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iOS.m
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iOS.m
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function iOS(numConditions)
if ~exist('numConditions','var')
numConditions = 2;
end
% Initialize Saving
gd.Internal.save.path = 'D:\';
gd.Internal.save.base = '0000_c1c2';
gd.Internal.save.index = '1';
% Initialize Timing
gd.Experiment.timing.baselineDur = 2; %seconds
gd.Experiment.timing.stimDur = 4; %seconds
gd.Experiment.timing.postDur = 1; %seconds
gd.Experiment.timing.ITI = 25; %seconds
gd.Experiment.timing.numTrials = 35;
gd.Experiment.timing.avgFirst = 2.5; %seconds
gd.Experiment.timing.avgLast = 7; %seconds
% Initialize Stimulus
gd.Experiment.stim.frequency = 10; %hz
gd.Experiment.stim.wailDuration = 0.0499; %seconds
gd.Experiment.stim.voltage = 5; %volts
gd.Experiment.stim.bidirectional = true; %boolean
if numConditions == 1
gd.Internal.daq.piezos = table({true},{'Dev1'},{'ao0'},'VariableNames',{'Active','Device','Port'});
elseif numConditions == 2
gd.Internal.daq.piezos = table({true;true},{'Dev1';'Dev1'},{'ao0';'ao1'},'VariableNames',{'Active','Device','Port'});
end
% Initialize Imaging
gd.Internal.imaging.port = 'COM2';
gd.Internal.imaging.initFile = 'C:\Users\Adesnik\Documents\MATLAB\iOS\T_1m60_12-bits_2_tap_ext_trig.ccf';
gd.Internal.imaging.subsampleFactor = 1;
gd.Internal.imaging.dim = repmat(1024/gd.Internal.imaging.subsampleFactor,1,2);
gd.Experiment.imaging.frameRate = 59; %hz
gd.Experiment.imaging.numFrames2Avg = floor(59/2); % half second averaging of frames
gd.Experiment.GreenImage = zeros(gd.Internal.imaging.dim);
% Default Settings
gd.Experiment.Trial = [];
gd.Internal.daq.samplingFrequency = 30000;
gd.Internal.isRunning = false;
gd.Internal.viewHandle = [];
% Display parameters
gd.Internal.Display.units = 'normalized';
gd.Internal.Display.position = [.225, .15, .5, .75];
%% GREG'S SETTINGS
gd.Experiment.timing.baselineDur = 1; %seconds
gd.Experiment.timing.stimDur = 4; %seconds
gd.Experiment.timing.postDur = 2; %seconds
gd.Experiment.timing.ITI = 6; %seconds
gd.Experiment.timing.numTrials = 35;
gd.Experiment.timing.avgFirst = 2; %seconds
gd.Experiment.timing.avgLast = 7; %seconds
gd.Experiment.stim.frequency = 20; %hz
gd.Experiment.stim.wailDuration = 0.02; %seconds
gd.Experiment.stim.voltage = 5; %volts
gd.Experiment.stim.bidirectional = true; %boolean
%% Generate GUI
fprintf('Starting up...\n');
% Create figure
gd.gui.fig = figure(...
'NumberTitle', 'off',...
'Name', 'Intrinsic Optical Signal Imaging',...
'Units', gd.Internal.Display.units,...
'Position', gd.Internal.Display.position,...
'ToolBar', 'none',...
'MenuBar', 'none',...
'Visible', 'off');
% Panels
gd.gui.file.panel = uipanel(...
'Title', 'File Information',...
'Parent', gd.gui.fig,...
'Units', 'Normalized',...
'Position', [0, .9, 1, .1]);
gd.gui.control.panel = uipanel(...
'Title', 'Prep',...
'Parent', gd.gui.fig,...
'Units', 'Normalized',...
'Position', [0,0,.4,.6]);
gd.gui.timing.panel = uipanel(...
'Title', 'Timing',...
'Parent', gd.gui.fig,...
'Units', 'Normalized',...
'Position', [0,.6,.25,.3]);
gd.gui.stim.panel = uipanel(...
'Title', 'Stimulus',...
'Parent', gd.gui.fig,...
'Units', 'Normalized',...
'Position', [.25,.6,.35,.3]);
gd.gui.experiment.panel = uipanel(...
'Title', 'Experiment',...
'Parent', gd.gui.fig,...
'Units', 'Normalized',...
'Position', [.6,.6,.4,.3]);
for cindex = 1:numConditions
gd.gui.data(cindex).panel = uipanel(...
'Title', sprintf('Stimulus %d',cindex),...
'Parent', gd.gui.fig,...
'Units', 'Normalized',...
'Position', [.4,.6-cindex*.6/numConditions,.6,.6/numConditions]);
end
% File selection
% select directory
gd.gui.file.dir = uicontrol(...
'Style', 'pushbutton',...
'String', 'Dir',...
'Parent', gd.gui.file.panel,...
'Units', 'normalized',...
'Position', [0,0,.2,1],...
'Callback', @(hObject,eventdata)ChooseDir(hObject, eventdata, guidata(hObject)));
% basename input
gd.gui.file.base = uicontrol(...
'Style', 'edit',...
'String', gd.Internal.save.base,...
