Merge branch 'work_on_fields' into 'NIFTy_5'

Work on fields

See merge request ift/nifty-dev!41

demos/getting_started_3.py

@@ -22,9 +22,8 @@ if __name__ == '__main__':
     ht = ift.HarmonicTransformOperator(harmonic_space, position_space)
     power_space = A.value.domain[0]
     power_distributor = ift.PowerDistributor(harmonic_space, power_space)
-    position = {}
-    position['xi'] = ift.Field.from_random('normal', harmonic_space)
-    position = ift.MultiField(position)
+    position = ift.MultiField.from_dict(
+        {'xi': ift.Field.from_random('normal', harmonic_space)})
 
     xi = ift.Variable(position)['xi']
     Amp = power_distributor(A)
@@ -35,6 +34,7 @@ if __name__ == '__main__':
 
     # apply some nonlinearity
     signal = ift.PointwisePositiveTanh(correlated_field)
+
     # Building the Line of Sight response
     LOS_starts, LOS_ends = get_random_LOS(100)
     R = ift.LOSResponse(position_space, starts=LOS_starts,

nifty5/compat.py

+from __future__ import absolute_import, division, print_function
+from builtins import (ascii, bytes, chr, dict, filter, hex, input,
+                      map, next, oct, open, pow, range, round,
+                      super, zip)
+from functools import reduce

nifty5/data_objects/distributed_do.py

@@ -16,9 +16,8 @@
 # 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 builtins import *
-from functools import reduce
+from __future__ import absolute_import, division, print_function
+from ..compat import *
 import numpy as np
 from .random import Random
 from mpi4py import MPI

nifty5/data_objects/random.py

@@ -16,7 +16,8 @@
 # NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik
 # and financially supported by the Studienstiftung des deutschen Volkes.
 
-from builtins import object
+from __future__ import absolute_import, division, print_function
+from ..compat import *
 import numpy as np
 
 

nifty5/dobj.py

@@ -16,6 +16,10 @@
 # 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 *
+
+
 try:
     from mpi4py import MPI
     if MPI.COMM_WORLD.Get_size() == 1:

nifty5/domain_tuple.py

@@ -16,9 +16,8 @@
 # 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 builtins import *
-from functools import reduce
+from __future__ import absolute_import, division, print_function
+from .compat import *
 from .domains.domain import Domain
 
 
@@ -138,26 +137,11 @@ class DomainTuple(object):
     def __eq__(self, x):
         if self is x:
             return True
-        x = DomainTuple.make(x)
-        return self is x
+        return self is DomainTuple.make(x)
 
     def __ne__(self, x):
         return not self.__eq__(x)
 
-    def compatibleTo(self, x):
-        return self.__eq__(x)
-
-    def subsetOf(self, x):
-        return self.__eq__(x)
-
-    def unitedWith(self, x):
-        if self is x:
-            return self
-        x = DomainTuple.make(x)
-        if self is not x:
-            raise ValueError("domain mismatch")
-        return self
-
     def __str__(self):
         res = "DomainTuple, len: " + str(len(self))
         for i in self:

nifty5/domains/dof_space.py

@@ -16,6 +16,8 @@
 # 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 *
 import numpy as np
 from .structured_domain import StructuredDomain
 

nifty5/domains/domain.py

@@ -16,6 +16,8 @@
 # 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 *
 import abc
 from ..utilities import NiftyMetaBase
 

nifty5/domains/gl_space.py

@@ -16,7 +16,8 @@
 # NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik
 # and financially supported by the Studienstiftung des deutschen Volkes.
 
-from __future__ import division
+from __future__ import absolute_import, division, print_function
+from ..compat import *
 import numpy as np
 from .structured_domain import StructuredDomain
 

nifty5/domains/hp_space.py

@@ -16,7 +16,8 @@
 # NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik
 # and financially supported by the Studienstiftung des deutschen Volkes.
 
