sigma_clip¶

astropy.stats.
sigma_clip
(data, sigma=3, sigma_lower=None, sigma_upper=None, maxiters=5, cenfunc='median', stdfunc='std', axis=None, masked=True, return_bounds=False, copy=True, grow=False)[source]¶ Perform sigmaclipping on the provided data.
The data will be iterated over, each time rejecting values that are less or more than a specified number of standard deviations from a center value.
Clipped (rejected) pixels are those where:
data < cenfunc(data [,axis=int])  (sigma_lower * stdfunc(data [,axis=int])) data > cenfunc(data [,axis=int]) + (sigma_upper * stdfunc(data [,axis=int]))
Invalid data values (i.e., NaN or inf) are automatically clipped.
For an objectoriented interface to sigma clipping, see
SigmaClip
.Note
scipy.stats.sigmaclip
provides a subset of the functionality in this class. Also, its input data cannot be a masked array and it does not handle data that contains invalid values (i.e., NaN or inf). Also note that it uses the mean as the centering function.If your data is a
ndarray
with no invalid values and you want to use the mean as the centering function withaxis=None
and iterate to convergence, thenscipy.stats.sigmaclip
is ~2530% faster than the equivalent settings here (sigma_clip(data, cenfunc='mean', maxiters=None, axis=None)
). Parameters
 dataarray_like or
MaskedArray
The data to be sigma clipped.
 sigma
float
, optional The number of standard deviations to use for both the lower and upper clipping limit. These limits are overridden by
sigma_lower
andsigma_upper
, if input. The default is 3. sigma_lower
float
orNone
, optional The number of standard deviations to use as the lower bound for the clipping limit. If
None
then the value ofsigma
is used. The default isNone
. sigma_upper
float
orNone
, optional The number of standard deviations to use as the upper bound for the clipping limit. If
None
then the value ofsigma
is used. The default isNone
. maxiters
int
orNone
, optional The maximum number of sigmaclipping iterations to perform or
None
to clip until convergence is achieved (i.e., iterate until the last iteration clips nothing). If convergence is achieved prior tomaxiters
iterations, the clipping iterations will stop. The default is 5. cenfunc{‘median’, ‘mean’} or
callable()
, optional The statistic or callable function/object used to compute the center value for the clipping. If using a callable function/object and the
axis
keyword is used, then it must be able to ignore NaNs (e.g.,numpy.nanmean
) and has anaxis
keyword to return an array with axis dimension(s) removed. The default is'median'
. stdfunc{‘std’, ‘mad_std’} or
callable()
, optional The statistic or callable function/object used to compute the standard deviation about the center value. If using a callable function/object and the
axis
keyword is used, then it must be able to ignore NaNs (e.g.,numpy.nanstd
) and has anaxis
keyword to return an array with axis dimension(s) removed. The default is'std'
. axis
None
orint
ortuple
ofint
, optional The axis or axes along which to sigma clip the data. If
None
, then the flattened data will be used.axis
is passed to thecenfunc
andstdfunc
. The default isNone
. maskedbool, optional
If
True
, then aMaskedArray
is returned, where the mask isTrue
for clipped values. IfFalse
, then andarray
and the minimum and maximum clipping thresholds are returned. The default isTrue
. return_boundsbool, optional
If
True
, then the minimum and maximum clipping bounds are also returned. copybool, optional
If
True
, then thedata
array will be copied. IfFalse
andmasked=True
, then the returned masked array data will contain the same array as the inputdata
(ifdata
is andarray
orMaskedArray
). IfFalse
andmasked=False
, the input data is modified inplace. The default isTrue
. grow
float
orFalse
, optional Radius within which to mask the neighbouring pixels of those that fall outwith the clipping limits (only applied along
axis
, if specified). As an example, for a 2D image a value of 1 will mask the nearest pixels in a cross pattern around each deviant pixel, while 1.5 will also reject the nearest diagonal neighbours and so on.
 dataarray_like or
 Returns
 resultarray_like
If
masked=True
, then aMaskedArray
is returned, where the mask isTrue
for clipped values and where the input mask wasTrue
.If
masked=False
, then andarray
is returned.If
return_bounds=True
, then in addition to the masked array or array above, the minimum and maximum clipping bounds are returned.If
masked=False
andaxis=None
, then the output array is a flattened 1Dndarray
where the clipped values have been removed. Ifreturn_bounds=True
then the returned minimum and maximum thresholds are scalars.If
masked=False
andaxis
is specified, then the outputndarray
will have the same shape as the inputdata
and containnp.nan
where values were clipped. If the inputdata
was a masked array, then the outputndarray
will also containnp.nan
where the input mask wasTrue
. Ifreturn_bounds=True
then the returned minimum and maximum clipping thresholds will be bendarray
s.
See also
Notes
The best performance will typically be obtained by setting
cenfunc
andstdfunc
to one of the builtin functions specified as as string. If one of the options is set to a string while the other has a custom callable, you may in some cases see better performance if you have the bottleneck package installed.Examples
This example uses a data array of random variates from a Gaussian distribution. We clip all points that are more than 2 sample standard deviations from the median. The result is a masked array, where the mask is
True
for clipped data:>>> from astropy.stats import sigma_clip >>> from numpy.random import randn >>> randvar = randn(10000) >>> filtered_data = sigma_clip(randvar, sigma=2, maxiters=5)
This example clips all points that are more than 3 sigma relative to the sample mean, clips until convergence, returns an unmasked
ndarray
, and does not copy the data:>>> from astropy.stats import sigma_clip >>> from numpy.random import randn >>> from numpy import mean >>> randvar = randn(10000) >>> filtered_data = sigma_clip(randvar, sigma=3, maxiters=None, ... cenfunc=mean, masked=False, copy=False)
This example sigma clips along one axis:
>>> from astropy.stats import sigma_clip >>> from numpy.random import normal >>> from numpy import arange, diag, ones >>> data = arange(5) + normal(0., 0.05, (5, 5)) + diag(ones(5)) >>> filtered_data = sigma_clip(data, sigma=2.3, axis=0)
Note that along the other axis, no points would be clipped, as the standard deviation is higher.