count_ripples.m~

acer=0;

%%
if acer==0
addpath('/home/raleman/Documents/MATLAB/analysis-tools-master'); %Open Ephys data loader. 
addpath('/home/raleman/Documents/GitHub/CorticoHippocampal')
addpath('/home/raleman/Documents/internship')
else
addpath('D:\internship\analysis-tools-master'); %Open Ephys data loader.
addpath('C:\Users\Welt Meister\Documents\Donders\CorticoHippocampal\CorticoHippocampal')
   
end
%%
%Rat=26;

for Rat=26:27
if Rat==26
nFF=[
%    {'rat26_Base_II_2016-03-24'                         }
%    {'rat26_Base_II_2016-03-24_09-47-13'                }
%    {'rat26_Base_II_2016-03-24_12-55-58'                }
%    {'rat26_Base_II_2016-03-24_12-57-57'                }
    
   
    {'rat26_nl_base_III_2016-03-30_10-32-57'            }
    {'rat26_nl_base_II_2016-03-28_10-40-19'             }
    {'rat26_nl_baseline2016-03-01_11-01-55'             }
    {'rat26_plusmaze_base_2016-03-08_10-24-41'}
    
    
    
    {'rat26_novelty_I_2016-04-12_10-05-55'          }
    {'rat26_novelty_II_2016-04-13_10-23-29'             }
    {'rat26_for_2016-03-21_10-38-54'                    }
    {'rat26_for_II_2016-03-23_10-49-50'                 }
    
    ];

% labelconditions=[
%     {'Baseline_1' 
%      'Baseline_2'}
%      'Baseline_3'
%      'PlusMaze'
%      'Novelty_1'
%      'Novelty_2'
%      'Foraging_1'
%      'Foraging_2'
%     ];

labelconditions=[
    {'PlusMaze'
                }
     
     'Novelty_1'
     'Novelty_2'
     'Foraging_1'
     'Foraging_2'
    ];


else
nFF=[
    {'rat27_nl_base_2016-03-28_15-01-17'                   }
    {'rat27_NL_baseline_2016-02-26_12-50-26'               }
    {'rat27_nl_base_III_2016-03-30_14-36-57'               }
    
    {'rat27_plusmaze_base_2016-03-14_14-52-48'             }
    {'rat27_plusmaze_base_II_2016-03-24_14-10-08'          }
    
    {'rat27_for_2016-03-21_15-03-05'                       }
    {'Rat27_for_II_2016-03-23_15-06-59'                    }
    
    %{'rat27_novelty_II_2016-04-13_14-37-58'                }  %NO .MAT files found. 
    %{'rat27_novelty_II_2016-04-13_16-29-42'                } %No (complete).MAT files found.
    {'rat27_novelty_I_2016-04-11_14-34-55'                 }
  
%     {'rat27_plusmaze_dis_2016-03-10_14-35-18'              }
%     {'rat27_plusmaze_dis_II_2016-03-16_14-36-07'           }
%     {'rat27_plusmaze_dis_II_2016-03-18_14-46-24'           }
%     {'rat27_plusmaze_jit_2016-03-08_14-46-31'              }
%     {'rat27_plusmaze_jit_II_2016-03-16_15-02-27'           }
%     {'rat27_plusmaze_swrd_qPCR_2016-04-15_14-28-41'        }
%     {'rat27_watermaze_dis_morning_2016-04-06_10-18-36'     }
%     {'rat27_watermaze_jitter_afternoon_2016-04-06_15-41-51'}  
    ]

labelconditions=[
    { 
    %'Baseline_1'}
    %'Baseline_2'
    %'Baseline_3'
    'PlusMaze_1'} 
    'PlusMaze_2'
    
    'Foraging_1'
    
     'Foraging_2'
     'Novelty_1'
    
    
     
    ];

    
end

%% Go to main directory
if acer==0
    cd(strcat('/home/raleman/Documents/internship/',num2str(Rat)))
    addpath /home/raleman/Documents/internship/fieldtrip-master/
    InitFieldtrip()

    cd(strcat('/home/raleman/Documents/internship/',num2str(Rat)))
    clc
else
    cd(strcat('D:\internship\',num2str(Rat)))
    addpath D:\internship\fieldtrip-master
    InitFieldtrip()

    % cd(strcat('/home/raleman/Documents/internship/',num2str(Rat)))
    cd(strcat('D:\internship\',num2str(Rat)))
    clc
end
%% Select experiment to perform. 
inter=1;
granger=0;
%Select length of window in seconds:
ro=[1200];
coher=0;
selectripples=0;
mergebaseline=0;
%%

%Make labels
label1=cell(7,1);
label1{1}='Hippo';
label1{2}='Hippo';
label1{3}='Parietal';
label1{4}='Parietal';
label1{5}='PFC';
label1{6}='PFC';
label1{7}='Reference';

label2=cell(7,1);
label2{1}='Monopolar';
label2{2}='Bipolar';
label2{3}='Monopolar';
label2{4}='Bipolar';
label2{5}='Monopolar';
label2{6}='Bipolar';
label2{7}='Monopolar';

%%

 for iii=1:length(nFF)

    
 clearvars -except nFF iii labelconditions inter granger Rat ro label1 label2 coher selectripples acer mergebaseline
if acer==0
    cd(strcat('/home/raleman/Documents/internship/',num2str(Rat)))
else
    cd(strcat('D:\internship\',num2str(Rat)))
end

cd(nFF{iii})



% error('stop here')  
%%
%for level=1:length(ripple)-1;    
 for level=1:1
     
if ro==1200 && inter==0 && granger==0
run('newest_load_data.m')
else
[sig1,sig2,ripple,carajo,veamos,CHTM,RipFreq2,timeasleep]=newest_only_ripple_level(level);    
end

% ripple=ripple2;
  %Get p and q.
  %Get averaged time signal.
[p,q,timecell,Q,~,~]=getwin2(carajo{:,:,level},veamos{level},sig1,sig2,label1,label2,ro,ripple(level),CHTM(level+1));
% SUS=SU(:,level).';

if selectripples==1

[ran]=rip_select(q);
    % 
    p=p([ran]);
    q=q([ran]);
    Q=Q([ran]);
    timecell=timecell([ran]);
end


%if ro==1200 && inter==0 || granger==1
if ro==1200 && inter==0 && granger==0

SUS=SU{level}.';
% SUS2=SU2(:,level).';
SUS2=SU2{level}.';
%SUQ2=SUQ(:,level).';
SUQ2=SUQ{level}.';

SUStimecell=timecell(1:length(SUS));
SUS2timecell=timecell(1:length(SUS2));
SUQ2timecell=timecell(1:length(SUQ2));

P1_SUS=avg_samples(SUS,SUStimecell);
P2_SUS=avg_samples(SUS2,SUS2timecell);

end
%p is wideband signal. 
%q is bandpassed signal. 
%timecell are the time labels. 
%Q is the envelope of the Bandpassed signal.  

% [p2,q2,timecell2,Q2,~,~]=getwin2(carajo2{:,:,level},veamos2{level},sig1,sig2,label1,label2,ro,ripple2(level),CHTM2(level+1));

%close all
%P1 bandpassed
%P2 widepassdw
% error('stop here please')



Files=dir(fullfile(cd,'*.mat'));


error('stop')




end
%%
end
end