renamings

demos/wiener_filter_via_curvature.py

@@ -58,7 +58,7 @@ if __name__ == "__main__":
     data_domain = R.target[0]
 
     noiseless_data = R(mock_signal)
-    noise_amplitude = noiseless_data.std()/signal_to_noise
+    noise_amplitude = noiseless_data.val.std()/signal_to_noise
     N = ift.DiagonalOperator(
         ift.Field.full(data_domain, noise_amplitude**2))
     noise = ift.Field.from_random(

nifty4/__init__.py

@@ -2,10 +2,9 @@ from .version import __version__
 
 from . import dobj
 
-from .domain_object import DomainObject
-
-from .spaces.field_array import FieldArray
-from .spaces.space import Space
+from .spaces.domain import Domain
+from .spaces.unstructured_domain import UnstructuredDomain
+from .spaces.structured_domain import StructuredDomain
 from .spaces.rg_space import RGSpace
 from .spaces.lm_space import LMSpace
 from .spaces.hp_space import HPSpace
@@ -55,7 +54,7 @@ from .sugar import *
 from .plotting.plot import plot
 from . import library
 
-__all__ = ["DomainObject", "FieldArray", "Space", "RGSpace", "LMSpace",
+__all__ = ["Domain", "UnstructuredDomain", "StructuredDomain", "RGSpace", "LMSpace",
            "HPSpace", "GLSpace", "DOFSpace", "PowerSpace", "DomainTuple",
            "LinearOperator", "EndomorphicOperator", "ScalingOperator",
            "DiagonalOperator", "FFTOperator", "FFTSmoothingOperator",

nifty4/domain_tuple.py

@@ -17,7 +17,7 @@
 # and financially supported by the Studienstiftung des deutschen Volkes.
 
 from functools import reduce
-from .domain_object import DomainObject
+from .spaces.domain import Domain
 
 
 class DomainTuple(object):
@@ -28,12 +28,10 @@ class DomainTuple(object):
         self._axtuple = self._get_axes_tuple()
         shape_tuple = tuple(sp.shape for sp in self._dom)
         self._shape = reduce(lambda x, y: x + y, shape_tuple, ())
-        self._dim = reduce(lambda x, y: x * y, self._shape, 1)
-        self._accdims = (1,)
+        self._size = reduce(lambda x, y: x * y, self._shape, 1)
         prod = 1
         for dom in self._dom:
-            prod *= dom.dim
-            self._accdims += (prod,)
+            prod *= dom.size
 
     def _get_axes_tuple(self):
         i = 0
@@ -60,16 +58,16 @@ class DomainTuple(object):
     def _parse_domain(domain):
         if domain is None:
             return ()
-        if isinstance(domain, DomainObject):
+        if isinstance(domain, Domain):
             return (domain,)
 
         if not isinstance(domain, tuple):
             domain = tuple(domain)
         for d in domain:
-            if not isinstance(d, DomainObject):
+            if not isinstance(d, Domain):
                 raise TypeError(
                     "Given object contains something that is not an "
-                    "instance of DomainObject class.")
+                    "instance of Domain class.")
         return domain
 
     def __getitem__(self, i):
@@ -80,8 +78,8 @@ class DomainTuple(object):
         return self._shape
 
     @property
-    def dim(self):
-        return self._dim
+    def size(self):
+        return self._size
 
     @property
     def axes(self):

nifty4/field.py

@@ -35,7 +35,7 @@ class Field(object):
 
     Parameters
     ----------
-    domain : None, DomainTuple, tuple of DomainObjects, or single DomainObject
+    domain : None, DomainTuple, tuple(Domain), or Domain
 
     val : None, Field, data_object, or scalar
         The values the array should contain after init. A scalar input will
@@ -156,7 +156,7 @@ class Field(object):
             'pm1', 'normal', 'uniform' are the supported arguments for this
             method.
 
-        domain : DomainObject
+        domain : DomainTuple
             The domain of the output random field
 
         dtype : type
@@ -201,7 +201,7 @@ class Field(object):
         return self._domain.shape
 
     @property
-    def dim(self):
+    def size(self):
         """ Returns the total number of pixel-dimensions the field has.
 
