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rINSTCONTROL/@MyFit/MyFit.m
cf350848b797confint-fix

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MyFit.m
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classdef MyFit < handle
properties (Access=public)
Data;
init_params=[];
scale_init=[];
lim_lower;
lim_upper;
enable_plot;
plot_handle;
save_name;
save_dir;
end
properties (GetAccess=public, SetAccess=private)
Fit;
Gui;
Fitdata;
coeffs;
fit_name='Linear'
end
properties (Access=private)
Parser;
FitStruct;
enable_gui=1;
hline_init;
end
properties (Dependent=true)
fit_function;
fit_tex;
fit_params;
fit_param_names;
valid_fit_names;
n_params;
scaled_params;
init_param_fun;
x_vec;
end
events
NewFit;
NewInitVal;
end
%%Public methods
methods (Access=public)
%Constructor function
function this=MyFit(varargin)
createFitStruct(this);
createParser(this);
parse(this.Parser,varargin{:});
parseInputs(this);
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
%If the data is appropriate, generates initial
%parameters
if validateData(this)
genInitParams(this);
else
this.init_params=ones(1,this.n_params);
end
%Sets the scale_init to 1, this is used for the GUI.
this.scale_init=ones(1,this.n_params);
if this.enable_gui
createGui(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
%Fits the trace using currently set parameters, depending on the
%model.
function fitTrace(this)
this.Fit.x=this.x_vec;
switch this.fit_name
case 'Linear'
%Fits polynomial of order 1
this.coeffs=polyfit(this.Data.x,this.Data.y,1);
this.Fit.y=polyval(this.coeffs,this.Fit.x);
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 {'Exponential','Gaussian','Lorentzian'}
doFit(this);
end
%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
%% Callbacks
%Save function callback
function saveCallback(this,~,~)
assert(~isempty(this.save_dir),'Save directory is not specified');
assert(ischar(this.save_dir),...
['Save directory is not specified.',...
' Should be of type char but is %s.'], ...
class(this.save_dir))
try
this.Fit.save('name',this.save_name,...
'save_dir',this.save_dir)
catch
error(['Attempted to save to directory %s',...
' with file name %s, but failed'],this.save_dir,...
this.save_name);
end
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)/25);
%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, ~, ~)
if validateData(this)
fitTrace(this);
else
error(['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));
end
end
function clearFitCallback(this,~,~)
clearFit(this);
end
function initParamCallback(this,~,~)
genInitParams(this);
updateGui(this);
end
%Generates model-dependent initial parameters, lower and upper
%boundaries.
function genInitParams(this)
switch this.fit_name
case 'Exponential'
[this.init_params,this.lim_lower,this.lim_upper]=...
initParamExponential(this.Data.x,this.Data.y);
case 'Gaussian'
[this.init_params,this.lim_lower,this.lim_upper]=...
initParamGaussian(this.Data.x,this.Data.y);
case 'Lorentzian'
[this.init_params,this.lim_lower,this.lim_upper]=...
initParamLorentzian(this.Data.x,this.Data.y);
otherwise
this.init_params=ones(1,this.n_params);
end
end
%Plots the trace contained in the Fit MyTrace object.
function plotFit(this,varargin)
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.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);
else
set(this.hline_init,'XData',this.x_vec,'YData',y_vec);
end
end
end
methods(Access=private)
%Creates the GUI of MyFit, in separate file.
createGui(this);
%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,'save_dir',[]);
addParameter(p,'save_name',[]);
this.Parser=p;
end
%Sets the class variables to the inputs from the inputParser.
function parseInputs(this)
for i=1:length(this.Parser.Parameters)
%Takes the value from the inputParser to the appropriate
%property.
if isprop(this,this.Parser.Parameters{i})
this.(this.Parser.Parameters{i})=...
this.Parser.Results.(this.Parser.Parameters{i});
end
end
end
%Does the fit with the currently set parameters
function doFit(this)
%Fits with the below properties. Chosen for maximum accuracy.
this.Fitdata=fit(this.Data.x,this.Data.y,this.fit_function,...
'Lower',this.lim_lower,'Upper',this.lim_upper,...
'StartPoint',this.init_params, ....
'MaxFunEvals',2000,'MaxIter',2000,'TolFun',1e-9);
%Puts the y values of the fit into the struct.
this.Fit.y=this.Fitdata(this.Fit.x);
%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
function triggerNewInitVal(this)
notify(this,'NewInitVal');
end
%Creates the struct used to get all things relevant to the fit
%model
function createFitStruct(this)
%Adds fits
addFit(this,'Linear','a*x+b','$$ax+b$$',{'a','b'},...
{'Gradient','Offset'})
addFit(this,'Quadratic','a*x^2+b*x+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','a/((x-c)^2+(b/2)^2)+d',...
'$$\frac{a}{(x-c)^2+(b/2)^2}+d$$',{'a','b','c','d'},...
{'Amplitude','Width','Center','Offset'});
addFit(this,'Exponential','a*exp(b*x)+c',...
'$$ae^{bx}+c$$',{'a','b','c'},...
{'Amplitude','Rate','Offset'});
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=25*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
%Adds a fit to the list of fits
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,','),')'];
anon_fit_fun=str2func(vectorize([args,fit_function]));
this.FitStruct.(fit_name).anon_fit_fun=anon_fit_fun;
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
%% Get and set functions
methods
%% Set functions
%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
assert(ismember(fit_name,this.valid_fit_names),...
'%s is not a supported fit name',fit_name); %#ok<MCSUP>
this.fit_name=fit_name;
end
%% Get functions for dependent variables
%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 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
end
end
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