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behavior_onsets/Emo_LM_per_illuminance.m

+%% Extracting Stimulation Onsets (Task and Light Inputs) of the Emo Task
+
+% This code extracts the onsets under different light conditions(3 Blue conditions, Orange, Dark)
+
+% VERSION_07 : 
+% Output of this version: 
+% Emo_B1 Emo_B2, Emo_B3, Emo_O, Emo_D
+% Neut_B1, Neut_B2, Neut_B3, Neut_O, Neut_D 
+ 
+
+function Emo_LM_v05(modul, check, paths, subs_info, H)
+
+%modul = 1 to include a parametric modulation according to light intensity
+
+if isempty(subs_info)==1
+    return
+end
+
+
+%% Define parameters and sbj file
+TR = 2340; % TR of the scan in ms
+LM_dir='LM'; % folder's name containing all log manager files.
+
+%%
+for id=1:size(subs_info,1)
+        cd(paths.data);
+
+    subject_info = char(subs_info(id));
+    subject_ID = subject_info(5:7);
+    switch subject_info(13)
+        case 'm'
+            subject_session = 'M';
+        case 'e'
+            subject_session = 'E';
+    end
+    
+    entry_table = ['HILIGHT_', subject_ID '_' subject_session] ;
+    index = strcmp(H.subject_Ids, entry_table) ;
+    patient_data = H(index,:) ;
+        
+% inform on the status of the analysis and load the correspondent log file
+disp(['Processing subject ' subject_ID]);
+cd(strcat(subject_info ,'/' ,LM_dir));
+file = strcat('HL_E_', subject_ID ,'_forLM.csv'); % name of log file have to be consistent
+
+% if no log file return a warning
+
+if isempty(file)
+    warning(['No logfile found for N-back task of subject ' subject_ID])
+    return
+end
+
+
+%retrieve info from the log file
+T = readtable(char(file));% read the .csv file
+     
+    % Get when the experiment started
+    start= unique(T.time_Pygaze_start_recording);
+    start_exp = str2double(start(1));   
+    
+    % Get type of Sound (emotional or neutral) and time of appearance
+    Type=T.Sound;
+    ind_nan=strcmp(Type,'NA');
+    Type(ind_nan)=[];
+    Type = char(Type);
+    Soun_app= T.time_Sound_app(5:end,:);
+    ind_neutral = 'N'==Type(:,1);
+    ind_emotion = 'A'==Type(:,1);
+    Tps_neutral = (str2double(Soun_app(ind_neutral))-start_exp)/TR; %time expressed in scans
+    Tps_emotion = (str2double(Soun_app(ind_emotion))-start_exp)/TR;  %time expressed in scans
+    All_tps= zeros(length(Type),1);
+    All_tps(ind_neutral,:)= Tps_neutral;
+    All_tps(ind_emotion,:)= Tps_emotion;
+    
+    
+%%%%%%%%%%%%%% Get light condition and duration
+
+    light_changes = find(abs(any(diff(char(T.Light_Condition)),2)) > 0);
+    
+    % Preallocate array with 2 columns (start and duration) for each light
+    % cond
+    light_start_dur= struct();
+    countb=0;
+    counto=0;
+    countd=0;
+    for lights= 1:length(light_changes)
+        curr_cond = T.Light_Condition{light_changes(lights)+1};
+        curr_light = curr_cond(1);
+        if strcmp(curr_light, 'B')==1
+            countb=countb+1;
+            thecount=countb;
+        else
+            counto=counto+1;
+            thecount=counto;
+        end
+        curr_int = curr_cond(2);
+        curr_loop = curr_cond(3);
+        countd= countd+1;
+        
+        % Start calculating light/dark onsets and durations
+        light_start_dur.(curr_light).onset(thecount)= (str2double...
+            (T.time_Light_Loop_Sequence(light_changes(lights)+1))-start_exp)/TR;
+        
+        dark_on= unique(T.(sprintf('time_%s%sD%s_inner_loop',curr_light, curr_int, curr_loop)));
+
+        light_start_dur.D.onset(countd)= (str2double(dark_on(1))-start_exp)/TR;
+        
+        light_start_dur.(curr_light).endLight(thecount) = light_start_dur.D.onset(countd);
+        
+        
+        light_start_dur.(curr_light).duration(thecount)= (light_start_dur.D.onset...
