Diffusion Instrument Control (Toptica-laser-control-class) Browse

MyFit.m
5d0d9e5cc8bfToptica-laser-control…

MyFit.m
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			classdef MyFit < dynamicprops
			%Note that dynamicprops classes are handle classes.
			properties (Access=public)
			Data; %MyTrace object contains the data to be fitted to
			init_params=[]; %Contains the initial parameters
			scale_init=[]; %Contains the scale variables for the initial parameters, used for GUI purposes
			lim_lower;
			lim_upper;
			enable_plot; %If enabled, plots initial parameters in the plot_handle
			plot_handle;

			%Calibration values supplied externally
			CalVals=struct();

			init_color='c';
			end

			properties (GetAccess=public, SetAccess=private)
			Fit; %MyTrace object containing the fit
			Gui; %Gui handles
			%Output structures from fit:
			Fitdata;
			Gof;
			FitInfo;
			%Contains information about all the fits and their parameters
			FitStruct;
			coeffs;
			%The name of the fit used.
			fit_name='Linear'
			end

			properties (Access=private)
			%Structure used for initializing GUI of userpanel
			UserGui;
			Parser; %Input parser for constructor
			enable_gui=1;
			hline_init; %Handle for the plotted init values
			%Private struct used for saving file information when there is no
			%gui
			SaveInfo
			end

			%Dependent variables with no set methods
			properties (Dependent=true, SetAccess=private)
			%These grab and set the appropriate field of the FitStruct
			fit_function;
			anon_fit_fun;
			fit_tex;
			fit_params;
			fit_param_names;
			valid_fit_names;
			n_params;
			%Initial parameters scaled according to the GUI
			scaled_params;
			%These are used to create the usergui
			n_user_fields;
			user_field_tags;
			user_field_names;
			user_field_vals;
			%Vector used for plotting, depends on the data trace
			x_vec;
			%Variables used for saving
			fullpath;
			save_path;
			end

			%Dependent variables with associated set methods
			properties (Dependent=true)
			filename;
			base_dir;
			session_name;
			end

			events
			NewFit;
			NewInitVal;
			end

			%Parser function
			methods (Access=private)
			%Creates parser for constructor
			function createParser(this)
			p=inputParser;
			addParameter(p,'fit_name','Linear',@ischar)
			addParameter(p,'Data',MyTrace());
			addParameter(p,'Fit',MyTrace());
			addParameter(p,'x',[]);
			addParameter(p,'y',[]);
			addParameter(p,'enable_gui',1);
			addParameter(p,'enable_plot',0);
			addParameter(p,'plot_handle',[]);
			addParameter(p,'base_dir',this.SaveInfo.filename);
			addParameter(p,'session_name',this.SaveInfo.session_name);
			addParameter(p,'filename',this.SaveInfo.base_dir);
			this.Parser=p;
			end
			end
			%Public methods
			methods (Access=public)
			%Constructor function
			function this=MyFit(varargin)
			%Sets the default parameters for the save directory and
			%filename.
			this.SaveInfo.filename='placeholder';
			this.SaveInfo.session_name='placeholder';
			this.SaveInfo.base_dir=getLocalSettings('measurement_base_dir');

			%We first create the FitStruct, which contains all the
			%information about the available fits.
			createFitStruct(this);
			%We now create the parser for parsing the arguments to the
			%constructor, and parse the variables.
			createParser(this);
			parse(this.Parser,varargin{:});
			parseInputs(this);

			%Loads values into the CalVals struct depending on the type of
			%fit
			initCalVals(this);

			%Allows us to load either x/y data or a MyTrace object directly
			if ismember('Data',this.Parser.UsingDefaults) &&...
			~ismember('x',this.Parser.UsingDefaults) &&...
			~ismember('y',this.Parser.UsingDefaults)

			this.Data.x=this.Parser.Results.x;
			this.Data.y=this.Parser.Results.y;
			end

			%Sets the scale_init to 1, this is used for the GUI.
			this.scale_init=ones(1,this.n_params);
			this.init_params=ones(1,this.n_params);
			%Creates the structure that contains variables for calibration
			%of fit results
			createUserGuiStruct(this);

			%Creates the gui if the flag is enabled. This function is in a
			%separate file.
			if this.enable_gui; createGui(this); end

			%If the data is appropriate, generates initial
			%parameters
			if validateData(this); genInitParams(this); end
			end

			%Deletion function of object
			function delete(this)
			if this.enable_gui
			%Avoids loops
			set(this.Gui.Window,'CloseRequestFcn','');
			%Deletes the figure
			delete(this.Gui.Window);
			%Removes the figure handle to prevent memory leaks
			this.Gui=[];
			end
			if ~isempty(this.hline_init); delete(this.hline_init); end
			if ~isempty(this.Fit.hlines); delete(this.Fit.hlines{:}); end
			end

