ENH: Add suppress_warnings

Author: larsoner

nibabel/testing/__init__.py

@@ -10,6 +10,7 @@
 from os.path import dirname, abspath, join as pjoin
 
 import numpy as np
+from warnings import catch_warnings, simplefilter
 
 # set path to example data
 data_path = abspath(pjoin(dirname(__file__), '..', 'tests', 'data'))
@@ -49,3 +50,12 @@ def assert_allclose_safely(a, b, match_nans=True):
     if b.dtype.kind in 'ui':
         b = b.astype(float)
     assert_true(np.allclose(a, b))
+
+
+class suppress_warnings(catch_warnings):
+    """ Version of ``catch_warnings`` class that suppresses warnings
+    """
+    def __enter__(self):
+        res = super(suppress_warnings, self).__enter__()
+        simplefilter('ignore')
+        return res

nibabel/tests/test_analyze.py

@@ -17,7 +17,6 @@
 import logging
 import pickle
 import itertools
-import warnings
 
 import numpy as np
 
@@ -36,7 +35,8 @@
                            assert_array_almost_equal)
 
 from ..testing import (assert_equal, assert_not_equal, assert_true,
-                       assert_false, assert_raises, data_path)
+                       assert_false, assert_raises, data_path,
+                       suppress_warnings)
 
 from .test_wrapstruct import _TestLabeledWrapStruct
 from . import test_spatialimages as tsi
@@ -99,7 +99,7 @@ def test_empty(self):
 
     def _set_something_into_hdr(self, hdr):
         # Called from test_bytes test method.  Specific to the header data type
-        with warnings.catch_warnings(record=True):
+        with suppress_warnings():
             hdr.set_data_shape((1, 2, 3))
 
     def test_checks(self):
@@ -109,7 +109,7 @@ def test_checks(self):
         assert_equal(self._dxer(hdr_t), '')
         hdr = hdr_t.copy()
         hdr['sizeof_hdr'] = 1
-        with warnings.catch_warnings(record=True):
+        with suppress_warnings():
             assert_equal(self._dxer(hdr), 'sizeof_hdr should be ' +
                          str(self.sizeof_hdr))
         hdr = hdr_t.copy()
@@ -129,7 +129,7 @@ def test_log_checks(self):
         HC = self.header_class
         # magic
         hdr = HC()
-        with warnings.catch_warnings(record=True):
+        with suppress_warnings():
             hdr['sizeof_hdr'] = 350 # severity 30
             fhdr, message, raiser = self.log_chk(hdr, 30)
         assert_equal(fhdr['sizeof_hdr'], self.sizeof_hdr)
@@ -144,7 +144,7 @@ def test_log_checks(self):
         # datatype not recognized
         hdr = HC()
         hdr['datatype'] = -1 # severity 40
-        with warnings.catch_warnings(record=True):
+        with suppress_warnings():
             fhdr, message, raiser = self.log_chk(hdr, 40)
         assert_equal(message, 'data code -1 not recognized; '
                            'not attempting fix')

nibabel/tests/test_arraywriters.py

@@ -8,7 +8,6 @@
 from platform import python_compiler, machine
 from distutils.version import LooseVersion
 import itertools
-import warnings
 import numpy as np
 
 from ..externals.six import BytesIO
@@ -28,7 +27,7 @@
                         assert_equal, assert_not_equal,
                         assert_raises)
 
-from ..testing import assert_allclose_safely
+from ..testing import assert_allclose_safely, suppress_warnings
 from ..checkwarns import ErrorWarnings
 
 
@@ -135,7 +134,7 @@ def test_no_scaling():
         kwargs = (dict(check_scaling=False) if awt == ArrayWriter
                   else dict(calc_scale=False))
         aw = awt(arr, out_dtype, **kwargs)
-        with warnings.catch_warnings(record=True):  # cast to real from cplx
+        with suppress_warnings():  # cast to real from cplx
             back_arr = round_trip(aw)
             exp_back = arr.astype(float)
         if out_dtype in IUINT_TYPES:
@@ -643,7 +642,7 @@ def test_float_int_min_max():
             continue
         for out_dt in IUINT_TYPES:
             try:
-                with warnings.catch_warnings(record=True):  # overflow
+                with suppress_warnings():  # overflow
                     aw = SlopeInterArrayWriter(arr, out_dt)
             except ScalingError:
                 continue

nibabel/tests/test_casting.py

@@ -3,12 +3,12 @@
 import os
 
 from platform import machine
-import warnings
 import numpy as np
 
 from ..casting import (float_to_int, shared_range, CastingError, int_to_float,
                        as_int, int_abs, floor_log2, able_int_type, best_float,
                        ulp, longdouble_precision_improved)
+from ..testing import suppress_warnings
 
 from numpy.testing import (assert_array_almost_equal, assert_array_equal)
 