+            (countd)-light_start_dur.(curr_light).onset(thecount));
+        
+        light_start_dur.(curr_light).names(thecount) = {curr_cond};
+        
+        if  exist('curr_dark','var') == 1
+            index_lastDark= strcmp(light_start_dur.D.names, curr_dark);
+            lastDark=light_start_dur.D.onset(index_lastDark);
+            light_start_dur.D.duration(index_lastDark)= light_start_dur.(curr_light).onset(thecount) - lastDark;  
+            light_start_dur.D.endLight(index_lastDark)= light_start_dur.(curr_light).onset(thecount);
+        end
+        
+        curr_dark=sprintf('%s%sD%s',curr_light, curr_int, curr_loop);
+        light_start_dur.D.names(countd) = {curr_dark};
+    end
+    
+%%%%%%%%%% Seperation of Blue Light Intensities
+
+start_light_6Con = struct();
+countB1=0;
+countB2=0;
+countB3=0;
+
+for ii = 1: length(light_start_dur.B.names)
+    if contains(light_start_dur.B.names(ii),'B1')
+        countB1 = countB1 + 1;
+        start_light_6Con.B1.onset(countB1)= light_start_dur.B.onset(ii);
+        start_light_6Con.B1.duration(countB1)= light_start_dur.B.duration(ii);
+        start_light_6Con.B1.names(countB1)= light_start_dur.B.names(ii);
+        start_light_6Con.B1.endLight(countB1)= light_start_dur.B.endLight(ii);
+    elseif contains(light_start_dur.B.names(ii),'B2')
+        countB2 = countB2 + 1;
+        start_light_6Con.B2.onset(countB2)= light_start_dur.B.onset(ii);
+        start_light_6Con.B2.duration(countB2)= light_start_dur.B.duration(ii);
+        start_light_6Con.B2.names(countB2)= light_start_dur.B.names(ii);
+        start_light_6Con.B2.endLight(countB2)= light_start_dur.B.endLight(ii);
+    elseif contains(light_start_dur.B.names(ii),'B3')
+        countB3 = countB3 + 1;
+        start_light_6Con.B3.onset(countB3)= light_start_dur.B.onset(ii);
+        start_light_6Con.B3.duration(countB3)= light_start_dur.B.duration(ii);
+        start_light_6Con.B3.names(countB3)= light_start_dur.B.names(ii);
+        start_light_6Con.B3.endLight(countB3)= light_start_dur.B.endLight(ii);
+    end
+end
+    
+start_light_6Con.O = light_start_dur.O ;
+start_light_6Con.D = light_start_dur.D;
+
+%%%%%%%%%%%%%%%%%%%%%
+    
+    % Take Emotional and Neutral sounds appearing during one of each
+    % condition
+    type_lights= {'B', 'O', 'D'};
+    sounds_in_cond=struct();
+    
+    for curr_light = 1:length(type_lights)
+        temp= light_start_dur.(type_lights{curr_light});
+        count_em=0;
+        count_neutr=0;
+        for temp_size=1:length(temp.onset)
+            for emot=1:length(Tps_emotion)
+                if curr_light==3 && temp_size==20
+                    if Tps_emotion(emot)>temp.onset(temp_size)
+                        count_em=count_em+1;
+                        sounds_in_cond.(type_lights{curr_light}).emotional(count_em)= Tps_emotion(emot);
+                        sounds_in_cond.(type_lights{curr_light}).indexEm(count_em)= find(All_tps==Tps_emotion(emot));
+                        sounds_in_cond.(type_lights{curr_light}).names(count_em)=(temp.names(temp_size));
+                    end
+                else
+                    if Tps_emotion(emot)>temp.onset(temp_size) && Tps_emotion(emot)<temp.endLight(temp_size)
+                        count_em=count_em+1;
+                        sounds_in_cond.(type_lights{curr_light}).emotional(count_em)= Tps_emotion(emot);
+                        sounds_in_cond.(type_lights{curr_light}).indexEm(count_em)= find(All_tps==Tps_emotion(emot));
+                        sounds_in_cond.(type_lights{curr_light}).names(count_em)=(temp.names(temp_size));
