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: Clear nifti1 module warnings
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@effigies
effigies committed Dec 27, 2022
commit cfc5abe65c032ef70938e14a9d6966b04cf02cf6
18 changes: 9 additions & 9 deletions nibabel/tests/test_nifti1.py
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8000
Original file line number Diff line number Diff line change
Expand Up @@ -719,23 +719,23 @@ def test_recoded_fields(self):
assert hdr.get_value_label('slice_code') == 'alternating decreasing'

def test_general_init(self):
with clear_and_catch_warnings() as warns:
with clear_and_catch_warnings(modules=(nifti1,)) as warns:
warnings.filterwarnings('ignore', 'get_zooms', FutureWarning)
warnings.filterwarnings('ignore', 'set_zooms', FutureWarning)
warnings.filterwarnings('ignore', 'Unknown (spatial|time) units',
UserWarning)
super(TestNifti1PairHeader, self).test_general_init()

def test_from_header(self):
with clear_and_catch_warnings() as warns:
with clear_and_catch_warnings(modules=(nifti1,)) as warns:
warnings.filterwarnings('ignore', 'get_zooms', FutureWarning)
warnings.filterwarnings('ignore', 'set_zooms', FutureWarning)
warnings.filterwarnings('ignore', 'Unknown (spatial|time) units',
UserWarning)
super(TestNifti1PairHeader, self).test_from_header()

def test_data_shape_zooms_affine(self):
with clear_and_catch_warnings() as warns:
with clear_and_catch_warnings(modules=(nifti1,)) as warns:
warnings.filterwarnings('ignore', 'get_zooms', FutureWarning)
warnings.filterwarnings('ignore', 'set_zooms', FutureWarning)
warnings.filterwarnings('ignore', 'Unknown (spatial|time) units',
Expand Down Expand Up @@ -1207,7 +1207,7 @@ def test_zooms_edge_cases(self):
img = img_klass(arr, aff)

# Unknown units = 2 warnings
with clear_and_catch_warnings() as warns:
with clear_and_catch_warnings(modules=(nifti1,)) as warns:
warnings.simplefilter('always')
assert_array_almost_equal(img.header.get_zooms(units='norm'),
(1, 1, 1, 1))
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It's unclear to me why (in Python 2 only) this is failing to raise warnings.

Expand All @@ -1216,7 +1216,7 @@ def test_zooms_edge_cases(self):
units='norm', raise_unknown=True)

img.header.set_xyzt_units(xyz='meter')
with clear_and_catch_warnings() as warns:
with clear_and_catch_warnings(modules=(nifti1,)) as warns:
warnings.simplefilter('always')
assert_array_almost_equal(img.header.get_zooms(units='norm'),
(1000, 1000, 1000, 1))
Expand All @@ -1232,7 +1232,7 @@ def test_zooms_edge_cases(self):
(0.001, 0.001, 0.001, 1))

img.header.set_xyzt_units(t='sec')
with clear_and_catch_warnings() as warns:
with clear_and_catch_warnings(modules=(nifti1,)) as warns:
warnings.simplefilter('always')
assert_array_equal(img.header.get_zooms(units='norm'),
(1, 1, 1, 1))
Expand Down Expand Up @@ -1277,7 +1277,7 @@ def test_zooms_edge_cases(self):

# Non-temporal t units are not transformed
img.header.set_zooms((1, 1, 1, 1.5), units=('mm', 'ppm'))
with clear_and_catch_warnings() as warns:
with clear_and_catch_warnings(modules=(nifti1,)) as warns:
warnings.simplefilter('always')
assert_array_almost_equal(img.header.get_zooms(units='norm'),
(1, 1, 1, 1.5))
Expand All @@ -1287,7 +1287,7 @@ def test_zooms_edge_cases(self):

# Non-temporal t units are not normalized
img.header.set_zooms((2, 2, 2, 3.5), units='norm')
with clear_and_catch_warnings() as warns:
with clear_and_catch_warnings(modules=(nifti1,)) as warns:
warnings.simplefilter('always')
assert_array_almost_equal(img.header.get_zooms(units='norm'),
(2, 2, 2, 3.5))
Expand All @@ -1310,7 +1310,7 @@ def test_zooms_edge_cases(self):
units='badparam')

def test_no_finite_values(self):
with clear_and_catch_warnings() as warns:
with clear_and_catch_warnings(modules=(nifti1,)) as warns:
warnings.filterwarnings('ignore', 'get_zooms', FutureWarning)
warnings.filterwarnings('ignore', 'set_zooms', FutureWarning)
warnings.filterwarnings('ignore', 'Unknown (spatial|time) units',
Expand Down
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