-
Notifications
You must be signed in to change notification settings - Fork 2
/
pupilPower.m
1233 lines (1132 loc) · 38.4 KB
/
pupilPower.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
classdef pupilPower < analysisCore
%PUPILPOWER Calculate power for each trial from EDF file pupil data
%------------------PUBLIC PROPERTIES----------%
properties
%> filename to use
fileName char
%> eyelink parsed edf data
pupilData eyelinkAnalysis
%> plot verbosity
verbose = true
%> normalise the pupil diameter to the baseline?
normaliseBaseline logical = true
%> remove mean of each trial before computing FFT
detrend logical = true
%> linear detrend each trial before computing FFT
detrendLinear logical = false
%> normalise the plots of power vs luminance?
normalisePowerPlots logical = true
%> color map to use
colorMap char = 'turbo';
%> actual R G B luminance maxima for display, if [1 1 1] then use 0<->1
%> floating point range
maxLuminances double = [1 1 1]
%> use hanning window?
useHanning logical = false
%> smooth the pupil data?
smoothPupil logical = true;
%> smoothing window in milliseconds
smoothWindow double = 30;
%> smooth method
smoothMethod char = 'gaussian'
%> draw error bars on raw pupil plots
drawError logical = true
%> error bars
error char = 'SE';
%> downsample raw pupil for plotting only (every N points)
downSample double = 20;
%> the calibration data from the display++
calibrationFile = ''
%> use simple luminance maxima or the linear regression
simpleMode = false
%> show 2nd harmonic plots
plotHarmonics = false
%> fitting function
fit = 'smoothingspline'
%> conversion to diameter? true/false | calibration value | measured
%> diameter
useDiameter = {false, 9250, 8}
end
properties (Hidden = true)
%> default R G B luminance maxima, if [1 1 1] then use 0<->1
%> floating point range, compatibility with older code, use
%> maxLumiances
defLuminances double = [1 1 1]
%> choose which sub-variables to plot, empty plots all
xpoints = []
%> trial numbers to exclude
excludeTrials = []
%> show the frequencies
showFrequencies = true
end
%------------------VISIBLE PROPERTIES----------%
properties (SetAccess = {?analysisCore}, GetAccess = public)
meanPowerValues
varPowerValues
meanPhaseValues
varPhaseValues
meanPupil
varPupil
meanTimes
modifiedPupil
modifiedTimes
meanF
meanP
varP
SortedPupil struct
taggingFrequency = []
transitionTime;
end
%------------------PROTECTED PROPERTIES----------%
properties (SetAccess = {?analysisCore}, GetAccess = public, Hidden = true)
meanPowerValues0
varPowerValues0
meanPowerValues2
varPowerValues2
meanPhaseValues0
varPhaseValues0
meanPhaseValues2
varPhaseValues2
powerValues cell
phaseValues cell
powerValues0 cell
phaseValues0 cell
powerValues2 cell
phaseValues2 cell
metadata struct
rawPupil cell
rawTimes cell
rawF cell
rawP cell
isLoaded logical = false
isCalculated logical = false
maxTime
end
%------------------PRIVATE PROPERTIES----------%
properties (SetAccess = private, GetAccess = private)
%> the monitor calibration object
c
%> processed luminance data fits
l
%> raw data removed, cannot reparse from EDF events.
isRawDataRemoved = false
%> allowed properties passed to object upon construction, see parseArgs
allowedProperties = {'calibrationFile','useHanning','defLuminances','fileName','pupilData',...
'normaliseBaseline','normalisePowerPlots','error','colorMap',...
