diff --git a/@MyDaq/MyDaq.m b/@MyDaq/MyGeneralPlot.m
similarity index 97%
rename from @MyDaq/MyDaq.m
rename to @MyDaq/MyGeneralPlot.m
index db5d5b8..7dcad9b 100644
--- a/@MyDaq/MyDaq.m
+++ b/@MyDaq/MyGeneralPlot.m
@@ -1,1041 +1,1041 @@
-% Acquisition and analysis program that receives data from Collector. Can
-% also be used for analysis of previously acquired traces.
-classdef MyDaq < handle
-    properties
-        %Contains GUI handles
-        Gui
-        %Main figure
-        Figure
-        %main axes
-        main_plot
-        
-        %Contains Reference trace (MyTrace object)
-        Ref
-        %Contains Data trace (MyTrace object)
-        Data
-        %Contains Background trace (MyTrace object)
-        Background
-
-        %List of all the programs with run files
-        ProgramList= MyProgramDescriptor.empty()
-        %Struct containing Cursor objects
-        Cursors=struct()
-        %Struct containing Cursor labels
-        CrsLabels=struct()
-        %Struct containing MyFit objects
-        Fits=struct()
-        %Input parser for class constructor
-        ConstructionParser
-        %Struct for listeners
-        Listeners=struct()
-
-        %Sets the colors of fits, data and reference
-        fit_color='k'
-        data_color='b'
-        ref_color='r'
-        bg_color='c'
-        
-        default_ext='.txt' % default data file extension
-    end
-    
-    properties (Dependent=true)
-        save_dir
-        open_fits
-        open_crs
-    end
-    
-    properties (Dependent=true, SetAccess=private, GetAccess=public)
-        %Properties for saving files
-        base_dir
-        session_name
-        filename % File name is always returned with extension
-    end
-    
-    methods (Access=public)
-        %% Class functions
-        %Constructor function
-        function this=MyDaq(varargin)
-            
-            %We grab the guihandles from a GUI made in Guide.
-            this.Gui=guihandles(eval('GuiDaq'));
-            
-            %Assign the handle of main figure to a property for
-            %compatibility with Matalb apps
-            this.Figure = this.Gui.figure1;
-            this.main_plot = this.Gui.figure1.CurrentAxes;        
-            
-            % Parse inputs
-            p=inputParser;
-            addParameter(p,'collector_handle',[]);
-            this.ConstructionParser=p;
-            parse(p, varargin{:});
-            
-            %Sets a listener to the collector
-            if ~isempty(p.Results.collector_handle)
-                this.Listeners.Collector.NewDataWithHeaders=...
-                    addlistener(p.Results.collector_handle,...
-                    'NewDataWithHeaders',...
-                    @(~,eventdata) acquireNewData(this,eventdata));
-            else
-                errordlg(['No collector handle was supplied. ',...
-                    'DAQ will be unable to acquire data'],...
-                    'Error: No collector');
-            end
-            
-            % Initialize traces
-            this.Ref=MyTrace();
-            this.Data=MyTrace();
-            this.Background=MyTrace();
-
-            %The list of instruments is automatically populated from the
-            %run files. Select programs that are enabled and can produce 
-            %traces.
-            FullProgList = getIcPrograms();
-            ind = [FullProgList.enabled] & [FullProgList.data_source];
-            
-            this.ProgramList = FullProgList(ind);
-            
-            %This function sets all the callbacks for the GUI. If a new
-            %button is made, the associated callback must be put in the
-            %initGui function
-            initGui(this);
-            
-            % Initialize the menu based on the available programs
-            set(this.Gui.InstrMenu,'String',[{'Select the application'},...
-                {this.ProgramList.title}]);
-            
-            % Add a property to the menu for storing the program file
-            % names
-            if ~isprop(this.Gui.InstrMenu, 'ItemsData')
-                addprop(this.Gui.InstrMenu, 'ItemsData');
-            end
-            
-            set(this.Gui.InstrMenu,'ItemsData',0:length(this.ProgramList));
-            
-            % Add Data, Ref and Bg traces in the proper order on the plot
-            % as empty lines.
-            hold(this.main_plot,'on');
-            this.Background.hlines{1}=line(this.main_plot, ...
-                'XData',[],'YData',[],'Color',this.bg_color);
-            this.Ref.hlines{1}=line(this.main_plot, ...
-                'XData',[],'YData',[],'Color',this.ref_color);
-            this.Data.hlines{1}=line(this.main_plot, ...
-                'XData',[],'YData',[],'Color',this.data_color);
-            
-            %Initializes saving locations
-            this.base_dir=getLocalSettings('measurement_base_dir');
-            this.session_name='placeholder';
-            this.filename='placeholder';
-        end
-        
-        function delete(this)
-            %Deletes the MyFit objects and their listeners
-            cellfun(@(x) deleteListeners(this,x), this.open_fits);
-            structfun(@(x) delete(x), this.Fits);
-            
-            %Deletes other listeners
-            if ~isempty(fieldnames(this.Listeners))
-                cellfun(@(x) deleteListeners(this, x),...
-                    fieldnames(this.Listeners));
-            end
-            
-            %A class destructor should never through errors, so enclose the
-            %attempt to close figure into try-catch structure
-            try
-                this.Gui.figure1.CloseRequestFcn='';
-                %Deletes the figure
-                delete(this.Gui.figure1);
-                %Removes the figure handle to prevent memory leaks
-                this.Gui=[];
-            catch
-            end
-        end
-    end
-    
-    methods (Access=private)      
-
-        %Sets callback functions for the GUI
-        initGui(this)
-        
-        %Executes when the GUI is closed
-        function closeFigure(this,~,~)
-            delete(this);
-        end
-        
-        %Updates fits
-        function updateFits(this)            
-            %Pushes data into fits in the form of MyTrace objects, so that
-            %units etc follow. Also updates user supplied parameters.
-            for i=1:length(this.open_fits)
-                switch this.open_fits{i}
-                    case {'Linear','Quadratic','Gaussian',...
-                            'Exponential','Beta'}
-                        this.Fits.(this.open_fits{i}).Data=...
-                            getFitData(this,'VertData');
-                    case {'Lorentzian','DoubleLorentzian'}
-                        this.Fits.(this.open_fits{i}).Data=...
-                            getFitData(this,'VertData');
-                        %Here we push the information about line spacing
-                        %into the fit object if the reference cursors are
-                        %open. Only for Lorentzian fits.
-                        if isfield(this.Cursors,'VertRef')
-                            ind=findCursorData(this,'Data','VertRef');
-                            this.Fits.(this.open_fits{i}).CalVals.line_spacing=...
-                                range(this.Data.x(ind));
-                        end
-                    case {'G0'}
-                        this.Fits.G0.MechTrace=getFitData(this,'VertData');
-                        this.Fits.G0.CalTrace=getFitData(this,'VertRef');
-                end
-            end
-        end
-        
-        % If vertical cursors are on, takes only data within cursors. If 
-        %the cursor is not open, it takes all the data from the selected
-        %trace in the analysis trace selection dropdown
-        function Trace=getFitData(this,varargin)
-            %Parses varargin input
-            p=inputParser;
-            addOptional(p,'name','',@ischar);
-            parse(p,varargin{:})
-            name=p.Results.name;
-            
-            %Finds out which trace the user wants to fit.
-            trc_opts=this.Gui.SelTrace.String;
-            trc_str=trc_opts{this.Gui.SelTrace.Value};
-            % Note the use of copy here! This is a handle
-            %class, so if normal assignment is used, this.Fits.Data and
-            %this.(trace_str) will refer to the same object, causing roblems.
-            %Name input is the name of the cursor to be used to extract data.
-            Trace=copy(this.(trc_str));
-            %If the cursor is open for the trace we are analyzing, we take
-            %only the data enclosed by the cursor.
-            if isfield(this.Cursors,name)
-                ind=findCursorData(this, trc_str, name);
-                Trace.x=this.(trc_str).x(ind);
-                Trace.y=this.(trc_str).y(ind);
-            end
-        end
-        
-        %Finds data between named cursors in the given trace
-        function ind=findCursorData(this, trc_str, name)
-            crs_pos=sort([this.Cursors.(name){1}.Location,...
-                this.Cursors.(name){2}.Location]);
-            ind=(this.(trc_str).x>crs_pos(1) & this.(trc_str).x<crs_pos(2));
-        end
-        
-        %Creates either horizontal or vertical cursors
-        function createCursors(this,name,type)
-            %Checks that the cursors are of valid type
-            assert(strcmp(type,'Horz') || strcmp(type,'Vert'),...
-                'Cursorbars must be vertical or horizontal.');
-
-            %Sets the correct color for the cursor
-            switch name
-                case 'HorzData'
-                    color=[0,0,1];
-                    crs_type='Horizontal';
-                case 'VertData'
-                    color=[1,0,0];
-                    crs_type='Vertical';
-                case 'VertRef'
-                    color=[0.5,0,0.5];
-                    crs_type='Vertical';
-            end
-            
-            %Creates first cursor
-            this.Cursors.(name){1}=cursorbar(this.main_plot,...
-                'TargetMarkerStyle','none',...
-                'ShowText','off','CursorLineWidth',0.5,...
-                'Orientation',crs_type,'Tag',sprintf('%s1',name));
-            %Creates second cursor by duplicating the first.
