def convert(input_file, outputfile, recenter=False, nrn_order=False, single_point_soma=False):
'''Run the appropriate converter
Args:
input_file(str): path to input file
outputfile(str): path to output file
recenter(bool): whether to recenter the morphology based on the
center of gravity of the soma
nrn_order(bool): whether to traverse the neuron in the NEURON fashion
single_point_soma(bool):For SWC only
'''
kwargs = {}
if nrn_order:
kwargs['options'] = Option.nrn_order
neuron = Morphology(input_file, **kwargs)
output_ext = Path(outputfile).suffix
if single_point_soma and output_ext.lower() != '.swc':
raise Exception('Single point soma is only applicable for swc output')
if output_ext.lower() not in ('.swc', '.asc', '.h5', ):
raise Exception('Output file format should be one swc, asc or h5')
output_ext = output_ext[1:] # Remove the dot
try:
converter = {MorphologyVersion.MORPHOLOGY_VERSION_SWC_1: from_swc,
MorphologyVersion.MORPHOLOGY_VERSION_ASC_1: from_h5_or_asc,
MorphologyVersion.MORPHOLOGY_VERSION_H5_1: from_h5_or_asc,
MorphologyVersion.MORPHOLOGY_VERSION_H5_1_1: from_h5_or_asc,
MorphologyVersion.MORPHOLOGY_VERSION_H5_2: from_h5_or_asc
}[neuron.version]
except KeyError as e:
raise Exception(
'No converter for morphology type: {}'.format(neuron.version)) from e
logger.info('Original soma type: %s', neuron.soma_type)
new = converter(neuron, output_ext)
if single_point_soma:
soma_to_single_point(new.soma)
if recenter:
transform.translate(new, -1 * new.soma.center)
new.write(outputfile)
try:
# pylint: disable=import-outside-toplevel
from morph_tool.neuron_surface import get_NEURON_surface
logger.info('Soma surface as computed by NEURON:\n'
'before conversion: %s\n'
'after conversion: %s',
get_NEURON_surface(input_file),
get_NEURON_surface(outputfile))
except: # noqa pylint: disable=bare-except
logger.info('Final NEURON soma surface check was skipped probably because BluePyOpt'
' or NEURON is not installed')
def _get_surface(filename, extension):
if extension == 'h5':
raise NotImplementedError
if extension == 'asc':
return get_NEURON_surface(filename)
if extension == 'swc':
return get_NEURON_surface(filename)
raise NotImplementedError
def soma_surface(input_file, quiet):
'''Get soma surface as computed by NEURON'''
# pylint: disable=import-outside-toplevel
from morph_tool.neuron_surface import get_NEURON_surface
if quiet:
L.setLevel(logging.WARNING)
try:
click.echo('Soma surface: {}'.format(get_NEURON_surface(input_file)))
except ImportError as e:
raise ImportError('''the NEURON module is not installed.
- if you are on the cluster, you can try: module load nix/hpc/neuron
- otherwise, get it here: https://github.com/neuronsimulator/nrn and compile it...'''
) from e
def convert(input_file,
outputfile,
recenter=False,
nrn_order=False,
single_point_soma=False,
sanitize=False):
"""Run the appropriate converter.
Args:
input_file(str): path to input file
outputfile(str): path to output file
recenter(bool): whether to recenter the morphology based on the
center of gravity of the soma
nrn_order(bool): whether to traverse the neuron in the NEURON fashion
single_point_soma(bool): For SWC only
sanitize(bool): whether to sanitize the morphology
"""
kwargs = {}
if nrn_order:
kwargs['options'] = Option.nrn_order
neuron = Morphology(input_file, **kwargs)
if sanitize:
neuron.remove_unifurcations()
output_ext = Path(outputfile).suffix
if single_point_soma and output_ext.lower() != '.swc':
raise Exception('Single point soma is only applicable for swc output')
if output_ext.lower() not in (
'.swc',
'.asc',
'.h5',
):
raise Exception('Output file format should be one swc, asc or h5')
output_ext = output_ext[1:] # Remove the dot
try:
converter = {
'swc': from_swc,
'asc': from_h5_or_asc,
'h5': from_h5_or_asc,
}[neuron.version[0]]
except KeyError as e:
raise Exception(
f'No converter for morphology type: {neuron.version}') from e
L.info('Original soma type: %s', neuron.soma_type)
new = converter(neuron, output_ext)
if single_point_soma:
soma_to_single_point(new.soma)
if recenter:
transform.translate(new, -1 * new.soma.center)
try:
new.write(outputfile)
except WriterError as e:
raise MorphToolException('Use `sanitize` option for converting') from e
try:
# pylint: disable=import-outside-toplevel
from morph_tool.neuron_surface import get_NEURON_surface
L.info(
'Soma surface as computed by NEURON:\n'
'before conversion: %s\n'
'after conversion: %s', get_NEURON_surface(input_file),
get_NEURON_surface(outputfile))
except: # noqa pylint: disable=bare-except
L.info(
'Final NEURON soma surface check was skipped probably because BluePyOpt'
' or NEURON is not installed')