Merge branch 'master' into misc_tweaks

.gitlab-ci.yml

@@ -16,21 +16,38 @@ before_script:
   - pip install --upgrade -r ci/requirements.txt
 
 
-test_all:
+test_min:
   stage: test
   script:
     - python setup.py build_ext --inplace
-    - nosetests
+    - nosetests -vv
+
+test_mpi:
+  stage: test
+  script:
     - ci/install_pyHealpix.sh
     - ci/install_mpi4py.sh
     - python setup.py build_ext --inplace
-    - nosetests
+    - nosetests -vv
+
+test_mpi_fftw:
+  stage: test
+  script:
+    - ci/install_pyHealpix.sh
+    - ci/install_mpi4py.sh
     - ci/install_pyfftw.sh
     - python setup.py build_ext --inplace
-    - nosetests
+    - nosetests -vv
+
+test_mpi_fftw_hdf5:
+  stage: test
+  script:
+    - ci/install_pyHealpix.sh
+    - ci/install_mpi4py.sh
+    - ci/install_pyfftw.sh
     - ci/install_h5py.sh
     - python setup.py build_ext --inplace
-    - nosetests --with-coverage --cover-package=nifty --cover-branches
+    - nosetests -vv --with-coverage --cover-package=nifty --cover-branches
     - >
       coverage report | grep TOTAL | awk '{ print "TOTAL: "$6; }'
 

nifty/config/nifty_config.py

@@ -29,9 +29,7 @@ __all__ = ['dependency_injector', 'nifty_configuration']
 dependency_injector = keepers.DependencyInjector(
                                    [('mpi4py.MPI', 'MPI'),
                                     'pyHealpix',
-                                    'plotly',
-                                    'pylab',
-                                    'healpy'])
+                                    'plotly'])
 
 dependency_injector.register('pyfftw', lambda z: hasattr(z, 'FFTW_MPI'))
 

nifty/field.py

@@ -1054,7 +1054,7 @@ class Field(Loggable, Versionable, object):
             dotted = diagonalOperator(x, spaces=spaces)
             return dotted.sum(spaces=spaces)
 
-    def norm(self, q=2):
+    def norm(self):
         """ Computes the Lq-norm of the field values.
 
         Parameters
@@ -1068,11 +1068,7 @@ class Field(Loggable, Versionable, object):
             The Lq-norm of the field values.
 
         """
-
-        if q == 2:
-            return (self.dot(x=self)) ** (1 / 2)
-        else:
-            return self.dot(x=self ** (q - 1)) ** (1 / q)
+        return np.sqrt(np.abs(self.dot(x=self)))
 
     def conjugate(self, inplace=False):
         """ Retruns the complex conjugate of the field.

nifty/operators/composed_operator/composed_operator.py

@@ -131,9 +131,6 @@ class ComposedOperator(LinearOperator):
     def _adjoint_inverse_times(self, x, spaces):
         return self._times_helper(x, spaces, func='adjoint_inverse_times')
 
-    def _inverse_adjoint_times(self, x, spaces):
-        return self._times_helper(x, spaces, func='inverse_adjoint_times')
-
     def _times_helper(self, x, spaces, func):
         space_index = 0
         if spaces is None:

nifty/operators/invertible_operator_mixin/invertible_operator_mixin.py

@@ -103,8 +103,3 @@ class InvertibleOperatorMixin(object):
                                                 b=x,
                                                 x0=x0)
         return result
-
-    #MR FIXME: why? shouldn't this be equivalent to the adjoint inverse?
-    def _inverse_adjoint_times(self, x, spaces):
-        raise NotImplementedError(
-            "no generic instance method 'inverse_adjoint_times'.")

nifty/operators/linear_operator/linear_operator.py

@@ -269,10 +269,6 @@ class LinearOperator(Loggable, object):
         raise NotImplementedError(
             "no generic instance method 'adjoint_inverse_times'.")
 
