A common requirement in signal processing is to detect peaks in
a signal and to measure their positions, heights, and widths. A
common way to do this is to make use of the fact that the first derivative of a peak has a
downward-going zero-crossing at the peak maximum. But the presence
of random noise in real experimental signal will cause many false
zero-crossing simply due to the noise. To avoid this problem, the
technique described here first smooths
the first derivative of the signal, before looking for
downward-going zero-crossings, and then it takes only those zero
crossings whose slope exceeds a certain predetermined minimum
(called the "slope threshold") at a point where the original
signal exceeds a certain minimum (called
the "amplitude threshold"). By carefully adjusting the
smoothwidth, slope threshold, and amplitude threshold, it's
possible to detect only the desired peaks and ignore peaks that
are too small, too wide, or too narrow. Moreover, because
smoothing can distort peak signals, reducing peak heights and
increasing peak widths, this technique estimates the position,
height, and width of each peak by least-squares
curve-fitting of a segment of the original unsmoothed signal in the vicinity of
the zero-crossing. Thus, even if heavy smoothing of the first
derivative is necessary to provide reliable discrimination against
noise peaks, the peak parameters extracted by curve fitting are
not distorted. (This is useful primarily for signals that have
several data points in each peak, not for spikes that have only
one or two points). This technique is capable of measuring peak
positions and heights quite accurately, but the measurements of
peak widths and areas is accurate only if the peaks are
approximately Gaussian in shape. (For the most accurate
measurement of highly overlapped peaks, iPeak
version 3 and above is capable of utilizing non-linear iterative curve fitting).
The routine is now available in several different versions:
function
P=findpeaks(x,y,SlopeThreshold,AmpThreshold,SmoothWidth,FitWidth,smoothtype)
This is my basic command-line function to locate and measure the
positive peaks in a noisy data sets. It detects peaks by looking
for downward zero-crossings in the smoothed first derivative that
exceed SlopeThreshold and peak amplitudes that exceed
AmpThreshold, and determines the position, height, and approximate
width of each peak by least-squares curve-fitting the top part of
the peak. Returns a list (in matrix P) containing the peak
number and the estimated position, height, width, and area of each
peak. It can find and measure over 1000 peaks per
second in very large signals. Version 5.0 (December,
2012) has improved error catching for very noisy data.
The data are passed to the findpeaks function in the
vectors x and y (x = independent variable, y = dependent
variable). The other parameters are user-adjustable:
SlopeThreshold - Slope of the smoothed
first-derivative that is taken to indicate a peak. This
discriminates on the basis of peak width. Larger values of this
parameter will neglect broad features of the signal. A
reasonable initial value for Gaussian peaks is
0.7*WidthPoints^-2, where WidthPoints is the number of data
points in the half-width of the peak. AmpThreshold - Discriminates on the basis of peak height.
Any peaks with height less than this value are ignored. SmoothWidth - Width of the smooth function that is
applied to data before the slope is measured. Larger values of
SmoothWidth will neglect small, sharp features. A reasonable
value is typically about equal to 1/2 of the number of data
points in 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 typically
about equal to 1/2 of the number of data points in the
half-width of the peaks. The minimum value is 3. Smoothtype (added
in Version 4, Sept. 2011) determines the smoothing algorithm
(see http://terpconnect.umd.edu/~toh/spectrum/Smoothing.html)
If smoothtype=1, rectangular (sliding-average
or boxcar)
If smoothtype=2, triangular (2 passes of
sliding-average)
If smoothtype=3, pseudo-Gaussian (3 passes of
sliding-average)
Basically, higher values yield greater reduction in
high-frequency noise, at the expense of slower execution. For a
comparison of these smoothing types, see SmoothingComparison.html.
Optimization of peak finding The optimum
values of the input arguments for findpeaks and related functions
depend on the signal and on which features of the signal are
important for your work. Rough values for these parameters can be
estimated based on the width of the peaks that you wish to detect,
as described above, but in many cases it will be best to fine-tune
these parameters for your particular signal.
In the example shown on the left (using the interactive peak
detector iPeak program described below), the
important parts of the signal are two broad peaks at
x=4 and x=6, the second one half the height of the
first. The small jagged features are just random noise. We want to
detect the two peaks but ignore the noise. (The detected peaks are
numbered 1,2,3,...in the lower panel of this graphic). This is
what it looks like if the AmpThreshold is too small or too large, if the
SlopeThreshold is too small or too large, if
the SmoothWidth is too small or too large, if
the FitWidth is too small or too large. If
these parameters are in the optimum range for this objective, the
findpeaks functions will return something like this (although the
exact values will vary with the noise and with the value of
FitWidth):
Peak# Position
Height
Width
Area
1
3.9649
0.99919
1.8237
1.94
2
5.8675
0.53817
1.6671
0.95516 How
is 'findpeaks' different from 'max' in Matlab or 'findpeaks' in
the Signal Processing Toolkit?
The 'max' function simply returns the largest single
value in a vector. Findpeaks in the Signal
Processing Toolbox can be used to find the values and
indices of all the peaks in a vector that are higher than a
specified peak height and are separated from their neighbors by a
specified minimum distance. My version of findpeaks accepts
both an independent variable (x) and dependent variable (y)
vectors, finds the places where the average curvature over a
specified region is concave down, fits that region with a
least-squares fit, and returns the peak position (in x units),
height, width, and area, of any peak that exceeds a specified
height. For example, let's create a noisy series of peaks (plotted
on the right) and apply each of the functions to the resulting data.
Now, anyone looking at this plot of data would count 16 peaks,
with peak heights averaging about 10 units. Every time the
statements are run, the random noise is different, but you would
still count the 16 peaks. But the findpeaks function in the Signal
Processing Toolbox, [PKS,LOCS]=findpeaks(y,'MINPEAKHEIGHT',5,'MINPEAKDISTANCE',11)
counts anywhere from 11 to 20 peaks, with an average height (PKS) of 11.5.
In contrast, my findpeaks function returns 16 peaks every time,
with a mean height of 10 ħ0.3.
findpeaks(x,y,0.001,5,11,11,3)
It also measures the width and area, if the peaks are Gaussian (or
Lorentzian, in the variant findpeaksL). On the other hand, findpeaks in the Signal Processing
Toolbox works better for peaks that have only 1-3 data
points on the peak; my function is better for peaks that
have a lot of points.
findvalleys.
There is also a similar function for finding valleys (minima), called findvalleys.m, which works the same way
as findpeaks.m, except that it locates minima instead of
maxima. Only valleys above (that is, more positive or less
negative than) the AmpThreshold are detected; if you wish to
detect valleys that have negative minima, then AmpThreshold must
be set more negative than that.
