initial commit.

.gitignore

+*.html
+*.o
+*.so
+*.pyc
+*.log
+*.egg
+*.egg-info
+*.png
+*.pdf
+*.tiff
+*~
+
+.git/
+.svn/
+.spyderproject
+
+demos/
+!demos/demo_faraday.py
+!demos/demo_faraday_map.npy
+!demos/demo_excaliwir.py
+
+#demos/demo_imaging*.py
+#demos/demo_wiener.py
+#demos/test.txt
\ No newline at end of file

README.rst

+NIFTY -- Numerical Information Field Theory
+===========================================
+
+**NIFTY** project homepage: `<http://www.mpa-garching.mpg.de/ift/nifty/>`_
+
+Summary
+-------
+
+Description
+...........
+
+**NIFTY**, "\ **N**\umerical **I**\nformation **F**\ield **T**\heor\ **y**\ ",
+is a versatile library designed to enable the development of signal inference
+algorithms that operate regardless of the underlying spatial grid and its
+resolution. Its object-oriented framework is written in Python, although it
+accesses libraries written in Cython, C++, and C for efficiency.
+
+NIFTY offers a toolkit that abstracts discretized representations of continuous
+spaces, fields in these spaces, and operators acting on fields into classes.
+Thereby, the correct normalization of operations on fields is taken care of
+automatically without concerning the user. This allows for an abstract
+formulation and programming of inference algorithms, including those derived
+within information field theory. Thus, NIFTY permits its user to rapidly
+prototype algorithms in 1D, and then apply the developed code in
+higher-dimensional settings of real world problems. The set of spaces on which
+NIFTY operates comprises point sets, *n*-dimensional regular grids, spherical
+spaces, their harmonic counterparts, and product spaces constructed as
+combinations of those.
+
+Class & Feature Overview
+........................
+
+The NIFTY library features three main classes: **spaces** that represent
+certain grids, **fields** that are defined on spaces, and **operators** that
+apply to fields.
+
+- `Spaces <http://www.mpa-garching.mpg.de/ift/nifty/space.html>`_
+
+    - ``point_space`` -- unstructured list of points 
+    - ``rg_space`` -- *n*-dimensional regular Euclidean grid
+    - ``lm_space`` -- spherical harmonics
+    - ``gl_space`` -- Gauss-Legendre grid on the 2-sphere
+    - ``hp_space`` -- `HEALPix <http://sourceforge.net/projects/healpix/>`_
+        grid on the 2-sphere
+    - ``nested_space`` -- arbitrary product of grids
+
+- `Fields <http://www.mpa-garching.mpg.de/ift/nifty/field.html>`_
+
+    - ``field`` -- generic class for (discretized) fields::
+
+    field.cast_domain   field.hat           field.power        field.smooth
+    field.conjugate     field.inverse_hat   field.pseudo_dot   field.tensor_dot
+    field.dim           field.norm          field.set_target   field.transform
+    field.dot           field.plot          field.set_val      field.weight
+
+- `Operators <http://www.mpa-garching.mpg.de/ift/nifty/operator.html>`_
+
+    - ``diagonal_operator`` -- purely diagonal matrices in a specified basis
+    - ``projection_operator`` -- projections onto subsets of a specified basis
+    - ``vecvec_operator`` -- matrices derived from the outer product of a
+        vector
+    - ``response_operator`` -- exemplary responses that include a convolution,
+        masking and projection
+    - (and more)
+
+- (and more)
+
+*Parts of this summary are taken* [1]_.
+
+Installation
+------------
+
+Requirements
+............
+
+- `Python <http://www.python.org/>`_ (v2.7.x)
+
+    - `NumPy <http://www.numpy.org/>`_ and `SciPy <http://www.scipy.org/>`_
+    - `matplotlib <http://matplotlib.org/>`_
+    - `multiprocessing <http://docs.python.org/2/library/multiprocessing.html>`_
+        (standard library)
+
+- `GFFT <https://github.com/mrbell/gfft>`_ (v0.1.0) -- Generalized Fast Fourier
+    Transformations for Python
+
+- `HEALPy <https://github.com/healpy/healpy>`_ (v1.4 without openmp) -- A
+    Python wrapper for `HEALPix <http://sourceforge.net/projects/healpix/>`_
+- `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
+
+Download
+........
+
+The latest release is tagged **v0.2.0** and is available as a source package
+at `<https://github.com/mselig/nifty/tags>`_. The current version can be
+obtained by cloning the repository::
+
+    git clone git://github.com/mselig/nifty.git
+    cd nifty
+
+Installation
+............
+
+NIFTY is 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
+---------------
+
+Please, acknowledge the use of NIFTY in your publication(s) by using a phrase
+such as the following:
+
+*"Some of the results in this publication have been derived using the NIFTY
+[M. Selig et al., 2013] package."*
+
+References
+..........
+
+.. [1] M. Selig et al., "NIFTY -- Numerical Information Field Theory -- a
+    versatile Python library for signal inference", submitted to IEEE, 2013;
+    `arXiv:XXXX.XXXX <http://www.arxiv.org/abs/XXXX.XXXX>`_
+
+Release Notes
+-------------
+
+The NIFTY package is licensed under the
+`GPLv3 <http://www.gnu.org/licenses/gpl.html>`_ and is distributed *without any
+warranty*.
+
+**NIFTY** project homepage: `<http://www.mpa-garching.mpg.de/ift/nifty/>`_
+