+                    end
+                end
+            end
+            for neut= 1:length(Tps_neutral)
+                if curr_light==3 && temp_size==20
+                    if Tps_neutral(neut)>temp.onset(temp_size)
+                        count_neutr=count_neutr+1;
+                        sounds_in_cond.(type_lights{curr_light}).neutral(count_neutr)= Tps_neutral(neut);
+                        sounds_in_cond.(type_lights{curr_light}).indexNe(count_neutr)= find(All_tps==Tps_neutral(neut));
+                        sounds_in_cond.(type_lights{curr_light}).names(count_neutr)=(temp.names(temp_size));
+                    end
+                else
+                    if Tps_neutral(neut)>temp.onset(temp_size) && Tps_neutral(neut)<temp.endLight(temp_size)
+                        count_neutr=count_neutr+1;
+                        sounds_in_cond.(type_lights{curr_light}).neutral(count_neutr)= Tps_neutral(neut);
+                        sounds_in_cond.(type_lights{curr_light}).indexNe(count_neutr)= find(All_tps==Tps_neutral(neut));
+                        sounds_in_cond.(type_lights{curr_light}).names(count_neutr)=(temp.names(temp_size));
+                    end
+                end
+            end
+        end
+    end
+    
+  
+    
+%%% Seperation of sounds by blue light intensities %%%
+
+Sounds_6Con = struct();
+countSB1=0;
+countSB2=0;
+countSB3=0;
+
+for ii = 1: length(sounds_in_cond.B.names)
+    if contains(sounds_in_cond.B.names(ii),'B1')
+        countSB1 = countSB1 + 1;
+        Sounds_6Con.B1.emotional(countSB1)= sounds_in_cond.B.emotional(ii);
+        Sounds_6Con.B1.indexEm(countSB1)= sounds_in_cond.B.indexEm(ii);
+        Sounds_6Con.B1.neutral(countSB1)= sounds_in_cond.B.neutral(ii);
+        Sounds_6Con.B1.indexNe(countSB1)= sounds_in_cond.B.indexNe(ii);
+        Sounds_6Con.B1.names(countSB1)= sounds_in_cond.B.names(ii);
+    elseif contains(sounds_in_cond.B.names(ii),'B2')
+        countSB2 = countSB2 + 1;
+        Sounds_6Con.B2.emotional(countSB2)= sounds_in_cond.B.emotional(ii);
+        Sounds_6Con.B2.indexEm(countSB2)= sounds_in_cond.B.indexEm(ii);
+        Sounds_6Con.B2.neutral(countSB2)= sounds_in_cond.B.neutral(ii);
+        Sounds_6Con.B2.indexNe(countSB2)= sounds_in_cond.B.indexNe(ii);
+        Sounds_6Con.B2.names(countSB2)= sounds_in_cond.B.names(ii);
+    elseif contains(sounds_in_cond.B.names(ii),'B3')
+        countSB3 = countSB3 + 1;
+        Sounds_6Con.B3.emotional(countSB3)= sounds_in_cond.B.emotional(ii);
+        Sounds_6Con.B3.indexEm(countSB3)= sounds_in_cond.B.indexEm(ii);
+        Sounds_6Con.B3.neutral(countSB3)= sounds_in_cond.B.neutral(ii);
+        Sounds_6Con.B3.indexNe(countSB3)= sounds_in_cond.B.indexNe(ii);
+        Sounds_6Con.B3.names(countSB3)= sounds_in_cond.B.names(ii);
+    end
+end
+    
+Sounds_6Con.O = sounds_in_cond.O ;
+Sounds_6Con.D = sounds_in_cond.D;  
+
+
+%%%%%%% Mel intensity added
+
+    mod_B1_sounds =  zeros(length(Sounds_6Con.B1.names),1);
+    mod_B1_sounds(contains(Sounds_6Con.B1.names, sprintf('B1'))')= 37;
+    
+    mod_B2_sounds =  zeros(length(Sounds_6Con.B2.names),1);
+    mod_B2_sounds(contains(Sounds_6Con.B2.names, sprintf('B2'))')= 92;
+    
+    mod_B3_sounds =  zeros(length(Sounds_6Con.B3.names),1);
+    mod_B3_sounds(contains(Sounds_6Con.B3.names, sprintf('B3'))')= 190;
+    
+    mod_O_sounds =  zeros(length(Sounds_6Con.O.names),1);
+    mod_O_sounds(contains(Sounds_6Con.O.names, sprintf('O'))')= 0.16;
+
+
+    
+%%% prepare files for SPM  
+    
+    onsets= [{Sounds_6Con.B1.emotional'} {Sounds_6Con.B2.emotional'} {Sounds_6Con.B3.emotional'} {Sounds_6Con.O.emotional'}...
