Denoise data using an empirical Bayesian method with a Cauchy prior
XDEN = wdenoise(X)
XDEN = wdenoise(X,LEVEL)
XDEN = wdenoise(___,Name,Value)
[XDEN,DENOISEDCFS] = wdenoise(___)
[XDEN,DENOISEDCFS,ORIGCFS] = wdenoise(___)
denoises the data in
XDEN = wdenoise(
X using an empirical Bayesian method
with a Cauchy prior. By default, the
sym4 wavelet is used
with a posterior median threshold rule. Denoising is down to the minimum of
wmaxlev(N,'sym4') where N is the
number of samples in the data. (For more information, see
X is a real-valued vector, matrix, or timetable.
X is a matrix,
wdenoise denoises each column of
X is a timetable,
wdenoise must contain real-valued vectors
in separate variables, or one real-valued matrix of data.
X is assumed to be uniformly sampled.
X is a timetable and the timestamps are
not linearly spaced,
wdenoise issues a
Obtain the denoised version of a noisy signal using default values.
load noisdopp xden = wdenoise(noisdopp);
Plot the original and denoised signals.
plot([noisdopp' xden']) legend('Original Signal','Denoised Signal')
Denoise a timetable of noisy data down to level 5 using block thresholding.
Load a noisy dataset.
Denoise the data down to level 5 using block thresholding by setting the name-value pair
xden = wdenoise(wnoisydata,5,'DenoisingMethod','BlockJS');
Plot the original data and the denoised data.
h1 = plot(wnoisydata.t,[wnoisydata.noisydata(:,1) xden.noisydata(:,1)]); h1(2).LineWidth = 2; legend('Original','Denoised')
Denoise a signal in different ways and compare results.
Load a datafile that contains clean and noisy versions of a signal. Plot the signals.
load fdata.mat plot(fNoisy,'r-') hold on plot(fClean,'b-') grid on legend('Noisy','Clean');
Denoise the signal using the
db1 wavelets, with a nine-level wavelet decomposition. Plot the results.
cleansym = wdenoise(fNoisy,9,'Wavelet','sym4'); cleandb = wdenoise(fNoisy,9,'Wavelet','db1'); figure plot(cleansym) title('Denoised - sym') grid on
figure plot(cleandb) title('Denoised - db') grid on
Compute the SNR of each denoised signal. Confirm that using the
sym4 wavelet produces a better result.
snrsym = -20*log10(norm(abs(fClean-cleansym))/norm(fClean))
snrsym = 35.9623
snrdb = -20*log10(norm(abs(fClean-cleandb))/norm(fClean))
snrdb = 32.2672
Load in a file which contains noisy data of 100 time series. Every time series is a noisy version of
fClean. Denoise the time series twice, estimating the noise variance differently in each case.
load fdataTS.mat cleanTSld = wdenoise(fdataTS,9,'NoiseEstimate','LevelDependent'); cleanTSli = wdenoise(fdataTS,9,'NoiseEstimate','LevelIndependent');
Compare one of the noisy time series with its two denoised versions.
figure plot(fdataTS.Time,fdataTS.fTS15) title('Original') grid on
figure plot(cleanTSli.Time,cleanTSli.fTS15) title('Level Independent') grid on
figure plot(cleanTSld.Time,cleanTSld.fTS15) title('Level Dependent') grid on
X— Input data
Input data, specified as a matrix, vector, or timetable of real values. If
X is a vector, it must have at least two samples.
X is a matrix or timetable, it must have at least
LEVEL— Level of wavelet decomposition
Level of wavelet decomposition, specified as a positive integer.
LEVEL is a positive integer less than or equal to
N is the number of samples in the data.
LEVEL defaults to the
For James-Stein block thresholding,
'BlockJS', there must be
coefficients at the coarsest resolution level,
comma-separated pairs of
the argument name and
Value is the corresponding value.
Name must appear inside single quotes (
' '). You can
specify several name and value pair arguments in any order as
'Wavelet','db6','DenoisingMethod','Bayes'denoises using the Daubechies
db6wavelet and the empirical Bayesian method.
'Wavelet'— Name of wavelet
Name of wavelet, specified as a character array, to use for denoising.
The wavelet must be orthogonal or biorthogonal. Orthogonal and
biorthogonal wavelets are designated as type 1 and type 2 wavelets
respectively in the wavelet manager,
Valid built-in orthogonal wavelet families begin with
the number of vanishing moments for all families except
N is the number of filter
Valid biorthgonal wavelet families begin with
Nd are the
number of vanishing moments in the reconstruction
(synthesis) and decomposition (analysis) wavelet.
Determine valid values for the vanishing moments by using
waveinfo with the
wavelet family short name. For example, enter
wavemngr('type',WNAME) to determine if a wavelet
is orthogonal (returns 1) or biorthogonal (returns 2).
'DenoisingMethod'— Denoising method
Denoising method, specified as a character array, used to determine
the denoising thresholds for the data
Bayes - Empirical Bayes
This method uses a threshold rule based on assuming measurements have independent prior distributions given by a mixture model. Because measurements are used to estimate the weight in the mixture model, the method tends to work better with more samples. By default, the posterior median rule is used to measure risk .
