# Question about using the "fit_mutiple_gaussians" from File Exchange

조회 수: 1(최근 30일)
Teshan Rezel 2022년 7월 21일
답변: Mathieu NOE 2022년 7월 21일
Hi folks,
The file in question can be found here.
I am sure I'm using it wrong so please bear with me!
I am trying to input my own data to analyse, but the result looks wrong, as per the image below.
I tried to inout my data as follows, replacing the "x" parameter with my data. May I ask if anyone can point out what I'm doing wrong please?
numGaussians = 4;
myPath = 'F:\Histogram Analysis.xlsx';
centers = randi(100, 1, numGaussians);
% Make widths in the range 0 - 20
sigmas = randi(20, 1, numGaussians);
% Make amplitudes in the range 0 - 40
amplitudes = randi([10, 40], 1, numGaussians);
% Make signal that is the sum of all Gaussians
% g = gaussian(x, peakPosition, width)
x = data.(1)(2:end);
% x = linspace(0, 150, 1000);
y = zeros(1, numel(x));
% y = data.(1)(2:end);
hFig = figure;
##### 댓글 수: 2표시숨기기 이전 댓글 수: 1
Teshan Rezel 2022년 7월 21일
@Mathieu NOE thank you, I've amended the post!

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### 채택된 답변

Mathieu NOE 2022년 7월 21일
here the code a bit simplified
but the results with a 4 gaussian model does not really fit well. I think this come mostly from the distorded shape of the major peak , so another model should be used IMHO
clearvars
% Demo to fit multiple Gaussians to data.
clc; % Clear the command window.
fprintf('Beginning to run %s.m.\n', mfilename);
clear global;
workspace; % Make sure the workspace panel is showing.
format long g;
format compact;
fontSize = 20;
y = x;
x = 1:numel(y);
% First specify how many Gaussians there will be.
numGaussians = 4;
% estimated parameters
% peaks y values
[PKS,LOCS]= findpeaks(y,'NPeaks',numGaussians);
amplitudes = PKS;
centers = x(LOCS);
sigmas = x(LOCS)/30;
% Put all the parameters into a table for convenience in looking at, and using, the results.
tActual = table((1:numGaussians)', amplitudes(:), centers(:), sigmas(:), 'VariableNames', {'Number', 'Amplitude', 'Mean', 'Width'});
% Now sort parameters in order of increasing mean, just so it's easier to think about (though it's not required).
tActual = sortrows(tActual, 3);
tActual.Number = (1:numGaussians)' % Unsort the first column of numbers.
% Sum up the component curves to make our test signal that we will analyze to try to guess the component curves from.
legendStrings = cell(numGaussians, 1);
%----------------------------------------------------------------------------------------------------------------------------------
% Initial Gaussian Parameters
initialGuesses = [tActual.Mean(:), tActual.Width(:)];
% Add a little noise so that our first guess is not dead on accurate.
initialGuesses = initialGuesses + 2 * rand(size(initialGuesses))
startingGuesses = reshape(initialGuesses', 1, [])
global c NumTrials TrialError
% warning off
% Initializations
NumTrials = 0; % Track trials
TrialError = 0; % Track errors
% t and y must be row vectors.
tFit = reshape(x, 1, []);
y = reshape(y, 1, []);
%-------------------------------------------------------------------------------------------------------------------------------------------
% Perform an iterative fit using the FMINSEARCH function to optimize the height, width and center of the multiple Gaussians.
options = optimset('TolX', 1e-4, 'MaxFunEvals', 10^12); % Determines how close the model must fit the data
% First, set some options for fminsearch().
options.TolFun = 1e-4;
options.TolX = 1e-4;
options.MaxIter = 100000;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% HEAVY LIFTING DONE RIGHT HERE:
% Run optimization
[parameter, fval, flag, output] = fminsearch(@(lambda)(fitgauss(lambda, tFit, y)), startingGuesses, options);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%----------------------------------------------------------------------------------------------------------------
% Now plot results.
yhat = PlotComponentCurves(x, y, tFit, c, parameter);
% Compute the residuals between the actual y and the estimated y and put that into the graph's title.
meanResidual = mean(abs(y - yhat));
fprintf('The mean of the absolute value of the residuals is %f.\n', meanResidual);
caption = sprintf('Estimation of %d Gaussian Curves that will fit data. Mean Residual = %f.', numGaussians, meanResidual);
title(caption, 'FontSize', fontSize, 'Interpreter', 'none');
drawnow;
% Make table for the fitted, estimated results.
