Merge pull request #13 from mselig/develop

Develop to Master

.gitignore

@@ -12,8 +12,21 @@
 .spyderproject
 build
 
+rg/*
+!rg/__init__.py
+!rg/nifty_rg.py
+!rg/nifty_power_conversion_rg.py
+!rg/gfft_rg.py
+!rg/powerspectrum.py
+
+lm/*
+!lm/__init__.py
+!lm/nifty_lm.py
+!lm/nifty_power_conversion_lm.py
+
 demos/*
 !demos/__init__.py
+!demos/demos_core.py
 !demos/demo_faraday.py
 !demos/demo_faraday_map.npy
 !demos/demo_excaliwir.py

README.rst

@@ -87,19 +87,21 @@ Requirements
         (standard library)
 
 *   `GFFT <https://github.com/mrbell/gfft>`_ (v0.1.0) - Generalized Fast
-    Fourier Transformations for Python
+    Fourier Transformations for Python - **optional**
 
 *   `HEALPy <https://github.com/healpy/healpy>`_ (v1.4 without openmp) - A
-    Python wrapper for `HEALPix <http://sourceforge.net/projects/healpix/>`_
+    Python wrapper for `HEALPix <http://sourceforge.net/projects/healpix/>`_ -
+    **optional**
 
 *   `libsharp-wrapper <https://github.com/mselig/libsharp-wrapper>`_ (v0.1.2
     without openmp) - A Python wrapper for the
-    `libsharp <http://sourceforge.net/projects/libsharp/>`_ library
+    `libsharp <http://sourceforge.net/projects/libsharp/>`_ library -
+    **optional**
 
 Download
 ........
 
-The latest release is tagged **v0.9.0** and is available as a source package
+The latest release is tagged **v1.0.6** and is available as a source package
 at `<https://github.com/mselig/nifty/tags>`_. The current version can be
 obtained by cloning the repository::
 
@@ -109,14 +111,25 @@ obtained by cloning the repository::
 Installation
 ............
 
-NIFTY is installed using Distutils by running the following command::
+*   NIFTY can be installed using `PyPI <https://pypi.python.org/pypi>`_ and
+    **pip** by running the following command::
 
-    python setup.py install
+        pip install nifty
 
-Alternatively, a private or user specific installation can be done by::
+    Alternatively, a private or user specific installation can be done by::
 
-    python setup.py install --user
-    python setup.py install --install-lib=/SOMEWHERE
+        pip install --user nifty
+
+
+*   NIFTY can be installed using **Distutils** by running the following
+    command::
+
+        python setup.py install
+
+    Alternatively, a private or user specific installation can be done by::
+
+        python setup.py install --user
+        python setup.py install --install-lib=/SOMEWHERE
 
 Acknowledgement
 ---------------

__init__.py

@@ -20,43 +20,24 @@
 ## along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 from __future__ import division
-from nifty_core import *
+from nifty_core import * ## imports `about`
 from nifty_cmaps import *
 from nifty_power import *
 from nifty_tools import *
 from nifty_explicit import *
 
-#from nifty_power_conversion import *
+## optional submodule `rg`
+try:
+    from rg import *
+except(ImportError):
+    pass
 
+## optional submodule `lm`
+try:
+    from lm import *
+except(ImportError):
+    pass
 
-##-----------------------------------------------------------------------------
+from demos import *
+from pickling import *
 
-import copy_reg as cr
-from types import MethodType as mt
-
-
-def _pickle_method(method):
-    fct_name = method.im_func.__name__
-    obj = method.im_self
-    cl = method.im_class
-    ## handle mangled function name
-    if(fct_name.startswith("__"))and(not fct_name.endswith("__")):
-        cl_name = cl.__name__.lstrip("_")
-        fct_name = "_" + cl_name + fct_name
-    return _unpickle_method, (fct_name, obj, cl)
-
-
-def _unpickle_method(fct_name, obj, cl):
-    for oo in cl.__mro__:
-        try:
-            fct = oo.__dict__[fct_name]
-        except(KeyError):
-            pass
-        else:
-            break
-    return fct.__get__(obj, cl)
-
-## enable instance methods pickling
-cr.pickle(mt, _pickle_method, _unpickle_method)
-
-##-----------------------------------------------------------------------------
\ No newline at end of file

demos/__init__.py

@@ -19,5 +19,5 @@
 ## You should have received a copy of the GNU General Public License
 ## along with this program. If not, see <http://www.gnu.org/licenses/>.
 
