Merge pull request #254 from Eric89GXL/clean-tests

MRG: Cleaner tests

In the process of working on #253 I was a little bit surprised by the number of warnings during testing. This cleans that up, and fixes a couple minor errors along the way.

Author: matthew-brett

doc/source/coordinate_systems.rst

@@ -55,7 +55,7 @@ the array.
     >>> slice_1 = epi_img_data[:, 30, :]
     >>> slice_2 = epi_img_data[:, :, 16]
     >>> show_slices([slice_0, slice_1, slice_2])
-    >>> plt.suptitle("Center slices for EPI image")
+    >>> plt.suptitle("Center slices for EPI image")  # doctest: +SKIP
 
 We collected an anatomical image in the same session.  We can load that image
 and look at slices in the three axes:
@@ -77,7 +77,7 @@ and look at slices in the three axes:
     >>> show_slices([anat_img_data[28, :, :],
     ...              anat_img_data[:, 33, :],
     ...              anat_img_data[:, :, 28]])
-    >>> plt.suptitle("Center slices for anatomical image")
+    >>> plt.suptitle("Center slices for anatomical image")  # doctest: +SKIP
 
 As is usually the case, we had a different field of view for the anatomical
 scan, and so the anatomical image has a different shape, size, and orientation

doc/source/neuro_radio_conventions.rst

@@ -95,7 +95,7 @@ Here we are showing the middle slice of :download:`an image
     >>> img_data = img.get_data()
     >>> a_slice = img_data[:, :, 28]
     >>> # Need transpose to put first axis left-right, second bottom-top
-    >>> plt.imshow(a_slice.T, cmap="gray", origin="lower")
+    >>> plt.imshow(a_slice.T, cmap="gray", origin="lower")  # doctest: +SKIP
 
 This slice does have the voxels from the right of isocenter towards the right
 of the screen, neurology style.

nibabel/imageglobals.py

@@ -30,6 +30,7 @@
 logger = logging.getLogger('nibabel.global')
 logger.addHandler(logging.StreamHandler())
 
+
 class ErrorLevel(object):
     """ Context manager to set log error level
     """
@@ -45,3 +46,15 @@ def __exit__(self, exc, value, tb):
         global error_level
         error_level = self._original_level
         return False
+
+
+class LoggingOutputSuppressor(object):
+    """Context manager to prevent global logger from printing"""
+    def __enter__(self):
+        self.orig_handlers = logger.handlers
+        for handler in self.orig_handlers:
+            logger.removeHandler(handler)
+
+    def __exit__(self, exc, value, tb):
+        for handler in self.orig_handlers:
+            logger.addHandler(handler)

nibabel/nicom/dicomwrappers.py

@@ -169,7 +169,7 @@ def rotation_matrix(self):
         """
         iop = self.image_orient_patient
         s_norm = self.slice_normal
-        if None in (iop, s_norm):
+        if iop is None or s_norm is None:
             return None
         R = np.eye(3)
         # np.fliplr(iop) gives matrix F in
@@ -235,7 +235,7 @@ def slice_indicator(self):
         """
         ipp = self.image_position
         s_norm = self.slice_normal
-        if None in (ipp, s_norm):
+        if ipp is None or s_norm is None:
             return None
         return np.inner(ipp, s_norm)
 