>>
x=[0:.01:50];y=cos(x);P=findvalleys(x,y,0,-1,5,5)
P =
1.0000 3.1416
-1.0000
2.3549 0
2.0000 9.4248
-1.0000
2.3549 0
3.0000 15.7080
-1.0000
2.3549 0
4.0000 21.9911
-1.0000
2.3549 0
5.0000 28.2743
-1.0000
2.3549 0
6.0000 34.5575
-1.0000
2.3549 0
7.0000 40.8407
-1.0000
2.3549 0
8.0000 47.1239
-1.0000
2.3549 0 The accuracy of the measurements of peak position,
height, width, and area by the findpeaks function depends on the
shape of the peaks, the
extent of peak overlap, and signal-to-noise ratio. The width and
area measurements particularly are strongly influenced by peak
overlap, noise, and the choice of FitWidth. Isolated peaks of
Gaussian shape are measured most accurately. For peak of Lorentzian
shape, use findpeaksL.m
instead (the only difference is that the reported peak heights,
widths, and areas will be more accurate if the peak are actually
Lorentzian). See "ipeakdemo.m" below for an accuracy trial for
Gaussian peaks. For the most accurate measurements of highly
overlapping peaks of various shapes, use peakfit.m
or the Interactive
Peak Fitter (ipf.m).
For a direct comparison of the accuracy of findpeaks vs
peakfit, run the script peakfitVSfindpeaks.m.
This script (figure on the left) generates four very noisy
peaks of different heights and widths, then applies
findpeaks.m and peakfit.m to measure the peaks and
compares the results. The peaks detected by findpeaks are
labeled "Peak 1", "Peak 2", etc. If you run this script
several times, you'll find that both methods work well
most of the time, with peakfit giving smaller errors in
most cases, but occasionally findpeaks will miss the first
(lowest) peak and rarely it will detect an extra peak that
is not there if the signal is very noisy.
findpeaksb.mis a variant of findpeaks.m that more accurately
measures peak parameters by using iterative least-square
curve fitting based on peakfit.m. This
yields better peak parameter values that findpeaks alone,
because it can be set for different peak shapes and it
fits the entire peak, not just the top part, and because
it has provision for background subtraction (linear or
quadratic). This function works best with isolated peaks
that do not overlap. For version 3, the syntax is P
= findpeaksb(x,y, SlopeThreshold, AmpThreshold,
smoothwidth, peakgroup, smoothtype, windowspan, PeakShape,
extra, background
correction mode). The first seven input arguments
are exactly the same as for the findpeaks.m function; if
you have been using findpeaks or iPeak to find and measure
peaks in your signals, you can use those same input
argument values for findpeaksb.m. The remaining four input
arguments of are for the peakfit function: "windowspan"
specifies the number of data points over which each peak
is fit to the model shape (it must be large enough to
cover the entire peak and get down to the background on
both sides of the peak); "PeakShape" specifies the model
peak shape: "peakshape" (1=Gaussian, 2=Lorentzian, etc),
"extra" is the shape modifier variable that is used for
the Voigt, Pearson, exponentially broadened Gaussian and
Lorentzian, Gaussian/Lorentzian blend, and bifurcated
Gaussian and Lorentzian shapes to fine-tune the peak
shape; "background
correction" is 0, 1, 2, or 3 for no, linear,
quadratic, or flat background subtraction.
The peak table returned by the function
has a 6th column listing the percent
fitting errors for each peak. The
demonstration script DemoFindPeaksb.m
shows how findpeaksb works with multiple
peaks on a curved background.
Here is a simple example with three Gaussians on a linear
background, comparing plain findpeaks to
findpeaksb with and without background
subtraction:
x=1:.2:100;Heights=[1 2 3];Positions=[20 50
80];Widths=[3 3 3]; y=2-(x./50)+modelpeaks(x,3,1,Heights,Positions,Widths)+.02*randn(size(x));plot(x,y); disp('
Peak
Position
Height
Width
Area %
error') PlainFindpeaks=findpeaks(x,y,.00005,.5,30,20,3) NoBackgroundSubtraction=findpeaksb(x,y,.00005,.5,30,20,3,150,1,0,0) LinearBackgroundSubtraction=findpeaksb(x,y,.00005,.5,30,20,3,150,1,0,1) findpeaksb3.m is a variant of
findpeaksb.m that fits each detected peak along with the previous
and following peaks found by findpeaks.m, so as to deal better
with overlap of the adjacent peaks. The syntax is function FPB=findpeaksb3(x,y,
SlopeThreshold, AmpThreshold, smoothwidth, peakgroup,
smoothtype, PeakShape, extra, NumTrials, AUTOZERO, ShowPlots).
The demonstration script DemoFindPeaksb3.m shows
how findpeaksb3 works with multiple overlapping
Lorentzian peaks, as in the example on the left.
The
function findpeaksplot.m
is a simple variant of findpeaks.m that also plots the x,y
data and numbers the peaks on the graph (if any are
found). An example is shown on the right.
The function peakstats.m
uses the same algorithm as findpeaks, but it computes and
returns a table of summary statistics of the peak
intervals (the x-axis interval between adjacent detected
peaks), heights, widths, and areas, listing the maximum,
minimum, average, and percent standard deviation of each,
and optionally plotting the x,y data with numbered peaks
in figure window 1, printing the table of peak statistics
in the command window, and plotting the histograms
of the peak intervals, heights, widths, and areas in the
four quadrants of figure window 2. Type "help peakstats".
The syntax is the same as findpeaks, with the addition of
a 8th input argument to control the display and plotting.
Example:
>>
x=[0:.1:1000];y=5+5.*cos(x)+randn(size(x));PS=peakstats(x,y,0,-1,15,23,3,1);
Peak Summary Statistics
158 peaks detected
Interval
Height
Width
Area
Maximum
6.6195
10.8991
4.7749 47.3653
Minimum
5.9086
9.1022
2.4123 26.3111
Mean
6.2833
10.0183
3.2346 34.4027
% STD
1.7362
3.2154
13.028 10.9314
With the last input argument omitted or equal to
zero, the plotting and printing in the command window are
omitted; the numerical values of the peak statistics table
are returned as a 4x4 array, in the same order as the
example above.
FindpeaksE.m
is a variant of findpeaks.m that additionally estimates
the percent relative fitting error of each peak (assuming
a Gaussian peak shape) and returns it in the 6th column of
the peak table.
Example:
Peak start and end. Defining
the "start" and "end" of the peak (the x-values where the peak
begins and ends) is a bit arbitrary because typical peak shapes
approach the baseline asymptotically far from the peak maximum.