__init__.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/>.
+
+from __future__ import division
+from nifty_core import *
+#from nifty_power import *
+#from nifty_cmaps 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/demo_faraday.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/>.
+
+"""
+    ..                  __   ____   __
+    ..                /__/ /   _/ /  /_
+    ..      __ ___    __  /  /_  /   _/  __   __
+    ..    /   _   | /  / /   _/ /  /   /  / /  /
+    ..   /  / /  / /  / /  /   /  /_  /  /_/  /
+    ..  /__/ /__/ /__/ /__/    \___/  \___   /  demo
+    ..                               /______/
+
+    NIFTY demo applying transformations to the "Faraday Map" [#]_.
+
+    References
+    ----------
+    .. [#] N. Opermann et. al., "An improved map of the Galactic Faraday sky",
+        Astronomy & Astrophysics, Volume 542, id.A93, 06/2012;
+        `arXiv:1111.6186 <http://www.arxiv.org/abs/1111.6186>`_
+
+"""
+from __future__ import division
+from nifty import *
+from nifty.nifty_cmaps import *
+
+
+about.warnings.off()
+about.infos.off()
+
+
+##-----------------------------------------------------------------------------
+
+## spaces
+h  = hp_space(128)
+l  = lm_space(383)
+g  = gl_space(384) ## nlon == 767
+g_ = gl_space(384, nlon=768)
+r  = rg_space([768, 384], dist=[1/360, 1/180])
+r_ = rg_space([256, 128], dist=[1/120, 1/60])
+
+## map
+m = field(h, val=np.load("demo_faraday_map.npy"))
+
+## projection operator
+Sk = None
+
+##-----------------------------------------------------------------------------
+
+
+
+##=============================================================================
+
+def run(projection=False, power=False):
+    """
+        Runs the demo.
+
+        Parameters
+        ----------
+        projection : bool, *optional*
+            Whether to additionaly include projections in the demo or not. If
+            ``projection == True`` the projection operator `Sk` will be
+            defined. (default: False)
+        power : bool, *optional*
+            Whether to additionaly show power spectra in the demo or not.
+            (default: False)
+
+    """
+    global Sk
+    ## start in hp_space
+    m0 = m
+
+    ## transform to lm_space
+    m1 = m0.transform(l)
+    if(projection):
+        ## define projection operator
+        powerindex = l.get_power_index()
+        Sk = projection_operator(l, assign=powerindex)
+        ## project quadrupole
+        m2 = Sk(m0, band=2)
+
+    ## transform to gl_space
+    m3 = m1.transform(g)
+
+    ## transform to rg_space
+    m4 = m1.transform(g_) ## auxiliary gl_space
+    m4.cast_domain(r) ## rg_space cast
+    m4.set_val(np.roll(m4.val[::-1, ::-1], g.nlon()//2, axis=1)) ## rearrange
+    if(power):
+        ## restrict to central window
+        m5 = field(r_, val=m4[128:256, 256:512]).transform()
+
+    ## plots
+    m0.plot(title=r"$m$ on a HEALPix grid", vmin=-4, vmax=4, cmap=ncmap.fm())
+    if(power):
+        m1.plot(title=r"angular power spectrum of $m$", vmin=1E-2, vmax=1E+1, mono=False)
+    if(projection):
+        m2.plot(title=r"quadrupole of $m$ on a HEALPix grid", vmin=-4, vmax=4, cmap=ncmap.fm())
+    m3.plot(title=r"$m$ on a spherical Gauss-Legendre grid", vmin=-4, vmax=4, cmap=ncmap.fm())
+    m4.plot(title=r"$m$ on a regular 2D grid", vmin=-4, vmax=4, cmap=ncmap.fm())
+    if(power):
+        m5.plot(title=r"(restricted) Fourier power spectrum of $m$", vmin=1E-3, vmax=1E+0, mono=False)
+
+##=============================================================================
+

