Merge branch 'cleanup' into 'NIFTy_5'

Cleanup

See merge request ift/nifty-dev!98

demos/getting_started_3.py

@@ -72,8 +72,8 @@ if __name__ == '__main__':
 
     # set up minimization and inversion schemes
     ic_sampling = ift.GradientNormController(iteration_limit=100)
-    ic_newton = ift.DeltaEnergyController(
-        name='Newton', tol_rel_deltaE=1e-8, iteration_limit=100)
+    ic_newton = ift.GradInfNormController(
+        name='Newton', tol=1e-7, iteration_limit=1000)
     minimizer = ift.NewtonCG(ic_newton)
 
     # build model Hamiltonian
@@ -91,7 +91,7 @@ if __name__ == '__main__':
     # number of samples used to estimate the KL
     N_samples = 20
     for i in range(2):
-        KL = ift.KL_Energy(position, H, N_samples, want_metric=True)
+        KL = ift.KL_Energy(position, H, N_samples)
         KL, convergence = minimizer(KL)
         position = KL.position
 

nifty5/__init__.py

@@ -54,9 +54,9 @@ from .probing import probe_with_posterior_samples, probe_diagonal, \
     StatCalculator
 
 from .minimization.line_search import LineSearch
-from .minimization.line_search_strong_wolfe import LineSearchStrongWolfe
 from .minimization.iteration_controllers import (
-    IterationController, GradientNormController, DeltaEnergyController)
+    IterationController, GradientNormController, DeltaEnergyController,
+    GradInfNormController)
 from .minimization.minimizer import Minimizer
 from .minimization.conjugate_gradient import ConjugateGradient
 from .minimization.nonlinear_cg import NonlinearCG
@@ -66,12 +66,11 @@ from .minimization.descent_minimizers import (
 from .minimization.scipy_minimizer import (ScipyMinimizer, L_BFGS_B, ScipyCG)
 from .minimization.energy import Energy
 from .minimization.quadratic_energy import QuadraticEnergy
-from .minimization.line_energy import LineEnergy
 from .minimization.energy_adapter import EnergyAdapter
 from .minimization.kl_energy import KL_Energy
 
 from .sugar import *
-from .plotting.plot import Plot
+from .plot import Plot
 
 from .library.amplitude_model import AmplitudeModel
 from .library.inverse_gamma_model import InverseGammaModel

nifty5/data_objects/distributed_do.py

@@ -32,7 +32,7 @@ __all__ = ["ntask", "rank", "master", "local_shape", "data_object", "full",
            "local_data", "ibegin", "ibegin_from_shape", "np_allreduce_sum",
            "np_allreduce_min", "np_allreduce_max",
            "distaxis", "from_local_data", "from_global_data", "to_global_data",
-           "redistribute", "default_distaxis", "is_numpy",
+           "redistribute", "default_distaxis", "is_numpy", "absmax", "norm",
            "lock", "locked", "uniform_full", "transpose", "to_global_data_rw",
            "ensure_not_distributed", "ensure_default_distributed"]
 
@@ -553,3 +553,22 @@ def ensure_default_distributed(arr):
     if arr._distaxis != 0:
         arr = redistribute(arr, dist=0)
     return arr
+
+
+def absmax(arr):
+    if arr._data.size == 0:
+        tmp = np.array(0, dtype=arr._data.dtype)
+    else:
+        tmp = np.asarray(np.linalg.norm(arr._data, ord=np.inf))
+    res = np.empty_like(tmp)
+    _comm.Allreduce(tmp, res, MPI.MAX)
+    return res[()]
+
+
+def norm(arr, ord=2):
+    if ord == np.inf:
+        return absmax(arr)
+    tmp = np.asarray(np.linalg.norm(np.atleast_1d(arr._data), ord=ord) ** ord)
+    res = np.empty_like(tmp)
+    _comm.Allreduce(tmp, res, MPI.SUM)
+    return res[()] ** (1./ord)

nifty5/data_objects/numpy_do.py

@@ -31,7 +31,7 @@ __all__ = ["ntask", "rank", "master", "local_shape", "data_object", "full",
            "local_data", "ibegin", "ibegin_from_shape", "np_allreduce_sum",
            "np_allreduce_min", "np_allreduce_max",
            "distaxis", "from_local_data", "from_global_data", "to_global_data",
-           "redistribute", "default_distaxis", "is_numpy",
+           "redistribute", "default_distaxis", "is_numpy", "absmax", "norm",
            "lock", "locked", "uniform_full", "to_global_data_rw",
            "ensure_not_distributed", "ensure_default_distributed"]
 
