def main():
"""
Program entry point.
"""
args = process_args()
print('Parsing and resolving model: ' + args.lems_file)
model = Model()
if args.I is not None:
for dir in args.I:
model.add_include_directory(dir)
model.import_from_file(args.lems_file)
resolved_model = model.resolve()
print('Building simulation')
sim = SimulationBuilder(resolved_model).build()
#sim.dump("Afterbuild:")
if args.dlems:
print('Exporting as: ' + dlems_info)
from lems.dlems.exportdlems import export_component
target = model.targets[0]
sim_comp = model.components[target]
target_net = sim_comp.parameters['target']
target_comp = model.components[target_net]
dlems_file_name = args.lems_file.replace('.xml', '.json')
if dlems_file_name == args.lems_file:
dlems_file_name = args.lems_file + '.json'
if target_comp.type == 'network':
for child in target_comp.children:
if child.type == 'population':
comp = model.components[child.parameters['component']]
export_component(model,
comp,
sim_comp,
child.id,
file_name=dlems_file_name)
else:
export_component(model, sim_comp, target_comp)
else:
print('Running simulation')
sim.run()
process_simulation_output(sim, args)
def test_load_get_dom(self):
model = Model()
file_name = 'lems/test/hhcell_resaved2.xml'
model.import_from_file(file_name)
dom0 = model.export_to_dom()
def load_model(model_filename, folder=None):
"Load model from filename"
fp_xml = lems_file(model_filename, folder)
model = Model()
model.import_from_file(fp_xml)
# modelextended = model.resolve()
return model
def main(args=None):
"""
Program entry point.
"""
if args is None:
args = process_args()
print('Parsing and resolving model: '+args.lems_file)
model = Model()
if args.I is not None:
for dir in args.I:
model.add_include_directory(dir)
model.import_from_file(args.lems_file)
resolved_model = model.resolve()
print('Building simulation')
sim = SimulationBuilder(resolved_model).build()
#sim.dump("Afterbuild:")
if args.dlems:
print('Exporting as: '+dlems_info)
from lems.dlems.exportdlems import export_component
target = model.targets[0]
sim_comp = model.components[target]
target_net = sim_comp.parameters['target']
target_comp = model.components[target_net]
dlems_file_name = args.lems_file.replace('.xml', '.json')
if dlems_file_name == args.lems_file:
dlems_file_name = args.lems_file + '.json'
if target_comp.type == 'network':
for child in target_comp.children:
if child.type == 'population':
comp = model.components[child.parameters['component']]
export_component(model, comp, sim_comp, child.id, file_name=dlems_file_name)
else:
export_component(model, sim_comp, target_comp)
else:
print('Running simulation')
sim.run()
process_simulation_output(sim, model, args)
def load_model(self):
"Load model from filename"
# instantiate LEMS lib
model = Model()
model.import_from_file(self.xml_location)
self.XSD_validate_XML()
# Do some preprocessing on the template to easify rendering
self.pp_pow(model)
noisepresent, nsigpresent = self.pp_noise(model)
couplinglist = self.pp_cplist(model)
svboundaries = self.pp_bound(model)
return model, svboundaries, couplinglist, noisepresent, nsigpresent
def get_component_types(srcdir):
"""Obtain a list of all defined component types.
Does not return anything. Fills global variables.
It works in two stages.
First, from the XML comp_definition files, we read all the models and get the required metadata:
- names,
- the xml source file in which it is defined,
- description of the component.
Next, we read all the XML files to get an ordered list of components.
We get this list by reading the XML files and parsing them rather than
using the LEMS API used above because the LEMS API does not guarantee what
order the components will be returned in. By using the file as the source
here, we ensure that we get the component list in the same order in which
they are defined in the XML file.
