GaussianKDE1DimV1#
- class zfit.pdf.GaussianKDE1DimV1(obs, data, bandwidth=None, weights=None, truncate=False, *, extended=None, norm=None, name='GaussianKDE1DimV1', label=None)[source]#
Bases:
KDEHelper
,WrapDistribution
EXPERIMENTAL, `FEEDBACK WELCOME.
<zfit/zfit#new>`_ Exact, one dimensional, (truncated) Kernel Density Estimation with a Gaussian Kernel.
This implementation features an exact implementation as is preferably used for smaller (max. ~ a few thousand points) data sets. For larger data sets, methods such as
KDE1DimGrid
that bin the dataset may be more efficient Kernel Density Estimation is a non-parametric method to approximate the density of given points.\[f_h(x) = \frac{1}{nh} \sum_{i=1}^n K\Big(\frac{x-x_i}{h}\Big)\]where the kernel in this case is a (truncated) Gaussian
\[K = \exp \Big(\frac{(x - x_i)^2}{\sigma^2}\Big)\]The bandwidth of the kernel can be estimated in different ways. It can either be a global bandwidth, corresponding to a single value, or a local bandwidth, each corresponding to one data point.
Usage
The KDE can be instantiated by using a numpy-like data sample, preferably a
zfit.Data
object. This will be used as the mean of the kernels. The bandwidth can either be given as a parameter (with length 1 for a global one or length equal to the data size) - a rather advanced concept for methods such as cross validation - or determined from the data automatically, either through a simple method like scott or silverman rule of thumbs or through an iterative, adaptive method.Examples#
# generate some example kernels size = 150 data = np.random.normal(size=size, loc=2, scale=3) limits = (-15, 5) obs = zfit.Space("obs1", limits=limits) kde_silverman = zfit.pdf.GaussianKDE1DimV1(data=data, obs=obs, bandwidth='silverman') # for a better smoothing of the kernels, use an adaptive approach kde = zfit.pdf.GaussianKDE1DimV1(data=data, obs=obs, bandwidth='adaptive')
- type data:
TypeVar
(ParamTypeInput
, zfit.core.interfaces.ZfitParameter,Union
[int
,float
,complex
,Tensor
, zfit.core.interfaces.ZfitParameter])- param data:
Data sample to approximate the density from. The points represent positions of the kernel, the \(x_i\). This is preferrably a
ZfitData
, but can also be an array-like object.If the data has weights, they will be taken into account. This will change the count of the events, whereas weight \(w_i\) of \(x_i\) will scale the value of \(K_i( x_i)\), resulting in a factor of :math:`frac{w_i}{sum w_i} `.
If no weights are given, each kernel will be scaled by the same constant \(\frac{1}{n_{data}}\).
- type obs:
- param obs:
Observable space of the KDE. As with any other PDF, this will be used as the default norm, but does not define the domain of the PDF. Namely, this can be a smaller space than data, as long as the name of the observable match. Using a larger dataset is actually good practice avoiding bountary biases, see also Boundary bias and padding.
- type bandwidth:
Union
[TypeVar
(ParamTypeInput
, zfit.core.interfaces.ZfitParameter,Union
[int
,float
,complex
,Tensor
, zfit.core.interfaces.ZfitParameter]),str
]- param bandwidth:
Valid pre-defined options are {‘silverman’, ‘scott’, ‘adaptive’}.Bandwidth of the kernel, often also denoted as \(h\). For a Gaussian kernel, this corresponds to sigma. This can be calculated using pre-defined options or by specifying a numerical value that is broadcastable to data – a scalar or an array-like object with the same size as data.
A scalar value is usually referred to as a global bandwidth while an array holds local bandwidths
- param The bandwidth can also be a parameter:
- param which should be used with caution. However:
:param : :param it allows to use it in cross-valitadion with a likelihood method.: :type weights:
None
|ndarray
|Tensor
:param weights:Weights of each eventin data, can be None or Tensor-like with shape compatible with data. Instead of using this parameter, it is preferred to use a
ZfitData
as data that contains weights. This will change the count of the events, whereas weight \(w_i\) of \(x_i\) will scale the value of \(K_i( x_i)\), resulting in a factor of :math:`frac{w_i}{sum w_i} `.If no weights are given, each kernel will be scaled by the same constant \(\frac{1}{n_{data}}\).