'maxLuminances','smoothPupil','smoothMethod','drawError','downSample','useDiameter'}
end
%=======================================================================
methods
%=======================================================================
% ===================================================================
%> @brief class constructor
%>
%> @param
%> @return
% ===================================================================
function me = pupilPower(varargin)
defaults.measureRange = [0.5667 0.5667 + (0.5667*5)];
defaults.baselineWindow = [-0.1 0.1];
defaults.plotRange = [];
if ~exist('turbo.m','file')
defaults.colorMap = 'jet';
end
varargin = optickaCore.addDefaults(varargin,defaults);
me = me@analysisCore(varargin); %superclass constructor
if nargin>0; me.parseArgs(varargin, me.allowedProperties); end
if ~isempty(me.fileName)
[p,f,~] = fileparts(me.fileName);
if ~isempty(p) && (exist(p,'dir') == 7)
me.rootDirectory = p;
else
me.rootDirectory = pwd;
end
me.name = f;
else
if isempty(me.name); me.name = 'pupilPower'; end
me.rootDirectory = pwd;
%run(me);
end
end
% ===================================================================
%> @brief validate
% ===================================================================
function set.maxLuminances(me,value)
if all( [1 3] == size(value) )
me.maxLuminances = value;
elseif all( [3 1] == size(value) )
me.maxLuminances = value';
else
me.maxLuminances = [1 1 1];
end
end
% ===================================================================
%> @brief run full analysis and plot the result
%>
%> @param force: reload the EDF and reparse
%> @return
% ===================================================================
function [handles,data] = run(me, force)
if ~me.simpleMode;loadCalibration(me); fitLuminances(me);end
if isempty(me.l); me.simpleMode = true; end
if ~exist('force','var') || isempty(force); force = false; end
if ~isempty(me.pupilData);me.pupilData.useDiameter = me.useDiameter;end
me.load(force);
if isempty(me.metadata);warning('No data was loaded...');return;end
if isfield(me.metadata.ana,'onFrames')
me.taggingFrequency = (me.metadata.sM.screenVals.fps/me.metadata.ana.onFrames) / 2;
me.transitionTime = me.metadata.ana.onFrames * (1/me.metadata.sM.screenVals.fps);
else
me.taggingFrequency = me.metadata.ana.frequency;
me.transitionTime = (1/me.metadata.ana.frequency)/2;
end
me.calculate();
if me.doPlots; [handles,data] = me.plot(); end
end
% ===================================================================
%> @brief plot the parsed data
%>
%> @param
%> @return
% ===================================================================
function [handles,data] = plot(me)
if ~me.isCalculated; return; end
[fixColor,fixName,fColor,varColor,varName,tColor,trlColor,trlColors,...
tit,colorLabels,step,colorMin,colorMax] = makecolors(me);
data.fixName = fixName;
data.varName = varName;
data.trlColors = trlColors;
function spawnMe(src, ~)
fnew = figure('Color',[1 1 1],'Units','normalized','Position',[0 0.5 1 0.5]);
na = copyobj(src,fnew);
na.Position = [0.1 0.1 0.8 0.8];
end
handles.h1=figure;figpos(2,[1000 500]);set(handles.h1,'Color',[1 1 1],'NumberTitle','off',...
'Name',['pupilPower: ' me.pupilData.file],'Papertype','a4','PaperUnits','centimeters',...
'PaperOrientation','landscape','Renderer','painters');
switch varName
case 'Grey'
plotColor = [0.5 0.5 0.5];
case 'Yellow'
plotColor = [0.8 0.8 0];
otherwise
plotColor = zeros(1,3); plotColor(1,tColor) = 0.8;
end
switch fixName
case 'Grey'
lineColor = [0.5 0.5 0.5];
case 'Yellow'
lineColor = [0.8 0.8 0];
otherwise
lineColor = zeros(1,3); lineColor(1,fColor) = 0.8;
end
pCorrect = (length(me.pupilData.correct.idx)/length(me.pupilData.trials))*100;
if me.simpleMode && max(me.maxLuminances) > 1
mode = 'simple';
elseif me.simpleMode && max(me.maxLuminances) == 1
mode = 'none';
else
mode = 'full';
end
t2 = sprintf('%i / %i = %.2f%% | background: %s',...
length(me.pupilData.correct.idx),length(me.pupilData.trials), ...
pCorrect,num2str(me.metadata.ana.backgroundColor,'%.3f '));
if isempty(me.xpoints)
start = 1;
finish = length(colorLabels);
numVars = finish;
else
start = me.xpoints(1);
finish = me.xpoints(2);
numVars = (finish-start) + 1;
end
cstep = trlColors(start:finish); csteps = cstep;
csteps(numVars+1) = cstep(numVars);
PL = stairs(1:numVars+1, csteps, 'Color',plotColor,'LineWidth',2);
PL.Parent.FontSize = 11;
PL.Parent.XTick = 1.5:1:numVars+0.5;
PL.Parent.XTickLabel = colorLabels;
PL.Parent.XTickLabelRotation = 30;
xlim([0.5 numVars+1.5])
ax = axis;
line([ax(1) ax(2)],[fixColor(1) fixColor(1)],'Color',lineColor,'Linewidth',2);
if max(me.maxLuminances) == 1
xlabel('Step (0 <-> 1)')
else
xlabel('Step (cd/m^2)')
end
ylim([min(csteps)-step(1) max(csteps)+step(1)])
%set(gca,'ytick',colorMin-step:2*step:colorMax+step)
ylabel('Luminance (cd/m^2)')
title([tit t2]);
box on; grid on;
handles.h2=figure;figpos(1,[0.9 0.9],[],'%');set(handles.h2,'Color',[1 1 1],'NumberTitle','off',...
