%% CorSE Algorithm for Functional Connectivity
% This algorithm calculates the correlated spectral entropy (CorSE) based functional 
%connectivity between % two time series. For more information, 
%<http://journal.frontiersin.org/article/10.3389/fncom.2016.00112/full Kapucu et al.(2016)>. Please cite the paper if you have used or inspired by the method.

%Copyright (c) 2016, Kapucu
%All rights reserved.
%Redistribution and use in source and binary forms, with or without
%modification, are permitted provided that the following conditions are met:
%* Redistributions of source code must retain the above copyright notice, this
  %list of conditions and the following disclaimer.
%* Redistributions in binary form must reproduce the above copyright notice,
  %this list of conditions and the following disclaimer in the documentation
  %and/or other materials provided with the distribution
%THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
%AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
%IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
%DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
%FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
%DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
%SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
%CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
%OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
%OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

%Select the .h5 file for yor analysis
[file,path] = uigetfile('*.h5');


TargetFile=[path file];
Plate_type=h5readatt(TargetFile, '/DataInfo/', 'Plate type');
if strcmp(Plate_type, '12-well plate')
    final_ch_col = 8;
    final_ch_row = 8;
    final_well_col = 4;
    final_well_row = 3;
elseif strcmp(Plate_type, '48-well plate')
    final_ch_col = 4;
    final_ch_row = 4;
    final_well_col = 8;
    final_well_row = 6;
else
    disp('Unknown MEA layout!')
    
    
    
end

ExcludedWells=h5read(TargetFile, '/DataInfo/ExcludedWells');
disp('Note the excluded wells!:')
disp(ExcludedWells)
InactiveChannels=h5read(TargetFile, '/DataInfo/InactiveChannels');
disp('Inactive channels!:')
disp(InactiveChannels)
%%
prompt='Select your well.Please, use capital letters, e.g. A1:';
MyWell = inputdlg(prompt);
MyWell=MyWell{:};
%%
well_row=double(MyWell(1)-64);

well_col=str2double(MyWell(2:end));


%%
splitter=@(x) strsplit(x, '/'); 
RecordedWells={h5info(TargetFile).Groups(1).Groups.Name};
if ~any(strcmp(cellfun(@(z) z{end}, cellfun(splitter,RecordedWells, 'UniformOutput',false), 'UniformOutput',false), MyWell)) 
    error(['Either well ' MyWell ' ' 'is excluded or it does not exist in the corresponding layout!']);
end
 
 
 %%
 
  
for i = 1 : final_ch_row
      
    for j = 1 : final_ch_col
          
        try
            temp = h5read(TargetFile, strcat('/Data/', MyWell, '/', num2str(i) , num2str(j)));
        catch
            disp(['The channel ' MyWell '_' num2str(i) num2str(j) ' is not recorded in the file'])
            temp=[];
        end
            DataCell{final_ch_row*(i-1)+j,7} = temp';
            DataCell{final_ch_row*(i-1)+j,1} = ['CH' num2str(i) num2str(j)];
            
    end
end
   

    Spectral_entropy_HighPass_data_adaptive;