         Effectively, all values from shape are multiplied.
@@ -211,7 +211,7 @@ class Field(object):
         out : int
             The dimension of the Field.
         """
-        return self._domain.dim
+        return self._domain.size
 
     @property
     def real(self):

nifty4/operators/response_operator.py

@@ -17,7 +17,7 @@
 # and financially supported by the Studienstiftung des deutschen Volkes.
 
 from ..field import Field
-from ..spaces.field_array import FieldArray
+from ..spaces.unstructured_domain import UnstructuredDomain
 from ..domain_tuple import DomainTuple
 from .linear_operator import LinearOperator
 from .fft_smoothing_operator import FFTSmoothingOperator
@@ -30,7 +30,7 @@ class GeometryRemover(LinearOperator):
     def __init__(self, domain):
         super(GeometryRemover, self).__init__()
         self._domain = DomainTuple.make(domain)
-        target_list = [FieldArray(dom.shape) for dom in self._domain]
+        target_list = [UnstructuredDomain(dom.shape) for dom in self._domain]
         self._target = DomainTuple.make(target_list)
 
     @property

nifty4/spaces/dof_space.py

@@ -17,10 +17,10 @@
 # and financially supported by the Studienstiftung des deutschen Volkes.
 
 import numpy as np
-from .space import Space
+from .structured_domain import StructuredDomain
 
 
-class DOFSpace(Space):
+class DOFSpace(StructuredDomain):
     def __init__(self, dof_weights):
         super(DOFSpace, self).__init__()
         self._dvol = tuple(dof_weights)
@@ -35,7 +35,7 @@ class DOFSpace(Space):
         return (len(self._dvol),)
 
     @property
-    def dim(self):
+    def size(self):
         return len(self._dvol)
 
     def scalar_dvol(self):

nifty4/domain_object.py → nifty4/spaces/domain.py

@@ -16,19 +16,15 @@
 # NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik
 # and financially supported by the Studienstiftung des deutschen Volkes.
 
-from __future__ import division
 import abc
-from .utilities import NiftyMeta
+from ..utilities import NiftyMeta
 from future.utils import with_metaclass
 import numpy as np
 
 
-class DomainObject(with_metaclass(
+class Domain(with_metaclass(
         NiftyMeta, type('NewBase', (object,), {}))):
-    """The abstract class that can be used as a domain for a field.
-
-    This holds all the information and functionality a field needs to know
-    about its domain and how the data of the field are stored.
+    """The abstract class repesenting a (structured or unstructured) domain.
     """
 
     def __init__(self):
@@ -45,16 +41,16 @@ class DomainObject(with_metaclass(
         return result_hash
 
     def __eq__(self, x):
-        """Checks if two domain_objects are equal.
+        """Checks if two domains are equal.
 
         Parameters
         ----------
-        x: domain_object
-            The domain_object `self` is compared to.
+        x: Domain
+            The domain `self` is compared to.
 
         Returns
         -------
-        bool: True iff `self` and x describe the same manifold.
+        bool: True iff `self` and x describe the same domain.
         """
         if self is x:  # shortcut for simple case
             return True
@@ -70,47 +66,22 @@ class DomainObject(with_metaclass(
 
     @abc.abstractproperty
     def shape(self):
-        """The domain-object's shape contribution to the underlying array.
+        """The shape of the array-like object required to store information
+        living on the domain.
 
         Returns
         -------
-        tuple of ints: shape of the underlying array-like object
+        tuple of ints: shape of the required array-like object
         """
         raise NotImplementedError
 
     @abc.abstractproperty
-    def dim(self):
-        """ Returns the number of pixel-dimensions the object has.
-
-        Returns
-        -------
-        int: number of pixels
-        """
-        raise NotImplementedError
-
-    @abc.abstractmethod
-    def scalar_dvol(self):
-        """Returns the volume factors of this domain as a floating
-        point scalar, if the volume factors are all identical, otherwise
-        returns None.
+    def size(self):
+        """Number of data elements associated with this domain.
+        Equivalent to the products over all entries in the domain's shape.
 