You might define the peak start and end points as the x values
where the y value is some small fraction, say 1%, of the peak
height, but then the random noise on the baseline is likely to be
a large fraction of the signal amplitude at that point. Smoothing
to reduce noise is likely to distort and broaden peaks,
effectively changing their start and end points. One solution to
this dilemma is to fit each peak to a model shape, then calculate
the peak start and end from the model expression. That
minimizes the noise problem by fitting the data over the entire
peak, but it works only if the peaks can be accurately modeled by
available fitting programs. For example, Gaussian peaks can
be shown to reach a fraction a of the peak
height at x=pħsqrt(w^2 log(1/a))/(2
sqrt(log(2))) where p is the peak position and w
is the peak width. So, for example if a=.01, x=pħw*sqrt((log(2)+log(5))/(2
log(2)))=1.288784*w. Lorentzian peaks can
be shown to reach a fraction a of the peak height at x=pħsqrt[(w^2
- aw^2)/a]/2. If a=.01, x=pħ(3/2
sqrt(11)*w)=4.97493*w. The findpeaks variants findpeaksGSS.m and findpeaksLSS.m, for Gaussian and
Lorentzian peaks respectively, compute the peak start and end
positions in this manner and return them in the 6th and 7th
columns of the peak table P. (For greater accuracy with
overlapping peaks, use peakfit.m
or the Interactive Peak Fitter (ipf.m)
and calculate the start and end from the peak positions and width
using the formulas above).
findpeaksfit.m is a findpeaks variant
that is essentially a serial combination of findpeaks.m and peakfit.m. It uses the
number of peaks found and the peak positions and widths determined
by findpeaks as input for the peakfit.m function, which then fits
the entire signal with the specified peak model. This
combination yields better values that findpeaks alone, because
peakfit fits the entire peak, not just the top part, and it deals
with non-Gaussian and overlapped peaks. However, it fits only
those peaks that are found by findpeaks. The syntax is
function [P,FitResults,LowestError,BestStart,xi,yi] =
findpeaksfit(x,y,SlopeThreshold,AmpThreshold,smoothwidth,peakgroup,smoothtype,peakshape,extra,NumTrials,baseline
correction mode,fixedparameters,plots)
The first seven input arguments are exactly the same as for the
findpeaks.m
function; if you have been using findpeaks or iPeak to find and
measure peaks in your signals, you can use those same input
argument values for findpeaksfit.m. The remaining six input
arguments of findpeaksfit.m are for the peakfit function; if you
have been using peakfit.m or ipf.m
to fit peaks in your signals, you can use those same input
argument values for findpeaksfit.m. Type "help findpeaksfit" for
more information.
Note: findpeaksfit.m differs from findpeaksb.m
in that findpeaksfit.m
fits all the found peaks at one time with a single multi-peak
model, whereas findpeaksb.m
fits each peak separately with a single-peak model. As a
result, findpeaksfit.m works better with a relatively
small number of peak that overlap, whereas findpeaksb.m
works better with a large number of isolated non-overlapping
peaks
.
findsteps.m
Syntax: P=findsteps(x,y,SlopeThreshold,AmpThreshold,peakgroup)
locates positive steps in noisy x-y time series data, by computing
the first derivative of y that exceed SlopeThreshold, computes the
step height as the difference between the maximum and minimum y
values over a number of data point equal to "Peakgroup". Returns
list (P) with step number, x position, and the step height of each
step detected; "SlopeThreshold" and "AmpThreshold" control step
sensitivity; higher values will neglect smaller features. See findsteps.png
for a real example. Rectangular pulses.
Rectangular pulses (square waves) require a different approach,
based on amplitude discrimination rather than differentiation. The
function "findsquarepulse.m"
(syntax S=findsquarepulse(t,y,threshold) locates the
rectangular pulses in the signal t,y that exceed a y-value of
"threshold" and determines their start time, average height
(relative to the baseline) and width. DemoFindsquare.m creates a test signal
and calls findsquarepulse.m to demonstrate. If the
signal is very noisy, some preliminary rectangular smoothing (e.g. using fastsmooth.m) before calling
findsquarepulse.m may be helpful to eliminate false
peaks.
Using the peak table. All these peak
finding functions return the peak table as a matrix, with one row
for each peak detected and with several columns listing the peak
number, position, height, width, and area in columns 1 - 5 (with
additional columns included for the variants findpeaksnr.m, findpeaksGSS.m, and findpeaksLSS.m). You
can assign this matrix to a variable (e.g. P, in the
examples above) and then use Matlab/Octave functions
to extract specific information from that matrix. For example:
[P(:,2) P(:,3)]is the time
series of peak heights (peak position in the 1st column and peak
height in the 2nd column) mean(P(:,3))
returns the average peak height of all peaks (because
peak height is in column 3); max(P(:,3))
returns the maximum peak height; hist(P(:,3))
displays the histogram of peak heights; std(P(:,4))/mean(P(:,4))
returns the relative standard deviation of the peak widths (column
4) for
n=1:length(P)-1;d(n)=max(P(n+1,2)-P(n,2));end creates "d" as the
vector of x-axis distance between adjacent peaks (because peak
position is in column 2).
Using my val2ind.m function
(download this function and place in the Matlab path): val2ind(P(:,3),7.5)
returns the peak number of the peak whose height (column
3) is closest to 7.5; P(val2ind(P(:,2),7.5),3) returns
the peak height (column 3) of the peak whose position (column
2) is closest to 7.5;
and so on.
DemoFindPeak.m is a
simple demonstration script using the findpeaks function
on noisy synthetic data. Numbers the peaks and prints out
the peak table in the Matlab command window:
DemoFindPeakSNR
is a variant of DemoFindPeak.m
that uses findpeaksnr.m
to compute
the signal-to-noise ratio (SNR) of each peak and
returns it in the 5th column.
DemoFindPeaksb.m
is a similar demonstration script that uses
the findpeaksb function on noisy synthetic
data consisting of several Gaussian peaks
superimposed on a curved background.
(The findpeaks function would not give
accurate measurements of peak height, width,
and area for this signal, because it does not
correct for the background). Peak
# Position
Height
Width
Area Fitting
error Measuredpeaks =
1
599.13
1.0059
49.533
53.044 9.6798
2
799.44
1.0206
45.073
48.974 8.6772
3
1000
3.9501
49.221
206.99 2.2302
4
1200.8
1.9413
49.133
101.54 5.195
5
1599.8
3.9979
49.138
209.14 2.4324
.....