- type truncate:
- param truncate:
If a truncated Gaussian kernel should be used with the limits given by the
obs
lower and upper limits. This can cause NaNs in case datapoints are outside the limits.- type extended:
Union
[bool
,TypeVar
(ParamTypeInput
, zfit.core.interfaces.ZfitParameter,Union
[int
,float
,complex
,Tensor
, zfit.core.interfaces.ZfitParameter]),None
]- param extended:
The overall yield of the PDF. If this is parameter-like, it will be used as the yield, the expected number of events, and the PDF will be extended. An extended PDF has additional functionality, such as the
ext_*
methods and thecounts
(for binned PDFs).- type norm:
- param norm:
Normalization of the PDF. By default, this is the same as the default space of the PDF.
- param extended:
The overall yield of the PDF. If this is parameter-like, it will be used as the yield, the expected number of events, and the PDF will be extended. An extended PDF has additional functionality, such as the
ext_*
methods and thecounts
(for binned PDFs).- type name:
- param name:
Name of the PDF. Maybe has implications on the serialization and deserialization of the PDF. For a human-readable name, use the label.
- type label:
- param label:
Human-readable name or label of the PDF for a better description, to be used with plots etc. Has no programmatical functional purpose as identification.
- add_cache_deps(cache_deps, allow_non_cachable=True)#
Add dependencies that render the cache invalid if they change.
- analytic_integrate(limits, norm=None, *, params=None)#
Analytical integration over function and raise Error if not possible.
- Parameters:
limits (
Union
[Tuple
[Tuple
[float
,...
]],Tuple
[float
,...
],bool
,Space
]) – Limits of the integration.norm (
Union
[Tuple
[Tuple
[float
,...
]],Tuple
[float
,...
],bool
,Space
]) – Normalization of the integration. By default, this is the same as the default space of the PDF.False
means no normalization and returns the unnormed integral.params (
TypeVar
(ParamTypeInput
, zfit.core.interfaces.ZfitParameter,Union
[int
,float
,complex
,Tensor
, zfit.core.interfaces.ZfitParameter])) – Mapping of the parameter names to the actual values. The parameter names refer to the names of the parameters, typicallyParameter
, that the model was _initialized_ with, not the name of the models parametrization.
- Return type:
- Returns:
The integral value
- Raises:
AnalyticIntegralNotImplementedError – If no analytical integral is available (for this limits).
NormRangeNotImplementedError – if the norm argument is not supported. This means that no analytical normalization is available, explicitly: the analytical integral over the limits = norm is not available.
- as_func(norm=False)#
Return a
Function
with the functionmodel(x, norm=norm)
.
- copy(**override_parameters)#
Creates a copy of the model.
Note: the copy model may continue to depend on the original initialization arguments.
- Parameters:
**override_parameters – String/value dictionary of initialization arguments to override with new value.
- Return type:
- Returns:
- A new instance of
type(self)
initialized from the union of self.parameters and override_parameters, i.e.,
dict(self.parameters, **override_parameters)
.
- A new instance of
- create_extended(yield_, name=None, *, name_addition=None)#
Return an extended version of this pdf with yield
yield_
. The parameters are shared.- Parameters:
yield – Yield (expected number of events) of the PDF. This is the expected number of events. If this is parameter-like, it will be used as the yield, the expected number of events, and the PDF will be extended. An extended PDF has additional functionality, such as the
ext_*
methods and thecounts
(for binned PDFs).name (
str
|None
) – New name of the PDF. IfNone
, the name of the PDF with a trailing “_ext” is used.
- Returns:
a new PDF that is extended
- Return type:
ZfitPDF
- create_projection_pdf(*, limits=None, obs=None, options=None, name=None, label=None, extended=None, norm=None)#
Create a PDF projection by integrating out some dimensions.
The new projection pdf is still fully dependent on the pdf it was created with.