-            this.Cursors.(name){2}=this.Cursors.(name){1}.duplicate;
-            set(this.Cursors.(name){2},'Tag',sprintf('%s2',name))
-            %Sets the cursor colors
-            cellfun(@(x) setCursorColor(x, color),this.Cursors.(name));
-            %Makes labels for the cursors
-            labelCursors(this,name,type,color);
-            %We add some listeners to the cursors, which update the labels
-            %when they are moved and so on.
-            addCursorListeners(this,name,type);
-            %We call the update function so that the labels are set
-            %correctly.
-            cellfun(@(x) notify(x, 'UpdateCursorBar'), this.Cursors.(name));
-        end
-        
-        %Labels cursors of a certain type and color
-        function labelCursors(this, name, type, color)
-            switch name
-                case {'VertData', 'HorzData'}
-                    lbl_str=name(1);
-                case {'VertRef'}
-                    lbl_str='R';
-            end
-            %Creates text boxes in a placeholder position
-            this.CrsLabels.(name)=cellfun(@(x) text(0,0,...
-                [lbl_str,x.Tag(end)]),this.Cursors.(name),...
-                'UniformOutput',0);
-            %Sets colors and properties on the labels.
-            cellfun(@(x) set(x,'Color',color,'EdgeColor',color,...
-                'FontWeight','bold','FontSize',10,...
-                'HorizontalAlignment','center',...
-                'VerticalAlignment','middle'), this.CrsLabels.(name));
-            positionCursorLabels(this, name, type);
-        end
-        
-        %Resets the position of the labels 
-        function positionCursorLabels(this, name, type)
-            switch type
-                case {'Horz','horizontal'}
-                    %To set the offset off the side of the axes
-                    xlim=get(this.main_plot,'XLim');
-                    %Empirically determined nice point for labels
-                    scale=1.03;
-                    if this.Gui.LogX.Value
-                        scale_log=((10^scale)/10)^(log10(xlim(2)/xlim(1)));
-                        xloc=scale_log*xlim(2)-(scale_log-1)*xlim(1);
-                    else
-                        xloc=scale*xlim(2)-(scale-1)*xlim(1);
-                    end
-                    %Sets the position of the cursor labels
-                    cellfun(@(x,y) set(x, 'Position',...
-                        [xloc,y.Location,0]),...
-                        this.CrsLabels.(name),this.Cursors.(name));
-                    
-                case {'Vert','vertical'}
-                    %To set the offset off the top of the axes
-                    ylim=get(this.main_plot,'YLim');
-                    %Empirically determined nice point for labels
-                    scale=1.05;
-                    if this.Gui.LogY.Value
-                        scale_log=((10^scale)/10)^(log10(ylim(2)/ylim(1)));
-                        yloc=scale_log*ylim(2)-(scale_log-1)*ylim(1);
-                    else
-                        yloc=scale*ylim(2)-(scale-1)*ylim(1);
-                    end
-                    %Sets the position of the cursor labels
-                    cellfun(@(x,y) set(x, 'Position',...
-                        [y.Location,yloc,0]),...
-                        this.CrsLabels.(name),this.Cursors.(name));
-            end
-            %Setting the position causes the line to update
-            cellfun(@(x) set(x, 'Location', x.Location),...
-                this.Cursors.(name));
-        end
-        
-        %Adds listeners for cursors
-        function addCursorListeners(this,name,type)
-            switch type
-                case {'Horz','horizontal'}
-                    %Sets the update function of the cursor to move the
-                    %label.
-                    this.Listeners.(name).Update=cellfun(@(x) ...
-                        addlistener(x,'UpdateCursorBar',...
-                        @(src, ~) horzCursorUpdate(this, src)),...
-                        this.Cursors.(name),'UniformOutput',0);
-                case {'Vert','vertical'}
-                    %Sets the update function of the cursors to move the
-                    %text
-                    this.Listeners.(name).Update=cellfun(@(x) ...
-                        addlistener(x,'UpdateCursorBar',...
-                        @(src, ~) vertCursorUpdate(this, src)),...
-                        this.Cursors.(name),'UniformOutput',0);
-                    %Sets the update function for end drag to update the
-                    %data in the fit objects
-                    this.Listeners.(name).EndDrag=cellfun(@(x) ...
-                        addlistener(x,'EndDrag',...
-                        @(~,~) updateFits(this)),this.Cursors.(name),...
-                        'UniformOutput',0);
-            end
-        end
-        
-        %Updates the cursors to fill the axes. Basically if the axes are
-        %resized the cursors will only fill part/more of the axes than what
-        %you see.
-        function updateCursors(this)
-            for i=1:length(this.open_crs)
-                type=this.Cursors.(this.open_crs{i}){1}.Orientation;
-                name=this.open_crs{i};
-                switch type
-                    case 'vertical'
-                        cellfun(@(x) set(x.TopHandle, 'YData',...
-                            this.main_plot.YLim(2)), this.Cursors.(name));
-                        cellfun(@(x) set(x.BottomHandle, 'YData',...
-                            this.main_plot.YLim(1)), this.Cursors.(name));
-                    case 'horizontal'
-                        cellfun(@(x) set(x.TopHandle, 'XData',...
-                            this.main_plot.XLim(2)), this.Cursors.(name));
-                        cellfun(@(x) set(x.BottomHandle, 'XData',...
-                            this.main_plot.XLim(1)), this.Cursors.(name));
-                end
-                %Updates the position of the cursor labels
-                positionCursorLabels(this,name,type);
-            end
-
-        end
-        
-        %Deletes the cursors, their listeners and their labels.
-        function deleteCursors(this, name)
-            if contains(name,'Data')
-                %Resets the edit boxes which contain cursor positions
-                this.Gui.(sprintf('Edit%s1',name(1))).String='';
-                this.Gui.(sprintf('Edit%s2',name(1))).String='';
-                this.Gui.(sprintf('Edit%s2%s1',name(1),name(1))).String='';
-            end
-            %Deletes cursor listeners
-            cellfun(@(x) deleteListeners(this,x.Tag), this.Cursors.(name));
-            %Deletes the cursors themselves
-            cellfun(@(x) delete(x), this.Cursors.(name));
-            this.Cursors=rmfield(this.Cursors,name);
-            %Deletes cursor labels
-            cellfun(@(x) delete(x), this.CrsLabels.(name));
-            this.CrsLabels=rmfield(this.CrsLabels,name);            
-        end
-        
-        function copyPlot(this)
-            %Conditions sizes
-            posn=this.main_plot.OuterPosition;
-            posn=posn.*[1,1,0.82,1.1];
-            %Creates a new figure, this is to avoid copying all the buttons
-            %etc to the clipboard.
-            newFig = figure('visible','off','Units',this.main_plot.Units,...
-                'Position',posn);
-            
-            %Copies the current axes into the new figure.
-            newAxes = copyobj(this.main_plot,newFig);
-            
-            newAxes.Color = 'none';
-            newAxes.XColor = [0, 0, 0];
-            newAxes.YColor = [0, 0, 0];
-            
-            %Prints the figure to the clipboard
-            print(newFig,'-clipboard','-dbitmap');
-            %Deletes the figure
-            delete(newFig);
-        end
-        
-        %Resets the axis to be tight around the plots.
-        function updateAxis(this)
-            axis(this.main_plot, 'tight');
-        end
-    end
-    
-    methods (Access=public)
-        %% Callbacks
-        
-        %Callback for copying the plot to clipboard
-        function copyPlotCallback(this,~,~)
-            copyPlot(this);
-        end
-        
-        %Callback for centering cursors
-        function centerCursorsCallback(this, ~, ~)
-            if ~this.Gui.LogX.Value
-                x_pos=mean(this.main_plot.XLim);
-            else
-                x_pos=10^(mean(log10(this.main_plot.XLim)));
-            end
-            
-            if ~this.Gui.LogY.Value
-                y_pos=mean(this.main_plot.YLim);
-            else
-                y_pos=10^(mean(log10(this.main_plot.YLim)));
-            end
-                        
-            for i=1:length(this.open_crs)
-                switch this.Cursors.(this.open_crs{i}){1}.Orientation
-                    case 'horizontal'
-                        pos=y_pos;
-                    case 'vertical'
-                        pos=x_pos;
-                end
-                
-                %Centers the position
-                cellfun(@(x) set(x,'Location',pos), ...
-                    this.Cursors.(this.open_crs{i}));
-                %Triggers the UpdateCursorBar event, which triggers
-                %listener callback to reposition text
-                cellfun(@(x) notify(x,'UpdateCursorBar'),...
-                    this.Cursors.(this.open_crs{i}));
-                %Triggers the EndDrag event, updating the data in the fit
-                %objects.
-                cellfun(@(x) notify(x,'EndDrag'),...
-                    this.Cursors.(this.open_crs{i}));
-            end
-        end
-        
-        %Callback for creating vertical data cursors
-        function cursorButtonCallback(this, hObject, ~)
-            name=erase(hObject.Tag,'Button');
-            %Gets the first four characters of the tag (Vert or Horz)
-            type=name(1:4);
-            
-            %Changes the color of the button and appropriately creates or
-            %deletes the cursors.
