fipgui.m

function varargout = fipgui(varargin)
    % FIPGUI MATLAB code for fipgui.fig
    %      FIPGUI, by itself, creates a new FIPGUI or raises the existing
    %      singleton*.
    %
    %      H = FIPGUI returns the handle to a new FIPGUI or the handle to
    %      the existing singleton*.
    %
    %      FIPGUI('CALLBACK',hObject,eventData,handles,...) calls the local
    %      function named CALLBACK in FIPGUI.M with the given input arguments.
    %
    %      FIPGUI('Property','Value',...) creates a new fipgui or raises the
    %      existing singleton*.  Starting from the left, property value pairs are
    %      applied to the GUI before fipgui_OpeningFcn gets called.  An
    %      unrecognized property name or invalid value makes property application
    %      stop.  All inputs are passed to fipgui_OpeningFcn via varargin.
    %
    %      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
    %      instance to run (singleton)".
    %
    % See also: GUIDE, GUIDATA, GUIHANDLES

    % Edit the above text to modify the response to help fipgui

    % Last Modified by GUIDE v2.5 23-Jul-2020 10:44:09

    % Begin initialization code - DO NOT EDIT
    gui_Singleton = 1;
    gui_State = struct('gui_Name', mfilename, ...
        'gui_Singleton', gui_Singleton, ...
        'gui_OpeningFcn', @fipgui_OpeningFcn, ...
        'gui_OutputFcn', @fipgui_OutputFcn, ...
        'gui_LayoutFcn', [], ...
        'gui_Callback', []);

    if nargin && ischar(varargin{1})
        gui_State.gui_Callback = str2func(varargin{1});
    end

    if nargout
        [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
    else
        gui_mainfcn(gui_State, varargin{:});
    end

    % End initialization code - DO NOT EDIT
end

% --- Executes just before fipgui is made visible.
function fipgui_OpeningFcn(hObject, eventdata, handles, varargin)
    % This function has no output args, see OutputFcn.
    % hObject    handle to figure
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    structure with handles and user data (see GUIDATA)
    % varargin   command line arguments to fipgui (see VARARGIN)

    % Parameters
    handles.computer_dependent_delay = 0.00015; % seconds
    handles.sample_rate_factor = 10; % how much faster DAQ samples than camera
    handles.exposureGap = 0;
    handles.plotLookback = 10;
    handles.settingsGroup = 'FIPGUI';

    % Defaults
    handles.crop_roi = false;
    handles.masks = false;
    handles.callback_path = false;
    handles.callback = @(x, y) false;
    handles.ao_waveform_path = false;
    handles.ao_waveform_file = false;
    handles.calibColors = 'k';
    handles.calibImg.cdata = false;

    % Populate dropdowns
    imaqreset();
    [adaptors, devices, formats, IDs] = getCameraHardware();
    nDevs = length(adaptors);

    if nDevs == 0
        error('MATLAB IMAQ detected no available Orca camera devices to connect to. Fix this and restart MATLAB.');
    end

    options = {};

    for i = 1:nDevs
        options{i} = [adaptors{i} ' ' devices{i} ' ' formats{i}];
    end

    set(handles.cam_pop, 'String', options);

    % Recover settings from last time
    grp = handles.settingsGroup;
    set(handles.camport_pop, 'Value', getpref(grp, 'camport_pop', 1));
    set(handles.ref_pop, 'Value', getpref(grp, 'ref_pop', 2));
    set(handles.sig_pop, 'Value', getpref(grp, 'sig_pop', 3));

    try
        set(handles.ai_logging_check, 'Value', getpref(grp, 'ai_logging_check'));
    catch e
        set(handles.ai_logging_check, 'Value', true);
    end

    rate_txt = getpref(grp, 'rate_txt', get(handles.rate_txt, 'String'));

    if isnan(str2double(rate_txt))
        rate_txt = '10';
        warning(['Invalid rate text, setting to default value of ' rate_txt]);
    end

    set(handles.rate_txt, 'String', rate_txt);
    set(handles.cam_pop, 'Value', getpref(grp, 'cam_pop', get(handles.cam_pop, 'Value')));

    set(handles.savepath, 'String', getpref(grp, 'savepath', get(handles.savepath, 'String')));
    set(handles.sunet_id, 'String', getpref(grp, 'sunet_id', get(handles.sunet_id, 'String')));
    set(handles.experiment, 'String', getpref(grp, 'experiment', get(handles.experiment, 'String')));

    ao_waveform_txt = getpref(grp, 'ao_waveform_txt', get(handles.ao_waveform_txt, 'String'));

    if numel(ao_waveform_txt) > 1 && ao_waveform_txt(1) == '0'
        ao_waveform_txt = '<None>';
        warning(['Invalid ao waveform text, setting to default value of ' ao_waveform_txt]);
    end

    set(handles.ao_waveform_txt, 'String', ao_waveform_txt);
    set(handles.callback_txt, 'String', getpref(grp, 'callback_txt', get(handles.callback_txt, 'String')));