-pass
+from demos_core import *
 

demos/demo_faraday.py

@@ -48,7 +48,7 @@ about.infos.off()
 ##-----------------------------------------------------------------------------
 
 # (global) Faraday map
-m = field(hp_space(128), val=np.load("demo_faraday_map.npy"))
+m = field(hp_space(128), val=np.load(os.path.join(get_demo_dir(),"demo_faraday_map.npy")))
 
 ##-----------------------------------------------------------------------------
 

demos/demos_core.py

+## NIFTY (Numerical Information Field Theory) has been developed at the
+## Max-Planck-Institute for Astrophysics.
+##
+## Copyright (C) 2015 Max-Planck-Society
+##
+## 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 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/>.
+
+"""
+    NIFTY provides a number of demonstrations that you can run either using
+    ``execfile`` provided with (absolute or relative) file names or using
+    ``run -m`` providing the module name. You can retrieve the directory of
+    the NIFTY demos calling :py:func:`get_demo_dir`.
+
+"""
+import os
+import nifty as nt
+
+def get_demo_dir():
+    """
+        Returns the path of the NIFTY demos directory.
+
+    """
+    return os.path.split(nt.demos.__file__)[0]
+

lm/__init__.py

+## NIFTY (Numerical Information Field Theory) has been developed at the
+## Max-Planck-Institute for Astrophysics.
+##
+## Copyright (C) 2015 Max-Planck-Society
+##
+## 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 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/>.
+
+from __future__ import division
+from nifty import about
+#from nifty_lm import *
+try:
+    import libsharp_wrapper_gl as gl
+except(ImportError):
+    try:
+        import healpy as hp
+    except(ImportError):
+        about.infos.cprint("INFO: neither libsharp_wrapper_gl nor healpy available.")
+        pass ## import nothing
+    else:
+        from nifty_lm import lm_space,hp_space ## import lm & hp
+        ## TODO: change about
+else:
+    try:
+        import healpy as hp
+    except(ImportError):
+        from nifty_lm import lm_space,gl_space ## import lm & gl
+    else:
+        from nifty_lm import lm_space,gl_space,hp_space ## import all 3
+from nifty_power_conversion_lm import *
+