'Parent', gd.gui.file.panel,...
'Units', 'normalized',...
'Position', [.3,.4,.4,.6],...
'Callback', @(hObject,eventdata)CreateFilename(guidata(hObject),true));
gd.gui.file.baseText = uicontrol(...
'Style', 'text',...
'String', 'Basename',...
'Parent', gd.gui.file.panel,...
'Units', 'normalized',...
'Position', [.2,.4,.1,.6]);
% file index
gd.gui.file.index = uicontrol(...
'Style', 'edit',...
'String', gd.Internal.save.index,...
'Parent', gd.gui.file.panel,...
'Units', 'normalized',...
'Position', [.8,.4,.2,.6],...
'Callback', @(hObject,eventdata)CreateFilename(guidata(hObject),false));
gd.gui.file.indexText = uicontrol(...
'Style', 'text',...
'String', 'File Index',...
'Parent', gd.gui.file.panel,...
'Units', 'normalized',...
'Position', [.7,.4,.1,.6]);
% display filename
gd.gui.file.filename = uicontrol(...
'Style', 'text',...
'String', '',...
'Parent', gd.gui.file.panel,...
'Units', 'normalized',...
'Position', [.2,0,.8,.35]);
% Image control
% preview
gd.gui.control.preview = uicontrol(...
'Style', 'togglebutton',...
'String', 'Preview',...
'Parent', gd.gui.control.panel,...
'Units', 'normalized',...
'Position', [0,.9,.33,.1],...
'Callback', @(hObject,eventdata)PreviewImage(hObject, eventdata, guidata(hObject)));
% capture image
gd.gui.control.capture = uicontrol(...
'Style', 'pushbutton',...
'String', 'Capture Image',...
'Parent', gd.gui.control.panel,...
'Units', 'normalized',...
'Position', [.33,.9,.34,.1],...
'BackgroundColor', [0,1,0],...
'Callback', @(hObject,eventdata)CaptureImage(hObject, eventdata, guidata(hObject)));
% select ROI
gd.gui.control.ROI = uicontrol(...
'Style', 'togglebutton',...
'String', 'Select ROI',...
'Parent', gd.gui.control.panel,...
'Units', 'normalized',...
'Position', [.67,.9,.33,.1],...
'Enable', 'off',...
'Callback', @(hObject,eventdata)SelectROI(hObject, eventdata, guidata(hObject)));
% axis
gd.gui.control.axes = axes(...
'Parent', gd.gui.control.panel,...
'Units', 'normalized',...
'UserData', cindex,...
'Position', [0,0,1,.9]);
axis off
% Timing control
% Baseline duration
gd.gui.timing.baselineDur = uicontrol(...
'Style', 'edit',...
'Parent', gd.gui.timing.panel,...
'String', gd.Experiment.timing.baselineDur,...
'Units', 'normalized',...
'Position', [.7,.85,.3,.15],...
'UserData', {'timing','baselineDur', 0, []},...
'Callback', @(hObject,eventdata)ChangeStim(hObject, eventdata, guidata(hObject)));
gd.gui.timing.baselineDurText = uicontrol(...
'Style', 'text',...
'Parent', gd.gui.timing.panel,...
'String', 'Baseline (s)',...
'HorizontalAlignment', 'right',...
'Units', 'normalized',...
'Position', [0,.85,.65,.1]);
% Stimulus duration
gd.gui.timing.stimDur = uicontrol(...
'Style', 'edit',...
'Parent', gd.gui.timing.panel,...
'String', gd.Experiment.timing.stimDur,...
'Units', 'normalized',...
'Position', [.7,.7,.3,.15],...
'UserData', {'timing','stimDur', 0.001, []},...
'Callback', @(hObject,eventdata)ChangeStim(hObject, eventdata, guidata(hObject)));
gd.gui.timing.stimDurText = uicontrol(...
'Style', 'text',...
'Parent', gd.gui.timing.panel,...
'String', 'Stimulus (s)',...
'HorizontalAlignment', 'right',...
'Units', 'normalized',...
'Position', [0,.7,.65,.1]);
% Post stimulus duration
gd.gui.timing.postDur = uicontrol(...
'Style', 'edit',...
'Parent', gd.gui.timing.panel,...
'String', gd.Experiment.timing.postDur,...
'Units', 'normalized',...
'Position', [.7,.55,.3,.15],...
'UserData', {'timing','postDur', 0, []},...
'Callback', @(hObject,eventdata)ChangeStim(hObject, eventdata, guidata(hObject)));
gd.gui.timing.postDurText = uicontrol(...
'Style', 'text',...
'Parent', gd.gui.timing.panel,...
'String', 'Post-Stim (s)',...
'HorizontalAlignment', 'right',...
'Units', 'normalized',...
'Position', [0,.55,.65,.1]);
% ITI
gd.gui.timing.ITI = uicontrol(...
'Style', 'edit',...
'Parent', gd.gui.timing.panel,...
'String', gd.Experiment.timing.ITI,...
'Units', 'normalized',...
'Position', [.7,.4,.3,.15],...
'UserData', {'timing','ITI', 0, []},...
'Callback', @(hObject,eventdata)ChangeStim(hObject, eventdata, guidata(hObject)));
gd.gui.timing.ITIText = uicontrol(...