'Name',['pupilPower: ' me.pupilData.file],'Papertype','a4','PaperUnits','centimeters',...
'PaperOrientation','landscape','Renderer','painters');
if me.showFrequencies
tl = tiledlayout(handles.h2,2,3,'TileSpacing','tight');
ax1 = nexttile(tl,[1 3]);
else
tl = tiledlayout(handles.h2,2,1,'TileSpacing','tight');
ax1 = nexttile(tl);
end
ax1.ButtonDownFcn = @spawnMe;
tl.Padding = 'tight';
tl.Title.String = me.pupilData.file;
tl.Title.Interpreter = 'none';
tl.Title.FontWeight = 'bold';
traceColor = colormap(me.colorMap);
traceColor_step = floor(length(traceColor)/numVars);
f = round(me.metadata.ana.onFrames) * (1 / me.metadata.sM.screenVals.fps);
if isfield(me.metadata.ana,'flashFirst') && me.metadata.ana.flashFirst == true
m = 0:2:100;
else
m = 1:2:101;
end
for i = 1 : floor(me.metadata.ana.trialDuration / f / 2) + 1
rectangle('Position',[f*m(i) -10000 f 20000],'FaceColor',[0.8 0.8 0.8 0.3],'EdgeColor','none')
end
maxp = -inf;
minp = inf;
a = 0;
for i = start : finish
hold on
t = me.meanTimes{i};
p = me.meanPupil{i};
e = me.varPupil{i};
if isempty(t); continue; end
c = traceColor((a*traceColor_step)+1,:);
if me.pupilData.sampleRate > 500
idx = circshift(logical(mod(1:length(t),me.downSample)), -(me.downSample-1)); %downsample every N as less points to draw
t(idx) = [];
p(idx) = [];
e(idx) = [];
end
if me.normaliseBaseline
idx = t >= me.baselineWindow(1) & t <= me.baselineWindow(2);
mn = mean(p(idx));
p = p - mn;
end
idx = t >= me.measureRange(1) & t <= me.measureRange(2);
if me.detrend
m = mean(p(idx),'omitnan');
if ~isnan(m); p = p - mean(p(idx)); end
end
idx = t >= me.measureRange(1) & t <= me.measureRange(2);
maxp = max([maxp max(p(idx)+e(idx))]);
minp = min([minp min(p(idx)-e(idx))]);
if ~isempty(p)
if me.drawError
PL1 = analysisCore.areabar(t,p,e,c,0.2,...
'Color', c, 'LineWidth', 2,'DisplayName',colorLabels{i});
try
row = dataTipTextRow('Color',repmat({num2str(trlColors(i))},length(t),1));
PL1.plot.DataTipTemplate.DataTipRows(end+1) = row;
PL1.plot.DataTipTemplate.DataTipRows(1).Label = 'Time';
PL1.plot.DataTipTemplate.DataTipRows(2).Label = 'Power';
end
else
PL1 = plot(t,p,'color', c,...
'LineWidth', 1,'DisplayName',colorLabels{i});
try
PL1.DataTipTemplate.DataTipRows(1).Label = 'Time';
PL1.DataTipTemplate.DataTipRows(2).Label = 'Power';
end
end
a = a + 1;
end
end
line([me.measureRange(1) me.measureRange(1)],[minp maxp],...
'Color',[0.2 0.2 0.2 0.8],'linestyle',':','LineWidth',3);
line([me.measureRange(2) me.measureRange(2)],[minp maxp],...