-from __future__ import division
+from __future__ import absolute_import, division, print_function
+from ..compat import *
 import numpy as np
 from .structured_domain import StructuredDomain
 

nifty5/domains/lm_space.py

@@ -16,7 +16,8 @@
 # NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik
 # and financially supported by the Studienstiftung des deutschen Volkes.
 
-from __future__ import division
+from __future__ import absolute_import, division, print_function
+from ..compat import *
 import numpy as np
 from .structured_domain import StructuredDomain
 from ..field import Field

nifty5/domains/log_rg_space.py

-from functools import reduce
+# 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 ..sugar import exp
-
 import numpy as np
-
 from .. import dobj
 from ..field import Field
 from .structured_domain import StructuredDomain

nifty5/domains/power_space.py

@@ -16,6 +16,8 @@
 # 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 *
 import numpy as np
 from .structured_domain import StructuredDomain
 from .. import dobj

nifty5/domains/rg_space.py

@@ -16,9 +16,8 @@
 # NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik
 # and financially supported by the Studienstiftung des deutschen Volkes.
 
-from __future__ import division
-from builtins import range
-from functools import reduce
+from __future__ import absolute_import, division, print_function
+from ..compat import *
 import numpy as np
 from .structured_domain import StructuredDomain
 from ..field import Field

nifty5/domains/structured_domain.py

@@ -16,6 +16,8 @@
 # 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 *
 import abc
 from .domain import Domain
 import numpy as np

nifty5/domains/unstructured_domain.py

@@ -16,8 +16,9 @@
 # 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 .domain import Domain
-from functools import reduce
 
 
 class UnstructuredDomain(Domain):

nifty5/energies/hamiltonian.py

@@ -16,6 +16,8 @@
 # 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 ..library.gaussian_energy import GaussianEnergy
 from ..minimization.energy import Energy
 from ..models.variable import Variable

nifty5/energies/kl.py

-from builtins import *
+# 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 ..minimization.energy import Energy
 from ..utilities import memo, my_sum
 

nifty5/extra/energy_and_model_tests.py

@@ -16,8 +16,8 @@
 # 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 builtins import *
+from __future__ import absolute_import, division, print_function
+from ..compat import *
 import numpy as np
 from ..sugar import from_random
 from ..minimization.energy import Energy

nifty5/extra/operator_tests.py

@@ -16,6 +16,8 @@
 # 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 *
 import numpy as np
 from ..sugar import from_random
 from ..field import Field

nifty5/field.py

@@ -16,12 +16,11 @@
 # 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 builtins import *
+from __future__ import absolute_import, division, print_function
+from .compat import *
 import numpy as np
 from . import utilities
 from .domain_tuple import DomainTuple
-from functools import reduce
 from . import dobj
 
 
@@ -110,7 +109,7 @@ class Field(object):
     @staticmethod
     def from_local_data(domain, arr):
         return Field(DomainTuple.make(domain),
-            dobj.from_local_data(domain.shape, arr))
+                     dobj.from_local_data(domain.shape, arr))
 
     def to_global_data(self):
         """Returns an array containing the full data of the field.
@@ -215,14 +214,14 @@ class Field(object):
         """Field : The real part of the field"""
         if not np.issubdtype(self.dtype, np.complexfloating):
             return self
-        return Field(self._domain, self.val.real)
+        return Field(self._domain, self._val.real)
 
     @property
     def imag(self):
         """Field : The imaginary part of the field"""
         if not np.issubdtype(self.dtype, np.complexfloating):
             raise ValueError(".imag called on a non-complex Field")
-        return Field(self._domain, self.val.imag)
+        return Field(self._domain, self._val.imag)
 
     def scalar_weight(self, spaces=None):
         """Returns the uniform volume element for a sub-domain of `self`.
@@ -338,14 +337,14 @@ class Field(object):
             raise TypeError("The dot-partner must be an instance of " +
                             "the NIFTy field class")
 
