Merge branch 'master' into tests

nifty/domain_object.py

@@ -48,6 +48,11 @@ class DomainObject(Versionable, Loggable, object):
         raise NotImplementedError(
             "There is no generic dim for DomainObject.")
 
+    @abc.abstractmethod
+    def weight(self, x, power=1, axes=None, inplace=False):
+        raise NotImplementedError(
+            "There is no generic weight-method for DomainObject.")
+
     def pre_cast(self, x, axes=None):
         return x
 

nifty/field.py

@@ -90,7 +90,7 @@ class Field(Loggable, Versionable, object):
             elif isinstance(val, Field):
                 distribution_strategy = val.distribution_strategy
             else:
-                self.logger.info("Datamodel set to default!")
+                self.logger.debug("distribution_strategy set to default!")
                 distribution_strategy = gc['default_distribution_strategy']
         elif distribution_strategy not in DISTRIBUTION_STRATEGIES['global']:
             raise ValueError(
@@ -151,11 +151,11 @@ class Field(Loggable, Versionable, object):
 
     def power_analyze(self, spaces=None, log=False, nbin=None, binbounds=None,
                       real_signal=True):
-        # assert that all spaces in `self.domain` are either harmonic or
+        # check if all spaces in `self.domain` are either harmonic or
         # power_space instances
         for sp in self.domain:
             if not sp.harmonic and not isinstance(sp, PowerSpace):
-                raise AttributeError(
+                self.logger.info(
                     "Field has a space in `domain` which is neither "
                     "harmonic nor a PowerSpace.")
 
@@ -287,11 +287,12 @@ class Field(Loggable, Versionable, object):
 
     def power_synthesize(self, spaces=None, real_signal=True,
                          mean=None, std=None):
-        # assert that all spaces in `self.domain` are either of signal-type or
+
+        # check if all spaces in `self.domain` are either of signal-type or
         # power_space instances
         for sp in self.domain:
             if not sp.harmonic and not isinstance(sp, PowerSpace):
-                raise AttributeError(
+                self.logger.info(
                     "Field has a space in `domain` which is neither "
                     "harmonic nor a PowerSpace.")
 
@@ -347,7 +348,8 @@ class Field(Loggable, Versionable, object):
         if real_signal:
             result_val_list = [harmonic_domain.hermitian_decomposition(
                                     x.val,
-                                    axes=x.domain_axes[power_space_index])[0]
+                                    axes=x.domain_axes[power_space_index],
+                                    preserve_gaussian_variance=True)[0]
                                for x in result_list]
         else:
             result_val_list = [x.val for x in result_list]
@@ -556,10 +558,9 @@ class Field(Loggable, Versionable, object):
 
         new_val = self.get_val(copy=False)
 
+        spaces = utilities.cast_axis_to_tuple(spaces, len(self.domain))
         if spaces is None:
             spaces = range(len(self.domain))
-        else:
-            spaces = utilities.cast_axis_to_tuple(spaces, len(self.domain))
 
         for ind, sp in enumerate(self.domain):
             if ind in spaces:
@@ -571,17 +572,11 @@ class Field(Loggable, Versionable, object):
         new_field.set_val(new_val=new_val, copy=False)
         return new_field
 
-    def dot(self, x=None, bare=False):
-        if isinstance(x, Field):
-            try:
-                assert len(x.domain) == len(self.domain)
-                for index in xrange(len(self.domain)):
-                    assert x.domain[index] == self.domain[index]
-            except AssertionError:
-                raise ValueError(
-                    "domains are incompatible.")
-            # extract the data from x and try to dot with this
-            x = x.get_val(copy=False)
+    def dot(self, x=None, spaces=None, bare=False):
+
+        if not isinstance(x, Field):
+            raise ValueError("The dot-partner must be an instance of " +
+                             "the NIFTy field class")
 