'Color',[0.2 0.2 0.2 0.8],'linestyle',':','LineWidth',3);
data.minDiameter = minp;
data.maxDiameter = maxp;
data.diameterRange = maxp - minp;
xlabel('Time (secs)')
if me.useDiameter{1} == false
ylabel('Pupil Diameter (area)')
else
ylabel('Pupil Diameter (mm)')
end
if me.normaliseBaseline
title(['Normalised Pupil (mode: ' mode '|bg: ' num2str(me.metadata.ana.backgroundColor,'%.3f ') '): # Trials = ' num2str(me.metadata.ana.trialNumber) ' | Subject = ' me.metadata.ana.subject ' | baseline = ' num2str(me.baselineWindow,'%.2f ') 'secs' ' | Range = ' num2str(data.diameterRange,'%.2f')]);
else
title(['Raw Pupil (mode: ' mode '|bg: ' num2str(me.metadata.ana.backgroundColor,'%.3f ') '): # Trials = ' num2str(me.metadata.ana.trialNumber) ' | Subject = ' me.metadata.ana.subject ' | Range = ' num2str(data.diameterRange,'%.2f')])
end
xlim([me.measureRange(1)-0.2 me.measureRange(2)+0.2]);
if minp == 0; minp = -1;end
if maxp==0; maxp = 1; end
if minp <= 0
ylim([minp+(minp/7) maxp+(maxp/7)]);
else
ylim([minp-(minp/7) maxp+(maxp/7)]);
end
legend(colorLabels(start:finish),'FontSize',10,'Location','northwest'); %'Position',[0.955 0.75 0.04 0.24]
box on; grid on;
ax1.XMinorGrid = 'on';
ax1.FontSize = 12;
if me.showFrequencies
ax2 = nexttile(tl);
ax2.ButtonDownFcn = @spawnMe;
maxP = 0;
a=0;
for i = start : finish %1: length(me.meanF)
hold on
c = traceColor((a*traceColor_step)+1,:);
F = me.meanF{i};
P = me.meanP{i};
idx = F < 20;
F = F(idx);
P = P(idx);
maxP = max([maxP max(P)]);
PL2 = plot(F,P,'color', [c 0.6],...
'LineWidth', 2,...
'Marker','o','DisplayName',colorLabels{i},...
'MarkerSize', 5,'MarkerFaceColor',traceColor((a*traceColor_step)+1,:),...
'MarkerEdgeColor', 'none');
try
row = dataTipTextRow('Color',repmat({num2str(trlColors(i))},length(t),1));
PL2.DataTipTemplate.DataTipRows(end+1) = row;
PL2.DataTipTemplate.DataTipRows(1).Label = 'Frequency';
PL2.DataTipTemplate.DataTipRows(2).Label = 'Power';
end
a = a + 1;
end
xlim([-0.1 floor(me.metadata.ana.frequency*4)]);
if maxP==0; maxP=1; end
ylim([0 maxP+(maxP/20)]);
xlabel('Frequency (Hz)');
ylabel('Power');
if ~me.detrend && ~me.normaliseBaseline
ax2.YScale = 'log';
ylabel('Power [log]');
end
line([me.taggingFrequency me.taggingFrequency],[ax2.YLim(1) ax2.YLim(2)],...
'Color',[0.3 0.3 0.3 0.5],'linestyle',':','LineWidth',2);
if me.plotHarmonics
line([me.taggingFrequency*2 me.taggingFrequency*2],[ax2.YLim(1) ax2.YLim(2)],...
'Color',[0.3 0.3 0.3 0.5],'linestyle',':','LineWidth',2);
line([0 0],[ax2.YLim(1) ax2.YLim(2)],...
'Color',[0.3 0.3 0.3 0.5],'linestyle',':','LineWidth',2);
end
title(['FFT Power: range = ' num2str(me.measureRange,'%.2f ') 'secs | F = ' num2str(me.taggingFrequency) 'Hz\newlineHanning = ' num2str(me.useHanning)]);
box on; grid on; grid minor;
ax2.FontSize = 12;
else
ax2 = [];
end
if me.showFrequencies
ax3 = nexttile(tl,[1 2]);
else
ax3 = nexttile(tl);
end
ax3.ButtonDownFcn = @spawnMe;
is0=false;
is2=false;
hold on
if exist('colororder','file')>0; colororder({'k','k'});end
yyaxis right
pv = me.meanPhaseValues(start:finish);
if min(pv) < 0; pv = pv + abs(min(pv)); end
phase1H = analysisCore.areabar(cstep,pv,...
me.varPhaseValues(start:finish),[0.6 0.6 0.3],0.25,'LineWidth',1.5,'DisplayName','Phase-H1');
try
phase1H.plot.DataTipTemplate.DataTipRows(1).Label = 'Luminance';
phase1H.plot.DataTipTemplate.DataTipRows(2).Label = 'Phase';
end
if me.plotHarmonics
is2=true;
hold on
pv2 = me.meanPhaseValues2(start:finish);
if min(pv2) < 0; pv2 = pv2 + abs(min(pv2)); end
phase2H = analysisCore.areabar(cstep,pv2,...
