merged latest unit branch

README.md

@@ -101,7 +101,7 @@ Starting with a fresh Ubuntu installation move to a folder like
 
         git clone https://gitlab.mpcdf.mpg.de/ift/pyHealpix.git
         cd pyHealpix
-        autoreconf -i && ./configure && sudo make install
+        autoreconf -i && ./configure && make -j4 && sudo make install
         cd ..
 
 -   Finally, NIFTy:
@@ -135,7 +135,7 @@ For pyHealpix, use:
 
     git clone https://gitlab.mpcdf.mpg.de/ift/pyHealpix.git
     cd pyHealpix
-    autoreconf -i && ./configure --prefix=$HOME/.local && make install
+    autoreconf -i && ./configure --prefix=$HOME/.local && make -j4 && make install
     cd ..
 
 ### Installation on OS X 10.11
@@ -156,7 +156,7 @@ may cause trouble.
 
         git clone https://gitlab.mpcdf.mpg.de/ift/pyHealpix.git
         cd pyHealpix
-        autoreconf -i && ./configure && sudo make install
+        autoreconf -i && ./configure --prefix=`python-config --prefix` && make -j4 && sudo make install
         cd ..
 
 -   Install NIFTy:

nifty/domain_object.py

@@ -17,13 +17,14 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 import abc
+from nifty.nifty_meta import NiftyMeta
 
 from keepers import Loggable,\
                     Versionable
 
 
 class DomainObject(Versionable, Loggable, object):
-    __metaclass__ = abc.ABCMeta
+    __metaclass__ = NiftyMeta
 
     def __init__(self):
         # _global_id is used in the Versioning module from keepers

nifty/energies/energy.py

@@ -16,10 +16,14 @@
 # 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.nifty_meta import NiftyMeta
+
 from keepers import Loggable
 
 
 class Energy(Loggable, object):
+    __metaclass__ = NiftyMeta
+
     def __init__(self, position):
         self._cache = {}
         try:

nifty/minimization/quasi_newton_minimizer.py

@@ -17,6 +17,7 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 import abc
+from nifty.nifty_meta import NiftyMeta
 
 import numpy as np
 
@@ -26,7 +27,7 @@ from .line_searching import LineSearchStrongWolfe
 
 
 class QuasiNewtonMinimizer(Loggable, object):
-    __metaclass__ = abc.ABCMeta
+    __metaclass__ = NiftyMeta
 
     def __init__(self, line_searcher=LineSearchStrongWolfe(), callback=None,
                  convergence_tolerance=1E-4, convergence_level=3,

nifty/nifty_meta.py

+# -*- coding: utf-8 -*-
+
+import abc
+
+
+class DocStringInheritor(type):
+    """
+    A variation on
+    http://groups.google.com/group/comp.lang.python/msg/26f7b4fcb4d66c95
+    by Paul McGuire
+    """
+    def __new__(meta, name, bases, clsdict):
+        if not('__doc__' in clsdict and clsdict['__doc__']):
+            for mro_cls in (mro_cls for base in bases
+                            for mro_cls in base.mro()):
+                doc = mro_cls.__doc__
+                if doc:
+                    clsdict['__doc__'] = doc
+                    break
+        for attr, attribute in clsdict.items():
+            if not attribute.__doc__:
+                for mro_cls in (mro_cls for base in bases
+                                for mro_cls in base.mro()
+                                if hasattr(mro_cls, attr)):
+                    doc = getattr(getattr(mro_cls, attr), '__doc__')
+                    if doc:
+                        if isinstance(attribute, property):
+                            clsdict[attr] = property(attribute.fget,
+                                                     attribute.fset,
+                                                     attribute.fdel,
+                                                     doc)
+                        else:
+                            attribute.__doc__ = doc
+                        break
+        return super(DocStringInheritor, meta).__new__(meta, name,
+                                                       bases, clsdict)
+
+
+class NiftyMeta(DocStringInheritor, abc.ABCMeta):
+    pass

nifty/operators/composed_operator/composed_operator.py

@@ -54,10 +54,6 @@ class ComposedOperator(LinearOperator):
                 self._target += op.target
         return self._target
 
-    @property
-    def implemented(self):
-        return True
-
     @property
     def unitary(self):
         return False

nifty/operators/diagonal_operator/diagonal_operator.py

@@ -85,13 +85,11 @@ class DiagonalOperator(EndomorphicOperator):
 
     # ---Overwritten properties and methods---
 
-    def __init__(self, domain=(), implemented=True,
+    def __init__(self, domain=(),
                  diagonal=None, bare=False, copy=True,
                  distribution_strategy=None):
         self._domain = self._parse_domain(domain)
 
