[Introduction]
[Signal
arithmetic] [Signals
and
noise] [Smoothing]
[Differentiation]
[Peak
Sharpening] [Harmonic
analysis] [Fourier
convolution] [Fourier
deconvolution] [Fourier
filter] [Peak
area
measurement] [Linear
Least
Squares] [Multicomponent
Spectroscopy] [Iterative
Curve
Fitting] [Hyperlinear
quantitative
absorption spectrophotometry] [Appendix
and
Case Studies] [Peak
Finding
and Measurement] [iPeak]
[iSignal]
[Peak
Fitters] [iFilter]
[iPower]
[List
of
downloadable software] [Interactive
tools]

[Smoothing Algorithms] [Noise Reduction] [End Effects] [Examples] [The problem with smoothing] [Optimization] [When should you smooth a signal?] [When should you NOT smooth a signal?] [Dealing with spikes] [Video Demonstration] [Spreadsheets] [Matlab/Octave] [Interactive tools] [Have a question? Email me]

In many experiments in science, the true signal
amplitudes (y-axis values) change rather smoothly as a function
of the x-axis values, whereas many kinds of noise are seen as
rapid, random changes in amplitude from point to point within
the signal. In the latter situation it may be useful in some
cases to attempt to reduce the noise by a process called *smoothing*. In smoothing,
the data points of a signal are modified so that individual
points that are *higher *than the immediately adjacent points (presumably
because of noise) are reduced, and points that are *lower *than the adjacent
points are increased. This naturally leads to a smoother signal
(and a slower step response to signal changes) . As long as the
true underlying signal is actually smooth, then the true signal
will not be much distorted by smoothing, but the high frequency
noise will be reduced. In terms of the frequency components
of a signal, a smoothing operation acts as a low-pass
filter, reducing the high-frequency components and passing
the low-frequency components with little change.

**Smoothing algorithms**. Most smoothing algorithms are based on the
"*shift and multiply*" technique, in which a group of adjacent points in the
original data are multiplied point-by-point by a set of numbers
(coefficients) that defines the smooth shape, the products are
added up and divided by the sum of the coefficients, which
becomes one point of smoothed data, then the set of coefficients
is shifted one point down the original data and the process is
repeated. The simplest
smoothing
algorithm is the *rectangular
boxcar *or *unweighted
sliding-average
smooth*; it simply replaces each
point in the signal with the average of *m* adjacent points, where *m* is a positive integer called the *smooth width*. For example,
for a 3-point smooth (*m* = 3):

for j = 2 to n-1, where S_{j} the j^{th} point in the smoothed
signal, Y_{j}
the j^{th}
point in the original signal, and n is the total number of
points in the signal. Similar smooth operations can be
constructed for any desired smooth width, *m*. Usually *m* is an odd number. If the noise in the data is "white
noise" (that is, evenly distributed over all frequencies) and
its standard deviation is *D*, then the standard deviation of the noise remaining in
the signal after the first pass of an unweighted sliding-average
smooth will be approximately s over the square root of *m* (*D*/sqrt(*m*)), where *m* is the smooth width. Despite its simplicity, this
smooth
is actually optimum for the common problem of reducing
white noise while keeping the *sharpest
step response*. The response to a
step change is in fact *linear*, so this filter has the advantage of responding
completely with no residual effect withing its *response time*, which is
equal to the smooth width divided by the sampling rate.
Smoothing can be performed either *du**ring *data
acquisition, by programming the digitizer to measure and average
multiple readings and save only the average, or *after *data acquisition ("post-run"), by storing all the
acquired data in memory and smoothing the stored data. The
latter requires more memory but is more flexible.

The *triangular smooth *is like the
rectangular smooth, above, except that it implements a *weighted
*smoothing function. For a 5-point smooth (*m* = 5):

for j = 3 to n-2, and similarly for other smooth widths
(see the spreadsheet UnitGainSmooths.xls).
In
both of these cases, the integer in the denominator is the *sum of the coefficients* in
the numerator, which results in a “unit-gain” smooth that has no
effect on the signal where it is a straight line and which
preserves the area under peaks.

It is often useful to apply a smoothing operation more than
once, that is, to smooth an already smoothed signal, in order to
build longer and more complicated smooths. For example, the
5-point triangular smooth above is equivalent to two passes of a
3-point rectangular smooth. *Three *passes of a 3-point rectangular smooth result in a
7-point "*pseudo-Gaussian*" or *haystack *smooth, for which the coefficients are in the ratio
1:3:6:7:6:3:1. The general rule is that *n* passes of a *w*-width smooth results in a combined smooth width of *n***w*-*n*+1.
For example, 3 passes of a 17-point smooth results in a 49-point
smooth. These multi-pass smooths are more effective at reducing
high-frequency noise in the signal than a rectangular smooth but
exhibit slower step response.