    % Setup DAQ
    rate = str2double(get(handles.rate_txt, 'String'));
    fs = rate * handles.sample_rate_factor;
    devices = daq.getDevices();
    device = devices(1);
    handles.dev = device;

    s = daq.createSession('ni');
    s.Rate = fs;
    s.IsContinuous = true;

    try
        camCh = s.addCounterOutputChannel(device.ID, getCurrentPopupString(handles.camport_pop), 'PulseGeneration');
        camCh.Frequency = rate;
        camCh.InitialDelay = 0;
        camCh.DutyCycle = 0.1;
        disp(['Camera should be connected to ' camCh.Terminal]);

        refCh = s.addCounterOutputChannel(device.ID, getCurrentPopupString(handles.ref_pop), 'PulseGeneration');
        refCh.Frequency = rate / 2;
        refCh.InitialDelay = 1 / rate * 0.05;
        refCh.DutyCycle = 0.45;
        disp(['Reference LED should be connected to ' refCh.Terminal]);

        sigCh = s.addCounterOutputChannel(device.ID, getCurrentPopupString(handles.sig_pop), 'PulseGeneration');
        sigCh.Frequency = rate / 2;
        sigCh.InitialDelay = 1 / rate * 1.05;
        sigCh.DutyCycle = 0.45;
        disp(['Signal LED should be connected to ' sigCh.Terminal]);
    catch e
        disp(e);
        setpref('FIPGUI', 'camport_pop', 1);
        setpref('FIPGUI', 'ref_pop', 2);
        setpref('FIPGUI', 'sig_pop', 3);
        error('Restart MATLAB');
    end

    % Enable analog input logging
    ch = addAnalogInputChannel(s, handles.dev.ID, [0:7], 'Voltage');
    lh = addlistener(s, 'DataAvailable', @(src, event) 0); % add a dummy listener
    disp(['(optional for logging) Analog inputs should be connected to ai0 - ai7']);

    % Enable analog output
    ao0 = addAnalogOutputChannel(s, handles.dev.ID, 'ao0', 'Voltage');
    ao1 = addAnalogOutputChannel(s, handles.dev.ID, 'ao1', 'Voltage');
    ao2 = addAnalogOutputChannel(s, handles.dev.ID, 'ao2', 'Voltage');
    ao3 = addAnalogOutputChannel(s, handles.dev.ID, 'ao3', 'Voltage');
    disp(['(optional) Analog outputs should be connected to ao0 - ao3']);
    % This listener is enabled later if analog outputs are not used, and will
    % continuously set the outputs to zero.
    lh_ao = addlistener(s, 'DataRequired', @load_zero_valued_ao_data);

    % Workaround for s.IsRunning bug. (see main acquisition for details)
    % Load and send a short AO waveform.
    load_zero_valued_ao_data(s, '');
    s.startBackground();
    stop(s);

    handles.lh_ao = lh_ao;
    handles.camCh = camCh;
    handles.refCh = refCh;
    handles.sigCh = sigCh;
    handles.s = s;

    % Setup camera
    camDeviceN = get(handles.cam_pop, 'Value');
    vid = videoinput(adaptors{camDeviceN}, IDs(camDeviceN), formats{camDeviceN});
    src = getselectedsource(vid);
    vid.FramesPerTrigger = 1;
    vid.TriggerRepeat = Inf;
    vid.ROIPosition = [0 0 vid.VideoResolution];

    handles.vid = vid;
    handles.src = src;

    % Some more updates based on the defaults loaded earlier
    % Update rate
    rate_txt_Callback(handles.rate_txt, [], handles);

    % Update callback file information
    [pathname, filename] = fileparts(get(handles.callback_txt, 'String'));
    addpath(pathname);
    handles.callback_path = pathname;
    [~, basename, ext] = fileparts(filename);

    if strcmp(basename, '<None>')
        handles.callback = @(x, y) false;
    else
        handles.callback = str2func(basename);
    end

    % Update analog output waveform
    [pathname, filename, ext] = fileparts(get(handles.ao_waveform_txt, 'String'));
    [~, basename, ext] = fileparts(filename);

    if strcmp(basename, '<None>')
        handles.ao_waveform_path = false;
        handles.ao_waveform_file = false;
    else
        handles.ao_waveform_path = pathname;
        handles.ao_waveform_file = [filename ext];
    end

    % Disable acquisition until calibration is run
    set(handles.acquire_tgl, 'Enable', 'off');

    % Choose default command line output for fipgui
    handles.output = hObject;

    % Update handles structure
    guidata(hObject, handles);
    update_camera_exposure_time(handles);

    % UIWAIT makes fipgui wait for user response (see UIRESUME)
    % uiwait(handles.fipgui);
end

% --- Outputs from this function are returned to the command line.
function varargout = fipgui_OutputFcn(hObject, eventdata, handles)
    % varargout  cell array for returning output args (see VARARGOUT);
    % hObject    handle to figure
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    structure with handles and user data (see GUIDATA)

    % Get default command line output from handles structure
    varargout{1} = handles.output;
end

% --- Executes on button press in snap_btn.
function snap_btn_Callback(hObject, eventdata, handles)
    % hObject    handle to snap_btn (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    structure with handles and user data (see GUIDATA)
    snapframe = getsnapshot(handles.vid);

    % Display the frame
    figure();
    imagesc(snapframe);
    colorbar();
end

% --- Executes on button press in calibframe_btn.
function calibframe_btn_Callback(hObject, eventdata, handles)
    % hObject    handle to calibframe_btn (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    structure with handles and user data (see GUIDATA)

