Merge remote-tracking branch 'upstream/master' into rel/2.5.0

effigies · effigies · commit d1bd90ea4552 · 2019-08-01T20:28:00.000-04:00
diff --git a/.gitmodules b/.gitmodules
@@ -6,7 +6,7 @@
 	url = git://github.com/matthew-brett/nitest-minc2.git
 [submodule "nipy-ecattest"]
 	path = nibabel-data/nipy-ecattest
-	url = https://github.com/freec84/nipy-ecattest
+	url = https://github.com/effigies/nipy-ecattest
 [submodule "nibabel-data/nitest-freesurfer"]
 	path = nibabel-data/nitest-freesurfer
 	url = https://bitbucket.org/nipy/nitest-freesurfer.git
diff --git a/nibabel-data/nipy-ecattest b/nibabel-data/nipy-ecattest
@@ -1 +1 @@
-Subproject commit 12c9ee6d18d50235e3453897a4be60c19bf126c0
+Subproject commit 9a0a592057bc16894c20c77b03ea1ebb5f8ca8f9
diff --git a/nibabel/__init__.py b/nibabel/__init__.py
@@ -35,16 +35,27 @@
 For more detailed information see the :ref:`manual`.
 """
 
-
-def setup_test():
-    """ Set numpy print options to "legacy" for new versions of numpy
-
-    If imported into a file, nosetest will run this before any doctests.
-    """
-    import numpy
+# Package-wide test setup and teardown
+_test_states = {
+    # Numpy changed print options in 1.14; we can update docstrings and remove
+    # these when our minimum for building docs exceeds that
+    'legacy_printopt': None,
+    }
+
+def setup_package():
+    """ Set numpy print style to legacy="1.13" for newer versions of numpy """
+    import numpy as np
     from distutils.version import LooseVersion
-    if LooseVersion(numpy.__version__) >= LooseVersion('1.14'):
-        numpy.set_printoptions(legacy="1.13")
+    if LooseVersion(np.__version__) >= LooseVersion('1.14'):
+        if _test_states.get('legacy_printopt') is None:
+            _test_states['legacy_printopt'] = np.get_printoptions().get('legacy')
+        np.set_printoptions(legacy="1.13")
+
+def teardown_package():
+    """ Reset print options when tests finish """
+    import numpy as np
+    if _test_states.get('legacy_printopt') is not None:
+        np.set_printoptions(legacy=_test_states.pop('legacy_printopt'))
 
 
 # module imports
diff --git a/nibabel/affines.py b/nibabel/affines.py
@@ -6,7 +6,6 @@
 import numpy as np
 
 from six.moves import reduce
-from . import setup_test  # noqa
 
 
 class AffineError(ValueError):
diff --git a/nibabel/brikhead.py b/nibabel/brikhead.py
@@ -295,8 +295,8 @@ def __init__(self, info):
         --------
         >>> fname = os.path.join(datadir, 'example4d+orig.HEAD')
         >>> header = AFNIHeader(parse_AFNI_header(fname))
-        >>> header.get_data_dtype()
-        dtype('int16')
+        >>> header.get_data_dtype().str
+        '<i2'
         >>> header.get_zooms()
         (3.0, 3.0, 3.0, 3.0)
         >>> header.get_data_shape()
diff --git a/nibabel/casting.py b/nibabel/casting.py
@@ -8,7 +8,6 @@
 from platform import processor, machine
 
 import numpy as np
-from . import setup_test  # noqa
 
 
 class CastingError(Exception):
diff --git a/nibabel/ecat.py b/nibabel/ecat.py
@@ -559,9 +559,9 @@ def _check_affines(self):
         affs = [self.get_frame_affine(i) for i in range(nframes)]
         if affs:
             i = iter(affs)
-            first = i.next()
+            first = next(i)
             for item in i:
-                if not np.all(first == item):
+                if not np.allclose(first, item):
                     return False
         return True
 
@@ -760,7 +760,7 @@ def __init__(self, dataobj, affine, header,
 
         Parameters
         ----------
-        dataabj : array-like
+        dataobj : array-like
             image data
         affine : None or (4,4) array-like
             homogeneous affine giving relationship between voxel coords and
@@ -811,6 +811,7 @@ def __init__(self, dataobj, affine, header,
             file_map = self.__class__.make_file_map()
         self.file_map = file_map
         self._data_cache = None
+        self._fdata_cache = None
 