lm/nifty_power_conversion_lm.py

+## NIFTY (Numerical Information Field Theory) has been developed at the
+## Max-Planck-Institute for Astrophysics.
+##
+## Copyright (C) 2014 Max-Planck-Society
+##
+## Author: Maksim Greiner, 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 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/>.
+
+#from nifty import *
+import numpy as np
+from nifty import pi,                                                        \
+                  about,                                                     \
+                  field,                                                     \
+                  sqrt,exp,log
+
+
+def power_backward_conversion_lm(k_space,p,mean=None):
+    """
+        This function is designed to convert a theoretical/statistical power
+        spectrum of a log-normal field to the theoretical power spectrum of
+        the underlying Gaussian field.
+        The function only works for power spectra defined for lm_spaces
+
+        Parameters
+        ----------
+        k_space : nifty.rg_space,
+            a regular grid space with the attribute `Fourier = True`
+        p : np.array,
+            the power spectrum of the log-normal field.
+            Needs to have the same number of entries as
+            `k_space.get_power_indices()[0]`
+        mean : float, *optional*
+            specifies the mean of the log-normal field. If `mean` is not
+            specified the function will use the monopole of the power spectrum.
+            If it is specified the function will NOT use the monopole of the
+            spectrum. (default: None)
+            WARNING: a mean that is too low can violate positive definiteness
+            of the log-normal field. In this case the function produces an
+            error.
+
+        Returns
+        -------
+        mean : float,
+            the recovered mean of the underlying Gaussian distribution.
+        p1 : np.array,
+            the power spectrum of the underlying Gaussian field, where the
+            monopole has been set to zero. Eventual monopole power has been
+            shifted to the mean.
+
+        References
+        ----------
+        .. [#] M. Greiner and T.A. Ensslin, "Log-transforming the matter power spectrum";
+            `arXiv:1312.1354 <http://arxiv.org/abs/1312.1354>`_
+    """
+
+    p = np.copy(p)
+    if(mean is not None):
+        p[0] = 4*pi*mean**2
+
+    klen = k_space.get_power_indices()[0]
+    C_0_Omega = field(k_space,val=0)
+    C_0_Omega.val[:len(klen)] = p*sqrt(2*klen+1)/sqrt(4*pi)
+    C_0_Omega = C_0_Omega.transform()
+
+    if(np.any(C_0_Omega.val<0.)):
+        raise ValueError(about._errors.cstring("ERROR: spectrum or mean incompatible with positive definiteness.\n Try increasing the mean."))
+        return None
+
+    lC = log(C_0_Omega)
+
+    Z = lC.transform()
+
+    spec = Z.val[:len(klen)]
+
+    mean = (spec[0]-0.5*sqrt(4*pi)*log((p*(2*klen+1)/(4*pi)).sum()))/sqrt(4*pi)
+
+    spec[0] = 0.
+
+    spec = spec*sqrt(4*pi)/sqrt(2*klen+1)
+
+    spec = np.real(spec)
+
+    if(np.any(spec<0.)):
+        spec = spec*(spec>0.)
+        about.warnings.cprint("WARNING: negative modes set to zero.")
+
+    return mean.real,spec
+
+
+def power_forward_conversion_lm(k_space,p,mean=0):
+    """
+        This function is designed to convert a theoretical/statistical power
+        spectrum of a Gaussian field to the theoretical power spectrum of
+        the exponentiated field.
+        The function only works for power spectra defined for lm_spaces
+
+        Parameters
+        ----------
+        k_space : nifty.rg_space,
+            a regular grid space with the attribute `Fourier = True`
+        p : np.array,
+            the power spectrum of the Gaussian field.
+            Needs to have the same number of entries as
+            `k_space.get_power_indices()[0]`
+        m : float, *optional*
+            specifies the mean of the Gaussian field (default: 0).
+
+        Returns
+        -------
+        p1 : np.array,
+            the power spectrum of the exponentiated Gaussian field.
+
+        References
+        ----------
+        .. [#] M. Greiner and T.A. Ensslin, "Log-transforming the matter power spectrum";
+            `arXiv:1312.1354 <http://arxiv.org/abs/1312.1354>`_
+    """
+    m = mean
+    klen = k_space.get_power_indices()[0]
+    C_0_Omega = field(k_space,val=0)
+    C_0_Omega.val[:len(klen)] = p*sqrt(2*klen+1)/sqrt(4*pi)
+    C_0_Omega = C_0_Omega.transform()
+
+    C_0_0 = (p*(2*klen+1)/(4*pi)).sum()
+
+    exC = exp(C_0_Omega+C_0_0+2*m)
+
+    Z = exC.transform()
+
+    spec = Z.val[:len(klen)]
+
+    spec = spec*sqrt(4*pi)/sqrt(2*klen+1)
+
+    spec = np.real(spec)
+
+    if(np.any(spec<0.)):
+        spec = spec*(spec>0.)
+        about.warnings.cprint("WARNING: negative modes set to zero.")
+
+    return spec
\ No newline at end of file

nifty_explicit.py

@@ -38,20 +38,20 @@
 
 """
 from __future__ import division
-from nifty_core import *
-#from sys import stdout as so
-#import numpy as np
-#import pylab as pl
-#from matplotlib.colors import LogNorm as ln
-#from matplotlib.ticker import LogFormatter as lf
-#from multiprocessing import Pool as mp
-#from multiprocessing import Value as mv
-#from multiprocessing import Array as ma
-#from nifty_core import about,                                                \
-#                       space,                                                \
-#                       field,                                                \
-#                       operator,diagonal_operator,identity,vecvec_operator,  \
-#                       probing
+#from nifty_core import *
+from sys import stdout as so
+import numpy as np
+import pylab as pl
+from matplotlib.colors import LogNorm as ln
+from matplotlib.ticker import LogFormatter as lf
+from multiprocessing import Pool as mp
+from multiprocessing import Value as mv
+from multiprocessing import Array as ma
+from nifty_core import about,                                                \
+                       space,                                                \
+                       field,                                                \
+                       operator,diagonal_operator,identity,vecvec_operator,  \
+                       probing
 
 
 ##-----------------------------------------------------------------------------
@@ -691,7 +691,7 @@ class explicit_operator(operator):
                 If it is no square matrix.
 