@@ -141,3 +141,11 @@ def ensure_not_distributed(arr, axes):
 
 def ensure_default_distributed(arr):
     return arr
+
+
+def absmax(arr):
+    return np.linalg.norm(arr, ord=np.inf)
+
+
+def norm(arr, ord=2):
+    return np.linalg.norm(np.atleast_1d(arr), ord=ord)

nifty5/extra/energy_and_model_tests.py → nifty5/extra.py

@@ -20,14 +20,61 @@ from __future__ import absolute_import, division, print_function
 
 import numpy as np
 
-from ..compat import *
-from ..linearization import Linearization
-from ..sugar import from_random
+from .compat import *
+from .field import Field
+from .linearization import Linearization
+from .sugar import from_random
 
-__all__ = ["check_value_gradient_consistency",
+__all__ = ["consistency_check", "check_value_gradient_consistency",
            "check_value_gradient_metric_consistency"]
 
 
+def _assert_allclose(f1, f2, atol, rtol):
+    if isinstance(f1, Field):
+        return np.testing.assert_allclose(f1.local_data, f2.local_data,
+                                          atol=atol, rtol=rtol)
+    for key, val in f1.items():
+        _assert_allclose(val, f2[key], atol=atol, rtol=rtol)
+
+
+def _adjoint_implementation(op, domain_dtype, target_dtype, atol, rtol):
+    needed_cap = op.TIMES | op.ADJOINT_TIMES
+    if (op.capability & needed_cap) != needed_cap:
+        return
+    f1 = from_random("normal", op.domain, dtype=domain_dtype)
+    f2 = from_random("normal", op.target, dtype=target_dtype)
+    res1 = f1.vdot(op.adjoint_times(f2))
+    res2 = op.times(f1).vdot(f2)
+    np.testing.assert_allclose(res1, res2, atol=atol, rtol=rtol)
+
+
+def _inverse_implementation(op, domain_dtype, target_dtype, atol, rtol):
+    needed_cap = op.TIMES | op.INVERSE_TIMES
+    if (op.capability & needed_cap) != needed_cap:
+        return
+    foo = from_random("normal", op.target, dtype=target_dtype)
+    res = op(op.inverse_times(foo))
+    _assert_allclose(res, foo, atol=atol, rtol=rtol)
+
+    foo = from_random("normal", op.domain, dtype=domain_dtype)
+    res = op.inverse_times(op(foo))
+    _assert_allclose(res, foo, atol=atol, rtol=rtol)
+
+
+def _full_implementation(op, domain_dtype, target_dtype, atol, rtol):
+    _adjoint_implementation(op, domain_dtype, target_dtype, atol, rtol)
+    _inverse_implementation(op, domain_dtype, target_dtype, atol, rtol)
+
+
+def consistency_check(op, domain_dtype=np.float64, target_dtype=np.float64,
+                      atol=0, rtol=1e-7):
+    _full_implementation(op, domain_dtype, target_dtype, atol, rtol)
+    _full_implementation(op.adjoint, target_dtype, domain_dtype, atol, rtol)
+    _full_implementation(op.inverse, target_dtype, domain_dtype, atol, rtol)
+    _full_implementation(op.adjoint.inverse, domain_dtype, target_dtype, atol,
+                         rtol)
+
+
 def _get_acceptable_location(op, loc, lin):
     if not np.isfinite(lin.val.sum()):
         raise ValueError('Initial value must be finite')

nifty5/extra/__init__.py

-from .operator_tests import consistency_check
-from .energy_and_model_tests import *