In all these smooths, the width of the smooth *m* is chosen to be an odd
integer, so that the smooth coefficients are symmetrically
balanced around the central point, which is important because it
preserves the x-axis position of peaks and other features in the
signal. (This is especially critical for analytical and
spectroscopic applications because the peak positions are often
important measurement objectives).

Note that we are assuming here that the x-axis intervals of the
signal is uniform, that is, that the difference between the
x-axis values of adjacent points is the same throughout the
signal. This is also assumed in many of the other
signal-processing techniques described in this essay, and it is
a very common (but not necessary) characteristic of signals that
are acquired by automated and computerized equipment.

The *Savitzky-Golay*
smooth is based on the least-squares fitting of polynomials to
segments of the data. The algorithm is discussed in http://www.wire.tu-bs.de/OLDWEB/mameyer/cmr/savgol.pdf.
Compared to the sliding-average smooths, the Savitzky-Golay
smooth is less effective at reducing noise, but more effective
at retaining the shape of the original signal. It is
capable of differentiation
as well as smoothing. The algorithm is more complex and
the computational times are greater than the smooth types
discussed above, but with modern computers the difference is not
significant and code
in
various languages is widely available online. See SmoothingComparison.html.

The shape of any smoothing algorithm can be determined by
applying that smooth to a *delta
function*, a signal consisting of all
zeros except for one point, as demonstrated by the simple
Matlab/Octave script DeltaTest.m.

**Noise reduction**.
Smoothing usually
reduces the noise in a signal. If the noise is "white" (that is,
evenly distributed over all frequencies) and its standard
deviation is *D*, then the standard deviation of the noise remaining in
the signal after one pass of a rectangular smooth will be
approximately *D*/sqrt(*m*), where *m* is the smooth width. If a triangular smooth is used
instead, the noise will be slightly less, about *D**0.8/sqrt(*m*). Smoothing operations can be applied more than once:
that is, a previously-smoothed signal can be smoothed again. In
some cases this can be useful if there is a great deal of
high-frequency noise in the signal. However, the noise reduction
for white noise is less in each successive smooth. For example,
*three *passes
of a rectangular smooth reduces white noise by a factor of
approximately *D**0.7/sqrt(*m*), only a slight improvement over two passes.

The
frequency
distribution of noise, designated by noise color,
substantially effects the ability of smoothing to reduce noise.
The Matlab/Octave function “NoiseColorTest.m”
compares the effect of a 20-point boxcar (unweighted sliding
average) smooth on the standard deviation of white, pink, and
blue noise, all of which have an original
unsmoothed standard deviation of 1.0. Because smoothing is
a low-pass filter process, it effects low frequency (pink and
red) noise less, and effects high-frequency (blue and violet)
noise more, than it does white noise.

Original unsmoothed noise |
1 |

Smoothed |
0.1 |

Smoothed |
0.55 |

Smoothed |
0.01 |

Smoothed |
0.98 |

Note that the computation of standard
deviation is independent of the order of the data and thus of
its frequency distribution; sorting a set of data does not
change its standard deviation. The standard deviation of a
sine wave is independent of its frequency. Smoothing, however,
changes both the frequency distribution and standard deviation
of a data set.

**End effects and the
lost points problem.** In the equations
above, the 3-point rectangular smooth is defined only for j = 2
to n-1. There is not enough data in the signal to define a
complete 3-point smooth for the first point in the signal (j =
1) or for the last point (j = n) , because there are no data
points before the first point or after the last point.
(Similarly, a 5-point smooth is defined only for j = 3 to n-2,
and therefore a smooth can not be calculated for the first two
points or for the last two points). In general, for an *m*-width smooth, there will
be (*m*-1)/2
points at the beginning of the signal and (*m*-1)/2 points at the end of the signal for which a
complete *m*-width
smooth can not be calculated the usual way. What to do? There
are two approaches. One is to accept the loss of points and trim
off those points or replace them with zeros in the smooth
signal. (That's the approach taken in most of the figures in
this paper). The other approach is to use *progressively
smaller smooths* at the ends of the
signal, for example to use 2, 3, 5, 7... point smooths for
signal points 1, 2, 3,and 4..., and for points n, n-1, n-2,
n-3..., respectively. The later approach may be preferable if
the edges of the signal contain critical information, but it
increases execution time. The fastsmooth
function discussed below can utilize
either of these two methods.

