Curve fitting with loop
Hi all, I have multiple sets of data to be fitted using a custom fitting function. I would like to do it such that I will only have to provide one initial guess for the first set of data, and after the computer managed to get the solution of the parameters for the first set of data, it will use the solution of the first set of data as the initial guess for the second set of data, so on and forth.
I have attached my data and code for the fitting:
%% Preparation
clear;clc
%data = importdata("Experimental dataTransient AbsorptionFCPIB-293K-2.5mW-400nm-Jan072021 -ibg -bg -chirp.csv"); % insert file path within parenthesis
data = importdata("FCPIB-293K-2.5mW-400nm-Jan072021 -ibg -bg -chirp.csv"); % insert file path within parenthesis
%% Preamble
% Fundamental constants
h = 4.0135667696*10^-15; % units: eV/ Hz
c = 3*10^8; % SI units
kB = 8.617333268*10^-5; % units: eV/ K
% Clean up of data to select range of values
wavelength = data(1:end, 1);
delay_t = data(1, 1:end); % conatains all of the delay times
E = (h*c)./(wavelength*10^-9); % contains all of the probe energies
Range_E = E>=1.5 & E<=2.2;
Range_T = delay_t>=0.5 & delay_t<=1000;
% for one delay time
T = find(Range_T);
T_min = min(T);
T_max = max(T);
t = min(T); % choose an integer b/w T_min and T_max
delaytime = delay_t(1, t);
% Data for fitting
E_p = E(Range_E); % selected probe energies
delta_Abs = -1*data(Range_E,t);
delta_Abs_norm = delta_Abs./max(delta_Abs); % normalised delta_Abs
Range_Efit = E_p>=1.65 & E_p<=max(E_p);
E_fit = E_p(Range_Efit);
delta_Abs_norm_fit = delta_Abs_norm(Range_Efit);
% Fitting function
function F = MB(y, E_fit)
F = y(1).*exp(-(E_fit./(8.617333268*10^-5.*y(2)))) + y(3);
end
%% Curve fitting options
% Initial parameter guess and bounds
lb = [0, 293, -Inf]; ub = [Inf, Inf, Inf];
y0 = [4*10^7, 900, 2];
% lsqcurvefit and choose between different algorithm that lsqcurvefit employs (3C1, comment those lines that are not choosen and uncomment the line that is choosen, if not, matlab will take the last line of "optim_lsq" by default)
% optim_lsq = optimoptions(‘lsqcurvefit’, ‘Algorithm’, ‘levenberg-marquardt’, ‘MaxFunctionEvaluations’,10^5, ‘MaxIterations’, 10^5, ‘FunctionTolerance’,10^-10, ‘StepTolerance’, 10^-10);
optim_lsq = optimoptions(‘lsqcurvefit’, ‘Algorithm’, ‘trust-region-reflective’, ‘MaxFunctionEvaluations’,10^5, ‘MaxIterations’,10^5, ‘FunctionTolerance’,10^-20, ‘StepTolerance’, 10^-20);
% optim_lsq = optimoptions(‘lsqcurvefit’, ‘Algorithm’, ‘interior-point’, ‘MaxFunctionEvaluations’,1000, ‘MaxIterations’, 1000, ‘FunctionTolerance’,10^-20, ‘StepTolerance’, 10^-20);
% Solver for lsqcurvefit
[y, residualnorm, residual, exitflag, output, lambda, jacobian] = lsqcurvefit(@MB, y0, E_fit, delta_Abs_norm_fit, lb, ub);
%% Error bars calculation
ci = nlparci(y, residual, ‘Jacobian’, jacobian);
PCI = table(ci(:,1), y(:), ci(:,2),’VariableNames’,{‘CI 0.025′,’y’,’CI 0.975′});
Parameter_CI = table2array(PCI);
upper_bar = (Parameter_CI(:,3) – Parameter_CI(:,2))./2;
lower_bar = (Parameter_CI(:,2) – Parameter_CI(:,1))./2;
%% Plot command
plot(E_p, delta_Abs_norm,’Black’)
hold on
plot(E_fit, MB(y, E_fit), ‘LineWidth’, 1.0, ‘Color’, ‘red’)
xlabel(‘Probe Photon Energy (eV)’)
ylabel(‘Normalised Delta A (a.u.)’)