@@ -304,7 +304,7 @@ def get_affine(self):
         # column, slice)
         vox = self.voxel_sizes
         ipp = self.image_position
-        if None in (orient, vox, ipp):
+        if any(p is None for p in (orient, vox, ipp)):
             raise WrapperError('Not enough information for affine')
         aff = np.eye(4)
         aff[:3, :3] = orient * np.array(vox)
@@ -786,7 +786,7 @@ def image_position(self):
         md_rows, md_cols = (self.get('Rows'), self.get('Columns'))
         iop = self.image_orient_patient
         pix_spacing = self.get('PixelSpacing')
-        if None in (ipp, md_rows, md_cols, iop, pix_spacing):
+        if any(x is None for x in (ipp, md_rows, md_cols, iop, pix_spacing)):
             return None
         # PixelSpacing values are python Decimal in pydicom 0.9.7
         pix_spacing = np.array(list(map(float, pix_spacing)))
@@ -881,8 +881,8 @@ def none_or_close(val1, val2, rtol=1e-5, atol=1e-6):
     >>> none_or_close([0,1], [0,2])
     False
     """
-    if (val1, val2) == (None, None):
+    if val1 is None and val2 is None:
         return True
-    if None in (val1, val2):
+    if val1 is None or val2 is None:
         return False
     return np.allclose(val1, val2, rtol, atol)

nibabel/nifti1.py

@@ -1061,7 +1061,7 @@ def set_slope_inter(self, slope, inter=None):
             raise HeaderDataError('Slope cannot be 0 or infinite')
         if inter in (np.inf, -np.inf):
             raise HeaderDataError('Intercept cannot be infinite')
-        if np.diff(np.isnan([slope, inter])):
+        if np.isnan(slope) ^ np.isnan(inter):
             raise HeaderDataError('None or both of slope, inter should be nan')
         self._structarr['scl_slope'] = slope
         self._structarr['scl_inter'] = inter

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

@@ -35,7 +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
@@ -45,6 +46,7 @@
 
 PIXDIM0_MSG = 'pixdim[1,2,3] should be non-zero; setting 0 dims to 1'
 
+
 class TestAnalyzeHeader(_TestLabeledWrapStruct):
     header_class = AnalyzeHeader
     example_file = header_file
@@ -97,7 +99,8 @@ def test_empty(self):
 
     def _set_something_into_hdr(self, hdr):
         # Called from test_bytes test method.  Specific to the header data type
-        hdr.set_data_shape((1, 2, 3))
+        with suppress_warnings():
+            hdr.set_data_shape((1, 2, 3))
 
     def test_checks(self):
         # Test header checks
@@ -106,8 +109,9 @@ def test_checks(self):
         assert_equal(self._dxer(hdr_t), '')
         hdr = hdr_t.copy()
         hdr['sizeof_hdr'] = 1
-        assert_equal(self._dxer(hdr), 'sizeof_hdr should be ' +
-                     str(self.sizeof_hdr))
+        with suppress_warnings():
+            assert_equal(self._dxer(hdr), 'sizeof_hdr should be ' +
+                         str(self.sizeof_hdr))
         hdr = hdr_t.copy()
         hdr['datatype'] = 0
         assert_equal(self._dxer(hdr), 'data code 0 not supported\n'
@@ -125,8 +129,9 @@ def test_log_checks(self):
         HC = self.header_class
         # magic
         hdr = HC()
-        hdr['sizeof_hdr'] = 350 # severity 30
-        fhdr, message, raiser = self.log_chk(hdr, 30)
+        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)
         assert_equal(message,
                      'sizeof_hdr should be {0}; set sizeof_hdr to {0}'.format(
@@ -139,15 +144,16 @@ def test_log_checks(self):
         # datatype not recognized
         hdr = HC()
         hdr['datatype'] = -1 # severity 40
-        fhdr, message, raiser = self.log_chk(hdr, 40)
+        with suppress_warnings():
+            fhdr, message, raiser = self.log_chk(hdr, 40)
         assert_equal(message, 'data code -1 not recognized; '
                            'not attempting fix')
         assert_raises(*raiser)
         # datatype not supported
         hdr['datatype'] = 255 # severity 40
         fhdr, message, raiser = self.log_chk(hdr, 40)
         assert_equal(message, 'data code 255 not supported; '
-                           'not attempting fix')
+                     'not attempting fix')
         assert_raises(*raiser)
         # bitpix
         hdr = HC()

nibabel/tests/test_arraywriters.py

@@ -8,7 +8,6 @@
 from platform import python_compiler, machine
 from distutils.version import LooseVersion
 import itertools
-
 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
 