me.varPhaseValues2(start:finish),[0.6 0.6 0.6],0.25,'LineWidth',1,'DisplayName','Phase-H2');
try
phase2H.plot.DataTipTemplate.DataTipRows(1).Label = 'Luminance';
phase2H.plot.DataTipTemplate.DataTipRows(2).Label = 'Phase';
end
mn = min([min(pv-me.varPhaseValues) min(pv2-me.varPhaseValues2)]);
mx = max([max(pv+me.varPhaseValues) max(pv2+me.varPhaseValues2)]);
else
mn = min(pv-me.varPhaseValues);
mx = max(pv+me.varPhaseValues);
end
ylim([mn mx]);
%PL3b = plot(trlColors,rad2deg(A),'k-.','Color',[0.6 0.6 0.3],'linewidth',1);
ylabel('Phase (deg)');
data.X=cstep;
data.phaseY=me.meanPhaseValues(start:finish);
data.phaseE=me.varPhaseValues(start:finish);
box on; grid on;
yyaxis left
hold on
if me.normalisePowerPlots
m0 = me.meanPowerValues0(start:finish) / max(me.meanPowerValues0(start:finish));
e0 = me.varPowerValues0(start:finish) / max(me.meanPowerValues0(start:finish));
else
m0 = me.meanPowerValues0(start:finish);
e0 = me.varPowerValues0(start:finish);
end
data.m0=m0;
data.e0=e0;
if me.plotHarmonics && max(me.meanPowerValues0) > 0.1 % only if there is a significant response
is0 = true;
h0PH = analysisCore.areabar(cstep,m0,e0,[0.5 0.5 0.7],0.1,...
'Marker','o','LineWidth',1,'DisplayName','H0');
try %#ok<*TRYNC>
h0PH.plot.DataTipTemplate.DataTipRows(1).Label = 'Luminance';
h0PH.plot.DataTipTemplate.DataTipRows(2).Label = 'Power';
end
end
if me.normalisePowerPlots
m2 = me.meanPowerValues2(start:finish) / max(me.meanPowerValues2(start:finish));
e2 = me.varPowerValues2(start:finish) / max(me.meanPowerValues2(start:finish));
else
m2 = me.meanPowerValues2(start:finish);
e2 = me.varPowerValues2(start:finish);
end
data.m2=m2';
data.e2=e2';
if me.plotHarmonics && max(me.meanPowerValues2) > 0.1 % only if there is a significant response
is2 = true;
h2PH = analysisCore.areabar(cstep,m2,e2,[0.7 0.4 0],0.1,...
'Marker','o','LineWidth',1,'DisplayName','H2');
try %#ok<*TRYNC>
h2PH.plot.DataTipTemplate.DataTipRows(1).Label = 'Luminance';
h2PH.plot.DataTipTemplate.DataTipRows(2).Label = 'Power';
end
end
if me.normalisePowerPlots
m = me.meanPowerValues(start:finish) / max(me.meanPowerValues(start:finish));
e = me.varPowerValues(start:finish) / max(me.meanPowerValues(start:finish));
else
m = me.meanPowerValues(start:finish);
e = me.varPowerValues(start:finish);
end
m = m';
e = e';
data.m=m;
data.e=e;
xx = linspace(min(cstep),max(cstep),500);
warning off
[f, gof] = fit(cstep',m',me.fit);
disp(gof)
warning on
yy = feval(f,xx);
ymin = find(yy==min(yy));
ymin = xx(ymin);
idx = find(m==min(m));
minC = cstep(idx);
ratio = fixColor / minC;
ratio2 = fixColor / ymin;
h1PH = analysisCore.areabar(cstep,m,e,[0.7 0.2 0.2],0.2,...
'LineWidth',2,'DisplayName','H1');
try
h1PH.plot.DataTipTemplate.DataTipRows(1).Label = 'Luminance';
h1PH.plot.DataTipTemplate.DataTipRows(2).Label = 'Power';
end
fitH = plot(xx,yy,'r--','LineWidth',1,'DisplayName','H1-Fit');
if is0
mx = max([max(m+e) max(m0+e0)]);
mn = min([min(m-e) min(m0-e0)]);
else
mx = max(m+e);
mn = min(m-e);
end
ylim([mn mx]);
pr = (m .* m0);
pr = (pr / max(pr)) * mx;
data.minColor = minC;
data.ratio = ratio;
data.ratio2 = ratio2;
ax3.FontSize = 12;
ax3.XTick = cstep;
ax3.XTickLabel = colorLabels(start:finish);
ax3.XTickLabelRotation = 45;
pad = max(diff(cstep))/10;
ax3.XLim = [ min(cstep) - pad max(cstep) + pad];
if fixColor <= max(cstep) && fixColor >= min(cstep)
line([fixColor fixColor],[ax3.YLim(1) ax3.YLim(2)],...
'lineStyle',':','Color',[0.3 0.3 0.3 0.5],'linewidth',2);
end
if ymin <= max(cstep) && ymin >= min(cstep)
line([ymin ymin],[ax3.YLim(1) ax3.YLim(2)],...
