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Start work on the waveform testing class
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‎code/DAQmx_Scanners/waveformTester.m

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classdef waveformTester < handle
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% Minimal code needed to acquire data from one channel of a 2-photon microscope
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%
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% waveformTester
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%
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%
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% Description:
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% This is a tutorial class to explore the scan waveform. The waveform for the X mirror
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% is played out of AO0 and sent to the X scan control card. It's also copied to AI0.
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% AI1 gets the galvo position feedback signal. Parameters are set by editing the properties.
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%
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%
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% Instructions
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% Start the class with the device ID of your NI acquisition board as an input argument.
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% Quit by closing the window showing the scanned image stream. Doing this will gracefully
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% stop the acquisition.
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% The X mirror should be on AO-0
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% The Y mirror should be on AO-1
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%
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% Inputs
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% hardwareDeviceID - [Optional, default is 'Dev1'] A string defining the device ID of your
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% NI acquisition board. Use the command "daq.getDevices" to find the ID
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% of your board. By default this is 'Dev1'
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% saveFname - An optional string defining the relative or absolute path of a file to which data
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% should be written. Data will be written as a TIFF stack. If not supplied, no data
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% are saved to disk.
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%
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%
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%
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% Examples
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% The following example shows how to list the available DAQ devices and start
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% waveformTester.
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%
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% >> listDeviceIDs
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% The devices on your system are:
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% aux1
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% aux2
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% Dev1
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% scan
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%
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% >> S=waveformTester('Dev2') % By default it's 'Dev1'
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% >> S.stop % stops the scanning
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% >> S.start % re-starts the scanning
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% >> S.delete % (or close the figure window)
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%
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%
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% % Acquire using 'Dev1' and save data to a file
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% >> S = waveformTester('Dev1','testImageStack.tiff')
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%
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% Requirements
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% DAQmx and the Vidrio dabs.ni.daqmx wrapper
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%
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% See Also:
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% minimalScanner
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% Define properties that we will use for the acquisition. The properties are "protected" to avoid
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% the user changing them at the command line. Doing so would cause the acquisition to exhibit errors
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% because there is no mechanism for handling changes to these parameters on the fly.
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properties (SetAccess=private)
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% These properties are specific to scanning and image construction
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galvoAmp = 1.5 % Scanner amplitude (defined as peak-to-peak/2)
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pixelsPerLine = 256 % Number pixels per line
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waveform % The scanner waveforms will be stored here
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numReps=4 % How many times to repeat this waveform in one acquisiion
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fillFraction = 0.85 % 1-fillFraction is considered to be the turn-around time and is excluded from the image
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% Properties for the analog input end of things
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hAITask %The AI task handle will be kept here
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AIChan = [0,1]
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AIterminalConfig = 'DAQmx_Val_PseudoDiff' %Valid values: 'DAQmx_Val_Cfg_Default', 'DAQmx_Val_RSE', 'DAQmx_Val_NRSE', 'DAQmx_Val_Diff', 'DAQmx_Val_PseudoDiff'
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AIrange = 0.5 % Digitise over +/- this range.
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% Properties for the analog output end of things
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hAOTask % The AO task handle will be kept here
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AOChans = 0
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% These properties are common to both tasks
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DAQDevice = 'Dev1'
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sampleRate = 128E3 % The sample rate at which the board runs (Hz)
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end % close properties block
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properties (Hidden,SetAccess=private)
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% These properties hold information relevant to the plot window
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% They are hidden as well as protected for neatness.
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hFig % The handle to the figure which shows the data is stored here
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hAxes % Handle for the image axes
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hPltData % Handle produced by imagesc
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hTitle % Handle that stores the plot title
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end
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methods
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function obj=waveformTester
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% This method is the "constructor", it runs when the class is instantiated.
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% Call a method to connect to the DAQ. If the following line fails, the Tasks are
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% cleaned up gracefully and the object is deleted. This is all done by the method
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% call and by the destructor
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obj.connectToDAQandSetUpChannels
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fprintf('Please see "help waveformTester" for usage information\n')
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% Build the figure window and have it shut off the acquisition when closed.
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obj.hFig = clf;
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set(obj.hFig, 'Name', 'Close figure to stop acquisition', 'CloseRequestFcn', @obj.windowCloseFcn)
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%Make an empty axis and fill with a blank image
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obj.hAxes = axes('Parent', obj.hFig, 'Position', [0.05 0.05 0.9 0.9]);
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obj.hPltData = plot(obj.hAxes, obj.waveform);
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set(obj.hAxes, 'Box', 'on')
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% Start the acquisition
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obj.start
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fprintf('Close figure to quit acquisition\n')
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end % close constructor
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function delete(obj)
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% This method is the "destructor". It runs when an instance of the class is deleted.