			%Close figure callback simply calls delete function for class
			function closeFigure(this,~,~)
			delete(this);
			end

			%Saves the metadata
			function saveParams(this,varargin)
			p=inputParser;
			addParameter(p,'save_user_params',true);
			addParameter(p,'save_gof',true);
			parse(p,varargin{:});
			%Flags for saving the user parameters or goodness of fit
			save_user_params=p.Results.save_user_params;
			save_gof=p.Results.save_gof;

			assert(~isempty(this.coeffs) && ...
			length(this.coeffs)==this.n_params,...
			['The number of calculated coefficients (%i) is not',...
			' equal to the number of parameters (%i).', ...
			' Perform a fit before trying to save parameters.'],...
			length(this.coeffs),this.n_params);

			%Creates combined strings of form: Linewidth (b), where
			%Linewidth is the parameter name and b is the parameter tag
			headers=cellfun(@(x,y) sprintf('%s (%s)',x,y),...
			this.fit_param_names, this.fit_params,'UniformOutput',0);
			save_data=this.coeffs;

			if save_user_params
			%Creates headers for the user fields
			user_field_headers=cellfun(@(x,y) ...
			sprintf('%s. %s',this.UserGui.Fields.(x).parent,y),...
			this.user_field_tags,this.user_field_names,...
			'UniformOutput',0)';
			%Appends the user headers and data to the save data
			headers=[headers, user_field_headers];
			save_data=[save_data,this.user_field_vals'];
			end

			if save_gof
			%Appends GOF headers and data to the save data
			headers=[headers,fieldnames(this.Gof)'];
			save_data=[save_data,struct2array(this.Gof)];
			end

			%Find out at the end how many columns we have
			n_columns=length(headers);

			%Sets the column width. Pads 2 for legibility.
			col_width=cellfun(@(x) length(x), headers)+2;
			%Min column width of 24
			col_width(col_width<24)=24;

			%Create the right directories
			if ~exist(this.base_dir,'dir')
			mkdir(this.base_dir)
			end

			if ~exist(this.save_path,'dir')
			mkdir(this.save_path)
			end

			%We automatically append to the file if it already exists,
			%otherwise create a new file
			if exist(this.fullpath,'file')
			fileID=fopen(this.fullpath,'a');
			fprintf('Appending data to %s \n',this.fullpath);
			else
			fileID=fopen(this.fullpath,'w');
			pre_fmt_str=repmat('%%%is\\t',1,n_columns);
			fmt_str=sprintf([pre_fmt_str,'\r\n'],col_width);
			fprintf(fileID,fmt_str,headers{:});
			end

			pre_fmt_str_nmb=repmat('%%%i.15e\\t',1,n_columns);
			nmb_fmt_str=sprintf([pre_fmt_str_nmb,'\r\n'],col_width);
			fprintf(fileID,nmb_fmt_str,save_data);

			fclose(fileID);
			end

			%We can load a fit from a file with appropriately formatted columns
			%We simply load the coefficients from the file into the fit.
			function loadFit(this,fullfilename,varargin)
			p=inputParser;
			addParameter(p,'line_no',1);
			parse(p,varargin{:})
			n=p.Results.line_no;

			load_table=readtable(fullfilename);
			load_names=fieldnames(load_table);
			for i=1:this.n_params
			this.coeffs(i)=load_table.(load_names{i})(n);
			end
			end

			%This function is used to set the coefficients, to avoid setting it
			%to a number not equal to the number of parameters
			function setFitParams(this,coeffs)
			assert(length(coeffs)==this.n_params,...
			['The length of the coefficient vector (currently %i) ',...
			'must be equal to the number of parameters (%i)'],...
			length(this.coeffs),this.n_params)
			this.coeffs=coeffs;
			end

			%Initializes the CalVals structure.
			function initCalVals(this)
			switch this.fit_name
			case 'Lorentzian'
			%Line spacing is the spacing between all the lines,
			%i.e. number of lines times the spacing between each
			%one
			this.CalVals.line_spacing=1;
			case 'DoubleLorentzian'
			this.CalVals.line_spacing=1;
			end
			end

			%Fits the trace using currently set parameters, depending on the
			%model.
			function fitTrace(this)
			switch this.fit_name
			case 'Linear'
			%Fits polynomial of order 1
			this.coeffs=polyfit(this.Data.x,this.Data.y,1);
			case 'Quadratic'
			%Fits polynomial of order 2
			this.coeffs=polyfit(this.Data.x,this.Data.y,2);
			this.Fit.y=polyval(this.coeffs,this.Fit.x);
			case {'Lorentzian','LorentzianGrad','Gaussian',...
			'DoubleLorentzian','DoubleLorentzianGrad',...
			'Exponential','Gorodetsky2000',...
			'Gorodetsky2000plus'}
			doFit(this)
			otherwise
			error('Selected fit is invalid');
			end

