Why won't fitpeaks work on my data?

Hi, I have a Raman spectrum in a .txt file, with one column of my x axis values and another with my y axis. I am trying to write a script so I can conduct bulk analysis of lots of spectra, but I am struggling!

I am using the following code to read in my data.

data = importdata('RamanData.txt');
plot(data);
[pks,loc] = findpeaks(data);
findpeaks(data)

MATLAB plots my data (alongside a diagonal line?)

I also get these errors:

Error using findpeaks
Expected Y to be a vector.

Error in findpeaks>parse_inputs (line 199)
validateattributes(Yin,{'double','single'},{'nonempty','real','vector'},...
    
Error in findpeaks (line 136)
= parse_inputs(isInMATLAB,Yin,varargin{:});

Error in FindPeak (line 3)
[pks,loc] = findpeaks(data);

Is this an error in my data set up, script or should I be using a different function?

Answer 1

[Rik]

I guess boldly:

Your txt file contains both the magnitude and the wavelength. The plot function gave you a plot with two lines: one with the magnitude and one with the wavelenghts. That is why your x-axis is 0-1700, instead of 470(?) to 2000 nm(?).

You need to separate the matrix that importdata returned into the two respective vectors. Then you can supply the wavelength only to findpeaks.

You can confirm this by looking at the size of data.

[Sam]

Thank you very much, I was not aware that only the wavelength was required!

Answer 2

[Image Analyst]

It's the magnitude that is required if you want to get indexes.

data = importdata('RamanData.txt');
wavelengths = data(:, 1); % Wavelengths in column 1
magnitude = data(:, 2); % Signal magnitude in column 2
plot(wavelengths, magnitude, 'b-', 'LineWidth', 2);
[peakValues, indexesOfPeaks] = findpeaks(magnitude);
wavelengthsOfPeaks = wavelengths(indexesOfPeaks);

Or specify wavelength as the second input if you want wavelength for location instead of indexes.

data = importdata('RamanData.txt');
wavelengths = data(:, 1); % Wavelengths in column 1
magnitude = data(:, 2); % Signal magnitude in column 2
plot(wavelengths, magnitude, 'b-', 'LineWidth', 2);
[peakValues, wavelengthsOfPeaks] = findpeaks(magnitude, wavelengths);