VVOR 1.0

analize.m

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+% Jorge Rey Martinez 2017
+% Inputs
+% t = time array
+% e = eye velocity array
+% h = head velocity array
+% s = Boolean, true if register is supresed VVOR false if VVOR
+function analize(t,e,h,s)
+if isOctave
+    scrsz = get(0,'ScreenSize');
+else
+    scrsz = get(groot,'ScreenSize');
+end
+if s == 1
+    figure1 = figure('Name','VORS PLOTS','NumberTitle','off','Position',[1 scrsz(4)/1.2 scrsz(3)/1.01 scrsz(4)/1.2]);
+else
+    figure1 = figure('Name','VVOR PLOTS','NumberTitle','off','Position',[1 scrsz(4)/1.2 scrsz(3)/1.01 scrsz(4)/1.2]);
+end
+figure(figure1);
+%Original plot
+subplot(3,2,1)
+plot(t,h,'b',t,e,'r','LineWidth',1.25)
+title('Test Results - RAW data')
+xlabel('Time in secs')
+ylabel('Velocity in deg/sec')
+ylim([-400 +400])
+legend ('Head velocity','Eye velocity')
+%Desaccaded plot
+subplot(3,2,2)
+if s == 1
+    desacE = medfilt1(e,35);
+else
+    desacE = medfilt1(e,30);
+end
+plot(t,h,'b',t,desacE,'r','LineWidth',1.25)
+title('Test Results - Desaccaded data')
+xlabel('Time in secs')
+ylabel('Velocity in deg/sec')
+ylim([-400 +400])
+legend ('Head velocity','Eye velocity')
+%get positive/neagtive data
+limit = size(t);
+posH = [];
+posE = [];
+negH = [];
+negE = [];
+for n = 1:limit
+    if h(n) > 0
+        posH = vertcat(posH,h(n));
+        if desacE(n) > 0
+            posE = vertcat(posE,desacE(n));
+        else
+            posE = vertcat(posE,0);
+        end
+    end
+    if h(n) < 0
+        negH = vertcat(negH,h(n));
+        if desacE(n) < 0
+            negE = vertcat(negE,desacE(n));
+        else
+            negE = vertcat(negE,0);
+        end
+    end
+end
+%Positive-Negative plots
+subplot(3,2,5)
+plot([posH,posE],'LineWidth',1.25)
+title('Positive vs Negative data - Desaccaded data')
+xlabel('Time in samples')
+ylabel('Velocity in deg/sec')
+hold on
+plot([negH,negE],'LineWidth',1.25)
+hold off
+legend ('Head velocity','Eye velocity','Head velocity','Eye velocity')
+%XY ploy & regresion line
+subplot(3,2,6)
+hold on
+if isOctave
+    scatter(negH,negE,'c','.');
+    scatter(posH,posE,'b','.');
+else
+    scatter(negH,negE,'.b');
+    scatter(posH,posE,'.','MarkerEdgeColor',[0 .7 .7]);
+end
+title('Head vs Eye plot - Desaccaded data')
+xlabel('Head Velocity in deg/sec')
+ylabel('Eye Velocity in deg/sec')
+negB = negH\negE;
+posB = posH\posE;
+calcNegE = negB*negH;
+calcPosE = posB*posH;
+plot(negH,calcNegE,posH,calcPosE,'LineWidth',5)
+if s == 1
+    plot(negH,negH,'r',posH,posH,'r','LineWidth',1.5)
+    legend ('Negative data','Positive data','Negative regresion','Positive regresion','No Suppression line','Location','eastoutside')
+else
+    plot(negH,negH,'g',posH,posH,'g','LineWidth',1.5)
+    legend ('Negative data','Positive data','Negative regresion','Positive regresion','Normality line','Location','eastoutside')
+end
+hold off
+%axis square
+%Fourier plots
+subplot(3,2,3)
+[fHead,P1Head] = fourier(h);
+[fEye,P1Eye] = fourier(e);
+hold on
+stem(fHead,P1Head,'b');
+title('Single-Side Amplitude Spectrum of Head and Eye - RAW data')
+xlabel('f (Hz)')
+ylabel('|P1(f)|')
+xlim([0 5])
+stem(fEye,P1Eye,'r');
+legend('Head','Eye')
+hold off
+%Desacade Fourier
+subplot(3,2,4)
+[fHead,P1Head] = fourier(h);
+[fEye,P1Eye] = fourier(desacE);
+hold on
+stem(fHead,P1Head,'b');
+title('Single-Side Amplitude Spectrum of Head and Eye - Desaccaded data')
+xlabel('f (Hz)')
+ylabel('|P1(f)|')
+xlim([0 5])
+stem(fEye,P1Eye,'r');
+legend('Head','Eye')
+hold off
+%Numerical data
+aucPosEye = trapz(posE);
+aucPosHead = trapz(posH);
+aucNegEye = trapz(negE);
+aucNegHead = trapz(negH);
+gainPos = (aucPosEye/aucPosHead);
+gainNeg = (aucNegEye/aucNegHead);
+velGainPos = mean(findpeaks(posE))/mean(findpeaks(posH));
+velGainNeg = mean(findpeaks(abs(negE)))/mean(findpeaks(abs(negH)));
+prePosPeakE = mean(findpeaks(posE));
+preNegPeakE = mean(findpeaks(abs(negE)));
+if prePosPeakE > preNegPeakE
+    peakE = prePosPeakE;
+    peakH = mean(findpeaks(posH));
+else
+    peakE = -preNegPeakE;
+    peakH = -mean(findpeaks(abs(negH)));
+end
+result = strcat('+Area gain: ',num2str(gainPos),' -Area gain: ',num2str(gainNeg),' || +Slope: ',num2str(posB),' -Slope: ',num2str(negB),' || +Velocity gain: ',num2str(velGainPos),' -Velocity gain: ',num2str(velGainNeg),' || Head Maxs(deg/s):  ', num2str(peakH),' Eye Maxs: ',num2str(peakE),' || DCoff.: ', num2str(velGainPos-velGainNeg));
+display(result)
+if ~isOctave
+    mTextBox = uicontrol('style','text');
+    set(mTextBox,'String',result)
+    set(mTextBox,'FontSize',12)
+    set(mTextBox,'Position',[20 5 1300 25])
+    set(figure1,'MenuBar','figure')
+end
+

