# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
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'''Utility functions and for loading neurons'''
import logging
import os
import glob
from functools import partial
from neurom.core.population import Population
from neurom.exceptions import (RawDataError, NeuroMError)
from neurom.io.datawrapper import DataWrapper
from neurom.io import (swc, neurolucida)
from neurom.fst._core import FstNeuron
from neurom._compat import filter, StringType
L = logging.getLogger(__name__)
def _is_morphology_file(filepath):
""" Check if `filepath` is a file with one of morphology file extensions. """
return (
os.path.isfile(filepath) and
os.path.splitext(filepath)[1].lower() in ('.swc', '.h5', '.asc')
)
[docs]class NeuronLoader(object):
"""
Caching morphology loader.
Arguments:
directory: path to directory with morphology files
file_ext: file extension to look for (if not set, will pick any of .swc|.h5|.asc)
cache_size: size of LRU cache (if not set, no caching done)
"""
[docs] def __init__(self, directory, file_ext=None, cache_size=None):
self.directory = directory
self.file_ext = file_ext
if cache_size is not None:
from pylru import FunctionCacheManager
self.get = FunctionCacheManager(self.get, size=cache_size)
def _filepath(self, name):
""" File path to `name` morphology file. """
if self.file_ext is None:
candidates = glob.glob(os.path.join(self.directory, name + ".*"))
candidates = filter(_is_morphology_file, candidates)
try:
return next(candidates)
except StopIteration:
raise NeuroMError("Can not find morphology file for '%s' " % name)
else:
return os.path.join(self.directory, name + self.file_ext)
# pylint:disable=method-hidden
[docs] def get(self, name):
""" Get `name` morphology data. """
return load_neuron(self._filepath(name))
[docs]def get_morph_files(directory):
'''Get a list of all morphology files in a directory
Returns:
list with all files with extensions '.swc' , 'h5' or '.asc' (case insensitive)
'''
lsdir = [os.path.join(directory, m) for m in os.listdir(directory)]
return list(filter(_is_morphology_file, lsdir))
[docs]def load_neuron(filename):
'''Build section trees from an h5 or swc file'''
rdw = load_data(filename)
name = os.path.splitext(os.path.basename(filename))[0]
return FstNeuron(rdw, name)
[docs]def load_neurons(neurons,
neuron_loader=load_neuron,
name=None,
population_class=Population):
'''Create a population object from all morphologies in a directory\
of from morphologies in a list of file names
Parameters:
neurons: directory path or list of neuron file paths
neuron_loader: function taking a filename and returning a neuron
population_class: class representing populations
name (str): optional name of population. By default 'Population' or\
filepath basename depending on whether neurons is list or\
directory path respectively.
Returns:
neuron population object
'''
if isinstance(neurons, list) or isinstance(neurons, tuple):
files = neurons
name = name if name is not None else 'Population'
elif isinstance(neurons, StringType):
files = get_morph_files(neurons)
name = name if name is not None else os.path.basename(neurons)
pop = population_class([neuron_loader(f) for f in files], name=name)
return pop
[docs]def load_data(filename):
'''Unpack data into a raw data wrapper'''
ext = os.path.splitext(filename)[1].lower()
if ext not in _READERS:
raise NeuroMError('Do not have a loader for "%s" extension' % ext)
try:
return _READERS[ext](filename)
except Exception:
L.exception('Error reading file %s, using "%s" loader', filename, ext)
raise RawDataError('Error reading file %s' % filename)
def _load_h5(filename):
'''Delay loading of h5py until it is needed'''
from neurom.io import hdf5
return hdf5.read(filename,
remove_duplicates=False,
data_wrapper=DataWrapper)
_READERS = {
'.swc': partial(swc.read,
data_wrapper=DataWrapper),
'.h5': _load_h5,
'.asc': partial(neurolucida.read,
data_wrapper=DataWrapper)
}