			classdef MyDaq < handle
			properties
			%Contains GUI handles
			Gui;
			%Contains Reference trace (MyTrace object)
			Ref;
			%Contains Data trace (MyTrace object)
			Data;
			%Contains Background trace (MyTrace object)
			Background;
			%Cell containing MyInstrument objects
			Instruments;
			%Cell containing Cursor objects
			Cursors;
			%Struct containing MyFit objects
			Fits=struct();
			%Input parser
			Parser;
			%Listeners for deletion of MyFit objects
			ListenersDelete;
			%Listeners for new fits from MyFit objects
			ListenersNewFit;

			%Sets the colors of fits, data and reference
			fit_color='k';
			data_color='b';
			ref_color='r';

			%Properties for saving files
			base_dir;
			session_name;
			file_name;

			%Flag for enabling the GUI
			enable_gui;
			end

			properties (Dependent=true)
			save_dir;
			main_plot;
			end

			methods
			%Constructor function
			function this=MyDaq(varargin)
			createParser(this);
			parse(this.Parser,varargin{:});
			parseInputs(this);
			if this.enable_gui
			this.Gui=guihandles(eval('GuiDaq'));
			initGui(this);
			hold(this.main_plot,'on');
			end
			initDaq(this)
			end

			%Creates parser for constructor function
			function createParser(this)
			p=inputParser;
			addParameter(p,'enable_gui',1);
			this.Parser=p;
			end

			%Sets the class variables to the inputs from the inputParser.
			function parseInputs(this)
			for i=1:length(this.Parser.Parameters)
			%Takes the value from the inputParser to the appropriate
			%property.
			if isprop(this,this.Parser.Parameters{i})
			this.(this.Parser.Parameters{i})=...
			this.Parser.Results.(this.Parser.Parameters{i});
			end
			end
			end

			%Initializes the class depending on the computer name
			function initDaq(this)
			computer_name=getenv('computername');

			switch computer_name
			case 'LPQM1PCLAB2'
			initRt(this);
			case 'LPQM1PC18'
			initUhq(this);
			case 'LPQM1PC2'
			%Test case for testing on Nils' computer.
			otherwise
			error('Please create an initialization function for this computer')
			end

			%Initializes empty trace objects
			this.Ref=MyTrace;
			this.Data=MyTrace;
			this.Background=MyTrace;
			end

			%Sets callback functions for the GUI
			function initGui(this)
			set(this.Gui.BaseDir,'Callback',...
			@(hObject, eventdata) baseDirCallback(this, hObject, ...
			eventdata));
			set(this.Gui.SessionName,'Callback',...
			@(hObject, eventdata) sessionNameCallback(this, hObject, ...
			eventdata));
			set(this.Gui.FileName,'Callback',...
			@(hObject, eventdata) fileNameCallback(this, hObject, ...
			eventdata));
			set(this.Gui.SaveData,'Callback',...
			@(hObject, eventdata) saveDataCallback(this, hObject, ...
			eventdata));
			set(this.Gui.SaveRef,'Callback',...
			@(hObject, eventdata) saveRefCallback(this, hObject, ...
			eventdata));
			set(this.Gui.ShowData,'Callback',...
			@(hObject, eventdata) showDataCallback(this, hObject, ...
			eventdata));
			set(this.Gui.ShowRef,'Callback',...
			@(hObject, eventdata) showRefCallback(this, hObject, ...
			eventdata));
			set(this.Gui.DataToRef,'Callback',...
			@(hObject, eventdata) dataToRefCallback(this, hObject, ...
			eventdata));
			set(this.Gui.LogY,'Callback',...
			@(hObject, eventdata) logYCallback(this, hObject, ...
			eventdata));
			set(this.Gui.LogX,'Callback',...
			@(hObject, eventdata) logXCallback(this, hObject, ...
			eventdata));
			set(this.Gui.DataToBg,'Callback',...
			@(hObject, eventdata) dataToBgCallback(this, hObject, ...
			eventdata));
			set(this.Gui.RefToBg,'Callback',...
			@(hObject, eventdata) refToBgCallback(this, hObject, ...
			eventdata));
			set(this.Gui.ClearBg,'Callback',...
			@(hObject, eventdata) clearBgCallback(this, hObject, ...
			eventdata));
			set(this.Gui.AnalyzeMenu,'Callback',...
			@(hObject, eventdata) analyzeMenuCallback(this, hObject,...
			eventdata));
			set(this.Gui.AnalyzeMenu,'String',{'Select a routine...',...
			'Linear Fit','Quadratic Fit','Exponential Fit',...
			'Gaussian Fit','Lorentzian Fit'});
			end

			%Saves the data if the save data button is pressed.
			function saveDataCallback(this, ~, ~)
			save(this.Data,'save_dir',this.save_dir,'name',...
			genFileName(this))
			end

			%Saves the reference if the save ref button is pressed.
			function saveRefCallback(this, ~, ~)
			save(this.Ref,'save_dir',this.save_dir,'name',...
			genFileName(this))
			end

			%Generates appropriate file name for the save file.
			function savefile=genFileName(this)
			if get(this.Gui.AutoName,'Value')
			date_time = datestr(now,'yyyy-mm-dd_HH.MM.SS');
			else
			date_time='';
			end

			savefile=[this.file_name,date_time];
			end

			%Generates base_dir
			function baseDirCallback(this, hObject, ~)
			this.base_dir=get(hObject,'String');
			end

