if InitialDistribution:
return histo.convolution_estimation1(known_distribution,
InitialDistribution, Estimator,
NbIteration, Weight, Penalty,
Outside)
else :
return histo.convolution_estimation2(known_distribution,
MinInfBound,
Estimator, NbIteration, Weight,
Penalty, Outside)
# Extend _Histogram class
_FrequencyDistribution = interface.extend_class( _FrequencyDistribution, EstimateFunctions)
def Estimate(histo, itype, *args, **kargs):
"""Estimate function
This function is a dispatcher to several estimate functions depending on
the first argument and the type.
:param obj: the input object (may be histogram, sequence, compound, ...)
:param itype: string.
.. seealso::
:func:`~openalea.stat_tool.estimate.EstimateFunctions.estimate_nonparametric`,
:func:`~openalea.stat_tool.simulate.Simulate`.
"""
error.CheckArgumentsLength(args, 1)
possible_types = [_DiscreteParametricModel, _DiscreteMixture,
_Compound, _Convolution]
# filename
if(len(args)==1):
error.CheckType([args[0]], [str], arg_id=[1])
result = _Convolution(args[0])
# build from list of distributions
else:
arguments = []
#check that all arguments are correct
for arg, i in zip(args, range(0, len(args))):
error.CheckType([arg], [possible_types], variable_pos=[i+1])
arguments.append(arg)
result = _Convolution(arguments)
return result
# Extend _Convolution
interface.extend_class(_Convolution, interface.StatInterface)
# Extend _ConvolutionData
interface.extend_class(_ConvolutionData, interface.StatInterface)
:Author: Thomas Cokelaer <*****@*****.**>
:Revision: $Id$
"""
__version__ = "$Id$"
# import sys
# import os
# sys.path.append(os.path.abspath("."))
import interface
from openalea.stat_tool._stat_tool import _DiscreteDistributionData
# Extend _DistributionData class dynamically
interface.extend_class(_DiscreteDistributionData, interface.StatInterface)
__all__ = ["_DiscreteDistributionData", "Histogram"]
def Histogram(*args):
"""Construction of a frequency distribution from an object of type
list(int) or from an ASCII file.
In the file syntax, the frequencies *fi* for each possible value
*i* are given in two columns. In the case of an argument of type
(list(int)), it is simply assumed that each array element represents
one data item.
:param integer list: a list of integer values
:param string filename: a valid filename in the proper format (see syntax part)
assert inf_bound <= sup_bound
assert (sup_bound - inf_bound) < MAX_DIFF_BOUND
param = D_DEFAULT
proba = D_DEFAULT
cumul_threshold = CUMUL_THRESHOLD
return _DiscreteParametricModel(UNIFORM, \
inf_bound, sup_bound, param, proba, cumul_threshold)
def Multinomial():
"""to be done"""
raise NotImplementedError("Multinomial not yet implemented")
# Extend _DiscreteParametricModel
interface.extend_class( _DiscreteParametricModel, interface.StatInterface)
# Cast Functions
def ToDistribution(histo):
""" Cast an object of type `_DiscreteDistributionData` into an object
of type `_Distribution`.
:Parameters:
* `histo` (DiscreteDistributionData)
:Returns:
If the object histo contains a 'model' part, an object
of type `_Distribution` is returned, otherwise no object
is returned.