BlockJS - Block James-Stein
This method is based on determining an `optimal block size and threshold. The resulting block thresholding estimator yields simultaneously optimal global and local adaptivity .
FDR - False Discovery Rate
This method uses a threshold rule based on controlling the
expected ratio of false positive detections to all positive
FDR method works best
with sparse data. Choosing a ratio, or
Q-value, less than
yields an asymptotically minimax estimator .
Minimax - Minimax Estimation
This method uses a fixed threshold chosen to yield minimax
performance for mean square error against an ideal
procedure. The minimax principle is used in statistics to
design estimators. See
for more information.
SURE - Stein's Unbiased Risk
This method uses a threshold selection rule based on Stein’s Unbiased Estimate of Risk (quadratic loss function). One gets an estimate of the risk for a particular threshold value (t). Minimizing the risks in (t) gives a selection of the threshold value.
UniversalThreshold - Universal
This method uses a fixed-form threshold yielding minimax
performance multiplied by a small factor proportional to
'FDR', there is an optional argument
for the Q-value, which is the proportion of
false positives. Q is a real-valued scalar
0 < Q <= 1/2. To
'FDR' with a
Q-value, use a cell array where the second
element is the Q-value. For example,
unspecified, Q defaults to
'ThresholdRule'— Threshold rule
Threshold rule, specified as a character array, to use to shrink the
'ThresholdRule' is valid for
all denoising methods, but the valid options and defaults depend on the
denoising method. Rules possible for different denoising methods are
specified as follows:
'BlockJS': The only supported option is
'James-Stein'. You do not need to
'UniversalThreshold': Valid options
The default is
'Bayes': Valid options are
The default is
'FDR': The only supported option is
'Hard'. You do not need to define
'NoiseEstimate'— Method of estimating variance of noise
Method of estimating variance of noise in the data, specified as a
character array. Valid options are
'LevelIndependent' estimates the
variance of the noise based on the finest-scale
(highest-resolution) wavelet coefficients.
'LevelDependent' estimates the variance
of the noise based on the wavelet coefficients at each
For the block James-Stein estimator
'LevelIndependent' is the only
XDEN— Denoised data
Denoised vector, matrix, or timetable version of
For timetable input,
XDEN has the same variable names
and timestamps as the original timetable.
DENOISEDCFS— Denoised wavelet and scaling coefficients
Denoised wavelet and scaling coefficients of the denoised data
XDEN, returned in a cell array. The elements of
DENOISEDCFS are in order of decreasing resolution.
The final element of
DENOISEDCFS contains the
approximation (scaling) coefficients.
ORIGCFS— Original wavelet and scaling coefficients
Original wavelet and scaling coefficients of the data
X, returned in a cell array. The elements of
ORIGCFS are in order of decreasing resolution. The
final element of
ORIGCFS contains the approximation
The underlying model for the noisy signal is basically of the following form:
where time n is equally spaced.
In the simplest model, suppose that e(n) is a Gaussian white noise N(0,1) and the noise level σ is equal to 1.
The de-noising objective is to suppress the noise part of the signal s and to recover f.
The de-noising procedure proceeds in three steps:
Decomposition. Choose a wavelet, and choose a level
Compute the wavelet decomposition of the signal s at level
Detail coefficients thresholding. For each level from 1 to
N, select a threshold and apply soft thresholding to the
Reconstruction. Compute wavelet reconstruction based on the original
approximation coefficients of level
N and the modified detail
coefficients of levels from 1 to
More details about threshold selection rules are in Wavelet Denoising and Nonparametric Function Estimation, in the User's Guide, and in the help of the
 Abramovich, F., Y. Benjamini, D.L. Donoho, I.M. Johnstone (2006), “Adapting to Unknown Sparsity by Controlling the False Discovery Rate,” Ann. Statist., 34(2), pp. 584–653.
 Antoniadis, A., G. Oppenheim, Eds. (1995), Wavelets and Statistics, 103, Lecture Notes in Statistics, Springer Verlag.
 Cai, T.T. (2002), “On Block Thresholding in Wavelet Regression: Adaptivity, Block size, and Threshold Level,” Statistica Sinica, 12, pp. 1241–1273.
 Donoho, D.L. (1993), “Progress in wavelet analysis and WVD: a ten minute tour,” in Progress in wavelet analysis and applications, Y. Meyer, S. Roques, pp. 109–128. Frontières Ed.
 Donoho, D.L., I.M. Johnstone (1994), “Ideal Spatial Adaptation by Wavelet Shrinkage,” Biometrika, Vol. 81, pp. 425–455.
 Donoho, D.L. (1995), “De-noising by soft-thresholding,” IEEE Trans. on Inf. Theory, 42 3, pp. 613– 627.
 Donoho, D.L., I.M. Johnstone, G. Kerkyacharian, D. Picard (1995), “Wavelet Shrinkage: Asymptotia,” Jour. Roy. Stat. Soc., series B, Vol. 57, No. 2, pp. 301–369.
 Johnstone, I.M., B.W. Silverman (2004), “Needles and Straw in Haystacks: Empirical Bayes Estimates of Possibly Sparse Sequences,” Ann. Statist. 32(4), pp. 1594-1649.