         Returns
         -------
-        float or None: Volume factor
+        int: number of data elements
         """
         raise NotImplementedError
-
-    def dvol(self):
-        """Returns the volume factors of this domain, either as a floating
-        point scalar (if the volume factors are all identical) or as a
-        floating point array with a shape of `self.shape`.
-
-        Returns
-        -------
-        float or numpy.ndarray(dtype=float): Volume factors
-        """
-        return self.scalar_dvol()
-
-    def total_volume(self):
-        tmp = self.dvol()
-        return self.dim * tmp if np.isscalar(tmp) else np.sum(tmp)

nifty4/spaces/gl_space.py

@@ -18,10 +18,10 @@
 
 from __future__ import division
 import numpy as np
-from .space import Space
+from .structured_domain import StructuredDomain
 
 
-class GLSpace(Space):
+class GLSpace(StructuredDomain):
     """NIFTy subclass for Gauss-Legendre pixelizations [#]_ of the two-sphere.
 
     Parameters
@@ -79,7 +79,7 @@ class GLSpace(Space):
         return (np.int((self.nlat * self.nlon)),)
 
     @property
-    def dim(self):
+    def size(self):
         return np.int((self.nlat * self.nlon))
 
     def scalar_dvol(self):

nifty4/spaces/hp_space.py

@@ -18,10 +18,10 @@
 
 from __future__ import division
 import numpy as np
-from .space import Space
+from .structured_domain import StructuredDomain
 
 
-class HPSpace(Space):
+class HPSpace(StructuredDomain):
     """NIFTy subclass for HEALPix discretizations of the two-sphere [#]_.
 
     Parameters
@@ -65,10 +65,10 @@ class HPSpace(Space):
 
     @property
     def shape(self):
-        return (self.dim,)
+        return (self.size,)
 
     @property
-    def dim(self):
+    def size(self):
         return np.int(12 * self.nside * self.nside)
 
     def scalar_dvol(self):

nifty4/spaces/lm_space.py

@@ -18,12 +18,12 @@
 
 from __future__ import division
 import numpy as np
-from .space import Space
+from .structured_domain import StructuredDomain
 from ..field import Field, exp
 from .. import dobj
 
 
-class LMSpace(Space):
+class LMSpace(StructuredDomain):
     """NIFTy subclass for spherical harmonics components, for representations
     of fields on the two-sphere.
 
@@ -75,10 +75,10 @@ class LMSpace(Space):
 
     @property
     def shape(self):
-        return (self.dim, )
+        return (self.size, )
 
     @property
-    def dim(self):
+    def size(self):
         l = self._lmax
         m = self._mmax
         # the LMSpace consists of the full triangle (including -m's!),
@@ -91,7 +91,7 @@ class LMSpace(Space):
     def get_k_length_array(self):
         lmax = self._lmax
         mmax = self._mmax
-        ldist = np.empty((self.dim,), dtype=np.float64)
+        ldist = np.empty((self.size,), dtype=np.float64)
         ldist[0:lmax+1] = np.arange(lmax+1, dtype=np.float64)
         tmp = np.empty((2*lmax+2), dtype=np.float64)
         tmp[0::2] = np.arange(lmax+1)

nifty4/spaces/power_space.py

@@ -17,11 +17,11 @@
 # and financially supported by the Studienstiftung des deutschen Volkes.
 
 import numpy as np
-from .space import Space
+from .structured_domain import StructuredDomain
 from .. import dobj
 
 
-class PowerSpace(Space):
+class PowerSpace(StructuredDomain):
     """NIFTy class for spaces of power spectra.
 
     A power space is the result of a projection of a harmonic space where
@@ -90,7 +90,7 @@ class PowerSpace(Space):
 
     @staticmethod
     def useful_binbounds(space, logarithmic, nbin=None):
-        if not (isinstance(space, Space) and space.harmonic):
+        if not (isinstance(space, StructuredDomain) and space.harmonic):
             raise ValueError("first argument must be a harmonic space.")
         if logarithmic is None and nbin is None:
             return None
@@ -122,7 +122,7 @@ class PowerSpace(Space):
         super(PowerSpace, self).__init__()
         self._needed_for_hash += ['_harmonic_partner', '_binbounds']
 