'Style', 'text',...
'Parent', gd.gui.timing.panel,...
'String', 'ITI (s)',...
'HorizontalAlignment', 'right',...
'Units', 'normalized',...
'Position', [0,.4,.65,.1]);
% Frames to average
gd.gui.timing.avgFirst = uicontrol(...
'Style', 'edit',...
'Parent', gd.gui.timing.panel,...
'String', gd.Experiment.timing.avgFirst,...
'Units', 'normalized',...
'Position', [.4,.15,.3,.15],...
'UserData', {'timing','avgFirst', 0, []},...
'Callback', @(hObject,eventdata)ChangeStim(hObject, eventdata, guidata(hObject)));
gd.gui.timing.avgLast = uicontrol(...
'Style', 'edit',...
'Parent', gd.gui.timing.panel,...
'String', gd.Experiment.timing.avgLast,...
'Units', 'normalized',...
'Position', [.7,.15,.3,.15],...
'UserData', {'timing','avgLast', 0, []},...
'Callback', @(hObject,eventdata)ChangeStim(hObject, eventdata, guidata(hObject)));
gd.gui.experiment.avgText = uicontrol(...
'Style', 'text',...
'Parent', gd.gui.timing.panel,...
'String', 'Average (s)',...
'HorizontalAlignment', 'center',...
'Units', 'normalized',...
'Position', [0,.15,.4,.1]);
% Frame rate
gd.gui.timing.frameRate = uicontrol(...
'Style', 'edit',...
'Parent', gd.gui.timing.panel,...
'String', gd.Experiment.imaging.frameRate,...
'Units', 'normalized',...
'Position', [.7,0,.3,.15],...
'UserData', {'imaging','frameRate', 0, 59},...
'Callback', @(hObject,eventdata)ChangeStim(hObject, eventdata, guidata(hObject)));
gd.gui.timing.frameRateText = uicontrol(...
'Style', 'text',...
'Parent', gd.gui.timing.panel,...
'String', 'Frame Rate (Hz)',...
'HorizontalAlignment', 'right',...
'Units', 'normalized',...
'Position', [0,0,.65,.1]);
% Stimulus control
% Piezo toggle
gd.gui.stim.piezos = uitable(...
'Parent', gd.gui.stim.panel,...
'Units', 'normalized',...
'Position', [0,.6,1,.4],...
'ColumnName', {'Active?','Device','Port'},...
'ColumnEditable', [true, false, false],...
'ColumnFormat', {'logical','char','char','char'},...
'ColumnWidth', {50,50,75,50},...
'Data', table2cell(gd.Internal.daq.piezos));
% stimulus frequency
gd.gui.stim.frequency = uicontrol(...
'Style', 'edit',...
'Parent', gd.gui.stim.panel,...
'String', gd.Experiment.stim.frequency,...
'Units', 'normalized',...
'Position', [.35,.4,.15,.15],...
'UserData', {'stim','frequency', 0, []},...
'Callback', @(hObject,eventdata)ChangeStim(hObject, eventdata, guidata(hObject)));
gd.gui.stim.frequencyText = uicontrol(...
'Style', 'text',...
'Parent', gd.gui.stim.panel,...
'String', 'Frequency',...
'HorizontalAlignment', 'right',...
'Units', 'normalized',...
'Position', [0,.4,.35,.1]);
% voltage
gd.gui.stim.voltage = uicontrol(...
'Style', 'edit',...
'Parent', gd.gui.stim.panel,...
'String', gd.Experiment.stim.voltage,...
'Units', 'normalized',...
'Position', [.85,.4,.15,.15],...
'UserData', {'stim','voltage', 0, 5},...
'Callback', @(hObject,eventdata)ChangeStim(hObject, eventdata, guidata(hObject)));
gd.gui.stim.voltageText = uicontrol(...
'Style', 'text',...
'Parent', gd.gui.stim.panel,...
'String', 'Voltage',...
'HorizontalAlignment', 'right',...
'Units', 'normalized',...
'Position', [.5,.4,.35,.1]);
% wail duration
gd.gui.stim.wailDuration = uicontrol(...
'Style', 'edit',...
'Parent', gd.gui.stim.panel,...
'String', gd.Experiment.stim.wailDuration,...
'Units', 'normalized',...
'Position', [.35,.2,.15,.15],...
'UserData', {'stim','wailDuration', 0.02, []},...
'Callback', @(hObject,eventdata)ChangeStim(hObject, eventdata, guidata(hObject)));
gd.gui.stim.wailDurationText = uicontrol(...
'Style', 'text',...
'Parent', gd.gui.stim.panel,...
'String', 'Wail Duration',...
'HorizontalAlignment', 'right',...
'Units', 'normalized',...
'Position', [0,.2,.35,.1]);
% bidirectional toggle
gd.gui.stim.bidirectional = uicontrol(...
'Style', 'checkbox',...
'Parent', gd.gui.stim.panel,...
'Value', gd.Experiment.stim.bidirectional,...
'Units', 'normalized',...
'Position', [.9,.2,.1,.15],...