Peak Identification
The command line function idpeaks.m is
used for identifying peaks according to their x-axis maximum
positions. The syntax is
It finds peaks in the signal "DataMatrix" (x-values in column 1
and y-values in column 2), according to the peak detection
parameters "AmpT", "SlopeT", "SmoothWidth", "FitWidth" (see the
"findpeaks" function above), then compares the found peak
positions (x-values) to a database of known peaks, in the form of
an array of known peak maximum positions ('Positions') and
matching cell array of names ('Names'). If the position of a peak
found in the signal is closer to one of the
known peaks by less than the specified maximum error ('maxerror'),
that peak is considered a match and its peak position, name,
error, and peak amplitude (height) are entered into the output
cell array "IdentifiedPeaks". The full list of detected peaks,
identified or not, is returned in "AllPeaks". Use "cell2mat" to
access numeric elements of IdentifiedPeaks,e.g. cell2mat(IdentifiedPeaks(2,1))
returns the position of the first identified peak, cell2mat(IdentifiedPeaks(2,2))
returns its name, etc. Obviously for your own applications, it's up to you to
provide your own array of known peak maximum positions
('Positions') and matching cell array of names ('Names') for
your particular types of signals. The interactive iPeak function described in the next section
has this function built inas one of the
keystroke commands.
Example: Download idpeaks.zip, extract it, and place the
extracted files in the Matlab or Octave path. This
contains a high-resolution atomic emission spectrum of copper
('spectrum') and a data table of known Cu I and II atomic lines
('DataTable') containing their positions and names.
iPeak is a
keyboard-operated
interactive peak finder for time series data, based on the "findpeaks.m" function, for
Matlab only.It accepts data in a single vector,
a pair of vectors, or a matrix with the independent variable in
the first column and the dependent variable in the second
column:
Example 1:One input argument; data in single vector >> y=cos(.1:.1:100);ipeak(y)
Example 2: One input argument; data in two columns of a matrix >> x=[0:.01:5]';y=x.*sin(x.^2).^2;M=[x y];ipeak(M)
Example 3: Two input
arguments; data in separate x and y vectors >>
x=[0:.1:100];y=(x.*sin(x)).^2;ipeak(x,y);
Example 4: Additional
input argument (after the data) to control peak sensitivity.
>>
x=[0:.1:100];y=5+5.*cos(x)+randn(size(x));ipeak(x,y,10); or
>> ipeak([x;y],10); or
>> ipeak(humps(0:.01:2),3)
or >>
x=[0:.1:10];y=exp(-(x-5).^2);ipeak([x' y'],1)
The additional numeric argument is an estimate of maximum peak
density (PeakD), the ratio
of the typical peak width to the length of the entire data
record. Small values detect fewer peaks; larger values detect more peaks. It effects only the
starting values for
the peak detection parameters. (This is just a quick way to
set reasonable initial values of the peak detection parameters, rather
than specifying each one individually).
iPeak displays the entire
signal in the lower half of the Figure window and an adjustable
zoomed-in section in the upper window. Pan and zoom the portion
in the upper window using the cursor arrow keys. The peak closest to the center of
the upper window is labeled in the upper left of the top window,
and it peak position, height, and width are listed. The Spacebar/Tab
keysjump to the next/previous detected
peak and displays it in the upper window at the current zoom
setting (use
the up and down cursor arrow keys to adjust the zoom range). Or you can pressthe J key to jump to a specified peak
number (Version 5.7 and later).
Adjust the peak detection
parameters AmpThreshold (A/Z keys), SlopeThreshold (S/X), SmoothWidth
(D/C), FitWidth (F/V) so that it detects the
desired peaks and ignores those that are too small, too broad,
or too narrow to be of interest. You can also type in a specific value of
AmpThreshold by pressing Shift-A or a specific value of
SlopeThreshold by pressing Shift-S. Detected peaks are numbered from
left to right.
Press P to display the peak table of all the detected
peaks (Peak #, Position, Height, Width, Area, and percent
fitting error): Gaussian shape mode (press Shift-G to
change) Window span: 169 units Linear baseline subtraction
Peak# Position
Height
Width
Area Error
1
500.93
6.0585
34.446
222.17 9.5731
2
767.75
1.8841
105.58
211.77 25.979
3
1012.8
0.20158
35.914
7.7071 269.21
............. Press Shift-G to switch between Gaussian and
Lorentzian shape modes. Press Shift-P to save peak table
as disc file. Press U to switch between peak and valley
mode. Don't forget
that only valleys above (that is,
more positive or less negative than) the AmpThreshold are
detected; if you wish to detect valleys that have negative
minima, then AmpThreshold must be set more negative than
that. Note: to speed up the operation for
signals over 100,000 points in length, the lower window is
refreshed only when the number of detected peaks changes or if
the Enter key is pressed. Press K to see all
the keystroke commands.
Press U key to switch
between peak and valley mode.
If the density of data points on the peaks is too low
- less than about 4 points - the peaks may not be reliably
detected; you can improve reliability by using the
interpolation command (Shift-I) to re-sample the data
by linear interpolation to a larger number of
points. Conversely, if the density of data
points on the peaks of interest is very high - say, more than
100 points per peak - then you can speed up the operation of
iPeak by re-sampling to a smaller number
of points.
Peak
Summary Statistics.The E key prints a table
of summary statistics of the peak intervals (the x-axis
interval between adjacent detected peaks), heights, widths,
and areas, listing the maximum, minimum, average,
and percent standard deviation, and displaying the histogramsof the peak intervals, heights,
widths, and areas in figure windows 2 through 5. Peak Summary
Statistics 15 peaks detected No
baseline correction
Interval Height
Width Area Maximum
6.3795 10.5308
3.2354 34.943 Minimum
6.1649 9.7355
2.6671 29.9008 Mean
6.291
10.1559 3.0149 32.5771 %
STD 0.91178
1.904 5.2584 4.3022
Example
5: Six
input arguments. As above, but input arguments 3 to 6 directly
specifies initial values of AmpThreshold (AmpT), SlopeThreshold (SlopeT), SmoothWidth (SmoothW), FitWidth (FitW). PeakD is ignored in this case, so
just type a '0' as the second argument after the data matrix). >>
ipeak(datamatrix,0,.5,.0001,20,20);
Pressing 'L' toggles ON and OFF the peak labels in the
upper window.
Keystrokes allow you to pan
and zoom the upper window, to inspect each peak in detail if
desired. You
can set the initial values of pan and zoom in optional input
arguments 7
('xcenter') and
8 ('xrange'). See example 6 below.
The Y keytoggles between linear and log
y-axis scale in the lower window (a log axis is good for
inspecting signals with high dynamic range; it effects only the
lower window display and has no effect on the peak detection or
measurements).