-        if not (isinstance(harmonic_partner, Space) and
+        if not (isinstance(harmonic_partner, StructuredDomain) and
                 harmonic_partner.harmonic):
             raise ValueError("harmonic_partner must be a harmonic space.")
         if harmonic_partner.scalar_dvol() is None:
@@ -180,7 +180,7 @@ class PowerSpace(Space):
         return self.k_lengths.shape
 
     @property
-    def dim(self):
+    def size(self):
         return self.shape[0]
 
     def scalar_dvol(self):

nifty4/spaces/rg_space.py

@@ -20,13 +20,13 @@ from __future__ import division
 from builtins import range
 from functools import reduce
 import numpy as np
-from .space import Space
+from .structured_domain import StructuredDomain
 from ..field import Field, exp
 from .. import dobj
 
 
-class RGSpace(Space):
-    """NIFTy subclass for spaces of regular Cartesian grids.
+class RGSpace(StructuredDomain):
+    """NIFTy subclass for regular Cartesian grids.
 
     Parameters
     ----------
@@ -66,7 +66,7 @@ class RGSpace(Space):
             self._distances = tuple(temp)
 
         self._dvol = float(reduce(lambda x, y: x*y, self._distances))
-        self._dim = int(reduce(lambda x, y: x*y, self._shape))
+        self._size = int(reduce(lambda x, y: x*y, self._shape))
 
     def __repr__(self):
         return ("RGSpace(shape=%r, distances=%r, harmonic=%r)"
@@ -81,8 +81,8 @@ class RGSpace(Space):
         return self._shape
 
     @property
-    def dim(self):
-        return self._dim
+    def size(self):
+        return self._size
 
     def scalar_dvol(self):
         return self._dvol

nifty4/spaces/space.py → nifty4/spaces/structured_domain.py

@@ -17,28 +17,56 @@
 # and financially supported by the Studienstiftung des deutschen Volkes.
 
 import abc
-from ..domain_object import DomainObject
+from .domain import Domain
+import numpy as np
 
 
-class Space(DomainObject):
-    """The abstract base class for all NIFTy spaces.
+class StructuredDomain(Domain):
+    """The abstract base class for all structured NIFTy domains.
 
     An instance of a space contains information about the manifold's
-    geometry and enhances the functionality of DomainObject by methods that
+    geometry and enhances the functionality of Domain by methods that
     are needed for power spectrum analysis and smoothing.
     """
 
     def __init__(self):
-        super(Space, self).__init__()
+        super(StructuredDomain, self).__init__()
+
+    @abc.abstractmethod
+    def scalar_dvol(self):
+        """Returns the volume factors of this domain as a floating
+        point scalar, if the volume factors are all identical, otherwise
+        returns None.
+
+        Returns
+        -------
+        float or None: Volume factor
+        """
+        raise NotImplementedError
+
+    def dvol(self):
+        """Returns the volume factors of this domain, either as a floating
+        point scalar (if the volume factors are all identical) or as a
+        floating point array with a shape of `self.shape`.
+
+        Returns
+        -------
+        float or numpy.ndarray(dtype=float): Volume factors
+        """
+        return self.scalar_dvol()
+
+    def total_volume(self):
+        tmp = self.dvol()
+        return self.size * tmp if np.isscalar(tmp) else np.sum(tmp)
 
     @abc.abstractproperty
     def harmonic(self):
-        """ Returns True iff this space is a harmonic space."""
+        """ Returns True iff this domain is a harmonic domain."""
         raise NotImplementedError
 
     def get_k_length_array(self):
         """The length of the k vector for every pixel.
-        This method is only implemented for harmonic spaces.
+        This method is only implemented for harmonic domains.
 
         Returns
         -------
@@ -49,27 +77,26 @@ class Space(DomainObject):
 
     def get_unique_k_lengths(self):
         """ Returns an array of floats containing the unique k vector lengths
-        for this space.
-        This method is only implemented for harmonic spaces.
+        for this domain.
+        This method is only implemented for harmonic domains.
         """
         raise NotImplementedError
 
     def get_fft_smoothing_kernel_function(self, sigma):
         """This method returns a smoothing kernel function.
 