'Callback', @(hObject,eventdata)ChangeWail(hObject, eventdata, guidata(hObject)));
gd.gui.stim.bidirectionalText = uicontrol(...
'Style', 'text',...
'Parent', gd.gui.stim.panel,...
'String', 'Bidirectional',...
'HorizontalAlignment', 'right',...
'Units', 'normalized',...
'Position', [.5,.2,.35,.1]);
% View triggers
gd.gui.stim.view = uicontrol(...
'Style', 'togglebutton',...
'String', 'View',...
'Parent', gd.gui.stim.panel,...
'Units', 'normalized',...
'Position', [0,0,.5,.2],...
'Callback', @(hObject,eventdata)ViewTriggers(hObject, eventdata, guidata(hObject)));
% Test stimuli
gd.gui.stim.test = uicontrol(...
'Style', 'togglebutton',...
'String', 'Test',...
'Parent', gd.gui.stim.panel,...
'Units', 'normalized',...
'Position', [.5,0,.5,.2],...
'Callback', @(hObject,eventdata)TestTriggers(hObject, eventdata, guidata(hObject)));
% Experiment control
% Link
gd.gui.experiment.link = uicontrol(...
'Style', 'checkbox',...
'Parent', gd.gui.experiment.panel,...
'String', 'Link?',...
'Units', 'normalized',...
'Position', [0,.85,.5,.15],...
'Enable', 'off',...
'Value', true,...
'Callback', @(hObject,eventdata)Link(hObject, eventdata, guidata(hObject)));
if numConditions == 1
set(gd.gui.experiment.link,'Visible','off');
end
% Number of Trials
gd.gui.experiment.numTrials = uicontrol(...
'Style', 'edit',...
'Parent', gd.gui.experiment.panel,...
'String', gd.Experiment.timing.numTrials,...
'Units', 'normalized',...
'Position', [.7,.85,.3,.15],...
'UserData', {'timing','numTrials', 1, []},...
'Callback', @(hObject,eventdata)ChangeStim(hObject, eventdata, guidata(hObject)));
gd.gui.experiment.numTrialsText = uicontrol(...
'Style', 'text',...
'Parent', gd.gui.experiment.panel,...
'String', '# Trials',...
'HorizontalAlignment', 'right',...
'Units', 'normalized',...
'Position', [.5,.85,.2,.1]);
% Run experiment
gd.gui.experiment.run = uicontrol(...
'Style', 'togglebutton',...
'String', 'Run',...
'Parent', gd.gui.experiment.panel,...
'Units', 'normalized',...
'Position', [0,.5,1,.35],...
'Enable', 'off',...
'Callback', @(hObject,eventdata)RunExperiment(hObject, eventdata, guidata(hObject)));
% Restart experiment
gd.gui.experiment.restart = uicontrol(...
'Style', 'togglebutton',...
'String', 'Restart',...
'Parent', gd.gui.experiment.panel,...
'Units', 'normalized',...
'Position', [0,.25,1,.25],...
'Enable', 'off');
% Identify centroids
gd.gui.experiment.save = uicontrol(...
'Style', 'pushbutton',...
'String', 'Save & Mark',...
'Parent', gd.gui.experiment.panel,...
'Units', 'normalized',...
'Position', [0,0,1,.25],...
'Enable', 'off',...
'Callback', @(hObject,eventdata)Save(hObject, eventdata, guidata(hObject)));
% Data Displays
for cindex = 1:numConditions
% second axes
gd.gui.data(cindex).axesImg = axes(...
'Parent', gd.gui.data(cindex).panel,...
'Units', 'normalized',...
'UserData', cindex,...
'Position', [0,.2,.5,.8]);
axis off
% select frame slider
gd.gui.data(cindex).slider = uicontrol(...
'Style', 'slider',...
'Parent', gd.gui.data(cindex).panel,...
'Units', 'normalized',...
'Position', [.1,.1,.4,.1],...
'UserData', cindex,...
'Enable', 'off',...
'Callback', @(hObject,eventdata)ChangeImage(hObject, eventdata, guidata(hObject)));
gd.gui.data(cindex).sliderText = uicontrol(...
'Style', 'text',...
'String', '',...
'Parent', gd.gui.data(cindex).panel,...
'Units', 'normalized',...
'UserData', cindex,...
'Enable', 'off',...
'Position', [0,.1,.09,.1]);
% set first button
gd.gui.data(cindex).first = uicontrol(...
'Style', 'pushbutton',...
'String', 'First',...
'Parent', gd.gui.data(cindex).panel,...
'Units', 'normalized',...
'Position', [0,0,.25,.1],...
'UserData', {cindex,'first',[]},...
'Enable', 'off',...
'Callback', @(hObject,eventdata)SetMean(hObject, eventdata, guidata(hObject)));
% button to set last
gd.gui.data(cindex).last = uicontrol(...
'Style', 'pushbutton',...
'String', 'Last',...
'Parent', gd.gui.data(cindex).panel,...
'Units', 'normalized',...
'Position', [.25,0,.25,.1],...
'UserData', {cindex,'last',[]},...
'Enable', 'off',...
'Callback', @(hObject,eventdata)SetMean(hObject, eventdata, guidata(hObject)));
% mean axes
gd.gui.data(cindex).axesMean = axes(...