**Examples of smoothing**. A simple example
of smoothing is shown in Figure 4. The left half of this signal
is a noisy peak. The right half is the same peak after
undergoing a triangular smoothing algorithm. The noise is
greatly reduced while the peak itself is hardly changed. The
reduced noise allows the signal characteristics (peak position,
height, width, area, etc.) to be measured more accurately by
visual inspection.

*Figure 4. The left half of this signal is a
noisy peak. The right half is the same peak after undergoing a
***smoothing*** algorithm. The noise is greatly reduced while the
peak itself is hardly changed, making it easier to measure the
peak position, height, and width directly by graphical or
visual estimation (but it does not improve measurements made
by least-squares methods; see below).*

The larger the smooth width, the greater the noise
reduction, but also the greater the possibility that the signal
will be *distorted* by the smoothing operation. The
optimum choice of smooth width depends upon the width and shape
of the signal and the digitization interval. For peak-type
signals, the critical factor is the *smooth ratio*, the
ratio between the smooth width *m* and the number of
points in the half-width of the peak. In general, increasing the
smoothing ratio improves the signal-to-noise ratio but causes a
reduction in amplitude and in increase in the bandwidth of the
peak. Be aware that the smooth width can be expressed in two
different ways: (a) as the number of data points or (b) as the
x-axis interval (for spectroscopic data usually in nm or in
frequency units). The two are simply related: the number of data
points is simply the x-axis interval times the increment between
adjacent x-axis values. The *smooth ratio* is the same in
either case.

The figures above show examples of the effect of
three different smooth widths on noisy Gaussian-shaped peaks. In
the figure on the left, the peak has a (true) height of 2.0 and
there are 80 points in the half-width of the peak. The red line
is the original unsmoothed peak. The three superimposed green
lines are the results of smoothing this peak with a triangular
smooth of width (from top to bottom) 7, 25, and 51 points.
Because the peak width is 80 points, the *smooth
ratios* of these three smooths are
7/80 = 0.09, 25/80 = 0.31, and 51/80 = 0.64, respectively. As
the smooth width increases, the noise is progressively reduced
but the peak height also is reduced slightly. For the largest
smooth, the peak width is slightly increased. In the figure on
the right, the original peak (in red) has a true height of 1.0
and a half-width of 33 points. (It is also less noisy than the
example on the left.) The three superimposed green lines are the
results of the same three triangular smooths of width (from top
to bottom) 7, 25, and 51 points. But because the peak width in
this case is only 33 points, the *smooth
ratios* of these three smooths are
larger - 0.21, 0.76, and 1.55, respectively. You can see that
the peak distortion effect (reduction of peak height and
increase in peak width) is greater for the narrower peak because
the smooth ratios are higher. Smooth ratios of greater than 1.0
are seldom used because of excessive peak distortion. Note that
even in the worst case, the peak positions are not effected
(assuming that the original peaks were symmetrical and not
overlapped by other peaks). If retaining the shape of the peak
is more important than optimizing the signal-to-noise ratio, the
Savitzky-Golay has the advantage over sliding-average smooths.
In all cases, the total area under
the peak remains unchanged. If the peak widths vary
substantially, an adaptive smooth,
which allows the smooth width to vary across the signal, may be
used.

**The problem with smoothing **is that *it is often less
beneficial than you might think*. It's important
to point out that smoothing results such as illustrated in the
figure above may be *deceptively impressive* because they
employ a *single sample* of a noisy signal that is
smoothed to different degrees. This causes the viewer to
underestimate the contribution of *low-frequency* noise,
which is hard to estimate visually because there are so few
low-frequency cycles in the signal record. This problem can
visualized by recording a number of independent samples of a
noisy signal consisting of a single peak, as illustrated in the
two figures below. These figures show ten superimposed plots
with the same peak but with independent white noise, each
plotted with a different line color, unsmoothed on the left and
smoothed on the right. Inspection of the smoothed signals on the
right clearly shows the variation in peak position, height, and
width between the 10 samples caused by the low frequency noise
remaining in the smoothed signals. Without the noise, each peak
would have a peak height of 2, peak center at 500, and width of
150. Just because a signal looks smooth does not mean there is
no noise. Low-frequency noise remaining in the signals after
smoothing will still interfere with precise measurement of peak
position, height, and width.

x=1:1000; |
x=1:1000; |

(The generating scripts below each figure require that the functions gaussian.m, whitenoise.m, and fastsmooth.m be downloaded from http://tinyurl.com/cey8rwh.)

