def test_single_point_root_section():
m = Morphology()
points = []
diameters = []
# Too hide the warning: appending empty section
with captured_output():
with ostream_redirect(stdout=True, stderr=True):
m.append_root_section(PointLevel(points, diameters),
SectionType(2))
with setup_tempdir('test_single_point_root_section',
no_cleanup=True) as tmp_folder:
assert_raises(
SectionBuilderError, m.write,
os.path.join(tmp_folder, "h5/empty_vasculature.h5"))
m = Morphology()
points = [[1., 1., 1.]]
diameters = [2.]
m.append_root_section(PointLevel(points, diameters), SectionType(2))
with setup_tempdir('test_single_point_root_section',
no_cleanup=True) as tmp_folder:
assert_raises(SectionBuilderError, m.write,
os.path.join(tmp_folder, "h5/empty_vasculature.h5"))
def test_write_perimeter():
morpho = Morphology()
morpho.soma.points = [[0, 0, 0]]
morpho.soma.diameters = [2]
dendrite = morpho.append_root_section(
PointLevel([[0, 0, 0], [0, 5, 0]], [2, 2], [5, 6]),
SectionType.basal_dendrite)
dendrite.append_section(PointLevel([[0, 5, 0], [-5, 5, 0]], [2, 3],
[6, 7]))
dendrite.append_section(PointLevel([[0, 5, 0], [6, 5, 0]], [2, 3], [6, 8]))
with setup_tempdir('test_write_perimeter') as tmp_folder:
h5_out = os.path.join(tmp_folder, "test_write.h5")
morpho.write(h5_out)
assert_array_equal(
ImmutMorphology(h5_out).perimeters, [5., 6., 6., 7., 6., 8.])
# Cannot right a morph with perimeter data to ASC and SWC
for ext in ['swc', 'asc']:
out_path = os.path.join(tmp_folder, "test_write_perimeter." + ext)
assert_raises(WriterError, morpho.write, out_path)
def test_write_merge_only_child_asc_h5():
'''The root section has only one child
When writing, children should *not* be merged with their parent section.
Note: See `test_write_merge_only_child_swc` for the SWC case.
'''
morpho = Morphology()
morpho.soma.points = [[0, 0, 0]]
morpho.soma.diameters = [2]
root = morpho.append_root_section(
PointLevel([[0, 0, 0],
[0, 5, 0]],
[2, 2]),
SectionType.basal_dendrite)
child = root.append_section(PointLevel([[0, 5, 0], [0, 6, 0]], [2, 3]))
with setup_tempdir('test_write_merge_only_child') as tmp_folder:
for extension in ['asc', 'h5']:
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
filename = Path(tmp_folder, 'test.{}'.format(extension))
morpho.write(filename)
read = Morphology(filename)
root = read.root_sections[0]
assert_array_equal(root.points,
[[0, 0, 0],
[0, 5, 0]])
assert len(root.children) == 1
def test_write_no_soma():
morpho = Morphology()
dendrite = morpho.append_root_section(
PointLevel([[0, 0, 0],
[0, 5, 0]],
[2, 2]),
SectionType.basal_dendrite)
dendrite = morpho.append_root_section(
PointLevel([[0, 1, 0],
[0, 7, 0]],
[2, 2]),
SectionType.basal_dendrite)
with setup_tempdir('test_write_no_soma') as tmp_folder:
for ext in ['asc', 'h5', 'swc']:
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
outfile = os.path.join(tmp_folder, 'tmp.' + ext)
morpho.write(outfile)
assert_equal(err.getvalue().strip(),
'Warning: writing file without a soma')
read = Morphology(outfile)
assert_equal(len(read.soma.points), 0)
assert_equal(len(read.root_sections), 2)
assert_array_equal(read.root_sections[0].points, [[0, 0, 0], [0, 5, 0]])
assert_array_equal(read.root_sections[1].points, [[0, 1, 0], [0, 7, 0]])
def test_endoplasmic_reticulum():
neuron = Morphology(Path(_path, "simple.asc"))
reticulum = neuron.endoplasmic_reticulum
assert_equal(reticulum.section_indices, [])
assert_equal(reticulum.volumes, [])
assert_equal(reticulum.surface_areas, [])
assert_equal(reticulum.filament_counts, [])
reticulum.section_indices = [1, 1]
