Cleaning up. Making more files PEP8 compliant.

Abstracted the power_indices class from rg_space -> Implemented a lm_power_indices class.
In the middle of space-interface cleaning.

__init__.py

@@ -35,7 +35,6 @@ from keepers import about,\
 from nifty_cmaps import ncmap
 from nifty_core import space,\
                     point_space,\
-                    nested_space,\
                     field
 
 from nifty_mpi_data import distributed_data_object, d2o_librarian

dummys/MPI_dummy.py

@@ -16,7 +16,11 @@ MAX = np.max
 SUM = np.sum
 
 
-class _COMM_WORLD():
+class Comm(object):
+    pass
+
+
+class Intracomm(Comm):
     def __init__(self):
         self.rank = 0
         self.size = 1
@@ -111,4 +115,4 @@ COMPLEX = _datatype("MPI_COMPLEX")
 DOUBLE_COMPLEX = _datatype("MPI_DOUBLE_COMPLEX")
 
 
-COMM_WORLD = _COMM_WORLD()
+COMM_WORLD = Intracomm()

keepers/nifty_configuration.py

 # -*- coding: utf-8 -*-
 
 import ConfigParser
+import pprint
+
 
 class variable(object):
     def __init__(self, name, default_value_list, checker, genus='str'):
@@ -47,7 +49,7 @@ class variable(object):
         return self.name
 
     def __repr__(self):
-        return "<nifty variable '" + str(self.name) + "': " + \
+        return "<" + str(self.name) + "': " + \
                str(self.get_value()) + ">"
 
 
@@ -161,7 +163,9 @@ class configuration(object):
             item.set_value(temp_value)
 
     def __repr__(self):
-        return "<nifty configuration> \n" + self.variable_dict.__repr__()
+        return_string = ("<nifty configuration> \n" +
+                         pprint.pformat(self.variable_dict))
+        return return_string
 
 
 

keepers/nifty_default_config.py

@@ -6,6 +6,9 @@ from nifty_dependency_injector import dependency_injector
 from nifty_configuration import variable,\
                                 configuration
 
+
+
+
 global_dependency_injector = dependency_injector(
                                    ['h5py',
                                     ('mpi4py.MPI', 'MPI'),
@@ -23,12 +26,12 @@ variable_fft_module = variable('fft_module',
 variable_lm2gl = variable('lm2gl',
                           [True, False],
                           lambda z: z is True or z is False,
-                          'boolean')
+                          genus = 'boolean')
 
 variable_verbosity = variable('verbosity',
                               [1],
                               lambda z: z == abs(int(z)),
-                              'int')
+                              genus = 'int')
 
 variable_mpi_module = variable('mpi_module',
                                ['MPI', 'MPI_dummy'],
@@ -49,3 +52,12 @@ global_configuration = configuration(
                       variable_default_distribution_strategy
                       ],
                      path=os.path.expanduser('~') + "/.nifty/global_config")
+
+
+variable_default_comm = variable(
+                     'default_comm',
+                     ['COMM_WORLD'],
+                     lambda z: hasattr(global_dependency_injector[
+                                       global_configuration['mpi_module']], z))
+
+global_configuration.register(variable_default_comm)

lm/nifty_power_conversion_lm.py

@@ -21,8 +21,9 @@
 
 #from nifty import *
 import numpy as np
+from numpy import pi
 from nifty.keepers import about
-from nifty.nifty_core import pi, field
+from nifty.nifty_core import field
 from nifty.nifty_simple_math import sqrt, exp, log
 
 

nifty_mpi_data.py

@@ -32,30 +32,6 @@ MPI = gdi[gc['mpi_module']]
 h5py = gdi.get('h5py')
 pyfftw = gdi.get('pyfftw')
 
-
-## initialize the 'FOUND-packages'-dictionary
-#FOUND = {}
-#try:
-#    from mpi4py import MPI
-#    FOUND['MPI'] = True
-#except(ImportError):
-#    import mpi_dummy as MPI
-#    FOUND['MPI'] = False
-#
-#try:
-#    import pyfftw
-#    FOUND['pyfftw'] = True
-#except(ImportError):
-#    FOUND['pyfftw'] = False
-#
-#try:
-#    import h5py
-#    FOUND['h5py'] = True
-#    FOUND['h5py_parallel'] = h5py.get_config().mpi
-#except(ImportError):
-#    FOUND['h5py'] = False
-#    FOUND['h5py_parallel'] = False
-
 _maybe_fftw = ['fftw'] if ('pyfftw' in gdi) else []
 STRATEGIES = {
                 'all': ['not', 'equal', 'freeform'] + _maybe_fftw,
@@ -687,7 +663,7 @@ class distributed_data_object(object):
 
         if weights is not None:
             local_weights = self.distributor.extract_local_data(weights).\
-                flatten()
+                                flatten()
         else:
             local_weights = None
 

nifty_paradict.py

@@ -56,7 +56,7 @@ class point_space_paradict(space_paradict):
 
 class rg_space_paradict(space_paradict):
 