nifty_config

+## nifty configuration
+##
+## errors colour code
+0
+## warnings
+1
+## warnings colour code
+0
+## infos
+0
+## infos colour code
+0
+## multiprocessing
+1
+## hermitianize
+1
+## lm2gl
+1
+##
+##
\ No newline at end of file

nifty_power.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/>.
+
+"""
+    ..                     __   ____   __
+    ..                   /__/ /   _/ /  /_
+    ..         __ ___    __  /  /_  /   _/  __   __
+    ..       /   _   | /  / /   _/ /  /   /  / /  /
+    ..      /  / /  / /  / /  /   /  /_  /  /_/  /
+    ..     /__/ /__/ /__/ /__/    \___/  \___   /  power
+    ..                                  /______/
+
+    NIFTy offers a number of automatized routines for handling
+    power spectra. It is possible to draw a field from a random distribution
+    with a certain autocorrelation or, equivalently, with a certain
+    power spectrum in its conjugate space (see :py:func:`field.random`). In
+    NIFTy, it is usually assumed that such a field follows statistical
+    homogeneity and isotropy. Fields which are only statistically homogeneous
+    can also be created using the diagonal operator routine.
+
+    In the moment, NIFTy offers one additional routine for power spectrum
+    manipulation, the smooth_power function to smooth a power spectrum with a
+    Gaussian convolution kernel. This can be necessary in cases where power
+    spectra are reconstructed and reused in an interative algorithm, where
+    too much statistical variation might effect severely the results.
+
+"""
+
+from __future__ import division
+import numpy as np
+import smoothing as gs
+
+
+##-----------------------------------------------------------------------------
+
+def smooth_power(power,kindex,exclude=1,sigma=-1):
+    """
+    Smoothes a power spectrum via convolution with a Gaussian kernel.
+
+    Parameters
+    ----------
+    power : ndarray
+        The power spectrum to be smoothed.
+
+    kindex : ndarray
+        The array specifying the coordinate indices in conjugate space.
+
+    exclude : scalar
+        Excludes the first power spectrum entries from smoothing, indicated by
+        the given integer scalar (default=1, the monopol is not smoothed).
+
+    smooth_length : scalar
+        FWHM of Gaussian convolution kernel.
+
+    Returns
+    -------
+    smoothpower : ndarray
+        The smoothed power spectrum.
+
+    """
+    return gs.smooth_power(power,kindex,exclude=exclude,smooth_length=sigma)
+
+##-----------------------------------------------------------------------------
+

setup.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/>.
+
+from distutils.core import setup
+import os
+
+setup(name="nifty",
+      version="0.2.0",
+      description="Numerical Information Field Theory",
+      author="Marco Selig",
+      author_email="mselig@mpa-garching.mpg.de",
+      url="http://www.mpa-garching.mpg.de/ift/nifty/",
+      packages=["nifty"],
+      package_dir={"nifty": ""},
+      package_data={"nifty": ["demos/demo_excaliwir.py",
+                              "demos/demo_faraday.py",
+                              "demos/demo_faraday_map.npy"]},
+      data_files=[(os.path.expanduser('~') + "/.nifty", ["nifty_config"])])
\ No newline at end of file