nifty5/extra/operator_tests.py

-# 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
-
-import numpy as np
-
-from ..compat import *
-from ..field import Field
-from ..sugar import from_random
-
-__all__ = ["consistency_check"]
-
-
-def _assert_allclose(f1, f2, atol, rtol):
-    if isinstance(f1, Field):
-        return np.testing.assert_allclose(f1.local_data, f2.local_data,
-                                          atol=atol, rtol=rtol)
-    for key, val in f1.items():
-        _assert_allclose(val, f2[key], atol=atol, rtol=rtol)
-
-
-def adjoint_implementation(op, domain_dtype, target_dtype, atol, rtol):
-    needed_cap = op.TIMES | op.ADJOINT_TIMES
-    if (op.capability & needed_cap) != needed_cap:
-        return
-    f1 = from_random("normal", op.domain, dtype=domain_dtype)
-    f2 = from_random("normal", op.target, dtype=target_dtype)
-    res1 = f1.vdot(op.adjoint_times(f2))
-    res2 = op.times(f1).vdot(f2)
-    np.testing.assert_allclose(res1, res2, atol=atol, rtol=rtol)
-
-
-def inverse_implementation(op, domain_dtype, target_dtype, atol, rtol):
-    needed_cap = op.TIMES | op.INVERSE_TIMES
-    if (op.capability & needed_cap) != needed_cap:
-        return
-    foo = from_random("normal", op.target, dtype=target_dtype)
-    res = op(op.inverse_times(foo))
-    _assert_allclose(res, foo, atol=atol, rtol=rtol)
-
-    foo = from_random("normal", op.domain, dtype=domain_dtype)
-    res = op.inverse_times(op(foo))
-    _assert_allclose(res, foo, atol=atol, rtol=rtol)
-
-
-def full_implementation(op, domain_dtype, target_dtype, atol, rtol):
-    adjoint_implementation(op, domain_dtype, target_dtype, atol, rtol)
-    inverse_implementation(op, domain_dtype, target_dtype, atol, rtol)
-
-
-def consistency_check(op, domain_dtype=np.float64, target_dtype=np.float64,
-                      atol=0, rtol=1e-7):
-    full_implementation(op, domain_dtype, target_dtype, atol, rtol)
-    full_implementation(op.adjoint, target_dtype, domain_dtype, atol, rtol)
-    full_implementation(op.inverse, target_dtype, domain_dtype, atol, rtol)
-    full_implementation(op.adjoint.inverse, domain_dtype, target_dtype, atol,
-                        rtol)

nifty5/field.py

@@ -360,25 +360,20 @@ class Field(object):
         # For the moment, do this the explicit, non-optimized way
         return (self.conjugate()*x).sum(spaces=spaces)
 
-    def norm(self):
+    def norm(self, ord=2):
         """ Computes the L2-norm of the field values.
 
-        Returns
-        -------
-        float
-            The L2-norm of the field values.
-        """
-        return np.sqrt(abs(self.vdot(x=self)))
-
-    def squared_norm(self):
-        """ Computes the square of the L2-norm of the field values.
+        Parameters
+        ----------
+        ord : int, default=2
+            accepted values: 1, 2, ..., np.inf
 
         Returns
         -------
         float
-            The square of the L2-norm of the field values.
+            The L2-norm of the field values.
         """
-        return abs(self.vdot(x=self))
+        return dobj.norm(self._val, ord)
 
     def conjugate(self):
         """ Returns the complex conjugate of the field.

nifty5/linearization.py

@@ -152,6 +152,9 @@ class Linearization(object):
     def add_metric(self, metric):
         return self.new(self._val, self._jac, metric)
 
+    def with_want_metric(self):
+        return Linearization(self._val, self._jac, self._metric, True)
+
     @staticmethod
     def make_var(field, want_metric=False):
         from .operators.scaling_operator import ScalingOperator
@@ -163,3 +166,15 @@ class Linearization(object):
         from .operators.simple_linear_operators import NullOperator
         return Linearization(field, NullOperator(field.domain, field.domain),
                              want_metric=want_metric)
+
+    @staticmethod
+    def make_partial_var(field, constants, want_metric=False):
+        from .operators.scaling_operator import ScalingOperator
+        from .operators.simple_linear_operators import NullOperator
+        if len(constants) == 0:
+            return Linearization.make_var(field, want_metric)
+        else:
+            ops = [ScalingOperator(0. if key in constants else 1., dom)
+                   for key, dom in field.domain.items()]
+            bdop = BlockDiagonalOperator(fielld.domain, tuple(ops))
+            return Linearization(field, bdop, want_metric=want_metric)

nifty5/minimization/descent_minimizers.py

@@ -22,7 +22,7 @@ import numpy as np
 
 from ..compat import *
 from ..logger import logger
-from .line_search_strong_wolfe import LineSearchStrongWolfe
+from .line_search import LineSearch
 from .minimizer import Minimizer
 
 
@@ -40,10 +40,10 @@ class DescentMinimizer(Minimizer):
         Object that decides when to terminate the minimization.
     line_searcher : callable *optional*
         Function which infers the step size in the descent direction
-        (default : LineSearchStrongWolfe()).
+        (default : LineSearch()).
     """
 
-    def __init__(self, controller, line_searcher=LineSearchStrongWolfe()):
+    def __init__(self, controller, line_searcher=LineSearch()):
         self._controller = controller
         self.line_searcher = line_searcher
 