    % Run the camera and LED commands briefly to get illuminated frames
    nFrames = 4;
    i = 0;
    res = get(handles.vid, 'VideoResolution');
    frames = zeros(res(1), res(2), nFrames);
    set(handles.vid, 'ROIPosition', [0 0 res]);

    load_analog_output_data(handles, true);
    triggerconfig(handles.vid, 'hardware', 'RisingEdge', 'EdgeTrigger');
    start(handles.vid);
    startBackground(handles.s);

    while i < nFrames
        i = i + 1;
        frames(:, :, i) = getdata(handles.vid, 1, 'uint16');
    end

    stop(handles.vid);
    stop(handles.s);

    calibframe = max(frames, [], 3);

    % Fiber ROI GUI
    calibOut = calibrationgui(calibframe);
    masks = calibOut.masks;
    handles.calibColors = calibOut.colors;
    handles.calibImg = calibOut.figImg;
    handles.labels = calibOut.labels;

    % Use masks to determine how much we can crop
    all_masks = any(masks, 3);
    [rows, cols] = ind2sub(size(all_masks), find(all_masks));
    crop_roi = [min(cols), min(rows), max(cols) - min(cols) + 1, max(rows) - min(rows) + 1];
    masks = masks(min(rows):max(rows), min(cols):max(cols), :);
    handles.crop_roi = crop_roi;
    handles.masks = logical(masks);
    handles.vid.ROIPosition = crop_roi;
    % This also sets the exposureGap. This assumes bidirectional center-out
    % rolling shutter
    r_min = min(rows);
    r_max = max(rows);
    res = handles.vid.VideoResolution;
    r_center = res(1) / 2; % center row for orca
    row_range = min(r_max - r_min, ceil(max(abs(r_center - r_min), abs(r_center -r_max))));
    disp(row_range);
    full_frame_readout_time = 0.010; % camera and mode dependent, assumes Orca FAST mode
    handles.exposureGap = handles.computer_dependent_delay + full_frame_readout_time / (res(1) / 2) * row_range;
    guidata(hObject, handles);
    update_camera_exposure_time(handles)

    set(handles.acquire_tgl, 'Enable', 'on');
    set(handles.calibframe_lbl, 'Visible', 'off');

    % Update handles structure
    guidata(hObject, handles);
end

function [acquisitionPath, dataFile, metadataFile, calibFile, logAIFile] = get_save_details(handles)
    base_path = get(handles.savepath, 'String');
    sunet_id = get(handles.sunet_id, 'String');

    experiment = get(handles.experiment, 'String');
    dt = datestr(datetime('now'), 'yyyymmdd-HHMMSS');
    baseName = [experiment '_' dt];
    
    acquisitionPath = fullfile(base_path, sunet_id, baseName);
    mkdir(acquisitionPath);

    dataFile = fullfile(acquisitionPath, [baseName '_data.mat']);
    metadataFile = fullfile(acquisitionPath, [baseName '_metadata.mat']);
    calibFile = fullfile(acquisitionPath, [baseName '_calibration.jpg']);
    logAIFile = fullfile(acquisitionPath, [baseName '_logAI.csv']);
end

% Validate settings
function valid = settings_are_valid(handles)
    valid = true;
    ports = [get(handles.camport_pop, 'Value'), get(handles.ref_pop, 'Value'), get(handles.sig_pop, 'Value')];

    if length(unique(ports)) < length(ports)
        valid = false;
        errordlg('Two or more devices (e.g. reference LED and camera) are set to the same DAQ port. Please correct this to proceed.', 'Config error');
    end

end

% Analog output data must be loaded before a session is started
function load_analog_output_data(handles, disable_ao_out)

    if disable_ao_out
        analog_output_waveform_enabled = false;
    else
        analog_output_waveform_enabled = handles.ao_waveform_path;
    end

    if analog_output_waveform_enabled
        disp('Loading user defined AO output');
        user_waveform = load_user_ao_waveform(handles);
        disp(['AO waveform duration: ' num2str(size(user_waveform, 1) / handles.s.Rate) ' seconds']);
        handles.lh_ao.Enabled = false;
        queueOutputData(handles.s, user_waveform);
    else
        handles.lh_ao.Enabled = true;
        disp('Setting all analog output values to 0 V');
        load_zero_valued_ao_data(handles.s, '');
    end

end

% Verify user waveform is valid
function verify_user_ao_waveform(handles)
    disp('Verifying AO waveform.');
    load_user_ao_waveform(handles);
end

% Load a user specified AO waveform
% A valid analog output waveform .mat file must contain two variables:
%   rate - int. samples per second, must match handles.s.Rate
%   waveform - (N x 4) vector of voltage values
function user_waveform = load_user_ao_waveform(handles)
    t = load(fullfile(handles.ao_waveform_path, handles.ao_waveform_file));
    user_waveform = 0;

    if t.rate ~= handles.s.Rate
        error(['Waveform rate ' num2str(t.rate) ' does not match daq rate ' num2str(handles.s.Rate)]);
    else

        if size(t.waveform, 2) == 4
            user_waveform = t.waveform;
        else
            error(['Waveform has ' num2str(size(t.waveform, 2)) ' channels instead of 4.']);
        end

    end

    if max(abs(user_waveform(:))) > 10
        error('AO output waveform must be between +/- 10 V');
    end

end

% Call back function to load zero valued AO data
function load_zero_valued_ao_data(src, event)
    % minimum output is 0.5s of samples, for 4 channels
    src.queueOutputData(zeros(5000, 4));
end

