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‎README.md

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# Contents of this project
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* **scanAndAcquire_Minimal** - The least you need to scan the mirrors across a sample and obtain an image:
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1. Uni-directional scanning
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2. Displays image to screen only
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3. One channel only
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4. No correction for imaging artefacts
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* **scanAndAcquire_Minimal** - This tutorial function is the least you need to scan the mirrors across a sample and obtain an image:
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1. Uni-directional scanning.
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2. Displays image to screen only.
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3. One channel only.
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4. No correction for imaging artefacts.
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5. Scanning parameters are hard-coded into the function. User can change scanner amplitude, number of pixels in the image, and sample rate.
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* **scanAndAcquire_Basic** - The same as scanAndAcquire_Minimal but adds:
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1. Averaging using multiple samples per pixel
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2. Correction of the X mirror (fast axis) turn-around artefact
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* **scanAndAcquire_Basic** - This tutorial function is the least you need to get good images and save them to disk.
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It provides the same features as scanAndAcquire_Minimal but adds:
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1. Averaging using multiple samples per pixel.
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2. Correction of the X mirror (fast axis) turn-around artefact.
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3. Saving to disk as a TIFF stack. A function to read back the data is provided.
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* **scanAndAcquire_Polished** - The same as scanAndAcquire_Basic but adds the following features:
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1. All important parameters can be set via parameter/value pairs
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2. More error checks
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3. Acquisition of multiple channels
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4. Generation of scan patterns and image display are handled by external functions
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5. Adds an optional histogram overlay on top of the scan images
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6. Saving to disk with time-stamps in TIFF info
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7. Bidirectional scanning
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* **scanAndAcquire_OO** - The same features as scanAndAcquire_Polished but in an object-oriented interface.
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* **scannerGUI** - A simple GUI wrapper for scanAndAcquire_OO. Currently it only:
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1. Starts/stops scanning
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2. Switches back and forth between unidirectional and bidirectional modes.
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3. Allows update of the bidirectional phase delay
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4. Saving that can be toggled with a checkbox
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1. All important parameters can be set via parameter/value pairs.
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2. More error checks.
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3. Acquisition of multiple channels.
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4. Generation of scan patterns and image display are handled by external functions.
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5. Adds an optional histogram overlay on top of the scan images.
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6. Time-stamps added to the saved TIFF info.
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7. Bidirectional scanning.
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8. Improved buffering to allow for higher frame rates.
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* **scanAndAcquire_OO** - The same features as scanAndAcquire_Polished but in an object-oriented interface.
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The purpose of this it to contract procedural with object-oriented code.
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* **scannerGUI** - A simple GUI wrapper class for scanAndAcquire_OO.
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This showcases some of the advantages of using object-oriented techniques for data acquisition and GUI-building.
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The scannerGUI class is not supposed to be a complete GUI application.
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Its purpose is to demonstrate how easy it is to wrap an object with a GUI.
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Currently the scannerGUI provides the following features:
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1. Starts/stops scanning.
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2. Switches back and forth between unidirectional and bidirectional modes.
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3. Allows update of the bidirectional phase delay whilst scanning.
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4. Saving to disk.
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* The **buildingBlocks** folder contains code snippets to help teach the individual concepts from the above without providing a solution to the whole problem.
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‎buildingBlocks/analogInput.m

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‎buildingBlocks/analogInput_Continuous.m

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function analogInput_Continuous
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% Example showing how to record data continuously through an analog input channel
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%
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% function out = analogInput_Continuous
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%
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% Purpose
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% Records data comntinuously and plots to screen.
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% Displays positive values only.
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%
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% Rob Campbell - Basel 2016
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%Create a session using NI hardware
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s=daq.createSession('ni');
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s.Rate=20E3;
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%Add an analog input channel
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AI=s.addAnalogInputChannel('Dev1', 'ai2', 'Voltage');
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inputRange = 1;
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AI.Range = [-inputRange , inputRange]; %record over +/- 1 V
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% Number of samples to pull in at a time
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s.NumberOfScans = s.Rate*0.1;
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%Add a listener to get data back from this channel and plot it
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addlistener(s,'DataAvailable', @plotData);
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%Trigger the listener after all data have been acquired
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s.NotifyWhenDataAvailableExceeds=s.NumberOfScans;
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s.IsContinuous = true; %needed to provide continuous behavior
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%start the acquisition and block until finished
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clf
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s.startBackground
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fprintf('Press ctrl-c to quit\n');
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while 1
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pause(0.1)
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end
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% - - - - - - - - - - - - - - - - - - - - -
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function plotData(~,event)
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%Nested function to plot data
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t=event.TimeStamps;
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x=event.Data;
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plot(t,x)
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ylim([0,inputRange])
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grid
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end
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end

