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FIX: Python 3 compatibility issue while loading multiframe ECAT files #777

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Merged
merged 3 commits into from
Aug 2, 2019
Merged

FIX: Python 3 compatibility issue while loading multiframe ECAT files #777

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1a0d949
TEST: Add multiframe ECAT file for testing
effigies Jul 27, 2019
244bc37
FIX: Minor ECAT cleanups
effigies Jul 28, 2019
8b00fd0
PY3: Use next function on iterator while checking ECAT affines
effigies Jul 30, 2019
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2 changes: 1 addition & 1 deletion .gitmodules
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
2 changes: 1 addition & 1 deletion nibabel-data/nipy-ecattest
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Submodule nipy-ecattest updated 1 files
+ − ECAT7_testcase_multiframe.v
7 changes: 4 additions & 3 deletions nibabel/ecat.py
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Expand Up @@ -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

Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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):
Expand Down
14 changes: 13 additions & 1 deletion nibabel/tests/test_ecat_data.py
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Expand Up @@ -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'])
Expand All @@ -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,
)