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More reconciliation with mut_morphio (#875)
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This brings more formatting of the test file
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Benoit Coste authored Mar 5, 2021
1 parent 935a0d5 commit a29cfaa
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Showing 5 changed files with 168 additions and 181 deletions.
14 changes: 7 additions & 7 deletions neurom/check/tests/test_neuron_checks.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,8 @@
SWC_PATH = DATA_PATH / 'swc'
ASC_PATH = DATA_PATH / 'neurolucida'
H5V1_PATH = DATA_PATH / 'h5/v1'
MORPHIO_OFFSET = 0



def _load_neuron(name):
Expand Down Expand Up @@ -221,13 +223,12 @@ def test_nonzero_segment_lengths_bad_data():
'Single_axon.swc',
]

morphio_offset = 0
bad_ids = [[2, 23, 44, 65], [2], [2], [2], [2]]

for i, nrn in enumerate(_pick(files)):
ids = nrn_chk.has_all_nonzero_segment_lengths(nrn)
nt.assert_equal(ids.info,
[(id + morphio_offset, 0) for id in bad_ids[i]])
[(id + MORPHIO_OFFSET, 0) for id in bad_ids[i]])


def test_nonzero_segment_lengths_threshold():
Expand All @@ -240,9 +241,8 @@ def test_nonzero_segment_lengths_threshold():
ids = nrn_chk.has_all_nonzero_segment_lengths(nrn, threshold=0.25)

bad_ids = [(2, 0), (23, 0), (38, 9), (44, 0), (54, 7), (62, 2), (65, 0), (72, 4), (78, 6)]
morphio_offset = 0
nt.assert_equal(ids.info,
[(id + morphio_offset, val) for id, val in bad_ids])
[(id + MORPHIO_OFFSET, val) for id, val in bad_ids])


def test_nonzero_section_lengths_good_data():
Expand All @@ -263,7 +263,7 @@ def test_nonzero_section_lengths_bad_data():

ids = nrn_chk.has_all_nonzero_section_lengths(nrn)
nt.ok_(not ids.status)
nt.assert_equal(ids.info, [15])
nt.assert_equal(ids.info, [15 + MORPHIO_OFFSET])


def test_nonzero_section_lengths_threshold():
Expand All @@ -285,8 +285,7 @@ def test_has_nonzero_soma_radius():


def test_has_nonzero_soma_radius_bad_data():

nrn = load_neuron(SWC_PATH / 'Single_basal.swc')
nrn = load_neuron(SWC_PATH / 'soma_zero_radius.swc')
nt.assert_false(nrn_chk.has_nonzero_soma_radius(nrn).status)


Expand Down Expand Up @@ -394,6 +393,7 @@ def test_has_no_narrow_dendritic_section():
8 3 6 -4 0 10. 7
9 3 -5 -4 0 10. 7
""")
nrn = load_neuron(swc_content, reader='swc')
res = nrn_chk.has_no_narrow_neurite_section(nrn, dendrite_filter,
radius_threshold=5,
considered_section_min_length=0)
Expand Down
276 changes: 112 additions & 164 deletions neurom/check/tests/test_runner.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,33 +26,24 @@
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

from pathlib import Path
import os
from collections import OrderedDict
from copy import copy

from nose import tools as nt
from pathlib import Path

from neurom.check.runner import CheckRunner
from neurom.exceptions import ConfigError
from pathlib import Path
from nose import tools as nt

_path = os.path.dirname(os.path.abspath(__file__))
SWC_PATH = Path(__file__).parent / '../../../test_data/swc/'

SWC_PATH = Path(__file__).parent.parent.parent.parent / 'test_data/swc/'
NRN_PATH_0 = str(Path(SWC_PATH, 'Neuron.swc'))
NRN_PATH_1 = str(Path(SWC_PATH, 'Neuron_zero_length_sections.swc'))
NRN_PATH_2 = str(Path(SWC_PATH, 'Single_apical.swc'))
NRN_PATH_3 = str(Path(SWC_PATH, 'Single_basal.swc'))
NRN_PATH_4 = str(Path(SWC_PATH, 'Single_axon.swc'))
NRN_PATH_5 = str(Path(SWC_PATH, 'Single_apical_no_soma.swc'))

CONFIG = {
'checks': {
'structural_checks': [
'is_single_tree',
'has_soma_points',
'has_sequential_ids',
'has_increasing_ids',
'has_valid_soma',
'has_valid_neurites'
],
'neuron_checks': [
'has_basal_dendrite',
Expand All @@ -72,183 +63,140 @@
},
}

checks_not_in_morphio = OrderedDict([
('has_valid_neurites', 'Has valid neurites'),
('has_sequential_ids', 'Has sequential ids'),
('has_increasing_ids', 'Has increasing ids'),
('is_single_tree', 'Is single tree'),
])
CONFIG['checks']['structural_checks'] += list(checks_not_in_morphio.keys())