     @property
     def affine(self):
diff --git a/nibabel/nicom/dwiparams.py b/nibabel/nicom/dwiparams.py
@@ -21,7 +21,6 @@
 '''
 import numpy as np
 import numpy.linalg as npl
-from .. import setup_test as setup_module  # noqa
 
 
 def B2q(B, tol=None):
diff --git a/nibabel/nifti1.py b/nibabel/nifti1.py
@@ -28,7 +28,6 @@
 from .spm99analyze import SpmAnalyzeHeader
 from .casting import have_binary128
 from .pydicom_compat import have_dicom, pydicom as pdcm
-from . import setup_test  # noqa
 
 # nifti1 flat header definition for Analyze-like first 348 bytes
 # first number in comments indicates offset in file header in bytes
diff --git a/nibabel/quaternions.py b/nibabel/quaternions.py
@@ -27,7 +27,6 @@
 
 import math
 import numpy as np
-from . import setup_test  # noqa
 
 MAX_FLOAT = np.maximum_sctype(np.float)
 FLOAT_EPS = np.finfo(np.float).eps
diff --git a/nibabel/streamlines/trk.py b/nibabel/streamlines/trk.py
@@ -13,7 +13,7 @@
 
 from nibabel.openers import Opener
 from nibabel.py3k import asstr
-from nibabel.volumeutils import (native_code, swapped_code)
+from nibabel.volumeutils import (native_code, swapped_code, endian_codes)
 from nibabel.orientations import (aff2axcodes, axcodes2ornt)
 
 from .array_sequence import create_arraysequences_from_generator
@@ -266,10 +266,14 @@ def is_correct_format(cls, fileobj):
             return magic_number == cls.MAGIC_NUMBER
 
     @classmethod
-    def _default_structarr(cls):
+    def _default_structarr(cls, endianness=None):
         """ Return an empty compliant TRK header as numpy structured array
         """
-        st_arr = np.zeros((), dtype=header_2_dtype)
+        dt = header_2_dtype
+        if endianness is not None:
+            endianness = endian_codes[endianness]
+            dt = dt.newbyteorder(endianness)
+        st_arr = np.zeros((), dtype=dt)
 
         # Default values
         st_arr[Field.MAGIC_NUMBER] = cls.MAGIC_NUMBER
@@ -283,10 +287,10 @@ def _default_structarr(cls):
         return st_arr
 
     @classmethod
-    def create_empty_header(cls):
+    def create_empty_header(cls, endianness=None):
         """ Return an empty compliant TRK header as dict
         """
-        st_arr = cls._default_structarr()
+        st_arr = cls._default_structarr(endianness)
         return dict(zip(st_arr.dtype.names, st_arr.tolist()))
 
     @classmethod
@@ -396,7 +400,7 @@ def save(self, fileobj):
             of the TRK header data).
         """
         # Enforce little-endian byte order for header
-        header = self._default_structarr().newbyteorder('<')
+        header = self._default_structarr(endianness='little')
 
         # Override hdr's fields by those contained in `header`.
         for k, v in self.header.items():
diff --git a/nibabel/tests/test_ecat_data.py b/nibabel/tests/test_ecat_data.py
@@ -37,7 +37,7 @@ class TestNegatives(object):
         # unit: 1/cm
     )
 
-    @needs_nibabel_data('nitest-minc2')
+    @needs_nibabel_data('nipy-ecattest')
     def test_load(self):
         # Check highest level load of minc works
         img = self.opener(self.example_params['fname'])
@@ -50,3 +50,15 @@ def test_load(self):
         assert_almost_equal(data.min(), self.example_params['min'], 4)
         assert_almost_equal(data.max(), self.example_params['max'], 4)
         assert_almost_equal(data.mean(), self.example_params['mean'], 4)
+
+
+class TestMultiframe(TestNegatives):
+    example_params = dict(
+        fname=os.path.join(ECAT_TEST_PATH, 'ECAT7_testcase_multiframe.v'),
+        shape=(256, 256, 207, 3),
+        type=np.int16,
+        # Zeroed out image
+        min=0.0,
+        max=29170.67905,
+        mean=121.454,
+    )