legend(‘Experimental Data’, ‘Fitted Curve’)
Some background info regarding the data:
There’s a range of values in the first column and these corresponds to this quantity called wavelength. After I have extracted the wavelength from there, I’ll process it into this quantitiy call E. However, E takes a range of values and I’ll only need the values ranging from E = 1.5 to E = 2.2 (this is the data used for the scatterplot, it is named as E_p in my code)
After the first step is done, I’ll now need to choose the range of E_p (E_p = 1.65 to E_p = 2.2) for the fitting of my data (this is named as E_fit in my code) note: the range of values for fitting range of values for scatter plot
Subsequently, I’ll need to look at the first row of my data and select some of them (they need to be positive). Once I have selected them, I’ll need to select the data in the same column as them and this needs to correspond to both E_p and E_fit.
In conclusion, the data selected in 1. and 2. goes to the horizontal axis and the data selected in 3. goes to the vertical axis.
Thank you.Hi all, I have multiple sets of data to be fitted using a custom fitting function. I would like to do it such that I will only have to provide one initial guess for the first set of data, and after the computer managed to get the solution of the parameters for the first set of data, it will use the solution of the first set of data as the initial guess for the second set of data, so on and forth.
I have attached my data and code for the fitting:
%% Preparation
clear;clc
%data = importdata("Experimental dataTransient AbsorptionFCPIB-293K-2.5mW-400nm-Jan072021 -ibg -bg -chirp.csv"); % insert file path within parenthesis
data = importdata("FCPIB-293K-2.5mW-400nm-Jan072021 -ibg -bg -chirp.csv"); % insert file path within parenthesis
%% Preamble
% Fundamental constants
h = 4.0135667696*10^-15; % units: eV/ Hz
c = 3*10^8; % SI units
kB = 8.617333268*10^-5; % units: eV/ K
% Clean up of data to select range of values
wavelength = data(1:end, 1);
delay_t = data(1, 1:end); % conatains all of the delay times
E = (h*c)./(wavelength*10^-9); % contains all of the probe energies
Range_E = E>=1.5 & E<=2.2;
Range_T = delay_t>=0.5 & delay_t<=1000;
% for one delay time
T = find(Range_T);
T_min = min(T);
T_max = max(T);
t = min(T); % choose an integer b/w T_min and T_max
delaytime = delay_t(1, t);
% Data for fitting
E_p = E(Range_E); % selected probe energies
delta_Abs = -1*data(Range_E,t);
delta_Abs_norm = delta_Abs./max(delta_Abs); % normalised delta_Abs
Range_Efit = E_p>=1.65 & E_p<=max(E_p);
E_fit = E_p(Range_Efit);
delta_Abs_norm_fit = delta_Abs_norm(Range_Efit);
% Fitting function
function F = MB(y, E_fit)
F = y(1).*exp(-(E_fit./(8.617333268*10^-5.*y(2)))) + y(3);
end
%% Curve fitting options
% Initial parameter guess and bounds
lb = [0, 293, -Inf]; ub = [Inf, Inf, Inf];
y0 = [4*10^7, 900, 2];