-        self._implemented = bool(implemented)
-
         if distribution_strategy is None:
             if isinstance(diagonal, distributed_data_object):
                 distribution_strategy = diagonal.distribution_strategy
@@ -265,10 +263,6 @@ class DiagonalOperator(EndomorphicOperator):
     def domain(self):
         return self._domain
 
-    @property
-    def implemented(self):
-        return self._implemented
-
     @property
     def self_adjoint(self):
         if self._self_adjoint is None:
@@ -329,16 +323,12 @@ class DiagonalOperator(EndomorphicOperator):
                   distribution_strategy=self.distribution_strategy,
                   copy=copy)
 
-        # weight if the given values were `bare` and `implemented` is True
+        # weight if the given values were `bare` is True
         # do inverse weightening if the other way around
-        if bare and self.implemented:
+        if bare:
             # If `copy` is True, we won't change external data by weightening
             # Otherwise, inplace weightening would change the external field
             f.weight(inplace=copy)
-        elif not bare and not self.implemented:
-            # If `copy` is True, we won't change external data by weightening
-            # Otherwise, inplace weightening would change the external field
-            f.weight(inplace=copy, power=-1)
 
         # Reset the self_adjoint property:
         self._self_adjoint = None

nifty/operators/fft_operator/fft_operator.py

@@ -152,10 +152,6 @@ class FFTOperator(LinearOperator):
     def target(self):
         return self._target
 
-    @property
-    def implemented(self):
-        return True
-
     @property
     def unitary(self):
         return True

nifty/operators/linear_operator/linear_operator.py

@@ -82,9 +82,6 @@ class LinearOperator(Loggable, object):
 
     @abc.abstractproperty
     def domain(self):
-        """
-        asdff
-        """
         raise NotImplementedError
 
     @abc.abstractproperty

nifty/operators/projection_operator/projection_operator.py

@@ -140,10 +140,6 @@ class ProjectionOperator(EndomorphicOperator):
     def domain(self):
         return self._projection_field.domain
 
-    @property
-    def implemented(self):
-        return True
-
     @property
     def unitary(self):
         if self._unitary is None:

nifty/operators/propagator_operator/propagator_operator.py

@@ -123,10 +123,6 @@ class PropagatorOperator(InvertibleOperatorMixin, EndomorphicOperator):
     def domain(self):
         return self._domain
 
-    @property
-    def implemented(self):
-        return True
-
     @property
     def self_adjoint(self):
         return True

nifty/operators/smoothing_operator/smoothing_operator.py

@@ -53,10 +53,6 @@ class SmoothingOperator(EndomorphicOperator):
     def domain(self):
         return self._domain
 
-    @property
-    def implemented(self):
-        return True
-
     @property
     def self_adjoint(self):
         return True

nifty/plotting/__init__.py

 from descriptors import *
 from plots import *
 from figures import *
+from colormap import *
\ No newline at end of file