-    def __init__(self, num, complexity=2, zerocenter=False):
+    def __init__(self, num, complexity, zerocenter):
         self.ndim = len(np.array(num).flatten())
         space_paradict.__init__(
             self, num=num, complexity=complexity, zerocenter=zerocenter)
@@ -100,7 +100,7 @@ class nested_space_paradict(space_paradict):
 
 class lm_space_paradict(space_paradict):
 
-    def __init__(self, lmax, mmax=None):
+    def __init__(self, lmax, mmax):
         space_paradict.__init__(self, lmax=lmax)
         if mmax is None:
             mmax = -1
@@ -145,7 +145,7 @@ class lm_space_paradict(space_paradict):
 
 class gl_space_paradict(space_paradict):
 
-    def __init__(self, nlat, nlon=None):
+    def __init__(self, nlat, nlon):
         space_paradict.__init__(self, nlat=nlat)
         if nlon is None:
             nlon = -1

nifty_random.py

-## NIFTY (Numerical Information Field Theory) has been developed at the
-## Max-Planck-Institute for Astrophysics.
+# NIFTY (Numerical Information Field Theory) has been developed at the
+# Max-Planck-Institute for Astrophysics.
 ##
-## Copyright (C) 2013 Max-Planck-Society
+# Copyright (C) 2013 Max-Planck-Society
 ##
-## Author: Marco Selig
-## Project homepage: <http://www.mpa-garching.mpg.de/ift/nifty/>
+# Author: Marco Selig
+# Project homepage: <http://www.mpa-garching.mpg.de/ift/nifty/>
 ##
-## 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 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.
+# 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/>.
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
 from keepers import about
 from nifty_mpi_data import distributed_data_object
 
-##-----------------------------------------------------------------------------
+# -----------------------------------------------------------------------------
+
 
 class random(object):
     """
@@ -39,10 +40,10 @@ class random(object):
     """
     __init__ = None
 
-    ##+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+    # +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
     @staticmethod
-    def parse_arguments(domain,**kwargs):
+    def parse_arguments(domain, **kwargs):
         """
             Analyses the keyword arguments for supported or necessary ones.
 
@@ -91,18 +92,21 @@ class random(object):
             codomain : nifty.space, *optional*
                 A compatible codomain for power indexing (default: None).
             log : bool, *optional*
-                Flag specifying if the spectral binning is performed on logarithmic
+                Flag specifying if the spectral binning is performed on
+                logarithmic
                 scale or not; if set, the number of used bins is set
                 automatically (if not given otherwise); by default no binning
                 is done (default: None).
             nbin : integer, *optional*
-                Number of used spectral bins; if given `log` is set to ``False``;
+                Number of used spectral bins; if given `log` is set to
+                ``False``;
                 integers below the minimum of 3 induce an automatic setting;
                 by default no binning is done (default: None).
             binbounds : {list, array}, *optional*
                 User specific inner boundaries of the bins, which are preferred
                 over the above parameters; by default no binning is done
-                (default: None).            vmin : {scalar, list, ndarray, field}, *optional*
+                (default: None).
+            vmin : {scalar, list, ndarray, field}, *optional*
                 Lower limit of the uniform distribution if ``random == "uni"``
                 (default: 0).
 
@@ -121,24 +125,10 @@ class random(object):
             return [key]
 
         elif key == "gau":
-            """
-            if("mean" in kwargs):
-                mean = domain.enforce_values(kwargs.get("mean"),extend=False)
-            else:
-                mean = None
-            if("dev" in kwargs):
-                dev = domain.enforce_values(kwargs.get("dev"),extend=False)
-            else:
-                dev = None
-            if("var" in kwargs):
-                var = domain.enforce_values(kwargs.get("var"),extend=False)
-            else:
-                var = None
-            """
             mean = kwargs.get('mean', None)
             dev = kwargs.get('dev', None)
             var = kwargs.get('var', None)
-            return [key,mean,dev,var]
+            return [key, mean, dev, var]
 
         elif key == "syn":
             pindex = kwargs.get('pindex', None)
@@ -150,101 +140,51 @@ class random(object):
             spec = kwargs.get('spec', 1)
             codomain = kwargs.get('codomain', None)
 