-            if hObject.Value
-                hObject.BackgroundColor=[0,1,0.2];
-                createCursors(this,name,type);
-            else
-                hObject.BackgroundColor=[0.941,0.941,0.941];
-                deleteCursors(this,name);
-            end
-        end
-        
-        %Callback for the instrument menu
-        function instrMenuCallback(this, hObject,~)
-            val=hObject.Value;
-            if val==1
-                %Returns if we are on the dummy option ('Select instrument')
-                return
-            else
-                ind = hObject.ItemsData(val);
-            end
-
-            try
-                eval(this.ProgramList(ind).run_expr);
-            catch
-                errordlg(sprintf('An error occured while running %s',...
-                    this.ProgramList(ind).name))
-            end
-        end
-        
-        %Select trace callback. If we change the trace being analyzed, the
-        %fit objects are updated.
-        function selTraceCallback(this, ~, ~)
-            updateFits(this)
-        end
-        
-        %Saves the data if the save data button is pressed.
-        function saveCallback(this, src, ~)
-            switch src.Tag
-                case 'SaveData'
-                    saveTrace(this,'Data');
-                case 'SaveRef'
-                    saveTrace(this,'Ref');
-            end
-        end
-        
-        function saveTrace(this, trace_tag, varargin) 
-            p=inputParser();
-            % If file already exists, generate a uinique name rather than
-            % show user the overwrite dialog.
-            addParameter(p, 'make_unique_name', false, @islogical);
-            parse(p,varargin{:});
-            
-            %Check if the trace is valid (i.e. x and y are equal length)
-            %before saving
-            if ~this.(trace_tag).validatePlot
-                errordlg(sprintf('%s trace was empty, could not save',...
-                    trace_tag));
-                return
-            end
-            
-            fullfilename=fullfile(this.save_dir,this.filename);
-            
-            if p.Results.make_unique_name && exist(fullfilename, 'file')~=0
-                fullfilename = createUniqueFileName( ...
-                    fullfile(this.save_dir, this.filename)); 
-            end
-            
-            %Save in readable format using the method of MyTrace
-            save(this.(trace_tag), fullfilename)
-        end
-        
-        %Toggle button callback for showing the data trace.
-        function showDataCallback(this, hObject, ~)
-            if hObject.Value
-                hObject.BackgroundColor=[0,1,0.2];
-                setVisible(this.Data,this.main_plot,1);
-                updateAxis(this);
-            else
-                hObject.BackgroundColor=[0.941,0.941,0.941];
-                setVisible(this.Data,this.main_plot,0);
-                updateAxis(this);
-            end
-        end
-        
-        %Toggle button callback for showing the ref trace
-        function showRefCallback(this, hObject, ~)
-            if hObject.Value
-                hObject.BackgroundColor=[0,1,0.2];
-                setVisible(this.Ref,this.main_plot,1);
-                updateAxis(this);
-            else
-                hObject.BackgroundColor=[0.941,0.941,0.941];
-                setVisible(this.Ref,this.main_plot,0);
-                updateAxis(this);
-            end
-        end
-        
-        %Callback for moving the data to reference.
-        function dataToRefCallback(this, ~, ~)
-            if this.Data.validatePlot
-                % Copy Data to Reference and pass Reference the handle to 
-                % the line in the main plot
-                hline=getLineHandle(this.Ref, this.main_plot);
-                this.Ref=copy(this.Data);
-                if ~isempty(hline)
-                    this.Ref.hlines{1}=hline;
-                end
-                %Plot the reference trace and make it visible
-                plot(this.Ref, this.main_plot, 'Color',this.ref_color,...
-                    'make_labels',true);
-                setVisible(this.Ref, this.main_plot,1);
-                %Update the fit objects
-                updateFits(this);
-                %Change button color
-                this.Gui.ShowRef.Value=1;
-                this.Gui.ShowRef.BackgroundColor=[0,1,0.2];
-                
-            else
-                warning('Data trace was empty, could not move to reference')
-            end
-        end
-        
-        %Callback for ref to bg button. Sends the reference to background
-        function refToBgCallback(this, ~, ~)
-            if this.Ref.validatePlot
-                hline=getLineHandle(this.Background, this.main_plot);
-                this.Background=copy(this.Ref);
-                if ~isempty(hline)
-                    this.Background.hlines{1}=hline;
-                end
-                this.Background.plot(this.main_plot,...
-                    'Color',this.bg_color,'make_labels',true);
-                this.Background.setVisible(this.main_plot,1);
-            else
-                warning('Reference trace was empty, could not move to background')
-            end
-        end
-        
-        %Callback for data to bg button. Sends the data to background
-        function dataToBgCallback(this, ~, ~)
-            if this.Data.validatePlot
-                hline=getLineHandle(this.Background, this.main_plot);
-                this.Background=copy(this.Data);
-                if ~isempty(hline)
-                    this.Background.hlines{1}=hline;
-                end
-                this.Background.plot(this.main_plot,...
-                    'Color',this.bg_color,'make_labels',true);
-                this.Background.setVisible(this.main_plot,1);
-            else
-                warning('Data trace was empty, could not move to background')
-            end
-        end
-        
-        %Callback for clear background button. Clears the background
-        function clearBgCallback(this, ~, ~)
-            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 hObject.Value
-                this.main_plot.YScale='Log';
-                hObject.BackgroundColor=[0,1,0.2];
-            else
-                this.main_plot.YScale='Linear';
-                hObject.BackgroundColor=[0.941,0.941,0.941];
-            end
-            updateAxis(this);
-            updateCursors(this);
-        end
-        
-        %Callback for LogX button. Sets the XScale to log/lin. Updates the
-        %axis and cursors afterwards.
-        function logXCallback(this, hObject, ~)
-            if get(hObject,'Value')
-                set(this.main_plot,'XScale','Log');
-                set(hObject, 'BackgroundColor',[0,1,0.2]);
-            else
-                set(this.main_plot,'XScale','Linear');
-                set(hObject, 'BackgroundColor',[0.941,0.941,0.941]);
-            end
-            updateAxis(this);
-            updateCursors(this);
-        end
-        
-        %Base directory callback. Sets the base directory. Also
-        %updates fit objects with the new save directory.
-        function baseDirCallback(this, ~, ~)
-            for i=1:length(this.open_fits)
-                this.Fits.(this.open_fits{i}).base_dir=this.base_dir;
-            end
-        end
-        
-        %Callback for session name edit box. Sets the session name. Also
-        %updates fit objects with the new save directory.
-        function sessionNameCallback(this, ~, ~)
-            for i=1:length(this.open_fits)
-                this.Fits.(this.open_fits{i}).session_name=this.session_name;
-            end
-        end
-        
-        %Callback for the analyze menu (popup menu for selecting fits).
-        %Opens the correct MyFit object.
-        function analyzeMenuCallback(this, hObject, ~)
-            analyze_ind=hObject.Value;
-            %Finds the correct fit name by erasing spaces and other
-            %superfluous strings
-            analyze_name=hObject.String{analyze_ind};
-            analyze_name=erase(analyze_name,'Fit');
-            analyze_name=erase(analyze_name,'Calibration');
-            analyze_name=erase(analyze_name,' ');
-            
-            %Sets the correct tooltip
-            hObject.TooltipString=sprintf(this.Gui.AnalyzeTip{analyze_ind}) ;
-            
-            %Opens the correct analysis tool
-            switch analyze_name
-                case {'Linear','Quadratic','Exponential',...
-                        'Lorentzian','Gaussian',...
-                        'DoubleLorentzian'}
-                    openMyFit(this,analyze_name);
-                case 'g0'
-                    openMyG(this);
-                case 'Beta'
-                    openMyBeta(this);
-            end
-        end
-        
-        function openMyFit(this,fit_name)
-            %Sees if the MyFit object is already open, if it is, changes the
-            %focus to it, if not, opens it.
-            if ismember(fit_name,fieldnames(this.Fits))
-                %Changes focus to the relevant fit window
-                figure(this.Fits.(fit_name).Gui.Window);
-            else
-                %Gets the data for the fit using the getFitData function
-                %with the vertical cursors
-                DataTrace=getFitData(this,'VertData');
-                %Makes an instance of MyFit with correct parameters.
-                this.Fits.(fit_name)=launchFit(...
-                    fit_name,...
-                    'enable_plot',1,...
-                    'plot_handle',this.main_plot,...
-                    'Data',DataTrace,...
-                    'base_dir',this.base_dir,...
-                    'session_name',this.session_name,...
-                    'filename',this.filename);
-                
-                updateFits(this);
-                %Sets up a listener for the Deletion event, which
-                %removes the MyFit object from the Fits structure if it is
-                %deleted.
-                this.Listeners.(fit_name).Deletion=...
-                    addlistener(this.Fits.(fit_name),'ObjectBeingDestroyed',...
-                    @(src, eventdata) deleteFit(this, src, eventdata));
-                
-                %Sets up a listener for the NewFit. Callback plots the fit
-                %on the main plot.
-                this.Listeners.(fit_name).NewFit=...
-                    addlistener(this.Fits.(fit_name),'NewFit',...
-                    @(src, eventdata) plotNewFit(this, src, eventdata));
-                
-                %Sets up a listener for NewInitVal
-                this.Listeners.(fit_name).NewInitVal=...
-                    addlistener(this.Fits.(fit_name),'NewInitVal',...
-                    @(~,~) updateCursors(this));
-            end
-        end
-        
-        %Opens MyG class if it is not open.
-        function openMyG(this)
-            if ismember('G0',this.open_fits)
-                figure(this.Fits.G0.Gui.figure1);
-            else
-                %Populate the MyG class with the right data. We assume the
-                %mechanics is in the Data trace.