-    def _inverse_adjoint_times(self, x, spaces):
-        raise NotImplementedError(
-            "no generic instance method 'inverse_adjoint_times'.")
-
     def _check_input_compatibility(self, x, spaces, inverse=False):
         if not isinstance(x, Field):
             raise ValueError(

nifty/operators/smoothing_operator/smoothing_operator.py

@@ -39,11 +39,12 @@ class SmoothingOperator(EndomorphicOperator):
         can only live on one space or FieldType
     sigma : float
         Sets the length of the Gaussian convolution kernel
-    log_distances : boolean
-        States whether the convolution happens on the logarithmic grid or not.
+    log_distances : boolean *optional*
+        States whether the convolution happens on the logarithmic grid or not
+        (default: False).
     default_spaces : tuple of ints *optional*
         Defines on which space(s) of a given field the Operator acts by
-        default (default: None)
+        default (default: None).
 
     Attributes
     ----------
@@ -117,7 +118,6 @@ class SmoothingOperator(EndomorphicOperator):
                 raise NotImplementedError("For the given Space smoothing "
                                           " is not available.")
         else:
-            print 'new 4'
             return super(SmoothingOperator, cls).__new__(cls,
                                                          domain,
                                                          *args,

nifty/plotting/figures/figure_2D.py

 # -*- coding: utf-8 -*-
 
 from figure_from_plot import FigureFromPlot
-from nifty.plotting.plots import Heatmap, Mollweide
+from nifty.plotting.plots import Heatmap, HPMollweide, GLMollweide
 
 
 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:
-            (x, y) = plots[0].data.shape
+        if plots is not None:
+            if isinstance(plots[0], Heatmap) and width is None and \
+               height is None:
+                (x, y) = plots[0].data.shape
+
+                if x > y:
+                    width = 500
+                    height = int(500*y/x)
+                else:
+                    height = 500
+                    width = int(500 * y / x)
+
+                if isinstance(plots[0], GLMollweide) or \
+                   isinstance(plots[0], HPMollweide):
+                    xaxis = False if (xaxis is None) else xaxis
+                    yaxis = False if (yaxis is None) else yaxis
 
-            if x > y:
-                width = 500
-                height = int(500*y/x)
             else:
-                height = 500
-                width = int(500 * y / x)
-            if isinstance(plots[0], Mollweide):
-                if not xaxis:
-                    xaxis = False
-                if not yaxis:
-                    yaxis = False
+                width = None
+                height = None
 
         super(Figure2D, self).__init__(plots, title, width, height)
         self.xaxis = xaxis
         self.yaxis = yaxis
 
+    def at(self, plots):
+        return Figure2D(plots=plots,
+                        title=self.title,
+                        width=self.width,
+                        height=self.height,
+                        xaxis=self.xaxis,
+                        yaxis=self.yaxis)
+
     def to_plotly(self):
+
         plotly_object = super(Figure2D, self).to_plotly()
+
         if self.xaxis or self.yaxis:
             plotly_object['layout']['scene']['aspectratio'] = {}
         if self.xaxis:

nifty/plotting/figures/figure_3D.py

@@ -10,6 +10,15 @@ class Figure3D(FigureFromPlot):
         self.yaxis = yaxis
         self.zaxis = zaxis
 
+    def at(self, plots):
+        return Figure3D(plots=plots,
+                        title=self.title,
+                        width=self.width,
+                        height=self.height,
+                        xaxis=self.xaxis,
+                        yaxis=self.yaxis,
+                        zaxis=self.zaxis)
+
     def to_plotly(self):
         plotly_object = super(Figure3D, self).to_plotly()
         if self.xaxis or self.yaxis or self.zaxis:

nifty/plotting/figures/figure_base.py

 # -*- coding: utf-8 -*-
 
-from abc import abstractmethod
+import abc
 
 from nifty.plotting.plotly_wrapper import PlotlyWrapper
 
@@ -11,6 +11,10 @@ class FigureBase(PlotlyWrapper):
         self.width = width
         self.height = height
 
-    @abstractmethod
+    @abc.abstractmethod
+    def at(self):
+        raise NotImplementedError
+
+    @abc.abstractmethod
     def to_plotly(self):
         raise NotImplementedError

nifty/plotting/figures/multi_figure.py

@@ -10,13 +10,21 @@ plotly = gdi.get('plotly')
 