:returns: nothing
"""
for comp_definition in comp_definitions:
fullpath = "{}/{}.xml".format(srcdir, comp_definition)
"""Stage 1"""
model = Model(include_includes=False)
model.import_from_file(fullpath)
for comp_type in model.component_types:
comp_types[comp_type.name] = comp_type
comp_type_src[comp_type.name] = comp_definition
comp_type_desc[
comp_type.
name] = comp_type.description if comp_type.description is not None else "ComponentType: " + comp_type.name
"""Stage 2"""
ordered_comp_type_list = []
with open(fullpath) as fp:
for line in fp:
s = '<ComponentType name='
if s in line:
i = line.index(s)
e = line.find('"', i + len(s) + 1)
comp_type_defined = line[i + len(s) + 1:e]
ordered_comp_type_list.append(comp_type_defined)
ordered_comp_types[comp_definition] = ordered_comp_type_list
def test_load_write_xml(self):
model = Model()
file_name = 'lems/test/hhcell_resaved2.xml'
model.import_from_file(file_name)
file_name2 = 'lems/test/hhcell_resaved3.xml'
model.export_to_file(file_name2)
print("----------------------------------------------")
print(open(file_name2,'r').read())
print("----------------------------------------------")
print("Written generated LEMS to %s"%file_name2)
from lems.base.util import validate_lems
validate_lems(file_name2)
def validate_model(filename, name=None, config=None):
""" Check that a model is valid
Args:
filename (:obj:`str`): path to model
name (:obj:`str`, optional): name of model for use in error messages
config (:obj:`Config`, optional): whether to fail on missing includes
Returns:
:obj:`tuple`:
* nested :obj:`list` of :obj:`str`: nested list of errors (e.g., required ids missing or ids not unique)
* nested :obj:`list` of :obj:`str`: nested list of errors (e.g., required ids missing or ids not unique)
* :obj:`Model`: model
"""
config = config or get_config()
errors = []
warnings = []
model = None
with StandardOutputErrorCapturer(relay=False, level=StandardOutputErrorCapturerLevel.c):
valid, output = validate_neuroml2_lems_file(filename, exit_on_fail=False, return_string=True)
if not valid:
errors.append(['`{}` is not a valid LEMS file.'.format(filename), [[output]]])
return (errors, warnings, model)
core_types_dir = tempfile.mkdtemp()
jar_filename = get_path_to_jnml_jar()
with zipfile.ZipFile(jar_filename, 'r') as jar_file:
neuroml2_core_type_members = (name for name in jar_file.namelist() if name.startswith('NeuroML2CoreTypes/'))
jar_file.extractall(core_types_dir, members=neuroml2_core_type_members)
model = Model(include_includes=True, fail_on_missing_includes=config.VALIDATE_IMPORTED_MODEL_FILES)
model.add_include_directory(os.path.join(core_types_dir, 'NeuroML2CoreTypes'))
model.import_from_file(filename)
shutil.rmtree(core_types_dir)
return (errors, warnings, model)
reopen.close()
print("Written to %s" % dlems_file_name)
if __name__ == '__main__':
model = Model()
try:
lems_file = sys.argv[1]
except:
lems_file = '../NeuroML2/LEMSexamples/LEMS_NML2_Ex9_FN.xml'
model.add_include_directory('../NeuroML2/NeuroML2CoreTypes')
print('Importing LEMS file from: %s' % lems_file)
model.import_from_file(lems_file)
target = model.targets[0]
sim_comp = model.components[target]
target_net = sim_comp.parameters['target']
target_comp = model.components[target_net]
if target_comp.type == 'network':
for child in target_comp.children:
if child.type == 'population':
from lems.model.model import Model
import xml.etree.ElementTree as ET
import sys
import numpy as np
import matplotlib.pyplot as plt
from math import exp