         """
-        return self._inverse_adjoint_times(x,**kwargs)
+        return self.inverse_adjoint_times(x,**kwargs)
 
     def inverse_adjoint_times(self,x,**kwargs):
         """

nifty_power.py

@@ -42,12 +42,12 @@
 """
 from __future__ import division
 from scipy.interpolate import interp1d as ip ## FIXME: conflicts with sphinx's autodoc
-from nifty_core import *
-#import numpy as np
-#from nifty_core import about,                                                \
-#                       space,                                                \
-#                       field,                                                \
-#                       projection_operator
+#from nifty_core import *
+import numpy as np
+from nifty_core import about,                                                \
+                       space,                                                \
+                       field,                                                \
+                       projection_operator
 import smoothing as gs
 
 

nifty_tools.py

@@ -37,12 +37,12 @@
 
 """
 from __future__ import division
-from nifty_core import *
-#import numpy as np
-#from nifty_core import notification,about,                                   \
-#                       space,                                                \
-#                       field,                                                \
-#                       operator,diagonal_operator
+#from nifty_core import *
+import numpy as np
+from nifty_core import notification,about,                                   \
+                       space,                                                \
+                       field,                                                \
+                       operator,diagonal_operator
 
 
 ##-----------------------------------------------------------------------------
@@ -1006,6 +1006,8 @@ class steepest_descent(object):
         self.c = c ## 0 < c1 < c2 < 1
         self.note = notification(default=bool(note))
 
+        self._alpha = None ## last alpha
+
     ##+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 
     def __call__(self,x0,alpha=1,tol=1E-4,clevel=8,limii=100000):
@@ -1041,6 +1043,13 @@ class steepest_descent(object):
             raise TypeError(about._errors.cstring("ERROR: invalid input."))
         self.x = x0
 
+        ## check for exsisting alpha
+        if(alpha is None):
+            if(self._alpha is not None):
+                alpha = self._alpha
+            else:
+                alpha = 1
+
         clevel = max(1,int(clevel))
         limii = int(limii)
 
@@ -1091,6 +1100,10 @@ class steepest_descent(object):
         if(self.spam is not None):
             self.spam(self.x,ii)
 
+        ## memorise last alpha
+        if(alpha is not None):
+            self._alpha = alpha/a ## undo update
+
         return self.x,convergence
 
     ##+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

pickling.py

+## NIFTY (Numerical Information Field Theory) has been developed at the
+## Max-Planck-Institute for Astrophysics.
+##
+## Copyright (C) 2013 Max-Planck-Society
+##
+## 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 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/>.
+
+import copy_reg as cr
+from types import MethodType as mt
+
+
+##-----------------------------------------------------------------------------
+
+def _pickle_method(method):
+    fct_name = method.im_func.__name__
+    obj = method.im_self
+    cl = method.im_class
+    ## handle mangled function name
+    if(fct_name.startswith("__"))and(not fct_name.endswith("__")):
+        cl_name = cl.__name__.lstrip("_")
+        fct_name = "_" + cl_name + fct_name
+    return _unpickle_method, (fct_name, obj, cl)
+
+##-----------------------------------------------------------------------------
+
+def _unpickle_method(fct_name, obj, cl):
+    for oo in cl.__mro__:
+        try:
+            fct = oo.__dict__[fct_name]
+        except(KeyError):
+            pass
+        else:
+            break
+    return fct.__get__(obj, cl)
+
+##-----------------------------------------------------------------------------
+
+## enable instance methods pickling
+cr.pickle(mt, _pickle_method, _unpickle_method)
+

rg/__init__.py

+## NIFTY (Numerical Information Field Theory) has been developed at the
+## Max-Planck-Institute for Astrophysics.
+##
+## Copyright (C) 2015 Max-Planck-Society
+##
+## 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 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/>.
+
+from __future__ import division
+from nifty_rg import *
+from nifty_power_conversion_rg import *
+

rg/gfft_rg.py

+## NIFTY (Numerical Information Field Theory) has been developed at the
+## Max-Planck-Institute for Astrophysics.
+##
+## Copyright (C) 2015 Max-Planck-Society
+##
+## Author: Michael Bell, Henrik Junklewitz, 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 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/>.
+
+## This is a "plain" version of gfft.py that was originally created as part of
+## GFFT v0.1.0 by Michael Bell and Henrik Junklewitz.
+
+import numpy as np
+import warnings
+
+
+def gfft(inp, in_ax=[], out_ax=[], ftmachine='fft', in_zero_center=True, \
+    out_zero_center=True, enforce_hermitian_symmetry=False, W=6, alpha=1.5,\