- Parameters:
limits (
Union
[ZfitLimit
,Tensor
,ndarray
,Iterable
[float
],float
,Tuple
[float
],List
[float
],bool
,None
]) – Limits of the integration to project out. If not given, all observables that are not inobs
are projected on using the default limits of the observables.obs (
Union
[ZfitLimit
,Tensor
,ndarray
,Iterable
[float
],float
,Tuple
[float
],List
[float
],bool
,None
]) – Observables to project on. If not given, all observables that are not inlimits
are projected on.options –
Options for the integration. Additional options for the integration. Currently supported options are: - type: one of (
bins
)This hints that bins are integrated. A method that is vectorizable, non-dynamic and therefore less suitable for complicated functions is chosen.
- Return type:
ZfitPDF
- Returns:
A pdf without the dimensions from
limits
.
- create_sampler(n=None, limits=None, *, fixed_params=None, params=None)#
Create a
SamplerData
that acts asData
but can be resampled, also with changed parameters and (deprecated arguments)Deprecated: SOME ARGUMENTS ARE DEPRECATED:
(fixed_params)
. They will be removed in a future version. Instructions for updating: Useparams
instead.If
limits
is not specified,space
is used (if the space contains limits). Ifn
is None and the model is an extended pdf, ‘extended’ is used by default.
- Parameters:
The number of samples to be generated. Can be a Tensor that will be or a valid string. Currently implemented:
’extended’: samples
poisson(yield)
from each pdf that is extended.
limits (
Union
[Tuple
[Tuple
[float
,...
]],Tuple
[float
,...
],bool
,Space
]) – From which space to sample.fixed_params (
Union
[bool
,list
[ZfitParameter
],tuple
[ZfitParameter
],None
]) – A list ofParameters
that will be fixed during severalresample
calls. If True, all are fixed, if False, all are floating. If aParameter
is not fixed and its value gets updated (e.g. by aParameter.set_value()
call), this will be reflected inresample
. If fixed, the Parameter will still have the same value as theSamplerData
has been created with when it resamples.params (
TypeVar
(ParamTypeInput
, zfit.core.interfaces.ZfitParameter,Union
[int
,float
,complex
,Tensor
, zfit.core.interfaces.ZfitParameter])) – Mapping of the parameter names to the actual values. The parameter names refer to the names of the parameters, typicallyParameter
, that the model was _initialized_ with, not the name of the models parametrization.
- Return type:
- Returns:
- Raises:
NotExtendedPDFError – if ‘extended’ is chosen (implicitly by default or explicitly) as an option for
n
but the pdf itself is not extended.ValueError – if n is an invalid string option.
InvalidArgumentError – if n is not specified and pdf is not extended.
- property dtype: DType#
The dtype of the object.
- property extended: Parameter | None#
Return the yield (only for extended models).
- Returns:
The yield of the current model or None
- get_cache_deps(only_floating=True)#
Return a set of all independent
Parameter
that this object depends on.- Parameters:
only_floating (
bool
) – IfTrue
, only return floatingParameter
- Return type:
OrderedSet
- get_dependencies(only_floating: bool = True) ztyping.DependentsType #
DEPRECATED FUNCTION
Deprecated: THIS FUNCTION IS DEPRECATED. It will be removed in a future version. Instructions for updating: Use
get_params
instead if you want to retrieve the independent parameters orget_cache_deps
in case you need the numerical cache dependents (advanced).- Return type:
OrderedSet
- get_params(floating=True, is_yield=None, extract_independent=True, only_floating=<class 'zfit.util.checks.NotSpecified'>)#
Recursively collect parameters that this object depends on according to the filter criteria.
- Which parameters should be included can be steered using the arguments as a filter.
- None: do not filter on this. E.g.
floating=None
will return parameters that are floating as well as parameters that are fixed.
- None: do not filter on this. E.g.
True: only return parameters that fulfil this criterion
- False: only return parameters that do not fulfil this criterion. E.g.
floating=False
will return only parameters that are not floating.
- False: only return parameters that do not fulfil this criterion. E.g.