nifty/plotting/colormap/__init__.py

+from colormap import Colormap
+import colormaps
\ No newline at end of file

nifty/plotting/colormap/colormaps.py

+from nifty.plotting.colormap.colormap import Colormap
+
+
+def HighEnergyCmap():
+    """
+        Returns a color map often used in High Energy Astronomy.
+    """
+
+    red = [(0.0, 0.0),
+           (0.167, 0.0),
+           (0.333, 0.5),
+           (0.5, 1.0),
+           (0.667, 1.0),
+           (0.833, 1.0),
+           (1.0, 1.0)]
+
+    green = [(0.0, 0.0),
+             (0.167, 0.0),
+             (0.333, 0.0),
+             (0.5, 0.0),
+             (0.667, 0.5),
+             (0.833, 1.0),
+             (1.0, 1.0)]
+
+    blue = [(0.0, 0.0),
+            (0.167, 1.0),
+            (0.333, 0.5),
+            (0.5, 0.0),
+            (0.667, 0.0),
+            (0.833, 0.0),
+            (1.0, 1.0)]
+    return Colormap("High Energy", red, green, blue)
+
+
+def FaradayMapCmap():
+    """
+        Returns a color map used in reconstruction of 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>`_
+    """
+    red = [(0.0, 0.35),
+           (0.1, 0.4),
+           (0.2, 0.25),
+           (0.41, 0.47),
+           (0.5, 0.8),
+           (0.56, 0.96),
+           (0.59, 1.0),
+           (0.74, 0.8),
+           (0.8, 0.8),
+           (0.9, 0.5),
+           (1.0, 0.4)]
+
+    green = [(0.0, 0.0),
+             (0.2, 0.0),
+             (0.362, 0.88),
+             (0.5, 1.0),
+             (0.638, 0.88),
+             (0.8, 0.25),
+             (0.9, 0.3),
+             (1.0, 0.2)]
+
+    blue = [(0.0, 0.35),
+            (0.1, 0.4),
+            (0.2, 0.8),
+            (0.26, 0.8),
+            (0.41, 1.0),
+            (0.44, 0.96),
+            (0.5, 0.8),
+            (0.59, 0.47),
+            (0.8, 0.0),
+            (1.0, 0.0)]
+
+    return Colormap("Faraday Map", red, green, blue)
+
+
+def FaradayUncertaintyCmap():
+    """
+        Returns a color map used for the "Faraday Map Uncertainty".
+
+        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>`_
+    """
+    red = [(0.0, 1.0),
+           (0.1, 0.8),
+           (0.2, 0.65),
+           (0.41, 0.6),
+           (0.5, 0.7),
+           (0.56, 0.96),
+           (0.59, 1.0),
+           (0.74, 0.8),
+           (0.8, 0.8),
+           (0.9, 0.5),
+           (1.0, 0.4)]
+
+    green = [(0.0, 0.9),
+             (0.2, 0.65),
+             (0.362, 0.95),
+             (0.5, 1.0),
+             (0.638, 0.88),
+             (0.8, 0.25),
+             (0.9, 0.3),
+             (1.0, 0.2)]
+
+    blue = [(0.0, 1.0),
+            (0.1, 0.8),
+            (0.2, 1.0),
+            (0.41, 1.0),
+            (0.44, 0.96),
+            (0.5, 0.7),
+            (0.59, 0.42),
+            (0.8, 0.0),
+            (1.0, 0.0)]
+
+    return Colormap("Faraday Uncertainty", red, green, blue)
+
+
+def PlusMinusCmap():
+    """
+        Returns a color map useful for a zero-centerd range of values.
+    """
+    red = [(0.0, 1.0),
+           (0.1, 0.96),
+           (0.2, 0.84),
+           (0.3, 0.64),
+           (0.4, 0.36),
+           (0.5, 0.0),
+           (0.6, 0.0),
+           (0.7, 0.0),
+           (0.8, 0.0),
+           (0.9, 0.0),
+           (1.0, 0.0)]
+
+    green = [(0.0, 0.5),
+             (0.1, 0.32),
+             (0.2, 0.18),
+             (0.3, 0.08),
+             (0.4, 0.02),
+             (0.5, 0.0),
+             (0.6, 0.02),
+             (0.7, 0.08),
+             (0.8, 0.18),
+             (0.9, 0.32),
+             (1.0, 0.5)]
+
+    blue = [(0.0, 0.0),
+            (0.1, 0.0),
+            (0.2, 0.0),
+            (0.3, 0.0),
+            (0.4, 0.0),
+            (0.5, 0.0),
+            (0.6, 0.36),
+            (0.7, 0.64),
+            (0.8, 0.84),
+            (0.9, 0.96),
+            (1.0, 1.0)]
+
+    return Colormap("Plus Minus", red, green, blue)
+
+
+def PlankCmap():
+    """
+        Returns a color map similar to the one used for the "Planck CMB Map".
+    """
+    red = [(0.0, 0.0),
+           (0.1, 0.0),
+           (0.2, 0.0),
+           (0.3, 0.0),
+           (0.4, 0.0),
+           (0.5, 1.0),
+           (0.6, 1.0),
+           (0.7, 1.0),
+           (0.8, 0.83),
+           (0.9, 0.67),
+           (1.0, 0.5)]
+
+    green = [(0.0, 0.0),
+             (0.1, 0.0),
+             (0.2, 0.0),
+             (0.3, 0.3),
+             (0.4, 0.7),
+             (0.5, 1.0),
+             (0.6, 0.7),
+             (0.7, 0.3),
+             (0.8, 0.0),
+             (0.9, 0.0),
+             (1.0, 0.0)]
+
+    blue = [(0.0, 0.5),
+            (0.1, 0.67),
+            (0.2, 0.83),
+            (0.3, 1.0),
+            (0.4, 1.0),
+            (0.5, 1.0),
+            (0.6, 0.0),
+            (0.7, 0.0),
+            (0.8, 0.0),
+            (0.9, 0.0),
+            (1.0, 0.0)]
+
+    return Colormap("Planck-like", red, green, blue)

nifty/plotting/figures/figure_2D.py

@@ -7,6 +7,7 @@ from nifty.plotting.plots import Heatmap, Mollweide
 class Figure2D(FigureFromPlot):
     def __init__(self, plots, title=None, width=None, height=None,
                  xaxis=None, yaxis=None):
+        super(Figure2D, self).__init__(plots, title, width, height)
 
         # TODO: add sanitization of plots input
         if isinstance(plots[0], Heatmap) and not width and not height:
@@ -45,7 +46,7 @@ class Figure2D(FigureFromPlot):
                                                 showticklabels=False
                                             )
         if self.yaxis:
-            plotly_object['layout']['yaxis'] = self.yaxis._to_plotly()
+            plotly_object['layout']['yaxis'] = self.yaxis.to_plotly()
         elif not self.yaxis:
             plotly_object['layout']['yaxis'] = dict(showline=False)
 

nifty/plotting/figures/figure_base.py

 # -*- coding: utf-8 -*-
 
+from abc import abstractmethod
+
 from nifty.plotting.plotly_wrapper import PlotlyWrapper
 