fourier.m

@@ -0,0 +1,9 @@
+function [f,P1] = fourier(data)
+Fs = 250;                     % Sampling frequency
+[L,~] = size(data);           % Length of signal
+X = data;                     % Data
+Y = fft(X);
+P2 = abs(Y/L);
+P1 = P2(1:fix(L/2)+1);
+P1(2:end-1) = 2*P1(2:end-1);
+f = Fs*(0:(L/2))/L;

isOctave.m

@@ -0,0 +1,12 @@
+%%
+%% Return: true if the environment is Octave.
+%%
+function retval = isOctave
+  persistent cacheval;  % speeds up repeated calls
+
+  if isempty (cacheval)
+    cacheval = (exist ('OCTAVE_VERSION', 'builtin') > 0);
+  end
+
+  retval = cacheval;
+end

read.m

@@ -0,0 +1,95 @@
+function [t,e,h] = read(s)
+t = [];
+e = [];
+h = [];
+[file,directory] = uigetfile('.csv','Select "ASCII results File" to import');
+if file == 0
+    return
+end
+fullArchive = fullfile(directory,file);
+readFile = fopen(fullArchive);
+tline = fgetl(readFile);
+readnow = 0;
+timeData = '';
+eyeData = '';
+headData = '';
+while ischar(tline)
+
+    if readnow == 3
+        timeData = tline;
+    end
+    if readnow == 4
+        eyeData = tline;
+    end
+    if readnow == 5
+        headData = tline;
+        break
+    end
+    if s == 1
+        if strcmp(tline,'Test Type;VORS — Horizontal')||strcmp(tline,'Test Type;SRVO — Horizontal')||strcmp(tline,'Tipo de Prueba;SRVO — Horizontal')
+            readnow = 1;
+        end
+    else
+        if strcmp(tline,'Test Type;VVOR — Horizontal')||strcmp(tline,'Tipo de Prueba;RVVO — Horizontal')||strcmp(tline,'Test Type;RVVO — Horizontal')
+            readnow = 1;
+        end
+    end
+
+    if readnow > 0
+        readnow = readnow + 1;
+    end
+    tline = fgetl(readFile);
+end
+fclose(readFile);
+timeData = strrep(timeData, ',', '.');
+timeData = strsplit(timeData,';');
+timeData = timeData(2:end);
+eyeData = strrep(eyeData, ',', '.');
+eyeData = strsplit(eyeData,';');
+eyeData = eyeData(2:end);
+headData = strrep(headData, ',', '.');
+headData = strsplit(headData,';');
+headData = headData(2:end);
+[~,b] = size(timeData);
+for n = 1:b-1
+    t = vertcat(t,str2double(timeData{1,n}));
+    e = vertcat(e,str2double(eyeData{1,n}));
+    h = vertcat(h,str2double(headData{1,n}));
+end
+question = questdlg('Do you want to select a time period or do you want to use entrie data?','Select time window','SET TIME RANGE','USE ALL DATA','USE ALL DATA');
+if strcmp(question,'SET TIME RANGE')
+    prompt = {'Enter min value of seconds:','Enter max value of seconds:'};
+    dlg_title = 'Input range';
+    num_lines = 1;
+    defaultans = {'',''};
+    answer = inputdlg(prompt,dlg_title,num_lines,defaultans);
+    validation = 1;
+    [a,~] = size(answer);
+    if a < 2
+        display('Max and/or Min are/is missing')
+        validation = 0;
+    end
+    minim = str2double(answer{1,1});
+    maxim = str2double(answer{2,1});
+    if isnan(minim)||isnan(maxim)
+        display('Data must to be numeric. Decimal separator is "."')
+        validation = 0;
+    end
+    if maxim < minim
+        display('Max is < than Min')
+        validation = 0;
+    end
+    if validation == 1
+        [~,minpos] = min(abs(t-minim));
+        [~,maxpos] = min(abs(t-maxim));
+        t = t(minpos:maxpos);
+        e = e(minpos:maxpos);
+        h = h(minpos:maxpos);
+    end
+end
+
+
+
+
+
+