- Parameters:
floating (
bool
|None
) – if a parameter is floating, e.g. iffloating()
returnsTrue
is_yield (
bool
|None
) – if a parameter is a yield of the _current_ model. This won’t be applied recursively, but may include yields if they do also represent a parameter parametrizing the shape. So if the yield of the current model depends on other yields (or also non-yields), this will be included. If, however, just submodels depend on a yield (as their yield) and it is not correlated to the output of our model, they won’t be included.extract_independent (
bool
|None
) – If the parameter is an independent parameter, i.e. if it is aZfitIndependentParameter
.
- Return type:
set
[ZfitParameter
]
- get_yield()#
Return the yield (only for extended models).
- log_normalization(norm, *, options=None, params=None)#
Return the normalization of the function (usually the integral over
norm
).- Parameters:
norm (
Union
[Tuple
[Tuple
[float
,...
]],Tuple
[float
,...
],bool
,Space
]) – Normalization of the function. By default, this is thenorm
of the PDF (which by default is the same as the space of the PDF). Should beZfitSpace
to define the space to normalize over.options – |@doc:pdf.param.options||@docend:pdf.param.options|
params (
Optional
[Iterable
[ZfitParameter
]]) – Mapping of the parameter names to the actual values. The parameter names refer to the names of the parameters, typicallyParameter
, that the model was _initialized_ with, not the name of the models parametrization.
- Return type:
- Returns:
The normalization value
- log_pdf(x, norm=None, *, params=None)#
Log probability density function normalized over
norm_range
.- Parameters:
x (
Union
[float
,Tensor
]) – Data to evaluate the method on. Should beZfitData
or a mapping of obs to numpy-like arrays. If an array is given, the first dimension is interpreted as the events while the second is meant to be the dimensionality of a single event.norm (
Union
[Tuple
[Tuple
[float
,...
]],Tuple
[float
,...
],bool
,Space
]) – Normalization of the function. By default, this is thenorm
of the PDF (which by default is the same as the space of the PDF). Should beZfitSpace
to define the space to normalize over.params (
Optional
[Iterable
[ZfitParameter
]]) – Mapping of the parameter names to the actual values. The parameter names refer to the names of the parameters, typicallyParameter
, that the model was _initialized_ with, not the name of the models parametrization.
- Return type:
- Returns:
A
Tensor
of typeself.dtype
.
- property norm: Space | None | bool#
Return the current normalization range. If None and the
obs
have limits, they are returned.- Returns:
The current normalization range.
- property norm_range: Space | None | bool#
Return the current normalization range. If None and the
obs
have limits, they are returned. (deprecated)Deprecated: THIS FUNCTION IS DEPRECATED. It will be removed in a future version. Instructions for updating: Use the
norm
attribute instead.- Returns:
The current normalization range.
- normalization(norm=None, *, options=None, limits=None, params=None)#
Return the normalization of the function (usually the integral over
norm
). (deprecated arguments)Deprecated: SOME ARGUMENTS ARE DEPRECATED:
(limits)
. They will be removed in a future version. Instructions for updating: Usenorm
instead.- Parameters:
norm (
Union
[Tuple
[Tuple
[float
,...
]],Tuple
[float
,...
],bool
,Space
]) – Normalization of the function. By default, this is thenorm
of the PDF (which by default is the same as the space of the PDF). Should beZfitSpace
to define the space to normalize over.options – |@doc:pdf.param.options||@docend:pdf.param.options|
params (
Optional
[Iterable
[ZfitParameter
]]) – Mapping of the parameter names to the actual values. The parameter names refer to the names of the parameters, typicallyParameter
, that the model was _initialized_ with, not the name of the models parametrization.
- Return type:
- Returns:
The normalization value
- numeric_integrate(limits, norm=None, *, options=None, params=None)#
Numerical integration over the model.
- Parameters:
limits (
Union
[Tuple
[Tuple
[float
,...
]],Tuple
[float
,...
],bool
,Space
]) – Limits of the integration.norm (
Union
[Tuple
[Tuple
[float
,...
]],Tuple
[float
,...
