Fix gamma calibration (#164)

* use the correct channels for gamma cal as specified
* label output plots correctly

Author: nsteinme

+hw/+ptb/Window.m

@@ -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);
@@ -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);
@@ -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));
 

+srv/expServer.m

@@ -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);