'lineStyle',':','Color',[1.0 0.5 0.1 0.5],'linewidth',2);
end
if max(me.maxLuminances) == 1
xlabel('LuminanceStep (0 <-> 1)')
else
xlabel('Luminance Step (cd/m^2)')
end
if me.normalisePowerPlots
ylabel('Normalised Power')
else
ylabel('Power')
end
tit = sprintf('Harmonic Power: %s | %s Min@H1 = %.2f & Ratio = %.2f/%.2f', ...
tit, varName, data.minColor, data.ratio, data.ratio2);
title(tit);
if is2 && is0
leg = [h1PH.plot,phase1H.plot,fitH,h2PH.plot,phase2H.plot,h0PH.plot];
elseif is2 && ~is0
leg = [h1PH.plot,phase1H.plot,fitH,h2PH.plot,phase2H.plot];
elseif ~is2 && is0
leg = [h1PH.plot,phase1H.plot,fitH,h0PH.plot];
else
leg = [h1PH.plot,phase1H.plot,fitH];
end
legend(leg,'FontSize',10,'Location','southeast'); %'Position',[0.9125 0.2499 0.0816 0.0735],
box on; grid on;
handles.ax1 = ax1;
handles.ax2 = ax2;
handles.ax3 = ax3;
if exist('PL1','var');handles.PL1 = PL1;end
if exist('PL2','var');handles.PL2 = PL2;end
if exist('PL3a','var');handles.PL3a = phase1H;end
if exist('h0PH','var');handles.PL3 = h0PH;end
if exist('h1PH','var'); handles.PL4 = h1PH;end
if exist('h0h1PH','var');handles.PL5 = h0h1PH;end
if exist('h2PH','var');handles.PL6 = h2PH;end
if exist('phase2H','var'); handles.PL7 = phase1H;end
if exist('h0h1PH','var');handles.PL8 = h0h1PH;end
drawnow;
figure(handles.h2);
fontsize(14,'points');
fontname('Source Sans 3');
end
% ===================================================================
%> @brief
%>
%> @param
%> @return
% ===================================================================
function plotIndividualTrials(me,idx)
if isempty(me.modifiedPupil); warning('No data yet analysed');return;end
numVars = length(me.modifiedPupil);
if ~exist('idx','var'); idx = 1 : numVars; end
figure; hold on; colormap(me.colorMap);
box on; grid on
xlabel('Time (secs)')
ylabel('Pupil Diameter')
traceColor = colormap(me.colorMap);
traceColor_step = floor(length(traceColor)/numVars);
for i = idx
cl = traceColor(((i-1)*traceColor_step)+1,:);
x = cell2mat(me.modifiedTimes{i}(1:end)')';
y = cell2mat(me.modifiedPupil{i}(1:end)')';
plot(x, y, 'Color', cl,'LineWidth',2);
drawnow;
WaitSecs(1);
end
end
% ===================================================================
%> @brief save
%>
%> @param file filename to save to
%> @return
% ===================================================================
function save(me, file)
me.pupilData.removeRawData();
save(file,'me','-v7.3');
end
% ===================================================================
%> @brief save
%>
%> @param file filename to save to
%> @return
% ===================================================================
function fitLuminances(me)
if isempty(me.c); loadCalibration(me); end
if isa(me.c,'calibrateLuminance') && isempty(me.l)
l.igray = me.c.inputValues(1).in; %#ok<*PROP>
l.ired = me.c.inputValues(2).in;
l.igreen = me.c.inputValues(3).in;
l.iblue = me.c.inputValues(4).in;
l.x = me.c.ramp;
[l.fx, l.fgray] = analysisCore.linearFit(l.x, l.igray);
[~, l.fred] = analysisCore.linearFit(l.x, l.ired);
[~, l.fgreen] = analysisCore.linearFit(l.x, l.igreen);
[~, l.fblue] = analysisCore.linearFit(l.x, l.iblue);
l.fred(l.fred<0)=0; l.fgreen(l.fgreen<0)=0; l.fblue(l.fblue<0)=0; l.fgray(l.fgray<0)=0;
me.l = l;
end
end
% ===================================================================
%> @brief save
%>
%> @param file filename to save to
%> @return
% ===================================================================
function [x1, y1, x2, y2] = getLuminances(me, value, from, to)
if isempty(me.l); me.fitLuminances; end
l = me.l;
fx = l.fx;
switch from
case 'red'
fy = l.fred;
case 'green'
fy = l.fgreen;
case 'blue'
fy = l.fblue;
case 'gray'
fy = l.fgray;
end
switch to
case 'red'