 # TODO: add nice height and width defaults for multifigure
 class MultiFigure(FigureBase):
-    def __init__(self, rows, columns, title=None, width=None, height=None,
-                 subfigures=None):
+    def __init__(self, subfigures, title=None, width=None, height=None):
         if 'plotly' not in gdi:
             raise ImportError("The module plotly is needed but not available.")
         super(MultiFigure, self).__init__(title, width, height)
-        self.subfigures = np.empty((rows, columns), dtype=np.object)
-        self.subfigures[:] = subfigures
+        if subfigures is not None:
+            self.subfigures = np.asarray(subfigures, dtype=np.object)
+            if len(self.subfigures.shape) != 2:
+                raise ValueError("Subfigures must be a two-dimensional array.")
+
+
+    def at(self, subfigures):
+        return MultiFigure(subfigures=subfigures,
+                           title=self.title,
+                           width=self.width,
+                           height=self.height)
 
     @property
     def rows(self):
@@ -26,15 +34,15 @@ class MultiFigure(FigureBase):
     def columns(self):
         return self.subfigures.shape[1]
 
-    def add_subfigure(self, figure, row, column):
-        self.subfigures[row, column] = figure
-
     def to_plotly(self):
         title_extractor = lambda z: z.title if z else ""
-        sub_titles = tuple(np.vectorize(title_extractor)(self.subfigures.flatten()))
+        sub_titles = tuple(np.vectorize(title_extractor)(
+                                                    self.subfigures.flatten()))
 
-        specs_setter = lambda z: {'is_3d': True} if isinstance(z, Figure3D) else {}
-        sub_specs = list(map(list, np.vectorize(specs_setter)(self.subfigures)))
+        specs_setter = lambda z: ({'is_3d': True}
+                                  if isinstance(z, Figure3D) else {})
+        sub_specs = list(map(list, np.vectorize(specs_setter)(
+                                                             self.subfigures)))
 
         multi_figure_plotly_object = plotly.tools.make_subplots(
                                                    self.rows,
@@ -46,7 +54,7 @@ class MultiFigure(FigureBase):
                                                     width=self.width,
                                                     title=self.title)
 
-        #TODO resolve bug with titles and 3D subplots
+        # TODO resolve bug with titles and 3D subplots
 
         i = 1
         for index, fig in np.ndenumerate(self.subfigures):

nifty/plotting/plots/heatmaps/__init__.py

 # -*- coding: utf-8 -*-
 
-from mollweide import Mollweide
+from hpmollweide import HPMollweide
+from glmollweide import GLMollweide
 from heatmap import Heatmap

nifty/plotting/plots/heatmaps/glmollweide.py

+# -*- coding: utf-8 -*-
+
+from nifty import dependency_injector as gdi
+from heatmap import Heatmap
+import numpy as np
+
+from .mollweide_helper import mollweide_helper
+
+pyHealpix = gdi.get('pyHealpix')
+
+
+class GLMollweide(Heatmap):
+    def __init__(self, data, xsize=800, color_map=None,
+                 webgl=False, smoothing=False):
+        # smoothing 'best', 'fast', False
+        if 'pyHealpix' not in gdi:
+            raise ImportError(
+                "The module pyHealpix is needed but not available.")
+        self.xsize = xsize
+
+        super(GLMollweide, self).__init__(data, color_map, webgl, smoothing)
+
+    def at(self, data):
+        if isinstance(data, list):
+            data = [self._mollview(d) for d in data]
+        else:
+            data = self._mollview(data)
+        return GLMollweide(data=data,
+                           xsize=self.xsize,
+                           color_map=self.color_map,
+                           webgl=self.webgl,
+                           smoothing=self.smoothing)
+
+    @staticmethod
+    def _find_closest(A, target):
+        # A must be sorted
+        idx = A.searchsorted(target)
+        idx = np.clip(idx, 1, len(A)-1)
+        left = A[idx-1]
+        right = A[idx]
+        idx -= target - left < right - target
+        return idx
+
+    def _mollview(self, x):
+        xsize = self.xsize
+        nlat = x.shape[0]
+        nlon = x.shape[1]
+
+        res, mask, theta, phi = mollweide_helper(xsize)
+
+        ra = np.linspace(0, 2*np.pi, nlon+1)
+        dec = pyHealpix.GL_thetas(nlat)
+        ilat = self._find_closest(dec, theta)
+        ilon = self._find_closest(ra, phi)
+        ilon = np.where(ilon == nlon, 0, ilon)
+        res[mask] = x[ilat, ilon]
+        return res