         # Compute the dot respecting the fact of discrete/continous spaces
         if bare:
@@ -589,14 +584,21 @@ class Field(Loggable, Versionable, object):
         else:
             y = self.weight(power=1)
 
-        y = y.get_val(copy=False)
-
-        # Cast the input in order to cure dtype and shape differences
-        x = self.cast(x)
-
-        dotted = x.conjugate() * y
-
-        return dotted.sum()
+        if spaces is None:
+            x_val = x.get_val(copy=False)
+            y_val = y.get_val(copy=False)
+            result = (x_val.conjugate() * y_val).sum()
+            return result
+        else:
+            # create a diagonal operator which is capable of taking care of the
+            # axes-matching
+            from nifty.operators.diagonal_operator import DiagonalOperator
+            diagonal = y.val.conjugate()
+            diagonalOperator = DiagonalOperator(domain=y.domain,
+                                                diagonal=diagonal,
+                                                copy=False)
+            dotted = diagonalOperator(x, spaces=spaces)
+            return dotted.sum(spaces=spaces)
 
     def norm(self, q=2):
         """
@@ -834,7 +836,10 @@ class Field(Loggable, Versionable, object):
         hdf5_group.attrs['domain_axes'] = str(self.domain_axes)
         hdf5_group['num_domain'] = len(self.domain)
 
-        ret_dict = {'val': self.val}
+        if self._val is None:
+            ret_dict = {}
+        else:
+            ret_dict = {'val': self.val}
 
         for i in range(len(self.domain)):
             ret_dict['s_' + str(i)] = self.domain[i]
@@ -854,7 +859,12 @@ class Field(Loggable, Versionable, object):
         new_field.domain = tuple(temp_domain)
 
         exec('new_field.domain_axes = ' + hdf5_group.attrs['domain_axes'])
-        new_field._val = repository.get('val', hdf5_group)
+
+        try:
+            new_field._val = repository.get('val', hdf5_group)
+        except(KeyError):
+            new_field._val = None
+
         new_field.dtype = np.dtype(hdf5_group.attrs['dtype'])
         new_field.distribution_strategy =\
             hdf5_group.attrs['distribution_strategy']

nifty/field_types/field_array.py

 # -*- coding: utf-8 -*-
 
-import pickle
-
 import numpy as np
 
 from field_type import FieldType
@@ -29,14 +27,14 @@ class FieldArray(FieldType):
 
     def _to_hdf5(self, hdf5_group):
         hdf5_group['shape'] = self.shape
-        hdf5_group['dtype'] = pickle.dumps(self.dtype)
+        hdf5_group.attrs['dtype'] = self.dtype.name
 
         return None
 
     @classmethod
     def _from_hdf5(cls, hdf5_group, loopback_get):
         result = cls(
-            hdf5_group['shape'][:],
-            pickle.loads(hdf5_group['dtype'][()])
+            shape=hdf5_group['shape'][:],
+            dtype=np.dtype(hdf5_group.attrs['dtype'])
             )
         return result

nifty/field_types/field_type.py

@@ -5,6 +5,13 @@ from nifty.domain_object import DomainObject
 
 class FieldType(DomainObject):
 
+    def weight(self, x, power=1, axes=None, inplace=False):
+        if inplace:
+            result = x
+        else:
+            result = x.copy()
+        return result
+
     def process(self, method_name, array, inplace=True, **kwargs):
         try:
             result_array = self.__getattr__(method_name)(array,

nifty/operators/__init__.py

@@ -33,6 +33,8 @@ from fft_operator import *
 
 from invertible_operator_mixin import InvertibleOperatorMixin
 
+from projection_operator import ProjectionOperator
+
 from propagator_operator import PropagatorOperator
 
 from composed_operator import ComposedOperator

nifty/operators/diagonal_operator/diagonal_operator.py

@@ -90,10 +90,15 @@ class DiagonalOperator(EndomorphicOperator):
 