			%This function calculates the fit trace, using this.x_vec as
			%the x axis
			calcFit(this);
			%This function calculates user-defined parameters
			calcUserParams(this);
			%Sets the new initial parameters to be the fitted parameters
			this.init_params=this.coeffs;
			%Resets the scale variables for the GUI
			this.scale_init=ones(1,this.n_params);
			%Updates the gui if it is enabled
			if this.enable_gui; updateGui(this); end
			%Plots the fit if the flag is on
			if this.enable_plot; plotFit(this); end
			%Triggers new fit event
			triggerNewFit(this);
			end

			%This function calculates all the user-defined parameters shown in
			%the GUI. To add more parameters, add them in createUserGuiStruct,
			%then add them here when you wish to calculate them.
			function calcUserParams(this)
			switch this.fit_name
			case 'Lorentzian'
			this.mech_lw=this.coeffs(2); %#ok<MCNPR>
			this.mech_freq=this.coeffs(3); %#ok<MCNPR>
			this.Q=this.mech_freq/this.mech_lw; %#ok<MCNPR>
			this.opt_lw=convOptFreq(this,this.coeffs(2)); %#ok<MCNPR>
			this.Qf=this.mech_freq*this.Q; %#ok<MCNPR>
			case 'DoubleLorentzian'
			this.opt_lw1=convOptFreq(this,this.coeffs(2)); %#ok<MCNPR>
			this.opt_lw2=convOptFreq(this,this.coeffs(5)); %#ok<MCNPR>
			splitting=abs(this.coeffs(6)-this.coeffs(3));
			this.mode_split=convOptFreq(this,splitting); %#ok<MCNPR>
			case 'Exponential'
			this.tau=1/this.coeffs(2); %#ok<MCNPR>
			this.lw=this.coeffs(2)/pi; %#ok<MCNPR>
			this.Q=pithis.freqthis.tau; %#ok<MCNPR>
			this.Qf=this.Q*this.freq; %#ok<MCNPR>
			otherwise
			%If fit_name is not listed, do nothing
			end

			end

			%This function is used to convert the x-axis to frequency.
			function real_freq=convOptFreq(this,freq)
			real_freq=freqthis.spacingthis.line_no/this.CalVals.line_spacing;
			end

			%This struct is used to generate the UserGUI. Fields are seen under
			%tabs in the GUI. To create a new tab, you have to enter it under
			%this.UserGui.Tabs. A tab must have a tab_title and a field to add
			%Children. To add a field, use the addUserField function.
			function createUserGuiStruct(this)
			this.UserGui=struct('Fields',struct(),'Tabs',struct());
			switch this.fit_name
			case 'Lorentzian'
			%Parameters for the tab relating to mechanics
			this.UserGui.Tabs.Mech.tab_title='Mech.';
			this.UserGui.Tabs.Mech.Children={};
			addUserField(this,'Mech','mech_lw','Linewidth (Hz)',1,...
			'enable_flag','off')
			addUserField(this,'Mech','Q',...
			'Qualify Factor (x10^6)',1e6,...
			'enable_flag','off','conv_factor',1e6)
			addUserField(this,'Mech','mech_freq','Frequency (MHz)',1e6,...
			'conv_factor',1e6, 'enable_flag','off')
			addUserField(this,'Mech','Qf','Q\times f (10^{14} Hz)',1e14,...
			'conv_factor',1e14,'enable_flag','off');

			%Parameters for the tab relating to optics
			this.UserGui.Tabs.Opt.tab_title='Optical';
			this.UserGui.Tabs.Opt.Children={};
			addUserField(this,'Opt','spacing',...
			'Line Spacing (MHz)',1e6,'conv_factor',1e6,...
			'Callback', @(~,~) calcUserParams(this));
			addUserField(this,'Opt','line_no','Number of lines',10,...
			'Callback', @(~,~) calcUserParams(this));
			addUserField(this,'Opt','opt_lw','Linewidth (MHz)',1e6,...
			'enable_flag','off','conv_factor',1e6);

