def __nml2_doc(cls,file_name,optimized=False):
import sys
import logging
logging.basicConfig(level=logging.INFO, format="%(name)-19s %(levelname)-5s - %(message)s")
from neuroml.hdf5.NeuroMLHdf5Parser import NeuroMLHdf5Parser
if optimized:
currParser = NeuroMLHdf5Parser(None,optimized=True)
currParser.parse(file_name)
return currParser.get_nml_doc()
else:
from neuroml.hdf5.NetworkBuilder import NetworkBuilder
nmlHandler = NetworkBuilder()
currParser = NeuroMLHdf5Parser(nmlHandler)
currParser.parse(file_name)
nml2_doc = nmlHandler.get_nml_doc()
if currParser.nml_doc_extra_elements:
add_all_to_document(currParser.nml_doc_extra_elements,nml2_doc)
return nml2_doc
def _read_neuroml2(nml2_file_name_or_string, include_includes=False, verbose=False,
already_included=[], print_method=print_, optimized=False, base_path=None):
#print("................ Loading: %s"%nml2_file_name_or_string[:7])
base_path_to_use = os.path.dirname(os.path.realpath(nml2_file_name_or_string)) if base_path == None else base_path
if supressGeneratedsWarnings: warnings.simplefilter("ignore")
if not isinstance(nml2_file_name_or_string, str) or nml2_file_name_or_string.startswith('<'):
nml2_doc = nmlparsestring(nml2_file_name_or_string)
base_path_to_use = './' if base_path == None else base_path
elif nml2_file_name_or_string.endswith('.h5') or nml2_file_name_or_string.endswith('.hdf5'):
nml2_doc = NeuroMLHdf5Loader.load(nml2_file_name_or_string,optimized=optimized)
else:
nml2_doc = NeuroMLLoader.load(nml2_file_name_or_string)
if supressGeneratedsWarnings: warnings.resetwarnings()
if include_includes:
print_method('Including included files (included already: %s)' \
% already_included, verbose)
for include in nml2_doc.include:
incl_loc = os.path.abspath(os.path.join(base_path_to_use, include.href))
if incl_loc not in already_included:
print_method("Loading included NeuroML2 file: %s (base: %s, resolved: %s)" % (include.href, base_path_to_use, incl_loc),
verbose)
if incl_loc.endswith('.nml') or incl_loc.endswith('.xml'):
nml2_sub_doc = read_neuroml2_file(incl_loc, True,
verbose=verbose, already_included=already_included)
already_included.append(incl_loc)
add_all_to_document(nml2_sub_doc,nml2_doc)
elif incl_loc.endswith('.nml.h5'):
nml2_sub_doc = NeuroMLHdf5Loader.load(incl_loc)
already_included.append(incl_loc)
add_all_to_document(nml2_sub_doc,nml2_doc)
else:
raise Exception("Unrecognised extension on file: %s"%incl_loc)
nml2_doc.include = []
else:
if len(nml2_doc.include)>0:
print_method('NOT including included files, even though %s are included!'%len(nml2_doc.include), verbose)
nml2_doc.include = []
return nml2_doc
def get_nml_doc(self):
if not self.optimized:
nml2_doc = nmlHandler.get_nml_doc()
if self.nml_doc_extra_elements:
add_all_to_document(self.nml_doc_extra_elements, nml2_doc)
return nml2_doc
else:
nml_doc = neuroml.NeuroMLDocument(id=self.doc_id,
notes=self.doc_notes)
if self.nml_doc_extra_elements:
add_all_to_document(self.nml_doc_extra_elements, nml_doc)
nml_doc.networks.append(self.optimizedNetwork)
return nml_doc