Log scale (Y key) and background
correction mode (T key)
Example 6: Eight input arguments. As above, but input arguments 7 and 8 specify the initial pan and zoom settings, 'xcenter' and 'xrange', respectively. In this example, the x-axis data
are wavelengths in nanometers (nm), and the upper window zooms in on a very
small0.4 nm region centered on 249.7 nm.
(These data,
provided in the ZIP file, are from a
high-resolution atomic spectrum).
>> load
ipeakdata.mat >> ipeak(Sample1,0,100,0.05,3,4,249.7,0.4); Baseline correction modes. The T key cycles thebaseline correction mode from off, to linear, to quadratic,
to flat mode, then back to off. The current mode is displayed above the upper panel. When the
baseline correction mode
is OFF, peak heights are measured relative to zero. (Use this
mode when the
baseline is zero or if you have previously subtracted the baseline
from the entire signal using the Bkey). In thelinear orquadraticmodes,
peak heights are automatically measured relative to the local
baseline interpolated from the points at the ends of the segment displayed in
the upper panel; use
the zoom controls to isolate a group of peaks
so that the
signal returns to the local baseline at the beginning and end of the segment displayed in the upper window. The peak heights, widths, and areas in the peak table (R or P keys)will be automatically corrected for the baseline.Thelinear orquadraticmodes will
work best if the
peaks are well separated so that the signal returns to the local
baseline between the peaks. (If the peaks are highly overlapped, or if they are not
Gaussian in shape, the best results will be obtained by using
the curve fitting function - the N or M keys. The flat mode is used only for curve fitting
function, to account
for a flat baseline offset without reference to the edges
of the signal segment being fit).
Example 7: Nine input arguments. As example 6, but the 9^{th}
input argument sets
the background correction mode (equivalent to
pressing the T key)' 0=OFF; 1=linear; 2=quadratic,
3=flat. If not specified, itis initially OFF. >> ipeak(Sample1,0,100,0.00,3,4,249.7,0.4,1);
Converting to command-line functions. To aid in
writing your own scripts and function to automate processing, the
'Q' key prints out the findpeaks, findpeaksb, and
findpeaksfit commands for the segment of the signal in the upper
window and for the entire signal, with most or all of the input
arguments in place, so you can Copy and Paste into your own
scripts. The 'W' key similarly prints out the peakfit and
ipf commands.
Ensemble averaging.
For signals that contain repetitive waveform patterns occurring in
one continuous signal, with nominally the same shape except for
noise, the ensemble averaging function (Shift-E) can
compute the average of all the repeating waveforms. It works by
detecting a single peak in each repeat waveform in order to
synchronize the repeats (and therefore does not require that the
repeats be equally spaced or synchronized to an external reference
signal). To use this function, first adjust the peak detection
controls to detect only one peak in each repeat pattern,
then zoom in to isolate any one of those repeat patterns, and then
press Shift-E. The average waveform is displayed in Figure
2 and saved as EnsembleAverage.mat in the current directory.See iPeakEnsembleAverageDemo.m. Normal and Multiple Peak
fitting: The N key applies iterative
curve fitting to the detected
peaks that are displayed in the upper window (referred
to here as "Normal" curve fitting). The use of the iterative
least-squares function can result in more accurate peak
parameter measurements than the normal peak table (R or P keys), especially if the peaks are
non-Gaussian in shape or are highly overlapped. (If the peaks are superimposed on a
background, select
the baseline
correction mode using the
T key, then use the pan and zoom keys to
select a peak or a group of overlapping peaks in the upper
window, with the signal returning all the way to the local
baseline at the ends of the upper window if you are using the
linear or quadratic baseline modes). Make sure that the AmpThreshold, SlopeThreshold, SmoothWidth are
adjusted so that each peak is numbered once. Only numbered peaks are fit.Then press the N
key, type a number for the desired peak shape at the prompt in
the Command window and press Enter (1=Gaussian
(default), 2=Lorentzian, 3=logistic, 4=Pearson, 5=exponentially
broadened Gaussian; 6=equal-width Gaussians; 7=Equal-width
Lorentzians; 8=exponentially broadened equal-width Gaussian,
9=exponential pulse, 10=sigmoid, 11=Fixed-width Gaussian,
12=Fixed-width Lorentzian; 13=Gaussian/Lorentzian blend;
14=bifurcated Gaussian, 15=bifurcated Lorentzian, 16=Fixed-position Gaussians;
17=Fixed-position Lorentzians; 18=exponentially broadened Lorentzian; 19=alpha
function;20=Voigt profile), then
type in a number of repeat trial fits and press Enter(the default is 1; start with that
and then increase if necessary). If you have selected a
variable-shape peak (numbers 4, 5, 8 ,13, 14, 15, 18, or 20),
the program will ask you to type in a number that controls the
shape ("extra" in the peakfit input arguments). The program will
then perform the fit, display the results graphically in Figure
window 2, and print out a table of results in the command
window, e.g.:
Peak shape (1-8): 2 Number of trials: 1
Least-squares fit to
Lorentzian peak model Fitting Error 1.1581e-006% Peak#
Position Height Width
Area
1
100
1 50
71.652
2
350
1 100 146.13
3
700
1 200 267.77
Normal
Peak Fit (N key) applied to a group of six overlapping
Gaussians peaks
There is also a "Multiple" peak fit function (M
key) that will attempt to apply iterative curve fitting to allthe detected peaks in the signal
simultaneously. Before using this function, it's best to turn off the
automatic baseline
correction (T
key) and use the
multi-segment baseline correction function (B
key) to remove the background (because the baseline correction function will probably not be able
to subtract the baseline from the entire signal). Then press M and proceed as
for the normal curve fit. A multiple curve fit may take a minute
or so to complete if the number of peaks is large, possibly
longer than the Normal curve fitting function on
each group of peaks separately.
The N and M key fitting functions perform non-linear iterative curve fitting
using the peakfit.m
function. The number of peaks and the starting values of peak
positions and widths for the curve fit function are
automatically supplied by the the findpeaks function, so it is
essential that the peak detection variables in iPeak be adjust
so that all the peaks in the selected region are detected and
numbered once. (For more flexible curve fitting, use ipf.m,
which allows manual optimization of peak groupings and start
positions).
Example 8. This example generates four Gaussian
peaks, all with the exact same peak height (1.00) and area
(1.773). The first peak (at x=4) is isolated, the second peak
(x=9) is slightly overlapped with the third one, and the last two
peaks (at x= 13 and 15) are strongly overlapped.