 
@@ -135,8 +134,9 @@ def test_no_scaling():
         kwargs = (dict(check_scaling=False) if awt == ArrayWriter
                   else dict(calc_scale=False))
         aw = awt(arr, out_dtype, **kwargs)
-        back_arr = round_trip(aw)
-        exp_back = arr.astype(float)
+        with suppress_warnings():  # cast to real from cplx
+            back_arr = round_trip(aw)
+            exp_back = arr.astype(float)
         if out_dtype in IUINT_TYPES:
             exp_back = np.round(exp_back)
             if hasattr(aw, 'slope') and in_dtype in FLOAT_TYPES:
@@ -642,7 +642,8 @@ def test_float_int_min_max():
             continue
         for out_dt in IUINT_TYPES:
             try:
-                aw = SlopeInterArrayWriter(arr, out_dt)
+                with suppress_warnings():  # overflow
+                    aw = SlopeInterArrayWriter(arr, out_dt)
             except ScalingError:
                 continue
             arr_back_sc = round_trip(aw)

nibabel/tests/test_casting.py

@@ -3,12 +3,12 @@
 import os
 
 from platform import machine
-
 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 +23,8 @@ def test_shared_range():
             # (if this system generates that) or something smaller (because of
             # overflow)
             mn, mx = shared_range(ft, it)
-            ovs = ft(mx) + np.arange(2048, dtype=ft)
+            with suppress_warnings():
+                ovs = ft(mx) + np.arange(2048, dtype=ft)
             # Float16 can overflow to inf
             bit_bigger = ovs[np.isfinite(ovs)].astype(it)
             casted_mx = ft(mx).astype(it)
@@ -51,7 +52,8 @@ def test_shared_range():
                 assert_equal(mn, 0)
                 continue
             # And something larger for the minimum
-            ovs = ft(mn) - np.arange(2048, dtype=ft)
+            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)
             casted_mn = ft(mn).astype(it)

nibabel/tests/test_ecat.py

@@ -16,20 +16,20 @@
 from ..ecat import EcatHeader, EcatMlist, EcatSubHeader, EcatImage
 
 from unittest import TestCase
-
 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
 from .test_fileslice import slicer_samples
 
 ecat_file = os.path.join(data_path, 'tinypet.v')
 
+
 class TestEcatHeader(_TestWrapStructBase):
     header_class = EcatHeader
     example_file = ecat_file
@@ -111,7 +111,8 @@ def test_mlist(self):
                                             6.01670000e+04,   1.00000000e+00],
                                          [  1.68427580e+07,   6.01680000e+04,
                                             7.22000000e+04,   1.00000000e+00]])
-        assert_true(badordermlist.get_frame_order()[0][0] == 1)
+        with suppress_warnings():  # STORED order
+            assert_true(badordermlist.get_frame_order()[0][0] == 1)
 
     def test_mlist_errors(self):
         fid = open(self.example_file, 'rb')
@@ -130,18 +131,21 @@ def test_mlist_errors(self):
                                     6.01670000e+04,   1.00000000e+00],
                                  [  1.68427580e+07,   6.01680000e+04,
                                     7.22000000e+04,   1.00000000e+00]])        
-        series_framenumbers = mlist.get_series_framenumbers()
+        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
-        frames_order = mlist.get_frame_order()
+        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])
-        assert_raises(IOError,
-                      mlist.get_series_framenumbers)
+        with suppress_warnings():
+            assert_raises(IOError,
+                          mlist.get_series_framenumbers)
 
 
 
@@ -178,6 +182,7 @@ def test_subheader(self):
         ecat_calib_factor = self.hdr['ecat_calibration_factor']
         assert_equal(ecat_calib_factor, 25007614.0)
 
+
 class TestEcatImage(TestCase):
     image_class = EcatImage
     example_file = ecat_file