% --- Executes on button press in acquire_tgl.
function acquire_tgl_Callback(hObject, eventdata, handles)
    % hObject    handle to acquire_tgl (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    structure with handles and user data (see GUIDATA)

    addpath('utils');  % for circularBuffer

    % Hint: get(hObject,'Value') returns toggle state of acquire_tgl
    state = get(hObject, 'Value');

    if state
        % Pre-check for valid analog output waveform
        if handles.ao_waveform_path
            verify_user_ao_waveform(handles);
        end

        verify_callback_function(handles);

        % Disable all settings
        confControls = [
                    handles.camport_pop
                    handles.ref_pop
                    handles.sig_pop
                    handles.rate_txt
                    handles.cam_pop
                    handles.snap_btn
                    handles.calibframe_btn
                    handles.savepath
                    handles.sunet_id
                    handles.experiment
                    handles.callback_txt
                    handles.ai_logging_check
                    handles.ao_waveform_btn
                    handles.ao_waveform_clear_btn
                    handles.ao_waveform_txt
                    handles.callback_clear_btn
                    handles.callback_btn
                    handles.savepath_btn];

        for control = confControls
            set(control, 'Enable', 'off');
        end

        % Re-label button
        set(hObject, 'String', 'Stop acquisition');

        if settings_are_valid(handles)
            rate = str2double(get(handles.rate_txt, 'String'));

            [acquisitionDir, dataFile, metadataFile, calibFile, logAIFile] = get_save_details(handles);
            set(handles.acquisition_dir, 'String', acquisitionDir);

            save_metadata(metadataFile, handles.labels, rate);
            save_calibration(calibFile, handles.calibImg.cdata);

            if (ai_logging_is_enabled(handles))
                % Add listener for analog input logging
                lh = addlistener(handles.s, 'DataAvailable', @(src, event) logAIData(src, event, logAIFile));
                handles.s.NotifyWhenDataAvailableExceeds = round(handles.s.Rate * 1);
                disp('Added analog input channels and listener');
            end

            % Snap a quick dark frame
            darkframe = getsnapshot(handles.vid);

            if ~any(handles.masks(:))
                handles.masks = ones(handles.vid.VideoResolution);
                darkOffset = mean(darkframe(:));
            else
                darkOffset = applyMasks(handles.masks, darkframe);
            end
            
            nMasks = size(handles.masks, 3);

            lookback = handles.plotLookback;
            framesback = lookback * rate / 2;

            chunk_time = 15 * 60;
            chunk_size = chunk_time * rate / 2;

            buffer_size = max(framesback, chunk_size);
            ref = circularBuffer(zeros(buffer_size, nMasks)); 
            sig = circularBuffer(zeros(buffer_size, nMasks));

            i = 0;
            j = 0;
            chunk = 1;
            last_save = 1;

            vid = handles.vid;
            s = handles.s;

            % Set up plotting
            plot_fig = figure('CloseRequestFcn', @uncloseable);
            ha = tightSubplot(nMasks, 1, 0.1, 0.05, 0.10, plot_fig);
            yyaxes = zeros(nMasks, 2);
            lyy = zeros(nMasks, 2);
            t = -lookback:(2 / rate):0;
            ymax = 4;
            ybuf = 1.1;

            for k = 1:nMasks
                [yyax, l1, l2] = plotyy(ha(k), 0, 0, 0, 0);
                xlim(yyax(1), [-lookback 0]);
                xlim(yyax(2), [-lookback 0]);
                ylim(yyax(1), [0 ymax]);
                ylim(yyax(2), [0 ymax]);
                linkprop(yyax, {'Xlim'});
                set(l1, 'Color', handles.calibColors(k, :));
                set(l2, 'Color', handles.calibColors(k, :));
                set(l1, 'LineWidth', 2);
                set(l2, 'LineStyle', '--');

                if verLessThan('matlab', '8.4')
                    set(l1, 'LineSmoothing', 'on');
                    set(l2, 'LineSmoothing', 'on');
                end

                set(yyax, {'ycolor'}, {'k'; 'k'});
                ylabel(yyax(1), 'Signal');
                ylabel(yyax(2), 'Reference');
                setappdata(gca, 'LegendColorbarManualSpace', 1);
                setappdata(gca, 'LegendColorbarReclaimSpace', 1);
                yyaxes(k, :) = yyax;
                lyy(k, :) = [l1 l2];
            end

            triggerconfig(vid, 'hardware', 'RisingEdge', 'EdgeTrigger');
            load_analog_output_data(handles, false);
            start(vid);

            s.startBackground();

            handles.startTime = now();

            % Stop if value is set to false, or if the user-specified AO
            % finishes running
            if handles.ao_waveform_path
                disp('Waiting for user to end acquisition or AO waveform to finish...');
            else
                disp('Waiting for user to end acquisition...');
            end

            while get(hObject, 'Value')

                if ~s.IsRunning
                    disp('AO waveform output finished.');
                    set(hObject, 'Value', false); % Exit loop if AO output just finished
                    break
                end

                try
                    img = getdata(vid, 1, 'uint16');
                catch e
                    % Most likely cause for getting here is the s.IsRunning bug:
                    %   without the workaround implemented above in init, the very
                    %   first acquisition, if AO is enabled, will fail to stop
                    %   (s.IsRunning is True indefinitely despite the waveform
                    %   having stopped). As a side effect, the synchronization
                    %   of the AO waveform and digital counter channels appears
                    %   to be consistently different.
                    if j > 0
                        disp('ERROR: AO and counters may not be synced. See s.IsRunning bug comments');
                        warning('See s.IsRunning bug comments'); beep;
                    end

