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Fix gamma calibration #164

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Merged
merged 3 commits into from
Oct 1, 2019
Merged

Fix gamma calibration #164

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3a06667
use the correct channels for gamma cal as specified
nsteinme May 29, 2019
60b9e22
label output plots correctly
nsteinme May 29, 2019
1af596d
Merge branch 'dev' into fixGammaCal2
k1o0 Sep 30, 2019
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4 changes: 3 additions & 1 deletion +hw/+ptb/Window.m
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Original file line number Diff line number Diff line change
Expand Up @@ -645,6 +645,7 @@ function applyCalibration(obj, cal)
[light, clock, acqRate] = obj.measuredStim(colours, dev, lightIn, clockIn, clockOut);

%% assess the delay between digital and analog

[xc, lags ] = xcorr(light, clock, 1000, 'coeff');
% figure; plot(lags,xc)
[~,imax] = max(xc);
Expand All @@ -661,6 +662,7 @@ function applyCalibration(obj, cal)
tt = (1:ns)/acqRate;

figure; plot(tt,clock);
ylabel('clock signal'); title('Clock');

upCrossings = find(diff( clock > 1 ) == 1);
dnCrossings = find(diff( clock > 1 ) == -1);
Expand All @@ -672,7 +674,7 @@ function applyCalibration(obj, cal)
end
plot( tt, light ); hold on
xlabel('Time (s)');
ylabel('Signal (Volts)');
ylabel('Photodiode Signal (Volts)');
set(gca,'ylim',[0 1.1*max(light)]);
title(sprintf('In this plot. digital has been delayed by %2.2f ms', delay));

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13 changes: 7 additions & 6 deletions +srv/expServer.m
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Expand Up @@ -365,13 +365,14 @@ function whiteScreen()
function calibrateGamma()
stimWindow = rig.stimWindow;
DaqDev = rig.daqController.DaqIds;
lightIn = 'ai0'; % defaults from hw.ptb.Window
clockIn = 'ai1';
clockOut = 'port1/line0 (PFI4)';
log(['Please connect photodiode to %s, clockIn to %s and clockOut to %s.\r'...
'Press any key to contiue\n'],lightIn,clockIn,clockOut);
lightIn = 'ai1'; % defaults from hw.ptb.Window
clockIn = 'ai0';
clockOut = 'port1/line0';
clockOutHint = 'PFI4';
log(['Please connect photodiode to %s, clockIn to %s and clockOut to %s (%s).\r'...
'Press any key to contiue\n'],lightIn,clockIn,clockOut,clockOutHint);
pause; % wait for keypress
stimWindow.Calibration = stimWindow.calibration(DaqDev); % calibration
stimWindow.Calibration = stimWindow.calibration(DaqDev,lightIn, clockIn, clockOut); % calibration
pause(1);
saveGamma(stimWindow.Calibration);
stimWindow.applyCalibration(stimWindow.Calibration);
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