@@ -23,7 +23,7 @@ def test_shared_range():
             # (if this system generates that) or something smaller (because of
             # overflow)
             mn, mx = shared_range(ft, it)
-            with warnings.catch_warnings(record=True):
+            with suppress_warnings():
                 ovs = ft(mx) + np.arange(2048, dtype=ft)
             # Float16 can overflow to inf
             bit_bigger = ovs[np.isfinite(ovs)].astype(it)
@@ -52,7 +52,7 @@ def test_shared_range():
                 assert_equal(mn, 0)
                 continue
             # And something larger for the minimum
-            with warnings.catch_warnings(record=True):  # overflow
+            with suppress_warnings():  # overflow
                 ovs = ft(mn) - np.arange(2048, dtype=ft)
             # Float16 can overflow to inf
             bit_smaller = ovs[np.isfinite(ovs)].astype(it)

nibabel/tests/test_ecat.py

@@ -16,13 +16,12 @@
 from ..ecat import EcatHeader, EcatMlist, EcatSubHeader, EcatImage
 
 from unittest import TestCase
-import warnings
 from nose.tools import (assert_true, assert_false, assert_equal,
                         assert_not_equal, assert_raises)
 
 from numpy.testing import assert_array_equal, assert_array_almost_equal
 
-from ..testing import data_path
+from ..testing import data_path, suppress_warnings
 from ..tmpdirs import InTemporaryDirectory
 
 from .test_wrapstruct import _TestWrapStructBase
@@ -112,7 +111,7 @@ def test_mlist(self):
                                             6.01670000e+04,   1.00000000e+00],
                                          [  1.68427580e+07,   6.01680000e+04,
                                             7.22000000e+04,   1.00000000e+00]])
-        with warnings.catch_warnings(record=True):  # STORED order
+        with suppress_warnings():  # STORED order
             assert_true(badordermlist.get_frame_order()[0][0] == 1)
 
     def test_mlist_errors(self):
@@ -132,19 +131,19 @@ def test_mlist_errors(self):
                                     6.01670000e+04,   1.00000000e+00],
                                  [  1.68427580e+07,   6.01680000e+04,
                                     7.22000000e+04,   1.00000000e+00]])        
-        with warnings.catch_warnings(record=True):  # STORED order
+        with suppress_warnings():  # STORED order
             series_framenumbers = mlist.get_series_framenumbers()
         # first frame stored was actually 2nd frame acquired
         assert_true(series_framenumbers[0] == 2)
         order = [series_framenumbers[x] for x in sorted(series_framenumbers)]
         # true series order is [2,1,3,4,5,6], note counting starts at 1
         assert_true(order == [2, 1, 3, 4, 5, 6])
         mlist._mlist[0,0] = 0
-        with warnings.catch_warnings(record=True):
+        with suppress_warnings():
             frames_order = mlist.get_frame_order()
         neworder =[frames_order[x][0] for x in sorted(frames_order)] 
         assert_true(neworder == [1, 2, 3, 4, 5])
-        with warnings.catch_warnings(record=True):
+        with suppress_warnings():
             assert_raises(IOError,
                           mlist.get_series_framenumbers)
 

nibabel/tests/test_floating.py

@@ -5,12 +5,12 @@
 PY2 = sys.version_info[0] < 3
 
 import numpy as np
-import warnings
 
 from ..casting import (floor_exact, ceil_exact, as_int, FloatingError,
                        int_to_float, floor_log2, type_info, _check_nmant,
                        _check_maxexp, ok_floats, on_powerpc, have_binary128,
                        longdouble_precision_improved)
+from ..testing import suppress_warnings
 
 from nose import SkipTest
 from nose.tools import assert_equal, assert_raises, assert_true, assert_false
@@ -93,10 +93,10 @@ def test_check_nmant_nexp():
         assert_true(_check_nmant(t, nmant))
         assert_false(_check_nmant(t, nmant - 1))
         assert_false(_check_nmant(t, nmant + 1))
-        with warnings.catch_warnings(record=True):  # overflow
+        with suppress_warnings():  # overflow
             assert_true(_check_maxexp(t, maxexp))
         assert_false(_check_maxexp(t, maxexp - 1))
-        with warnings.catch_warnings(record=True):
+        with suppress_warnings():
             assert_false(_check_maxexp(t, maxexp + 1))
     # Check against type_info
     for t in ok_floats():

nibabel/tests/test_nifti1.py

@@ -32,7 +32,7 @@
 from nose.tools import (assert_true, assert_false, assert_equal,
                         assert_raises)
 