It should be clear that smoothing can seldom *completely
*eliminate noise, because most noise is spread out over a
wide range of frequencies, and smoothing simply reduces the
noise in *part *of its frequency range. Only for some
very specific types of noise (e.g. discrete frequency noise or
single-point spikes) is there hope of anything close to complete
noise elimination. Smoothing *does* make the signal
smoother and *it does* reduce the standard deviation of
the noise, but whether or not that makes for a *better
measurement* or not depends on the situation. And don't
assume that just because a little smoothing is good that more
will necessarily be better. Smoothing is like alcohol; sometimes
you really need it - but you should never overdo it.

The figure on the right below is another example
signal that illustrates some of these principles. The signal
consists of two Gaussian peaks, one located at x=50 and the
second at x=150. Both peaks have a peak height of 1.0 and a peak
half-width of 10, and a normally-distributed random white noise
with a standard deviation of 0.1 has been added to the entire
signal. The x-axis sampling interval, however, is different for
the two peaks; it's 0.1 for the first peak (from x=0 to 100) and
1.0 for the second peak (from x=100 to 200). This means
that the first peak is characterized
by
ten times more points that the second peak. It may *look* like the first peak
is noisier than the second, but that's just an illusion; the
signal-to-noise ratio for both peaks is 10. The second peak
looks less noisy only because there are fewer noise samples
there and we tend to underestimate the dispersion of small
samples. The result of this is that when the signal is smoothed,
the second peak is much more likely to be distorted by the
smooth (it becomes shorter and wider) than the first peak. The
first peak can tolerate a much wider smooth width, resulting in
a greater degree of noise reduction. (Similarly, if both peaks
are measured with the least-squares
curve fitting method, the fit of the first peak is more
stable with the noise and the measured parameters of that
peak will be about *3 times more
accurate *than the second peak,
because there are 10 times more data points in that peak, and
the measurement precision improves roughly with the square root
of the number of data points if the noise is white). You
can download the data file "udx" in TXT
format or in Matlab MAT format.

**Optimization of
smoothing.** As smooth width increases, the
smoothing ratio increases, noise is reduced quickly at first,
then more slowly, and the peak height is also reduced, slowly at
first, then more
quickly. The *noise reduction* depends on the smooth width, the smooth type (e.g.
rectangular, triangular, etc), and the noise color, but the *peak height reduction* also
depends on the peak width. The result is that the
signal-to-noise (defined as the ratio of the peak height of the
standard deviation of the noise) increases quickly at first,
then reaches a maximum. This is illustrated in the animation on
the left for a Gaussian peak with white noise (produced by this
Matlab/Octave script). The
maximum improvement in the signal-to-noise ratio depends on the
number of points in the peak: the more points in the peak, the
greater smooth widths can be employed and the greater the noise
reduction. This figure also illustrates that most of the noise
reduction is due to *high frequency* components of the noise, whereas much of the *low *frequency noise
remains in the signal even as it is smoothed.

Which is the best smooth ratio? It depends
on the purpose of the peak measurement. If the ultimate
objective of the measurement is to measure the peak height or
width, then smooth ratios below 0.2 should be used and the *Savitzky-Golay*
smooth is preferred. But if the objective of the measurement is
to measure the peak position (x-axis value of the peak), larger
smooth ratios can be employed if desired, because smoothing has
little effect on the peak position (unless peak is asymmetrical
or the increase in peak width is so much that it causes adjacent
peaks to overlap). If the peak is actually formed of two
underlying peaks that overlap so much that they appear to be one
peak, then curve
fitting is the only way to measure the parameters of the
underlying peaks. Unfortunately, the optimum signal-to-noise
ratio corresponds to a smooth ratio that significantly distorts
the peak, which is why curve fitting the unsmoothed data is
often preferred.

In *quantitative chemical analysis*
applications based on calibration by standard samples, the peak
height reduction caused by smoothing is not so important. If the
*same* signal processing operations are applied to the
samples and to the standards, the peak height reduction of the
standard signals will be exactly the same as that of the sample
signals and the effect will cancel out exactly. In such cases
smooth widths from 0.5 to 1.0 can be used if necessary to
further improve the signal-to-noise ratio, as shown in the
figure on the left (for a simple sliding-average rectangular
smooth). In practical analytical chemistry, absolute peak height
measurements are seldom required; calibration against standard
solutions is the rule. (Remember: the objective
of quantitative analysis is not to measure a signal but
rather to measure the concentration of the unknown.) It is very
important, however, to apply *exactly* the same signal
processing steps to the standard signals as to the sample
signals, otherwise a large systematic error may result.

