Various fixes

odl/_ufunc/_ufunc_ops.py

@@ -1,4 +1,4 @@
-# Copyright 2014-2019 The ODL contributors
+# Copyright 2014-2020 The ODL contributors
 #
 # This file is part of ODL.
 #
@@ -16,6 +16,7 @@
     'negative', 'degrees', 'rad2deg', 'radians', 'deg2rad', 'add', 'subtract'
 }
 
+
 def _ufunc_op_range(domain, nin, nout, types_dict):
     """Infer the range of a ufunc operator."""
     if nin == 1:
@@ -551,3 +552,5 @@ def _call(self, x):
 ufunc_funcs = type(
     'ufunc_funcs', (object,), {'__getattr__': staticmethod(ufunc_func_cls)}
 )()
+
+# TODO(kohr-h): doctest

odl/deform/linearized.py

@@ -367,11 +367,11 @@ def __init__(self, domain, displacement, interp='linear'):
         )
 
         try:
-            self.__displacement = (self.domain.tangent_bundle).element(
+            self.__displacement = self.domain.tangent_bundle.element(
                 displacement
             )
         except (ValueError, TypeError):
-            self.__displacement = (self.domain.tangent_bundle).element(
+            self.__displacement = self.domain.tangent_bundle.element(
                 [displacement]
             )
         self.__interp_byaxis = _normalize_interp(interp, domain.ndim)

odl/discr/diff_ops.py

@@ -135,7 +135,6 @@ def _call(self, x, out=None):
         if out is None:
             out = self.range.element()
 
-        # TODO: this pipes CUDA arrays through NumPy. Write native operator.
         finite_diff(x, axis=self.axis, dx=self.dx,
                     method=self.method, pad_mode=self.pad_mode,
                     pad_const=self.pad_const, out=out)
@@ -688,7 +687,7 @@ def __init__(self, domain, range=None, pad_mode='constant', pad_const=0):
                              ''.format(pad_mode_in))
         if pad_mode in ('order1', 'order1_adjoint',
                         'order2', 'order2_adjoint'):
-            # TODO: Add these pad modes
+            # TODO: add these pad modes
             raise ValueError('`pad_mode` {} not implemented for Laplacian.'
                              ''.format(pad_mode_in))
 

odl/discr/discr_ops.py

@@ -18,8 +18,7 @@
 from odl.discr.partition import uniform_partition
 from odl.operator import Operator
 from odl.space import tensor_space
-from odl.util import (
-    normalized_scalar_param_list, resize_array, safe_int_conv)
+from odl.util import normalized_scalar_param_list, resize_array, safe_int_conv
 from odl.util.numerics import _SUPPORTED_RESIZE_PAD_MODES
 
 __all__ = ('Resampling', 'ResizingOperator')

odl/discr/partition.py

@@ -1,4 +1,4 @@
-# Copyright 2014-2018 The ODL contributors
+# Copyright 2014-2020 The ODL contributors
 #
 # This file is part of ODL.
 #
@@ -14,17 +14,18 @@
 of partitions of intervals.
 """
 
-from __future__ import print_function, division, absolute_import
+from __future__ import absolute_import, division, print_function
+
 from builtins import object
+
 import numpy as np
 
 from odl.discr.grid import RectGrid, uniform_grid_fromintv
 from odl.set import IntervalProd
 from odl.util import (
-    normalized_index_expression, normalized_nodes_on_bdry,
-    normalized_scalar_param_list, safe_int_conv,
-    signature_string, indent, array_str, npy_printoptions)
-
+    array_str, indent, normalized_index_expression, normalized_nodes_on_bdry,
+    normalized_scalar_param_list, npy_printoptions, safe_int_conv,
+    signature_string)
 
 __all__ = ('RectPartition', 'uniform_partition_fromintv',
            'uniform_partition_fromgrid', 'uniform_partition',
@@ -1295,8 +1296,11 @@ def nonuniform_partition(*coord_vecs, **kwargs):
 