-        if x._domain != self._domain:
+        if x._domain is not self._domain:
             raise ValueError("Domain mismatch")
 
         ndom = len(self._domain)
         spaces = utilities.parse_spaces(spaces, ndom)
 
         if len(spaces) == ndom:
-            return dobj.vdot(self.val, x.val)
+            return dobj.vdot(self._val, x._val)
         # If we arrive here, we have to do a partial dot product.
         # For the moment, do this the explicit, non-optimized way
         return (self.conjugate()*x).sum(spaces=spaces)
@@ -378,7 +377,7 @@ class Field(object):
         Field
             The complex conjugated field.
         """
-        return Field(self._domain, self.val.conjugate())
+        return Field(self._domain, self._val.conjugate())
 
     # ---General unary/contraction methods---
 
@@ -386,14 +385,14 @@ class Field(object):
         return self
 
     def __neg__(self):
-        return Field(self._domain, -self.val)
+        return Field(self._domain, -self._val)
 
     def __abs__(self):
-        return Field(self._domain, abs(self.val))
+        return Field(self._domain, abs(self._val))
 
     def _contraction_helper(self, op, spaces):
         if spaces is None:
-            return getattr(self.val, op)()
+            return getattr(self._val, op)()
 
         spaces = utilities.parse_spaces(spaces, len(self._domain))
 
@@ -403,7 +402,7 @@ class Field(object):
             axes_list = reduce(lambda x, y: x+y, axes_list)
 
         # perform the contraction on the data
-        data = getattr(self.val, op)(axis=axes_list)
+        data = getattr(self._val, op)(axis=axes_list)
 
         # check if the result is scalar or if a result_field must be constr.
         if np.isscalar(data):
@@ -594,7 +593,7 @@ class Field(object):
     def __str__(self):
         return "nifty5.Field instance\n- domain      = " + \
                self._domain.__str__() + \
-               "\n- val         = " + repr(self.val)
+               "\n- val         = " + repr(self._val)
 
     def isEquivalentTo(self, other):
         """Determines (as quickly as possible) whether `self`'s content is
@@ -603,7 +602,7 @@ class Field(object):
             return True
         if not isinstance(other, Field):
             return False
-        if self._domain != other._domain:
+        if self._domain is not other._domain:
             return False
         return (self._val == other._val).all()
 
@@ -625,14 +624,14 @@ for op in ["__add__", "__radd__",
         def func2(self, other):
             # if other is a field, make sure that the domains match
             if isinstance(other, Field):
-                if other._domain != self._domain:
+                if other._domain is not self._domain:
                     raise ValueError("domains are incompatible.")
-                tval = getattr(self.val, op)(other.val)
+                tval = getattr(self._val, op)(other._val)
                 return Field(self._domain, tval)
 
             if (np.isscalar(other) or
                     isinstance(other, (dobj.data_object, np.ndarray))):
-                tval = getattr(self.val, op)(other)
+                tval = getattr(self._val, op)(other)
                 return Field(self._domain, tval)
 
             raise TypeError("should not arrive here")

nifty5/library/amplitude_model.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 *
 import numpy as np
-
 from ..domains.power_space import PowerSpace
 from ..domains.unstructured_domain import UnstructuredDomain
 from ..field import Field
@@ -58,7 +77,7 @@ def make_amplitude_model(s_space, Npixdof, ceps_a, ceps_k, sm, sv, im, iv,
     fields = {keys[0]: Field.from_random('normal', dof_space),
               keys[1]: Field.from_random('normal', param_space)}
 
-    position = MultiField(fields)
+    position = MultiField.from_dict(fields)
 
     dof_space = position[keys[0]].domain[0]
     kern = lambda k: _ceps_kernel(dof_space, k, ceps_a, ceps_k)
@@ -104,9 +123,7 @@ def create_cepstrum_amplitude_field(domain, cepstrum):
         for i in range(dim):
             ks = np.minimum(shape[i] - np.arange(shape[i]) +
                             1, np.arange(shape[i])) * dist[i]
-            fst_dims = (1,) * i
-            lst_dims = (1,) * (dim - i - 1)
-            q_array[i] += ks.reshape(fst_dims + (shape[i],) + lst_dims)
+            q_array[i] += ks.reshape((1,)*i + (shape[i],) + (1,)*(dim-i-1))
 
