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BF: deterministic order of slice_time deduction, warning if multiple match #647

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Merged
merged 6 commits into from
Jul 23, 2018
Merged

BF: deterministic order of slice_time deduction, warning if multiple match #647

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347eef9
BF: deterministic order of slice_time deduction, warning if multiple …
yarikoptic Jul 12, 2018
7ba14b1
DOC: minor typo
yarikoptic Jul 12, 2018
244c8cf
ENH(TST): basic test for consistent choice of slice_code in case of m…
yarikoptic Jul 13, 2018
748ce00
RF+NF: Use OrderedDict and OrderedSet in Recoder
yarikoptic Jul 18, 2018
a1400bd
ENH(TST): test that we issue a warning upon multiple matches
yarikoptic Jul 18, 2018
d756751
TEST: Ensure warning isn't suppressed
effigies Jul 19, 2018
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16 changes: 13 additions & 3 deletions nibabel/nifti1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1573,14 +1573,24 @@ def set_slice_times(self, slice_times):
so_recoder = self._field_recoders['slice_code']
labels = so_recoder.value_set('label')
labels.remove('unknown')
for label in labels:

matching_labels = []
# reversing the order so that "alternative" go last
for label in sorted(labels, reverse=True):
if np.all(st_order == self._slice_time_order(
label,
n_timed)):
break
else:
matching_labels.append(label)

if not matching_labels:
raise HeaderDataError('slice ordering of %s fits '
'with no known scheme' % st_order)
if len(matching_labels) > 1:
warnings.warn(
'Multiple slice orders satisfy: %s. Choosing the first one'
% ', '.join(matching_labels)
)
label = matching_labels[0]
# Set values into header
hdr['slice_start'] = slice_start
hdr['slice_end'] = slice_end
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13 changes: 13 additions & 0 deletions nibabel/tests/test_nifti1.py
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Expand Up @@ -558,6 +558,19 @@ def test_slice_times(self):
assert_equal(hdr['slice_end'], 5)
assert_array_almost_equal(hdr['slice_duration'], 0.1)

# Ambiguous case
hdr2 = self.header_class()
hdr2.set_dim_info(slice=2)
hdr2.set_slice_duration(0.1)
hdr2.set_data_shape((1, 1, 2))
hdr2.set_slice_times([0.1, 0]) # will generate warning that multiple match
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Want to check that the warning is generated? e.g.

with clear_and_catch_warnings() as w:
    hdr2.set_slice_times([0.1, 0])
    assert len(w) == 1

# but always must be choosing sequential one first
assert_equal(hdr2.get_value_label('slice_code'), 'sequential decreasing')
# and the other direction
hdr2.set_slice_times([0, 0.1])
assert_equal(hdr2.get_value_label('slice_code'), 'sequential increasing')


def test_intents(self):
ehdr = self.header_class()
ehdr.set_intent('t test', (10,), name='some score')
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2 changes: 1 addition & 1 deletion nibabel/volumeutils.py
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Expand Up @@ -97,7 +97,7 @@ def __init__(self, codes, fields=('code',), map_maker=dict):

Parameters
----------
codes : seqence of sequences
codes : sequence of sequences
Each sequence defines values (codes) that are equivalent
fields : {('code',) string sequence}, optional
names by which elements in sequences can be accessed
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