Merge branch 'master' of https://gitlab.science.ru.nl/mposthuma/bachelor-stage

Target_response_plot_test_experiment.m

+%% Initialize 
+%  Clean everythimg
+
+cfn = pb_clean('cd','U:\Documents\BIOLOGIE\STAGE\MATLAB\Data\test experiment'); % clean everything, and change directory
+
+% load epoched data
+l = dir('epoched_data_*.mat');
+for iL = 1:length(l)
+   load(l(iL).name);
+end
+%pa_sac2mat to save sac to mat file
+% load saccades
+l = dir(['sacdet' filesep 'sacdet*.mat']);
+load(['sacdet' filesep l(1).name]);
+
+
+%% Extract data
+
+% get epoched gaze data traces
+azimuth     = Data.epoch.AzGazeEpoched;
+elevation   = Data.epoch.ElGazeEpoched;
+
+%  Run over saccades
+for iS = 1:length(Sac)
+   trial_idx = Sac(iS,1);
+   
+   % Get timings
+   start_trial_idx   = (trial_idx-1)*360+1;
+   stimOn_idx        = start_trial_idx;
+   sacOn_idx         = Sac(iS,3) + start_trial_idx-1;
+   sacOff_idx        = Sac(iS,4) + start_trial_idx-1;
+   
+   % Super sac
+   SS(iS,1:4)  = Sac(iS,1:4);                            % trial / saccade nr / sacc on sample / sac off sample
+   SS(iS,5)    = 1/120 * 1000 *  Sac(iS,3);              % RT
+   SS(iS,6)    = 1/120 * 1000 *  (Sac(iS,4)-Sac(iS,3));  % Duration
+   SS(iS,7)    = azimuth(sacOn_idx);                     % Azimuth onset position
+   SS(iS,8)    = elevation(sacOn_idx);                   % Elevation onset position
+   SS(iS,9)    = azimuth(sacOff_idx);                    % Azimuth offset position 
+   SS(iS,10)   = elevation(sacOff_idx);                  % Elevation offset position
+   SS(iS,11)   = SS(iS,9) - SS(iS,7);                    % Azimuth Saccade amplitude
+   SS(iS,12)   = SS(iS,10) - SS(iS,8);                   % Elevation Saccade amplitude
+   SS(iS,13)   = Data.stimuli.azimuth(SS(iS,1));         % Target Azimuth
+   SS(iS,14)   = Data.stimuli.elevation(SS(iS,1));       % Target Elevation
+   SS(iS,15)   = max(abs(diff(sqrt(azimuth(sacOn_idx:sacOff_idx).^2+elevation(sacOn_idx:sacOff_idx).^2))));   % Max velocity
+   SS(iS,16)   = sqrt(SS(iS,11)^2+SS(iS,12)^2);
+   
+end
+
+
+%%
+
+% criteria
+sel_first   = SS(:,2)==1;                                   % only first saccade                     
+sel_timing  = SS(:,5)>80 & SS(:,5)<400;                     % between 80 - 400 ms
+
+sel_SS      = sel_first & sel_timing;                       % combine all selections
+nSS         = SS(sel_SS,:);
+n_sacc      = sum(sel_SS);
+
+
+c_title = {'Azimuth','Elevation'};
+
+col = pb_selectcolor(2,2);
+cfn = pb_newfig(cfn);
+for iS = 1:2
+   % get data
+   target   = nSS(:,12+iS);
+   resp     = nSS(:,10+iS);
+   
+   % graph
+   subplot(1,2,iS);
+   hold on;
+   axis square;
+   title(c_title{iS});
+   h(iS) = plot(target,resp,'o');
+   hr(iS) = pb_regplot(target,resp,'data',false);
+   xlabel('Target ($^{\circ}$)');
+   ylabel('Response ($^{\circ}$)')
+   xlim([-50 50]);
+   ylim([-50 50]);
+   pb_dline;
+end
+pb_nicegraph;
+
+% color
+for iH = 1:length(h)
+   h(iH).Color    = col(iH,:);
+   hr(iH).Color   = col(iH,:);
+end
+%% Main Sequence plots
+% amplitude = length of saccade = pythagoras of azimuth + elevation
+
+cfn = pb_newfig(cfn);
+sgtitle('Main Sequence')
+   
+iS 1:2
+    velocity = SS(:,15);
+    amplitude = abs(SS(:,16));
+    subplot(1,2,iS);
+    hold on;
+    axis square
+    h(iS) = plot(amplitude, velocity,'o');
+    xlabel('Amplitude');
+    ylabel('Peak velocity');
+
+
+
+
+   
+   
+   
+   

