version 2.0 (Alpha) 14-Jun-2004
    %
    % Principal Investigators and Developers:
    % ** Richard M. Leahy, PhD, Signal & Image Processing Institute,
    %    University of Southern California, Los Angeles, CA
    % ** John C. Mosher, PhD, Biophysics Group,
    %    Los Alamos National Laboratory, Los Alamos, NM
    % ** Sylvain Baillet, PhD, Cognitive Neuroscience & Brain Imaging Laboratory,
    %    CNRS, Hopital de la Salpetriere, Paris, France
    %
    % See BrainStorm website at http://neuroimage.usc.edu for further information.
    %
    % Copyright (c) 2004 BrainStorm by the University of Southern California
    % This software 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.
    %<autoend> ------------------------ 14-Jun-2004 17:09:51 -----------------------

    % History ---------------------------------------
    % -- Sylvain Baillet, Ph.D.
    % Cognitive Neuroscience & Brain Imagin Laboratory - CNRS - Paris France
    % March 2001
    % JCM 08-Sep-2003 commenting
    % -----------------------------------------------

    % MARKER_RANGE = [0 .128];
    % CHANNELS = [31:181]; % Channels to extract
    % DS_FOLDER = 'D:\Users\Silvin\BrainStorm\studies\IRCAM\steady3.ds';
    %
     ONLINE_AV = 0; % if set to 1, runs the online average of each trial and does not return the original data.
     ONLINE_SW_AV = 0; % Same thing but for sample-weighted average
    % MARKERS = [2]; % Array of markers to be read from the file - if empty, reads out all trials from all markers
    %
    % VERBOSE = 1;

    % [MARKERPARAM.names,MARKERPARAM.nsamples ,MARKERPARAM.trial_time] = bst_readmarkerfilectf(DS_FOLDER);

    n_markers = length(MARKERPARAM.nsamples);

    if isempty(MARKERS)
        MARKERS = 1:n_markers;
    end

    n_markers = length(MARKERS);

    for i = MARKERS

        % Are there several time from sync points for this marker ?
        utime = unique(MARKERPARAM.trial_time{i}(:,2));
        if length(utime) == 1 % NO
            % Read all trials at once
            %F = ds2brainstorm(DS_FOLDER,VERBOSE,0,CHANNELS,MARKER_RANGE,MARKERPARAM.trial_time{i}(:,1)');
            F = ds2brainstorm(DS_FOLDER,VERBOSE,0,CHANNELS,MARKERPARAM.trial_time{i}(2)+MARKER_RANGE,MARKERPARAM.trial_time{i}(1));

            % F is a MARKERPARAM.trial_time{i}(:,1)-long cell array
            %        DATA{i}  = zeros(length(CHANNELS),size(F{1},2),MARKERPARAM.nsamples(i)));
            for k = 1:length(MARKERPARAM.trial_time{i}(:,1))
                DATA{i}(:,:,k) = F{k};
                F{k} = [];
            end
            clear F

        else % YES
            % Read trial by trial
            for k = 1:MARKERPARAM.nsamples(i)
                F = ds2brainstorm(DS_FOLDER,VERBOSE,0,CHANNELS,MARKERPARAM.trial_time{i}(k,2)+MARKER_RANGE,MARKERPARAM.trial_time{i}(k,1));
                if k>1
                    if size(F{1},2) < size(DATA{i},2)
                        error('Please check the duration of MARKER_RANGE')
                    else
                        F{1} = F{1}(:,1:size(DATA{i},2));
                    end
                else
                    if ONLINE_AV == 0;
                        DATA{i} = zeros(length(CHANNELS),size(F{1},2),MARKERPARAM.nsamples(i));
                    else
                        DATA{i} = zeros(length(CHANNELS),size(F{1},2));
                    end

                end

                if ONLINE_AV == 0
                    DATA{i}(:,:,k) = F{1};
                else
                    DATA{i} = DATA{i}+F{1}/MARKERPARAM.nsamples(i);
                end

                if VERBOSE
                    fprintf('Trial %d\n',k);
                end

                clear F
            end

        end

    end

    % This part for averaging only

    %
    % for i = 1:n_markers
    %     data_av{i} = mean(DATA{i},3);
    %     figure, plot(MARKER_RANGE(1):1/SAMPLING_RATE:MARKER_RANGE(2),data_av{i}')
    %     title(['Marker ',num2str(i)])
    % end

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