-                MechTrace=getFitData(this,'VertData');
-                CalTrace=getFitData(this,'VertRef');
-                this.Fits.G0=MyG('MechTrace',MechTrace,'CalTrace',CalTrace,...
-                    'name','G0');
-                
-                %Adds listener for object being destroyed
-                this.Listeners.G0.Deletion=addlistener(this.Fits.G0,...
-                    'ObjectBeingDestroyed',...
-                    @(~,~) deleteObj(this,'G0'));
-            end
-        end
-        
-        %Opens MyBeta class if it is not open.
-        function openMyBeta(this)
-            if ismember('Beta', this.open_fits)
-                figure(this.Fits.Beta.Gui.figure1);
-            else
-                DataTrace=getFitData(this);
-                this.Fits.Beta=MyBeta('Data',DataTrace);
-                
-                %Adds listener for object being destroyed, to perform cleanup
-                this.Listeners.Beta.Deletion=addlistener(this.Fits.Beta,...
-                    'ObjectBeingDestroyed',...
-                    @(~,~) deleteObj(this,'Beta'));
-            end
-        end
-        
-        %Callback for load data button
-        function loadDataCallback(this, ~, ~)
-            if isempty(this.base_dir)
-                warning('Please input a valid folder name for loading a trace');
-                this.base_dir=pwd;
-            end
-
-            [load_name,path_name]=uigetfile(this.default_ext, ...
-                'Select the trace', this.base_dir);
-            if load_name==0
-                warning('No file was selected');
-                return
-            end
-            
-            load_path=[path_name,load_name];
-            
-            %Finds the destination trace from the GUI
-            dest_trc=this.Gui.DestTrc.String{this.Gui.DestTrc.Value};
-            
-            %Get the line handle from the trace to not create a new line
-            hline=getLineHandle(this.(dest_trc), this.main_plot);
-                
-            %Reset and load the destination trace
-            this.(dest_trc)=MyTrace.load(load_path);
-            
-            % Assign existing line handle to the trace
-            if ~isempty(hline)
-                this.(dest_trc).hlines{1}=hline;
-            end
-            
-            %Color and plot the right trace.
-            plot(this.(dest_trc), this.main_plot,...
-                'Color',this.(sprintf('%s_color',lower(dest_trc))),...
-                'make_labels',true);
-            %Update axis and cursors
-            updateAxis(this);
-            updateCursors(this);
-        end
-        
-        % Callback for open folder button
-        function openFolderCallback(this, hObject, eventdata)
-            dir=uigetdir(this.Gui.BaseDir.String);
-            if ~isempty(dir)
-                this.Gui.BaseDir.String=dir;
-            end
-            
-            % Execute the same callback as if the base directory edit 
-            % field was manually updated 
-            baseDirCallback(this, hObject, eventdata);
-        end
-    end
-    
-    methods (Access=public)
-        %% Listener functions 
-        %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);
-            updateAxis(this);
-            updateCursors(this);
-        end
-        
-        %Callback function for the NewData listener
-        function acquireNewData(this, EventData)
-            %Get the currently selected instrument
-            
-            val = this.Gui.InstrMenu.Value;
-            
-            ind = this.Gui.InstrMenu.ItemsData(val);
-            
-            if ind == 0
-                
-                % No application selected
-                return
-            end
-            
-            curr_instr_name = this.ProgramList(ind).name;
-            
-            %Check if the data originates from the currently selected
-            %instrument
-            if strcmp(EventData.src_name, curr_instr_name)
-                hline=getLineHandle(this.Data,this.main_plot);
-                %Copy the data from the source instrument
-                this.Data=copy(EventData.Trace);
-                %We give the new trace object the right line handle to plot in
-                if ~isempty(hline)
-                    this.Data.hlines{1}=hline;
-                end
-                plot(this.Data, this.main_plot,...
-                    'Color',this.data_color,...
-                    'make_labels',true)
-                updateAxis(this);
-                %Clears the fits when new data is acquired.
-                structfun(@(x) clearFit(x), this.Fits);
-                updateFits(this);
-                updateCursors(this);
-                
-                % If the save flag is on in EventData, save the new trace
-                % making sure that a unique filename is generated to not
-                % prompt the owerwrite dialog
-                if isprop(EventData, 'save') && EventData.save
-                    if isprop(EventData, 'filename_ending')
-                        % If present, use the file name ending supplied 
-                        % externally. By default filename_ending is empty.
-                        [~,fn,ext]=fileparts(this.filename);
-                        this.filename=[fn, EventData.filename_ending, ext];
-                        
-                        saveTrace(this, 'Data', 'make_unique_name', true);
-                        
-                        % Return the file name to its original value
-                        this.filename=[fn, ext];
-                    else
-                        saveTrace(this, 'Data', 'make_unique_name', true);
-                    end
-                end
-            end
-        end
-        
-        %Callback function for MyFit ObjectBeingDestroyed listener. 
-        %Removes the relevant field from the Fits struct and deletes the 
-        %listeners from the object.
-        function deleteFit(this, src, ~)
-            %Deletes the object from the Fits struct and deletes listeners 
-            deleteObj(this,src.fit_name);
-            
-            %Clears the fits
-            src.clearFit;
-            
-            %Updates cursors since the fits are removed from the plot
-            updateCursors(this);
-        end
-        
-        %Callback function for other analysis method deletion listeners.
-        %Does the same as above.
-        function deleteObj(this,name)
-            if ismember(name,this.open_fits)
-                this.Fits=rmfield(this.Fits,name);
-            end
-            deleteListeners(this, name);
-        end
-        
-        %Listener update function for vertical cursor
-        function vertCursorUpdate(this, src)
-            %Finds the index of the cursor. All cursors are tagged
-            %(name)1, (name)2, e.g. VertData2, ind is the number.
-            ind=str2double(src.Tag(end));
-            tag=src.Tag(1:(end-1));
-            %Moves the cursor labels
-            set(this.CrsLabels.(tag){ind},'Position',[src.Location,...
-                this.CrsLabels.(tag){ind}.Position(2),0]);
-            if strcmp(tag,'VertData')
-                %Sets the edit box displaying the location of the cursor
-                this.Gui.(sprintf('EditV%d',ind)).String=...
-                    num2str(src.Location);
-                %Sets the edit box displaying the difference in locations
-                this.Gui.EditV2V1.String=...
-                    num2str(this.Cursors.VertData{2}.Location-...
-                    this.Cursors.VertData{1}.Location);
-            end
-        end
-        
-        %Listener update function for horizontal cursor
-        function horzCursorUpdate(this, src)
-            %Finds the index of the cursor. All cursors are tagged
-            %(name)1, (name)2, e.g. VertData2, ind is the number.
-            ind=str2double(src.Tag(end));
-            tag=src.Tag(1:(end-1));
-            %Moves the cursor labels
-            set(this.CrsLabels.(tag){ind},'Position',...
-                [this.CrsLabels.(tag){ind}.Position(1),...
-                src.Location,0]);
-            if strcmp(tag,'HorzData')
-                %Sets the edit box displaying the location of the cursor
-                this.Gui.(sprintf('EditH%d',ind)).String=...
-                    num2str(src.Location);
-                %Sets the edit box displaying the difference in locations
-                this.Gui.EditH2H1.String=...
-                    num2str(this.Cursors.HorzData{2}.Location-...
-                    this.Cursors.HorzData{1}.Location);
-            end
-        end
-               
-        %Function that deletes listeners from the listeners struct,
-        %corresponding to an object of name obj_name
-        deleteListeners(this, obj_name);
-    end
-    
-    %Get functions for dependent variables without set functions
-    methods        
-        %Get function from save directory
-        function save_dir=get.save_dir(this)
-            save_dir=createSessionPath(this.base_dir,this.session_name);
-        end
-        
-        %Get function for open fits
-        function open_fits=get.open_fits(this)
-            open_fits=fieldnames(this.Fits);
-        end
-        
-        %Get function that displays names of open cursors
-        function open_crs=get.open_crs(this)
-            open_crs=fieldnames(this.Cursors);
-        end
-    end
-    
-    %Get and set functions for dependent properties with SetAccess
-    methods
-        function base_dir=get.base_dir(this)
-            try 
-                base_dir=this.Gui.BaseDir.String;
-            catch
-                base_dir=pwd;
-            end
-        end
-        
-        function set.base_dir(this,base_dir)
-            this.Gui.BaseDir.String=base_dir;
-        end
-        
-        function session_name=get.session_name(this)
-            try
-                session_name=this.Gui.SessionName.String;
-            catch
-                session_name='';
-            end
-        end
-        
-        function set.session_name(this,session_name)
-            this.Gui.SessionName.String=session_name;
-        end
-        
-        % Always return filename with extension
-        function filename=get.filename(this)
-            try
-                filename=this.Gui.FileName.String;
-                [~,~,ext]=fileparts(filename);
-                if isempty(ext)
-                    % Add default file extension
-                    filename=[filename, this.default_ext];
-                end
-            catch
-                filename=['placeholder', this.default_ext];
-            end
-        end
-        
-        function set.filename(this, str)
-            [~,fn,ext]=fileparts(str);
-            if strcmpi(ext, this.default_ext)
-                % By default display filename without extension
-                this.Gui.FileName.String=fn;
-            else
-                this.Gui.FileName.String=[fn,ext];
-            end
-        end
-        
-        function set.default_ext(this, str)
-            assert(ischar(str)&&(str(1)=='.'), ['Default file ' ...