ty = l.fred;
case 'green'
ty = l.fgreen;
case 'blue'
ty = l.fblue;
case 'gray'
ty = l.fgray;
end
[ix,~,~] = analysisCore.findNearest(fx, value);
x1 = fx(ix);
y1 = fy(ix);
[ix,~,~] = analysisCore.findNearest(ty, y1);
x2 = fx(ix);
y2 = ty(ix);
end
% ===================================================================
%> @brief save
%>
%> @param file filename to save to
%> @return
% ===================================================================
function [y, x] = getLuminance(me, value, color)
if isempty(me.l); me.fitLuminances; end
l = me.l;
fx = l.fx;
if ~exist('color','var') && length(value) == 3
fy{1} = l.fred;
fy{2} = l.fgreen;
fy{3} = l.fblue;
for i = 1:3
[ix,~,~] = analysisCore.findNearest(fx, value(i));
x(i) = fx(ix);
y(i) = fy{i}(ix);
end
else
switch color
case 'red'
fy = l.fred;
case 'green'
fy = l.fgreen;
case 'blue'
fy = l.fblue;
case 'gray'
fy = l.fgray;
end
for i = 1:length(value)
[ix,~,~] = analysisCore.findNearest(fx, value(i));
x(i) = fx(ix);
y(i) = fy(ix);
end
end
y( y < 0 ) = 0;
end
% ===================================================================
%> @brief make the color variables used in plotting
%>
%> @param
%> @return
% ===================================================================
function [fixColor,fixName,fColor,varColor,varName,tColor,trlColor,...
trlColors,tit,colorLabels,step,colorMin,colorMax] = ...
makecolors(me,fc,cs,ce,vals)
if ~exist('fc','var') || isempty(fc); fc = me.metadata.ana.colorFixed; end
if ~exist('cs','var') || isempty(cs); cs = me.metadata.ana.colorStart; end
if ~exist('ce','var') || isempty(ce); ce = me.metadata.ana.colorEnd; end
if ~exist('vals','var') || isempty(vals); vals = me.metadata.seq.nVar.values'; end
if size(me.maxLuminances,1) > 1; me.maxLuminances=me.maxLuminances';end
cNames = {'Red';'Green';'Blue';'Yellow';'Grey';'Cyan';'Purple'};
fColor=find(fc > 0); %get the position of not zero
if length(fColor) == 1 && fColor <= 3
elseif length(fColor) == 2 && all([1 2] == fColor)
fColor = 4;
elseif length(fColor) == 2 && all([1 3] == fColor)
fColor = 7;
elseif length(fColor) == 2 && all([2 3] == fColor)
fColor = 6;
elseif length(fColor) == 3 && isequal(fc(1),fc(2),fc(3))
fColor = 5;
else
warning('Cannot Define fixed color!');
end
if me.simpleMode
fix = fc .* me.maxLuminances;
else
fix = me.getLuminance(fc);
end
fixName = cNames{fColor};
switch fixName
case 'Grey'
fixColor = fix(1) + fix(2) + fix(3);
case 'Yellow'
fixColor = fix(1) + fix(2);
otherwise
fixColor = sum(fix(fColor));
end
if me.simpleMode
cE = ce .* me.maxLuminances;
cS = cs .* me.maxLuminances;
else
cE = me.getLuminance(ce);
cS = me.getLuminance(cs);
end
vColor=find(ce > 0); %get the position of not zero
if length(vColor)==3 && all([1 2 3] == vColor); vi = 5;
elseif length(vColor)==2 && all([1 2] == vColor); vi = 4;
elseif length(vColor)==2 && all([1 3] == vColor); vi = 7;
elseif length(vColor)==2 && all([2 3] == vColor); vi = 6;
else; vi = vColor;
end
varName = cNames{vi};
varColor = sum(cS(vColor));
if me.simpleMode
vals = cellfun(@(x) x .* me.maxLuminances, vals, 'UniformOutput', false);
else
vals = cellfun(@(x) getLuminance(me,x), vals, 'UniformOutput', false);
end
trlColor=cell2mat(vals);
tit = num2str(fix,'%.2f ');
tit = regexprep(tit,'0\.00','0');
tit = ['Fix color (' fixName ') = ' tit ' | Var color (' varName ')'];
colorChange= cE - cS;
tColor=find(colorChange~=0); %get the position of not zero
step=abs(colorChange(tColor)/me.metadata.ana.colorStep);
switch varName
case 'Yellow'
trlColors = trlColor(:,1)' + trlColor(:,2)';
colorMin = min(trlColor(:,1)) + min(trlColor(:,2));
colorMax = max(trlColor(:,1)) + max(trlColor(:,2));
otherwise
trlColors = trlColor(:,tColor)';
colorMax=max(trlColor(:,tColor));