'Parent', gd.gui.data(cindex).panel,...
'Units', 'normalized',...
'UserData', cindex,...
'Position', [.5,0,.5,1]);
axis off
end
try
gd = initCamera(gd); % initialize camera
CreateFilename(gd,false); % create initial filename
set(gd.gui.fig,'Visible','on')
catch
CreateFilename(gd,false); % create initial filename
set(gd.gui.fig,'Visible','on')
error('Camera not found -> try restarting MATLAB (figure visible only for testing)');
end
end
%% File Saving
function ChooseDir(hObject, eventdata, gd)
temp = uigetdir(gd.Internal.save.path, 'Choose directory to save to');
if ischar(temp)
gd.Internal.save.path = temp;
guidata(hObject, gd);
end
CreateFilename(gd,true);
end
function gd = CreateFilename(gd,reset)
% Create filename
gd.Internal.save.basename = fullfile(gd.Internal.save.path, get(gd.gui.file.base,'String'));
gd.Internal.save.filename = strcat(gd.Internal.save.basename, '_', get(gd.gui.file.index,'String'));
set(gd.gui.file.filename,'String',gd.Internal.save.filename);
% Determine if green image exists
if ~isempty(dir([gd.Internal.save.basename,'*']))
gd.Experiment.GreenImage = imread([gd.Internal.save.basename,'_green_image.tif']);
set(gd.gui.control.capture,'BackgroundColor',[.94,.94,.94]);
set(gd.gui.experiment.run,'Enable','on','BackgroundColor',[0,1,0]);
axes(gd.gui.control.axes);
if ~isempty(gd.gui.control.ROI.UserData)
gd.gui.control.ROI.UserData = getPosition(gd.gui.control.ROI.UserData);
imagesc(gd.Experiment.GreenImage); % display green image
gd=placeROI(gd);
else
imagesc(gd.Experiment.GreenImage); % display green image
end
axis off; colormap gray;
set(gd.gui.control.ROI,'Enable','on');
else
set(gd.gui.control.capture,'BackgroundColor',[0,1,0]);
set(gd.gui.experiment.run,'Enable','off','BackgroundColor',[.94,.94,.94]);
gd.Experiment.GreenImage = [];
axes(gd.gui.control.axes);
imagesc(zeros(gd.Internal.imaging.dim)); % display green image
axis off; colormap gray;
end
if reset
set(gd.gui.control.ROI,'Value',false,'UserData',[],'String','Select ROI');
end
guidata(gd.gui.fig, gd);
% Check if file exists
if ~isempty(dir([gd.Internal.save.filename,'*']))
set(gd.gui.file.filename,'BackgroundColor',[1,0,0]);
else
set(gd.gui.file.filename,'BackgroundColor',[.94,.94,.94]);
end
end
%% Prep
function gd = initCamera(gd)
% Initialize camera
gd.Internal.imaging.vid = videoinput('dalsa', 1, gd.Internal.imaging.initFile);
gd.Internal.imaging.src = getselectedsource(gd.Internal.imaging.vid);
gd.Internal.imaging.vid.FramesPerTrigger = 1;
gd.Internal.imaging.vid.TriggerRepeat = Inf; %set number of triggers to expect. set to Inf so any number of frames can be captured
triggerconfig(gd.Internal.imaging.vid, 'hardware', 'risingEdge-ttl', 'automatic'); %set camera to be triggered on rising edge of ttl pulse
cam_serial_cmmd(gd.Internal.imaging.port,'sem 3');
cam_serial_cmmd(gd.Internal.imaging.port,'sec 0');
mssg = cam_serial_cmmd(gd.Internal.imaging.port,'gcp');
sem_check = 0;
sec_check = 0;
for k = 1:numel(mssg)
if regexp(mssg{k},'Exposure Control.*disabled') %'.' = any single character, '*' = 0 or more times consecutively)
sec_check = 1;
disp('Exposure Control Set to ''disabled''')
elseif regexp(mssg{k},'Exposure Mode.*3')
sem_check = 1;
disp('Exposure Mode set to ''3''')
end
end
if sem_check == 0
error('iOS:camExpMode','Could not change camera to proper external tirgger mode (mode 3)')
elseif sec_check == 0
error('iOS:camExpControl','Could not set camera exposure control to disabled')
end
end
function PreviewImage(hObject, eventdata, gd)
if get(hObject,'Value') % start preview
% Update GUI
set(gd.gui.experiment.panel,'Visible','off');