For a more detailed comparison of all four smoothing types considered above, see SmoothingComparison.html.

**When should you smooth
a signal?** There are two reasons to smooth a signal:

(a)for cosmetic reasons, to prepare a nicer-looking or more dramatic graphic of a signal for visual inspection or publications, especially in order to emphasizelong-termbehavior overshort-term, or

(b)If the signal contains mostlyhigh-frequency("blue") noise, which can look bad but has less effect on the low-frequency signal components (e.g. the positions, heights, widths, and areas of peaks) than white noise.

(c)if the signal will be subsequently analyzed by a method that would be degraded by the presence of too much noise in the signal, for example if the heights of peaks are to be determinedvisually or graphicallyor by using the MAX function, of the the widths of peaks is measured by the halfwidth function, or if the location of maxima, minima, or inflection points in the signal is to be determined automatically by detecting zero-crossings in derivatives of the signal. Optimization of the amount and type of smoothing is important in these cases (see Differentiation.html#Smoothing). But generally, if a computer is available to make quantitative measurements, it's better to use least-squares methods on theunsmootheddata, rather than graphical estimates on smoothed data. If a commercial instrument has the option to smooth the data for you, it's best to disable the smoothing and record and save theunsmootheddata; you can always smooth it yourself later for visual presentation and it will be better to use the unsmoothed data for an least-squares fitting or other processing that you may want to do later. Smoothing can be used tolocate peaksbut it should not be used tomeasure peaks.

Care must be used in the design of algorithms that
employ smoothing. For example, in a popular technique for peak finding and
measurement, peaks are located by detecting downward
zero-crossings in the smoothed
first derivative, but the position, height, and width of
each peak is determined by least-squares
curve-fitting of a segment of original *unsmoothed* data in the
vicinity of the zero-crossing. That way, even if heavy
smoothing is necessary to provide reliable discrimination
against noise peaks, the peak parameters extracted by curve
fitting are not distorted by the smoothing.

**When should you NOT
smooth a signal? **One common
situation where you
should * not* smooth
signals is prior to statistical procedures such as least-squares
curve fitting, because:

(a)smoothing will not significantly improve the accuracy of parameter measurement by least-squares measurements between separate independent signal samples,

(b)all smoothing algorithms are at least slightly "lossy", entailing at least some change in signal shape and amplitude,

(c)it is harder to evaluate the fit by inspecting the residuals if the data are smoothed, becausesmoothed noise may be mistaken for an actual signal, and

(d)smoothing the signal will seriously underestimate the parameters errors predicted by propagation-of-error calculations and the bootstrap method. Even a visual estimate of the quality of the signal

**Dealing with spikes and
outliers. **Sometimes signals are
contaminated with very tall, narrow “spikes” or "outliers"
occurring at random intervals and with random amplitudes, but
with widths of only one or a few points. It not only looks ugly,
but it also upsets the assumptions of least-squares computations
because it is not *normally-distributed* random noise. This type of interference is difficult
to eliminate using the above smoothing methods without
distorting the signal. However, a “median” filter, which
replaces each point in the signal with the *median* (rather than the
average) of *m*
adjacent points, can completely eliminate narrow spikes with
little change in the signal, if the width of the spikes is only
one or a few points and equal to or less than *m*. See http://en.wikipedia.org/wiki/Median_filter.
The killspikes.m function uses a
different approach; it locates and eliminates the spikes by
"patches over them" using linear interpolation from the signal
before and after. Unlike conventional smooths, these functions
can be profitably applied *prior *to least-squares fitting functions. (On the other hand,
if it's the *spikes *that are actually the signal of interest, and other
components of the signal are interfering with their measurement,
see CaseStudies.html#G).