			case 'DoubleLorentzian'
			this.UserGui.Tabs.Opt.tab_title='Optical';
			this.UserGui.Tabs.Opt.Children={};
			addUserField(this,'Opt','spacing',...
			'Line Spacing (MHz)',1e6,'conv_factor',1e6,...
			'Callback', @(~,~) calcUserParams(this));
			addUserField(this,'Opt','line_no','Number of lines',10,...
			'Callback', @(~,~) calcUserParams(this));
			addUserField(this,'Opt','opt_lw1','Linewidth 1 (MHz)',1e6,...
			'enable_flag','off','conv_factor',1e6);
			addUserField(this,'Opt','opt_lw2','Linewidth 2 (MHz)',1e6,...
			'enable_flag','off','conv_factor',1e6);
			addUserField(this,'Opt','mode_split',...
			'Modal splitting (MHz)',1e6,...
			'enable_flag','off','conv_factor',1e6);
			case 'Exponential'
			this.UserGui.Tabs.Q.tab_title='Q';
			this.UserGui.Tabs.Q.Children={};
			addUserField(this,'Q','tau','\tau (s)',1,...
			'enable_flag','off')
			addUserField(this,'Q','lw','Linewidth (Hz)',1,...
			'enable_flag','off')
			addUserField(this,'Q','Q',...
			'Qualify Factor (x10^6)',1e6,...
			'enable_flag','off','conv_factor',1e6)
			addUserField(this,'Q','freq','Frequency (MHz)',1e6,...
			'conv_factor',1e6, 'enable_flag','on')
			addUserField(this,'Q','Qf','Q\times f (10^{14} Hz)',1e14,...
			'conv_factor',1e14,'enable_flag','off');
			otherwise
			%Do nothing if there is no defined user parameters
			end
			end

			%Parent is the parent tab for the userfield, tag is the tag given
			%to the GUI element, title is the text written next to the field,
			%initial value is the initial value of the property and change_flag
			%determines whether the gui element is enabled for writing or not.
			%conv_factor is used to have different units in the field. In the
			%program, the value is always saved as the bare value.
			function addUserField(this, parent, tag, title, ...
			init_val,varargin)
			%Parsing inputs
			p=inputParser();
			addRequired(p,'Parent');
			addRequired(p,'Tag');
			addRequired(p,'Title');
			addRequired(p,'init_val');
			addParameter(p,'enable_flag','on');
			addParameter(p,'Callback','');
			addParameter(p,'conv_factor',1);

			parse(p,parent,tag,title,init_val,varargin{:});
			tag=p.Results.Tag;

			%Populates the UserGui struct
			this.UserGui.Fields.(tag).parent=p.Results.Parent;
			this.UserGui.Fields.(tag).title=p.Results.Title;
			this.UserGui.Fields.(tag).init_val=p.Results.init_val;
			this.UserGui.Fields.(tag).enable_flag=...
			p.Results.enable_flag;
			this.UserGui.Fields.(tag).conv_factor=p.Results.conv_factor;
			this.UserGui.Fields.(tag).Callback=...
			p.Results.Callback;

			this.UserGui.Tabs.(p.Results.Parent).Children{end+1}=tag;
			%Adds the new property to the class
			addUserProp(this, tag);

			end

			%Every user field has an associated property, which is added by
			%this function. The get and set functions are set to use the GUI
			%through the getUserVal and setUserVal functions if the GUI is
			%enabled.
			function addUserProp(this,tag)
			prop=addprop(this,tag);
			if this.enable_gui
			prop.GetMethod=@(this) getUserVal(this,tag);
			prop.SetMethod=@(this, val) setUserVal(this, val, tag);
			prop.Dependent=true;
			end
			end

			%This function gets the value of the userprop from the GUI. The GUI
			%is the single point of truth
			function val=getUserVal(this, tag)
			conv_factor=this.UserGui.Fields.(tag).conv_factor;
			val=str2double(this.Gui.([tag,'Edit']).String)*conv_factor;
			end

			%As above, but instead we set the GUI through setting the property
			function setUserVal(this, val, tag)
			conv_factor=this.UserGui.Fields.(tag).conv_factor;
			this.Gui.([tag,'Edit']).String=num2str(val/conv_factor);
			end
			%Generates model-dependent initial parameters, lower and upper
			%boundaries.
			function genInitParams(this)
			assert(validateData(this), ['The data must be vectors of',...
			' equal length greater than the number of fit parameters.',...
			' Currently the number of fit parameters is %d, the',...
			' length of x is %d and the length of y is %d'],...
			this.n_params,length(this.Data.x),length(this.Data.y));
			%Cell for putting parameters in to be interpreted in the
			%parser. Element 1 contains the init params, Element 2 contains
			%the lower limits and Element 3 contains the upper limits.
			params={};

