peakfinder info.txt

Basic function to locate and measure the positive peaks in a noisy data sets. Detects peaks by loo

FINDPEAKS,  Version 1.6 October 26, 2006
Tom O'Haver, [e-mail]


findpeaks
function P=findpeaks(x,y,SlopeThreshold,AmpThreshold,smoothwidth,FitWidth)
Basic function to locate and measure the positive peaks in a noisy
data sets.  Detects peaks by looking for downward zero-crossings
 in the smoothed third derivative that exceed SlopeThreshold 
 and peak amplitudes that exceed AmpThreshold.  Determines, 
 position, height, and approximate width of each peak by least-squares 
 curve-fitting the log of top part of the peak with a parabola.
 Returns a list (in matrix P) containing the peak number and
 position, height, and width of each peak.
 The 4 parameters are:
 SlopeThreshold (SlopeT) - Slope of the smoothed third-derivative that is  
   taken to indicate a peak. Larger values will neglect small features.
 AmpThreshold (AmpT) - Any peaks with height less than this value are ignored.
 SmoothWidth - Width of smooth functions applied to data before slope is
   measured. Larger values will neglect small features. A reasonable value is 
   about equal to 1/2 of the half-width of the peaks.
 FitWidth - The number of points around the "top part" of the (unsmoothed)
   peak that are taken to estimate the peak heights, positions, and widths.
   A reasonable value is about equal to 1/2 of the half-width of the peaks. 

DemoFindPeak
A simple demonstration script using the findpeaks function on noisy synthetic data. Numbers the peaks and prints out the P matrix in the Matlab command window:

FindPeakSliders
Interactive findpeaks script for your own data. Requires 
Matlab 6.5. This can be used to  determine what values of the 
parameters give the most reliable peak detection.
Load your data set into the vectors x and y 
(x = independent variable, y = dependent variable), then run this 
m-file and adjust the four sliders to change the four arguments 
of the peakfind function. The range of the sliders is easily 
changed to suit a wide range of data types. The BG button is used 
for baseline (background) subtraction: click once on the BG button, then click on the baseline at five points starting to the left of the lowest x-value and ending to the right of the higest x-value. The background will be subtracted. You can repeat as 
needed.  (You can also change the number of baseline points by 
changing BaselinePoints in the function BG.m). Peak number and the 
estimated position, height, and width of each peak is returned 
in the matrix P:

DemoFindPeakSliders
A self-contained interactive demonstration of FindPeakSliders applied to noisy synthetic data set consisting of a random number of narrow peaks. Use the sliders to explore the effect of the variables SlopeThreshold (SlopeT), AmplitudeThreshold (AmpT), SmoothWidth (Smooth), and FitWidth (Fit). Peak number and the estimated position, height, and width of each peak is returned in the matrix P.

DemoFindPeakSliders2
A self-contained interactive demonstration of FindPeakSliders applied to
noisy synthetic data set consisting of a random number of narrow peaks. Requires Matlab 6.5.  Use the sliders to explore the effect of the variables SlopeThreshold (SlopeT), AmplitudeThreshold (AmpT), SmoothWidth (Smooth), and FitWidth (Fit). Peak number and the estimated 
 position, height, and width of each peak is returned in the matrix P.

FindPeakSlidersG
 Interactive findpeaks script with peak-zoom feature, 
 for pre-defined data in x,y. 
 Load a typical data set into the vectors x,y, then run this 
 m-file and adjust the 5 sliders to determine what values of the 
 parameters give the most reliable peak detection. Peak number and 
 position, height, and width of each peak is returned in the matrix P. 
 The 5 sliders are:
 SlopeThreshold (SlopeT) - Slope of the smoothed third-derivative that is  
   taken to indicate a peak. Larger values will neglect small features.
 AmpThreshold (AmpT) - Any peaks with height less than this value are ignored.
 SmoothWidth - Width of smooth functions applied to data before slope is
   measured. Larger values will neglect small features. The best value is 
   about equal to the half-width of the peaks.
 FitWidth - The number of points around the "top part" of the (unsmoothed)
   peak that are taken to determine the peak height, positions, and width.
   The best value is about equal to the half-width of the peaks.
 Peak - This slider zooms in on any one of the detected peaks, and shows
   the fitted top of the peak (FitWidth) as a blue curve. To see all the
   peaks, set the Peaks slider to zero (all the way down).
The BG button is used 
for baseline (background) subtraction: click once on the BG button, then click on the baseline at five points starting to the left of the lowest x-value and ending to the right of the higest x-value. The background will be subtracted. You can repeat as 
needed.  (You can also change the number of baseline points by 
changing BaselinePoints in the function BG.m). 
 Note: If the slider ranges are not appropriate for your data, change 
   them in lines 61 - 66.

DemoFindPeakSlidersG
Self-contained interactive demo of findpeaks function with 
peak-zoom feature. 

The remaning m-files in the folder are called by the above functions 
and scripts.