‎buildingBlocks/analogInput_SingleShot.m

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function varargout = analogInput_SingleShot
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% Example showing how to record two seconds
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%
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% function data = analogInput_SingleShot
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%
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% Purpose
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% Records two seconds of data and plots it to screen.
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% Optionally returns as output argument.
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%
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% Outputs
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% data - [optional] Returns the data vector that was plotted to screen.
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%
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%
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% Rob Campbell - Basel 2016
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%Create a session using NI hardware
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s=daq.createSession('ni');
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s.Rate=20E3; %Set the sample rate
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%Add an analog input channel
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AI=s.addAnalogInputChannel('Dev1', 'ai0', 'Voltage');
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AI.Range = [-1,1]; %record over +/- 1 V
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%Pull in 2 seconds worth of samples
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s.NumberOfScans = s.Rate*2;
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%start the acquisition and block until finished
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fprintf('Acquiring data...');
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[data,t]=s.startForeground;
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fprintf('\n');
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%Plot
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plot(t,data)
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%Release the DAQ session
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s.release;
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if nargout>0
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varargout{1} = data;
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end
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‎buildingBlocks/analogOutput_Continuous.m

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function addAnalogOutput_Continuous
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function analogOutput_Continuous
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% Play a continuous sine wave out of an analog output
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%
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% function analogOutput_Continuous
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%
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%
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% Instructions
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% Simply call the function. Quit with ctrl-C.
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% Connect AO0 of NI device Dev1 to an oscilloscope and run this function.
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% Quit with ctrl-C.
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%
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%
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% Rob Campbell - Basel 2015
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% Rob Campbell - Basel 2016
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%Build one cycle of a sine wave
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waveForm=sin(-pi : pi/1000 : pi);
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waveForm=sin(-pi : pi/1000 : pi)';
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%Set the sample rate to 2000 samples per second, so the waveform plays out in one second
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%queue the first cycle
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s.queueOutputData(dataToPlay);
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s.queueOutputData(waveForm);
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% START!

‎buildingBlocks/analogOutput_SingleShot.m

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function analogOutput_SingleShot
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% Play one cycle of a waveform out of an analog output
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%
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% function analogOutput_SingleShot
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%
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% Instructions
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% Connect AO0 of NI device Dev1 to an oscilloscope and run this function.
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%
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%
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% Rob Campbell - Basel 2015
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%
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% Rob Campbell - Basel 2016
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%Create a session using NI hardware
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%Build one cycle of a sine wave
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waveForm=sin(-pi : pi/1000 : pi);
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waveForm=sin(-pi : pi/1000 : pi)';
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%Set the sample rate to 2000 samples per second, so the waveform plays out in one second
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s.Rate = 2000;
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%Queue the data to the board
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s.queueOutputData(dataToPlay);
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s.queueOutputData(waveForm);
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%Play the waveform

‎buildingBlocks/anonymousFunctionExample.m

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function anonymousFunctionExample
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% Example - how to use anonymous functions in MATLAB
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%
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% function anonymousFunctionExample
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%
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% Purpose
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% Demo showing a few use-cases for anonymouse functions.
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%
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% For details see:
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% http://uk.mathworks.com/help/matlab/matlab_prog/anonymous-functions.html
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%
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%
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% Rob Campbell - Basel 2016
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% Create an anonymous function that makes a sine wave. It has one input argument
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% that determines the number of cucles in the sinwave
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sinWave = @(nCycles) ( sin(linspace(-nCycles*pi,nCycles*pi,100*nCycles)) );
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clf
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n=3;
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plot(sinWave(n))
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title(sprintf('%d cycles of a sine wave',n))
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set(gca,'XTickLabel',[],'YTickLabel',[])
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grid
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%Use a function handle (not an anonymous function) to calculate the mean of each vector in a cell array
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r = {rand(1,30), randn(1,150)*100, rand(1,1000)};
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fprintf('\nThe contents of cell array "r" are:\n')
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disp(r)
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fprintf('Use cellfun and a function handle to calculate the of each each vector in "r":\n' );
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disp(cellfun(@mean,r))
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fprintf('Use cellfun and an anonymous function to calculate 1.96 SD of each each vector in "r":\n' );
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SD95 = @(x) (std(x)*1.96);
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disp(cellfun(SD95,r))
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‎buildingBlocks/cleanUp.m

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% Demo of how to run a sub-function when the caller function ends.
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% The "cleanUp" function will run even if the caller crashes.
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%
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% Rob Campbell - Basel 2015
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% Rob Campbell - Basel 2016
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%
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% see: http://blogs.mathworks.com/loren/2008/03/10/keeping-things-tidy/
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%

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