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: Add units specification to tests
  • Loading branch information
@effigies
effigies committed Dec 26, 2022
commit 798fc4e655c4740c31660ccda6e0737a17e8f35c
2 changes: 1 addition & 1 deletion nibabel/analyze.py
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Original file line number Diff line number Diff line change
Expand Up @@ -399,7 +399,7 @@ def from_header(klass, header=None, check=True):
f"but output header {klass} does not support it")
obj.set_data_dtype(header.get_data_dtype())
obj.set_data_shape(header.get_data_shape())
obj.set_zooms(header.get_zooms())
obj.set_zooms(header.get_zooms(units='raw'))
if check:
obj.check_fix()
return obj
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2 changes: 1 addition & 1 deletion nibabel/nifti1.py
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Expand Up @@ -784,7 +784,7 @@ def get_data_shape(self):

Expanding number of dimensions gets default zooms

>>> hdr.get_zooms()
>>> hdr.get_zooms(units='canonical')
(1.0, 1.0, 1.0)

Notes
Expand Down
22 changes: 14 additions & 8 deletions nibabel/tests/test_analyze.py
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Expand Up @@ -91,7 +91,8 @@ def test_general_init(self):
assert_array_equal(np.diag(hdr.get_base_affine()),
[-1, 1, 1, 1])
# But zooms only go with number of dimensions
assert hdr.get_zooms() == (1.0,)
assert hdr.get_zooms(units='raw') == (1.0,)
assert hdr.get_zooms(units='canonical') == (1.0,)

def test_header_size(self):
assert self.header_class.template_dtype.itemsize == self.sizeof_hdr
Expand Down Expand Up @@ -437,7 +438,8 @@ def test_data_shape_zooms_affine(self):
else:
assert hdr.get_data_shape() == (0,)
# Default zoom - for 3D - is 1(())
assert hdr.get_zooms() == (1,) * L
assert hdr.get_zooms(units='raw') == (1,) * L
assert hdr.get_zooms(units='canonical') == (1,) * L
# errors if zooms do not match shape
if len(shape):
with pytest.raises(HeaderDataError):
Expand All @@ -455,11 +457,14 @@ def test_data_shape_zooms_affine(self):
hdr = self.header_class()
hdr.set_data_shape((1, 2, 3))
hdr.set_zooms((4, 5, 6))
assert_array_equal(hdr.get_zooms(), (4, 5, 6))
assert_array_equal(hdr.get_zooms(units='raw'), (4, 5, 6))
assert_array_equal(hdr.get_zooms(units='canonical'), (4, 5, 6))
hdr.set_data_shape((1, 2))
assert_array_equal(hdr.get_zooms(), (4, 5))
assert_array_equal(hdr.get_zooms(units='raw'), (4, 5))
assert_array_equal(hdr.get_zooms(units='canonical'), (4, 5))
hdr.set_data_shape((1, 2, 3))
assert_array_equal(hdr.get_zooms(), (4, 5, 1))
assert_array_equal(hdr.get_zooms(units='raw'), (4, 5, 1))
assert_array_equal(hdr.get_zooms(units='canonical'), (4, 5, 1))
# Setting zooms changes affine
assert_array_equal(np.diag(hdr.get_base_affine()),
[-4, 5, 1, 1])
Expand D 8000 own Expand Up @@ -529,12 +534,13 @@ def get_data_dtype(self): return np.dtype('i2')

def get_data_shape(self): return (5, 4, 3)

def get_zooms(self): return (10.0, 9.0, 8.0)
def get_zooms(self, units=None, raise_unknown=None): return (10.0, 9.0, 8.0)
converted = klass.from_header(C())
assert isinstance(converted, klass)
assert converted.get_data_dtype() == np.dtype('i2')
assert converted.get_data_shape() == (5, 4, 3)
assert converted.get_zooms() == (10.0, 9.0, 8.0)
assert converted.get_zooms(units='raw') == (10.0, 9.0, 8.0)
assert converted.get_zooms(units='canonical') == (10.0, 9.0, 8.0)

def test_base_affine(self):
klass = self.header_class
Expand Down Expand Up @@ -640,7 +646,7 @@ def get_data_shape(self):

class H4(H3):