set([gd.gui.control.capture,gd.gui.control.ROI],'Enable','off');
set(hObject,'String','Stop Preview','BackgroundColor',[0,0,0],'ForegroundColor',[1,1,1]);
if ~isempty(gd.gui.control.ROI.UserData)
gd.gui.control.ROI.UserData = getPosition(gd.gui.control.ROI.UserData); % save ROI info
end
% Display stream
temp_img = zeros(gd.Internal.imaging.vid.Videoresolution); % initialize image
hImage = image(temp_img,'Parent',gd.gui.control.axes); % initialize handle
pos = get(gd.gui.fig,'Position');
figure('Units','normalized','Position',[pos(1)+.21,pos(2),.3,.3]);
h = axes;
set(gd.Internal.imaging.vid,'UserData',h); % set histogram axis
setappdata(hImage,'UpdatePreviewWindowFcn',@iOS_update_livehistogram_display);
preview(gd.Internal.imaging.vid,hImage); % start preview
else % stop preview
set(hObject,'String','Stopping...'); drawnow;
stoppreview(gd.Internal.imaging.vid); % stop preview
h = get(gd.Internal.imaging.vid,'UserData');
if ishghandle(h)
delete(get(h,'Parent')); % delete histogram figure
end
axes(gd.gui.control.axes);
if ~isempty(gd.Experiment.GreenImage)
imagesc(gd.Experiment.GreenImage); %display subsampled image (so ROI has right dimensions)
else
imagesc(zeros(gd.Internal.imaging.dim));
end
axis off;
if ~isempty(gd.gui.control.ROI.UserData)
placeROI(gd);
end
set(gd.gui.experiment.panel,'Visible','on');
set([gd.gui.control.capture,gd.gui.control.ROI],'Enable','on');
set(hObject,'String','Preview','BackgroundColor',[.94,.94,.94],'ForegroundColor',[0,0,0]);
end
end
function iOS_update_livehistogram_display(obj,event,hImage)
set(hImage,'CData',event.Data);
axes(get(gcbo,'UserData'));
counts = imhist(event.Data);
imhist(event.Data)
% ylim([0 255^2])
perc_255 = (counts(end)/sum(counts))*100;
perc_254 = (counts(end-1)/sum(counts))*100;
img_mean = mean2(event.Data);
ymax = max(ylim)-max(ylim)*0.1;
hold on
text(25,ymax,['perc @ 255: ' num2str(perc_255)])
text(25,ymax-ymax*0.1,['perc @ 254: ' num2str(perc_254)])
text(25,ymax-ymax*0.2,['mean: ' num2str(img_mean)])
hold off
drawnow
end
function CaptureImage(hObject, eventdata, gd)
set(hObject,'String','Capturing...'); drawnow;
if ~isempty(gd.gui.control.ROI.UserData)
gd.gui.control.ROI.UserData = getPosition(gd.gui.control.ROI.UserData); % save ROI info
end
axes(gd.gui.control.axes);
img = captureSingleFrame(gd);
gd.Experiment.GreenImage = img(1:gd.Internal.imaging.subsampleFactor:end,1:gd.Internal.imaging.subsampleFactor:end);
axes(gd.gui.control.axes);
imagesc(gd.Experiment.GreenImage); % display subsampled image (so ROI has right dimensions)
axis off;
if ~isempty(gd.gui.control.ROI.UserData)
placeROI(gd);
end
guidata(hObject,gd);
imwrite(gd.Experiment.GreenImage,strcat(gd.Internal.save.basename,'_','green_image.tif')); %save to file (overwrites any previous image)
set(hObject,'String','Capture Image','BackgroundColor',[.94,.94,.94]);
set(gd.gui.control.ROI,'Enable','on');
set(gd.gui.experiment.run,'Enable','on','BackgroundColor',[0,1,0]);
end
function img = captureSingleFrame(gd)
temp_img = zeros(get(gd.Internal.imaging.vid,'Videoresolution')); %initialize image
hImage = image(temp_img,'Parent',gd.gui.control.axes); %initialize handle
flushdata(gd.Internal.imaging.vid) %remove any previous data
triggerconfig(gd.Internal.imaging.vid, 'manual'); %change trigger
preview(gd.Internal.imaging.vid,hImage); %preview image
start(gd.Internal.imaging.vid); %start recording
pause(0.100) %ensures recording started
trigger(gd.Internal.imaging.vid); %manually trigger frame
pause(0.100) %for some reason no data is collected if there is no pause. this is what makes it work!!!
