def test_convert(tmpdir):
for in_ext, out_ext in it.product(['asc', 'h5', 'swc'], repeat=2):
# A simple morphology
inname = DATA / f'simple.{in_ext}'
outname = Path(tmpdir, f'test.{out_ext}')
convert(inname, outname)
assert not diff(inname, outname)
# A more complex one
inname = DATA / f'tkb061126a4_ch0_cc2_h_zk_60x_1.{in_ext}'
outname = Path(tmpdir, f'test.{out_ext}')
convert(inname, outname)
diff_result = diff(inname, outname, rtol=1e-5, atol=1e-5)
assert not bool(diff_result), diff_result.info
def test_convert():
with setup_tempdir('test-convert') as tmp_dir:
for in_ext, out_ext in it.product(['asc', 'h5', 'swc'], repeat=2):
# A simple morphology
inname = os.path.join(DATA, 'simple.' + in_ext)
outname = os.path.join(tmp_dir, 'test.' + out_ext)
convert(inname, outname)
ok_(not diff(inname, outname))
# A more complex one
inname = os.path.join(DATA, 'tkb061126a4_ch0_cc2_h_zk_60x_1.' + in_ext)
outname = os.path.join(tmp_dir, 'test.' + out_ext)
convert(inname, outname)
diff_result = diff(inname, outname, rtol=1e-5, atol=1e-5)
ok_(not bool(diff_result), diff_result.info)
def test_same_conversion_as_asciitoh5():
'''Check that the morph-tool conversion to produces the same h5 files as asciitoh5 converter.
repo_base/02-morphology-repository-sanitized contains valid morphologies under ASC format
repo_base/03-morphology-repository-sanitized-asciitoh5ed
contains the expected conversion output
Note: asciitoh5 also reorder the neurites but not 'morph-tool convert'
so we compare the reordered files
'''
repo_base = '/gpfs/bbp.cscs.ch/project/proj30/jenkins/morph-tool/converter'
with tempfile.TemporaryDirectory() as folder:
sanitized = Path(repo_base, '02-morphology-repository-sanitized')
for path in tqdm(list(_walk(sanitized))):
morphio_morph = Path(folder, path.stem + '.h5')
convert(path, str(morphio_morph))
asciitoh5_morph = Path(
repo_base, '03-morphology-repository-sanitized-asciitoh5ed',
path.stem + '.h5')
diff_result = diff(Morphology(morphio_morph, Option.nrn_order),
asciitoh5_morph)
ok_(
not diff_result,
'mismatch:\n{}\n{}\n{}'.format(path, asciitoh5_morph,
diff_result.info))
def assert_conversion_works(input_file):
ext_in = input_file.lower().split('.')[-1]
name = os.path.basename(input_file).split('.')[0]
for ext_out in ['asc', 'h5', 'swc']:
output_file = os.path.join('/tmp', name + '.' + ext_out)
convert(input_file, output_file)
input = Morphology(input_file)
output = Morphology(output_file)
diff_result = diff(input, output)
ok_(
not diff_result,
'Difference between {} and {}: {}'.format(input_file, output_file,
diff_result.info))
try:
if ext_in == ext_out or {ext_in, ext_out} == {'asc', 'h5'}:
assert_array_almost_equal(
Morphology(input_file).soma.points,
Morphology(output_file).soma.points)
else:
surf1 = _get_surface(input_file, ext_in)
surf2 = _get_surface(output_file, ext_out)
try:
assert_allclose(surf1, surf2, 5e-1)
except Exception as e:
raise e
except NotImplementedError:
pass
def test__repair():
neuron = load_neuron(Path(DATA_PATH, 'valid.h5'))
axon = neuron.root_sections[0]
assert_equal(axon.type, SectionType.axon)
test_module.repair(neuron, axon, [axon], [axon], set(), y_extent=10000)
assert_equal(len(axon.children), 1)
assert_array_equal(axon.children[0].points[0], axon.points[-1])
ok_(not diff(neuron, DATA_PATH / 'axon-repair.h5'))
def test_self_graft():
'''Grafting a neuron with its own neuron'''
filename = DATA / 'neuron.asc'
new_axon = graft.find_axon(ImmutMorphology(filename))
neuron = Morphology(filename)
graft.graft_axon(neuron, new_axon)
expected = Morphology(filename)
assert not diff(expected, neuron)
def test__repair_no_intact_axon():
filename = Path(DATA_PATH, 'valid.h5')
neuron = load_neuron(filename)
axon = neuron.root_sections[0]
used_axon_branches = set()
test_module.repair(neuron,
axon, [], [axon],
used_axon_branches,
y_extent=10000)
# There should not be any repair
ok_(not diff(neuron, filename))
def test_convert_recenter():
with setup_tempdir('test-convert_recenter') as tmp_dir:
simple = os.path.join(DATA, 'simple.swc')
outname = os.path.join(tmp_dir, 'test.swc')
convert(simple, outname, recenter=True)
ok_(not diff(simple, outname)) #simple.swc is already centered
mut = morphio.Morphology(simple).as_mutable()
mut.soma.points = [[1, 1, 1], ]
inname = os.path.join(tmp_dir, 'moved.swc')
mut.write(inname)
convert(inname, outname, recenter=True)
simple = morphio.Morphology(simple)
centered_morph = morphio.Morphology(outname)
ok_(np.all((simple.points - centered_morph.points) == 1))
def test_convert_recenter(tmpdir):
simple = DATA / 'simple.swc'
outname = Path(tmpdir, 'test.swc')
convert(simple, outname, recenter=True)
assert not diff(simple, outname) #simple.swc is already centered
mut = morphio.Morphology(simple).as_mutable()
mut.soma.points = [
[1, 1, 1],
]
inname = Path(tmpdir, 'moved.swc')
mut.write(inname)
convert(inname, outname, recenter=True)
simple = morphio.Morphology(simple)
centered_morph = morphio.Morphology(outname)
assert np.all((simple.points - centered_morph.points) == 1)
def diff(morph1, morph2, quiet):
'''
Compare two morphology files.
Return exit code 0 if morphology objects stored in `file1` and `file2`
are deemed identical by MorphIO; and exit code 1 otherwise.
Morphologies with different formats can be compared.
MORPH1 and MORPH2 can be either filenames or morphio.Morpholgy objects
'''
if quiet:
L.setLevel(logging.WARNING)
result = morph_tool.diff(morph1, morph2)
if result:
L.info("Morphologies not identical")
L.info(result.info)
sys.exit(1)