			switch this.fit_name
			case 'Exponential'
			[params{1},params{2},params{3}]=...
			initParamExponential(this.Data.x,this.Data.y);
			case 'Gaussian'
			[params{1},params{2},params{3}]=...
			initParamGaussian(this.Data.x,this.Data.y);
			case 'Lorentzian'
			[params{1},params{2},params{3}]=...
			initParamLorentzian(this.Data.x,this.Data.y);
			case 'LorentzianGrad'
			[params{1},params{2},params{3}]=...
			initParamLorentzianGrad(this.Data.x,this.Data.y);
			case 'DoubleLorentzian'
			[params{1},params{2},params{3}]=...
			initParamDblLorentzian(this.Data.x,this.Data.y);
			case 'DoubleLorentzianGrad'
			[params{1},params{2},params{3}]=...
			initParamDblLorentzianGrad(this.Data.x,this.Data.y);
			case 'Gorodetsky2000'
			[params{1},params{2},params{3}]=...
			initParamGorodetsky2000(this.Data.x,this.Data.y);
			case 'Gorodetsky2000plus'
			[params{1},params{2},params{3}]=...
			initParamGorodetsky2000Plus(this.Data.x,this.Data.y);
			end

			%Validates the initial parameters
			p=createFitParser(this.n_params);
			parse(p,params{:});

			%Loads the parsed results into the class variables
			this.init_params=p.Results.init_params;
			this.lim_lower=p.Results.lower;
			this.lim_upper=p.Results.upper;

			%Resets scale init variables
			this.scale_init=ones(1,this.n_params);
			%Plots the fit function with the new initial parameters
			if this.enable_plot; plotInitFun(this); end
			if this.enable_gui; updateGui(this); end
			end

			%Calculates the trace object for the fit
			function calcFit(this)
			this.Fit.x=this.x_vec;
			input_coeffs=num2cell(this.coeffs);
			this.Fit.y=this.anon_fit_fun(this.Fit.x,input_coeffs{:});
			end
			%Plots the trace contained in the Fit MyTrace object after
			%calculating the new values
			function plotFit(this,varargin)
			calcFit(this);
			assert((isa(this.plot_handle,'matlab.graphics.axis.Axes')\|\|...
			isa(this.plot_handle,'matlab.ui.control.UIAxes')),...
			'plot_handle property must be defined to valid axis in order to plot')
			this.Fit.plotTrace(this.plot_handle,varargin{:});
			end

			%Clears the plots
			function clearFit(this)
			cellfun(@(x) delete(x), this.Fit.hlines);
			delete(this.hline_init);
			this.hline_init=[];
			this.Fit.hlines={};
			end

			%Function for plotting fit model with current initial parameters.
			function plotInitFun(this)
			%Substantially faster than any alternative - generating
			%anonymous functions is very cpu intensive.

			input_cell=num2cell(this.scaled_params);
			y_vec=feval(this.FitStruct.(this.fit_name).anon_fit_fun,...
			this.x_vec,input_cell{:});
			if isempty(this.hline_init)
			this.hline_init=plot(this.plot_handle,this.x_vec,y_vec,...
			'Color',this.init_color);
			else
			set(this.hline_init,'XData',this.x_vec,'YData',y_vec);
			end
			end
			end

			%Callbacks
			methods
			%Save fit function callback
			function saveFitCallback(this,~,~)
			assert(~isempty(this.base_dir),'Save directory is not specified');
			assert(ischar(this.base_dir),...
			['Save directory is not specified.',...
			' Should be of type char but is %s.'], ...
			class(this.base_dir))
			this.Fit.save('name',this.filename,...
			'base_dir',this.save_path)
			end

			%Callback for saving parameters
			function saveParamCallback(this,~,~)
			saveParams(this);
			end

			%Callback functions for sliders in GUI. Uses param_ind to find out
			%which slider the call is coming from, this was implemented to
			%speed up the callback.
			function sliderCallback(this, param_ind, hObject, ~)
			%Gets the value from the slider
			scale=get(hObject,'Value');
			%Updates the scale with a new value
			this.scale_init(param_ind)=10^((scale-50)/50);
			%Updates the edit box with the new value from the slider
			set(this.Gui.(sprintf('Edit_%s',this.fit_params{param_ind})),...
			'String',sprintf('%3.3e',this.scaled_params(param_ind)));
			if this.enable_plot; plotInitFun(this); end
			end

			%Callback function for edit boxes in GUI
			function editCallback(this, hObject, ~)
			init_param=str2double(get(hObject,'String'));
			tag=get(hObject,'Tag');
			%Finds the index where the fit_param name begins (convention is
			%after the underscore)
			fit_param=tag((strfind(tag,'_')+1):end);
			param_ind=strcmp(fit_param,this.fit_params);
			%Updates the slider to be such that the scaling is 1
			set(this.Gui.(sprintf('Slider_%s',fit_param)),...
			'Value',50);
			%Updates the correct initial parameter
			this.init_params(param_ind)=init_param;
			if this.enable_plot; plotInitFun(this); end
			%Triggers event for new init values
			triggerNewInitVal(this);
			end