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obj.hFig.delete %Closes the plot window
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obj.stop % Call the method that stops the DAQmx tasks
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% The tasks should delete automatically (which causes dabs.ni.daqmx.Task.delete to
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% call DAQmxClearTask on each task) but for paranoia we can delete manually:
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obj.hAITask.delete;
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obj.hAOTask.delete;
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end %close destructor
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function connectToDAQandSetUpChannels(obj)
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% Note how we try to name the methods in the most descriptive way possible
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% Attempt to connect to the DAQ and set it up. If we fail, we close the
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% connection to the DAQ and tidy up
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try
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% Create separate DAQmx tasks for the AI and AO
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obj.hAITask = dabs.ni.daqmx.Task('signalReceiver');
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obj.hAOTask = dabs.ni.daqmx.Task('waveformMaker');
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% Set up analog input and output voltage channels
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obj.hAITask.createAIVoltageChan(obj.DAQDevice, obj.AIChan, [], -obj.AIrange, obj.AIrange, [], [], obj.AIterminalConfig);
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obj.hAOTask.createAOVoltageChan(obj.DAQDevice, obj.AOChans);
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% * Set up the AI task
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% Configure the sampling rate and the number of samples so that we are reading back
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% data at the end of each frame
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obj.generateScanWaveforms %This will populate the waveforms property
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obj.hAITask.cfgSampClkTiming(obj.sampleRate,'DAQmx_Val_ContSamps', size(obj.waveforms,1) * 4);
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% Call an anonymous function function to read from the AI buffer and plot the images once per frame
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obj.hAITask.registerEveryNSamplesEvent(@obj.readAndDisplayScanData, size(obj.waveforms,1), false, 'Scaled');
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% * Set up the AO task
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% Set the size of the output buffer
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obj.hAOTask.cfgSampClkTiming(obj.sampleRate, 'DAQmx_Val_ContSamps', size(obj.waveforms,1));
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if obj.hAOTask.sampClkRate ~= obj.hAITask.sampClkRate
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fprintf(['WARNING: AI task sample clock rate does not match AO task sample clock rate. Scan lines will precess.\n', ...
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'This issue is corrected in polishedScanner, which uses a shared sample clock between AO and AI\n'])
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end
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% Allow sample regeneration (buffer is circular)
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obj.hAOTask.set('writeRegenMode', 'DAQmx_Val_AllowRegen');
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% Write the waveform to the buffer with a 5 second timeout in case it fails
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obj.hAOTask.writeAnalogData(obj.waveforms, 5)
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% Configure the AO task to start as soon as the AI task starts
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obj.hAOTask.cfgDigEdgeStartTrig(['/',obj.DAQDevice,'/ai/StartTrigger'], 'DAQmx_Val_Rising');
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catch ME
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errorDisplay(ME)
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%Tidy up if we fail
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obj.delete
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end
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end % close connectToDAQandSetUpChannels
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function start(obj)
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% This method starts acquisition on the AO then the AI task.
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% Acquisition begins immediately since there are no external triggers.
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try
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obj.hAOTask.start();
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obj.hAITask.start();
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catch ME
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errorDisplay(ME)
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%Tidy up if we fail
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obj.delete
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end
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end %close start
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function stop(obj)
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% Stop the AI and then AO tasks
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fprintf('Stopping the scanning AI and AO tasks\n');
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obj.hAITask.stop; % Calls DAQmxStopTask
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obj.hAOTask.stop;
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end %close stop
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function generateScanWaveforms(obj)
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% This method builds a simple ("unshaped") galvo waveform and stores it in the obj.waveform
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% The X waveform goes from +galvoAmp to -galvoAmp over the course of one line.
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xWaveform = linspace(-obj.galvoAmp, obj.galvoAmp, obj.pixelsPerLine);
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% Repeat the X waveform a few times to ease visualisation on-screen
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obj.waveform = repmat(xWaveform, 1, obj.numReps);
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%Report waveform properties
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fprintf('Scanning with a waveform of length %d and a line period of %0.3f ms\n', ...
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obj.imSize, (obj.sampleRate/length(obj.waveforms))*obj.numReps*1E3 );
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end %close generateScanWaveforms
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function readAndDisplayScanData(obj,src,evnt)
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% This callback method is run each time data have been acquired.
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% This happens because the of the listener set up in the method connectToDAQandSetUpChannels
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% on the "obj.hAITask.registerEveryNSamplesEvent" line.
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% Read data off the DAQ
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inData = readAnalogData(src,src.everyNSamples,'Scaled');
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obj.hPltData.YData = inData(:,1);
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end %close readAndDisplayScanData
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function windowCloseFcn(obj,~,~)
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% This runs when the user closes the figure window or if there is an error
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% Note it's also possible to run a clean-up callback function with hTask.registerDoneEvent
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fprintf('You closed the window. Shutting down DAQ.\n')
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obj.delete % simply call the destructor
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end %close windowCloseFcn
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end %close methods block
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end %close the vidrio.mixed.waveformTester class definition
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% Private functions not part of the class definition
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function errorDisplay(ME)
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fprintf('ERROR: %s\n',ME.message)
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for ii=1:length(ME.stack)
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fprintf(' on line %d of %s\n', ME.stack(ii).line, ME.stack(ii).name)
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end
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fprintf('\n')
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end

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