reticulum.volumes = [2, 2]
reticulum.surface_areas = [3, 3]
reticulum.filament_counts = [4, 4]
assert_equal(reticulum.section_indices, [1, 1])
assert_equal(reticulum.volumes, [2, 2])
assert_equal(reticulum.surface_areas, [3, 3])
assert_equal(reticulum.filament_counts, [4, 4])
with setup_tempdir('test-endoplasmic-reticulum') as folder:
path = Path(folder, 'with-reticulum.h5')
neuron.write(path)
neuron = Morphology(path)
reticulum = neuron.endoplasmic_reticulum
assert_equal(reticulum.section_indices, [1, 1])
assert_equal(reticulum.volumes, [2, 2])
assert_equal(reticulum.surface_areas, [3, 3])
assert_equal(reticulum.filament_counts, [4, 4])
def test_duplicate_different_diameter():
'''Test that starting a child section with a different diamete
work as expected'''
morpho = Morphology()
morpho.soma.points = [[0, 0, 0], [1, 1, 1]]
morpho.soma.diameters = [1, 1]
section = morpho.append_root_section(
PointLevel([[2, 2, 2], [3, 3, 3]], [4, 4]),
SectionType.axon,
)
section.append_section(PointLevel([[3, 3, 3], [4, 4, 4]], [10, 12]))
section.append_section(PointLevel([[3, 3, 3], [5, 5, 5]], [11, 12]))
with setup_tempdir('test_write_duplicate_different_diameter',
no_cleanup=True) as tmp_folder:
for ext in ['asc', 'h5', 'swc']:
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
outfile = os.path.join(tmp_folder, 'tmp.' + ext)
morpho.write(outfile)
read = Morphology(outfile)
assert_equal(len(read.root_sections[0].children), 2)
child1, child2 = read.root_sections[0].children
assert_array_equal(child1.points, [[3, 3, 3], [4, 4, 4]])
assert_array_equal(child2.points, [[3, 3, 3], [5, 5, 5]])
assert_array_equal(child1.diameters, [10, 12])
assert_array_equal(child2.diameters, [11, 12])
def test_write_empty_file():
'''Check that empty morphology are not written to disk'''
with captured_output() as (_, _):
with ostream_redirect(stdout=True, stderr=True):
with setup_tempdir('test_write_empty_file', no_cleanup=True) as tmp_folder:
for ext in ['asc', 'swc', 'h5']:
outname = os.path.join(tmp_folder, 'empty.' + ext)
Morphology().write(outname)
ok_(not os.path.exists(outname))
def test_write_soma_basic():
morpho = Morphology()
morpho.soma.points = [[0, 0, 0], [0, 0, 0], [0, 0, 0]]
morpho.soma.diameters = [2, 3, 3]
with setup_tempdir('test_write_soma_basic') as tmp_folder:
morpho.write(os.path.join(tmp_folder, "test_write.swc"))
morpho.write(Path(tmp_folder, "test_write_pathlib.swc"))
assert_equal(len(os.listdir(tmp_folder)), 2)
def test_mitochondria():
morpho = Morphology()
morpho.soma.points = [[0, 0, 0], [1, 1, 1]]
morpho.soma.diameters = [1, 1]
neuronal_section_ids = [0, 0]
relative_pathlengths = np.array([0.5, 0.6], dtype=np.float32)
diameters = [10, 20]
mito_id = morpho.mitochondria.append_root_section(
MitochondriaPointLevel(neuronal_section_ids, relative_pathlengths,
diameters))
mito_id.append_section(
MitochondriaPointLevel([0, 0, 0, 0], [0.6, 0.7, 0.8, 0.9],
[20, 30, 40, 50]))
with setup_tempdir('test_mitochondria') as tmp_folder:
morpho.write(os.path.join(tmp_folder, "test.h5"))
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
morpho.write(os.path.join(tmp_folder, "test.swc"))
assert_string_equal(
err.getvalue(),
"Warning: this cell has mitochondria, they cannot be saved in "
" ASC or SWC format. Please use H5 if you want to save them."
)
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
morpho.write(os.path.join(tmp_folder, "test.asc"))
assert_string_equal(
err.getvalue(),
"Warning: this cell has mitochondria, they cannot be saved in "
" ASC or SWC format. Please use H5 if you want to save them."