-        This method, which is only implemented for harmonic spaces, helps
-        smoothing fields that live in a position space that has this space as
-        its harmonic space. The returned function multiplies field values of a
-        field with a zero centered Gaussian which corresponds to a convolution
-        with a Gaussian kernel and sigma standard deviation in position space.
+        This method, which is only implemented for harmonic domains, helps
+        smoothing fields that live on a domain that has this domain as
+        its harmonic partner. The returned function multiplies field values of
+        a field with a zero centered Gaussian which corresponds to a
+        convolution with a Gaussian kernel and sigma standard deviation in
+        position space.
 
         Parameters
         ----------
         sigma : float
             A real number representing a physical scale on which the smoothing
-            takes place. The smoothing is defined with respect to the real
-            physical field and points that are closer together than one sigma
-            are blurred together. Mathematically sigma is the standard
+            takes place. Mathematically sigma is the standard
             deviation of a convolution with a normalized, zero-centered
             Gaussian that takes place in position space.
 

nifty4/spaces/field_array.py → nifty4/spaces/unstructured_domain.py

@@ -16,13 +16,13 @@
 # NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik
 # and financially supported by the Studienstiftung des deutschen Volkes.
 
-from ..domain_object import DomainObject
+from .domain import Domain
 from functools import reduce
 
 
-class FieldArray(DomainObject):
+class UnstructuredDomain(Domain):
     def __init__(self, shape):
-        super(FieldArray, self).__init__()
+        super(UnstructuredDomain, self).__init__()
         self._needed_for_hash += ["_shape"]
         try:
             self._shape = tuple([int(i) for i in shape])
@@ -30,15 +30,12 @@ class FieldArray(DomainObject):
             self._shape = (int(shape), )
 
     def __repr__(self):
-        return "FieldArray(shape=%r)" % (self.shape, )
+        return "UnstructuredDomain(shape=%r)" % (self.shape, )
 
     @property
     def shape(self):
         return self._shape
 
     @property
-    def dim(self):
+    def size(self):
         return reduce(lambda x, y: x*y, self.shape)
-
-    def scalar_dvol(self):
-        return 1.

nifty4/sugar.py

@@ -17,7 +17,7 @@
 # and financially supported by the Studienstiftung des deutschen Volkes.
 
 import numpy as np
-from .spaces.space import Space
+from .spaces.structured_domain import StructuredDomain
 from .spaces.power_space import PowerSpace
 from .field import Field, sqrt
 from .operators.diagonal_operator import DiagonalOperator
@@ -246,7 +246,7 @@ def create_composed_ht_operator(domain, codomain=None):
         codomain = [None]*len(domain)
     res = None
     for i, space in enumerate(domain):
-        if isinstance(space, Space) and space.harmonic:
+        if isinstance(space, StructuredDomain) and space.harmonic:
             tdom = domain if res is None else res.target
             op = HarmonicTransformOperator(tdom, codomain[i], i)
             res = op if res is None else op*res

test/test_field.py

@@ -33,7 +33,7 @@ class Test_Interface(unittest.TestCase):
                     [['domain', ift.DomainTuple],
                      ['val', ift.dobj.data_object],
                      ['shape', tuple],
-                     ['dim', (np.int, np.int64)]]))
+                     ['size', (np.int, np.int64)]]))
     def test_return_types(self, domain, attribute_desired_type):
         attribute = attribute_desired_type[0]
         desired_type = attribute_desired_type[1]

test/test_spaces/test_gl_space.py

@@ -31,7 +31,7 @@ CONSTRUCTOR_CONFIGS = [
             'nlon': 3,
             'harmonic': False,
             'shape': (6,),
-            'dim': 6,
+            'size': 6,
             }],
         [0, None, {
             'error': ValueError

test/test_spaces/test_hp_space.py

@@ -30,19 +30,19 @@ CONSTRUCTOR_CONFIGS = [
             'nside': 2,
             'harmonic': False,
             'shape': (48,),
-            'dim': 48,
+            'size': 48,
             }],
         [5, {
             'nside': 5,
             'harmonic': False,
             'shape': (300,),
-            'dim': 300,
+            'size': 300,
             }],
         [1, {
             'nside': 1,
             'harmonic': False,
             'shape': (12,),
-            'dim': 12,
+            'size': 12,
             }],
         [0, {
             'error': ValueError