                    set(hObject, 'Value', false); % Exit loop if AO output just finished
                    break
                end

                i = i + 1; % frame number
                j = ceil(i / 2); % sig/ref pair number

                avgs = applyMasks(handles.masks, img);
                avgs = avgs - darkOffset;

                if mod(i, 2) == 1% reference channel
                    ref(j, :) = avgs;
                    handles.callback(avgs, 'reference');
                else % signal channel
                    sig(j, :) = avgs;
                    handles.callback(avgs, 'signal');
                    
                    if (j > 1) & (mod(j, chunk_size) == 0)
                        save_data(dataFile, chunk, sig(last_save:j, :), ref(last_save:j, :));
                        chunk = chunk + 1;
                        last_save = last_save + chunk_size;
                    end
                end

                % Plotting
                jboth = 2 * floor(j / 2);

                if jboth > 0 && mod(i, 2) == 0
                    tlen = jboth - max(1, j - framesback);
                    tnow = t(end - tlen:end);

                    for k = 1:nMasks
                        sigmin = min(sig(max(1, j - framesback):jboth, k));
                        sigmax = max(sig(max(1, j - framesback):jboth, k));

                        refmin = min(ref(max(1, j - framesback):jboth, k));
                        refmax = max(ref(max(1, j - framesback):jboth, k));

                        % put axes on same scale, but allow zero to float
                        if sigmax - sigmin > refmax - refmin
                            spread = sigmax - sigmin;
                            mid = (refmax + refmin) / 2;
                            refmax = mid + spread / 2;
                            refmin = mid - spread / 2;
                        else
                            spread = refmax - refmin;
                            mid = (sigmax + sigmin) / 2;
                            sigmax = mid + spread / 2;
                            sigmin = mid - spread / 2;
                        end

                        % if max = min, don't try to update bounds
                        if sigmax > sigmin
                            ylim(yyaxes(k, 1), [sigmin sigmax]);
                        end

                        if refmax > refmin
                            ylim(yyaxes(k, 2), [refmin refmax]);
                        end

                        set(lyy(k, 1), 'XData', tnow, 'YData', sig(max(1, j - framesback):jboth, k));
                        set(lyy(k, 2), 'XData', tnow, 'YData', ref(max(1, j - framesback):jboth, k));
                    end

                end

                % Check to make sure camera acquisition is keeping up.
                elapsed_time = (now() - handles.startTime());

                if abs(elapsed_time * 24 * 3600 - (i) / rate) > 1% if camera acquisition falls behind more than 1 s...
                    fraction_frames_acquired = i / (elapsed_time * 24 * 3600 * rate);

                    if j > 0
                        disp(['fraction of frames acquired: ' num2str(fraction_frames_acquired)]);

                        if abs(fraction_frames_acquired - 0.5) < 0.04
                            warning('ERROR: Only got half as many frames as expected. Most likely check trigger connections; less likely: select a smaller ROI or lower speed and try again. Last resort: increase handles.computer_dependent_delay');
                        else
                            warning('ERROR: Camera acquisition fell behind! Select a smaller ROI or lower speed and try again. Last resort: increase handles.computer_dependent_delay'); beep;
                        end

                    end

                    set(hObject, 'Value', false);
                    break
                end

                set(handles.elapsed_txt, 'String', datestr(elapsed_time, 'HH:MM:SS'));
            end

            disp('...acquisition complete.');

            % Stop acquisition
            stop(vid);
            s.stop();

            if (ai_logging_is_enabled(handles))
                delete(lh); % delete analog input listener
            end

            set(handles.elapsed_txt, 'String', datestr(0, 'HH:MM:SS'));

            % Save data
            if j > 0
                save_data(dataFile, chunk, sig(last_save:j, :), ref(last_save:j, :));
            else
                warning(['No frames captured or saved! Check camera trigger connection is ' handles.camCh.Terminal '. Then restart MATLAB.']); beep;
            end

        end % end settings are valid check

        % Make the old plots closeable
        set(plot_fig, 'CloseRequestFcn', @closeable);

        % Re-enable all controls
        for control = confControls
            set(control, 'Enable', 'on');
        end

        % Re-label button
        set(hObject, 'String', 'Acquire data');
    end

end

function save_metadata(metadataFile, labels, framerate)
    save(metadataFile, 'labels', 'framerate', '-v7.3')
end

function save_calibration(calibFile, cdata)
    if any(cdata(:))
        imwrite(cdata, calibFile, 'JPEG')
    end
end

function save_data(dataFile, chunk, sig, ref)
    [spath, fname, ext] = fileparts(dataFile);
    final_file = fullfile(spath, [fname sprintf('_%03d', chunk) ext]);
    save(final_file, 'sig', 'ref', '-v7.3');
end

% --- Executes during object creation, after setting all properties.
function camport_pop_CreateFcn(hObject, eventdata, handles)
    % hObject    handle to camport_pop (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    empty - handles not created until after all CreateFcns called

    % Hint: popupmenu controls usually have a white background on Windows.
    %       See ISPC and COMPUTER.
    if ispc && isequal(get(hObject, 'BackgroundColor'), get(0, 'defaultUicontrolBackgroundColor'))
        set(hObject, 'BackgroundColor', 'white');
    end

end

% --- Executes on selection change in ref_pop.
function ref_pop_Callback(hObject, eventdata, handles)
    % hObject    handle to ref_pop (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    structure with handles and user data (see GUIDATA)