)
mito = ImmutMorphology(os.path.join(tmp_folder,
'test.h5')).mitochondria
assert_array_equal(mito.root_sections[0].diameters, diameters)
assert_array_equal(mito.root_sections[0].neurite_section_ids,
neuronal_section_ids)
assert_array_equal(mito.root_sections[0].relative_path_lengths,
relative_pathlengths)
assert_equal(len(mito.root_sections), 1)
mito = Morphology(os.path.join(tmp_folder, 'test.h5')).mitochondria
assert_equal(len(mito.root_sections), 1)
assert_equal(mito.root_sections[0].neurite_section_ids,
neuronal_section_ids)
assert_array_equal(mito.section(0).diameters, diameters)
assert_array_equal(
mito.section(0).neurite_section_ids, neuronal_section_ids)
def test_convert():
set_maximum_warnings(0)
with setup_tempdir('test-convert-file') as tmp_dir:
runner = CliRunner()
filename = Path(DATA, 'simple.asc')
output_name = Path(tmp_dir, 'simple.h5')
result = runner.invoke(cli, ['convert', 'file', str(filename), str(output_name)])
assert_equal(result.exit_code, 0, result.exception)
ok_(output_name.exists())
with setup_tempdir('test-convert-folder') as tmp_dir:
runner = CliRunner()
result = runner.invoke(cli, ['convert', 'folder', '-ext', 'swc',
str(DATA / 'input-convert'), tmp_dir])
assert_equal(result.exit_code, 0, result.exc_info)
n_converted_files = len(list(Path(tmp_dir).rglob('**/*.swc')))
assert_equal(n_converted_files, 2)
def test_convert_swc_contour_to_sphere():
with setup_tempdir('test_convert_swc_contour_to_sphere') as tmp_dir:
# needs to have a complex contour soma
simple = os.path.join(DATA, 'tkb061126a4_ch0_cc2_h_zk_60x_1.asc')
outname = os.path.join(tmp_dir, 'test.swc')
convert(simple, outname, single_point_soma=True)
m = morphio.Morphology(outname)
assert_equal(1, len(m.soma.points))
assert_equal(1, len(m.soma.diameters))
#value dumped from NEURON: h.area(0.5, sec=icell.soma[0])
np.testing.assert_approx_equal(m.soma.surface, 476.0504050847511)
def test_convert_sanitize():
with setup_tempdir('test_convert_sanitize') as tmp_dir:
# needs to have a complex contour soma
simple = os.path.join(DATA, 'single_child.asc')
outname = os.path.join(tmp_dir, 'single_child.swc')
with assert_raises(MorphToolException) as obj:
convert(simple, outname, single_point_soma=True)
assert_equal('Use `sanitize` option for converting', str(obj.exception))
convert(simple, outname, single_point_soma=True, sanitize=True)
m = morphio.Morphology(outname)
assert_equal(len(m.sections), 1)
def test_write_merge_only_child():
'''The root section has only one child
The child should be merged with its parent section
Special care must be given for the potential duplicate point
o
/
/ son 1
root child /
o--------o----------o<
\
\ son 2
\
o
'''
morpho = Morphology()
morpho.soma.points = [[0, 0, 0]]
morpho.soma.diameters = [2]
root = morpho.append_root_section(
PointLevel([[0, 0, 0],
[0, 5, 0]],
[2, 2]),
SectionType.basal_dendrite)
child = root.append_section(PointLevel([[0, 5, 0], [0, 6, 0]], [2, 3]))
son1 = child.append_section(PointLevel([[0, 6, 0], [0, 7, 0]], [2, 3]))
son2 = child.append_section(PointLevel([[0, 6, 0], [4, 5, 6]], [3, 3]))
with setup_tempdir('test_write_merge_only_child') as tmp_folder:
for extension in ['swc', 'asc', 'h5']:
with captured_output() as (_, err):
with ostream_redirect(stdout=True, stderr=True):
filename = os.path.join(tmp_folder, 'test.{}'.format(extension))
morpho.write(filename)
assert_equal(err.getvalue().strip(),
'Warning: section 1 is the only child of section: 0\nIt will be merged with the parent section')
read = Morphology(filename)
root = read.root_sections[0]
assert_array_equal(root.points,
[[0, 0, 0],
[0, 5, 0],
[0, 6, 0]])
assert_equal(len(root.children), 2)
assert_array_equal(root.children[0].points,
[[0, 6, 0], [0, 7, 0]])
assert_array_equal(root.children[1].points,
[[0, 6, 0], [4, 5, 6]])
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_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 feature_extractor(param_file,
paths_to_images_and_masks,
path_to_results,
verbose=0,
n_jobs=None,
drop_missing=False,
variance_thresh=0.0):
"""Extract features from images using the PyRadimoics package.