-from ..testing import data_path
+from ..testing import data_path, suppress_warnings
 
 from . import test_analyze as tana
 from . import test_spm99analyze as tspm
@@ -256,7 +256,7 @@ def test_freesurfer_hack(self):
         hdr.set_data_shape((too_big-1, 1, 1))
         assert_equal(hdr.get_data_shape(), (too_big-1, 1, 1))
         # The freesurfer case
-        with warnings.catch_warnings(record=True):
+        with suppress_warnings():
             hdr.set_data_shape((too_big, 1, 1))
         assert_equal(hdr.get_data_shape(), (too_big, 1, 1))
         assert_array_equal(hdr['dim'][:4], [3, -1, 1, 1])
@@ -271,7 +271,7 @@ def test_freesurfer_hack(self):
         assert_raises(HeaderDataError, hdr.set_data_shape, (1, 1, too_big))
         # Outside range of glmin raises error
         far_too_big = int(np.iinfo(glmin).max) + 1
-        with warnings.catch_warnings(record=True):
+        with suppress_warnings():
             hdr.set_data_shape((far_too_big-1, 1, 1))
         assert_equal(hdr.get_data_shape(), (far_too_big-1, 1, 1))
         assert_raises(HeaderDataError, hdr.set_data_shape, (far_too_big,1,1))
@@ -282,7 +282,7 @@ def test_freesurfer_hack(self):
         # Lists or tuples or arrays will work for setting shape
         for shape in ((too_big-1, 1, 1), (too_big, 1, 1)):
             for constructor in (list, tuple, np.array):
-                with warnings.catch_warnings(record=True):
+                with suppress_warnings():
                     hdr.set_data_shape(constructor(shape))
                 assert_equal(hdr.get_data_shape(), shape)
 

nibabel/tests/test_scaling.py

@@ -10,12 +10,12 @@
 from __future__ import division, print_function, absolute_import
 
 import numpy as np
-import warnings
 
 from ..externals.six import BytesIO
 from ..volumeutils import (calculate_scale, scale_min_max, finite_range,
                            apply_read_scaling, array_to_file, array_from_file)
 from ..casting import type_info
+from ..testing import suppress_warnings
 
 from numpy.testing import (assert_array_almost_equal, assert_array_equal)
 
@@ -242,7 +242,7 @@ def test_scaling_in_abstract():
                                 ):
         for in_type in np.sctypes[category0]:
             for out_type in np.sctypes[category1]:
-                with warnings.catch_warnings(record=True):  # overflow
+                with suppress_warnings():  # overflow
                     check_int_a2f(in_type, out_type)
 
 

nibabel/tests/test_spatialimages.py

@@ -10,7 +10,6 @@
 
 """
 from ..externals.six import BytesIO
-import warnings
 import numpy as np
 
 from ..spatialimages import (Header, SpatialImage, HeaderDataError,
@@ -24,6 +23,7 @@
 from numpy.testing import assert_array_equal, assert_array_almost_equal
 
 from .test_helpers import bytesio_round_trip
+from ..testing import suppress_warnings
 
 
 def test_header_init():
@@ -292,7 +292,7 @@ def test_get_shape(self):
         # Assumes all possible images support int16
         # See https://github.com/nipy/nibabel/issues/58
         img = img_klass(np.arange(1, dtype=np.int16), np.eye(4))
-        with warnings.catch_warnings(record=True):
+        with suppress_warnings():
             assert_equal(img.get_shape(), (1,))
             img = img_klass(np.zeros((2,3,4), np.int16), np.eye(4))
             assert_equal(img.get_shape(), (2,3,4))

nibabel/tests/test_spm99analyze.py

@@ -9,7 +9,6 @@
 
 import numpy as np
 import itertools
-import warnings
 
 from ..externals.six import BytesIO
 
@@ -33,7 +32,7 @@
 
 from nose.tools import assert_true, assert_false, assert_equal, assert_raises
 
-from ..testing import assert_allclose_safely
+from ..testing import assert_allclose_safely, suppress_warnings
 
 from . import test_analyze
 from .test_helpers import (bytesio_round_trip, bytesio_filemap, bz2_mio_error)
@@ -331,7 +330,7 @@ def test_no_scaling(self):
             img.set_data_dtype(out_dtype)
             img.header.set_slope_inter(slope, inter)
             rt_img = bytesio_round_trip(img)
-            with warnings.catch_warnings(record=True):  # invalid mult
+            with suppress_warnings():  # invalid mult
                 back_arr = rt_img.get_data()
             exp_back = arr.copy()
             if in_dtype not in COMPLEX_TYPES:
@@ -343,7 +342,7 @@ def test_no_scaling(self):
             else:
                 exp_back = exp_back.astype(out_dtype)
             # Allow for small differences in large numbers
-            with warnings.catch_warnings(record=True):  # invalid value
+            with suppress_warnings():  # invalid value
                 assert_allclose_safely(back_arr,
                                        exp_back * slope + inter)