nifty/plotting/plots/heatmaps/heatmap.py

@@ -6,14 +6,8 @@ from nifty.plotting.plotly_wrapper import PlotlyWrapper
 
 
 class Heatmap(PlotlyWrapper):
-    def __init__(self, data, color_map=None, webgl=False,
-                 smoothing=False):  # smoothing 'best', 'fast', False
-        if isinstance(data, list):
-            self.data = np.zeros((data[0].shape))
-            for arr in data:
-                self.data = np.add(self.data, arr)
-        else:
-            self.data = data
+    def __init__(self, data, color_map=None, webgl=False, smoothing=False):
+        # smoothing 'best', 'fast', False
 
         if color_map is not None:
             if not isinstance(color_map, Colormap):
@@ -22,6 +16,19 @@ class Heatmap(PlotlyWrapper):
         self.color_map = color_map
         self.webgl = webgl
         self.smoothing = smoothing
+        self.data = data
+
+    def at(self, data):
+        if isinstance(data, list):
+            temp_data = np.zeros((data[0].shape))
+            for arr in data:
+                temp_data = np.add(temp_data, arr)
+        else:
+            temp_data = data
+        return Heatmap(data=temp_data,
+                       color_map=self.color_map,
+                       webgl=self.webgl,
+                       smoothing=self.smoothing)
 
     @property
     def figure_dimension(self):
@@ -29,7 +36,9 @@ class Heatmap(PlotlyWrapper):
 
     def to_plotly(self):
         plotly_object = dict()
+
         plotly_object['z'] = self.data
+
         plotly_object['showscale'] = False
         if self.color_map:
             plotly_object['colorscale'] = self.color_map.to_plotly()

nifty/plotting/plots/heatmaps/hpmollweide.py

+# -*- coding: utf-8 -*-
+
+from nifty import dependency_injector as gdi
+from heatmap import Heatmap
+import numpy as np
+
+from .mollweide_helper import mollweide_helper
+
+pyHealpix = gdi.get('pyHealpix')
+
+
+class HPMollweide(Heatmap):
+    def __init__(self, data, xsize=800, color_map=None, webgl=False,
+                 smoothing=False):  # smoothing 'best', 'fast', False
+        if 'pyHealpix' not in gdi:
+            raise ImportError(
+                "The module pyHealpix is needed but not available.")
+        self.xsize = xsize
+        super(HPMollweide, self).__init__(data, color_map, webgl, smoothing)
+
+    def at(self, data):
+        if isinstance(data, list):
+            data = [self._mollview(d) for d in data]
+        else:
+            data = self._mollview(data)
+        return HPMollweide(data=data,
+                           xsize=self.xsize,
+                           color_map=self.color_map,
+                           webgl=self.webgl,
+                           smoothing=self.smoothing)
+
+    def _mollview(self, x):
+        xsize = self.xsize
+        res, mask, theta, phi = mollweide_helper(xsize)
+
+        ptg = np.empty((phi.size, 2), dtype=np.float64)
+        ptg[:, 0] = theta
+        ptg[:, 1] = phi
+        base = pyHealpix.Healpix_Base(int(np.sqrt(x.size/12)), "RING")
+        res[mask] = x[base.ang2pix(ptg)]
+        return res

nifty/plotting/plots/heatmaps/mollweide.py

-# -*- coding: utf-8 -*-
-
-from nifty import dependency_injector as gdi
-from heatmap import Heatmap
-
-pylab = gdi.get('pylab')
-healpy = gdi.get('healpy')
-
-
-class Mollweide(Heatmap):
-    def __init__(self, data, color_map=None, webgl=False,
-                 smoothing=False):  # smoothing 'best', 'fast', False
-        if 'pylab' not in gdi:
-            raise ImportError("The module pylab is needed but not available.")
-        if 'healpy' not in gdi:
-            raise ImportError("The module healpy is needed but not available.")
-        if isinstance(data, list):
-            data = [self._mollview(d) for d in data]
-        else:
-            data = self._mollview(data)
-        super(Mollweide, self).__init__(data, color_map, webgl, smoothing)
-
-    def _mollview(self, x, xsize=800):
-        x = healpy.pixelfunc.ma_to_array(x)
-        f = pylab.figure(None, figsize=(8.5, 5.4))
-        extent = (0.02, 0.05, 0.96, 0.9)
-        ax = healpy.projaxes.HpxMollweideAxes(f, extent)
-        img = ax.projmap(x, nest=False, xsize=xsize)
-        return img