def get_zooms(self):
def get_zooms(self, units=None, raise_unknown=None):
return 4., 5., 6.
exp_hdr = klass()
exp_hdr.set_data_dtype(np.dtype('u1'))
Expand Down
22 changes: 11 additions & 11 deletions nibabel/tests/test_nifti1.py
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Expand Up @@ -881,11 +881,11 @@ def test_set_qform(self):
img.set_qform(new_affine, 1, update_affine=False)
assert_array_almost_equal(img.affine, aff_affine)
# Clear qform using None, zooms unchanged
assert_array_almost_equal(hdr.get_zooms(), [1.1, 1.1, 1.1])
assert_array_almost_equal(hdr.get_zooms(units='raw'), [1.1, 1.1, 1.1])
img.set_qform(None)
qaff, code = img.get_qform(coded=True)
assert (qaff, code) == (None, 0)
assert_array_almost_equal(hdr.get_zooms(), [1.1, 1.1, 1.1])
assert_array_almost_equal(hdr.get_zooms(units='raw'), [1.1, 1.1, 1.1])
# Best affine similarly
assert_array_almost_equal(img.affine, hdr.get_best_affine())
# If sform is not set, qform should update affine
Expand Down Expand Up @@ -942,9 +942,9 @@ def test_set_sform(self):
assert_array_almost_equal(img.affine, aff_affine)
# zooms do not get updated when qform is 0
assert_array_almost_equal(img.get_qform(), orig_aff)
assert_array_almost_equal(hdr.get_zooms(), [2.2, 3.3, 4.3])
assert_array_almost_equal(hdr.get_zooms(units='raw'), [2.2, 3.3, 4.3])
img.set_qform(None)
assert_array_almost_equal(hdr.get_zooms(), [2.2, 3.3, 4.3])
assert_array_almost_equal(hdr.get_zooms(units='raw'), [2.2, 3.3, 4.3])
# Set sform using new_affine when qform is set
img.set_qform(qform_affine, 1)
img.set_sform(new_affine, 1)
Expand All @@ -953,7 +953,7 @@ def test_set_sform(self):
assert_array_almost_equal(saff, new_affine)
assert_array_almost_equal(img.affine, new_affine)
# zooms follow qform
assert_array_almost_equal(hdr.get_zooms(), [1.2, 1.2, 1.2])
assert_array_almost_equal(hdr.get_zooms(units='raw'), [1.2, 1.2, 1.2])
# Clear sform using None, best_affine should fall back on qform
img.set_sform(None)
assert hdr['sform_code'] == 0
Expand Down Expand Up @@ -1042,15 +1042,15 @@ def test_load_pixdims(self):
# Check qform, sform, pixdims are the same
assert_array_equal(img_hdr.get_qform(), qaff)
assert_array_equal(img_hdr.get_sform(), saff)
assert_array_equal(img_hdr.get_zooms(), [2, 3, 4])
assert_array_equal(img_hdr.get_zooms(units='raw'), [2, 3, 4])
# Save to stringio
re_simg = bytesio_round_trip(simg)
assert_array_equal(re_simg.get_fdata(), arr)
# Check qform, sform, pixdims are the same
rimg_hdr = re_simg.header
assert_array_equal(rimg_hdr.get_qform(), qaff)
assert_array_equal(rimg_hdr.get_sform(), saff)
assert_array_equal(rimg_hdr.get_zooms(), [2, 3, 4])
assert_array_equal(rimg_hdr.get_zooms(units='raw'), [2, 3, 4])

def test_affines_init(self):
# Test we are doing vaguely spec-related qform things. The 'spec' here
Expand All @@ -1064,20 +1064,20 @@ def test_affines_init(self):
hdr = img.header
assert hdr['qform_code'] == 0
assert hdr['sform_code'] == 2
assert_array_equal(hdr.get_zooms(), [2, 3, 4])
assert_array_equal(hdr.get_zooms(units='raw'), [2, 3, 4])
# This is also true for affines with header passed
qaff = np.diag([3, 4, 5, 1])
saff = np.diag([6, 7, 8, 1])
hdr.set_qform(qaff, code='scanner')
hdr.set_sform(saff, code='talairach')
assert_array_equal(hdr.get_zooms(), [3, 4, 5])
assert_array_equal(hdr.get_zooms(units='raw'), [3, 4, 5])
img = IC(arr, aff, hdr)
new_hdr = img.header
# Again affine is sort of anonymous space
assert new_hdr['qform_code'] == 0
assert new_hdr['sform_code'] == 2
assert_array_equal(new_hdr.get_sform(), aff)
assert_array_equal(new_hdr.get_zooms(), [2, 3, 4])
assert_array_equal(new_hdr.get_zooms(units='raw'), [2, 3, 4])
# But if no affine passed, codes and matrices stay the same
img = IC(arr, None, hdr)
new_hdr = img.header
Expand All @@ -1086,7 +1086,7 @@ def test_affines_init(self):
assert new_hdr['sform_code'] == 3 # Still talairach
assert_array_equal(new_hdr.get_sform(), saff)
# Pixdims as in the original header
assert_array_equal(new_hdr.get_zooms(), [3, 4, 5])
assert_array_equal(new_hdr.get_zooms(units='raw'), [3, 4, 5])

def test_read_no_extensions(self):
IC = self.image_class
Expand Down
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