smoothing.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/>.
+
+## TODO: optimize
+
+from __future__ import division
+import gfft as gf
+import numpy as np
+
+
+def smooth_power(power, k, exclude=1, smooth_length=None):
+    """
+    """
+    if smooth_length == 0:
+        # No smoothing requested, just return the input array.
+        return power
+
+    if (exclude > 0):
+        k = k[exclude:]
+        excluded_power = np.copy(power[:exclude])
+        power = power[exclude:]
+
+    kmin = k[0]
+    kdiff = np.abs(k[:-1] - k[1:])
+
+    # Use the maximum difference between k values to define the bin width.
+    # This should ensure that we always have some points in each bin.
+    dk = np.max(kdiff)
+    nk = int(max(k - kmin) / dk + 1.)
+
+    if (smooth_length is None) or (smooth_length < 0):
+        #smooth_length = np.abs(k[0]-k[-1])/(3*nk)
+        smooth_length = dk
+
+    # Store the number of data points that have contributed to each bin
+#    counter = np.zeros(nk, dtype=float)
+    counter = np.zeros(nk, dtype=np.int)
+    # The binned power spectrum
+    pbinned = np.zeros(nk, dtype=power.dtype)
+    # do the binning
+    for i in range(len(k)):
+        ndx = int((k[i] - kmin) / dk)
+        pbinned[ndx] += power[i]
+        counter[ndx] += 1
+    pbinned = pbinned / counter
+
+    nmirror = int(5 * smooth_length / dk) + 2
+    zpbinned = np.r_[(2 * pbinned[0] - pbinned[1:nmirror][::-1]), pbinned,
+                     (2 * pbinned[-1] - pbinned[-nmirror:-1][::-1])]
+    zpbinned = np.maximum(0, zpbinned)
+
+    tpbinned = np.fft.fftshift(np.fft.fft(zpbinned))
+    tkernel = gaussian_kernel(zpbinned.size, dk, smooth_length)
+    pbinned2 = np.fft.ifft(np.fft.ifftshift(tpbinned * tkernel))
+
+    pbinned2 = np.abs(pbinned2[nmirror - 1:-nmirror + 1])
+
+    # Un-bin the results
+    power2 = np.zeros(len(power), dtype=power.dtype)
+    for i in range(len(k)):
+        ndx = int((k[i] - kmin) / dk)
+        power2[i] = pbinned2[ndx]
+
+    if(exclude > 0):
+        return np.r_[excluded_power, power2]
+    else:
+        return power2
+
+
+def smooth_field(val, fourier, zero_center, enforce_hermitian_symmetry, vol, \
+    smooth_length=0.):
+        """
+        A function to smooth a regularly spaced field with a Gaussian smoothing
+        kernel.
+
+        Args:
+            val: An ndarray containing the field values to be smoothed.
+            fourier: A boolean indicating whether the field is in Fourier space
+                or not.
+            zero_center: A list of booleans stating whether the field is
+                zero centered or not along each axis.
+            enforce_hermitian_symmetry: A flag indicating whether the input
+                field should be considered one half of a hermetian symmetric field
+            vol: An iterable containing the pixel space volume of each axis on
+                the regular grid.
+            smooth_length: The standard deviation of the Gaussian smoothing
+                kernel, in units of dist. [0]
+
+        Returns:
+            sval: The smoothed field values.
+        """
+
+#        if smooth_length == 0.:
+#            return val
+#
+        if(fourier):
+            tfield = val
+            vol = 1/np.array(val.shape)/vol
+        else:
+#
+            tfield = gf.gfft(val, ftmachine='fft', \
+                in_zero_center=zero_center, out_zero_center=True, \
+                enforce_hermitian_symmetry=enforce_hermitian_symmetry, W=-1, \
+                alpha=-1, verbose=False)
+
+        # Construct the Fourier transformed smoothing kernel
+        tkernel = gaussian_kernel(val.shape, vol, smooth_length)
+        # Multiply the smoothing kernel and the transformed spectrum
+        tfield = tfield*tkernel
+#
+        if(fourier):
+            sfield = tfield
+        else:
+#
+            # Transform back to the signal space using GFFT.
+            sfield = gf.gfft(tfield, ftmachine='ifft', \
+                in_zero_center=True, out_zero_center=zero_center, \
+                enforce_hermitian_symmetry=enforce_hermitian_symmetry, W=-1, \
+                alpha=-1, verbose=False)
+
+        return sfield
+
+
+def gaussian_kernel(nx, dx, smooth_length):
+    """
+    Returns an image of the Fourier transform of a Gaussian smoothing kernel.
+
+    Args:
+        nx: A scalar or iterable of axis lengths defining the grid on which the
+            smoothing kernel shall be applied.
+        dx: A scalar or iterable of pixel volumes defining the grid on which the
+            smoothing kernel shall be applied.
+        smooth_length: The standard deviation of the Gaussian smoothing kernel,
+            defined in units of dx.
+
+    Returns:
+        kernel: The Fourier transform of the Gaussian smoothing kernel.
+    """
+    ## FIXME: out source lambda function
+
+    # The Fourier transform of a Gaussian function having amplitude 1.
+    func = lambda x: np.exp(-2.*np.pi**2*x**2*smooth_length**2)
+
+    ## TODO: check necessity of checks
+
+    if np.isscalar(nx) and np.isscalar(dx):
+        ndim = 1
+        nx = [nx]
+        dx = [dx]
+    elif np.isscalar(nx) and not np.isscalar(dx) or \
+        not np.isscalar(nx) and np.isscalar(dx):
+            raise Exception("nx and dx must both be scalars or arrays. "+\
+                "No mixtures allowed!")