@@ -144,8 +144,7 @@ class RelaxedNewton(DescentMinimizer):
 
     def __init__(self, controller, line_searcher=None):
         if line_searcher is None:
-            line_searcher = LineSearchStrongWolfe(
-                preferred_initial_step_size=1.)
+            line_searcher = LineSearch(preferred_initial_step_size=1.)
         super(RelaxedNewton, self).__init__(controller=controller,
                                             line_searcher=line_searcher)
 
@@ -161,8 +160,7 @@ class NewtonCG(DescentMinimizer):
 
     def __init__(self, controller, line_searcher=None):
         if line_searcher is None:
-            line_searcher = LineSearchStrongWolfe(
-                preferred_initial_step_size=1.)
+            line_searcher = LineSearch(preferred_initial_step_size=1.)
         super(NewtonCG, self).__init__(controller=controller,
                                        line_searcher=line_searcher)
 
@@ -201,7 +199,7 @@ class NewtonCG(DescentMinimizer):
 
 
 class L_BFGS(DescentMinimizer):
-    def __init__(self, controller, line_searcher=LineSearchStrongWolfe(),
+    def __init__(self, controller, line_searcher=LineSearch(),
                  max_history_length=5):
         super(L_BFGS, self).__init__(controller=controller,
                                      line_searcher=line_searcher)
@@ -266,7 +264,7 @@ class VL_BFGS(DescentMinimizer):
     Microsoft
     """
 
-    def __init__(self, controller, line_searcher=LineSearchStrongWolfe(),
+    def __init__(self, controller, line_searcher=LineSearch(),
                  max_history_length=5):
         super(VL_BFGS, self).__init__(controller=controller,
                                       line_searcher=line_searcher)

nifty5/minimization/energy_adapter.py

@@ -13,14 +13,8 @@ class EnergyAdapter(Energy):
         self._op = op
         self._constants = constants
         self._want_metric = want_metric
-        if len(self._constants) == 0:
-            tmp = self._op(Linearization.make_var(self._position, want_metric))
-        else:
-            ops = [ScalingOperator(0. if key in self._constants else 1., dom)
-                   for key, dom in self._position.domain.items()]
-            bdop = BlockDiagonalOperator(self._position.domain, tuple(ops))
-            tmp = self._op(Linearization(self._position, bdop,
-                                         want_metric=want_metric))
+        lin = Linearization.make_partial_var(position, constants, want_metric)
+        tmp = self._op(lin)
         self._val = tmp.val.local_data[()]
         self._grad = tmp.gradient
         self._metric = tmp._metric

nifty5/minimization/iteration_controllers.py

@@ -21,6 +21,7 @@ from __future__ import absolute_import, division, print_function
 from ..compat import *
 from ..logger import logger
 from ..utilities import NiftyMetaBase
+import numpy as np
 
 
 class IterationController(NiftyMetaBase()):
@@ -145,6 +146,48 @@ class GradientNormController(IterationController):
         return self.CONTINUE
 
 
+class GradInfNormController(IterationController):
+    def __init__(self, tol=None, convergence_level=1, iteration_limit=None,
+                 name=None):
+        self._tol = tol
+        self._convergence_level = convergence_level
+        self._iteration_limit = iteration_limit
+        self._name = name
+
+    def start(self, energy):
+        self._itcount = -1
+        self._ccount = 0
+        return self.check(energy)
+
+    def check(self, energy):
+        self._itcount += 1
+
+        crit = energy.gradient.norm(np.inf) / abs(energy.value)
+        if self._tol is not None and crit <= self._tol:
+            self._ccount += 1
+        else:
+            self._ccount = max(0, self._ccount-1)
+
+        # report
+        if self._name is not None:
+            logger.info(
+                "{}: Iteration #{} energy={:.6E} crit={:.2E} clvl={}"
+                .format(self._name, self._itcount, energy.value,
+                        crit, self._ccount))
+
+        # Are we done?
+        if self._iteration_limit is not None:
+            if self._itcount >= self._iteration_limit:
+                logger.warning(
+                    "{} Iteration limit reached. Assuming convergence"
+                    .format("" if self._name is None else self._name+": "))
+                return self.CONVERGED
+        if self._ccount >= self._convergence_level:
+            return self.CONVERGED
+
+        return self.CONTINUE
+
+
 class DeltaEnergyController(IterationController):
     def __init__(self, tol_rel_deltaE, convergence_level=1,
                  iteration_limit=None, name=None):