			%Callback function for analyze button in GUI. Checks if the data is
			%ready for fitting.
			function analyzeCallback(this, ~, ~)
			assert(validateData(this),...
			['The length of x is %d and the length of y is',...
			' %d. The lengths must be equal and greater than ',...
			'the number of fit parameters to perform a fit'],...
			length(this.Data.x),length(this.Data.y))
			fitTrace(this);
			end

			%Callback for clearing the fits on the axis.
			function clearFitCallback(this,~,~)
			clearFit(this);
			end

			%Callback function for generate init parameters button. Updates GUI
			%afterwards
			function initParamCallback(this,~,~)
			genInitParams(this);
			updateGui(this);
			end
			end

			%Private methods
			methods(Access=private)
			%Creates the GUI of MyFit, in separate file.
			createGui(this);

			%Creates a panel for the GUI, in separate file
			createTab(this, tab_tag, bg_color, button_h);

			%Creats two vboxes (from GUI layouts) to display values of
			%quantities
			createUnitBox(this, bg_color, h_parent, name);

			%Creates edit box inside a UnitDisp for showing label and value of
			%a quantity. Used in conjunction with createUnitBox
			createUnitDisp(this,varargin);



			%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

			%Does the fit with the currently set parameters
			function doFit(this)
			ft=fittype(this.fit_function,'coefficients',this.fit_params);
			opts=fitoptions('Method','NonLinearLeastSquares',...
			'Lower',this.lim_lower,...
			'Upper',this.lim_upper,...
			'StartPoint',this.scaled_params,...
			'MaxFunEvals',2000,...
			'MaxIter',2000,...
			'TolFun',1e-9,...
			'TolX',1e-9);
			%Fits with the below properties. Chosen for maximum accuracy.
			[this.Fitdata,this.Gof,this.FitInfo]=...
			fit(this.Data.x,this.Data.y,ft,opts);
			%Puts the coeffs into the class variable.
			this.coeffs=coeffvalues(this.Fitdata);
			end

			%Triggers the NewFit event such that other objects can use this to
			%e.g. plot new fits
			function triggerNewFit(this)
			notify(this,'NewFit');
			end

			%Triggers the NewInitVal event
			function triggerNewInitVal(this)
			notify(this,'NewInitVal');
			end