% First make numGaussians row by 3 column matrix: Column 1 = amplitude, column 2 = mean, column 3 = width.
% parameter % Print to command window.
estimatedMuSigma = reshape(parameter, 2, [])';
gaussianParameters = [c, estimatedMuSigma];
% Now sort parameters in order of increasing mean
gaussianParameters = sortrows(gaussianParameters, 2);
tActual % Display actual table in the command window.
% Create table of the output parameters and display it below the actual, true parameters.
tEstimate = table((1:numGaussians)', c(:), estimatedMuSigma(:, 1), estimatedMuSigma(:, 2), 'VariableNames', {'Number', 'Amplitude', 'Mean', 'Width'})
% Plot the error as a function of trial number.
hFigError = figure();
hFigError.Name = 'Errors';
semilogy(TrialError, 'b-');
% hFigError.WindowState = 'maximized';
grid on;
xlabel('Trial Number', 'FontSize', fontSize)
ylabel('Error', 'FontSize', fontSize)
caption = sprintf('Errors for all %d trials.', length(TrialError));
title(caption, 'FontSize', fontSize, 'Interpreter', 'none');
message = sprintf('Done!\nHere is the result!\nNote: there could be multiple ways\n(multiple sets of Gaussians)\nthat you could achieve the same sum (same test curve).');
fprintf('Done running %s.m.\n', mfilename);
msgbox(message);
%=======================================================================================================================================================
function yhat = PlotComponentCurves(x, y, t, c, parameter)
try
fontSize = 20;
% Get the means and widths.
means = parameter(1 : 2 : end);
widths = parameter(2 : 2 : end);
% Now plot results.
hFig2 = figure;
hFig2.Name = 'Fitted Component Curves';
% plot(x, y, '--', 'LineWidth', 2)
hold on;
yhat = zeros(1, length(t));
numGaussians = length(c);
legendStrings = cell(numGaussians + 2, 1);
for k = 1 : numGaussians
% Get each component curve.
thisEstimatedCurve = c(k) .* gaussian(t, means(k), widths(k));
% Plot component curves.
plot(x, thisEstimatedCurve, '-', 'LineWidth', 2);
hold on;
% Overall curve estimate is the sum of the component curves.
yhat = yhat + thisEstimatedCurve;
legendStrings{k} = sprintf('Estimated Gaussian %d', k);
end
% Plot original summation curve, that is the actual curve.
plot(x, y, 'r-', 'LineWidth', 1)
% Plot estimated summation curve, that is the estimate of the curve.
plot(x, yhat, 'k--', 'LineWidth', 2)
grid on;
xlabel('X', 'FontSize', fontSize)
ylabel('Y', 'FontSize', fontSize)
caption = sprintf('Estimation of %d Gaussian Curves that will fit data.', numGaussians);
title(caption, 'FontSize', fontSize, 'Interpreter', 'none');
grid on
legendStrings{numGaussians+1} = sprintf('Actual original signal');
legendStrings{numGaussians+2} = sprintf('Sum of all %d Gaussians', numGaussians);
legend(legendStrings);
xlim(sort([x(1) x(end)]));
hFig2.WindowState = 'maximized';
drawnow;
catch ME
% Some error happened if you get here.
callStackString = GetCallStack(ME);
errorMessage = sprintf('Error in program %s.\nTraceback (most recent at top):\n%s\nError Message:\n%s', ...
mfilename, callStackString, ME.message);
WarnUser(errorMessage);
end
end % of PlotComponentCurves
%=======================================================================================================================================================
function theError = fitgauss(lambda, t, y)
% Fitting function for multiple overlapping Gaussians, with statements
% added (lines 18 and 19) to slow the progress and plot each step along the
% way, for educational purposes.