    % Hints: contents = cellstr(get(hObject,'String')) returns ref_pop contents as cell array
    %        contents{get(hObject,'Value')} returns selected item from ref_pop
    f = handles.refCh.Frequency;
    i = handles.refCh.InitialDelay;
    d = handles.refCh.DutyCycle;
    handles.s.removeChannel(chIdx(handles.s, handles.refCh));

    handles.refCh = handles.s.addCounterOutputChannel(handles.dev.ID, getCurrentPopupString(hObject), 'PulseGeneration');
    handles.refCh.Frequency = f;
    handles.refCh.InitialDelay = i;
    handles.refCh.DutyCycle = d;
    disp(['Signal LED should be connected to ' handles.refCh.Terminal]);

    % Update handles structure
    guidata(hObject, handles);
end

% --- Executes during object creation, after setting all properties.
function ref_pop_CreateFcn(hObject, eventdata, handles)
    % hObject    handle to ref_pop (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    empty - handles not created until after all CreateFcns called

    % Hint: popupmenu controls usually have a white background on Windows.
    %       See ISPC and COMPUTER.
    if ispc && isequal(get(hObject, 'BackgroundColor'), get(0, 'defaultUicontrolBackgroundColor'))
        set(hObject, 'BackgroundColor', 'white');
    end

end

% --- Executes on selection change in sig_pop.
function sig_pop_Callback(hObject, eventdata, handles)
    % hObject    handle to sig_pop (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    structure with handles and user data (see GUIDATA)

    % Hints: contents = cellstr(get(hObject,'String')) returns sig_pop contents as cell array
    %        contents{get(hObject,'Value')} returns selected item from sig_pop
    f = handles.sigCh.Frequency;
    i = handles.sigCh.InitialDelay;
    d = handles.sigCh.DutyCycle;
    handles.s.removeChannel(chIdx(handles.s, handles.sigCh));

    handles.sigCh = handles.s.addCounterOutputChannel(handles.dev.ID, getCurrentPopupString(hObject), 'PulseGeneration');
    handles.sigCh.Frequency = f;
    handles.sigCh.InitialDelay = i;
    handles.sigCh.DutyCycle = d;
    disp(['Signal LED should be connected to ' handles.sigCh.Terminal]);

    % Update handles structure
    guidata(hObject, handles);
end

% --- Executes during object creation, after setting all properties.
function sig_pop_CreateFcn(hObject, eventdata, handles)
    % hObject    handle to sig_pop (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    empty - handles not created until after all CreateFcns called

    % Hint: popupmenu controls usually have a white background on Windows.
    %       See ISPC and COMPUTER.
    if ispc && isequal(get(hObject, 'BackgroundColor'), get(0, 'defaultUicontrolBackgroundColor'))
        set(hObject, 'BackgroundColor', 'white');
    end

end

function rate_txt_Callback(hObject, eventdata, handles)
    % hObject    handle to rate_txt (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    structure with handles and user data (see GUIDATA)

    % Hints: get(hObject,'String') returns contents of rate_txt as text
    %        str2double(get(hObject,'String')) returns contents of rate_txt as a double
    rate = str2double(get(handles.rate_txt, 'String'));
    fs = rate * handles.sample_rate_factor;
    set(handles.s, 'Rate', fs);
    set(handles.camCh, 'Frequency', rate);
    set(handles.refCh, 'Frequency', rate / 2);
    set(handles.refCh, 'InitialDelay', 1 / rate * 0.05);
    set(handles.sigCh, 'Frequency', rate / 2);
    set(handles.sigCh, 'InitialDelay', 1 / rate * 1.05);

    % Update handles structure
    guidata(hObject, handles);
    update_camera_exposure_time(handles);
end

% --- Executes during object creation, after setting all properties.
function rate_txt_CreateFcn(hObject, eventdata, handles)
    % hObject    handle to rate_txt (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    empty - handles not created until after all CreateFcns called

    % Hint: edit controls usually have a white background on Windows.
    %       See ISPC and COMPUTER.
    if ispc && isequal(get(hObject, 'BackgroundColor'), get(0, 'defaultUicontrolBackgroundColor'))
        set(hObject, 'BackgroundColor', 'white');
    end

end

% --- Executes on selection change in camport_pop.
function camport_pop_Callback(hObject, eventdata, handles)
    % hObject    handle to camport_pop (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    structure with handles and user data (see GUIDATA)

    % Hints: contents = cellstr(get(hObject,'String')) returns camport_pop contents as cell array
    %        contents{get(hObject,'Value')} returns selected item from camport_pop
    f = handles.camCh.Frequency;
    i = handles.camCh.InitialDelay;
    d = handles.camCh.DutyCycle;
    handles.s.removeChannel(chIdx(handles.s, handles.camCh));

    handles.camCh = handles.s.addCounterOutputChannel(handles.dev.ID, getCurrentPopupString(hObject), 'PulseGeneration');
    handles.camCh.Frequency = f;
    handles.camCh.InitialDelay = i;
    handles.camCh.DutyCycle = d;
    disp(['Camera should be connected to ' handles.camCh.Terminal]);

    % Update handles structure
    guidata(hObject, handles);
end

function update_camera_exposure_time(handles)
    rate = str2double(get(handles.rate_txt, 'String'));
    handles.src.ExposureTime = 1 / rate - handles.exposureGap;
end

function cam_pop_Callback(hObject, eventdata, handles)
    % hObject    handle to cam_pop (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    structure with handles and user data (see GUIDATA)

