8000 ENH: Add get/set_zooms(units='norm') to manipulate zooms in mm/s units by effigies · Pull Request #567 · nipy/nibabel · GitHub
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ENH: Add get/set_zooms(units='norm') to manipulate zooms in mm/s units #567

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ENH: Add get/set_zooms(units='norm') to manipulate zooms in mm/s units #567

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3f3b450
ENH: Add get_norm_zooms for zooms in mm/s units
effigies Oct 24, 2017
d26acfb
ENH: Add get_norm_zooms for MGHHeader
effigies Dec 18, 2017
de9323c
ENH: Add set_norm_zooms
effigies Dec 21, 2017
5c30366
FIX: Various unit issues
effigies Dec 21, 2017
4b86d3e
TEST: Test get/set_norm_zooms
effigies Dec 21, 2017
eb1d8ff
TEST: Fix warnings
effigies Dec 21, 2017
6ba8b66
RF: get_norm_zooms -> get_zooms(units="canonical")
effigies Jan 12, 2018
1357a3b
TEST: Update get_zooms tests
effigies Jan 13, 2018
096da88
FIX: Set default t_code even if no t_zoom
effigies Jan 13, 2018
798fc4e
TEST: Add units specification to tests
effigies Feb 19, 2018
f31aba5
TEST: Add setup/teardown to try to catch warnings properly [WIP]
effigies Feb 19, 2018
27234c3
TEST: Try using clear_and_catch_warnings
effigies Feb 19, 2018
8899bc7
RF: Add units parameter to set_zooms
effigies Mar 12, 2018
da54665
TEST: More complete zoom testing, revert unnecessary change
effigies Mar 12, 2018
1620f31
TEST: Improve warning filters, check set_zooms behavior more thoroughly
effigies Mar 12, 2018
5d96f5c
TEST: Explicitly test non-temporal t_units during set_zooms(units="no…
effigies Mar 12, 2018
233f7f0
TEST: Filter warnings for unmodified superclass tests only
effigies Mar 12, 2018
4babf08
ENH: Add units/raise_unknown to MINC/ECAT get_zooms
effigies Mar 12, 2018
6cd83f7
ENH: Validate units parameter in all get/set_zooms
effigies Mar 13, 2018
94cbd0d
FIX: Correct and simplify NIFTI logic
effigies Mar 14, 2018
cfc5abe
TEST: Clear nifti1 module warnings
effigies Mar 20, 2018
3562921
TEST: Check edge cases
effigies Mar 20, 2018
d9199ca
TEST: Add unit to bad set_zoom call
effigies Mar 20, 2018
98e43a0
TEST: Check get_zooms units arg in MINC/ECAT
effigies Mar 20, 2018
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TEST: Update get_zooms tests
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@effigies
effigies committed Dec 26, 2022
commit 1357a3b8bd231e81f0e9a27ba466e85f53e742e4
39 changes: 24 additions & 15 deletions nibabel/freesurfer/tests/test_mghformat.py
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Original file line number Diff line number Diff line change
Expand Up @@ -351,49 +351,58 @@ def check_dtypes(self, expected, actual):
# MGH requires the actual to be a big endian version of expected
assert expected.newbyteorder('>') == actual

def test_norm_zooms_edge_cases(self):
def test_zooms_edge_cases(self):
img_klass = self.image_class
aff = np.eye(4)
arr = np.arange(120, dtype=np.int16).reshape((2, 3, 4, 5))
img = img_klass(arr, aff)

assert_array_almost_equal(img.header.get_zooms(),
assert_array_almost_equal(img.header.get_zooms(units='raw'),
(1, 1, 1, 0))
assert_array_almost_equal(img.header.get_norm_zooms(),
assert_array_almost_equal(img.header.get_zooms(units='canonical'),
(1, 1, 1, 0))

img.header.set_zooms((1, 1, 1, 2000))
assert_array_almost_equal(img.header.get_zooms(),
assert_array_almost_equal(img.header.get_zooms(units='raw'),
(1, 1, 1, 2000))
assert_array_almost_equal(img.header.get_norm_zooms(),
assert_array_almost_equal(img.header.get_zooms(units='canonical'),
(1, 1, 1, 2))
assert_array_almost_equal(img.header.get_zooms(), (1, 1, 1, 2))

img.header.set_norm_zooms((2, 2, 2, 3))
assert_array_almost_equal(img.header.get_zooms(),
assert_array_almost_equal(img.header.get_zooms(units='raw'),
(2, 2, 2, 3000))
assert_array_almost_equal(img.header.get_norm_zooms(),
assert_array_almost_equal(img.header.get_zooms(units='canonical'),
(2, 2, 2, 3))
assert_array_almost_equal(img.header.get_zooms(), (2, 2, 2, 3))