CONFIG_COLOR = copy(CONFIG)
CONFIG_COLOR['color'] = True

REF_0 = {
'files': {
NRN_PATH_0: {
"Is single tree": True,
"Has soma points": True,
"Has sequential ids": True,
"Has increasing ids": True,
"Has valid soma": True,
"Has valid neurites": True,
"Has basal dendrite": True,
"Has axon": True,
"Has apical dendrite": True,
"Has all nonzero segment lengths": True,
"Has all nonzero section lengths": True,
"Has all nonzero neurite radii": True,
"Has nonzero soma radius": True,
"ALL": True
}
},
"STATUS": "PASS"
}

REF_1 = {
'files': {
NRN_PATH_1: {
"Is single tree": True,
"Has soma points": True,
"Has sequential ids": True,
"Has increasing ids": True,
"Has valid soma": True,
"Has valid neurites": True,
"Has basal dendrite": True,
"Has axon": True,
"Has apical dendrite": True,
"Has all nonzero segment lengths": False,
"Has all nonzero section lengths": False,
"Has all nonzero neurite radii": True,
"Has nonzero soma radius": True,
"ALL": False
}
},
"STATUS": "FAIL"
}

REF_2 = {
'files': {
NRN_PATH_2: {
"Is single tree": True,
"Has soma points": True,
"Has sequential ids": True,
"Has increasing ids": True,
"Has valid soma": True,
"Has valid neurites": True,
"Has basal dendrite": False,
"Has axon": False,
"Has apical dendrite": True,
"Has all nonzero segment lengths": False,
"Has all nonzero section lengths": True,
"Has all nonzero neurite radii": True,
"Has nonzero soma radius": True,
"ALL": False
}
},
"STATUS": "FAIL"
}

REF_3 = {
'files': {
NRN_PATH_3: {
"Is single tree": True,
"Has soma points": True,
"Has sequential ids": True,
"Has increasing ids": True,
"Has valid soma": True,
"Has valid neurites": True,
"Has basal dendrite": True,
"Has axon": False,
"Has apical dendrite": False,
"Has all nonzero segment lengths": False,
"Has all nonzero section lengths": True,
"Has all nonzero neurite radii": True,
"Has nonzero soma radius": False,
"ALL": False
}
},
"STATUS": "FAIL"
}

REF_4 = {
'files': {
NRN_PATH_4: {
"Is single tree": True,
"Has soma points": True,
"Has sequential ids": True,
"Has increasing ids": True,
"Has valid soma": True,
"Has valid neurites": True,
"Has basal dendrite": False,
"Has axon": True,
"Has apical dendrite": False,
"Has all nonzero segment lengths": False,
"Has all nonzero section lengths": True,
"Has all nonzero neurite radii": True,
"Has nonzero soma radius": True,
"ALL": False
}
},
"STATUS": "FAIL"
}


REF_5 = {
'files': {
NRN_PATH_5: {
"Is single tree": True,
"Has soma points": False,
"Has sequential ids": True,
"Has increasing ids": True,
"Has valid soma": False,
"Has valid neurites": False,
"ALL": False
}
},
"STATUS": "FAIL"
}

def _run_test(path, ref, config=CONFIG, should_pass=False):
'''Run checkers with the passed "config" on file "path"
and compare the results to "ref"'''
results = CheckRunner(config).run(path)
nt.assert_dict_equal(dict(results['files'][path]), ref)
nt.assert_equal(results['STATUS'],
"PASS" if should_pass else "FAIL")

ref = dict([
("Has soma points", True),
("Has valid soma", True),
("Has basal dendrite", True),
("Has axon", True),
("Has apical dendrite", True),
("Has all nonzero segment lengths", True),
("Has all nonzero section lengths", True),
("Has all nonzero neurite radii", True),
("Has nonzero soma radius", True),
("ALL", True)
])
ref.update({(item.replace('_', ' ').capitalize(), True) for item in checks_not_in_morphio.values()})

def test_ok_neuron():
checker = CheckRunner(CONFIG)
summ = checker.run(NRN_PATH_0)
nt.assert_equal(summ, REF_0)