     # Fill cepstrum field (all non-zero modes)
     no_zero_modes = (slice(1, None),) * dim
@@ -117,10 +134,9 @@ def create_cepstrum_amplitude_field(domain, cepstrum):
     # Fill cepstrum field (zero-mode subspaces)
     for i in range(dim):
         # Prepare indices
-        fst_dims = (slice(None),) * i
-        lst_dims = (slice(None),) * (dim - i - 1)
-        sl = fst_dims + (slice(1, None),) + lst_dims
-        sl2 = fst_dims + (0,) + lst_dims
+        fst_dims = (slice(None),)*i
+        sl = fst_dims + (slice(1, None),)
+        sl2 = fst_dims + (0,)
 
         # Do summation
         cepstrum_field[sl2] = np.sum(cepstrum_field[sl], axis=i)

nifty5/library/apply_data.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 *
+
+
 def ApplyData(data, var, model_data):
     # TODO This is rather confusing. Delete that eventually.
     from ..operators.diagonal_operator import DiagonalOperator

nifty5/library/bernoulli_energy.py

@@ -16,8 +16,9 @@
 # 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 numpy import inf, isnan
-
 from ..minimization.energy import Energy
 from ..operators.sandwich_operator import SandwichOperator
 from ..sugar import log, makeOp
@@ -35,10 +36,10 @@ class BernoulliEnergy(Energy):
         self._d = d
 
         p_val = self._p.value
-        self._value = -self._d.vdot(log(p_val)) - (1. - d).vdot(log(1.-p_val))
+        self._value = -self._d.vdot(log(p_val)) - (1.-d).vdot(log(1.-p_val))
         if isnan(self._value):
             self._value = inf
-        metric = makeOp(1./((p_val) * (1.-p_val)))
+        metric = makeOp(1. / (p_val * (1.-p_val)))
         self._gradient = self._p.jacobian.adjoint_times(metric(p_val-d))
 
         self._metric = SandwichOperator.make(self._p.jacobian, metric)

nifty5/library/correlated_fields.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 *
+from ..operators.fft_operator import FFTOperator
+from ..field import Field
+from ..multi.multi_field import MultiField
+from ..models.local_nonlinearity import PointwiseExponential
+from ..operators.power_distributor import PowerDistributor
+from ..models.variable import Variable
+from ..domain_tuple import DomainTuple
+from ..operators.domain_distributor import DomainDistributor
+from ..operators.harmonic_transform_operator \
+    import HarmonicTransformOperator
+
 def make_correlated_field(s_space, amplitude_model):
     '''
     Method for construction of correlated fields
@@ -8,21 +39,14 @@ def make_correlated_field(s_space, amplitude_model):
 
     amplitude_model : model for correlation structure
     '''
-    from ..operators.fft_operator import FFTOperator
-    from ..field import Field
-    from ..multi.multi_field import MultiField
-    from ..models.local_nonlinearity import PointwiseExponential
-    from ..operators.power_distributor import PowerDistributor
-    from ..models.variable import Variable
     h_space = s_space.get_default_codomain()
     ht = FFTOperator(h_space, s_space)
     p_space = amplitude_model.value.domain[0]
     power_distributor = PowerDistributor(h_space, p_space)
-    position = {}
-    position['xi'] = Field.from_random('normal', h_space)
-    position['tau'] = amplitude_model.position['tau']
-    position['phi'] = amplitude_model.position['phi']
-    position = MultiField(position)
+    position = MultiField.from_dict({
+        'xi': Field.from_random('normal', h_space),
+        'tau': amplitude_model.position['tau'],
+        'phi': amplitude_model.position['phi']})
 
     xi = Variable(position)['xi']
     A = power_distributor(amplitude_model)
@@ -39,16 +63,6 @@ def make_mf_correlated_field(s_space_spatial, s_space_energy,