% Author: T. C. O'Haver, 2006
global c NumTrials TrialError
try
A = zeros(length(t), round(length(lambda) / 2));
for j = 1 : length(lambda) / 2
A(:,j) = gaussian(t, lambda(2 * j - 1), lambda(2 * j))';
end
c = A \ y';
z = A * c;
theError = norm(z - y');
% Penalty so that heights don't become negative.
if sum(c < 0) > 0
theError = theError + 1000000;
end
NumTrials = NumTrials + 1;
TrialError(NumTrials) = theError;
catch ME
% Some error happened if you get here.
callStackString = GetCallStack(ME);
errorMessage = sprintf('Error in program %s.\nTraceback (most recent at top):\n%s\nError Message:\n%s', ...
mfilename, callStackString, ME.message);
WarnUser(errorMessage);
end
end % of fitgauss()
%=======================================================================================================================================================
function g = gaussian(x, peakPosition, width)
% gaussian(x,pos,wid) = gaussian peak centered on pos, half-width=wid
% x may be scalar, vector, or matrix, pos and wid both scalar
% T. C. O'Haver, 1988
% Examples: gaussian([0 1 2],1,2) gives result [0.5000 1.0000 0.5000]
% plot(gaussian([1:100],50,20)) displays gaussian band centered at 50 with width 20.
g = exp(-((x - peakPosition) ./ (0.60056120439323 .* width)) .^ 2);
end % of gaussian()
%=======================================================================================================================================================
% Gets a string describing the call stack where each line is the filename, function name, and line number in that file.
% Sample usage
% try
% % Some code that might throw an error......
% catch ME
% callStackString = GetCallStack(ME);
% errorMessage = sprintf('Error in program %s.\nTraceback (most recent at top):\n%s\nError Message:\n%s', ...
% mfilename, callStackString, ME.message);
% WarnUser(errorMessage);
% end
function callStackString = GetCallStack(errorObject)
try
theStack = errorObject.stack;
callStackString = '';
stackLength = length(theStack);
% Get the date of the main, top level function:
% d = dir(theStack(1).file);
% fileDateTime = d.date(1:end-3);
if stackLength <= 3
% Some problem in the OpeningFcn
% Only the first item is useful, so just alert on that.
[folder, baseFileName, ext] = fileparts(theStack(1).file);
baseFileName = sprintf('%s%s', baseFileName, ext); % Tack on extension.
callStackString = sprintf('%s in file %s, in the function %s, at line %d\n', callStackString, baseFileName, theStack(1).name, theStack(1).line);
else
% Got past the OpeningFcn and had a problem in some other function.
for k = 1 : length(theStack)-3
[folder, baseFileName, ext] = fileparts(theStack(k).file);
baseFileName = sprintf('%s%s', baseFileName, ext); % Tack on extension.
callStackString = sprintf('%s in file %s, in the function %s, at line %d\n', callStackString, baseFileName, theStack(k).name, theStack(k).line);
end
end
catch ME
errorMessage = sprintf('Error in program %s.\nTraceback (most recent at top):\nError Message:\n%s', ...
mfilename, ME.message);
WarnUser(errorMessage);
end
end % from callStackString
%==========================================================================================================================
% Pops up a warning message, and prints the error to the command window.
function WarnUser(warningMessage)
if nargin == 0
return; % Bail out if they called it without any arguments.
end
try
fprintf('%s\n', warningMessage);
uiwait(warndlg(warningMessage));
% Write the warning message to the log file
folder = 'C:\Users\Public\Documents\MATLAB Settings';
if ~exist(folder, 'dir')
mkdir(folder);
end
fullFileName = fullfile(folder, 'Error Log.txt');
fid = fopen(fullFileName, 'at');
if fid >= 0
fprintf(fid, '\nThe error below occurred on %s.\n%s\n', datestr(now), warningMessage);
fprintf(fid, '-------------------------------------------------------------------------------\n');
fclose(fid);
end
catch ME
message = sprintf('Error in WarnUser():\n%s', ME.message);
fprintf('%s\n', message);
uiwait(warndlg(message));
end
end % from WarnUser()

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