>> x=[0:.01:20]; >> y=exp(-(x-4).^2)+exp(-(x-9).^2)+exp(-(x-13).^2)+exp(-(x-15).^2); >> ipeak(x,y)
By itself, iPeak does a fairly good just of measuring peaks
positions and heights by fitting just the top part of the peaks,
because the
peaks are Gaussian, but the areas and widths of the last two peaks (which should be 1.665 like the others) are quite a bit too large because of the overlap:
Peak# Position
Height
Width
Area
1
4
1
1.6651 1.7727
2
9
1
1.6651 1.7727
3
13.049
1.0198
1.8381 1.9956
4
14.951
1.0198
1.8381 1.9956
In this case, curve fitting
(using the N or M keys) does a much better job,
even if the overlap is even greater, but only if
the peak shape is known:
Peak#
Position
Height
Width
Area
1
4
1
1.6651 1.7724
2
9
1
1.6651 1.7725
3
13
1
1.6651 1.7725
4
15
0.99999
1.6651 1.7724
Note 1: If the peaks are too overlapped to be detected
and numbered separately, try pressing the H key to
activate the sharpen function before pressing M
(version 4.0 and above only).This does not effect the signal
itself, only the peak detection. Note 2: If you plan to use a variable-shape
peak (numbers 4, 5, 8 ,13, 14, 15,
18, or 20) for the Multiple
peak fit, it's a good idea to obtain a reasonable value for the
requested "extra" shape parameter by performing a Normal
peak fit on an isolated single peak (or small group of
partly-overlapping peaks) of the same shape, then use
that value for the Multiple curve fit of the entire
signal. Note 3: Although the peak widths can vary from peak to peak, the curve
fit routines assume that the peak shape is the same for all peaks in one
fitting operation, so if the peak shape varies across the
signal, use the Normal peak fit to fit each section with
a different shape rather than the Multiple peak fit. Peak
identification. There is an optional "peak
identification" function if optional input arguments 9 ('MaxError'), 10 ('Positions'), and 11 ('Names') are included. The "I" key
toggles this function ON and OFF. This function compares the
found peak positions (maximum x-values) to a reference database
of known peaks, in the form of an array of known peak maximum
positions ('Positions') and matching cell array of names
('Names'). If the position of a found peak in the signal is
closer to one of the known peaks by less than the specified
maximum error ('MaxError'), then that peak is considered a match
and its name is displayed next to the peak in the upper window.
When when the 'O' key is pressed (the letter 'O'), the
peak positions, names, errors, and amplitudes are printed out in
a table in the command window.
Example
9: Eleven input arguments. As above, but also specifies
'MaxError', 'Positions', and 'Names' in optional input
arguments 9, 10, and 11, for peak identification function.
Pressing the 'I' key toggles off and on the peak
identification labels in the upper window.These data (provided in the ZIP
file) are from a high-resolution atomic spectrum (x-axis in
nanometers).
The peak identification function applied to a high-resolution
atomic spectrum.
Three peaks near 296 nm isolated and identified. Press
the I key to display the peak ID names.
Pressing "O" prints the peak positions, names,
errors, and amplitudes in a table in the command window.
Name
Position Error
Amplitude 'Mg I 295.2'
[295.2]
[0.058545] [129.27] 'Cu
296.1 nm' [296.1]
[0.045368] [124.6]
'Hg 297.6 nm'
[297.6] [0.023142]
[143.95]
Here is another example, from a
large atomic emission spectrum with over 10,000 data points and
many hundreds of peaks. The reference table of known peaks in
this case is taken from Table 1 of ASTM
C1301 - 95(2009)e1. With the settings I was using, 10
peaks were identified, shown in the table below. You can see
that some of these elements have more than one line identified.
Obviously, the lower the settings of the AmpThreshold,
SlopeThreshold, and SmoothWidth, the more peaks will be
detected; and the higher the setting of "MaxError", the more
peaks will be close enough to be considered identified. In this
example, the element names in the table below are hot-linked to
the screen image of the corresponding peak detected as
identified by iPeak. Some of these lines, especially Nickel
231.66nm, Silicon 288.18nm, and Iron 260.1nm, are rather weak
and have poor signal-to-noise ratios, so their identification
might be in doubt (especially Iron, since its wavelength error
is greater than the rest). It's up to the experimenter to decide
which peaks are strong enough to be significant. In this
example, I used an independently published table of element
wavelengths, rather than data acquired on that same instrument,
which depends on the accurate wavelength calibration of the
instrument; in fact, the wavelength calibration is likely
excellent, based
on the very small error for the two well-known and relatively
strong Sodium lines at 589 and 589.59 nm. (Even so, I set
MaxError to 0.2 nm in this example to loosen up the wavelength
matching requirements).
Note: The
ZIP file contains the latest version of the iPeak function as
well as some sample data to demonstrate peak identification
(Example 8). Obviously for your own applications, it's
up to you to provide your own array of known peak maximum
positions ('Positions') and matching cell array of names
('Names') for your particular types of signals.
Keyboard Controls (version
6.01):
Pan signal left and right...Coarse pan: <
or >
Fine pan:
left or right cursor arrow keys
Nudge
one point
left or right: [ and ] Zoom
in and out.............Coarse zoom: / or '
Fine
zoom: up or down cursor arrow keys
Resets pan and zoom.........ESC Select entire signal........Ctrl-A Refresh entire plot.........Enter (Updates
cursor position in lower plot)
Change plot color...........Shift-C (cycles
through standard colors)
Adjust AmpThreshold.........A,Z (Larger
values ignore short peaks) Type
in AmpThreshold........Shift-A (Type value and press
Enter)
Adjust SlopeThreshold.......S,X (Larger
values ignore broad peaks) Type
in SlopeThreshold......Shift-S(Type value and press Enter) Adjust SmoothWidth..........D,C
(Larger values ignore sharp peaks}
Adjust FitWidth.............F,V (Adjust to
cover just top part of peaks)
Toggle sharpen mode ........H Helps detect
overlapped peaks.
Baseline correction.........B, then click
baseline at multiple points
Restore original signal.....G to cancel
previous background subtraction
Invert signal...............- Invert
(negate) the signal (flip + and -)
Set minimum to zero.........0 (Zero) Sets minimum
signal to zero Interpolate signal..........Shift-I
Interpolate (re-sample) to N points
Toggle log y mode OFF/ON....YPlot log Y axis on lower graph
Cycles baseline modes.......T 0=none; 1=linear;
2=quadratic; 3=Flat. Toggle valley
mode OFF/ON...U Switch to valley mode
Gaussian/Lorentzian switch..Shift-G Switch
between Gaussian/Lorentzian mode
Print peak table............P Prints Peak
#, Position, Height, Width
Save peak table.............Shift-P Saves
peak table as disc file
Step through peaks..........Space/Tab Jumps
to next/previous peak Jump to peak number.........J Type peak number and press Enter
Normal peak fit.............N Fit peaks in
upper window with peakfit.m
Multiple peak fit...........M Fit all peaks
in signal with peakfit.m Ensemble
average all peaks..Shift-E (Read instructions first)
Print keyboard commands.....K Prints this
list
Print findpeaks arguments...Q Prints
findpeaks function with arguments.