stoppreview(gd.Internal.imaging.vid); %stop preview
stop(gd.Internal.imaging.vid); %stop recording
triggerconfig(gd.Internal.imaging.vid, 'hardware', 'risingEdge-ttl', 'automatic'); %change trigger back to external
vid_data = getdata(gd.Internal.imaging.vid); %collect recorded frame
img = uint8(single(vid_data)/(2^12-1)*(2^8-1)); %convert frame to uint8
end
function SelectROI(hObject, eventdata, gd)
if get(hObject,'Value')
placeROI(gd);
set(hObject,'String','Delete ROI');
else
delete(gd.gui.control.ROI.UserData);
gd.gui.control.ROI.UserData = [];
if ~isempty(gd.Experiment.Trial)
if get(gd.gui.experiment.link,'Value')
UpdatePlots(1,gd);
else
for cindex = 1:gd.Experiment.numStim
UpdatePlots(cindex,gd);
end
end
end
set(hObject,'String','Select ROI');
end
end
function gd = placeROI(gd)
axes(gd.gui.control.axes)
fcn = makeConstrainToRectFcn('impoly',get(gd.gui.control.axes,'XLim'),get(gd.gui.control.axes,'YLim'));
if isempty(gd.gui.control.ROI.UserData)
gd.gui.control.ROI.UserData = impoly(gd.gui.control.axes,'Closed',1,'PositionConstraintFcn',fcn);
else
gd.gui.control.ROI.UserData = impoly(gd.gui.control.axes,gd.gui.control.ROI.UserData,'Closed',1,'PositionConstraintFcn',fcn);
end
addNewPositionCallback(gd.gui.control.ROI.UserData,@MoveROI);
if ~isempty(gd.Experiment.Trial)
if get(gd.gui.experiment.link,'Value')
UpdatePlots(1,gd);
else
for cindex = 1:gd.Experiment.numStim
UpdatePlots(cindex,gd);
end
end
end
end
function MoveROI(pos)
h = get(gco,'Parent');
gd = guidata(h);
if ~isempty(gd.Experiment.Trial)
if get(gd.gui.experiment.link,'Value')
UpdatePlots(1,gd);
else
for cindex = 1:gd.Experiment.numStim
UpdatePlots(cindex,gd);
end
end
end
end
%% Stimuli
function ChangeStim(hObject, eventdata, gd)
newValue = str2num(get(hObject,'String'));
UD = get(hObject,'UserData');
if isempty(newValue) % not a number
set(hObject,'String',gd.Experiment.(hObject.UserData{1}).(hObject.UserData{2}));
elseif ~isempty(UD{3}) && newValue < UD{3} % lower bound
set(hObject,'String',UD{3});
gd.Experiment.(UD{1}).(UD{2}) = UD{3};
guidata(hObject,gd);
elseif ~isempty(UD{4}) && newValue > UD{4} % upper bound
set(hObject,'String',UD{4});
gd.Experiment.(UD{1}).(UD{2}) = UD{4};
guidata(hObject,gd);
else % valid input
gd.Experiment.(UD{1}).(UD{2}) = newValue;
guidata(hObject, gd);
end
if get(gd.gui.stim.view,'Value')
ViewTriggers(gd.gui.stim.view, [], gd);
end
end
function ChangeWail(hObject, eventdata, gd)
gd.Experiment.stim.bidirectional = get(hObject,'Value');
guidata(hObject,gd);
if get(gd.gui.stim.view,'Value')
ViewTriggers(gd.gui.stim.view, [], gd);
end
end
function ViewTriggers(hObject, eventdata, gd)
if get(hObject,'Value')
gd=refresh(gd); % update inputs
Fs = gd.Internal.daq.samplingFrequency;
Triggers = generateTriggers(gd);
if isempty(gd.Internal.viewHandle) || ~ishghandle(gd.Internal.viewHandle) % figure doesn't exist
pos = get(gd.gui.fig,'OuterPosition');
pos2 = get(gd.gui.stim.panel,'Position');
pos = [pos(1),.1,pos(3),pos(2)+pos(4)*pos2(2)-.11];
gd.Internal.viewHandle = figure('NumberTitle','off','Name','Single Trial Triggers',...
'Units','normalized','OuterPosition',pos);
guidata(hObject,gd);
else
figure(gd.Internal.viewHandle);
end
cla; hold on;
Color = {'r','b','g','c'};
x = [0,gd.Experiment.timing.baselineDur];
y = [min(Triggers(:)),max(Triggers(:))];
patch(x([1,1,2,2]),[y,flip(y)],Color{4},'EdgeAlpha',0,'FaceAlpha',.2);
x = [gd.Experiment.timing.avgFirst,gd.Experiment.timing.avgLast];
patch(x([1,1,2,2]),[y,flip(y)],Color{3},'EdgeAlpha',0,'FaceAlpha',.2);
x = 0:1/Fs:(size(Triggers,1)-1)/Fs;
for index = 1:2
plot(x,Triggers(:,index),Color{index});
end
axis tight
ylabel('Voltage');
xlabel('Time (s)');
legend('Baseline','Avg Period','Piezo','Camera');
hold off;
else
if ~isempty(gd.Internal.viewHandle) && ishghandle(gd.Internal.viewHandle) % figure doesn't exist
delete(gd.Internal.viewHandle);
end
end
end
function TestTriggers(hObject, eventdata, gd)
if get(hObject,'Value')
DAQ = daq.createSession('ni');
DAQ.Rate = gd.Internal.daq.samplingFrequency;
PD = get(gd.gui.stim.piezos,'Data');
ActivePiezos = [PD{:,1}];
if ~any(ActivePiezos)
set(hObject,'Value',false);
error('Requires at least one active piezo!');
end
for index = find(ActivePiezos)
[~,id] = DAQ.addAnalogOutputChannel(gd.Internal.daq.piezos.Device{index},gd.Internal.daq.piezos.Port{index},'Voltage');
DAQ.Channels(id).Name = sprintf('O_Piezo%d',index);
end
Triggers = generateTriggers(gd);
Triggers = repmat(Triggers(:,1),1,nnz(ActivePiezos));
set(hObject,'String','Testing...'); drawnow;