     @property
     def symmetric(self):
+        if self._symmetric is None:
+            self._symmetric = (self._diagonal.val.imag == 0).all()
         return self._symmetric
 
     @property
     def unitary(self):
+        if self._unitary is None:
+            self._unitary = (self._diagonal.val *
+                             self._diagonal.val.conjugate() == 1).all()
         return self._unitary
 
     # ---Added properties and methods---
@@ -134,11 +139,11 @@ class DiagonalOperator(EndomorphicOperator):
             # Otherwise, inplace weightening would change the external field
             f.weight(inplace=copy, power=-1)
 
-        # check if the operator is symmetric:
-        self._symmetric = (f.val.imag == 0).all()
+        # Reset the symmetric property:
+        self._symmetric = None
 
-        # check if the operator is unitary:
-        self._unitary = (f.val * f.val.conjugate() == 1).all()
+        # Reset the unitarity property
+        self._unitary = None
 
         # store the diagonal-field
         self._diagonal = f
@@ -154,9 +159,7 @@ class DiagonalOperator(EndomorphicOperator):
         # the one of x, reshape the local data of self and apply it directly
         active_axes = []
         if spaces is None:
-            if self.domain != ():
-                for axes in x.domain_axes:
-                    active_axes += axes
+            active_axes = range(len(x.shape))
         else:
             for space_index in spaces:
                 active_axes += x.domain_axes[space_index]
@@ -167,6 +170,8 @@ class DiagonalOperator(EndomorphicOperator):
             local_diagonal = self._diagonal.val.get_local_data(copy=False)
         else:
             # create an array that is sub-slice compatible
+            self.logger.warn("The input field is not sub-slice compatible to "
+                             "the distribution strategy of the operator.")
             redistr_diagonal_val = self._diagonal.val.copy(
                 distribution_strategy=axes_local_distribution_strategy)
             local_diagonal = redistr_diagonal_val.get_local_data(copy=False)

nifty/operators/fft_operator/fft_operator.py

 
+import numpy as np
+
 import nifty.nifty_utilities as utilities
 from nifty.spaces import RGSpace,\
                          GLSpace,\
@@ -33,7 +35,8 @@ class FFTOperator(LinearOperator):
 
     # ---Overwritten properties and methods---
 
-    def __init__(self, domain=(), target=None, module=None):
+    def __init__(self, domain=(), target=None, module=None,
+                 domain_dtype=None, target_dtype=None):
 
         self._domain = self._parse_domain(domain)
 
@@ -69,7 +72,18 @@ class FFTOperator(LinearOperator):
         self._backward_transformation = TransformationCache.create(
             backward_class, self.target[0], self.domain[0], module=module)
 
-    def _times(self, x, spaces, dtype=None):
+        # Store the dtype information
+        if domain_dtype is None:
+            self.domain_dtype = None
+        else:
+            self.domain_dtype = np.dtype(domain_dtype)
+
+        if target_dtype is None:
+            self.target_dtype = None
+        else:
+            self.target_dtype = np.dtype(target_dtype)
+
+    def _times(self, x, spaces):
         spaces = utilities.cast_axis_to_tuple(spaces, len(x.domain))
         if spaces is None:
             # this case means that x lives on only one space, which is
@@ -87,12 +101,13 @@ class FFTOperator(LinearOperator):
             result_domain = list(x.domain)
             result_domain[spaces[0]] = self.target[0]
 
-        result_field = x.copy_empty(domain=result_domain, dtype=dtype)
+        result_field = x.copy_empty(domain=result_domain,
+                                    dtype=self.target_dtype)
         result_field.set_val(new_val=new_val, copy=False)
 
         return result_field
 
-    def _inverse_times(self, x, spaces, dtype=None):
+    def _inverse_times(self, x, spaces):
         spaces = utilities.cast_axis_to_tuple(spaces, len(x.domain))
         if spaces is None:
             # this case means that x lives on only one space, which is
@@ -110,7 +125,8 @@ class FFTOperator(LinearOperator):
             result_domain = list(x.domain)
             result_domain[spaces[0]] = self.domain[0]
 
