Add bidirectional scanning phase delay as input argument. BUGFIX: use the actual sampling rate when calculating stuff, not the desired sampling rate.

Author: raacampbell

completed/private/plotImageData.m

@@ -1,4 +1,4 @@
-function plotImageData(imData,h,saveFname,scanPattern)
+function plotImageData(imData,h,saveFname,bidiPhaseDelay)
 	%Plot (and optionally save) data produced by scanAndAcquire_Polished
 	%
 	% function plotImageData(imData,h,saveFname,scanPattern)
@@ -15,44 +15,52 @@ function plotImageData(imData,h,saveFname,scanPattern)
 	% h - plot handles structure produced by scanAndAcquire_Polished
 	% saveFname - [string] the relative or absolute path of a file to which data should be saved. 
 	%             If empty, no data are saved.
-	% scanPattern - [string] Either 'uni' or 'bidi' depending on the scan pattern used.
+	% bidiPhaseDelay - [optional] If missing or empty, we assume the images are acquired using a uni-directional
+	%                  scan pattern. If bidiPhaseDelay is present, it is a scalar used to correct the phase
+	% 			       offset between the outgoing and return scanlines.
 	%
 	%
 	% Rob Campbell - Basel 2016
 
+	if nargin<4
+		bidiPhaseDelay=[];
+	end
 
 	imSize = size(get(h(1).hAx,'CData'),1);
 
 	%The number of points on one line (larger then imSize if fillFraction < 1)
 	pointsPerLine = ceil(size(imData,1) / imSize); 
 
 	timeStamp = now*60^2*24*1E3; %MATLAB serial date in ms. This is used for saving. 
-	
+
+	%The analog input range is in the CLIM property of the image axes
+	AI_range = get(h(1).imAx,'CLim');
+	AI_range = AI_range(2);
+
 	for chan = 1:size(imData,2)
 
 		im = reshape(imData(:,chan), pointsPerLine, imSize);
 		im = -rot90(im);
 
 		%Remove the turn-around artefact 
-		switch lower(scanPattern)
-			case 'bidi'
-				%Flip the even rows if data were acquired bidirectionally
-				im(2:2:end,:) = fliplr(im(2:2:end,:));
+		if ~isempty(bidiPhaseDelay)
+			%Flip the even rows if data were acquired bidirectionally
+			im(2:2:end,:) = fliplr(im(2:2:end,:));
 
-				phaseShift=26; %TODO: put this elsewhere!
-				im(1:2:end,:) = circshift(im(1:2:end,:),-phaseShift,2);
-				im(2:2:end,:) = circshift(im(2:2:end,:), phaseShift,2);
+			im(1:2:end,:) = circshift(im(1:2:end,:),-bidiPhaseDelay,2);
+			im(2:2:end,:) = circshift(im(2:2:end,:), bidiPhaseDelay,2);
 
-				im = fliplr(im); %To keep it in the same orientation as the uni-directional scan
+			im = fliplr(im); %To keep it in the same orientation as the uni-directional scan
 
-				im = im(:,1+phaseShift:end-phaseShift); %Trim the turnaround on one edge (BADLY)
-			case 'uni'
-				im = im(:,end-imSize+1:end); %Trim the turnaround on one edge
+			im = im(:,1+bidiPhaseDelay:end-bidiPhaseDelay); %Trim the turnaround on one edge (BADLY)
+			set(h(chan).imAx,'XLim',[1,size(im,2)]);
+		else
+			im = im(:,end-imSize+1:end); %Trim the turnaround on one edge
 		end
 
 		%Update image
 		set(h(chan).hAx,'CData',im);
-		set(h(chan).imAx,'CLim',[0,2],'XLim',[1,size(im,2)]); %TODO: This is potentially a problem point should we choose to use a different digitisation range
+
 
 
 		if h(chan).histAx ~= 0
@@ -62,7 +70,7 @@ function plotImageData(imData,h,saveFname,scanPattern)
 			%Keep the axes of the histogram looking nice
 			set(h(chan).histAx, ...
 				'YTick', [], ...
-				'XLim', [-0.1,2], ... %TODO: This is potentially a problem point should we choose to use a different digitisation range
+				'XLim', [-0.1,AI_range], ... 
 				'Color', 'None', ...
 				'Box', 'Off');
 