    % Hints: get(hObject,'String') returns contents of cam_pop as text
    %        str2double(get(hObject,'String')) returns contents of cam_pop as a double
    % Setup camera
    rate = str2double(get(handles.rate_txt, 'String'));
    [adaptors, devices, formats, IDs] = getCameraHardware();
    camDeviceN = get(hObject, 'Value');
    vid = videoinput(adaptors{camDeviceN}, IDs(camDeviceN), formats{camDeviceN});
    src = getselectedsource(vid);
    vid.FramesPerTrigger = 1;
    vid.TriggerRepeat = Inf;

    handles.vid = vid;
    handles.src = src;

    % Choose default command line output for fipgui
    handles.output = hObject;

    % Update handles structure
    guidata(hObject, handles);
    update_camera_exposure_time(handles);

    % Disable acquisition until calibration is run
    set(handles.acquire_tgl, 'Enable', 'off');
    set(handles.calibframe_lbl, 'Visible', 'on');
end

% --- Executes during object creation, after setting all properties.
function cam_pop_CreateFcn(hObject, eventdata, handles)
    % hObject    handle to cam_pop (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    empty - handles not created until after all CreateFcns called

    % Hint: edit controls usually have a white background on Windows.
    %       See ISPC and COMPUTER.
    if ispc && isequal(get(hObject, 'BackgroundColor'), get(0, 'defaultUicontrolBackgroundColor'))
        set(hObject, 'BackgroundColor', 'white');
    end

end

% --- Executes during object creation, after setting all properties.
function savepath_CreateFcn(hObject, eventdata, handles)
    % hObject    handle to savepath (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    empty - handles not created until after all CreateFcns called

    % Hint: edit controls usually have a white background on Windows.
    %       See ISPC and COMPUTER.
    if ispc && isequal(get(hObject, 'BackgroundColor'), get(0, 'defaultUicontrolBackgroundColor'))
        set(hObject, 'BackgroundColor', 'white');
    end

end

% --- Executes during object creation, after setting all properties.
function callback_txt_CreateFcn(hObject, eventdata, handles)
    % hObject    handle to callback_txt (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    empty - handles not created until after all CreateFcns called

    % Hint: edit controls usually have a white background on Windows.
    %       See ISPC and COMPUTER.
    if ispc && isequal(get(hObject, 'BackgroundColor'), get(0, 'defaultUicontrolBackgroundColor'))
        set(hObject, 'BackgroundColor', 'white');
    end

end

% --- Executes on button press in savepath_btn.
function savepath_btn_Callback(hObject, eventdata, handles)
    % hObject    handle to savepath_btn (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    structure with handles and user data (see GUIDATA)
    selpath = uigetdir('.', 'Top-level data dir');
    set(handles.savepath, 'String', selpath);

    % Update handles structure
    guidata(hObject, handles);
end

% --- Executes on button press in callback_btn.
function callback_btn_Callback(hObject, eventdata, handles)
    % hObject    handle to callback_btn (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    structure with handles and user data (see GUIDATA)
    [filename, pathname] = uigetfile('', 'Select a .m function file');

    if handles.callback_path
        rmpath(handles.callback_path);
    end

    addpath(pathname);
    handles.callback_path = pathname;
    [~, basename, ext] = fileparts(filename);
    handles.callback = str2func(basename);
    set(handles.callback_txt, 'String', fullfile([pathname filename]));

    % Update handles structure
    guidata(hObject, handles);
    verify_callback_function(handles);
end

function savepath_Callback(hObject, eventdata, handles)
    % hObject    handle to save_txt (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    structure with handles and user data (see GUIDATA)

    % Hints: get(hObject,'String') returns contents of save_txt as text
    %        str2double(get(hObject,'String')) returns contents of save_txt as a double
end

function callback_txt_Callback(hObject, eventdata, handles)
    % hObject    handle to callback_txt (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    structure with handles and user data (see GUIDATA)

    % Hints: get(hObject,'String') returns contents of callback_txt as text
    %        str2double(get(hObject,'String')) returns contents of callback_txt as a double
    [path, file, ext] = fileparts(get(hObject, 'String'));

    if handles.callback_path
        rmpath(handles.callback_path);
    end

    addpath(path);
    handles.callback_path = path;
    handles.callback = str2func(file);

    % Update handles structure
    guidata(hObject, handles);
end

function verify_callback_function(handles)

    if handles.callback_path
        handles.callback(0, 'test');
    end

end

% --- Executes on button press in callback_clear_btn.
function callback_clear_btn_Callback(hObject, eventdata, handles)
    % hObject    handle to callback_clear_btn (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    structure with handles and user data (see GUIDATA)
    handles.callback_path = false;
    handles.callback = @(x, y) false;
    set(handles.callback_txt, 'String', '<None>');

    % Update handles structure
    guidata(hObject, handles);
end

% --- Executes when user attempts to close fipgui.
function fipgui_CloseRequestFcn(hObject, eventdata, handles)
    % hObject    handle to fipgui (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    structure with handles and user data (see GUIDATA)