			%Toggle button callback for showing the data trace.
			function showDataCallback(this, hObject, ~)
			if get(hObject,'Value')
			set(hObject, 'BackGroundColor',[0,1,.2]);
			setVisible(this.Data,this.main_plot,1);
			else
			set(hObject, 'BackGroundColor',[0.941,0.941,0.941]);
			setVisible(this.Data,this.main_plot,0);
			end
			end

			%Toggle button callback for showing the ref trace
			function showRefCallback(this, hObject, ~)
			if get(hObject,'Value')
			set(hObject, 'BackGroundColor',[0,1,0.2]);
			setVisible(this.Ref,this.main_plot,1);
			else
			set(hObject, 'BackGroundColor',[0.941,0.941,0.941]);
			setVisible(this.Ref,this.main_plot,0);
			end
			end

			%Callback for moving the data to reference.
			function dataToRefCallback(this, hObject, ~)
			this.Ref.x=this.Data.x;
			this.Ref.y=this.Data.y;
			this.Ref.plotTrace(this.main_plot);
			this.Ref.setVisible(this.main_plot,1);
			set(this.Gui.ShowRef,'Value',1);
			set(this.Gui.ShowRef, 'BackGroundColor',[0,1,.2]);
			end

			%Callback for ref to bg button. Sends the reference to background
			function refToBgCallback(this, ~, ~)
			this.Background.x=this.Ref.x;
			this.Background.y=this.Ref.y;
			this.Background.plotTrace(this.main_plot);
			this.Background.setVisible(this.main_plot,1);
			end

			%Callback for data to bg button. Sends the data to background
			function dataToBgCallback(this, ~, ~)
			this.Background.x=this.Data.x;
			this.Background.y=this.Data.y;
			this.Background.plotTrace(this.main_plot);
			this.Background.setVisible(this.main_plot,1);
			end

			%Callback for clear background button. Clears the background
			function clearBgCallback(this, hObject, ~)
			this.Background.x=[];
			this.Background.y=[];
			this.Background.setVisible(this.main_plot,0);
			end

			%Callback for LogY button. Sets the YScale to log/lin
			function logYCallback(this, hObject, ~)
			if get(hObject,'Value')
			set(this.main_plot,'YScale','Log');
			set(hObject, 'BackGroundColor',[0,1,.2]);
			else
			set(this.main_plot,'YScale','Linear');
			set(hObject, 'BackGroundColor',[0.941,0.941,0.941]);
			end
			end

			%Callback for LogX button. Sets the XScale to log/lin
			function logXCallback(this, hObject, ~)
			if get(hObject,'Value')
			set(this.main_plot,'XScale','Log');
			set(hObject, 'BackGroundColor',[0,1,.2]);
			else
			set(this.main_plot,'XScale','Linear');
			set(hObject, 'BackGroundColor',[0.941,0.941,0.941]);
			end
			end

			%Callback for the analyze menu (popup menu for selecting fits).
			%Opens the correct MyFit object.
			function analyzeMenuCallback(this, hObject, ~)
			analyze_list=get(hObject,'String');
			analyze_ind=get(hObject,'Value');
			%Finds the correct fit name
			analyze_name=analyze_list{analyze_ind};
			analyze_name=analyze_name(1:(strfind(analyze_name,' ')-1));
			analyze_name=[upper(analyze_name(1)),analyze_name(2:end)];

			%Sees if the fit object is already open, if it is, changes the
			%focus to it, if not, opens it.
			if ismember(analyze_name,fieldnames(this.Fits))
			%Changes focus to the relevant fit window
			figure(this.Fits.(analyze_name).Gui.Window);
			elseif analyze_ind~=1
			%Makes an instance of MyFit with correct parameters.
			this.Fits.(analyze_name)=MyFit('fit_name',analyze_name,...
			'enable_plot',1,'plot_handle',this.main_plot,...
			'Data',this.Data);
			%Sets up a listener for the BeingDeleted event, which
			%removes the MyFit object from the Fits structure if it is
			%deleted.
			this.ListenersDelete.(analyze_name)=...
			addlistener(this.Fits.(analyze_name),'BeingDeleted',...
			@(src, eventdata) deleteFit(this, src, eventdata));
			%Sets up a listener for the NewFit. Callback plots the fit
			%on the main plot.
			this.ListenersNewFit.(analyze_name)=...
			addlistener(this.Fits.(analyze_name),'NewFit',...
			@(src, eventdata) plotNewFit(this, src, eventdata));
			end
			end

			%Callback for session name edit box. Sets the session name.
			function sessionNameCallback(this, hObject, ~)
			this.session_name=get(hObject,'String');
			end

			%Callback for filename edit box. Sets the file name.
			function fileNameCallback(this, hObject,~)
			this.file_name=get(hObject,'String');
			end

			%Callback function for NewFit listener. Plots the fit in the
			%window using the plotFit function of the MyFit object
			function plotNewFit(this, src, ~)
			src.plotFit('Color',this.fit_color);
			end

			%Callback function for BeingDeleted listener. Removes the relevant
			%field from the Fits struct.
			function deleteFit(this, src, ~)
			if ismember(src.fit_name, fieldnames(this.Fits))
			this.Fits=rmfield(this.Fits,src.fit_name);
			end
			end

			%Get function from save directory
			function save_dir=get.save_dir(this)
			save_dir=[this.base_dir,datestr(now,'yyyy-mm-dd '),...
			this.session_name,'\'];
			end

			%Get function for the plot handles
			function main_plot=get.main_plot(this)
			if this.enable_gui
			main_plot=this.Gui.figure1.CurrentAxes;
			else
			main_plot=[];
			end
			end
			end
			end

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