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NIFTy
Commit 9159c1aa authored by Martin Reinecke's avatar Martin Reinecke
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re-organization

parent d16f65da
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nifty5/__init__.py
View file @ 9159c1aa
......@@ -47,11 +47,9 @@ from .operators.smoothness_operator import SmoothnessOperator
from .operators.symmetrizing_operator import SymmetrizingOperator
from .operators.vdot_operator import VdotOperator
from .operators.block_diagonal_operator import BlockDiagonalOperator
from .operators.kl import SampledKullbachLeiblerDivergence
from .operators.hamiltonian import Hamiltonian
from .operators.gaussian_energy import GaussianEnergy
from .operators.poissonian_energy import PoissonianEnergy
from .operators.bernoulli_energy import BernoulliEnergy
from .operators.energy_operators import (
EnergyOperator, GaussianEnergy, PoissonianEnergy, BernoulliEnergy,
Hamiltonian, SampledKullbachLeiblerDivergence)
from .probing.utils import probe_with_posterior_samples, probe_diagonal, \
StatCalculator
......
nifty5/operators/bernoulli_energy.py deleted 100644 → 0
View file @ d16f65da
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
# Copyright(C) 2013-2018 Max-Planck-Society
#
# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik
# and financially supported by the Studienstiftung des deutschen Volkes.
from __future__ import absolute_import, division, print_function
from ..compat import *
from ..operators.operator import EnergyOperator
from ..operators.sandwich_operator import SandwichOperator
from ..sugar import makeOp
from ..linearization import Linearization
class BernoulliEnergy(EnergyOperator):
def __init__(self, p, d):
self._p = p
self._d = d
@property
def domain(self):
return self._p.domain
def apply(self, x):
x = self._p(x)
v = x.log().vdot(-self._d) - (1.-x).log().vdot(1.-self._d)
if not isinstance(x, Linearization):
return v
met = makeOp(1./(x.val*(1.-x.val)))
met = SandwichOperator.make(x.jac, met)
return v.add_metric(met)
nifty5/operators/gaussian_energy.py deleted 100644 → 0
View file @ d16f65da
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
# Copyright(C) 2013-2018 Max-Planck-Society
#
# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik
# and financially supported by the Studienstiftung des deutschen Volkes.
from __future__ import absolute_import, division, print_function
from ..compat import *
from ..operators.operator import EnergyOperator
from ..operators.sandwich_operator import SandwichOperator
from ..domain_tuple import DomainTuple
from ..linearization import Linearization
class GaussianEnergy(EnergyOperator):
def __init__(self, mean=None, covariance=None, domain=None):
super(GaussianEnergy, self).__init__()
self._domain = None
if mean is not None:
self._checkEquivalence(mean.domain)
if covariance is not None:
self._checkEquivalence(covariance.domain)
if domain is not None:
self._checkEquivalence(domain)
if self._domain is None:
raise ValueError("no domain given")
self._mean = mean
self._icov = None if covariance is None else covariance.inverse
def _checkEquivalence(self, newdom):
if self._domain is None:
self._domain = newdom
else:
if self._domain is not newdom:
raise ValueError("domain mismatch")
@property
def domain(self):
return self._domain
def apply(self, x):
residual = x if self._mean is None else x-self._mean
icovres = residual if self._icov is None else self._icov(residual)
res = .5*residual.vdot(icovres)
if not isinstance(x, Linearization):
return res
metric = SandwichOperator.make(x.jac, self._icov)
return res.add_metric(metric)