while get(hObject,'Value')
DAQ.queueOutputData(Triggers);
DAQ.startForeground;
if ~get(hObject,'Value')
break
end
end
clear DAQ;
set(hObject,'String','Test');
else
set(hObject,'String','Stopping...'); drawnow;
end
end
function Triggers = generateTriggers(gd)
t = gd.Experiment.timing;
s = gd.Experiment.stim;
Fs = gd.Internal.daq.samplingFrequency;
Fr = gd.Experiment.imaging.frameRate;
% Initialize Triggers
trialDuration = t.baselineDur + t.stimDur + t.postDur;
numScansPerTrial = round(trialDuration*Fs);
Triggers = zeros(numScansPerTrial,2);
% Build piezo triggers
piezoTrigs = generatePiezoTrig(s.wailDuration, s.bidirectional, s.frequency, ceil(t.stimDur*Fs), Fs);
piezoTrigs = piezoTrigs*s.voltage; % scale to proper voltage
startTrig = round(t.baselineDur*Fs)+1;
endTrig = startTrig+numel(piezoTrigs)-1;
Triggers(startTrig:endTrig,1) = piezoTrigs;
% Add camera triggers
Triggers(1:ceil(Fs/Fr):end,2) = 1;
end
function trig = generatePiezoTrig(duration, bidirectional, freq, numScans, Fs)
% Create half wave
f = 1/duration;
t = (0:1/Fs:duration/2)';
halfwave = -0.5*cos(2*pi*f*t)+0.5;
% Create wave
if ~bidirectional
wave = [halfwave;flip(halfwave)];
else
% Create full wave
f = 1/(2*duration);
t = (0:1/Fs:duration)';
midwave = cos(2*pi*f*t);
wave = [halfwave;midwave;-flip(halfwave)];
end
% Determine if duration of wave is longer than single period for desired frequency
numScansPerWail = round(1/freq*Fs);
stim_lag = numScansPerWail - numel(wave);
if stim_lag < 0 %wave is longer than single period
warning('Wail duration parameter is longer than single period for desired frequency. Frequency will set to the maximum frequency allowed with the given duration.');
stim_lag = 0;
end
% Build single wail
single_stim = [wave;zeros(stim_lag,1)]; %single period
numScansPerWail = numel(single_stim);
% Build for entire duraiton
numWails = floor(numScans/numScansPerWail);
trig = repmat(single_stim,numWails,1);
end
function gd=refresh(gd)
gd.Experiment.timing.baselineDur = str2double(get(gd.gui.timing.baselineDur,'String'));
gd.Experiment.timing.stimDur = str2double(get(gd.gui.timing.stimDur,'String'));
gd.Experiment.timing.postDur = str2double(get(gd.gui.timing.postDur,'String'));
gd.Experiment.timing.ITI = str2double(get(gd.gui.timing.ITI,'String'));
end
%% Experiment
function RunExperiment(hObject, eventdata, gd)
if get(hObject,'Value')
%% Check if any piezos are active
PD = get(gd.gui.stim.piezos,'Data');
ActivePiezos = [PD{:,1}];
if ~any(ActivePiezos)
set(hObject,'Value',false);
error('No piezos active -> at least one piezo needs to be active');
end
%% Determine filename to save to
if exist([gd.Internal.save.filename,'.mat'], 'file')
answer = questdlg(sprintf('File already exists! Continue?\n%s', gd.Internal.save.filename), 'Overwrite file?', 'Yes', 'No', 'No');
if strcmp(answer, 'No')
set(hObject,'Value',false);
return
end
end
%% Update GUI
set(hObject,'String','Stop','BackgroundColor',[0,1,0]);
gd.Experiment.numStim = nnz(ActivePiezos);
set(gd.gui.experiment.save,'BackgroundColor',[.94,.94,.94]);
set([gd.gui.control.preview,gd.gui.control.capture,gd.gui.experiment.save],'Enable','off');
set(gd.gui.experiment.restart,'Enable','on');
if gd.Experiment.numStim>1
set(gd.gui.experiment.link,'Enable','on');
end
gd.Internal.isRunning = true;
guidata(hObject,gd);
%% Initialize DAQ
Fs = gd.Internal.daq.samplingFrequency;
% Initialize DAQ
DAQ = daq.createSession('ni');
DAQ.Rate = Fs;
% Piezos
for index = find(ActivePiezos)
[~,id] = DAQ.addAnalogOutputChannel(gd.Internal.daq.piezos.Device{index},gd.Internal.daq.piezos.Port{index},'Voltage');
DAQ.Channels(id).Name = sprintf('O_Piezo%d',index);
end
% Camera
[~,id]=DAQ.addDigitalChannel('Dev1','port0/line0','OutputOnly'); % camera trigger
DAQ.Channels(id).Name = 'O_CameraTrigger';
%% Create Triggers
% Initialize Experiment struct
gd.Experiment.filename = gd.Internal.save.filename; % record file saved to
gd.Experiment.timing.init = datestr(now); % record date & time information
% Create triggers
gd = refresh(gd); % update inputs
Triggers = generateTriggers(gd);
totalFrames = sum(Triggers(:,2)==1);
frameTime = find(Triggers(:,2)==1)/Fs;
badFrames = frameTime < .150; % camera doesn't expose fully until after ~150ms
numBadFrames = nnz(badFrames);
numFrames = floor((totalFrames-numBadFrames)/gd.Experiment.imaging.numFrames2Avg);
lastFrameIndex = totalFrames - rem(totalFrames-numBadFrames,gd.Experiment.imaging.numFrames2Avg);
% Determine frames to average over for baseline and stim