-        result_field = x.copy_empty(domain=result_domain, dtype=dtype)
+        result_field = x.copy_empty(domain=result_domain,
+                                    dtype=self.domain_dtype)
         result_field.set_val(new_val=new_val, copy=False)
 
         return result_field

nifty/operators/fft_operator/transformations/rg_transforms.py

@@ -592,6 +592,7 @@ class GFFT(Transform):
 
         # Array for storing the result
         return_val = None
+        result_dtype = np.result_type(np.complex, self.codomain.dtype)
 
         for slice_list in utilities.get_slice_list(temp_inp.shape, axes):
 
@@ -601,7 +602,7 @@ class GFFT(Transform):
             else:
                 # initialize the return_val object if needed
                 if return_val is None:
-                    return_val = np.empty_like(temp_inp)
+                    return_val = np.empty_like(temp_inp, dtype=result_dtype)
                 inp = temp_inp[slice_list]
 
             inp = self.fft_machine.gfft(
@@ -622,12 +623,11 @@ class GFFT(Transform):
             else:
                 return_val[slice_list] = inp
 
-        result_dtype = np.result_type(np.complex, self.codomain.dtype)
         if isinstance(val, distributed_data_object):
             new_val = val.copy_empty(dtype=result_dtype)
             new_val.set_full_data(return_val, copy=False)
             return_val = new_val
         else:
-            return_val = return_val.astype(result_type, copy=False)
+            return_val = return_val.astype(result_dtype, copy=False)
 
         return return_val

nifty/operators/linear_operator/linear_operator.py

@@ -127,7 +127,7 @@ class LinearOperator(Loggable, object):
             self_domain = self.target
 
         if spaces is None:
-            if self_domain != () and self_domain != x.domain:
+            if self_domain != x.domain:
                 raise ValueError(
                     "The operator's and and field's domains don't "
                     "match.")

nifty/operators/projection_operator/__init__.py

+# -*- coding: utf-8 -*-
+
+from projection_operator import ProjectionOperator

nifty/operators/projection_operator/projection_operator.py

+# -*- coding: utf-8 -*-
+import numpy as np
+
+from nifty.field import Field
+
+from nifty.operators.endomorphic_operator import EndomorphicOperator
+
+
+class ProjectionOperator(EndomorphicOperator):
+
+    # ---Overwritten properties and methods---
+
+    def __init__(self, projection_field):
+        if not isinstance(projection_field, Field):
+            raise TypeError("The projection_field must be a NIFTy-Field"
+                            "instance.")
+        self._projection_field = projection_field
+        self._unitary = None
+
+    def _times(self, x, spaces):
+        # if the domain matches directly
+        # -> multiply the fields directly
+        if x.domain == self.domain:
+            # here the actual multiplication takes place
+            dotted = (self._projection_field * x).sum()
+            return self._projection_field * dotted
+
+        # if the distribution_strategy of self is sub-slice compatible to
+        # the one of x, reshape the local data of self and apply it directly
+        active_axes = []
+        if spaces is None:
+            active_axes = range(len(x.shape))
+        else:
+            for space_index in spaces:
+                active_axes += x.domain_axes[space_index]
+
+        axes_local_distribution_strategy = \
+            x.val.get_axes_local_distribution_strategy(active_axes)
+        if axes_local_distribution_strategy == \
+           self._projection_field.distribution_strategy:
+            local_projection_vector = \
+                self._projection_field.val.get_local_data(copy=False)
+        else:
+            # create an array that is sub-slice compatible
+            self.logger.warn("The input field is not sub-slice compatible to "
+                             "the distribution strategy of the operator. "
+                             "Performing an probably expensive "
+                             "redistribution.")
+            redistr_projection_val = self._projection_field.val.copy(
+                distribution_strategy=axes_local_distribution_strategy)
+            local_projection_vector = \
+                redistr_projection_val.get_local_data(copy=False)
+
+        local_x = x.val.get_local_data(copy=False)
+
+        l = len(local_projection_vector.shape)
+        sublist_projector = range(l)
+        sublist_x = np.arange(len(local_x.shape)) + l
+
+        for i in xrange(l):
+            a = active_axes[i]
+            sublist_x[a] = i
+
+        dotted = np.einsum(local_projection_vector, sublist_projector,
+                           local_x, sublist_x)
+
+        # get those elements from sublist_x that haven't got contracted
+        sublist_dotted = sublist_x[sublist_x >= l]
+
+        remultiplied = np.einsum(local_projection_vector, sublist_projector,
+                                 dotted, sublist_dotted,
+                                 sublist_x)
+        result_field = x.copy_empty(dtype=remultiplied.dtype)
+        result_field.val.set_local_data(remultiplied, copy=False)
+        return result_field
+
+    def _inverse_times(self, x, spaces):
+        raise NotImplementedError("The ProjectionOperator is a singular "
+                                  "operator and therefore has no inverse.")
+
+    # ---Mandatory properties and methods---
+
+    @property
+    def domain(self):
+        return self._projection_field.domain
+
+    @property
+    def implemented(self):
+        return True
+
+    @property
+    def unitary(self):
+        if self._unitary is None:
+            self._unitary = (self._projection_field.val == 1).all()
+        return self._unitary
+
+    @property
+    def symmetric(self):
+        return True