nifty5/operators/hamiltonian.py deleted 100644 → 0
View file @ d16f65da
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
# Copyright(C) 2013-2018 Max-Planck-Society
#
# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik
# and financially supported by the Studienstiftung des deutschen Volkes.
from __future__ import absolute_import, division, print_function
from ..compat import *
from .operator import EnergyOperator
from .gaussian_energy import GaussianEnergy
from .sampling_enabler import SamplingEnabler
from ..linearization import Linearization
class Hamiltonian(EnergyOperator):
def __init__(self, lh, ic_samp=None):
super(Hamiltonian, self).__init__()
self._lh = lh
self._prior = GaussianEnergy(domain=lh.domain)
self._ic_samp = ic_samp
@property
def domain(self):
return self._lh.domain
def apply(self, x):
if self._ic_samp is None or not isinstance(x, Linearization):
return self._lh(x) + self._prior(x)
else:
lhx = self._lh(x)
prx = self._prior(x)
mtr = SamplingEnabler(lhx.metric, prx.metric.inverse,
self._ic_samp, prx.metric.inverse)
return (lhx+prx).add_metric(mtr)
nifty5/operators/kl.py deleted 100644 → 0
View file @ d16f65da
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
# Copyright(C) 2013-2018 Max-Planck-Society
#
# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik
# and financially supported by the Studienstiftung des deutschen Volkes.
from __future__ import absolute_import, division, print_function
from ..compat import *
from .operator import EnergyOperator
from ..utilities import my_sum
class SampledKullbachLeiblerDivergence(EnergyOperator):
def __init__(self, h, res_samples):
"""
# MR FIXME: does h have to be a Hamiltonian? Couldn't it be any energy?
h: Hamiltonian
N: Number of samples to be used
"""
super(SampledKullbachLeiblerDivergence, self).__init__()
self._h = h
self._res_samples = tuple(res_samples)
@property
def domain(self):
return self._h.domain
def apply(self, x):
return (my_sum(map(lambda v: self._h(x+v), self._res_samples)) *
(1./len(self._res_samples)))
nifty5/operators/operator.py
View file @ 9159c1aa
......@@ -52,13 +52,6 @@ for f in ["sqrt", "exp", "log", "tanh", "positive_tanh"]:
setattr(Operator, f, func(f))
class EnergyOperator(Operator):
_target = DomainTuple.scalar_domain()
@property
def target(self):
return EnergyOperator._target
class _FunctionApplier(Operator):
def __init__(self, domain, funcname):
from ..sugar import makeDomain
......@@ -150,36 +143,3 @@ class _OpSum(_CombinedOperator):
def apply(self, x):
raise NotImplementedError
class SquaredNormOperator(EnergyOperator):
def __init__(self, domain):
super(SquaredNormOperator, self).__init__()
self._domain = domain
@property
def domain(self):
return self._domain
def apply(self, x):
return Field(self._target, x.vdot(x))
class QuadraticFormOperator(EnergyOperator):
def __init__(self, op):
from .endomorphic_operator import EndomorphicOperator
super(QuadraticFormOperator, self).__init__()
if not isinstance(op, EndomorphicOperator):
raise TypeError("op must be an EndomorphicOperator")
self._op = op
@property
def domain(self):
return self._op.domain
def apply(self, x):
if isinstance(x, Linearization):
jac = self._op(x)
val = Field(self._target, 0.5 * x.vdot(jac))
return Linearization(val, jac)
return Field(self._target, 0.5 * x.vdot(self._op(x)))
nifty5/operators/poissonian_energy.py deleted 100644 → 0
View file @ d16f65da
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
# Copyright(C) 2013-2018 Max-Planck-Society
#
# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik
# and financially supported by the Studienstiftung des deutschen Volkes.
from __future__ import absolute_import, division, print_function
from numpy import inf, isnan
from ..compat import *
from ..operators.operator import EnergyOperator
from ..operators.sandwich_operator import SandwichOperator
from ..sugar import makeOp
from ..linearization import Linearization
class PoissonianEnergy(EnergyOperator):
def __init__(self, op, d):
self._op, self._d = op, d
@property
def domain(self):
return self._op.domain
def apply(self, x):
x = self._op(x)
res = x.sum() - x.log().vdot(self._d)
if not isinstance(x, Linearization):
return res
metric = SandwichOperator.make(x.jac, makeOp(1./x.val))
return res.add_metric(metric)
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