startup.m

 addpath(genpath('C:\Users\marc_\OneDrive\Documents\Studie\STAGE\MATLAB Code'));
 init_biofysica
+pb_setlatex
 

test_experiment.m

-cfn = pb_clean('cd','C:\Users\marc_\OneDrive\Documents\Studie\STAGE\MATLAB Code\Data\Recordings\test experiment');
+%% Raw data conversion + Save preprocessed Data
+cfn = pb_clean('cd','U:\Documents\BIOLOGIE\STAGE\MATLAB\Data\test experiment');
 
 l = dir('converted_data*.mat');
 if isempty(l)
@@ -83,7 +84,7 @@ for i = 1:3:10
     
     i
 end
-%%
+%% Epoch data
 
 fs          = 120;
 duration    = 3;
@@ -158,55 +159,3 @@ end
 
 fn = strrep('preprocessed_data_JJH-0001-21-04-15-0001.mat','preprocessed','epoched');
 save(fn,'Data');
-%%
-if ~exist('sacdet','dir')
-       mkdir('sacdet')
-end
-
-cfn   = pb_clean('cd','C:\Users\marc_\OneDrive\Documents\Studie\STAGE\MATLAB Code\Data\Recordings\test experiment');
-path  = pb_getdir('cdir',cd);
-cd(path)
-
-%  Load data
-l     = dir('epoched*.mat');
-
-if isempty(l); return; end
-fn    = l(1).name;
-load(fn);
-
-%  Switch to sacdet folder
-path  = [path filesep 'sacdet'];
-cd(path)
-%%	Run sacdet over epoched data
-%  Read converted data file, preprocess all blocks, and store data
-
-l     = dir('*.sac');
-if ~isempty(l); return; end
-
-
-%% Make hv & csv and run sacdet
-
-
-Dlen        = length(Data.epoch);
-fs          = 120;
-duration    = 3;
-samples     = duration * fs;
-
-for iB = 1:Dlen
-
-   % Saving calibrated data
-   fname                   = fcheckext(['sacdet_' fn(14:end-5) '_block_' num2str(iB) '_azel'] ,'.hv');
-   fid                     = fopen([path filesep fname],'w','l');
-   AZEL                    = [Data.epoch(iB).AzGazeEpoched; Data.epoch(iB).ElGazeEpoched];
-   
-   fwrite(fid,AZEL,'float');
-   fclose(fid);
-   
-   fn_csv = [path filesep fname];
-   VC2csv(fn_csv,fs,samples,1:length(Data.epoch(iB).AzGazeEpoched)/samples);
-   
-   if ~isfile(fn_csv(1:end-3)) == 1
-       pa_sacdet;
-       pause;
-   end
-end
\ No newline at end of file

test_experiment_sacdet.m

+%% pb_vSacDet.m
+cfn = pb_clean ('cd','U:\Documents\BIOLOGIE\STAGE\MATLAB\Data\test experiment');
+path = pb_getdir('cdir',cd);
+cd(path)
+
+l = dir('epoched*.mat');
+if isempty(1); return; end
+fn = l(1).name;n
+load(fn);
+
+if ~exist('sacdet','dir')
+    mkdir('sacdet')
+end
+path = [path filesep 'sacdet'];
+cd(path)
+
+%%
+
+Dlen = length(Data.epoch);
+fs = 120;
+duration = 3;
+samples = duration*fs;
+
+for iB = 1:Dlen
+    fname = fcheckext(['sacdet_' fn(14:end-5) '_block_' num2str(iB) '_azel'] ,'.hv');
+    fid = fopen([path filesep fname],'w','l');
+    AZEL = [Data.epoch(iB).AzGazeEpoched;Data.epoch(iB).ElGazeEpoched];
+    
+    fwrite(fid,AZEL,'float');
+    fclose(fid);
+    
+    fn_csv = [path filesep fname];
+    VC2csv(fn_csv,fs,samples,1:length(Data.epoch(iB).AzGazeEpoched)/samples);
+    
+    if ~isfile(fn_csv(1:end-3))==1
+        pa_sacdet;
+        pause;
+    end
+end
+    
\ No newline at end of file