def sanitize_all(input_folder, output_folder, nprocesses=1):
'''Sanitize all morphologies in input_folder and its sub-directories.
See :func:`~neuror.sanitize.sanitize` for more information on the sanitization process.
Args:
input_folder (str|pathlib.Path): input neuron
output_folder (str|pathlib.Path): output name
.. note:: the sub-directory structure is maintained.
'''
set_maximum_warnings(0)
morphologies = list(iter_morphologies(Path(input_folder)))
func = partial(_sanitize_one,
input_folder=input_folder,
output_folder=output_folder)
if nprocesses == 1:
results = map(func, morphologies)
else:
results = Pool(nprocesses).imap_unordered(func,
morphologies,
chunksize=100)
errored_paths = list(filter(None, tqdm(results, total=len(morphologies))))
if errored_paths:
L.info('Files in error:')
for path in errored_paths:
L.info(path)
def sanitize_all(input_folder, output_folder, nprocesses=1):
'''Sanitize all morphologies in input_folder and its sub-directories.
Note: the sub-directory structure is maintained.
- fixes non zero segments
- raises if the morphology has no soma
- raises if the morphology has negative diameters
Args:
input_folder (str|pathlib.Path): input neuron
output_folder (str|pathlib.Path): output name
'''
set_maximum_warnings(0)
morphologies = list(iter_morphologies(Path(input_folder)))
func = partial(_sanitize_one,
input_folder=input_folder,
output_folder=output_folder)
if nprocesses == 1:
results = map(func, morphologies)
else:
results = Pool(nprocesses).imap_unordered(func,
morphologies,
chunksize=100)
errored_paths = list(filter(None, tqdm(results, total=len(morphologies))))
if errored_paths:
L.info('Files in error:')
for path in errored_paths:
L.info(path)
def test_run_converter():
for ext_in in ['asc', 'swc', 'h5']:
assert_conversion_works(os.path.join(_path,
'circle_contour.' + ext_in))
# # real_neuron.asc prints a lot of warning that we do not care about
set_maximum_warnings(0)
assert_conversion_works(os.path.join(_path, 'real_neuron.asc'))
assert_conversion_works(os.path.join(_path, 'real_neuron2.asc'))
def test_convert_file(tmpdir):
set_maximum_warnings(0)
runner = CliRunner()
filename = Path(DATA, 'simple.asc')
output_name = Path(tmpdir, 'simple.h5')
result = runner.invoke(
cli,
['convert', 'file', str(filename),
str(output_name)])
assert result.exit_code == 0, result.exception
assert output_name.exists()
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)