],bool
,Space
]) – Normalization of the integration. By default, this is the same as the default space of the PDF.False
means no normalization and returns the unnormed integral.options –
Options for the integration. Additional options for the integration. Currently supported options are: - type: one of (
bins
)This hints that bins are integrated. A method that is vectorizable, non-dynamic and therefore less suitable for complicated functions is chosen.
params (
TypeVar
(ParamTypeInput
, zfit.core.interfaces.ZfitParameter,Union
[int
,float
,complex
,Tensor
, zfit.core.interfaces.ZfitParameter])) – Mapping of the parameter names to the actual values. The parameter names refer to the names of the parameters, typicallyParameter
, that the model was _initialized_ with, not the name of the models parametrization.
- Return type:
- Returns:
The integral value
- classmethod register_additional_repr(**kwargs)#
Register an additional attribute to add to the repr.
- Parameters:
an (any keyword argument. The value has to be gettable from the instance (has to be)
self. (attribute or callable method of)
- classmethod register_analytic_integral(cls, func, limits=None, priority=50, *, supports_norm=None, supports_norm_range=None, supports_multiple_limits=None)#
Register an analytic integral with the class. (deprecated arguments)
Deprecated: SOME ARGUMENTS ARE DEPRECATED:
(supports_norm_range)
. They will be removed in a future version. Instructions for updating: Usesupports_norm
instead.- Parameters:
func (
Callable
) –A function that calculates the (partial) integral over the axes
limits
. The signature has to be the following:- x (
ZfitData
, None): the data for the remaining axes in a partial integral. If it is not a partial integral, this will be None.
- x (
limits (
ZfitSpace
): the limits to integrate over.- norm_range (
ZfitSpace
, None): Normalization range of the integral. If not
supports_supports_norm_range
, this will be None.
- norm_range (
params (Dict[param_name,
zfit.Parameters
]): The parameters of the model.model (
ZfitModel
):The model that is being integrated.
limits (
Union
[Tuple
[Tuple
[float
,...
]],Tuple
[float
,...
],bool
,Space
]) – If aSpace
is given, it is used as limits. Otherwise arguments to instantiate a Range class can be given as follows.|limits_init|priority (
int
|float
) – Priority of the function. If multiple functions cover the same space, the one with the highest priority will be used.supports_multiple_limits (
bool
|None
) – IfTrue
, the ``limits` given to the integration function can have multiple limits. IfFalse
, only simple limits will pass through and multiple limits will be auto-handled.supports_norm (
bool
|None
) – IfTrue
,norm
argument to the function may not beNone
. IfFalse
,norm
will always beNone
and care is taken of the normalization automatically.
- Return type:
- register_cacher(cacher)#
Register a
cacher
that caches values produces by this instance; a dependent.- Parameters:
cacher (ztyping.CacherOrCachersType)
- classmethod register_inverse_analytic_integral(func)#
Register an inverse analytical integral, the inverse (unnormalized) cdf.
- reset_cache_self()#
Clear the cache of self and all dependent cachers.
- sample(n=None, limits=None, *, x=None, params=None)#
Sample
n
points withinlimits
from the model.If
limits
is not specified,space
is used (if the space contains limits). Ifn
is None and the model is an extended pdf, ‘extended’ is used by default.- Parameters:
The number of samples to be generated. Can be a Tensor that will be or a valid string. Currently implemented:
’extended’: samples
poisson(yield)
from each pdf that is extended.
limits (
Union
[Tuple
[Tuple
[float
,...
]],Tuple
[float
,...
],bool
,Space
]) – In which region to sample inparams (
TypeVar
(ParamTypeInput
, zfit.core.interfaces.ZfitParameter,Union
[int
,float
,complex
,Tensor
, zfit.core.interfaces.ZfitParameter])) – Mapping of the parameter names to the actual values. The parameter names refer to the names of the parameters, typicallyParameter
, that the model was _initialized_ with, not the name of the models parametrization.
- Returns:
The observables are the
limits
- Return type:
Data(n_obs, n_samples)
- Raises:
NotExtendedPDFError – if ‘extended’ is (implicitly by default or explicitly) chosen as an option for
n
but the pdf itself is not extended.ValueError – if n is an invalid string option.
InvalidArgumentError – if n is not specified and pdf is not extended.