Preliminary results are stored for re-entering the process in case of
abortion.
Args:
param_file (str):
samples (list):
Kwargs:
verbose (int): The level of verbosity during extraction.
n_jobs (int): The number of CPUs to distribute the extraction process.
Defaults to available - 1.
Returns:
(dict): The extracted image features.
"""
global TMP_FEATURE_DIR, TIMEOUT
_check_is_file(param_file)
# Setup temporary directory to store preliminary results.
path_tempdir = utils.setup_tempdir(TMP_FEATURE_DIR)
# Set number of available CPUs.
if n_jobs is None:
n_jobs = cpu_count() - 1 if cpu_count() > 1 else cpu_count()
if verbose > 0:
print('Initiated feature extraction.')
# Extract features.
results = Parallel(n_jobs=n_jobs, verbose=verbose, timeout=TIMEOUT)(
delayed(_extract_features)(param_file=param_file,
case=path_to_images_and_masks,
path_tempdir=path_tempdir,
verbose=verbose)
for path_to_images_and_masks in paths_to_images_and_masks)
def test_write_basic():
morpho = Morphology()
morpho.soma.points = [[0, 0, 0]]
morpho.soma.diameters = [2]
dendrite = morpho.append_root_section(PointLevel([[0, 0, 0], [0, 5, 0]], [2, 2]),
SectionType.basal_dendrite)
dendrite.append_section(PointLevel([[0, 5, 0], [-5, 5, 0]], [2, 3]))
dendrite.append_section(PointLevel([[0, 5, 0], [6, 5, 0]], [2, 3]))
axon = morpho.append_root_section(
PointLevel([[0, 0, 0],
[0, -4, 0]],
[2, 2]),
SectionType.axon)
axon.append_section(PointLevel([[0, -4, 0],
[6, -4, 0]],
[2, 4]))
axon = axon.append_section(PointLevel([[0, -4, 0],
[-5, -4, 0]],
[2, 4]))
with setup_tempdir('test_write_basic') as tmp_folder:
morpho.write(Path(tmp_folder, "test_write.asc"))
morpho.write(Path(tmp_folder, "test_write.swc"))
h5_out = Path(tmp_folder, "test_write.h5")
morpho.write(h5_out)
expected = [[0., 0., 0.], [0., 5., 0.], [0., 5., 0.], [-5., 5., 0.],
[0., 5., 0.], [6., 5., 0.], [0., 0., 0.], [0., -4., 0.],
[0., -4., 0.], [6., -4., 0.], [0., -4., 0.], [-5., -4., 0.]]
assert_array_equal(ImmutMorphology(Path(tmp_folder, "test_write.asc")).points, expected)
assert_array_equal(ImmutMorphology(Path(tmp_folder, "test_write.swc")).points, expected)
h5_morph = ImmutMorphology(Path(tmp_folder, "test_write.h5"))
assert_array_equal(h5_morph.points, expected)
assert h5_morph.version == ('h5', 1, 2)
import h5py
with h5py.File(h5_out, 'r') as h5_file:
assert '/perimeters' not in h5_file.keys()
def test_roundtrip(self):
with setup_tempdir() as tmp_dir:
output = Path(tmp_dir, "output.csv")
self.test_obj_sorted.to_csv(str(output))
new = self.ids_cls.from_csv(str(output))
assert self.test_obj_sorted == new
def test_roundtrip(self):
with setup_tempdir() as tmp_dir:
output = Path(tmp_dir, "output.csv")
self.test_obj_sorted.to_csv(str(output))
new = test_module.CircuitNodeIds.from_csv(str(output))
assert self.test_obj_sorted == new