			%Creates the struct used to get all things relevant to the fit
			%model. Ensure that fit parameters are listed alphabetically, as
			%otherwise the anon_fit_fun will not work properly.
			function createFitStruct(this)
			%Adds fits
			addFit(this,'Linear','a*x+b','$$ax+b$$',{'a','b'},...
			{'Gradient','Offset'})
			addFit(this,'Quadratic','ax^2+bx+c','$$ax^2+bx+c$$',...
			{'a','b','c'},{'Quadratic coeff.','Linear coeff.','Offset'});
			addFit(this,'Gaussian','a*exp(-((x-c)/b)^2/2)+d',...
			'$$ae^{-\frac{(x-c)^2}{2b^2}}+d$$',{'a','b','c','d'},...
			{'Amplitude','Width','Center','Offset'});
			addFit(this,'Lorentzian','1/piab/2/((x-c)^2+(b/2)^2)+d',...
			'$$\frac{a}{\pi}\frac{b/2}{(x-c)^2+(b/2)^2}+d$$',...
			{'a','b','c','d'},...
			{'Amplitude','Width','Center','Offset'});
			addFit(this,'LorentzianGrad','1/piab/2/((x-c)^2+(b/2)^2)+d*(x-c)+e',...
			'$$\frac{a}{\pi}\frac{b/2}{(x-c)^2+(b/2)^2}+d*(x-b)+e$$',...
			{'a','b','c','d','e'},...
			{'Amplitude','Width','Center','Gradient','Offset'});
			addFit(this,'Exponential','aexp(bx)+c',...
			'$$ae^{bx}+c$$',{'a','b','c'},...
			{'Amplitude','Rate','Offset'});
			addFit(this,'DoubleLorentzian',...
			'1/pib/2a/((x-c)^2+(b/2)^2)+1/pie/2d/((x-f)^2+(e/2)^2)+g',...
			'$$\frac{a}{\pi}\frac{b/2}{(x-c)^2+(b/2)^2}+\frac{d}{\pi}\frac{e/2}{(x-f)^2+(e/2)^2}+g$$',...
			{'a','b','c','d','e','f','g'},...
			{'Amplitude 1','Width 1','Center 1','Amplitude 2',...
			'Width 2','Center 2','Offset'});
			addFit(this,'DoubleLorentzianGrad',...
			'1/pib/2a/((x-c)^2+(b/2)^2)+1/pie/2d/((x-f)^2+(e/2)^2)+g*(x-c)+h',...
			'$$\frac{a}{\pi}\frac{b/2}{(x-c)^2+(b/2)^2}+\frac{d}{\pi}\frac{e/2}{(x-f)^2+(e/2)^2}+g*x+h$$',...
			{'a','b','c','d','e','f','g','h'},...
			{'Amplitude 1','Width 1','Center 1','Amplitude 2',...
			'Width 2','Center 2','Gradient','Offset'});
			addFit(this,'Gorodetsky2000',...
			['aabs( (k0^2/4 - kex^2/4 + gamma^2/4 - (x-b).^2 + ik0.*(x-b))',...
			'./( (k0 + kex)^2/4 + gamma^2/4 - (x-b).^2 + i.(x-b)(k0 + kex) )).^2+c*(x-b)'],...
			['$$a\left\|\frac{\kappa_0^2/4-\kappa_{ex}^2/4+\gamma^2/4-(x-b)^2+i\kappa_0(x-b)/2}',...
			'{(\kappa_0+\kappa_{ex})^2/4+\gamma^2/4-(x-b)^2+i(x-b)(\kappa_0+\kappa_{ex})}\right\|^2$$+c(x-b)'],...
			{ 'a','b','c','gamma','k0', 'kex'},...
			{'Background','Center','BG Slope','Mode splitting',...
			'Intrinsic','Extrinsic'});
			% addFit(this,'Gorodetsky2000plus',...
			% ['(a+cx)abs( (k0^2/4 - kex^2/4 + gamma^2/4 - (x-b).^2 + ik0.(x-b))',...
			% './( (k0 + kex)^2/4 + gamma^2/4 - (x-b).^2 + i.(x-b)(k0 + kex) )).^2+d'],...
			% ['$$\left[a+cx+dx^2\right]\left\|\frac{\kappa_0^2/4-\kappa_{ex}^2/4+\gamma^2/4-(x-b)^2+i\kappa_0(x-b)/2}',...
			% '{(\kappa_0+\kappa_{ex})^2/4+\gamma^2/4-(x-b)^2+i(x-b)(\kappa_0+\kappa_{ex})}\right\|^2$$'],...
			% { 'a','b','c','d','gamma','k0', 'kex'},...
			% {'Baseline','Center','Lin. Coeff',...
			% 'Background','Mode splitting','Intrinsic','Extrinsic'});
			addFit(this,'Gorodetsky2000plus',...
			['(a+cx+dx.^2+ex.^2)abs( (k0^2/4 - kex^2/4 + gamma^2/4 - (x-b).^2 + ik0.(x-b))',...
			'./( (k0 + kex)^2/4 + gamma^2/4 - (x-b).^2 + i.(x-b)(k0 + kex) )).^2+f'],...
			['$$\left[a+cx+dx^2\right]\left\|\frac{\kappa_0^2/4-\kappa_{ex}^2/4+\gamma^2/4-(x-b)^2+i\kappa_0(x-b)/2}',...
			'{(\kappa_0+\kappa_{ex})^2/4+\gamma^2/4-(x-b)^2+i(x-b)(\kappa_0+\kappa_{ex})}\right\|^2$$'],...
			{ 'a','b','c','d','e','f','gamma','k0', 'kex'},...
			{'Baseline','Center','Lin. Coeff','Quad. Coeff','Cubic Coeff.',...
			'Background','Mode splitting','Intrinsic','Extrinsic'});

			end

			%Adds a fit to the list of fits. See above for real examples
			%fit_function: the function used to fit to in MATLAB form
			%fit_tex: the fit function written in tex for display in the GUI
			%fit_params: the fit parameters
			%fit_param_names: longer names of fit parameters for GUI
			function addFit(this,fit_name,fit_function,fit_tex,fit_params,...
			fit_param_names)
			this.FitStruct.(fit_name).fit_function=fit_function;
			this.FitStruct.(fit_name).fit_tex=fit_tex;
			this.FitStruct.(fit_name).fit_params=fit_params;
			this.FitStruct.(fit_name).fit_param_names=fit_param_names;
			%Generates the anonymous fit function from the above
			args=['@(x,', strjoin(fit_params,','),')'];
			this.FitStruct.(fit_name).anon_fit_fun=...
			str2func(vectorize([args,fit_function]));
			end

			%Updates the GUI if the edit or slider boxes are changed from
			%elsewhere.
			function updateGui(this)
			%Converts the scale variable to the value between 0 and 100
			%necessary for the slider
			slider_vals=50*log10(this.scale_init)+50;
			for i=1:this.n_params
			set(this.Gui.(sprintf('Edit_%s',this.fit_params{i})),...
			'String',sprintf('%3.3e',this.scaled_params(i)));
			set(this.Gui.(sprintf('Slider_%s',this.fit_params{i})),...
			'Value',slider_vals(i));
			end
			end