link = "https://raw.githubusercontent.com/NeuroML/NeuroML2/master/NeuroML2CoreTypes/NeuroMLCoreDimensions.xml"
nml2_dims_contents = urllib.urlopen(link).read()
nml2_dims_file = tempfile.NamedTemporaryFile(delete=False)
nml2_dims_file.write(nml2_dims_contents)
nml2_dims_file.close()
model = Model()
model.import_from_file(nml2_dims_file.name)
def get_si_value(nml2_value):
return model.get_numeric_value(nml2_value, None)
cell_doc = loaders.NeuroMLLoader.load("../../../NeuroML2/SingleCompMuscle.cell.nml")
k_slow = loaders.NeuroMLLoader.load("../../../NeuroML2/k_slow.channel.nml").ion_channel[0]
k_fast = loaders.NeuroMLLoader.load("../../../NeuroML2/k_fast.channel.nml").ion_channel[0]
ca_boyle = loaders.NeuroMLLoader.load("../../../NeuroML2/ca_boyle.channel.nml").ion_channel[0]
ca_pool = loaders.NeuroMLLoader.load("../../../NeuroML2/CaPool.nml").fixed_factor_concentration_models[0]
tree = ET.parse('../../../NeuroML2/ca_boyle.channel.nml')
cell = cell_doc.cells[0]
d = cell.morphology.segments[0].distal
p = cell.morphology.segments[0].proximal
return "<br/>%s<span %s><i>%s</i></span>"%(spacer4,grey_small_style_dark, desc)
files = ["Cells", "Synapses", "Channels", "Inputs", "Networks", "PyNN", "NeuroMLCoreDimensions", "NeuroMLCoreCompTypes"]
comp_types = {}
comp_type_src = {}
comp_type_desc = {}
ordered_comp_types = {}
for file in files:
fullfile = "%s/%s.xml"%(nml_src,file)
print "\n---------- Reading LEMS file: "+fullfile
model = Model(include_includes=False)
model.import_from_file(fullfile)
for comp_type in model.component_types:
comp_types[comp_type.name] = comp_type
comp_type_src[comp_type.name] = file
comp_type_desc[comp_type.name] = comp_type.description if comp_type.description is not None else "ComponentType: "+comp_type.name
ordered_comp_type_list = []
with open(fullfile) as fp:
for line in fp:
s = '<ComponentType name='
if s in line:
i = line.index(s)
e = line.find('"', i+len(s)+1)
comp_type_defined = line[i+len(s)+1: e]
ordered_comp_type_list.append(comp_type_defined)
ordered_comp_types[file] = ordered_comp_type_list
files = [
"Cells", "Synapses", "Channels", "Inputs", "Networks", "PyNN",
"NeuroMLCoreDimensions", "NeuroMLCoreCompTypes"
]
comp_types = {}
comp_type_src = {}
comp_type_desc = {}
ordered_comp_types = {}
for file in files:
fullfile = "%s/%s.xml" % (nml_src, file)
print "\n---------- Reading LEMS file: " + fullfile
model = Model(include_includes=False)
model.import_from_file(fullfile)
for comp_type in model.component_types:
comp_types[comp_type.name] = comp_type
comp_type_src[comp_type.name] = file
comp_type_desc[
comp_type.
name] = comp_type.description if comp_type.description is not None else "ComponentType: " + comp_type.name
ordered_comp_type_list = []
with open(fullfile) as fp:
for line in fp:
s = '<ComponentType name='
if s in line:
i = line.index(s)
e = line.find('"', i + len(s) + 1)
comp_type_defined = line[i + len(s) + 1:e]
def main(srcdir, destdir):
"""Main parser and generator function.
:param srcdir: directory holding source NeuroML Core Type XML files
:type srcdir: str
:param destdir: directory where generated files should be stored
:type destdir: str
:returns: nothing
"""
# If not defined or empty, download a new copy to a temporary directory
if not srcdir or src == "":
print("No src directory specified. Cloning NeuroML2 repo")
tempdir = tempfile.TemporaryDirectory()
tmpsrcdir = tempdir.name
print("Temporariy directory: {}".format(tmpsrcdir))
clone_command = [
"git", "clone", "--depth", "1", "--branch", nml_branch, GitHubRepo,
tmpsrcdir
]
subprocess.run(clone_command)
else:
