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grabStream.m
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grabStream.m
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function [data, scannerOut] = grabStream(rig, prop, hIm, fStatus, fStripe)
%GRABSTREAM Grab images and display data online
% data = grabStream(rig, scancfg, grabcfg, hIm);
% Scans and records images according to parameters specified
% <rig> rig control structure as generated by rigStartup
% <scancfg> scan configuration structure
% <grabcfg> grab configuration structure
% <hIm> Handle of an image for online data display. EraseMode
% should be 'none'.
% <fStatus> (optional) Function handle of status update function
% which is called by grabStream to e.g. update status
% text information. Arguments: fStatus(percent, text).
% <fStripe> (optional) Handle of a fucntion that is being called
% after each stripe has been acquired and displayed on
% screen. Arguments: fStripe(cdata, yIndices).
%
% grabStream(rig, scancfg, grabcfg, hIm, fStatus);
% If the function is called without output argument it uses less memory
% since data doesn't have to be stored. Can be used for "focus" mode,
% when no data is acquired.
%
% See also raw2pixeldata, makeScanPatternXYZ
%
% Revision history:
% 01.11.2018: moved all hard-coded DAQ functions to rigClass (and upgraded to .NET interface)
% 18.06.2015: extensive modification to work with session based DAQ, added z-scanning, INP
% 29.01.2009: added output of scannerOut to variable svxyz, SS
% 13.11.2007: added fStripe functionality, BJ
% 28.04.2006: created, BJ
scancfg = prop.scancfg;
grabcfg = prop.grabcfg;
% process inputs and outputs
isGrabbing = (nargout > 0);
if nargin < 4, fStatus = @(varargin) NaN; end
% Check input arguments
checkCfg();
% set lines per display stripe (smallest divisor of nLinesPerFrame >= 10)
nLinesPerStripe=find((rem(scancfg.nLinesPerFrame, 1:scancfg.nLinesPerFrame) == 0) & ((1:scancfg.nLinesPerFrame) >= 40), 1);
% initialize
iAcquiredLines = 0;
outdata = zeros(scancfg.nPixelsPerLine, scancfg.nLinesPerFrame, rig.AItask.AIChannels.Count, 'int16');
data = zeros([scancfg.nPixelsPerLine scancfg.nLinesPerFrame rig.AItask.AIChannels.Count grabcfg.nFrames*scancfg.piezoStepsN], 'int16');
% AI acquisition is continuous and will be stopped after all the expected data are collected
rig.setupAIlistener(@samplesAcquiredFun, nLinesPerStripe * scancfg.nInSamplesPerLine)
% AO
nOutSamplesPerLine = (rig.AOrate / rig.AIrate) * scancfg.nInSamplesPerLine;
scannerOut = makeScanPattern(nOutSamplesPerLine, scancfg.fillFraction, scancfg.nLinesPerFrame, scancfg.scanAmp, scancfg.scanOffset, ...
scancfg.scanAngle, scancfg.bidirectional, scancfg.zoom, scancfg.piezoStepsN, scancfg.phaseStepsN);
scannerOut(:,1:2) = circshift(scannerOut(:,1:2), round(-(rig.AOrate / rig.AIrate) * scancfg.sampleLag));
rig.queueOutputData(scannerOut); %queueOutputData(rig.aoSession, repmat(scannerOut(:, 1:3), [grabcfg.nFrames 1]));
% figure(45), plot3(scannerOut(:, 1), scannerOut(:, 2), scannerOut(:, 5)), xlim([-1.1 1.1]), ylim([-1.1 1.1])
% figure(46), plot(scannerOut)
% display
cax = (get(hIm, 'Parent')); if numel(cax) == 1, cax = {cax}; end
set([cax{:}], 'XLim', [0 scancfg.nPixelsPerLine], 'YLim', [0 scancfg.nLinesPerFrame])
set(hIm, 'XData', [1 scancfg.nPixelsPerLine]-0.5);
set(hIm, 'YData', [1 scancfg.nLinesPerFrame]-0.5);
fps = rig.AIrate / (scancfg.nLinesPerFrame * scancfg.nInSamplesPerLine);
%% START
% restartDio(rig);
t = tic;
rig.start();
rig.shutterOpen()
rig.hwTrigger()
rig.isScanning = true;
% cleanup if interrupted
cleanupObj = onCleanup(@(varargin) rig.stopAndCleanup);
try
%WAIT until done
if isGrabbing
waitfor(rig, 'isScanning', false)
else
fStatus(NaN, ['live view @ ', num2str(fps, 3), ' fps ...']);
waitfor(rig, 'isScanning', false)
end
catch
warning(lasterr)
end
rig.stopAndCleanup
rig.isScanning = false;
% delete(rig.ailh);
% NESTED FUNCTIONS
function samplesAcquiredFun(raw)
nCurrentFrame = floor(iAcquiredLines / scancfg.nLinesPerFrame) + 1;
if ~rig.isScanning || (isGrabbing && (nCurrentFrame > grabcfg.nFrames)) , rig.isScanning = false; pause(0), return, end
%%GET RAW DATA , SHAPE INTO IMAGE
%raw = event.Data;
yIndices = mod(iAcquiredLines, scancfg.nLinesPerFrame) + (1:nLinesPerStripe);
outdata(:, yIndices ,:, :) = raw2pixeldata(raw', scancfg.nInSamplesPerLine, scancfg.fillFraction, 0, scancfg.nPixelsPerLine, scancfg.bidirectional);
iAcquiredLines = iAcquiredLines + nLinesPerStripe;
if isGrabbing
%%copY SINGLE FRAME BUFFER INTO LARGE MULTIFRAME OUTPUT MATRIX
data(:, yIndices, :, nCurrentFrame) = outdata(:, yIndices, :);
percent = (iAcquiredLines / scancfg.nLinesPerFrame) / double(grabcfg.nFrames);
if toc(t) >= 0.2 %refreshing too often will overload the system
fStatus(percent, ['acquiring @ ', num2str(fps, 2), ' fps ...']);
t = tic;
end
end
%% update CHANNEL FIGURE WITH LAST IMAGE
for iChan = 1:length(hIm)
set(hIm(iChan), 'XData', [1 scancfg.nPixelsPerLine]-0.5);
set(hIm(iChan), 'YData', [1 scancfg.nLinesPerFrame]-0.5);
set(hIm(iChan), 'CData', mean(outdata(:,:,iChan,:),4)');
end
if nargin >=6, fStripe(outdata, yIndices); end
pause(0) %makes this callback interruptable (to stop acquisition)
end
function checkCfg()
maxGalvoFreq = 1000;
minInSamplesPerLine = rig.AIrate/maxGalvoFreq/(1+scancfg.bidirectional);
if scancfg.nInSamplesPerLine < minInSamplesPerLine
%scancfg.nInSamplesPerLine = minInSamplesPerLine;
%warning(['Number of samples cannot be smaller than ' num2str(minInSamplesPerLine) '. Set automatically to ' num2str(minInSamplesPerLine) '.']);
warning(['Number of samples cannot be smaller than ' num2str(minInSamplesPerLine) ])
end
%scancfg.fillFraction = floor(scancfg.fillFractionMax*scancfg.nInSamplesPerLine/scancfg.nPixelsPerLine)*scancfg.nPixelsPerLine/scancfg.nInSamplesPerLine;
end
end