nifty/spaces/gl_space/gl_space.py

@@ -131,10 +131,9 @@ class GLSpace(Space):
     def weight(self, x, power=1, axes=None, inplace=False):
         nlon = self.nlon
         nlat = self.nlat
-
+        vol = gl.vol(nlat) ** power
         weight = np.array(list(itertools.chain.from_iterable(
-            itertools.repeat(x ** power, nlon)
-            for x in gl.vol(nlat))))
+                          itertools.repeat(x, nlon) for x in vol)))
 
         if axes is not None:
             # reshape the weight array to match the input shape
@@ -209,7 +208,7 @@ class GLSpace(Space):
     def _to_hdf5(self, hdf5_group):
         hdf5_group['nlat'] = self.nlat
         hdf5_group['nlon'] = self.nlon
-        hdf5_group['dtype'] = self.dtype.name
+        hdf5_group.attrs['dtype'] = self.dtype.name
 
         return None
 
@@ -218,7 +217,7 @@ class GLSpace(Space):
         result = cls(
             nlat=hdf5_group['nlat'][()],
             nlon=hdf5_group['nlon'][()],
-            dtype=np.dtype(hdf5_group['dtype'][()])
+            dtype=np.dtype(hdf5_group.attrs['dtype'])
             )
 
         return result

nifty/spaces/hp_space/hp_space.py

@@ -209,13 +209,13 @@ class HPSpace(Space):
 
     def _to_hdf5(self, hdf5_group):
         hdf5_group['nside'] = self.nside
-        hdf5_group['dtype'] = self.dtype.name
+        hdf5_group.attrs['dtype'] = self.dtype.name
         return None
 
     @classmethod
     def _from_hdf5(cls, hdf5_group, repository):
         result = cls(
             nside=hdf5_group['nside'][()],
-            dtype=np.dtype(hdf5_group['dtype'][()])
+            dtype=np.dtype(hdf5_group.attrs['dtype'])
             )
         return result

nifty/spaces/lm_space/lm_space.py

@@ -111,7 +111,8 @@ class LMSpace(Space):
         super(LMSpace, self).__init__(dtype)
         self._lmax = self._parse_lmax(lmax)
 