colorMin=min(trlColor(:,tColor));
end
colorLabels = num2cell(trlColors);
colorLabels = cellfun(@(x) num2str(x,'%.2f'), colorLabels, 'UniformOutput', false);
end
% ===================================================================
%> @brief do the FFT
%>
%> @param p the raw signal
%> @return
% ===================================================================
function [P, f, A, p1, p0, p2, A0, A2] = doFFT(me,p)
useX = true;
L = length(p);
if me.useHanning
win = hanning(L, 'periodic');
P = fft(p.*win');
else
P = fft(p);
end
if useX
Pi = fft(p);
P = abs(Pi/L);
P=P(1:floor(L/2)+1);
P(2:end-1) = 2*P(2:end-1);
f = me.pupilData.sampleRate * (0:(L/2))/L;
else
Pi = fft(p);
NumUniquePts = ceil((L+1)/2);
P = abs(Pi(1:NumUniquePts));
f = (0:NumUniquePts-1)*me.pupilData.sampleRate/L;
end
idx = analysisCore.findNearest(f, me.taggingFrequency);
p1 = P(idx);
A = angle(Pi(idx));
idx = analysisCore.findNearest(f, 0);
p0 = P(idx);
A0 = angle(Pi(idx));
idx = analysisCore.findNearest(f, me.taggingFrequency*2);
p2 = P(idx);
A2 = angle(Pi(idx));
end
end
%=======================================================================
methods (Access = protected) %------------------PRIVATE METHODS
%=======================================================================
% ===================================================================
%> @brief
%>
%> @param
%> @return
% ===================================================================
function load(me, force)
if ~exist('force','var') || isempty(force); force = false; end
if me.isLoaded && ~force; return; end
try
if ~isempty(me.fileName)
me.pupilData=eyelinkAnalysis('file',me.fileName,'dir',me.rootDirectory);
else
me.pupilData=eyelinkAnalysis;
me.fileName = me.pupilData.file;
me.rootDirectory = me.pupilData.dir;
end
[~,fn] = fileparts(me.pupilData.file);
if isempty(fn) || ~exist([me.pupilData.dir,filesep,fn,'.mat'],'file'); warning('No file specified!');return;end
me.metadata = load([me.pupilData.dir,filesep,fn,'.mat']); %load .mat of same filename with .edf
if isa(me.metadata.sM,'screenManager') && ~isempty(me.metadata.sM.gammaTable)
if ~isempty(me.metadata.sM.gammaTable.inputValuesTest)
l = me.metadata.sM.gammaTable.inputValuesTest;
else
l = me.metadata.sM.gammaTable.inputValues;
end
me.maxLuminances(1) = l(2).in(end);
me.maxLuminances(2) = l(3).in(end);
me.maxLuminances(3) = l(4).in(end);
elseif max(me.defLuminances) > 1
me.maxLuminances = me.defLuminances;
end
me.pupilData.correctValue = 1;
me.pupilData.incorrectValue = -100;
me.pupilData.breakFixValue = -1;
me.pupilData.plotRange = [-0.5 3.5];
me.pupilData.measureRange = me.measureRange;
me.pupilData.pixelsPerCm = me.metadata.sM.pixelsPerCm;
me.pupilData.distance = me.metadata.sM.distance;
me.pupilData.useDiameter = me.useDiameter;
fprintf('\n<strong>--->>></strong> LOADING raw EDF data: \n')
parseSimple(me.pupilData);
me.maxTime = max(me.pupilData.correct.timeRange(:,2));
me.pupilData.removeRawData();me.isRawDataRemoved=true;
me.isLoaded = true;
catch ME
getReport(ME);
me.isLoaded = false;
rethrow(ME)
end
end
% ===================================================================
%> @brief
%>
%> @param
%> @return
% ===================================================================
function calculate(me)
if ~me.isLoaded; return; end
Fs1 = me.pupilData.sampleRate; % Sampling frequency
T1 = 1/Fs1; % Sampling period
smoothSamples = me.smoothWindow / (T1 * 1e3);
me.SortedPupil = struct();
me.powerValues={}; me.phaseValues={};
me.powerValues0={}; me.phaseValues0={};
me.powerValues2={}; me.phaseValues2={};
me.rawP = {}; me.rawF = {}; me.rawPupil = {}; me.rawTimes={};
vars = unique(me.metadata.seq.outIndex);
idx = me.pupilData.correct.idx;