- set_norm_range(norm: ztyping.LimitsTypeInput)#
Set the normalization range (temporarily if used with contextmanager). (deprecated)
Deprecated: THIS FUNCTION IS DEPRECATED. It will be removed in a future version. Instructions for updating: Prefer to create a new PDF with
norm
set or wrap the existing in aTruncatedPDF
.
- set_yield(value)#
Make the model extended inplace by setting a yield. If possible, prefer to use
create_extended
.This does not alter the general behavior of the PDF. The
pdf
andintegrate
and similar methods will continue to return the same - normalized to 1 - values. However, not only can this parameter be accessed viaget_yield
, the methodsext_pdf
andext_integral
provide a version ofpdf
andintegrate
respecetively that is multiplied by the yield.These can be useful for plotting and for binned likelihoods.
- Parameters:
value – Yield (expected number of events) of the PDF. This is the expected number of events. If this is parameter-like, it will be used as the yield, the expected number of events, and the PDF will be extended. An extended PDF has additional functionality, such as the
ext_*
methods and thecounts
(for binned PDFs).
- to_binned(space, extended=None, norm=None, name=None, label=None)#
Convert to binned pdf, returns self if already binned.
- to_truncated(limits=None, *, obs=None, extended=None, norm=None, name=None, label=None)#
Convert the PDF to a truncated version with possibly different and multiple limits.
The arguments are the same as for
TruncatedPDF
, the only difference being that if no limits are given, the limit of the PDF is used, thereby truncating the PDF to its original limits.- Parameters:
pdf – The PDF to be truncated.
limits (
Union
[ZfitSpace
,Iterable
[ZfitSpace
],None
]) – The limits to truncate the PDF. Can be a single limit or multiple limits.obs –
Observables of the model. This will be used as the default space of the PDF and, if not given explicitly, as the normalization range.
The default space is used for example in the sample method: if no sampling limits are given, the default space is used.
If the observables are binned and the model is unbinned, the model will be a binned model, by wrapping the model in a
BinnedFromUnbinnedPDF
, equivalent to callingto_binned()
.The observables are not equal to the domain as it does not restrict or truncate the model outside this range.
extended – The overall yield of the PDF. If this is parameter-like, it will be used as the yield, the expected number of events, and the PDF will be extended. An extended PDF has additional functionality, such as the
ext_*
methods and thecounts
(for binned PDFs).If None, the PDF will be extended if the original PDF is extended. IfTrue
and the original PDF is extended, the yield will be scaled to the fraction of the total integral that is within the limits. Therefore, the overall yield is comparable, i.e. the pdfs can be plotted “on top of each other”.norm – Normalization of the PDF. By default, this is the same as the default space of the PDF.
name (
str
|None
) – Name of the PDF. Maybe has implications on the serialization and deserialization of the PDF. For a human-readable name, use the label.label (
str
|None
) – Human-readable name or label of the PDF for a better description, to be used with plots etc. Has no programmatical functional purpose as identification.
- to_unbinned()#
Convert to unbinned pdf, returns self if already unbinned.
- unnormalized_pdf(x: ztyping.XType) ztyping.XType #
PDF “unnormalized”. Use
functions
for unnormalized pdfs. this is only for performance in special cases. (deprecated)Deprecated: THIS FUNCTION IS DEPRECATED. It will be removed in a future version. Instructions for updating: Use
pdf(norm=False)
instead- Parameters:
x (
Union
[float
,Tensor
]) – Data to evaluate the method on. Should beZfitData
or a mapping of obs to numpy-like arrays. If an array is given, the first dimension is interpreted as the events while the second is meant to be the dimensionality of a single event.- Return type:
- Returns:
1-dimensional
tf.Tensor
containing the unnormalized pdf.
- update_integration_options(draws_per_dim=None, mc_sampler=None, tol=None, max_draws=None, draws_simpson=None)#
Set the integration options.
- Parameters:
max_draws (default ~1'000'000) – Maximum number of draws when integrating . Typically 500’000 - 5’000’000.
tol – Tolerance on the error of the integral. typically 1e-4 to 1e-8
draws_per_dim – The draws for MC integration to do per iteration. Can be set to
'auto
’.draws_simpson – Number of points in one dimensional Simpson integration. Can be set to
'auto'
.