nifty/plotting/plots/heatmaps/mollweide_helper.py

+# -*- coding: utf-8 -*-
+
+import numpy as np
+
+
+def mollweide_helper(xsize):
+    xsize = int(xsize)
+    ysize = int(xsize/2)
+    res = np.full(shape=(ysize, xsize), fill_value=np.nan,
+                  dtype=np.float64)
+    xc = (xsize-1)*0.5
+    yc = (ysize-1)*0.5
+    u, v = np.meshgrid(np.arange(xsize), np.arange(ysize))
+    u = 2*(u-xc)/(xc/1.02)
+    v = (v-yc)/(yc/1.02)
+
+    mask = np.where((u*u*0.25 + v*v) <= 1.)
+    t1 = v[mask]
+    theta = 0.5*np.pi-(
+        np.arcsin(2/np.pi*(np.arcsin(t1) + t1*np.sqrt((1.-t1)*(1+t1)))))
+    phi = -0.5*np.pi*u[mask]/np.maximum(np.sqrt((1-t1)*(1+t1)), 1e-6)
+    phi = np.where(phi < 0, phi+2*np.pi, phi)
+    return res, mask, theta, phi

nifty/plotting/plots/scatter_plots/cartesian.py

@@ -4,16 +4,14 @@ from scatter_plot import ScatterPlot
 
 
 class Cartesian(ScatterPlot):
-    def __init__(self, x, y, label, line, marker, showlegend=True):
-        super(Cartesian, self).__init__(label, line, marker)
-        self.x = x
-        self.y = y
+    def __init__(self, data, label, line, marker, showlegend=True):
+        super(Cartesian, self).__init__(data, label, line, marker)
         self.showlegend = showlegend
 
     @abstractmethod
     def to_plotly(self):
         plotly_object = super(Cartesian, self).to_plotly()
-        plotly_object['x'] = self.x
-        plotly_object['y'] = self.y
+        plotly_object['x'] = self.data[0]
+        plotly_object['y'] = self.data[1]
         plotly_object['showlegend'] = self.showlegend
         return plotly_object

nifty/plotting/plots/scatter_plots/cartesian_2D.py

@@ -4,17 +4,20 @@ from cartesian import Cartesian
 
 
 class Cartesian2D(Cartesian):
-    def __init__(self, x=None, y=None, x_start=0, x_step=1,
-                 label='', line=None, marker=None, showlegend=True,
+    def __init__(self, data, label='', line=None, marker=None, showlegend=True,
                  webgl=True):
-        if y is None:
-            raise Exception('Error: no y data to plot')
-        if x is None:
-            x = range(x_start, len(y) * x_step, x_step)
-        super(Cartesian2D, self).__init__(x, y, label, line, marker,
+        super(Cartesian2D, self).__init__(data, label, line, marker,
                                           showlegend)
         self.webgl = webgl
 
+    def at(self, data):
+        return Cartesian2D(data=data,
+                           label=self.label,
+                           line=self.line,
+                           marker=self.marker,
+                           showlegend=self.showlegend,
+                           webgl=self.webgl)
+
     @property
     def figure_dimension(self):
         return 2

nifty/plotting/plots/scatter_plots/cartesian_3D.py

@@ -4,11 +4,17 @@ from cartesian import Cartesian
 
 
 class Cartesian3D(Cartesian):
-    def __init__(self, x, y, z, label='', line=None, marker=None,
+    def __init__(self, data, label='', line=None, marker=None,
                  showlegend=True):
-        super(Cartesian3D, self).__init__(x, y, label, line, marker,
+        super(Cartesian3D, self).__init__(data, label, line, marker,
                                           showlegend)
-        self.z = z
+
+    def at(self, data):
+        return Cartesian3D(data=data,
+                           label=self.label,
+                           line=self.line,
+                           marker=self.marker,
+                           showlegend=self.showlegend)
 
     @property
     def figure_dimension(self):
@@ -16,6 +22,6 @@ class Cartesian3D(Cartesian):
 
     def to_plotly(self):
         plotly_object = super(Cartesian3D, self).to_plotly()
-        plotly_object['z'] = self.z
+        plotly_object['z'] = self.data[2]
         plotly_object['type'] = 'scatter3d'
         return plotly_object

nifty/plotting/plots/scatter_plots/geo.py

@@ -3,26 +3,31 @@ from scatter_plot import ScatterPlot