# It's legal to set zooms for spatial dimensions only
img.header.set_norm_zooms((3, 3, 3))
assert_array_almost_equal(img.header.get_zooms(),
assert_array_almost_equal(img.header.get_zooms(units='raw'),
(3, 3, 3, 3000))
assert_array_almost_equal(img.header.get_norm_zooms(),
assert_array_almost_equal(img.header.get_zooms(units='canonical'),
(3, 3, 3, 3))
assert_array_almost_equal(img.header.get_zooms(), (3, 3, 3, 3))

arr = np.arange(24, dtype=np.int16).reshape((2, 3, 4))
img = img_klass(arr, aff)

assert_array_almost_equal(img.header.get_zooms(), (1, 1, 1))
assert_array_almost_equal(img.header.get_norm_zooms(), (1, 1, 1))
assert_array_almost_equal(img.header.get_zooms(units='raw'),
(1, 1, 1))
assert_array_almost_equal(img.header.get_zooms(units='canonical'),
(1, 1, 1))

img.header.set_zooms((2, 2, 2))
assert_array_almost_equal(img.header.get_zooms(), (2, 2, 2))
assert_array_almost_equal(img.header.get_norm_zooms(), (2, 2, 2))
assert_array_almost_equal(img.header.get_zooms(units='raw'),
(2, 2, 2))
assert_array_almost_equal(img.header.get_zooms(units='canonical'),
(2, 2, 2))

img.header.set_norm_zooms((3, 3, 3))
assert_array_almost_equal(img.header.get_zooms(), (3, 3, 3))
ass 8000 ert_array_almost_equal(img.header.get_norm_zooms(), (3, 3, 3))
assert_array_almost_equal(img.header.get_zooms(units='raw'),
(3, 3, 3))
assert_array_almost_equal(img.header.get_zooms(units='canonical'),
(3, 3, 3))

# Cannot set TR as zoom for 3D image
assert_raises(HeaderDataError, img.header.set_zooms, (4, 4, 4, 5))
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32 changes: 19 additions & 13 deletions nibabel/tests/test_nifti1.py
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Expand Up @@ -1176,7 +1176,7 @@ def test_static_dtype_aliases(self):
img_rt = bytesio_round_trip(img)
assert img_rt.get_data_dtype() == effective_dt

def test_norm_zooms_edge_cases(self):
def test_zooms_edge_cases(self):
img_klass = self.image_class
arr = np.arange(120, dtype=np.int16).reshape((2, 3, 4, 5))
aff = np.eye(4)
Expand All @@ -1186,47 +1186,53 @@ def test_norm_zooms_edge_cases(self):
# Unknown units = 2 warnings
with warnings.catch_warnings(record=True) as warns:
warnings.simplefilter('always')
assert_array_almost_equal(img.header.get_norm_zooms(),
assert_array_almost_equal(img.header.get_zooms(units='canonical'),
(1, 1, 1, 1))
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It's unclear to me why (in Python 2 only) this is failing to raise warnings.

assert_equal(len(warns), 2)
assert_raises(ValueError, img.header.get_norm_zooms, True)
assert_raises(ValueError, img.header.get_zooms,
units='canonical', raise_unknown=True)

img.header.set_xyzt_units(xyz='meter')
with warnings.catch_warnings(record=True) as warns:
warnings.simplefilter('always')
assert_array_almost_equal(img.header.get_norm_zooms(),
assert_array_almost_equal(img.header.get_zooms(units='canonical'),
(1000, 1000, 1000, 1))
assert_equal(len(warns), 1)
assert_raises(ValueError, img.header.get_norm_zooms, True)
assert_raises(ValueError, img.header.get_zooms,
units='canonical', raise_unknown=True)