tmpsrcdir = srcdir
# TODO: add LEMS examples
# We can't do this at the moment, because the LEMS python bits are in
# pyneuroml, while we point to the libNeuroML docs for the NeuroML2 usage
# examples. pyneuroml does not currently have docs on RTD, and some more
# work will be required to tell our templates when an example is NeuroML
# and when it is LEMS so it can point to the correct docs.
# exampledirs = [tmpsrcdir + "/examples/", tmpsrcdir + "/LEMSexamples/"]
exampledirs = [tmpsrcdir + "/examples/"]
tmpsrcdir = tmpsrcdir + "/NeuroML2CoreTypes/"
# Get current commit
commit_command = ["git", "log", "-1", "--pretty=format:%H"]
output = subprocess.run(commit_command,
capture_output=True,
cwd=tmpsrcdir,
text=True)
nml_commit = output.stdout
# read the downloaded files
get_component_types(tmpsrcdir)
# get examples
get_comp_examples(exampledirs)
# get python signatures
get_libneuroml_signatures()
if not destdir or destdir == "":
destdir = "."
print("Output files will be written to {} directory".format(destdir))
for comp_definition in comp_definitions:
fullpath = "{}/{}.xml".format(tmpsrcdir, comp_definition)
outputfile = "{}/{}.md".format(destdir, comp_definition)
"""Stage 1"""
model = Model(include_includes=False)
model.import_from_file(fullpath)
print("Processing {}".format(fullpath))
print("Writing output to {}".format(outputfile))
ast_doc = open(outputfile, 'w')
"""Page header"""
print(asttemplates.page_header.render(
comp_definition=comp_definition,
comp_description=format_description(model.description),
GitHubCompSources=GitHubCompSources,
nml_version=nml_version,
nml_branch=nml_branch,
nml_date=nml_date,
nml_commit=nml_commit),
file=ast_doc)
"""Dimensions and units"""
if "Dimensions" in comp_definition:
dimensions = model.dimensions
dimensions = sorted(dimensions, key=lambda dim: dim.name)
units = model.units
units = sorted(units, key=lambda unit: unit.symbol)
# lables are translated as lowercase in jupyter, so we append two
# consecutive underscores to differentiate same ones, like M and m.
symbols = []
for unit in units:
if unit.symbol.lower() in symbols:
unit.symbol = unit.symbol + "__"
symbols.append(unit.symbol.lower())
print(asttemplates.dimension.render(
comp_definition=comp_definition,
dimensions=dimensions,
units=units),
file=ast_doc)
# Get factors
for unit in units:
unit.factors = []
for unit2 in units:
if unit.symbol != unit2.symbol and unit.dimension == unit2.dimension:
si_val = model.get_numeric_value(
"1%s" % unit.symbol.replace("__", ""),
unit.dimension)
unit_val = (
(Decimal(si_val) /
Decimal(math.pow(10, unit2.power))) /
Decimal(unit2.scale)) - Decimal(unit2.offset)
conversion = float(unit_val)
# to catch 60.0001 etc.
if conversion > 1 and int(conversion) != conversion:
if conversion - int(conversion) < 0.001:
conversion = int(conversion)
if conversion > 10000:
conversion = '%.2e' % conversion
else:
conversion = '%s' % conversion
if conversion.endswith('.0'):
conversion = conversion[:-2]
unit.factors.append([conversion, unit2.symbol])
print(asttemplates.unit.render(comp_definition=comp_definition,
units=units),
file=ast_doc)
"""Component Types"""
for o_comp_type in ordered_comp_types[comp_definition]:
o_comp_type = o_comp_type.replace('rdf:', 'rdf_')
comp_type = model.component_types[o_comp_type]
"""Header"""
cno = None
if " cno_00" in str(comp_type.description):
cno = comp_type.description.split(" ")[-1]
comp_type.description = comp_type.description.replace(cno, "")
comp_type.description = format_description(comp_type.description)
if len(comp_type.description) > 0:
if comp_type.description[-1] not in "!.":
comp_type.description += "."