_run_test(os.path.join(SWC_PATH, 'Neuron.swc'),
ref,
should_pass=True)

def test_ok_neuron_color():
checker = CheckRunner(CONFIG_COLOR)
summ = checker.run(NRN_PATH_0)
nt.assert_equal(summ, REF_0)
_run_test(os.path.join(SWC_PATH, 'Neuron.swc'),
ref,
CONFIG_COLOR,
should_pass=True)


def test_zero_length_sections_neuron():
checker = CheckRunner(CONFIG)
summ = checker.run(NRN_PATH_1)
nt.assert_equal(summ, REF_1)
expected = dict([
("Has soma points", True),
("Has valid soma", True),
("Has basal dendrite", True),
("Has axon", True),
("Has apical dendrite", True),
("Has all nonzero segment lengths", False),
("Has all nonzero section lengths", False),
("Has all nonzero neurite radii", True),
("Has nonzero soma radius", True),
("ALL", False)
])
expected.update({(item, True) for item in checks_not_in_morphio.values()})
_run_test(os.path.join(SWC_PATH, 'Neuron_zero_length_sections.swc'),
expected)


def test_single_apical_neuron():
checker = CheckRunner(CONFIG)
summ = checker.run(NRN_PATH_2)
nt.assert_equal(summ, REF_2)
expected = dict([
("Has soma points", True),
("Has valid soma", True),
("Has basal dendrite", False),
("Has axon", False),
("Has apical dendrite", True),
("Has all nonzero segment lengths", False),
("Has all nonzero section lengths", True),
("Has all nonzero neurite radii", True),
("Has nonzero soma radius", True),
("ALL", False)
])
expected.update({(item, True) for item in checks_not_in_morphio.values()})
_run_test(os.path.join(SWC_PATH, 'Single_apical.swc'),
expected)


def test_single_basal_neuron():
checker = CheckRunner(CONFIG)
summ = checker.run(NRN_PATH_3)
nt.assert_equal(summ, REF_3)
expected = dict(
([
("Has soma points", True),
("Has valid soma", True),
("Has basal dendrite", True),
("Has axon", False),
("Has apical dendrite", False),
("Has all nonzero segment lengths", False),
("Has all nonzero section lengths", True),
("Has all nonzero neurite radii", True),
("Has nonzero soma radius", False), # Should be True, will be fixed by v2
("ALL", False)
]))
expected.update({(item, True) for item in checks_not_in_morphio.values()})
_run_test(os.path.join(SWC_PATH, 'Single_basal.swc'),
expected)


def test_single_axon_neuron():
checker = CheckRunner(CONFIG)
summ = checker.run(NRN_PATH_4)
nt.assert_equal(summ, REF_4)
expected = dict([
("Has soma points", True),
("Has valid soma", True),
("Has basal dendrite", False),
("Has axon", True),
("Has apical dendrite", False),
("Has all nonzero segment lengths", False),
("Has all nonzero section lengths", True),
("Has all nonzero neurite radii", True),
("Has nonzero soma radius", True),
("ALL", False)
])
expected.update({(item, True) for item in checks_not_in_morphio.values()})
_run_test(os.path.join(SWC_PATH, 'Single_axon.swc'),
expected)


def test_single_apical_no_soma():
checker = CheckRunner(CONFIG)
summ = checker.run(NRN_PATH_5)
nt.assert_equal(summ, REF_5)
expected = dict([('Has soma points', False),
('Has valid soma', False),
('ALL', False)])
expected.update({(item, True) for item in checks_not_in_morphio.values()})
expected['Has valid neurites'] = False
_run_test(os.path.join(SWC_PATH, 'Single_apical_no_soma.swc'),
expected)


def test_directory_input():
checker = CheckRunner(CONFIG)
summ = checker.run(SWC_PATH)
nt.eq_(summ['files'][NRN_PATH_0]['Has axon'], True)
nt.eq_(summ['files'][NRN_PATH_2]['Has axon'], False)
nt.eq_(summ['files'][os.path.join(SWC_PATH, 'Single_axon.swc')]['Has axon'], True)
nt.eq_(summ['files'][os.path.join(SWC_PATH, 'Single_apical.swc')]['Has axon'], False)


@nt.raises(IOError)
Expand Down
1 change: 0 additions & 1 deletion neurom/core/tests/test_iter.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -117,7 +117,6 @@ def test_iter_sections_ipreorder():
assert_sequence_equal([s.id + MORPHIO_OFFSET for n in POP.neurites for s in n.iter_sections(Tree.ipreorder)],
[2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 2, 3, 4])


def test_iter_sections_ipostorder():
assert_sequence_equal([s.id + MORPHIO_OFFSET for n in POP.neurites for s in n.iter_sections(Tree.ipostorder)],
[3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 22, 20, 18, 16, 14, 12, 10, 8, 6, 4, 2, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 43, 41, 39, 37, 35, 33, 31, 29, 27, 25, 23, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 64, 62, 60, 58, 56, 54, 52, 50, 48, 46, 44, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 85, 83, 81, 79, 77, 75, 73, 71, 69, 67, 65, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 22, 20, 18, 16, 14, 12, 10, 8, 6, 4, 2, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 22, 20, 18, 16, 14, 12, 10, 8, 6, 4, 2, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 43, 41, 39, 37, 35, 33, 31, 29, 27, 25, 23, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 64, 62, 60, 58, 56, 54, 52, 50, 48, 46, 44, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 85, 83, 81, 79, 77, 75, 73, 71, 69, 67, 65, 2, 3, 4])
Expand Down
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