img.header.set_xyzt_units(xyz='mm', t='sec')
assert_array_almost_equal(img.header.get_norm_zooms(),
assert_array_almost_equal(img.header.get_zooms(units='canonical'),
(1, 1, 1, 1))
img.header.set_xyzt_units(xyz='micron', t='sec')
assert_array_almost_equal(img.header.get_norm_zooms(),
assert_array_almost_equal(img.header.get_zooms(units='canonical'),
(0.001, 0.001, 0.001, 1))

img.header.set_xyzt_units(t='sec')
with warnings.catch_warnings(record=True) as warns:
warnings.simplefilter('always')
assert_array_equal(img.header.get_norm_zooms(), (1, 1, 1, 1))
assert_array_equal(img.header.get_zooms(units='canonical'),
(1, 1, 1, 1))
assert_equal(len(warns), 1)
assert_raises(ValueError, img.header.get_norm_zooms, True)
assert_raises(ValueError, img.header.get_zooms,
units='canonical', raise_unknown=True)

img.header.set_xyzt_units(xyz='mm', t='msec')
assert_array_almost_equal(img.header.get_norm_zooms(),
assert_array_almost_equal(img.header.get_zooms(units='canonical'),
(1, 1, 1, 0.001))

img.header.set_xyzt_units(xyz='mm', t='usec')
assert_array_almost_equal(img.header.get_norm_zooms(),
assert_array_almost_equal(img.header.get_zooms(units='canonical'),
(1, 1, 1, 0.000001))

# Verify `set_norm_zooms` resets units
img.header.set_xyzt_units(xyz='meter', t='usec')
assert_equal(img.header.get_xyzt_units(), ('meter', 'usec'))
img.header.set_norm_zooms((2, 2, 2, 2.5))
assert_array_almost_equal(img.header.get_norm_zooms(), (2, 2, 2, 2.5))
assert_array_almost_equal(img.header.get_zooms(), (2, 2, 2, 2.5))
assert_array_almost_equal(img.header.get_zooms(units='canonical'),
(2, 2, 2, 2.5))
assert_array_almost_equal(img.header.get_zooms(units='raw'),
(2, 2, 2, 2.5))
assert_equal(img.header.get_xyzt_units(), ('mm', 'sec'))


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14 changes: 7 additions & 7 deletions nibabel/tests/test_spatialimages.py
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628C
Original file line number Diff line number Diff line change
Expand Up @@ -528,27 +528,27 @@ def test_slicer(self):
assert (sliced_data == img.get_data()[sliceobj]).all()
assert (sliced_data == img.get_fdata()[sliceobj]).all()

def test_norm_zooms(self):
def test_zooms(self):
''' Should be true for all images '''
img_klass = self.image_class
arr = np.arange(120, dtype=np.int16).reshape((2, 3, 4, 5))
aff = np.eye(4)
img = img_klass(arr, aff)
img.header.set_norm_zooms((2, 2, 2, 2.5))
assert_array_equal(img.header.get_norm_zooms(), (2, 2, 2, 2.5))
assert_array_equal(img.header.get_zooms(units='canonical'), (2, 2, 2, 2.5))

def test_norm_zooms_edge_cases(self):
def test_zooms_edge_cases(self):
''' Override for classes where *_norm_zooms != *_zooms '''
img_klass = self.image_class
arr = np.arange(120, dtype=np.int16).reshape((2, 3, 4, 5))
aff = np.eye(4)
img = img_klass(arr, aff)
img.header.set_zooms((2, 2, 2, 2.5))
assert_array_equal(img.header.get_zooms(), (2, 2, 2, 2.5))
assert_array_equal(img.header.get_norm_zooms(), (2, 2, 2, 2.5))
assert_array_equal(img.header.get_zooms(units='raw'), (2, 2, 2, 2.5))
assert_array_equal(img.header.get_zooms(units='canonical'), (2, 2, 2, 2.5))
img.header.set_norm_zooms((2, 2, 2, 2.5))
assert_array_equal(img.header.get_zooms(), (2, 2, 2, 2.5))
assert_array_equal(img.header.get_norm_zooms(), (2, 2, 2, 2.5))
assert_array_equal(img.header.get_zooms(units='raw'), (2, 2, 2, 2.5))
assert_array_equal(img.header.get_zooms(units='canonical'), (2, 2, 2, 2.5))


class MmapImageMixin:
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0