-    def hermitian_decomposition(self, x, axes=None):
+    def hermitian_decomposition(self, x, axes=None,
+                                preserve_gaussian_variance=False):
         hermitian_part = x.copy_empty()
         anti_hermitian_part = x.copy_empty()
         hermitian_part[:] = x.real
@@ -145,7 +146,6 @@ class LMSpace(Space):
 
     def copy(self):
         return self.__class__(lmax=self.lmax,
-                              mmax=self.mmax,
                               dtype=self.dtype)
 
     def weight(self, x, power=1, axes=None, inplace=False):
@@ -193,13 +193,13 @@ class LMSpace(Space):
 
     def _to_hdf5(self, hdf5_group):
         hdf5_group['lmax'] = self.lmax
-        hdf5_group['dtype'] = self.dtype.name
+        hdf5_group.attrs['dtype'] = self.dtype.name
         return None
 
     @classmethod
     def _from_hdf5(cls, hdf5_group, repository):
         result = cls(
             lmax=hdf5_group['lmax'][()],
-            dtype=np.dtype(hdf5_group['dtype'][()])
+            dtype=np.dtype(hdf5_group.attrs['dtype'])
             )
         return result

nifty/spaces/power_space/power_space.py

@@ -73,7 +73,7 @@ class PowerSpace(Space):
     @property
     def total_volume(self):
         # every power-pixel has a volume of 1
-        return reduce(lambda x, y: x*y, self.pindex.shape)
+        return float(reduce(lambda x, y: x*y, self.pindex.shape))
 
     def copy(self):
         distribution_strategy = self.pindex.distribution_strategy
@@ -85,14 +85,8 @@ class PowerSpace(Space):
                               dtype=self.dtype)
 
     def weight(self, x, power=1, axes=None, inplace=False):
-        total_shape = x.shape
-
-        axes = cast_axis_to_tuple(axes, len(total_shape))
-        if len(axes) != 1:
-            raise ValueError(
-                "axes must be of length 1.")
-
-        reshaper = [1, ] * len(total_shape)
+        reshaper = [1, ] * len(x.shape)
+        # we know len(axes) is always 1
         reshaper[axes[0]] = self.shape[0]
 
         weight = self.rho.reshape(reshaper)
@@ -179,8 +173,9 @@ class PowerSpace(Space):
         new_ps = EmptyPowerSpace()
         # reset class
         new_ps.__class__ = cls
+        # call instructor so that classes are properly setup
+        super(PowerSpace, new_ps).__init__(np.dtype(hdf5_group.attrs['dtype']))
         # set all values
-        new_ps.dtype = np.dtype(hdf5_group.attrs['dtype'])
         new_ps._harmonic_domain = repository.get('harmonic_domain', hdf5_group)
         new_ps._log = hdf5_group['log'][()]
         exec('new_ps._nbin = ' + hdf5_group.attrs['nbin'])
@@ -191,6 +186,8 @@ class PowerSpace(Space):
         new_ps._rho = hdf5_group['rho'][:]
         new_ps._pundex = hdf5_group['pundex'][:]
         new_ps._k_array = repository.get('k_array', hdf5_group)
+        new_ps._ignore_for_hash += ['_pindex', '_kindex', '_rho', '_pundex',
+                                   '_k_array']
 
         return new_ps
 

nifty/spaces/rg_space/rg_space.py

@@ -150,7 +150,8 @@ class RGSpace(Space):
         self._distances = self._parse_distances(distances)
         self._zerocenter = self._parse_zerocenter(zerocenter)
 
-    def hermitian_decomposition(self, x, axes=None):
+    def hermitian_decomposition(self, x, axes=None,
+                                preserve_gaussian_variance=False):
         # compute the hermitian part
         flipped_x = self._hermitianize_inverter(x, axes=axes)
         flipped_x = flipped_x.conjugate()
@@ -160,8 +161,39 @@ class RGSpace(Space):
 
         # use subtraction since it is faster than flipping another time
         anti_hermitian_part