Print ipeak arguments.......W Prints ipeak
function with all arguments.
Print report................R Prints Peak
table and parameters
Print peak statistics.......E prints mean,
std of peak intervals, heights, etc.
Peak labels ON/OFF......... L Label all
peaks detected in upper window.
Peak ID ON/OFF..............I Identifies
closest peaks in 'Names' database.
Print peak IDs..............O Prints table
of peaks IDs
demoipeak.m is a
simple demo function that generates a noisy signal
with peaks, calls iPeak, and then prints out a table
of the actual peak parameters and a list of the
peaks detected and measured by iPeak for comparison.
Before running this demo, ipeak.m
must be downloaded and placed in the Matlab path.
The ZIP file at http://terpconnect.umd.edu/~toh/spectrum/ipeak6.zip contains several demo
functions (ipeakdemo.m, ipeakdemo1.m, etc) that
illustrate various aspects of the iPeak function and
how it can be used effectively. Download the zip
file, right-click and select "Extract all", then put
the resulting files in the Matlab path and run them
by typing their names at the Matlab command window
prompt. To test for the proper installation and
operation of iPeak, run testipeak.
ipeakdemo: effect of
the peak detection parameters
Four
Gaussian peaks with the same heights but different
widths (10, 30, 50 and 70 units) This demonstrates the
effect of SlopeThreshold and SmoothWidth
on peak detection. Increasing SlopeThreshold (S
key) will discriminate against the broader peaks.
Increasing SmoothWidth (D key) will
discriminate against the narrower peaks and noise.
FitWidth (F/V keys) controls
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 ordinarily about equal to
1/2 of the number of data points in the half-width
of the peaks. In this case, where the peak widths are
quite different, set it to about 1/2 of the number of data
points in the narrowest peak.
ipeakdemo1: the baseline
correction mode
Demonstration
of background correction, for separated, narrow peaks on
a large baseline. Each time you run this demo, you will
get a different set of peaks and noise. A table of the
actual peak positions, heights, widths, and areas is
printed out in the command window. Jump to the
next/previous peaks using the Spacebar/Tab keys.
Hint: Set the
linear
baseline correction mode (T key),
adjust the zoom setting so that the peaks are shown
one at a time in the upper window, then press the P
key to display the peak table.
ipeakdemo2: peak
overlap and the curve fitting functions.
Demonstration
of error caused by overlapping peaks on a large offset
baseline. Each time you run this demo, you will get a
different set of peaks and noise. A table of the
actual peak positions, heights, widths, and areas is
printed out in the command window. (Jump to the
next/previous peaks using the Spacebar/Tab
keys).
Hint: Use
the B key and click on the baseline points, then
press the P key to display the peak table. Or
turn on the background
correction mode (T key) and use the
Normal curve fit (N key) with peak shape
1 (Gaussian).
ipeakdemo3: Baseline shift caused by
overlapping peaks
Demonstration
of overlapping Lorentzian peaks, without an added
background. A table of the actual peak
positions, heights, widths, and areas is printed out in
the command window; in this example, the true peak heights
are 1,2 3,...10. Overlap of peaks can cause significant
errors in measuring peak parameters, especially for
Lorentzian peaks, because they have gently sloping sides
that contribute to the baseline of any peaks in the
region.
Hint: turn
OFF the background
correction mode (T key) and use the
Normal curve fit (N key) to fit small groups of
2-5 peaks numbered in the upper window, with peak
shape 2 (Lorentzian). For the
greatest accuracy in measuring a particular peak,
include one or two additional peaks on either side, to
help account for the baseline shift caused by
the sides of those neighboring peaks. Alternatively,
if the total number of peaks is not too great, you can
use the Multiple curve fit (M key) to fit the
entire signal in the lower window.
ipeakdemo4: dealing
with very noisy signals
Detection
and measurement of four peaks in a very noisy signal.
The signal-to-noise ratio of first peak is 2. Each time you
run this demo, you will get a different set of noise. A table of the
actual peak positions, heights, widths, and areas is
printed out in the command window. Jump to the
next/previous peaks using the Spacebar/Tab keys.
The peak at
x=100 is usually detected, but the accuracy of peak
parameter measurement is poor because of the low
signal-to-noise ratio. ipeakdemo6 is similar
but has the option of different kinds on noise
(white, pink, proportional, etc).
Hint: With
very noisy signals it is usually best to increase SmoothWidth
and FitWidth to help reduce the effect
of the noise.
ipeakdemo5: dealing
with highly overlapped peaks
In this demo
the peaks are so highly overlapped that only one or
two of the highest peaks yield distinct maxima that
are detected by iPeak. The height, width, and area
estimates are highly inaccurate because of this
overlap. The normal peak fit function ('N' key) would be
useful in this case, but it depends on iPeak for the
number of peaks and for the initial guesses, and so
it would fit only the peaks that were found and
numbered.
To help in
this case, pressing the 'H' key will activate the
peak sharpen function that decreases peak width and
increases peak height of all the peaks, making it easier
to detect and number all the peaks for use by the
peakfit function (N
key). Note: peakfit fits the original unmodified peaks; the
sharpening is used only to help locate the peaks to
provide peakfit with suitable starting values..
Which to use: iPeak, ipf, or peakfit? Download these
Matlab demos that compare iPeak.m with ipf.m and peakfit.m
for signals with a few peaks and signals
with many peaks and that shows how to
adjust iPeak to detect broad or narrow peaks.
These are self-contained demos that include all required Matlab
functions. Just place them in your path and click Run or type their name at
the command prompt. Or you can download all these demos together
in idemos.zip. For peak fitting, the N-key
and M-key functions of iPeak have the advantage of using
the peak positions and widths determined by the automatic peak
finder routine as the first-guess vector for peakfit.m, often
resulting in faster and more robust fits that ipf.m or peakfit.m
themselves with default first guesses.
Try fitting the x,y data in ipeakexampledata.mat
for some examples of using
iPeak for fitting overlapping peaks. On the
other hand, ipf.m is better for fitting peaks that don't make
distinct maxima and thus are not detected detected by
the automatic peak finder routine.
Peak Finding and
Measurement Spreadsheet
The spreadsheet pictured above implements the "findpeaks" peak finding and measurement
method in a spreadsheet. The input x,y data are contained
in Sheet1, column A and B, rows 8 to 263. You can Copy and Paste
your own data there. The amplitude threshold and slope threshold
are set in cells B3 and E3,
respectively.