-            ## check which domain should be taken for powerindexing
-            if domain.check_codomain(codomain) == True and\
-                codomain.fourier == True:
-                fourier_domain = codomain
-            elif domain.fourier == True:
-                fourier_domain = domain
+            # check which domain should be taken for powerindexing
+            if domain.check_codomain(codomain) and codomain.harmonic:
+                harmonic_domain = codomain
+            elif domain.harmonic:
+                harmonic_domain = domain
             else:
-                fourier_domain = domain.get_codomain()
+                harmonic_domain = domain.get_codomain()
 
-            ## building kpack
-            if pindex != None and kindex != None:
+            # building kpack
+            if pindex is not None and kindex is not None:
                 pindex = distributed_data_object(pindex,
                                                  distribution_strategy='fftw')
                 kpack = [pindex, kindex]
             else:
                 kpack = None
 
-            ## simply put size and kindex into enforce_power
-            ## if one or both are None, enforce power will fix that
-            spec = fourier_domain.enforce_power(spec, size=size, kindex=kindex)
-
-
-
-            return [key, spec, kpack, fourier_domain, log, nbin, binbounds]
-
-
-            '''
-            ## explicit power indices
-            if ("pindex" in kwargs) and ("kindex" in kwargs):
-                kindex = kwargs.get("kindex")
-                if(kindex is None):
-                    spec = domain.enforce_power(kwargs.get("spec",1),size=kwargs.get("size",None))
-                    kpack = None
-                else:
-                    spec = domain.enforce_power(kwargs.get("spec",1),size=len(kindex),kindex=kindex)
-                    pindex = kwargs.get("pindex",None)
-                    if(pindex is None):
-                        kpack = None
-                    else:
-                        kpack = [pindex,kindex]
-
-
-
-            ## implicit power indices
-            else:
-                try:
-                    domain.set_power_indices(**kwargs)
-                except:
-                    codomain = kwargs.get("codomain",None)
-                    if(codomain is None):
-                        spec = domain.enforce_power(kwargs.get("spec",1),size=kwargs.get("size",None))
-                        kpack = None
-                    else:
-                        domain.check_codomain(codomain)
-                        codomain.set_power_indices(**kwargs)
-                        kindex = codomain.power_indices.get("kindex")
-                        spec = domain.enforce_power(kwargs.get("spec",1),size=len(kindex),kindex=kindex,codomain=codomain)
-                        kpack = [codomain.power_indices.get("pindex"),kindex]
-                else:
-                    kindex = domain.power_indices.get("kindex")
-                    spec = domain.enforce_power(kwargs.get("spec",1),size=len(kindex),kindex=kindex)
-                    kpack = [domain.power_indices.get("pindex"),kindex]
-            '''
+            # simply put size and kindex into enforce_power
+            # if one or both are None, enforce power will fix that
+            spec = harmonic_domain.enforce_power(spec,
+                                                 size=size,
+                                                 kindex=kindex)
 
+            return [key, spec, kpack, harmonic_domain, log, nbin, binbounds]
 
         elif key == "uni":
-            """
-            if("vmin" in kwargs):
-                vmin = domain.enforce_values(kwargs.get("vmin"),extend=False)
-            else:
-                vmin = 0
-            if("vmax" in kwargs):
-                vmax = domain.enforce_values(kwargs.get("vmax"),extend=False)
-            else:
-                vmax = 1
-            """
-            vmin = domain.datatype(kwargs.get('vmin', 0))
-            vmax = domain.datatype(kwargs.get('vmax', 1))
-            return [key,vmin,vmax]
+            vmin = domain.dtype(kwargs.get('vmin', 0))
+            vmax = domain.dtype(kwargs.get('vmax', 1))
+            return [key, vmin, vmax]
 
         else:
-            raise KeyError(about._errors.cstring("ERROR: unsupported random key '"+str(key)+"'."))
+            raise KeyError(about._errors.cstring(
+                "ERROR: unsupported random key '" + str(key) + "'."))
 
-    ##+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+    # +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
     @staticmethod
-    def pm1(datatype=np.int, shape=1):
+    def pm1(dtype=np.dtype('int'), shape=1):
         """
             Generates random field values according to an uniform distribution
             over {+1,-1} or {+1,+i,-1,-i}, respectively.
 
             Parameters
             ----------
-            datatype : type, *optional*
-                Data type of the field values (default: np.int).
+            dtype : type, *optional*
+                Data type of the field values (default: int).
             shape : {integer, tuple, list, ndarray}, *optional*
                 Split up dimension of the space (default: 1).
 
@@ -254,26 +194,29 @@ class random(object):
                 Random field values (with correct dtype and shape).
 