-                'extension must be a character string startign ' ...
-                'with ''.'''])
-            this.default_ext=str;
-        end
-    end
+% Acquisition and analysis program that receives data from Collector. Can
+% also be used for analysis of previously acquired traces.
+classdef MyDaq < handle
+    properties
+        %Contains GUI handles
+        Gui
+        %Main figure
+        Figure
+        %main axes
+        main_plot
+        
+        %Contains Reference trace (MyTrace object)
+        Ref
+        %Contains Data trace (MyTrace object)
+        Data
+        %Contains Background trace (MyTrace object)
+        Background
+
+        %List of all the programs with run files
+        ProgramList= MyProgramDescriptor.empty()
+        %Struct containing Cursor objects
+        Cursors=struct()
+        %Struct containing Cursor labels
+        CrsLabels=struct()
+        %Struct containing MyFit objects
+        Fits=struct()
+        %Input parser for class constructor
+        ConstructionParser
+        %Struct for listeners
+        Listeners=struct()
+
+        %Sets the colors of fits, data and reference
+        fit_color='k'
+        data_color='b'
+        ref_color='r'
+        bg_color='c'
+        
+        default_ext='.txt' % default data file extension
+    end
+    
+    properties (Dependent=true)
+        save_dir
+        open_fits
+        open_crs
+    end
+    
+    properties (Dependent=true, SetAccess=private, GetAccess=public)
+        %Properties for saving files
+        base_dir
+        session_name
+        filename % File name is always returned with extension
+    end
+    
+    methods (Access=public)
+        %% Class functions
+        %Constructor function
+        function this=MyDaq(varargin)
+            
+            %We grab the guihandles from a GUI made in Guide.
+            this.Gui=guihandles(eval('GuiDaq'));
+            
+            %Assign the handle of main figure to a property for
+            %compatibility with Matalb apps
+            this.Figure = this.Gui.figure1;
+            this.main_plot = this.Gui.figure1.CurrentAxes;        
+            
+            % Parse inputs
+            p=inputParser;
+            addParameter(p,'collector_handle',[]);
+            this.ConstructionParser=p;
+            parse(p, varargin{:});
+            
+            %Sets a listener to the collector
+            if ~isempty(p.Results.collector_handle)
+                this.Listeners.Collector.NewDataWithHeaders=...
+                    addlistener(p.Results.collector_handle,...
+                    'NewDataWithHeaders',...
+                    @(~,eventdata) acquireNewData(this,eventdata));
+            else
+                errordlg(['No collector handle was supplied. ',...
+                    'DAQ will be unable to acquire data'],...
+                    'Error: No collector');
+            end
+            
+            % Initialize traces
+            this.Ref=MyTrace();
+            this.Data=MyTrace();
+            this.Background=MyTrace();
+
+            %The list of instruments is automatically populated from the
+            %run files. Select programs that are enabled and can produce 
+            %traces.
+            FullProgList = getIcPrograms();
+            ind = [FullProgList.enabled] & [FullProgList.data_source];
+            
+            this.ProgramList = FullProgList(ind);
+            
+            %This function sets all the callbacks for the GUI. If a new
+            %button is made, the associated callback must be put in the
+            %initGui function
+            initGui(this);
+            
+            % Initialize the menu based on the available programs
+            set(this.Gui.InstrMenu,'String',[{'Select the application'},...
+                {this.ProgramList.title}]);
+            
+            % Add a property to the menu for storing the program file
+            % names
+            if ~isprop(this.Gui.InstrMenu, 'ItemsData')
+                addprop(this.Gui.InstrMenu, 'ItemsData');
+            end
+            
+            set(this.Gui.InstrMenu,'ItemsData',0:length(this.ProgramList));
+            
+            % Add Data, Ref and Bg traces in the proper order on the plot
+            % as empty lines.
+            hold(this.main_plot,'on');
+            this.Background.hlines{1}=line(this.main_plot, ...
+                'XData',[],'YData',[],'Color',this.bg_color);
+            this.Ref.hlines{1}=line(this.main_plot, ...
+                'XData',[],'YData',[],'Color',this.ref_color);
+            this.Data.hlines{1}=line(this.main_plot, ...
+                'XData',[],'YData',[],'Color',this.data_color);
+            
+            %Initializes saving locations
+            this.base_dir=getLocalSettings('measurement_base_dir');
+            this.session_name='placeholder';
+            this.filename='placeholder';
+        end
+        
+        function delete(this)
+            %Deletes the MyFit objects and their listeners
+            cellfun(@(x) deleteListeners(this,x), this.open_fits);
+            structfun(@(x) delete(x), this.Fits);
+            
+            %Deletes other listeners
+            if ~isempty(fieldnames(this.Listeners))
+                cellfun(@(x) deleteListeners(this, x),...
+                    fieldnames(this.Listeners));
+            end
+            
+            %A class destructor should never through errors, so enclose the
+            %attempt to close figure into try-catch structure
+            try
+                this.Gui.figure1.CloseRequestFcn='';
+                %Deletes the figure
+                delete(this.Gui.figure1);
+                %Removes the figure handle to prevent memory leaks
+                this.Gui=[];
+            catch
+            end
+        end
+    end
+    
+    methods (Access=private)      
+
+        %Sets callback functions for the GUI
+        initGui(this)
+        
+        %Executes when the GUI is closed
+        function closeFigure(this,~,~)
+            delete(this);
+        end
+        
+        %Updates fits
+        function updateFits(this)            
+            %Pushes data into fits in the form of MyTrace objects, so that
+            %units etc follow. Also updates user supplied parameters.
+            for i=1:length(this.open_fits)
+                switch this.open_fits{i}
+                    case {'Linear','Quadratic','Gaussian',...
+                            'Exponential','Beta'}
+                        this.Fits.(this.open_fits{i}).Data=...
+                            getFitData(this,'VertData');
+                    case {'Lorentzian','DoubleLorentzian'}
+                        this.Fits.(this.open_fits{i}).Data=...
+                            getFitData(this,'VertData');
+                        %Here we push the information about line spacing
+                        %into the fit object if the reference cursors are
+                        %open. Only for Lorentzian fits.
+                        if isfield(this.Cursors,'VertRef')
+                            ind=findCursorData(this,'Data','VertRef');
+                            this.Fits.(this.open_fits{i}).CalVals.line_spacing=...
+                                range(this.Data.x(ind));
+                        end
+                    case {'G0'}
+                        this.Fits.G0.MechTrace=getFitData(this,'VertData');
+                        this.Fits.G0.CalTrace=getFitData(this,'VertRef');
+                end
+            end
+        end
+        
+        % If vertical cursors are on, takes only data within cursors. If 
+        %the cursor is not open, it takes all the data from the selected
+        %trace in the analysis trace selection dropdown
+        function Trace=getFitData(this,varargin)
+            %Parses varargin input
+            p=inputParser;
+            addOptional(p,'name','',@ischar);
+            parse(p,varargin{:})
+            name=p.Results.name;
+            
+            %Finds out which trace the user wants to fit.
+            trc_opts=this.Gui.SelTrace.String;
+            trc_str=trc_opts{this.Gui.SelTrace.Value};
+            % Note the use of copy here! This is a handle
+            %class, so if normal assignment is used, this.Fits.Data and
+            %this.(trace_str) will refer to the same object, causing roblems.
+            %Name input is the name of the cursor to be used to extract data.
+            Trace=copy(this.(trc_str));
+            %If the cursor is open for the trace we are analyzing, we take
+            %only the data enclosed by the cursor.
+            if isfield(this.Cursors,name)
+                ind=findCursorData(this, trc_str, name);
+                Trace.x=this.(trc_str).x(ind);
+                Trace.y=this.(trc_str).y(ind);
+            end
+        end
+        
+        %Finds data between named cursors in the given trace
+        function ind=findCursorData(this, trc_str, name)
+            crs_pos=sort([this.Cursors.(name){1}.Location,...
+                this.Cursors.(name){2}.Location]);
+            ind=(this.(trc_str).x>crs_pos(1) & this.(trc_str).x<crs_pos(2));
+        end
+        
+        %Creates either horizontal or vertical cursors
+        function createCursors(this,name,type)
+            %Checks that the cursors are of valid type
+            assert(strcmp(type,'Horz') || strcmp(type,'Vert'),...
+                'Cursorbars must be vertical or horizontal.');
+
+            %Sets the correct color for the cursor
+            switch name
+                case 'HorzData'
+                    color=[0,0,1];
+                    crs_type='Horizontal';
+                case 'VertData'
+                    color=[1,0,0];
+                    crs_type='Vertical';
+                case 'VertRef'
+                    color=[0.5,0,0.5];
+                    crs_type='Vertical';
+            end
+            
+            %Creates first cursor
+            this.Cursors.(name){1}=cursorbar(this.main_plot,...
+                'TargetMarkerStyle','none',...
+                'ShowText','off','CursorLineWidth',0.5,...
+                'Orientation',crs_type,'Tag',sprintf('%s1',name));
+            %Creates second cursor by duplicating the first.
+            this.Cursors.(name){2}=this.Cursors.(name){1}.duplicate;
+            set(this.Cursors.(name){2},'Tag',sprintf('%s2',name))
+            %Sets the cursor colors
+            cellfun(@(x) setCursorColor(x, color),this.Cursors.(name));
+            %Makes labels for the cursors
+            labelCursors(this,name,type,color);
+            %We add some listeners to the cursors, which update the labels
+            %when they are moved and so on.