Smoothing and differentiation are performed by the
convolution technique used by the spreadsheets
DerivativeSmoothing.xls described previously.
The Smooth Width and the Fit Width are both controlled by the
number of non-zero convolution coefficients in row 5,
columns J through Z. (In order to compute a
symmetrical first derivative, the coefficients in columns J to Q
must be the negatives of the positive
coefficients in columns S to Z). The original data
and the smoothed derivative are shown in the two charts on
Sheet1.
To detect peaks in the data, a series of three conditions
are tested for each data point in columns F, G, and H,
corresponding to the three nested loops in findpeaks.m:
Is the signal greater than Amplitude Threshold? (line
45 of findpeaks.m; column F in the spreadsheet)
Is there a downward directed zero crossing
in the smoothed first derivative? (line 43
of findpeaks.m; column G in the spreadsheet)
Is the slope of the derivative at that point
greater than the Slope Threshold? (line 44
of findpeaks.m; column H in the spreadsheet)
If the answer to all
three questions is yes
(highlighted by blue cell coloring), a peak is registered at
that point (column I), counted in column J, and assigned an
index number in column K.
For the first 10 peaks found, the x,y original unsmoothed
data are copied to Sheets 2 through 11, respectively, where that
segment of data is subjected to a Gaussian least-squares fit,
using the same technique as GaussianLeastSquares.xls.
The best-fit Gaussian parameter results are copied back to
Sheet1, in the table in columns AH-AK. (In its present
form. the spreadsheet is limited to measuring 10 peaks, although
it can detect any number of peaks. Also it is limited in Smooth
Width and Fit Width by the 17-point convolution coefficients).
The spreadsheet is available in OpenOffice (ods) and in Excel (xls) and (xlsx)
formats. They are functionally equivalent and differ only
in minor cosmetic aspects. An example
spreadsheet, with data, is available. A demo version, with a
calculated noisy waveform that you can modify, is also
available. Note: To enter data into the .xls and .xlsx
versions, click the "Enable Editing" button in the yellow bar
at the top.
To expand this spreadsheet to larger numbers of data points,
simply drag down row 263, columns A through K, so that the
formulas in those rows are replicated for the required number of
additional rows, then adjust the charts to accommodate the extra
rows. Expanding the spreadsheet to larger numbers of measured
peaks is more difficult. You'll have to drag down row 17,
columns AC through AK, and adjust the formulas in those rows for
the required number of additional peaks, then copy all of
Sheet11 and paste it into a series of new sheets (Sheet12,
Sheet13, etc), one for each additional peak, and finally adjust
the formulas in columns B and C in each of these additional
sheets to refer to the appropriate row in Sheet1. Modify these
additional equations in the same pattern as those for peaks
1-10.
A comparison of this spreadsheet to its Matlab/Octave
equivalent findpeaksplot.m is
instructive. On the positive side, the spreadsheet literally
"spreads out" the data and the calculations spatially over a
large number of cells and sheets, breaking down the discrete
steps in a very graphic way. In particular, the use of conditional
formatting in columns F through K make the peak detection
decision process more evident for each peak, and the
least-squares sheets 2 through 11 lay out every detail of those
calculations. Spreadsheet programs have many flexible and
easy-to-use formatting options to make displays more attractive.
On the down side, a spreadsheet as complicated as this one is
far more difficult to construct than its Matlab/Octave
equivalent. Much more serious, the spreadsheet is
less flexible and harder to expand to larger signals and larger
number of peaks. In contrast, the Matlab/Octave
equivalent, while requiring some understanding of programming,
is faster, much more flexible, and can
easily handle signals and smooth/fit widths of any size.
Moreover, because it is written as a Matlab/Octave function, it can be readily
employed as an element in your own custom
Matlab/Octave programs to perform
even larger tasks.
Obsolete version: FindPeakSliders, for
Matlab 6.5
This is an older version that used
mouse-controlled sliders for control. However, as the
program grew and more functions were added, it soon turned out
that the slider version became impractical because the screen
became cluttered more and more screen space would have to have
been devoted to controls display, reducing the screen space
available for plotting the all-important data. Moreover, the
slider function used does not work reliably in more recent
versions of Matlab. Development was halted in 2008 and it
therefore lacks all the important newer features of iPeak.
Interactive findpeaks script using mouse-controlled
sliders for interactive control. 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 sliders to
change the four arguments of the findpeaks function. The
four sliders correspond to the arguments of the findpeaks
function described above: SlopeThreshold (SlopeT), AmpThreshold
(AmpT), SmoothWidth (Smooth), and FitWidth
(Fit). The range of these sliders is easily changed in
lines 65 - 70 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 highest 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:
>> P P = 1.0000 45.0095 0.1328 4.0102 2.0000 90.5301 0.3655 4.7127 3.0000 94.9673 1.4075 4.0967 ......
A self-contained interactive demonstration of
FindPeakSliders applied to noisy synthetic data set
consisting of a random number of narrow peaks superimposed
on a gently curved background. Requires Matlab 6.5. Use the
sliders to explore the effect of the variables SlopeThreshold
(SlopeT), AmpThreshold (AmpT), SmoothWidth
(Smooth), and FitWidth (Fit), and the baseline
correct (BG) button. Peak number and the estimated
position, height, and width of each peak is returned in the
matrix P.
A self-contained interactive demonstration of
FindPeakSliders applied to a data set containing four simple
peaks with increasing peak height and peak width. Use this
to understand the difference between the variables
SlopeThreshold (SlopeT), which discriminates on the basis of
peak width, and AmpThreshold (AmpT), which discriminates on
the basis of peak amplitude. Peak number and the estimated
position, height, and width of each peak is returned in the
matrix P.
>> P P = 1.0000 49.9096 1.9895 20.1960 2.0000 126.1034 3.0585 42.3508 3.0000 201.3947 4.0752 63.3354 4.0000 299.9242 4.9925 82.2000
Interactive findpeaks script with peak-zoom feature, for predefined
data in x,y. Requires Matlab 6.5. Load a typical data set into the
vectors x,y, then run this m-file and adjust the 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. This version has an additional slider,
Peak, which 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).
Note: If the slider ranges are not appropriate for your data, change
them in lines 63-69.
DemoFindPeakSlidersG
A self-contained interactive demonstration of FindPeakSlidersG.
Requires Matlab 6.5.
Video Demonstration of
FindPeakSliders
This is a 26-second, 1.4 MByte video (PeakFind2.wmv)
of FindPeakSliders (version 1.1), showing the effect of varying the
four parameters SlopeThreshold (SlopeT), AmpThreshold
(AmpT), SmoothWidth, and FitWidth (labeled
"PeakWidth" in this video).