**
An alternative to smoothing **to reduce noise in the set of ten unsmoothed signals used above
is ensemble
averaging, which can be performed in this case very
simply by the Matlab/Octave code

**Con****densing oversampled signals**.
Sometimes
signals are recorded more densely (that is, with smaller x-axis
intervals) than really necessary to capture all the important
features of the signal. This results in larger-than-necessary
data sizes, which slows down signal processing procedures and
may tax storage capacity. To correct this, oversampled
signals can be reduced in size either by eliminating data points
(say, dropping every other point or every third point) or by
replacing groups of adjacent points by their averages. The later
approach has the advantage of *using* rather than *discarding* extraneous data points, and it acts like smoothing to
provide some measure of noise reduction. (If the noise in the
original signal is white, and the signal is condensed by
averaging every *n* points, the noise is reduced in the condensed signal
by the square root of *n*, but with *no change* in frequency distribution of the noise). The
Matlab/Octave script testcondense.m
demonstrates the effect of boxcar averaging using the condense.m function to reduce noise
without changing the noise color. Shows that the boxcar reduces the measured noise, removing the high frequency
components but has little effect on the the peak
parameters. Least-squares curve fitting on the condensed data is
faster and results in a lower fitting
error, but *no more accurate
measurement* of peak parameters.

**Video Demonstration.** This
18-second, 3 MByte video (Smooth3.wmv)
demonstrates the effect of triangular smoothing on a single
Gaussian peak with a peak height of 1.0 and peak width of 200.
The initial white noise amplitude is 0.3, giving an initial
signal-to-noise ratio of about 3.3. An attempt to measure the
peak amplitude and peak width of the noisy signal, shown at the
bottom of the video, are initially seriously inaccurate because
of the noise. As the smooth width is increased, however, the
signal-to-noise ratio improves and the accuracy of the
measurements of peak amplitude and peak width are improved.
However, above a smooth width of about 40 (smooth ratio 0.2),
the smoothing causes the peak to be shorter than 1.0 and wider
than 200, even though the signal-to-noise ratio continues to
improve as the smooth width is increased. (This demonstration
was created in Matlab 6.5.

SPECTRUM, the freeware Macintosh signal-processing application, includes rectangular and triangular smoothing functions for any number of points.

**Spreadsheets.** Smoothing can be
done in spreadsheets using the "shift and multiply" technique described above. In the spreadsheets smoothing.ods and smoothing.xls (screen image) the set of multiplying
coefficients is contained in the formulas that calculate the
values of each cell of the smoothed data in columns C and E.
Column C performs a 7-point rectangular smooth (1 1 1 1 1 1 1)
and column E does a 7-point triangular smooth (1 2 3 4 3 2 1),
applied to the data in column A. You can type in (or Copy and
Paste) any data you like into column A, and you can extend the
spreadsheet to longer columns of data by dragging the last row
of columns A, C, and E down as needed. But to change the smooth
width, you would have to change the equations in columns C or E
and copy the changes down the entire column. It's common
practice to divide the results by the sum of the coefficients so
that the net gain is unity and the area under the curve of the
smoothed signal is preserved. The spreadsheets UnitGainSmooths.xls and UnitGainSmooths.ods (screen image) contain a
collection of unit-gain convolution coefficients for
rectangular, triangular, and Gaussian smooths of width 3 to 29
in both vertical (column) and horizontal (row) format. You can
Copy and Paste these into your own spreadsheets.

The spreadsheets MultipleSmoothing.xls
and MultipleSmoothing.ods (screen image) demonstrate a
more flexible method in which the coefficients are contained in
a group of 17 adjacent cells (in row 5, columns I through Y),
making it easier to change the smooth shape and width (up to a *maximum *of 17) just by
changing those 17 cells. (To make a smaller smooth, just insert
zeros for the unused coefficients; in this example, a 7-point
triangular smooth is defined in columns N - T and the rest of
the coefficients are zeros ). In this spreadsheet, the smooth is
applied *three times* in succession, resulting in an effective maximum
smooth width of n*w-n+1 = 49 points applied to column G.

Compared to Matlab/Octave, spreadsheets are much slower, less
flexible, and less easily automated. For example, in these
spreadsheets, to change the signal or the number of points in
the signal, or to change the smooth width or type, you have to
modify the spreadsheet in several places, whereas to do the same
using the Matlab/Octave "fastsmooth" function (below), you need
only change the input arguments of a single line of code.
And combining several different techniques into one
spreadsheet is more complicated than writing
a Matlab/Octave script that does the same thing.