+            addCursorListeners(this,name,type);
+            %We call the update function so that the labels are set
+            %correctly.
+            cellfun(@(x) notify(x, 'UpdateCursorBar'), this.Cursors.(name));
+        end
+        
+        %Labels cursors of a certain type and color
+        function labelCursors(this, name, type, color)
+            switch name
+                case {'VertData', 'HorzData'}
+                    lbl_str=name(1);
+                case {'VertRef'}
+                    lbl_str='R';
+            end
+            %Creates text boxes in a placeholder position
+            this.CrsLabels.(name)=cellfun(@(x) text(0,0,...
+                [lbl_str,x.Tag(end)]),this.Cursors.(name),...
+                'UniformOutput',0);
+            %Sets colors and properties on the labels.
+            cellfun(@(x) set(x,'Color',color,'EdgeColor',color,...
+                'FontWeight','bold','FontSize',10,...
+                'HorizontalAlignment','center',...
+                'VerticalAlignment','middle'), this.CrsLabels.(name));
+            positionCursorLabels(this, name, type);
+        end
+        
+        %Resets the position of the labels 
+        function positionCursorLabels(this, name, type)
+            switch type
+                case {'Horz','horizontal'}
+                    %To set the offset off the side of the axes
+                    xlim=get(this.main_plot,'XLim');
+                    %Empirically determined nice point for labels
+                    scale=1.03;
+                    if this.Gui.LogX.Value
+                        scale_log=((10^scale)/10)^(log10(xlim(2)/xlim(1)));
+                        xloc=scale_log*xlim(2)-(scale_log-1)*xlim(1);
+                    else
+                        xloc=scale*xlim(2)-(scale-1)*xlim(1);
+                    end
+                    %Sets the position of the cursor labels
+                    cellfun(@(x,y) set(x, 'Position',...
+                        [xloc,y.Location,0]),...
+                        this.CrsLabels.(name),this.Cursors.(name));
+                    
+                case {'Vert','vertical'}
+                    %To set the offset off the top of the axes
+                    ylim=get(this.main_plot,'YLim');
+                    %Empirically determined nice point for labels
+                    scale=1.05;
+                    if this.Gui.LogY.Value
+                        scale_log=((10^scale)/10)^(log10(ylim(2)/ylim(1)));
+                        yloc=scale_log*ylim(2)-(scale_log-1)*ylim(1);
+                    else
+                        yloc=scale*ylim(2)-(scale-1)*ylim(1);
+                    end
+                    %Sets the position of the cursor labels
+                    cellfun(@(x,y) set(x, 'Position',...
+                        [y.Location,yloc,0]),...
+                        this.CrsLabels.(name),this.Cursors.(name));
+            end
+            %Setting the position causes the line to update
+            cellfun(@(x) set(x, 'Location', x.Location),...
+                this.Cursors.(name));
+        end
+        
+        %Adds listeners for cursors
+        function addCursorListeners(this,name,type)
+            switch type
+                case {'Horz','horizontal'}
+                    %Sets the update function of the cursor to move the
+                    %label.
+                    this.Listeners.(name).Update=cellfun(@(x) ...
+                        addlistener(x,'UpdateCursorBar',...
+                        @(src, ~) horzCursorUpdate(this, src)),...
+                        this.Cursors.(name),'UniformOutput',0);
+                case {'Vert','vertical'}
+                    %Sets the update function of the cursors to move the
+                    %text
+                    this.Listeners.(name).Update=cellfun(@(x) ...
+                        addlistener(x,'UpdateCursorBar',...
+                        @(src, ~) vertCursorUpdate(this, src)),...
+                        this.Cursors.(name),'UniformOutput',0);
+                    %Sets the update function for end drag to update the
+                    %data in the fit objects
+                    this.Listeners.(name).EndDrag=cellfun(@(x) ...
+                        addlistener(x,'EndDrag',...
+                        @(~,~) updateFits(this)),this.Cursors.(name),...
+                        'UniformOutput',0);
+            end
+        end
+        
+        %Updates the cursors to fill the axes. Basically if the axes are
+        %resized the cursors will only fill part/more of the axes than what
+        %you see.
+        function updateCursors(this)
+            for i=1:length(this.open_crs)
+                type=this.Cursors.(this.open_crs{i}){1}.Orientation;
+                name=this.open_crs{i};
+                switch type
+                    case 'vertical'
+                        cellfun(@(x) set(x.TopHandle, 'YData',...
+                            this.main_plot.YLim(2)), this.Cursors.(name));
+                        cellfun(@(x) set(x.BottomHandle, 'YData',...
+                            this.main_plot.YLim(1)), this.Cursors.(name));
+                    case 'horizontal'
+                        cellfun(@(x) set(x.TopHandle, 'XData',...
+                            this.main_plot.XLim(2)), this.Cursors.(name));
+                        cellfun(@(x) set(x.BottomHandle, 'XData',...
+                            this.main_plot.XLim(1)), this.Cursors.(name));
+                end
+                %Updates the position of the cursor labels
+                positionCursorLabels(this,name,type);
+            end
+
+        end
+        
+        %Deletes the cursors, their listeners and their labels.
+        function deleteCursors(this, name)
+            if contains(name,'Data')
+                %Resets the edit boxes which contain cursor positions
+                this.Gui.(sprintf('Edit%s1',name(1))).String='';
+                this.Gui.(sprintf('Edit%s2',name(1))).String='';
+                this.Gui.(sprintf('Edit%s2%s1',name(1),name(1))).String='';
+            end
+            %Deletes cursor listeners
+            cellfun(@(x) deleteListeners(this,x.Tag), this.Cursors.(name));
+            %Deletes the cursors themselves
+            cellfun(@(x) delete(x), this.Cursors.(name));
+            this.Cursors=rmfield(this.Cursors,name);
+            %Deletes cursor labels
+            cellfun(@(x) delete(x), this.CrsLabels.(name));
+            this.CrsLabels=rmfield(this.CrsLabels,name);            
+        end
+        
+        function copyPlot(this)
+            %Conditions sizes
+            posn=this.main_plot.OuterPosition;
+            posn=posn.*[1,1,0.82,1.1];
+            %Creates a new figure, this is to avoid copying all the buttons
+            %etc to the clipboard.
+            newFig = figure('visible','off','Units',this.main_plot.Units,...
+                'Position',posn);
+            
+            %Copies the current axes into the new figure.
+            newAxes = copyobj(this.main_plot,newFig);
+            
+            newAxes.Color = 'none';
+            newAxes.XColor = [0, 0, 0];
+            newAxes.YColor = [0, 0, 0];
+            
+            %Prints the figure to the clipboard
+            print(newFig,'-clipboard','-dbitmap');
+            %Deletes the figure
+            delete(newFig);
+        end
+        
+        %Resets the axis to be tight around the plots.
+        function updateAxis(this)
+            axis(this.main_plot, 'tight');
+        end
+    end
+    
+    methods (Access=public)
+        %% Callbacks
+        
+        %Callback for copying the plot to clipboard
+        function copyPlotCallback(this,~,~)
+            copyPlot(this);
+        end
+        
+        %Callback for centering cursors
+        function centerCursorsCallback(this, ~, ~)
+            if ~this.Gui.LogX.Value
+                x_pos=mean(this.main_plot.XLim);
+            else
+                x_pos=10^(mean(log10(this.main_plot.XLim)));
+            end
+            
+            if ~this.Gui.LogY.Value
+                y_pos=mean(this.main_plot.YLim);
+            else
+                y_pos=10^(mean(log10(this.main_plot.YLim)));
+            end
+                        
+            for i=1:length(this.open_crs)
+                switch this.Cursors.(this.open_crs{i}){1}.Orientation
+                    case 'horizontal'
+                        pos=y_pos;
+                    case 'vertical'
+                        pos=x_pos;
+                end
+                
+                %Centers the position
+                cellfun(@(x) set(x,'Location',pos), ...
+                    this.Cursors.(this.open_crs{i}));
+                %Triggers the UpdateCursorBar event, which triggers
+                %listener callback to reposition text
+                cellfun(@(x) notify(x,'UpdateCursorBar'),...
+                    this.Cursors.(this.open_crs{i}));
+                %Triggers the EndDrag event, updating the data in the fit
+                %objects.
+                cellfun(@(x) notify(x,'EndDrag'),...
+                    this.Cursors.(this.open_crs{i}));
+            end
+        end
+        
+        %Callback for creating vertical data cursors
+        function cursorButtonCallback(this, hObject, ~)
+            name=erase(hObject.Tag,'Button');
+            %Gets the first four characters of the tag (Vert or Horz)
+            type=name(1:4);
+            
+            %Changes the color of the button and appropriately creates or
+            %deletes the cursors.
+            if hObject.Value
+                hObject.BackgroundColor=[0,1,0.2];
+                createCursors(this,name,type);
+            else
+                hObject.BackgroundColor=[0.941,0.941,0.941];
+                deleteCursors(this,name);
+            end
+        end
+        
+        %Callback for the instrument menu
+        function instrMenuCallback(this, hObject,~)
+            val=hObject.Value;
+            if val==1
+                %Returns if we are on the dummy option ('Select instrument')
+                return
+            else
+                ind = hObject.ItemsData(val);
+            end
+
+            try
+                eval(this.ProgramList(ind).run_expr);
+            catch
+                errordlg(sprintf('An error occured while running %s',...