saccades.m

@@ -0,0 +1,88 @@
+% Jorge Rey Martinez 2017
+% Inputs
+% t = time array
+% e = eye velocity array
+% h = head velocity array
+% s = Boolean, true if register is supresed VVOR false if VVOR
+function saccades(t,e,h,s)
+if isOctave
+    scrsz = get(0,'ScreenSize');
+else
+    scrsz = get(groot,'ScreenSize');
+end
+if s == 1
+    figure2 = figure('Name','SACCADES VORS PLOT','NumberTitle','off','Position',[1 scrsz(4)/1.2 scrsz(3)/1.55 scrsz(4)/1.7]);
+else
+    figure2 = figure('Name','SACCADES VVOR PLOT','NumberTitle','off','Position',[1 scrsz(4)/1.2 scrsz(3)/1.55 scrsz(4)/1.7]);
+end
+figure(figure2);
+%SACCADES plot
+subplot(2,1,1)
+if s == 1
+    desacE = medfilt1(e,35);
+else
+    desacE = medfilt1(e,30);
+end
+sacE = e-desacE;
+plot(t,h,'b',t,sacE,'r','LineWidth',1.25)
+%Calculate Sacades per Second
+[peaks,locs] = findpeaks(abs(sacE),'MinPeakHeight',100,'MinPeakDistance',10);
+[npeaks,~] = size(peaks);
+[last,~]= size(t);
+sacSec = (npeaks)/(t(last)-t(1));
+[f,P1] = fourier(h);
+[~,ind] = max(P1);
+headFrec = f(ind);
+headPeriod = 1/headFrec;
+sacCyc = (npeaks)/((t(last)-t(1))/headPeriod);
+%PlotData
+string = ['Test Results - Saccades data (Saccades per second = ' num2str(sacSec) ' - Saccades per cycle = ' num2str(sacCyc) ' at ' num2str(headFrec) 'Hz. )'];
+title(string)
+xlabel('Time in secs')
+ylabel('Velocity in deg/sec')
+ylim([-400 +400])
+legend ('Head velocity','Eye velocity')
+%Plot Detectes Saccades
+%subplot(3,1,2)
+%findpeaks(abs(sacE),t,'MinPeakHeight',100,'MinPeakDistance',10);
+%ylim([0 +400]);
+%title('Detected Saccades Plot')
+%xlabel('Time in secs')
+%ylabel('Eye Velocity in deg/sec')
+%Get sacades on time
+headSacc = abs(h(locs));
+[sizeHead,~]= size (headSacc);
+pos = 1;
+sac0 = 0;
+sac50 = 0;
+sac100 = 0;
+sac150 = 0;
+sac200 = 0;
+sac250 = 0;
+while pos < sizeHead
+    if headSacc(pos) > 125
+        sac250 = sac250 + 1;
+    elseif headSacc(pos) > 100
+        sac200 = sac200 + 1;
+    elseif headSacc(pos) > 75
+        sac150 = sac150 + 1;
+    elseif headSacc(pos) > 50
+        sac100 = sac100 + 1;
+    elseif headSacc(pos) > 25
+        sac50 = sac50 + 1;   
+    elseif headSacc(pos) > 0
+        sac0 = sac0 + 1;  
+    end
+    pos = pos + 1;
+end
+subplot(2,1,2)
+total = sac0+sac50+sac100+sac150+sac200+sac250;
+dataX = [(sac0/total)*100,(sac50/total)*100,(sac100/total)*100,(sac150/total)*100,(sac200/total)*100,(sac250/total)*100];
+bar(dataX)
+Labels = {'0-25', '25-50', '50-75', '75-100', '100-125', '>125'};
+set(gca, 'XTick', 1:6, 'XTickLabel', Labels);
+string = ['Saccade count by head velocity (Total Saccades = ' num2str(npeaks) ')'];
+title(string)
+xlabel('Head velocity intervals in deg/sec')
+ylabel('% of sacaddes')
+

vvor.m

@@ -0,0 +1,15 @@
+s = 0;
+question = questdlg('Do you want to read the data from VVOR or from VVORS (suppressed) test?','Select test to read','VVOR','VORS (suppressed)','VVOR');
+if strcmp(question,'VORS (suppressed)')
+    s = 1;
+end
+[t,e,h] = read(s);
+if isempty(t)
+    display('No data was loaded')
+    return
+end
+analize(t,e,h,s);
+question = questdlg('Do you want to analize saccades?','Extended analysis','YES','NO','NO');
+if strcmp(question,'YES')
+saccades(t,e,h,s)   
+end