**Smoothing in Matlab** and **Octave**. The custom function
fastsmooth implements shift and
multiply type smooths using
a
recursive algorithm. (Click on this link to inspect the
code, or right-click to download for use within Matlab).
"Fastsmooth" is a Matlab function of the form **s=fastsmooth(a,w, type, edge)**. The argument "a" is the input signal vector; "w" is
the smooth width (a positive integer); "type" determines the
smooth type: type=1 gives a rectangular (sliding-average or
boxcar) smooth; type=2 gives a triangular
smooth, equivalent to two passes of a sliding average;
type=3 gives a pseudo-Gaussian smooth, equivalent to three
passes of a sliding average; these shapes are compared in the
figure on the left. (See SmoothingComparison.html
for a comparison of these smoothing modes). The argument "edge"
controls how the "edges" of the signal (the first w/2 points and
the last w/2 points) are handled. If edge=0, the edges are zero.
(In this mode the elapsed time is independent of the smooth
width. This gives the fastest execution time). If edge=1, the
edges are smoothed with progressively smaller smooths the closer
to the end. (In this mode the execution time increases with
increasing smooth widths). The smoothed signal is returned as
the vector "s". (You can leave off the last two input arguments:
fastsmooth(Y,w,type) smooths with edge=0 and fastsmooth(Y,w)
smooths with type=1 and edge=0). Compared to convolution-based
smooth algorithms, fastsmooth uses a simple recursive algorithm
that typically gives much faster execution times, especially for
large smooth widths; it can smooth a 1,000,000 point signal with
a 1,000 point sliding average in less than 0.1 second. Here's a
simple example of fastsmooth demonstrating the effect on white
noise (graphic).

`x=1:100;
y=randn(size(x));
plot(x,y,x,fastsmooth(y,5,3,1),'r')
xlabel('Blue: white noise. Red: smoothed
white noise.')`

SegmentedSmooth.m, illustrated
on the right, is a segmented multiple-width data
smoothing
function, based on the fastsmooth algorithm, which can be useful
if the widths of the peaks or the noise level varies
substantially across the signal. *The
syntax is the same as* *fastsmooth.m*, except that
the second input argument "smoothwidths" can be a *vector*: `SmoothY = SegmentedSmooth (Y,
smoothwidths, type, ends)`.
The function divides Y into a number of equal-length regions
defined by the length of the vector 'smoothwidths', then smooths
each region with a smooth of type 'type' and width defined by
the elements of vector 'smoothwidths'. In the graphic example in
the figure on the right, `smoothwidths=[31 52 91]`,
which divides up the signal into three regions and smooths the
first region with smoothwidth 31, the second with smoothwidth
51, and the last with smoothwidth 91. *Any number of smooth widths and sequence of smooth
widths can be used*. Type "help
SegmentedSmooth" for other examples examples. DemoSegmentedSmooth.m
demonstrates the operation with different signals consisting of
noisy variable-width peaks that get progressively wider, like
the figure on the right. If the peak widths increase regularly
across the signal, you can calculate a reasonable initial value
for the smoothwidths vector by giving only the number of
segments (NumSegments) , the first value, startw and the last
value, endw:

wstep=(endw-startw)/NumSegments;

smoothwidths=startw:wstep:endw;

Diederick has published a Savitzky-Golay smooth function in Matlab, which you can download from the Matlab File Exchange. It's included in the iSignal function. Greg Pittam has published a modification of the fastsmooth function that tolerates NaNs (Not a Number) in the data file (nanfastsmooth(Y,w,type,tol)) and a version for smoothing angle data (nanfastsmoothAngle(Y,w,type,tol)).

SmoothWidthTest.m is a simple
script that uses the fastsmooth function to demonstrate the
effect of smoothing on peak height, noise, and signal-to-noise
ratio of a peak. You can change the peak shape in line 7, the
smooth type in line 8, and the noise in line 9. A typical result
for a Gaussian peak with white noise smoothed with a
pseudo-Gaussian smooth is shown on the left. Here, as it is for
most peak shapes, the optimal signal-to-noise ratio occurs at a
smooth ratio of about 0.8. However, that optimum corresponds to
a *significant reduction in the peak
height*, which could be a serious
problem. A smooth width about *half *the width of the original unsmoothed peak produces less
distortion of the peak but still achieves a reasonable noise
reduction. SmoothVsCurvefit.m
is a similar script, but is also compares curve fitting as an alternative
method to measure the peak height *without
smoothing*.