+                    this.ProgramList(ind).name))
+            end
+        end
+        
+        %Select trace callback. If we change the trace being analyzed, the
+        %fit objects are updated.
+        function selTraceCallback(this, ~, ~)
+            updateFits(this)
+        end
+        
+        %Saves the data if the save data button is pressed.
+        function saveCallback(this, src, ~)
+            switch src.Tag
+                case 'SaveData'
+                    saveTrace(this,'Data');
+                case 'SaveRef'
+                    saveTrace(this,'Ref');
+            end
+        end
+        
+        function saveTrace(this, trace_tag, varargin) 
+            p=inputParser();
+            % If file already exists, generate a uinique name rather than
+            % show user the overwrite dialog.
+            addParameter(p, 'make_unique_name', false, @islogical);
+            parse(p,varargin{:});
+            
+            %Check if the trace is valid (i.e. x and y are equal length)
+            %before saving
+            if ~this.(trace_tag).validatePlot
+                errordlg(sprintf('%s trace was empty, could not save',...
+                    trace_tag));
+                return
+            end
+            
+            fullfilename=fullfile(this.save_dir,this.filename);
+            
+            if p.Results.make_unique_name && exist(fullfilename, 'file')~=0
+                fullfilename = createUniqueFileName( ...
+                    fullfile(this.save_dir, this.filename)); 
+            end
+            
+            %Save in readable format using the method of MyTrace
+            save(this.(trace_tag), fullfilename)
+        end
+        
+        %Toggle button callback for showing the data trace.
+        function showDataCallback(this, hObject, ~)
+            if hObject.Value
+                hObject.BackgroundColor=[0,1,0.2];
+                setVisible(this.Data,this.main_plot,1);
+                updateAxis(this);
+            else
+                hObject.BackgroundColor=[0.941,0.941,0.941];
+                setVisible(this.Data,this.main_plot,0);
+                updateAxis(this);
+            end
+        end
+        
+        %Toggle button callback for showing the ref trace
+        function showRefCallback(this, hObject, ~)
+            if hObject.Value
+                hObject.BackgroundColor=[0,1,0.2];
+                setVisible(this.Ref,this.main_plot,1);
+                updateAxis(this);
+            else
+                hObject.BackgroundColor=[0.941,0.941,0.941];
+                setVisible(this.Ref,this.main_plot,0);
+                updateAxis(this);
+            end
+        end
+        
+        %Callback for moving the data to reference.
+        function dataToRefCallback(this, ~, ~)
+            if this.Data.validatePlot
+                % Copy Data to Reference and pass Reference the handle to 
+                % the line in the main plot
+                hline=getLineHandle(this.Ref, this.main_plot);
+                this.Ref=copy(this.Data);
+                if ~isempty(hline)
+                    this.Ref.hlines{1}=hline;
+                end
+                %Plot the reference trace and make it visible
+                plot(this.Ref, this.main_plot, 'Color',this.ref_color,...
+                    'make_labels',true);
+                setVisible(this.Ref, this.main_plot,1);
+                %Update the fit objects
+                updateFits(this);
+                %Change button color
+                this.Gui.ShowRef.Value=1;
+                this.Gui.ShowRef.BackgroundColor=[0,1,0.2];
+                
+            else
+                warning('Data trace was empty, could not move to reference')
+            end
+        end
+        
+        %Callback for ref to bg button. Sends the reference to background
+        function refToBgCallback(this, ~, ~)
+            if this.Ref.validatePlot
+                hline=getLineHandle(this.Background, this.main_plot);
+                this.Background=copy(this.Ref);
+                if ~isempty(hline)
+                    this.Background.hlines{1}=hline;
+                end
+                this.Background.plot(this.main_plot,...
+                    'Color',this.bg_color,'make_labels',true);
+                this.Background.setVisible(this.main_plot,1);
+            else
+                warning('Reference trace was empty, could not move to background')
+            end
+        end
+        
+        %Callback for data to bg button. Sends the data to background
+        function dataToBgCallback(this, ~, ~)
+            if this.Data.validatePlot
+                hline=getLineHandle(this.Background, this.main_plot);
+                this.Background=copy(this.Data);
+                if ~isempty(hline)
+                    this.Background.hlines{1}=hline;
+                end
+                this.Background.plot(this.main_plot,...
+                    'Color',this.bg_color,'make_labels',true);
+                this.Background.setVisible(this.main_plot,1);
+            else
+                warning('Data trace was empty, could not move to background')
+            end
+        end
+        
+        %Callback for clear background button. Clears the background
+        function clearBgCallback(this, ~, ~)
+            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 hObject.Value
+                this.main_plot.YScale='Log';
+                hObject.BackgroundColor=[0,1,0.2];
+            else
+                this.main_plot.YScale='Linear';
+                hObject.BackgroundColor=[0.941,0.941,0.941];
+            end
+            updateAxis(this);
+            updateCursors(this);
+        end
+        
+        %Callback for LogX button. Sets the XScale to log/lin. Updates the
+        %axis and cursors afterwards.
+        function logXCallback(this, hObject, ~)
+            if get(hObject,'Value')
+                set(this.main_plot,'XScale','Log');
+                set(hObject, 'BackgroundColor',[0,1,0.2]);
+            else
+                set(this.main_plot,'XScale','Linear');
+                set(hObject, 'BackgroundColor',[0.941,0.941,0.941]);
+            end
+            updateAxis(this);
+            updateCursors(this);
+        end
+        
+        %Base directory callback. Sets the base directory. Also
+        %updates fit objects with the new save directory.
+        function baseDirCallback(this, ~, ~)
+            for i=1:length(this.open_fits)
+                this.Fits.(this.open_fits{i}).base_dir=this.base_dir;
+            end
+        end
+        
+        %Callback for session name edit box. Sets the session name. Also
+        %updates fit objects with the new save directory.
+        function sessionNameCallback(this, ~, ~)
+            for i=1:length(this.open_fits)
+                this.Fits.(this.open_fits{i}).session_name=this.session_name;
+            end
+        end
+        
+        %Callback for the analyze menu (popup menu for selecting fits).
+        %Opens the correct MyFit object.
+        function analyzeMenuCallback(this, hObject, ~)
+            analyze_ind=hObject.Value;
+            %Finds the correct fit name by erasing spaces and other
+            %superfluous strings
+            analyze_name=hObject.String{analyze_ind};
+            analyze_name=erase(analyze_name,'Fit');
+            analyze_name=erase(analyze_name,'Calibration');
+            analyze_name=erase(analyze_name,' ');
+            
+            %Sets the correct tooltip
+            hObject.TooltipString=sprintf(this.Gui.AnalyzeTip{analyze_ind}) ;
+            
+            %Opens the correct analysis tool
+            switch analyze_name
+                case {'Linear','Quadratic','Exponential',...
+                        'Lorentzian','Gaussian',...
+                        'DoubleLorentzian'}
+                    openMyFit(this,analyze_name);
+                case 'g0'
+                    openMyG(this);
+                case 'Beta'
+                    openMyBeta(this);
+            end
+        end
+        
+        function openMyFit(this,fit_name)
+            %Sees if the MyFit object is already open, if it is, changes the
+            %focus to it, if not, opens it.
+            if ismember(fit_name,fieldnames(this.Fits))
+                %Changes focus to the relevant fit window
+                figure(this.Fits.(fit_name).Gui.Window);
+            else
+                %Gets the data for the fit using the getFitData function
+                %with the vertical cursors
+                DataTrace=getFitData(this,'VertData');
+                %Makes an instance of MyFit with correct parameters.
+                this.Fits.(fit_name)=launchFit(...
+                    fit_name,...
+                    'enable_plot',1,...
+                    'plot_handle',this.main_plot,...
+                    'Data',DataTrace,...
+                    'base_dir',this.base_dir,...
+                    'session_name',this.session_name,...
+                    'filename',this.filename);
+                
+                updateFits(this);
+                %Sets up a listener for the Deletion event, which
+                %removes the MyFit object from the Fits structure if it is
+                %deleted.
+                this.Listeners.(fit_name).Deletion=...
+                    addlistener(this.Fits.(fit_name),'ObjectBeingDestroyed',...
+                    @(src, eventdata) deleteFit(this, src, eventdata));
+                
+                %Sets up a listener for the NewFit. Callback plots the fit
+                %on the main plot.
+                this.Listeners.(fit_name).NewFit=...
+                    addlistener(this.Fits.(fit_name),'NewFit',...
+                    @(src, eventdata) plotNewFit(this, src, eventdata));
+                
+                %Sets up a listener for NewInitVal
+                this.Listeners.(fit_name).NewInitVal=...
+                    addlistener(this.Fits.(fit_name),'NewInitVal',...
+                    @(~,~) updateCursors(this));
+            end
+        end
+        
+        %Opens MyG class if it is not open.
+        function openMyG(this)
+            if ismember('G0',this.open_fits)
+                figure(this.Fits.G0.Gui.figure1);
+            else
+                %Populate the MyG class with the right data. We assume the
+                %mechanics is in the Data trace.
+                MechTrace=getFitData(this,'VertData');
+                CalTrace=getFitData(this,'VertRef');
+                this.Fits.G0=MyG('MechTrace',MechTrace,'CalTrace',CalTrace,...