         """
-        size = np.prod(shape,axis=0,dtype=np.int,out=None)
+        size = np.prod(shape, axis=0, dtype=np.dtype('int'), out=None)
 
-        if(issubclass(datatype,np.complexfloating)):
-            x = np.array([1+0j,0+1j,-1+0j,0-1j],dtype=datatype)[np.random.randint(4,high=None,size=size)]
+        if(issubclass(dtype.type, np.complexfloating)):
+            x = np.array([1 + 0j, 0 + 1j, -1 + 0j, 0 - 1j],
+                         dtype=dtype)[np.random.randint(4,
+                                                        high=None,
+                                                        size=size)]
         else:
-            x = 2*np.random.randint(2,high=None,size=size)-1
+            x = 2 * np.random.randint(2, high=None, size=size) - 1
 
-        return x.astype(datatype).reshape(shape,order='C')
+        return x.astype(dtype).reshape(shape, order='C')
 
-    ##+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+    # +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
     @staticmethod
-    def gau(datatype=np.float64, shape=1, mean=None, dev=None, var=None):
+    def gau(dtype=np.dtype('float64'), shape=1, mean=None, dev=None, var=None):
         """
             Generates random field values according to a normal distribution.
 
             Parameters
             ----------
-            datatype : type, *optional*
-                Data type of the field values (default: np.float64).
+            dtype : type, *optional*
+                Data type of the field values (default: float64).
             shape : {integer, tuple, list, ndarray}, *optional*
                 Split up dimension of the space (default: 1).
             mean : {scalar, ndarray}, *optional*
@@ -296,51 +239,57 @@ class random(object):
                 `shape`.
 
         """
-        size = np.prod(shape,axis=0,dtype=np.int,out=None)
+        size = np.prod(shape, axis=0, dtype=np.dtype('int'), out=None)
 
-        if(issubclass(datatype,np.complexfloating)):
-            x = np.empty(size,dtype=datatype,order='C')
-            x.real = np.random.normal(loc=0,scale=np.sqrt(0.5),size=size)
-            x.imag = np.random.normal(loc=0,scale=np.sqrt(0.5),size=size)
+        if(issubclass(dtype.type, np.complexfloating)):
+            x = np.empty(size, dtype=dtype, order='C')
+            x.real = np.random.normal(loc=0, scale=np.sqrt(0.5), size=size)
+            x.imag = np.random.normal(loc=0, scale=np.sqrt(0.5), size=size)
         else:
-            x = np.random.normal(loc=0,scale=1,size=size)
+            x = np.random.normal(loc=0, scale=1, size=size)
 
         if(var is not None):
-            if(np.size(var)==1):
+            if(np.size(var) == 1):
                 x *= np.sqrt(np.abs(var))
-            elif(np.size(var)==size):
+            elif(np.size(var) == size):
                 x *= np.sqrt(np.absolute(var).flatten(order='C'))
             else:
-                raise ValueError(about._errors.cstring("ERROR: dimension mismatch ( "+str(np.size(var))+" <> "+str(size)+" )."))
+                raise ValueError(about._errors.cstring(
+                    "ERROR: dimension mismatch ( " + str(np.size(var)) +
+                    " <> " + str(size) + " )."))
         elif(dev is not None):
-            if(np.size(dev)==1):
+            if(np.size(dev) == 1):
                 x *= np.abs(dev)
-            elif(np.size(dev)==size):
+            elif(np.size(dev) == size):
                 x *= np.absolute(dev).flatten(order='C')
             else:
-                raise ValueError(about._errors.cstring("ERROR: dimension mismatch ( "+str(np.size(dev))+" <> "+str(size)+" )."))
+                raise ValueError(about._errors.cstring(
+                    "ERROR: dimension mismatch ( " + str(np.size(dev)) +
+                    " <> " + str(size) + " )."))
         if(mean is not None):
-            if(np.size(mean)==1):
+            if(np.size(mean) == 1):
                 x += mean
-            elif(np.size(mean)==size):
+            elif(np.size(mean) == size):
                 x += np.array(mean).flatten(order='C')
             else:
-                raise ValueError(about._errors.cstring("ERROR: dimension mismatch ( "+str(np.size(mean))+" <> "+str(size)+" )."))
+                raise ValueError(about._errors.cstring(
+                    "ERROR: dimension mismatch ( " + str(np.size(mean)) +
+                    " <> " + str(size) + " )."))
 