This effect is explored more completely by the text below, which
shows an experiment in Matlab or
Octave that creates a Gaussian peak, smooths it,
compares the smoothed and unsmoothed version, then uses the
max, halfwidth, and trapz functions
to print out the *peak height,
halfwidth, and area*. (max and trapz
are both built-in functions in Matlab and Octave, but you have
to download halfwidth.m. To learn
more about these functions, type "help" followed by the function
name).

x=[0:.1:10]';

y=exp(-(x-5).^2);

plot(x,y)

ysmoothed=fastsmooth(y,11,3,1);

plot(x,y,x,ysmoothed,'r')

disp([max(y) halfwidth(x,y,5) trapz(x,y)])

disp([max(ysmoothed) halfwidth(x,ysmoothed,5)
trapz(x,ysmoothed)]

1
1.6662 1.7725

0.78442
2.1327 1.7725

These
results
show that smoothing *reduces *the peak
height (from 1 to 0.784) and *increases *the peak
width (from 1.66 to 2.13), but has *no effect* on the peak
area, as long as you measure the *total
area* under the broadened peak.

Smoothing is useful if the signal
is contaminated by non-normal noise such as sharp spikes or if
the peak height, position, or width are measured by simple
methods, but there is no need to smooth the data if the noise is
white and the peak parameters are measured by least-squares
methods, because the results obtained on the unsmoothed data
will be more accurate (see CurveFittingC.html#Smoothing).

The Matlab/Octave user-defined function condense.m*, condense(y,n)*, returns a
condensed version of *y* in which each group of *n* points is replaced by its average, reducing the
length of *y*
by the factor *n*. (For *x,y* data sets, use this function on both independent
variable *x* **and** dependent variable *y* so that the features of
*y* will appear
at the same *x*
values).

The Matlab/Octave user-defined function medianfilter.m, *medianfilter(y,w)*,
performs a median-based filter operation that replaces each
value of *y*
with the median of *w* adjacent points (which must be a positive integer). killspikes.m is a threshold-based
filter for eliminating narrow spike artifacts. The syntax
is fy= killspikes(x, y, threshold, width). Each time
it finds a positive or negative jump in the data between y(n)
and y(n+1) that exceeds "threshold", it replaces the next
"width" points of data with a linearly interpolated segment
spanning x(n) to x(n+width+1), See killspikesdemo. Type "help
killspikes" at the command prompt.

ProcessSignal is a Matlab/Octave
command-line function that performs smoothing and
differentiation on the time-series data set x,y (column or row
vectors). It can employ all the types of smoothing
described above. Type "help ProcessSignal". Returns the
processed signal as a vector that has the same shape as x,
regardless of the shape of y. The syntax is **Processed=ProcessSignal(x, y,
DerivativeMode, w, type, ends, Sharpen, factor1, factor2,
SlewRate, MedianWidth)**

**iSignal** is an interactive
function for Matlab that performs smoothing for time-series
signals using *all the algorithms
discussed above*, including
the Savitzky-Golay smooth, a median filter, and a condense
function, with keystrokes that allow you to adjust the smoothing
parameters continuously while observing the effect on your
signal instantly, making it easy to observe how different types
and amounts of smoothing effect noise and signal, such as the
height, width, and areas of peaks. (Other functions include
differentiation, peak sharpening, interpolation, least-squares
peak measurement, and a frequency spectrum mode that shows how
smoothing and other functions can change the frequency spectrum
of your signals). The simple script “iSignalDeltaTest”
demonstrates the frequency response of iSignal's smoothing
functions by applying them to a single-point
spike, allowing you to change the smooth type and the
smooth width to see how the the frequency response changes. View
the code here or download the ZIP file with sample data for testing.

**iSignal** for Matlab. Click to
view larger figures.

**You try it:**
Here's an example of a very noisy signal with lots of
high-frequency (blue) noise *totally
obscuring a perfectly good peak* in
the center at x=150, height=1e-4; SNR=90. First, download
NoisySignal
into the Matlab path, then execute these statements:

`>> load NoisySignal
>> isignal(x,y);`

Use the **A** and **Z** keys to increase and decrease
the smooth width, and the **S** key to cycle through the
available smooth types. Hint: use the Gaussian smooth and keep
increasing the smooth width until the peak shows.

**Note:** you can right-click on any of
the m-file links on this site and select **Save Link As...**
to download them to your computer for use within Matlab.
Unfortunately, iSignal does not currently work in Octave.

An earlier version of his page is available in French, at http://www.besteonderdelen.nl/blog/?p=4169,
courtesy of Natalie Harmann and Anna Chekovsky.

Last updated February,
2017. This page is part of "**A Pragmatic Introduction to Signal Processing**", created and maintained by Prof. Tom O'Haver ,
Department of Chemistry and Biochemistry, The University of
Maryland at College Park. Comments, suggestions, bug reports,
and questions should be directed to Prof. O'Haver at toh@umd.edu.

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