% lsqcurvefit and choose between different algorithm that lsqcurvefit employs (3C1, comment those lines that are not choosen and uncomment the line that is choosen, if not, matlab will take the last line of "optim_lsq" by default)
% optim_lsq = optimoptions(‘lsqcurvefit’, ‘Algorithm’, ‘levenberg-marquardt’, ‘MaxFunctionEvaluations’,10^5, ‘MaxIterations’, 10^5, ‘FunctionTolerance’,10^-10, ‘StepTolerance’, 10^-10);
optim_lsq = optimoptions(‘lsqcurvefit’, ‘Algorithm’, ‘trust-region-reflective’, ‘MaxFunctionEvaluations’,10^5, ‘MaxIterations’,10^5, ‘FunctionTolerance’,10^-20, ‘StepTolerance’, 10^-20);
% optim_lsq = optimoptions(‘lsqcurvefit’, ‘Algorithm’, ‘interior-point’, ‘MaxFunctionEvaluations’,1000, ‘MaxIterations’, 1000, ‘FunctionTolerance’,10^-20, ‘StepTolerance’, 10^-20);
% Solver for lsqcurvefit
[y, residualnorm, residual, exitflag, output, lambda, jacobian] = lsqcurvefit(@MB, y0, E_fit, delta_Abs_norm_fit, lb, ub);
%% Error bars calculation
ci = nlparci(y, residual, ‘Jacobian’, jacobian);
PCI = table(ci(:,1), y(:), ci(:,2),’VariableNames’,{‘CI 0.025′,’y’,’CI 0.975′});
Parameter_CI = table2array(PCI);
upper_bar = (Parameter_CI(:,3) – Parameter_CI(:,2))./2;
lower_bar = (Parameter_CI(:,2) – Parameter_CI(:,1))./2;
%% Plot command
plot(E_p, delta_Abs_norm,’Black’)
hold on
plot(E_fit, MB(y, E_fit), ‘LineWidth’, 1.0, ‘Color’, ‘red’)
xlabel(‘Probe Photon Energy (eV)’)
ylabel(‘Normalised Delta A (a.u.)’)
legend(‘Experimental Data’, ‘Fitted Curve’)
Some background info regarding the data:
There’s a range of values in the first column and these corresponds to this quantity called wavelength. After I have extracted the wavelength from there, I’ll process it into this quantitiy call E. However, E takes a range of values and I’ll only need the values ranging from E = 1.5 to E = 2.2 (this is the data used for the scatterplot, it is named as E_p in my code)
After the first step is done, I’ll now need to choose the range of E_p (E_p = 1.65 to E_p = 2.2) for the fitting of my data (this is named as E_fit in my code) note: the range of values for fitting range of values for scatter plot
Subsequently, I’ll need to look at the first row of my data and select some of them (they need to be positive). Once I have selected them, I’ll need to select the data in the same column as them and this needs to correspond to both E_p and E_fit.
In conclusion, the data selected in 1. and 2. goes to the horizontal axis and the data selected in 3. goes to the vertical axis.
Thank you. Hi all, I have multiple sets of data to be fitted using a custom fitting function. I would like to do it such that I will only have to provide one initial guess for the first set of data, and after the computer managed to get the solution of the parameters for the first set of data, it will use the solution of the first set of data as the initial guess for the second set of data, so on and forth.
