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rINSTCONTROL/@MyFit/MyFit.m
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MyFit.m
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classdef MyFit < dynamicprops
%Note that dynamicprops classes are handle classes.
properties (Access=public)
Data;
init_params=[];
scale_init=[];
lim_lower;
lim_upper;
enable_plot;
plot_handle;
%Calibration values supplied externally
CalVals=struct();
init_color='c';
end
properties (GetAccess=public, SetAccess=private)
Fit;
Gui;
Fitdata;
FitStruct;
coeffs;
fit_name='Linear'
end
properties (Access=private)
%Structure used for initializing GUI of userpanel
UserGui;
Parser;
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;
n_user_fields;
user_field_tags;
user_field_names;
user_field_vals;
fullpath;
save_name;
save_dir;
save_path;
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,'save_dir',pwd);
addParameter(p,'save_name','placeholder');
this.Parser=p;
end
end
%Public methods
methods (Access=public)
%Constructor function
function this=MyFit(varargin)
createFitStruct(this);
createParser(this);
parse(this.Parser,varargin{:});
parseInputs(this);
initCalVals(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
%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);
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)
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
param_headers=cellfun(@(x,y) sprintf('%s (%s)',x,y),...
this.fit_param_names, this.fit_params,'UniformOutput',0);
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)';
headers=[param_headers user_field_headers];
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;
if ~exist(this.save_dir,'dir')
mkdir(this.save_dir)
end
if ~exist(this.save_path,'dir')
mkdir(this.save_path)
end
if exist(this.fullpath,'file')
fileID=fopen(this.fullpath,'a');
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,[this.coeffs,this.user_field_vals']);
fclose(fileID);
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)
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'}
doFit(this)
case {'Lorentzian','DoubleLorentzian'}
doFit(this);
otherwise
error('Selected fit is invalid');
end
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
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>
otherwise
end
end
function real_freq=convOptFreq(this,freq)
real_freq=freq*this.spacing*this.line_no/this.CalVals.line_spacing;
end
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);
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.
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
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
function val=getUserVal(this, tag)
conv_factor=this.UserGui.Fields.(tag).conv_factor;
val=str2double(this.Gui.([tag,'Edit']).String)*conv_factor;
end
function setUserVal(this, val, tag)
conv_factor=this.UserGui.Fields.(tag).conv_factor;
this.Gui.([tag,'Edit']).String=num2str(val/conv_factor);
end
% Callbacks
%Save fit function callback
function saveFitCallback(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
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
%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 'DoubleLorentzian'
[params{1},params{2},params{3}]=...
initParamDblLorentzian(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;
%Plots the fit function with the new initial parameters
if this.enable_plot; plotInitFun(this); 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.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
%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)
%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','1/pi*a*b/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,'Exponential','a*exp(b*x)+c',...
'$$ae^{bx}+c$$',{'a','b','c'},...
{'Amplitude','Rate','Offset'});
addFit(this,'DoubleLorentzian',...
'1/pi*b/2*a/((x-c)^2+(b/2)^2)+1/pi*e/2*d/((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'});
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
%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
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
% 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
function n_user_fields=get.n_user_fields(this)
n_user_fields=length(this.user_field_tags);
end
function user_field_tags=get.user_field_tags(this)
user_field_tags=fieldnames(this.UserGui.Fields);
end
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
function user_field_vals=get.user_field_vals(this)
user_field_vals=cellfun(@(x) this.(x), this.user_field_tags);
end
function fullpath=get.fullpath(this)
fullpath=[this.save_path,this.save_name,'.txt'];
end
function save_path=get.save_path(this)
save_path=createSessionPath(this.save_dir,this.session_name);
end
function save_dir=get.save_dir(this)
try
save_dir=this.Gui.SaveDir.String;
catch
save_dir=pwd;
end
end
function set.save_dir(this,save_dir)
this.Gui.SaveDir.String=save_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
function save_name=get.save_name(this)
try
save_name=this.Gui.FileName.String;
catch
save_name='placeholder';
end
end
function set.save_name(this,save_name)
this.Gui.SaveName=save_name;
end
end
end
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