function varargout = process_cohere2( varargin )
% PROCESS_COHERE2: Compute the coherence between one signal in one file, and all the signals in another file.
%
% USAGE:  OutputFiles = process_cohere2('Run', sProcess, sInputA, sInputB)

% @=============================================================================
% 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: Francois Tadel, 2012-2020; Hossein Shahabi, 2019-2020

eval(macro_method);
end


%% ===== GET DESCRIPTION =====
function sProcess = GetDescription() %#ok<DEFNU>
    % Description the process
    sProcess.Comment     = 'Coherence AxB [Deprecated]';
    sProcess.Category    = 'Custom';
    sProcess.SubGroup    = 'Connectivity';
    sProcess.Index       = 652;
    sProcess.Description = 'https://neuroimage.usc.edu/brainstorm/Tutorials/Connectivity';
    % Definition of the input accepted by this process
    sProcess.InputTypes  = {'data', 'results', 'matrix'};
    sProcess.OutputTypes = {'timefreq', 'timefreq', 'timefreq'};
    sProcess.nInputs     = 2;
    sProcess.nMinFiles   = 1;
    sProcess.isPaired    = 1;

    % === CONNECT INPUT
    sProcess = process_corr2('DefineConnectOptions', sProcess);
    % === REMOVE EVOKED REPONSE
    sProcess.options.removeevoked.Comment = 'Remove evoked response from each trial';
    sProcess.options.removeevoked.Type    = 'checkbox';
    sProcess.options.removeevoked.Value   = 0;
    sProcess.options.removeevoked.Group   = 'input';
    % === COHERENCE METHOD
    sProcess.options.cohmeasure.Comment = {...
        ['<B>Magnitude-squared Coherence</B><BR>' ...
        '|C|^2 = |Gxy|^2/(Gxx*Gyy)'], ...
        ['<B>Imaginary Coherence (2019)</B><BR>' ...
        'IC    = |imag(C)|'], ...
        ['<B>Lagged Coherence (2019)</B><BR>' ...
        'LC    = |imag(C)|/sqrt(1-real(C)^2)'], ...
        ['<FONT color="#777777"> Imaginary Coherence (before 2019)</FONT><BR>' ...
        '<FONT color="#777777"> IC    = imag(C)^2 / (1-real(C)^2) </FONT>']; ...
        'mscohere', 'icohere2019','lcohere2019', 'icohere'};
    sProcess.options.cohmeasure.Type    = 'radio_label';
    sProcess.options.cohmeasure.Value   = 'mscohere';
    % === Overlap
    sProcess.options.overlap.Comment = 'Overlap for PSD estimation:' ;
    sProcess.options.overlap.Type    = 'value';
    sProcess.options.overlap.Value   = {50, '%', []};
    % === MAX FREQUENCY RESOLUTION
    sProcess.options.maxfreqres.Comment = 'Maximum frequency resolution:';
    sProcess.options.maxfreqres.Type    = 'value';
    sProcess.options.maxfreqres.Value   = {2,'Hz',2};
    % === HIGHEST FREQUENCY OF INTEREST
    sProcess.options.maxfreq.Comment = 'Highest frequency of interest:';
    sProcess.options.maxfreq.Type    = 'value';
    sProcess.options.maxfreq.Value   = {60,'Hz',2};
    % === OUTPUT MODE
    sProcess.options.outputmode.Comment = {'Save individual results (one file per input file)', 'Concatenate input files before processing (one file)', 'Save average connectivity matrix (one file)'};
    sProcess.options.outputmode.Type    = 'radio';
    sProcess.options.outputmode.Value   = 1;
    sProcess.options.outputmode.Group   = 'output';
end


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


%% ===== RUN =====
function OutputFiles = Run(sProcess, sInputA, sInputB) %#ok<DEFNU>
    % Input options
    OPTIONS = process_corr2('GetConnectOptions', sProcess, sInputA, sInputB);
    if isempty(OPTIONS)
        OutputFiles = {};
        return
    end
     
    % Metric options
    OPTIONS.Method = 'cohere';
    OPTIONS.RemoveEvoked  = sProcess.options.removeevoked.Value;
    OPTIONS.MaxFreqRes    = sProcess.options.maxfreqres.Value{1};
    OPTIONS.MaxFreq       = sProcess.options.maxfreq.Value{1};
    OPTIONS.CohOverlap    = 0.50;  % First pre-define the overlap
    OPTIONS.pThresh       = 0.05;
    OPTIONS.CohMeasure    = sProcess.options.cohmeasure.Value; 

    % Change the overlap if it is specified
    if isfield(sProcess.options, 'overlap') && isfield(sProcess.options.overlap, 'Value') && ...
       iscell(sProcess.options.overlap.Value) && ~isempty(sProcess.options.overlap.Value) && ~isempty(sProcess.options.overlap.Value{1})
       OPTIONS.CohOverlap = sProcess.options.overlap.Value{1}/100 ; 
    end

    % Compute metric
    OutputFiles = bst_connectivity({sInputA.FileName}, {sInputB.FileName}, OPTIONS);
end