+        {Sounds_6Con.D.emotional'}... 
+        {Sounds_6Con.B1.neutral'} {Sounds_6Con.B2.neutral'} {Sounds_6Con.B3.neutral'} {Sounds_6Con.O.neutral'}... 
+        {Sounds_6Con.D.neutral'}]        
+       
+    
+    durations= [{zeros(size(Sounds_6Con.B1.emotional',1),1)} {zeros(size(Sounds_6Con.B2.emotional',1),1)}...
+        {zeros(size(Sounds_6Con.B3.emotional',1),1)} {zeros(size(Sounds_6Con.O.emotional',1),1)}...
+        {zeros(size(Sounds_6Con.D.emotional',1),1)}...
+        {zeros(size(Sounds_6Con.B1.neutral',1),1)} {zeros(size(Sounds_6Con.B2.neutral',1),1)}...
+        {zeros(size(Sounds_6Con.B3.neutral',1),1)} {zeros(size(Sounds_6Con.O.neutral',1),1)}...
+        {zeros(size(Sounds_6Con.D.neutral',1),1)}];
+         
+         
+   names = [{'Emo_B1'} {'Emo_B2'} {'Emo_B3'} {'Emo_O'} {'Emo_D'} {'Neut_B1'} {'Neut_B2'}...
+            {'Neut_B3'} {'Neut_O'} {'Neut_D'}]
+    
+ 
+    if modul == 0
+        
+    save (sprintf('onsets_emo_nomod_Mel_6Con_noblocks_%s.mat',entry_table),'onsets', 'durations', 'names');
+        
+    elseif modul ==1
+        for x=1:length(names)
+            if x==1
+                pmod(x).name{1}='lightmod_emot_B1';
+                pmod(x).param{1}= mod_B1_sounds';
+                pmod(x).poly{1} = 1;
+                
+            elseif x==2
+                pmod(x).name{1}='lightmod_emot_B2';
+                pmod(x).param{1}= mod_B2_sounds';
+                pmod(x).poly{1} = 1;
+                
+            elseif x==3
+                pmod(x).name{1}='lightmod_emot_B3';
+                pmod(x).param{1}= mod_B3_sounds';
+                pmod(x).poly{1} = 1;
+                
+            elseif x==6
+                pmod(x).name{1}='lightmod_neut_B1';
+                pmod(x).param{1}= mod_B1_sounds';
+                pmod(x).poly{1} = 1;
+                
+            elseif x==7
+                pmod(x).name{1}='lightmod_neut_B2';
+                pmod(x).param{1}= mod_B2_sounds';
+                pmod(x).poly{1} = 1;
+                
+            elseif x==8
+                pmod(x).name{1}='lightmod_neut_B3';
+                pmod(x).param{1}= mod_B3_sounds';
+                pmod(x).poly{1} = 1;
+                
+            elseif x==4
+                pmod(x).name{1}='lightmod_emo_O';
+                pmod(x).param{1}= mod_O_sounds';
+                pmod(x).poly{1} = 1;
+                
+            elseif x==9
+                pmod(x).name{1}='lightmod_neut_O';
+                pmod(x).param{1}= mod_O_sounds';
+                pmod(x).poly{1} = 1;
+                
+            else
+                pmod(x).name{1} = '';
+                pmod(x).param{1} = [];
+                pmod(x).poly{1} = [];
+            end
+        end
+             
+        save (sprintf('onsets_emo_lightmod_Mel_6Con_noblocks_%s.mat',entry_table),'onsets', 'durations', 'pmod', 'names');
+    end
+    
+    cd (paths.data)
+    
+end
+
+
+