I have attached my data and code for the fitting:
%% Preparation
clear;clc
%data = importdata("Experimental dataTransient AbsorptionFCPIB-293K-2.5mW-400nm-Jan072021 -ibg -bg -chirp.csv"); % insert file path within parenthesis
data = importdata("FCPIB-293K-2.5mW-400nm-Jan072021 -ibg -bg -chirp.csv"); % insert file path within parenthesis
%% Preamble
% Fundamental constants
h = 4.0135667696*10^-15; % units: eV/ Hz
c = 3*10^8; % SI units
kB = 8.617333268*10^-5; % units: eV/ K
% Clean up of data to select range of values
wavelength = data(1:end, 1);
delay_t = data(1, 1:end); % conatains all of the delay times
E = (h*c)./(wavelength*10^-9); % contains all of the probe energies
Range_E = E>=1.5 & E<=2.2;
Range_T = delay_t>=0.5 & delay_t<=1000;
% for one delay time
T = find(Range_T);
T_min = min(T);
T_max = max(T);
t = min(T); % choose an integer b/w T_min and T_max
delaytime = delay_t(1, t);
% Data for fitting
E_p = E(Range_E); % selected probe energies
delta_Abs = -1*data(Range_E,t);
delta_Abs_norm = delta_Abs./max(delta_Abs); % normalised delta_Abs
Range_Efit = E_p>=1.65 & E_p<=max(E_p);
E_fit = E_p(Range_Efit);
delta_Abs_norm_fit = delta_Abs_norm(Range_Efit);
% Fitting function
function F = MB(y, E_fit)
F = y(1).*exp(-(E_fit./(8.617333268*10^-5.*y(2)))) + y(3);
end
%% Curve fitting options
% Initial parameter guess and bounds
lb = [0, 293, -Inf]; ub = [Inf, Inf, Inf];
y0 = [4*10^7, 900, 2];
% lsqcurvefit and choose between different algorithm that lsqcurvefit employs (3C1, comment those lines that are not choosen and uncomment the line that is choosen, if not, matlab will take the last line of "optim_lsq" by default)
% optim_lsq = optimoptions(‘lsqcurvefit’, ‘Algorithm’, ‘levenberg-marquardt’, ‘MaxFunctionEvaluations’,10^5, ‘MaxIterations’, 10^5, ‘FunctionTolerance’,10^-10, ‘StepTolerance’, 10^-10);
optim_lsq = optimoptions(‘lsqcurvefit’, ‘Algorithm’, ‘trust-region-reflective’, ‘MaxFunctionEvaluations’,10^5, ‘MaxIterations’,10^5, ‘FunctionTolerance’,10^-20, ‘StepTolerance’, 10^-20);
% optim_lsq = optimoptions(‘lsqcurvefit’, ‘Algorithm’, ‘interior-point’, ‘MaxFunctionEvaluations’,1000, ‘MaxIterations’, 1000, ‘FunctionTolerance’,10^-20, ‘StepTolerance’, 10^-20);
% Solver for lsqcurvefit
[y, residualnorm, residual, exitflag, output, lambda, jacobian] = lsqcurvefit(@MB, y0, E_fit, delta_Abs_norm_fit, lb, ub);
%% Error bars calculation
ci = nlparci(y, residual, ‘Jacobian’, jacobian);
PCI = table(ci(:,1), y(:), ci(:,2),’VariableNames’,{‘CI 0.025′,’y’,’CI 0.975′});
Parameter_CI = table2array(PCI);
upper_bar = (Parameter_CI(:,3) – Parameter_CI(:,2))./2;
lower_bar = (Parameter_CI(:,2) – Parameter_CI(:,1))./2;
%% Plot command
plot(E_p, delta_Abs_norm,’Black’)
hold on
plot(E_fit, MB(y, E_fit), ‘LineWidth’, 1.0, ‘Color’, ‘red’)
xlabel(‘Probe Photon Energy (eV)’)
ylabel(‘Normalised Delta A (a.u.)’)
legend(‘Experimental Data’, ‘Fitted Curve’)
Some background info regarding the data:
There’s a range of values in the first column and these corresponds to this quantity called wavelength. After I have extracted the wavelength from there, I’ll process it into this quantitiy call E. However, E takes a range of values and I’ll only need the values ranging from E = 1.5 to E = 2.2 (this is the data used for the scatterplot, it is named as E_p in my code)
After the first step is done, I’ll now need to choose the range of E_p (E_p = 1.65 to E_p = 2.2) for the fitting of my data (this is named as E_fit in my code) note: the range of values for fitting range of values for scatter plot
Subsequently, I’ll need to look at the first row of my data and select some of them (they need to be positive). Once I have selected them, I’ll need to select the data in the same column as them and this needs to correspond to both E_p and E_fit.
In conclusion, the data selected in 1. and 2. goes to the horizontal axis and the data selected in 3. goes to the vertical axis.
Thank you. curve fitting MATLAB Answers — New Questions