else:
comp_type.description = ""
print(asttemplates.comp.render(comp_definition=comp_definition,
comp_type=comp_type,
cno=cno),
file=ast_doc)
"""Process parameters, derived parameters, texts, paths, expsures,
requirements and ports"""
params = {}
derived_params = {}
texts = {}
paths = {}
exposures = {}
requirements = {}
eventPorts = {}
"""Get lists of them all"""
for param in comp_type.parameters:
params[param] = comp_type.name
for derived_param in comp_type.derived_parameters:
derived_params[derived_param] = comp_type.name
for text in comp_type.texts:
texts[text] = comp_type.name
for path in comp_type.paths:
paths[path] = comp_type.paths
for exp in comp_type.exposures:
exposures[exp] = comp_type.name
for req in comp_type.requirements:
requirements[req] = comp_type.name
for ep in comp_type.event_ports:
eventPorts[ep] = comp_type.name
"""Get parent ComponentType if derived from one."""
extd_comp_type = get_extended_from_comp_type(comp_type.name)
"""Recursively go up the tree and get attributes inherited from ancestors."""
while extd_comp_type is not None:
for param in extd_comp_type.parameters:
pk = params.copy().keys()
for pp0 in pk:
if pp0.name == param.name:
del params[pp0]
params[param] = extd_comp_type.name
for derived_param in extd_comp_type.derived_parameters:
derived_params[derived_param] = extd_comp_type.name
for text in extd_comp_type.texts:
texts[text] = extd_comp_type.name
for path in extd_comp_type.paths:
paths[path] = extd_comp_type.paths
for exp in extd_comp_type.exposures:
ek = exposures.copy().keys()
for ee0 in ek:
if ee0.name == exp.name:
del exposures[ee0]
exposures[exp] = extd_comp_type.name
for req in extd_comp_type.requirements:
requirements[req] = extd_comp_type.name
for ep in extd_comp_type.event_ports:
eventPorts[ep] = extd_comp_type.name
"""Recurse up the next parent"""
extd_comp_type = get_extended_from_comp_type(
extd_comp_type.name)
if len(params) > 0:
keysort = sorted(params.keys(), key=lambda param: param.name)
print(asttemplates.params.render(title="Parameters",
comp_type=comp_type,
entries=params,
keysort=keysort),
file=ast_doc)
if len(derived_params) > 0:
keysort = sorted(derived_params.keys(),
key=lambda derived_param: derived_param.name)
print(asttemplates.params.render(title="Derived parameters",
comp_type=comp_type,
entries=derived_params,
keysort=keysort),
file=ast_doc)
if len(comp_type.texts
) > 0: # TODO: Check if Text elements are inherited...
print(asttemplates.misc2c.render(title="Text fields",
textlist=comp_type.texts),
file=ast_doc)
if len(comp_type.paths
) > 0: # TODO: Check if Path elements are inherited...
print(asttemplates.misc2c.render(title="Paths",
textlist=comp_type.paths),
file=ast_doc)
if len(comp_type.component_references) > 0:
print(asttemplates.misc3c.render(
title="Component References",
textlist=comp_type.component_references),
file=ast_doc)
if len(comp_type.children) > 0:
childlist = []
childrenlist = []
for child_or_children in comp_type.children:
if not child_or_children.multiple:
childlist.append(child_or_children)
else:
childrenlist.append(child_or_children)
if len(childlist) > 0:
print(asttemplates.misc3c.render(title="Child list",
textlist=childlist),
file=ast_doc)
if len(childrenlist) > 0:
print(asttemplates.misc3c.render(title="Children list",
textlist=childrenlist),
file=ast_doc)
if len(comp_type.constants) > 0:
print(asttemplates.constants.render(
title="Constants", textlist=comp_type.constants),
file=ast_doc)
if len(comp_type.properties) > 0:
print(asttemplates.properties.render(