+                    'name','G0');
+                
+                %Adds listener for object being destroyed
+                this.Listeners.G0.Deletion=addlistener(this.Fits.G0,...
+                    'ObjectBeingDestroyed',...
+                    @(~,~) deleteObj(this,'G0'));
+            end
+        end
+        
+        %Opens MyBeta class if it is not open.
+        function openMyBeta(this)
+            if ismember('Beta', this.open_fits)
+                figure(this.Fits.Beta.Gui.figure1);
+            else
+                DataTrace=getFitData(this);
+                this.Fits.Beta=MyBeta('Data',DataTrace);
+                
+                %Adds listener for object being destroyed, to perform cleanup
+                this.Listeners.Beta.Deletion=addlistener(this.Fits.Beta,...
+                    'ObjectBeingDestroyed',...
+                    @(~,~) deleteObj(this,'Beta'));
+            end
+        end
+        
+        %Callback for load data button
+        function loadDataCallback(this, ~, ~)
+            if isempty(this.base_dir)
+                warning('Please input a valid folder name for loading a trace');
+                this.base_dir=pwd;
+            end
+
+            [load_name,path_name]=uigetfile(this.default_ext, ...
+                'Select the trace', this.base_dir);
+            if load_name==0
+                warning('No file was selected');
+                return
+            end
+            
+            load_path=[path_name,load_name];
+            
+            %Finds the destination trace from the GUI
+            dest_trc=this.Gui.DestTrc.String{this.Gui.DestTrc.Value};
+            
+            %Get the line handle from the trace to not create a new line
+            hline=getLineHandle(this.(dest_trc), this.main_plot);
+                
+            %Reset and load the destination trace
+            this.(dest_trc)=MyTrace.load(load_path);
+            
+            % Assign existing line handle to the trace
+            if ~isempty(hline)
+                this.(dest_trc).hlines{1}=hline;
+            end
+            
+            %Color and plot the right trace.
+            plot(this.(dest_trc), this.main_plot,...
+                'Color',this.(sprintf('%s_color',lower(dest_trc))),...
+                'make_labels',true);
+            %Update axis and cursors
+            updateAxis(this);
+            updateCursors(this);
+        end
+        
+        % Callback for open folder button
+        function openFolderCallback(this, hObject, eventdata)
+            dir=uigetdir(this.Gui.BaseDir.String);
+            if ~isempty(dir)
+                this.Gui.BaseDir.String=dir;
+            end
+            
+            % Execute the same callback as if the base directory edit 
+            % field was manually updated 
+            baseDirCallback(this, hObject, eventdata);
+        end
+    end
+    
+    methods (Access=public)
+        %% Listener functions 
+        %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);
+            updateAxis(this);
+            updateCursors(this);
+        end
+        
+        %Callback function for the NewData listener
+        function acquireNewData(this, EventData)
+            %Get the currently selected instrument
+            
+            val = this.Gui.InstrMenu.Value;
+            
+            ind = this.Gui.InstrMenu.ItemsData(val);
+            
+            if ind == 0
+                
+                % No application selected
+                return
+            end
+            
+            curr_instr_name = this.ProgramList(ind).name;
+            
+            %Check if the data originates from the currently selected
+            %instrument
+            if strcmp(EventData.src_name, curr_instr_name)
+                hline=getLineHandle(this.Data,this.main_plot);
+                %Copy the data from the source instrument
+                this.Data=copy(EventData.Trace);
+                %We give the new trace object the right line handle to plot in
+                if ~isempty(hline)
+                    this.Data.hlines{1}=hline;
+                end
+                plot(this.Data, this.main_plot,...
+                    'Color',this.data_color,...
+                    'make_labels',true)
+                updateAxis(this);
+                %Clears the fits when new data is acquired.
+                structfun(@(x) clearFit(x), this.Fits);
+                updateFits(this);
+                updateCursors(this);
+                
+                % If the save flag is on in EventData, save the new trace
+                % making sure that a unique filename is generated to not
+                % prompt the owerwrite dialog
+                if isprop(EventData, 'save') && EventData.save
+                    if isprop(EventData, 'filename_ending')
+                        % If present, use the file name ending supplied 
+                        % externally. By default filename_ending is empty.
+                        [~,fn,ext]=fileparts(this.filename);
+                        this.filename=[fn, EventData.filename_ending, ext];
+                        
+                        saveTrace(this, 'Data', 'make_unique_name', true);
+                        
+                        % Return the file name to its original value
+                        this.filename=[fn, ext];
+                    else
+                        saveTrace(this, 'Data', 'make_unique_name', true);
+                    end
+                end
+            end
+        end
+        
+        %Callback function for MyFit ObjectBeingDestroyed listener. 
+        %Removes the relevant field from the Fits struct and deletes the 
+        %listeners from the object.
+        function deleteFit(this, src, ~)
+            %Deletes the object from the Fits struct and deletes listeners 
+            deleteObj(this,src.fit_name);
+            
+            %Clears the fits
+            src.clearFit;
+            
+            %Updates cursors since the fits are removed from the plot
+            updateCursors(this);
+        end
+        
+        %Callback function for other analysis method deletion listeners.
+        %Does the same as above.
+        function deleteObj(this,name)
+            if ismember(name,this.open_fits)
+                this.Fits=rmfield(this.Fits,name);
+            end
+            deleteListeners(this, name);
+        end
+        
+        %Listener update function for vertical cursor
+        function vertCursorUpdate(this, src)
+            %Finds the index of the cursor. All cursors are tagged
+            %(name)1, (name)2, e.g. VertData2, ind is the number.
+            ind=str2double(src.Tag(end));
+            tag=src.Tag(1:(end-1));
+            %Moves the cursor labels
+            set(this.CrsLabels.(tag){ind},'Position',[src.Location,...
+                this.CrsLabels.(tag){ind}.Position(2),0]);
+            if strcmp(tag,'VertData')
+                %Sets the edit box displaying the location of the cursor
+                this.Gui.(sprintf('EditV%d',ind)).String=...
+                    num2str(src.Location);
+                %Sets the edit box displaying the difference in locations
+                this.Gui.EditV2V1.String=...
+                    num2str(this.Cursors.VertData{2}.Location-...
+                    this.Cursors.VertData{1}.Location);
+            end
+        end
+        
+        %Listener update function for horizontal cursor
+        function horzCursorUpdate(this, src)
+            %Finds the index of the cursor. All cursors are tagged
+            %(name)1, (name)2, e.g. VertData2, ind is the number.
+            ind=str2double(src.Tag(end));
+            tag=src.Tag(1:(end-1));
+            %Moves the cursor labels
+            set(this.CrsLabels.(tag){ind},'Position',...
+                [this.CrsLabels.(tag){ind}.Position(1),...
+                src.Location,0]);
+            if strcmp(tag,'HorzData')
+                %Sets the edit box displaying the location of the cursor
+                this.Gui.(sprintf('EditH%d',ind)).String=...
+                    num2str(src.Location);
+                %Sets the edit box displaying the difference in locations
+                this.Gui.EditH2H1.String=...
+                    num2str(this.Cursors.HorzData{2}.Location-...
+                    this.Cursors.HorzData{1}.Location);
+            end
+        end
+               
+        %Function that deletes listeners from the listeners struct,
+        %corresponding to an object of name obj_name
+        deleteListeners(this, obj_name);
+    end
+    
+    %Get functions for dependent variables without set functions
+    methods        
+        %Get function from save directory
+        function save_dir=get.save_dir(this)
+            save_dir=createSessionPath(this.base_dir,this.session_name);
+        end
+        
+        %Get function for open fits
+        function open_fits=get.open_fits(this)
+            open_fits=fieldnames(this.Fits);
+        end
+        
+        %Get function that displays names of open cursors
+        function open_crs=get.open_crs(this)
+            open_crs=fieldnames(this.Cursors);
+        end
+    end
+    
+    %Get and set functions for dependent properties with SetAccess
+    methods
+        function base_dir=get.base_dir(this)
+            try 
+                base_dir=this.Gui.BaseDir.String;
+            catch
+                base_dir=pwd;
+            end
+        end
+        
+        function set.base_dir(this,base_dir)
+            this.Gui.BaseDir.String=base_dir;
+        end
+        
+        function session_name=get.session_name(this)
+            try
+                session_name=this.Gui.SessionName.String;
+            catch
+                session_name='';
+            end
+        end
+        
+        function set.session_name(this,session_name)
+            this.Gui.SessionName.String=session_name;
+        end
+        
+        % Always return filename with extension
+        function filename=get.filename(this)
+            try
+                filename=this.Gui.FileName.String;
+                [~,~,ext]=fileparts(filename);
+                if isempty(ext)
+                    % Add default file extension
+                    filename=[filename, this.default_ext];
+                end
+            catch
+                filename=['placeholder', this.default_ext];
+            end
+        end
+        
+        function set.filename(this, str)
+            [~,fn,ext]=fileparts(str);
+            if strcmpi(ext, this.default_ext)
+                % By default display filename without extension
+                this.Gui.FileName.String=fn;
+            else
+                this.Gui.FileName.String=[fn,ext];
+            end
+        end
+        
+        function set.default_ext(this, str)
+            assert(ischar(str)&&(str(1)=='.'), ['Default file ' ...
+                'extension must be a character string startign ' ...
+                'with ''.'''])
+            this.default_ext=str;
+        end
+    end
 end
\ No newline at end of file