    % Save settings for next time
    grp = handles.settingsGroup;
    setpref(grp, 'camport_pop', get(handles.camport_pop, 'Value'));
    setpref(grp, 'ref_pop', get(handles.ref_pop, 'Value'));
    setpref(grp, 'sig_pop', get(handles.sig_pop, 'Value'));
    setpref(grp, 'rate_txt', get(handles.rate_txt, 'String'));
    setpref(grp, 'cam_pop', get(handles.cam_pop, 'Value'));
    setpref(grp, 'savepath', get(handles.savepath, 'String'));
    setpref(grp, 'sunet_id', get(handles.sunet_id, 'String'));
    setpref(grp, 'experiment', get(handles.experiment, 'String'));
    setpref(grp, 'callback_txt', get(handles.callback_txt, 'String'));
    setpref(grp, 'ao_waveform_txt', get(handles.ao_waveform_txt, 'String'));
    setpref(grp, 'ai_logging_check', get(handles.ai_logging_check, 'Value'));

    % Hint: delete(hObject) closes the figure
    delete(hObject);
end

function uncloseable(src, callbackdata)
    % A dummy function that makes it impossible to close if used as the
    % CloseRequestFcn
    return
end

function closeable(src, callbackdata)
    % Does the right thing (closes the figure) if used as the CloseRequestFcn
    delete(src);
end

% --- Executes during object creation, after setting all properties.
function ao_waveform_txt_CreateFcn(hObject, eventdata, handles)
    % hObject    handle to ao_waveform_txt (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    empty - handles not created until after all CreateFcns called

    % Hint: edit controls usually have a white background on Windows.
    %       See ISPC and COMPUTER.
    if ispc && isequal(get(hObject, 'BackgroundColor'), get(0, 'defaultUicontrolBackgroundColor'))
        set(hObject, 'BackgroundColor', 'white');
    end

end

function ao_waveform_txt_Callback(hObject, eventdata, handles)
    % hObject    handle to ao_waveform_txt (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    structure with handles and user data (see GUIDATA)

    % Hints: get(hObject,'String') returns contents of ao_waveform_txt as text
    %        str2double(get(hObject,'String')) returns contents of ao_waveform_txt as a double
    [path, file, ext] = fileparts(get(hObject, 'String'));
    handles.ao_waveform_path = path;
    handles.ao_waveform_file = [file ext];

    % Update handles structure
    guidata(hObject, handles);
    verify_user_ao_waveform(handles);
end

% --- Executes on button press in ao_waveform_btn.
function ao_waveform_btn_Callback(hObject, eventdata, handles)
    % hObject    handle to ao_waveform_btn (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    structure with handles and user data (see GUIDATA)
    [filename, pathname] = uigetfile('ao_waveform.mat', 'Save AO waveform .mat file');
    handles.ao_waveform_path = pathname;
    handles.ao_waveform_file = filename;
    set(handles.ao_waveform_txt, 'String', fullfile([pathname filename]));
    % Update handles structure
    guidata(hObject, handles);
    verify_user_ao_waveform(handles);
end

% --- Executes on button press in ao_waveform_clear_btn.
function ao_waveform_clear_btn_Callback(hObject, eventdata, handles)
    % hObject    handle to ao_waveform_clear_btn (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    structure with handles and user data (see GUIDATA)
    handles.ao_waveform_path = false;
    handles.ao_waveform_file = false;
    set(handles.ao_waveform_txt, 'String', '<None>');

    % Update handles structure
    guidata(hObject, handles);
end

% --- Executes on button press in viewlog_btn.
function viewlog_btn_Callback(hObject, eventdata, handles)
    % hObject    handle to viewlog_btn (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    structure with handles and user data (see GUIDATA)
    [acquisitionDir, dataFile, metadataFile, calibFile, logAIFile] = get_save_details(handles);
    plotLogFile(logAIFile);
end

% --- Executes on button press in ai_logging_check.
function ai_logging_check_Callback(hObject, eventdata, handles)
    % hObject    handle to ai_logging_check (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    structure with handles and user data (see GUIDATA)
end

% Hint: get(hObject,'Value') returns toggle state of ai_logging_check
function is_enabled = ai_logging_is_enabled(handles)
    is_enabled = get(handles.ai_logging_check, 'Value');
end

function sunet_id_Callback(hObject, eventdata, handles)
    % hObject    handle to sunet_id (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    structure with handles and user data (see GUIDATA)

    % Hints: get(hObject,'String') returns contents of sunet_id as text
    %        str2double(get(hObject,'String')) returns contents of sunet_id as a double
end

% --- Executes during object creation, after setting all properties.
function sunet_id_CreateFcn(hObject, eventdata, handles)
    % hObject    handle to sunet_id (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    empty - handles not created until after all CreateFcns called

    % Hint: edit controls usually have a white background on Windows.
    %       See ISPC and COMPUTER.
    if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
        set(hObject,'BackgroundColor','white');
    end
end

function experiment_Callback(hObject, eventdata, handles)
    % hObject    handle to experiment (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    structure with handles and user data (see GUIDATA)

    % Hints: get(hObject,'String') returns contents of experiment as text
    %        str2double(get(hObject,'String')) returns contents of experiment as a double
end

% --- Executes during object creation, after setting all properties.
function experiment_CreateFcn(hObject, eventdata, handles)
    % hObject    handle to experiment (see GCBO)
    % eventdata  reserved - to be defined in a future version of MATLAB
    % handles    empty - handles not created until after all CreateFcns called

    % Hint: edit controls usually have a white background on Windows.
    %       See ISPC and COMPUTER.
    if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
        set(hObject,'BackgroundColor','white');
    end
end