title="Properties", textlist=comp_type.properties),
file=ast_doc)
if len(exposures) > 0:
keysort = sorted(exposures, key=lambda entry: entry.name)
print(asttemplates.exposures.render(title="Exposures",
comp_type=comp_type,
entries=exposures,
keysort=keysort),
file=ast_doc)
if len(requirements) > 0:
keysort = sorted(requirements, key=lambda entry: entry.name)
print(asttemplates.requirements.render(title="Requirements",
comp_type=comp_type,
entries=requirements,
keysort=keysort),
file=ast_doc)
if len(eventPorts) > 0:
keysort = sorted(eventPorts, key=lambda entry: entry.name)
print(asttemplates.eventPorts.render(title="Event Ports",
comp_type=comp_type,
entries=eventPorts,
keysort=keysort),
file=ast_doc)
if len(comp_type.attachments) > 0:
print(asttemplates.misc3c.render(
title="Attachments", textlist=comp_type.attachments),
file=ast_doc)
if comp_type.dynamics and comp_type.dynamics.has_content():
print(asttemplates.dynamics.render(title="Dynamics",
comp_type=comp_type),
file=ast_doc)
# Examples
"""
print("{} has: ".format(comp_type.name))
if comp_type_py_api[comp_type.name]:
print("\t1 Py def")
if len(comp_type_examples[comp_type.name]) > 0:
print("\t{} XML examples".format(len(comp_type_examples[comp_type.name])))
"""
if comp_type_py_api[comp_type.name] or len(
comp_type_examples[comp_type.name]) > 0:
print(asttemplates.examples.render(
title="Usage",
comp_type=comp_type,
lemsexamples=comp_type_examples[comp_type.name],
pysig=comp_type_py_api[comp_type.name]),
file=ast_doc)
ast_doc.close()
print("Finished processing {}".format(fullpath))
if not srcdir:
tempdir.cleanup()
print(open(dlems_file_name,'r').read())
print("Written to %s"%dlems_file_name)
if __name__ == '__main__':
model = Model()
try:
lems_file = sys.argv[1]
except:
lems_file = '../NeuroML2/NeuroML2CoreTypes/LEMS_NML2_Ex9_FN.xml'
print('Importing LEMS file from: %s'%lems_file)
model.import_from_file(lems_file)
target = model.targets[0]
sim_comp = model.components[target]
target_net = sim_comp.parameters['target']
target_comp = model.components[target_net]
if target_comp.type == 'network':
for child in target_comp.children:
if child.type == 'population':
#! /usr/bin/python
from lems.model.model import Model
import sys
model = Model()
file_name = 'examples/hhcell.xml'
#file_name = '../NeuroML2/NeuroML2CoreTypes/LEMS_NML2_Ex0_IaF.xml'
#file_name = '../NeuroML2/NeuroML2CoreTypes/LEMS_NML2_Ex3_Net.xml'
#file_name = '../org.neuroml.import/src/test/resources/BIOMD0000000185_LEMS.xml'
if len(sys.argv) == 2:
file_name = sys.argv[1]
model.import_from_file(file_name)
fn = '/tmp/hhmodel.xml'
model.export_to_file(fn)
print("----------------------------------------------")
print(open(fn, 'r').read())
print("----------------------------------------------")
print("Written generated LEMS to %s" % fn)
from lems.base.util import validate_lems
validate_lems(fn)
#! /usr/bin/python
from lems.model.model import Model
import sys
model = Model()
file_name = 'examples/hhcell.xml'
#file_name = '../NeuroML2/NeuroML2CoreTypes/LEMS_NML2_Ex0_IaF.xml'
#file_name = '../NeuroML2/NeuroML2CoreTypes/LEMS_NML2_Ex3_Net.xml'
#file_name = '../org.neuroml.import/src/test/resources/BIOMD0000000185_LEMS.xml'
if len(sys.argv) == 2:
file_name = sys.argv[1]
model.import_from_file(file_name)
fn = '/tmp/hhmodel.xml'
model.export_to_file(fn)
print("----------------------------------------------")
print(open(fn,'r').read())
print("----------------------------------------------")
print("Written generated LEMS to %s"%fn)
from lems.base.util import validate_lems
validate_lems(fn)