			%Checks if the class is ready to perform a fit
			function bool=validateData(this)
			bool=~isempty(this.Data.x) && ~isempty(this.Data.y) && ...
			length(this.Data.x)==length(this.Data.y) && ...
			length(this.Data.x)>=this.n_params;
			end
			end

			% Set function for nondependent variable
			methods
			%Set function for fit_name.
			function set.fit_name(this,fit_name)
			assert(ischar(fit_name),'The fit name must be a string');
			%Capitalizes the first letter
			fit_name=[upper(fit_name(1)),lower(fit_name(2:end))];
			%Checks it is a valid fit name
			ind=strcmpi(fit_name,this.valid_fit_names);%#ok<MCSUP>
			assert(any(ind),'%s is not a supported fit name',fit_name);

			this.fit_name=this.valid_fit_names{ind}; %#ok<MCSUP>
			end
			end

			% Get functions for dependent variables
			methods
			%Generates the valid fit names
			function valid_fit_names=get.valid_fit_names(this)
			valid_fit_names=fieldnames(this.FitStruct);
			end

			%Grabs the correct fit function from FitStruct
			function fit_function=get.fit_function(this)
			fit_function=this.FitStruct.(this.fit_name).fit_function;
			end

			%Grabs the correct tex string from FitStruct
			function fit_tex=get.fit_tex(this)
			fit_tex=this.FitStruct.(this.fit_name).fit_tex;
			end

			%Grabs the correct anon fit function from FitStruct
			function anon_fit_fun=get.anon_fit_fun(this)
			anon_fit_fun=this.FitStruct.(this.fit_name).anon_fit_fun;
			end


			%Grabs the correct fit parameters from FitStruct
			function fit_params=get.fit_params(this)
			fit_params=this.FitStruct.(this.fit_name).fit_params;
			end

			%Grabs the correct fit parameter names from FitStruct
			function fit_param_names=get.fit_param_names(this)
			fit_param_names=this.FitStruct.(this.fit_name).fit_param_names;
			end

			%Calculates the scaled initial parameters
			function scaled_params=get.scaled_params(this)
			scaled_params=this.scale_init.*this.init_params;
			end

			%Calculates the number of parameters in the fit function
			function n_params=get.n_params(this)
			n_params=length(this.fit_params);
			end

			%Generates a vector of x values for plotting
			function x_vec=get.x_vec(this)
			x_vec=linspace(min(this.Data.x),max(this.Data.x),1000);
			end

			%Used when creating the UserGUI, finds the number of user fields.
			function n_user_fields=get.n_user_fields(this)
			n_user_fields=length(this.user_field_tags);
			end

			%Finds all the user field tags
			function user_field_tags=get.user_field_tags(this)
			user_field_tags=fieldnames(this.UserGui.Fields);
			end

			%Finds all the titles of the user field tags
			function user_field_names=get.user_field_names(this)
			user_field_names=cellfun(@(x) this.UserGui.Fields.(x).title,...
			this.user_field_tags,'UniformOutput',0);
			end

			%Finds all the values of the user fields
			function user_field_vals=get.user_field_vals(this)
			user_field_vals=cellfun(@(x) this.(x), this.user_field_tags);
			end

			%Generates a full path for saving
			function fullpath=get.fullpath(this)
			fullpath=[this.save_path,this.filename,'.txt'];
			end

			%Generates a base path for saving
			function save_path=get.save_path(this)
			save_path=createSessionPath(this.base_dir,this.session_name);
			end
			end

			%Set and get functions for dependent variables with SetAccess
			methods
			%Gets the base dir from the gui
			function base_dir=get.base_dir(this)
			if this.enable_gui
			base_dir=this.Gui.BaseDir.String;
			else
			base_dir=this.SaveInfo.base_dir;
			end
			end

			function set.base_dir(this,base_dir)
			if this.enable_gui
			this.Gui.BaseDir.String=base_dir;
			else
			this.SaveInfo.base_dir=base_dir;
			end
			end

			function session_name=get.session_name(this)
			if this.enable_gui
			session_name=this.Gui.SessionName.String;
			else
			session_name=this.SaveInfo.session_name;
			end
			end

			function set.session_name(this,session_name)
			if this.enable_gui
			this.Gui.SessionName.String=session_name;
			else
			this.SaveInfo.session_name=session_name;
			end
			end

			function filename=get.filename(this)
			if this.enable_gui
			filename=this.Gui.FileName.String;
			else
			filename=this.SaveInfo.filename;
			end
			end

			function set.filename(this,filename)
			if this.enable_gui
			this.Gui.FileName.String=filename;
			else
			this.SaveInfo.filename=filename;
			end
			end
			end
			end

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rINSTCONTROL/@MyFit/MyFit.m
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MyFit.m
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