-        return x.astype(datatype).reshape(shape,order='C')
+        return x.astype(dtype).reshape(shape, order='C')
 
-    ##+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+    # +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
     @staticmethod
-    def uni(datatype=np.float64,shape=1,vmin=0,vmax=1):
+    def uni(dtype=np.dtype('float64'), shape=1, vmin=0, vmax=1):
         """
             Generates random field values according to an uniform distribution
             over [vmin,vmax[.
 
             Parameters
             ----------
-            datatype : type, *optional*
-                Data type of the field values (default: np.float64).
+            dtype : type, *optional*
+                Data type of the field values (default: float64).
             shape : {integer, tuple, list, ndarray}, *optional*
                 Split up dimension of the space (default: 1).
 
@@ -355,27 +304,28 @@ class random(object):
                 Random field values (with correct dtype and shape).
 
         """
-        size = np.prod(shape,axis=0,dtype=np.int,out=None)
-        if(np.size(vmin)>1):
+        size = np.prod(shape, axis=0, dtype=np.dtype('int'), out=None)
+        if(np.size(vmin) > 1):
             vmin = np.array(vmin).flatten(order='C')
-        if(np.size(vmax)>1):
+        if(np.size(vmax) > 1):
             vmax = np.array(vmax).flatten(order='C')
 
-        if(datatype in [np.complex64,np.complex128]):
-            x = np.empty(size,dtype=datatype,order='C')
-            x.real = (vmax-vmin)*np.random.random(size=size)+vmin
-            x.imag = (vmax-vmin)*np.random.random(size=size)+vmin
-        elif(datatype in [np.int8,np.int16,np.int32,np.int64]):
-            x = np.random.randint(min(vmin,vmax),high=max(vmin,vmax),size=size)
+        if(dtype in [np.dtype('complex64'), np.dtype('complex128')]):
+            x = np.empty(size, dtype=dtype, order='C')
+            x.real = (vmax - vmin) * np.random.random(size=size) + vmin
+            x.imag = (vmax - vmin) * np.random.random(size=size) + vmin
+        elif(dtype in [np.dtype('int8'), np.dtype('int16'), np.dtype('int32'),
+                       np.dtype('int64')]):
+            x = np.random.randint(
+                min(vmin, vmax), high=max(vmin, vmax), size=size)
         else:
-            x = (vmax-vmin)*np.random.random(size=size)+vmin
+            x = (vmax - vmin) * np.random.random(size=size) + vmin
 
-        return x.astype(datatype).reshape(shape,order='C')
+        return x.astype(dtype).reshape(shape, order='C')
 
-    ##+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+    # +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
     def __repr__(self):
         return "<nifty_core.random>"
 
-##-----------------------------------------------------------------------------
-
+# -----------------------------------------------------------------------------

operators/nifty_explicit.py

@@ -253,12 +253,12 @@ class explicit_operator(operator):
 #            about.infos.cprint("INFO: matrix size > 2 ** 20.")
         self.target = target
 
-        # check datatype
+        # check dtype
         if(np.any(np.iscomplex(val))):
-            datatype, purelyreal = max(min(val.dtype, self.domain.datatype), min(
-                val.dtype, self.target.datatype)), False
+            dtype, purelyreal = max(min(val.dtype, self.domain.dtype), min(
+                val.dtype, self.target.dtype)), False
         else:
-            datatype, purelyreal = max(min(val.dtype, self.domain.vol.dtype), min(
+            dtype, purelyreal = max(min(val.dtype, self.domain.vol.dtype), min(
                 val.dtype, self.target.vol.dtype)), True
         # weight if ... (given `domain` and `target`)
         if(isinstance(bare, tuple)):
@@ -271,9 +271,9 @@ class explicit_operator(operator):
         elif(not bare):
             val = self._calc_weight_rows(val, -1)
         if(purelyreal):
-            self.val = np.real(val).astype(datatype)
+            self.val = np.real(val).astype(dtype)
         else:
-            self.val = val.astype(datatype)
+            self.val = val.astype(dtype)
 
         # check hidden degrees of freedom
         self._hidden = np.array([self.domain.dim(split=False) < self.domain.dof(
@@ -455,12 +455,12 @@ class explicit_operator(operator):
             raise ValueError(about._errors.cstring("ERROR: dimension mismatch ( " + str(np.size(
                 newmatrix, axis=None)) + " <> " + str(self.nrow()) + " x " + str(self.ncol()) + " )."))
 
-        # check datatype
+        # check dtype
         if(np.any(np.iscomplex(val))):
-            datatype, purelyreal = max(min(val.dtype, self.domain.datatype), min(
-                val.dtype, self.target.datatype)), False
+            dtype, purelyreal = max(min(val.dtype, self.domain.dtype), min(
+                val.dtype, self.target.dtype)), False