     Parameters
     ----------
-    coord_vecs1, ... coord_vecsN : `array-like`
+    coord_vec1, ... coord_vecN : `array-like`
         Arrays of coordinates of the mid-points of the partition cells.
+
+    Other Parameters
+    ----------------
     min_pt, max_pt : float or sequence of floats, optional
         Vectors defining the lower/upper limits of the intervals in an
         `IntervalProd` (a rectangular box). ``None`` entries mean

odl/solvers/functional/default_functionals.py

@@ -1104,16 +1104,14 @@ def __init__(self, space, prior=None):
 
         Examples
         --------
-
-        Test that KullbackLeibler(x,x) = 0
+        Test that KullbackLeibler(x, x) = 0
 
         >>> space = odl.rn(3)
         >>> prior = 3 * space.one()
         >>> func = odl.solvers.KullbackLeibler(space, prior=prior)
         >>> func(prior)
         0.0
 
-
         Test that zeros in the prior are handled correctly
 
         >>> prior = space.zero()
@@ -1152,7 +1150,10 @@ def _call(self, x):
                 tmp = self.domain.ufuncs.log(x)
                 tmp += 1
                 tmp -= x
-                res = -self.domain.inner(tmp, self.domain.one())
+                res = self.domain.inner(tmp, self.domain.one())
+                if res != 0:
+                    # Avoid -0.0
+                    res = -res
             else:
                 # < x - g + xlogy(g, g/x), one >
                 g = self.prior
@@ -1164,7 +1165,7 @@ def _call(self, x):
                     tmp = scipy.special.xlogy(g, g / x)
                 tmp -= g
                 tmp += x
-                res = -self.domain.inner(tmp, self.domain.one())
+                res = self.domain.inner(tmp, self.domain.one())
 
         if not np.isfinite(res):
             # In this case, some element was less than or equal to zero

odl/solvers/nonsmooth/douglas_rachford.py

@@ -191,9 +191,6 @@ def douglas_rachford_pd(x, f, g, L, niter, tau=None, sigma=None,
         else:
             dom.assign(z1, x)
 
-        f.proximal(tau)(z1, out=p1)
-        # End of z1 as temporary
-
         f.proximal(tau)(z1, out=p1)
         # Now p1 = prox[tau*f](x - tau/2 * sum(Li^* vi))
         # Temporary z1 is no longer needed

odl/space/npy_tensors.py

@@ -12,6 +12,7 @@
 from future.utils import native
 
 import ctypes
+import inspect
 from builtins import object
 from functools import partial
 
@@ -20,10 +21,11 @@
 from odl.set.sets import ComplexNumbers, RealNumbers
 from odl.space.base_tensors import TensorSpace
 from odl.util import (
-    dtype_str, getargspec, is_numeric_dtype, is_real_dtype, signature_string)
+    dtype_str, is_numeric_dtype, is_real_dtype, signature_string)
 
 __all__ = ('NumpyTensorSpace',)
 
+getargspec = getattr(inspect, "getfullargspec", inspect.getargspec)
 _BLAS_DTYPES = (np.dtype('float32'), np.dtype('float64'),
                 np.dtype('complex64'), np.dtype('complex128'))
 
@@ -639,6 +641,7 @@ class NumpyTensorSpaceReduce(object):
             def __getattr__(self, name):
                 """Return ``self.name``."""
                 attr = getattr(np, name, None)
+                attr = getattr(attr, "_implementation", attr)  # for numpy >= 1.16
                 try:
                     spec = getargspec(attr)
                 except (ValueError, TypeError):

odl/space/pspace.py

@@ -21,11 +21,7 @@
 
 __all__ = ('ProductSpace',)
 
-
-try:
-    getargspec = inspect.getfullargspec
-except AttributeError:
-    getargspec = inspect.getargspec
+getargspec = getattr(inspect, "getfullargspec", inspect.getargspec)
 
 
 class ProductSpace(LinearSpace):

odl/test/operator/operator_test.py

@@ -23,10 +23,7 @@
 from odl.util.testutils import (
     all_almost_equal, noise_element, noise_elements, simple_fixture)
 
-try:
-    getargspec = inspect.getfullargspec
-except AttributeError:
-    getargspec = inspect.getargspec
+getargspec = getattr(inspect, "getfullargspec", inspect.getargspec)
 
 
 # --- Fixtures --- #