 
@@ -8,3 +10,7 @@ class FigureBase(PlotlyWrapper):
         self.title = title
         self.width = width
         self.height = height
+
+    @abstractmethod
+    def to_plotly(self):
+        raise NotImplementedError

nifty/plotting/figures/figure_from_plot.py

@@ -2,7 +2,6 @@
 
 # -*- coding: utf-8 -*-
 
-from abc import abstractmethod
 from figure_base import FigureBase
 
 
@@ -11,7 +10,6 @@ class FigureFromPlot(FigureBase):
         super(FigureFromPlot, self).__init__(title, width, height)
         self.plots = plots
 
-    @abstractmethod
     def to_plotly(self):
         data = [plt.to_plotly() for plt in self.plots]
         layout = {'title': self.title,

nifty/plotting/figures/multi_figure.py

 # -*- coding: utf-8 -*-
 
 import numpy as np
-
 from nifty import dependency_injector as gdi
-
 from figure_base import FigureBase
 from figure_3D import Figure3D
 
 plotly = gdi.get('plotly')
 
 
+# TODO: add nice height and width defaults for multifigure
 class MultiFigure(FigureBase):
-    def __init__(self, rows, columns, subfigures=None,
-                 title=None, width=None, height=None):
+    def __init__(self, rows, columns, title=None, width=None, height=None,
+                 subfigures=None):
         if 'plotly' not in gdi:
             raise ImportError("The module plotly is needed but not available.")
         super(MultiFigure, self).__init__(title, width, height)
@@ -31,43 +30,30 @@ class MultiFigure(FigureBase):
         self.subfigures[row, column] = figure
 
     def to_plotly(self):
-        sub_titles = self.subfigures.copy()
-        sub_titles = sub_titles.flatten
-        title_extractor = lambda z: z.title
-        sub_titles = np.vectorize(title_extractor)(sub_titles)
+        title_extractor = lambda z: z.title if z else ""
+        sub_titles = \
+            tuple(np.vectorize(title_extractor)(self.subfigures.flatten()))
 
-        sub_specs = self.subfigures.copy_empty()
         specs_setter = \
             lambda z: {'is_3d': True} if isinstance(z, Figure3D) else {}
-        sub_specs = np.vectorize(specs_setter)(sub_specs)
+        sub_specs = \
+            list(map(list, np.vectorize(specs_setter)(self.subfigures)))
+
         multi_figure_plotly_object = plotly.tools.make_subplots(
                                                    self.rows,
                                                    self.columns,
                                                    subplot_titles=sub_titles,
                                                    specs=sub_specs)
-
+        # TODO resolve bug with titles and 3D subplots
         for index, fig in np.ndenumerate(self.subfigures):
-            for plot in fig.plots:
-                multi_figure_plotly_object.append_trace(plot.to_plotly(),
-                                                        index[0]+1,
-                                                        index[1]+1)
+            if fig:
+                for plot in fig.plots:
+                    multi_figure_plotly_object.append_trace(plot.to_plotly(),
+                                                            index[0]+1,
+                                                            index[1]+1)
 
         multi_figure_plotly_object['layout'].update(height=self.height,
                                                     width=self.width,
                                                     title=self.title)
-        return multi_figure_plotly_object
-
-
-    @staticmethod
-    def from_figures_2cols(figures, title=None, width=None, height=None):
-        multi_figure = MultiFigure((len(figures)+1)/2, 2, title, width, height)
-
-        for i in range(0, len(figures), 2):
-            multi_figure.add_subfigure(figures[i], i/2, 0)
-
-        for i in range(1, len(figures), 2):
-            multi_figure.add_subfigure(figures[i], i/2, 1)
-
-        return multi_figure
-
 
+        return multi_figure_plotly_object

nifty/plotting/plotly_wrapper.py

 from abc import ABCMeta, abstractmethod
+from nifty.nifty_meta import NiftyMeta
 
 
 class PlotlyWrapper(object):
-    __metaclass__ = ABCMeta
+    __metaclass__ = NiftyMeta
 
     @abstractmethod
     def to_plotly(self):

nifty/plotting/plots/heatmaps/heatmap.py

 # -*- coding: utf-8 -*-
 
-from nifty.plotting.plots.plot import Plot
+from nifty.plotting.plotly_wrapper import PlotlyWrapper
 
 
-class Heatmap(Plot):
-    def __init__(self, data, label='', line=None, marker=None, webgl=False,
+class Heatmap(PlotlyWrapper):