completed/scanAndAcquire_Polished.m

@@ -27,6 +27,8 @@ function scanAndAcquire_Polished(hardwareDeviceID,varargin)
 % 'samplesPerPixel'  - Number of samples per pixel. [4 by default]
 % 'scanPattern'  - A string defining whether we do uni or bidirectional scanning: 'uni' or 'bidi'
 %				 'uni' by default
+% 'bidiPhase' - a scalar that defines the offset in pixels between the outgoing and return lines
+% 			    in bidirectional scanning. 26 by default. This parameter needs changing often and is sensitive.
 % 'enableHist'   - A boolean. True by default. If true, overlays an intensity histogram on top of the image.
 %
 %
@@ -83,6 +85,7 @@ function scanAndAcquire_Polished(hardwareDeviceID,varargin)
 	params.addParameter('sampleRate', 512E3, @(x) isnumeric(x) && isscalar(x));
 	params.addParameter('fillFraction', 0.9, @(x) isnumeric(x) && isscalar(x));
 	params.addParameter('scanPattern', 'uni', @(x) ischar(x));
+	params.addParameter('bidiPhase', 26,  @(x) isnumeric(x) && isscalar(x));
 	params.addParameter('enableHist', true, @(x) islogical (x) || x==0 || x==1);
 
 	%Process the input arguments in varargin using the inputParser object we just built
@@ -97,7 +100,12 @@ function scanAndAcquire_Polished(hardwareDeviceID,varargin)
 	sampleRate = params.Results.sampleRate;
 	fillFraction = params.Results.fillFraction;
 	scanPattern = params.Results.scanPattern;
+	bidiPhase = params.Results.bidiPhase;
 	enableHist = params.Results.enableHist;
+
+	if ~strcmpi(scanPattern,'bidi')
+		bidiPhase=[];
+	end
 	% - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
 
 
@@ -129,12 +137,12 @@ function scanAndAcquire_Polished(hardwareDeviceID,varargin)
 	% BUILD THE GALVO WAVEFORMS (using function in "private" sub-directory)
 	dataToPlay = generateGalvoWaveforms(imSize,amp,samplesPerPixel,fillFraction,scanPattern); 
 	%We want at least 250 ms of data in the queue, to be really certain don't we hit buffer underflows and the scanning stops
-	secondsOfDataInQueue = length(dataToPlay)/sampleRate;
+	secondsOfDataInQueue = length(dataToPlay)/s.Rate;
 	minDataThreshold = 0.25; %Must have at least this much data in the queue
 	nFramesToQueue = ceil(minDataThreshold/secondsOfDataInQueue);
 	dataToPlay = repmat(dataToPlay,nFramesToQueue ,1); %expand queued data accordingly
 
-	msOfDataInQueue = round( (length(dataToPlay)/sampleRate)*1000 );
+	msOfDataInQueue = round( (length(dataToPlay)/s.Rate)*1000 );
 	fprintf('There is %d ms of data in the output queue ', msOfDataInQueue)
 	if nFramesToQueue>1
 		fprintf('(queuing in blocks of %d frames)',nFramesToQueue)
@@ -143,7 +151,7 @@ function scanAndAcquire_Polished(hardwareDeviceID,varargin)
 
 	%- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
 	% PREPARE TO ACQUIRE
-	fps = sampleRate/length(dataToPlay);
+	fps = s.Rate/length(dataToPlay);
 	fps = fps * nFramesToQueue;
 	fprintf('Scanning with a frame size of %d by %d at %0.2f frames per second\n',imSize,imSize,fps)
 
@@ -184,7 +192,8 @@ function scanAndAcquire_Polished(hardwareDeviceID,varargin)
 	end
 
 	%Tweak settings on axes and figure elemenents
-	set([h(:).imAx], 'XTick',[], 'YTick', [])
+	set([h(:).imAx], 'XTick',[], 'YTick', [], 'CLim',[0,AI_range]) %note: we store the AI_range here
+
 	colormap gray
 
 	%- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
@@ -224,7 +233,7 @@ function plotData(~,event)
 		end
 
 		%External function call to function in private directory
-		plotImageData(downSampled,h,saveFname,scanPattern)
+		plotImageData(downSampled,h,saveFname,bidiPhase)
 
  	end %plotData