result = _DiscreteMixture(args[0])
# build list of weights and distributions
else:
nb_param = len(args)
if ((nb_param % 2) != 0):
raise TypeError("Number of parameters must be pair")
# Extract weights ands distributions
weights = []
dists = []
for i in xrange(nb_param / 2):
weights.append(args[i * 2])
error.CheckType([args[i * 2 + 1]], [types], arg_id=[i * 2 + 1])
error.CheckType([args[i * 2]], [float], arg_id=[i * 2])
#dists.append(_Distribution(args[i * 2 + 1]))
dists.append((args[i * 2 + 1]))
result = _DiscreteMixture(weights, dists)
return result
# Extend _DiscreteMixture
interface.extend_class(_DiscreteMixture, interface.StatInterface)
# Extend _DiscreteMixtureData
interface.extend_class(_DiscreteMixtureData, interface.StatInterface)
_DiscreteMixture.__doc__ = Mixture.__doc__
elif utype == "MovingAverage":
error.CheckArgumentsLength(args, 1, 1)
param = args[0]
# todo add CheckType for int and models
# param is a list of float, int
if isinstance(args[0], list):
# todo: check that sum equals 1
return vec.moving_average_regression_values(explanatory, response, param, Algorithm)
# or a set of distributions
# todo: test case of compound, convolution, mixture
else:
error.CheckType([param], [[_DiscreteParametricModel, _DiscreteMixture, _Convolution, _Compound]])
return vec.moving_average_regression_distribution(explanatory, response, param, Algorithm)
elif utype in ["NearestNeighbors", "NearestNeighbours"]:
error.CheckArgumentsLength(args, 1, 1)
span = args[0]
error.CheckType([span], [[float, int]])
assert span >= STAT_MINIMUM_SPAN
# todo: check this assert
return vec.nearest_neighbours_regression(explanatory, response, float(span), Weighting)
else:
raise TypeError("Bad Regression type. Must be in %s" % possible_types)
# Extend _Regression class dynamically
interface.extend_class(_Regression, interface.StatInterface)
error.CheckType([args[0]], [str])
result = _Compound(args[0])
possible_types = [_DiscreteParametricModel, _DiscreteMixture,
_Compound, _Convolution]
# build from two objects and optional threshold
if len(args)==2:
error.CheckType([args[0], args[1]],
[possible_types, possible_types],
variable_pos=[1,2])
if Threshold:
result = _Compound([args[0], args[1]], Threshold)
else:
result = _Compound([args[0], args[1]])
return result
# Extend _Compound
interface.extend_class(_Compound, interface.StatInterface)
# Extend _CompoundData
interface.extend_class(_CompoundData, interface.StatInterface)
#if InputTypes:
ret = _Vectors(obj, identifiers, InputTypes)
#else:
# ret = _Vectors(obj, [])
else:
# from a sequence
index_variable = error.ParseKargs(kargs, "IndexVariable", False,
[True, False])
error.CheckType([index_variable], [bool], variable_pos=[2])
ret = obj.build_vectors(index_variable)
return ret
interface.extend_class( _Vectors, interface.StatInterface)
def VectorDistance(*args, **kargs):
"""
Construction of an object of type vector_distance from types (and eventually weights)
of variables or from an ASCII file.
The type _VectorDistance implements standardization procedures. The objective of
standardization is to avoid the dependence on the variable type
(chosen among symbolic, ordinal, numeric and circular) and, for numeric variables,
on the choice of the measurement units by converting the original variables to
unitless variables.
:Parameters:
from enums import cluster_type
from enums import round_type
mode_type = round_type
__all__ = [
"_DistanceMatrix",
"_Cluster",
"_Dendrogram",
"Cluster",
"Transcode",
"Clustering",
"ToDistanceMatrix", ]
# Extend classes dynamically
interface.extend_class(_DistanceMatrix, interface.StatInterface)
interface.extend_class(_Cluster, interface.StatInterface)
interface.extend_class(_Dendrogram, interface.StatInterface)
def Cluster(obj, utype, *args, **kargs):
"""Clustering of values.
In the case of the clustering of values of a frequency distribution on the
basis of an information measure criterion (argument `Information`), both the
information measure ratio and the selected optimal step are given in the
shell window.
The clustering mode `Step` (and its variant `Information`) is naturally
adapted to numeric variables while the clustering mode `Limit` applies to
both symbolic (nominal) and numeric variables. In the case of a symbolic
:Author: Thomas Cokelaer <*****@*****.**>
:Revision: $Id$
"""
__version__ = "$Id$"
#import sys
#import os
#sys.path.append(os.path.abspath("."))
import interface
from openalea.stat_tool._stat_tool import _DiscreteDistributionData
# Extend _DistributionData class dynamically
interface.extend_class(_DiscreteDistributionData, interface.StatInterface)
__all__ = [
"_DiscreteDistributionData",
"Histogram",
]
def Histogram(*args):
"""Construction of a frequency distribution from an object of type
list(int) or from an ASCII file.
In the file syntax, the frequencies *fi* for each possible value
*i* are given in two columns. In the case of an argument of type
(list(int)), it is simply assumed that each array element represents
one data item.
if InitialDistribution:
return histo.convolution_estimation1(known_distribution,
InitialDistribution,
Estimator, NbIteration,
Weight, Penalty, Outside)
else:
return histo.convolution_estimation2(known_distribution,
MinInfBound, Estimator,
NbIteration, Weight, Penalty,
Outside)
# Extend _Histogram class
_FrequencyDistribution = interface.extend_class(_FrequencyDistribution,
EstimateFunctions)
def Estimate(histo, itype, *args, **kargs):
"""Estimate function
This function is a dispatcher to several estimate functions depending on
the first argument and the type.