nifty5/minimization/kl_energy.py

@@ -9,33 +9,32 @@ from .. import utilities
 
 
 class KL_Energy(Energy):
-    def __init__(self, position, h, nsamp, constants=[], _samples=None,
-                 want_metric=False):
+    def __init__(self, position, h, nsamp, constants=[], _samples=None):
         super(KL_Energy, self).__init__(position)
         self._h = h
         self._constants = constants
-        self._want_metric = want_metric
         if _samples is None:
             met = h(Linearization.make_var(position, True)).metric
             _samples = tuple(met.draw_sample(from_inverse=True)
                              for _ in range(nsamp))
         self._samples = _samples
-        if len(constants) == 0:
-            tmp = Linearization.make_var(position, want_metric)
-        else:
-            ops = [ScalingOperator(0. if key in constants else 1., dom)
-                   for key, dom in position.domain.items()]
-            bdop = BlockDiagonalOperator(position.domain, tuple(ops))
-            tmp = Linearization(position, bdop, want_metric=want_metric)
-        mymap = map(lambda v: self._h(tmp+v), self._samples)
-        tmp = utilities.my_sum(mymap) * (1./len(self._samples))
-        self._val = tmp.val.local_data[()]
-        self._grad = tmp.gradient
-        self._metric = tmp.metric
+
+        self._lin = Linearization.make_partial_var(position, constants)
+        v, g = None, None
+        for s in self._samples:
+            tmp = self._h(self._lin+s)
+            if v is None:
+                v = tmp.val.local_data[()]
+                g = tmp.gradient
+            else:
+                v += tmp.val.local_data[()]
+                g = g + tmp.gradient
+        self._val = v / len(self._samples)
+        self._grad = g * (1./len(self._samples))
+        self._metric = None
 
     def at(self, position):
-        return KL_Energy(position, self._h, 0, self._constants, self._samples,
-                         self._want_metric)
+        return KL_Energy(position, self._h, 0, self._constants, self._samples)
 
     @property
     def value(self):
@@ -45,11 +44,20 @@ class KL_Energy(Energy):
     def gradient(self):
         return self._grad
 
+    def _get_metric(self):
+        if self._metric is None:
+            lin = self._lin.with_want_metric()
+            mymap = map(lambda v: self._h(lin+v).metric, self._samples)
+            self._metric = utilities.my_sum(mymap)
+            self._metric = self._metric.scale(1./len(self._samples))
+
     def apply_metric(self, x):
+        self._get_metric()
         return self._metric(x)
 
     @property
     def metric(self):
+        self._get_metric()
         return self._metric
 
     @property

nifty5/minimization/line_energy.py

-# 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 *
-
-
-class LineEnergy(object):
-    """ Evaluates an underlying Energy along a certain line direction.
-
-    Given an Energy class and a line direction, its position is parametrized by
-    a scalar step size along the descent direction relative to a zero point.
-
-    Parameters
-    ----------
-    line_position : float
-        Defines the full spatial position of this energy via
-        self.energy.position = zero_point + line_position*line_direction
-    energy : Energy
-        The Energy object which will be evaluated along the given direction.
-    line_direction : Field
-        Direction used for line evaluation. Does not have to be normalized.
-    offset :  float *optional*
-        Indirectly defines the zero point of the line via the equation
-        energy.position = zero_point + offset*line_direction
-        (default : 0.).
-
-    Notes
-    -----
-    The LineEnergy is used in minimization schemes in order perform line
-    searches. It describes an underlying Energy which is restricted along one
-    direction, only requiring the step size parameter to determine a new
-    position.
-    """
-
-    def __init__(self, line_position, energy, line_direction, offset=0.):
-        self._line_position = float(line_position)
-        self._line_direction = line_direction
-
-        if self._line_position == float(offset):
-            self._energy = energy
-        else:
-            pos = energy.position \
-                + (self._line_position-float(offset))*self._line_direction
-            self._energy = energy.at(position=pos)
-
-    def at(self, line_position):
-        """ Returns LineEnergy at new position, memorizing the zero point.
-
-        Parameters
-        ----------
-        line_position : float
-            Parameter for the new position on the line direction.
-
-        Returns
-        -------
-            LineEnergy object at new position with same zero point as `self`.
-
-        """
-
-        return LineEnergy(line_position, self._energy, self._line_direction,
-                          offset=self._line_position)
-
-    @property
-    def energy(self):
-        """
-        Energy : The underlying Energy object
-        """
-        return self._energy
-
-    @property
-    def value(self):
-        """