:param obj: the input object (may be histogram, sequence, compound, ...)
:param itype: string.
.. seealso::
:func:`~openalea.stat_tool.estimate.EstimateFunctions.estimate_nonparametric`,
:func:`~openalea.stat_tool.estimate.EstimateFunctions.estimate_parametric`,
:func:`~openalea.stat_tool.estimate.EstimateFunctions.estimate_DiscreteMixture`,
from enums import cluster_type
from enums import round_type
mode_type = round_type
__all__ = [
"_DistanceMatrix",
"_Cluster",
"_Dendrogram",
"Cluster",
"Transcode",
"Clustering",
"ToDistanceMatrix",
]
# Extend classes dynamically
interface.extend_class(_DistanceMatrix, interface.StatInterface)
interface.extend_class(_Cluster, interface.StatInterface)
interface.extend_class(_Dendrogram, interface.StatInterface)
def Cluster(obj, utype, *args, **kargs):
"""Clustering of values.
In the case of the clustering of values of a frequency distribution on the
basis of an information measure criterion (argument `Information`), both the
information measure ratio and the selected optimal step are given in the
shell window.
The clustering mode `Step` (and its variant `Information`) is naturally
adapted to numeric variables while the clustering mode `Limit` applies to
both symbolic (nominal) and numeric variables. In the case of a symbolic
if isinstance(args[0], list):
# todo: check that sum equals 1
return vec.moving_average_regression_values(
explanatory, response, param, Algorithm)
# or a set of distributions
# todo: test case of compound, convolution, mixture
else:
error.CheckType([param], [[
_DiscreteParametricModel, _DiscreteMixture, _Convolution,
_Compound
]])
return vec.moving_average_regression_distribution(
explanatory, response, param, Algorithm)
elif utype in ["NearestNeighbors", "NearestNeighbours"]:
error.CheckArgumentsLength(args, 1, 1)
span = args[0]
error.CheckType([span], [[float, int]])
assert span >= STAT_MINIMUM_SPAN
#todo: check this assert
return vec.nearest_neighbours_regression(explanatory, response,
float(span), Weighting)
else:
raise TypeError("Bad Regression type. Must be in %s" % possible_types)
# Extend _Regression class dynamically
interface.extend_class(_Regression, interface.StatInterface)
error.CheckType([args[0]], [str], arg_id=[1])
result = _DiscreteMixture(args[0])
# build list of weights and distributions
else:
nb_param = len(args)
if ((nb_param % 2) != 0):
raise TypeError("Number of parameters must be pair")
# Extract weights ands distributions
weights = []
dists = []
for i in xrange(nb_param / 2):
weights.append(args[i * 2])
error.CheckType([args[i * 2 + 1]], [types], arg_id=[i * 2 + 1])
error.CheckType([args[i * 2]], [float], arg_id=[i * 2])
#dists.append(_Distribution(args[i * 2 + 1]))
dists.append((args[i * 2 + 1]))
result = _DiscreteMixture(weights, dists)
return result
# Extend _DiscreteMixture
interface.extend_class(_DiscreteMixture, interface.StatInterface)
# Extend _DiscreteMixtureData
interface.extend_class(_DiscreteMixtureData, interface.StatInterface)
_DiscreteMixture.__doc__ = Mixture.__doc__
Threshold = kargs.get("Threshold", None)
# filename
if len(args) == 1:
error.CheckType([args[0]], [str])
result = _Compound(args[0])
possible_types = [
_DiscreteParametricModel, _DiscreteMixture, _Compound, _Convolution
]
# build from two objects and optional threshold
if len(args) == 2:
error.CheckType([args[0], args[1]], [possible_types, possible_types],
variable_pos=[1, 2])
if Threshold:
result = _Compound([args[0], args[1]], Threshold)
else:
result = _Compound([args[0], args[1]])
return result
# Extend _Compound
interface.extend_class(_Compound, interface.StatInterface)
# Extend _CompoundData
interface.extend_class(_CompoundData, interface.StatInterface)