def setUp(self):
"""
Testing a complex hand-built morphology (from neuroml objects
rather than arrays)
"""
p = neuroml.Point3DWithDiam(x=0,y=0,z=0,diameter=50)
d = neuroml.Point3DWithDiam(x=50,y=0,z=0,diameter=50)
soma = neuroml.Segment(proximal=p, distal=d)
soma.name = 'Soma'
soma.id = 0
#now make an axon with 100 compartments:
parent = neuroml.SegmentParent(segments=soma.id)
parent_segment = soma
axon_segments = []
seg_id = 1
for i in range(100):
p = neuroml.Point3DWithDiam(x=parent_segment.distal.x,
y=parent_segment.distal.y,
z=parent_segment.distal.z,
diameter=0.1)
d = neuroml.Point3DWithDiam(x=parent_segment.distal.x+10,
y=parent_segment.distal.y,
z=parent_segment.distal.z,
diameter=0.1)
axon_segment = neuroml.Segment(proximal = p,
distal = d,
parent = parent)
axon_segment.id = seg_id
axon_segment.name = 'axon_segment_' + str(axon_segment.id)
#now reset everything:
parent = neuroml.SegmentParent(segments=axon_segment.id)
parent_segment = axon_segment
seg_id += 1
axon_segments.append(axon_segment)
test_morphology = am.ArrayMorphology()
test_morphology.segments.append(soma)
test_morphology.segments += axon_segments
test_morphology.id = "TestMorphology"
self.test_morphology = test_morphology
def segment_from_vertex_index(self, index):
print "index:"
print index
parent_index = self.connectivity[index]
node_x = self.vertices[index][0]
node_y = self.vertices[index][1]
node_z = self.vertices[index][2]
node_d = self.vertices[index][3]
parent_x = self.vertices[parent_index][0]
parent_y = self.vertices[parent_index][1]
parent_z = self.vertices[parent_index][2]
parent_d = self.vertices[parent_index][3]
p = neuroml.Point3DWithDiam(x=node_x,
y=node_y,
z=node_z,
diameter=node_d)
d = neuroml.Point3DWithDiam(x=parent_x,
y=parent_y,
z=parent_z,
diameter=parent_d)
seg = neuroml.Segment(proximal=p, distal=d, id=index)
if index > 1:
parent = neuroml.SegmentParent(segments=parent_index)
seg.parent = parent
return seg
def _morphology(self):
"""Return the morphology of the cell. Currently this is restricted to
`Neuron <#neuron>`_ objects.
"""
morph_name = "morphology_" + str(next(self.name()))
# Query for segments
query = segment_query.substitute(morph_name=morph_name)
qres = self.rdf.query(query, initNs=ns)
morph = neuroml.Morphology(id=morph_name)
for r in qres:
par = False
if r['par_id']:
par = neuroml.SegmentParent(segments=str(r['par_id']))
s = neuroml.Segment(name=str(r['seg_name']),
id=str(r['seg_id']),
parent=par)
else:
s = neuroml.Segment(name=str(r['seg_name']),
id=str(r['seg_id']))
if r['x_prox']:
loop_prox = neuroml.Point3DWithDiam(
*(r[x] for x in ['x_prox', 'y_prox', 'z_prox', 'd_prox']))
s.proximal = loop_prox
loop = neuroml.Point3DWithDiam(*(r[x]
for x in ['x', 'y', 'z', 'd']))
s.distal = loop
morph.segments.append(s)
# Query for segment groups
query = segment_group_query.substitute(morph_name=morph_name)
qres = self.rdf.query(query, initNs=ns)
for r in qres:
s = neuroml.SegmentGroup(id=r['gid'])
if r['member']:
m = neuroml.Member()
m.segments = str(r['member'])
s.members.append(m)
elif r['include']:
i = neuroml.Include()
i.segment_groups = str(r['include'])
s.includes.append(i)
morph.segment_groups.append(s)
return morph
def morphology(self):
morph_name = "morphology_" + str(self.name())
# Query for segments
query = segment_query.substitute(morph_name=morph_name)
qres = self['semantic_net'].query(query, initNs=ns)
morph = neuroml.Morphology(id=morph_name)
for r in qres:
par = False
if r['par_id']:
par = neuroml.SegmentParent(segments=str(r['par_id']))
s = neuroml.Segment(name=str(r['seg_name']),
id=str(r['seg_id']),
parent=par)
else:
s = neuroml.Segment(name=str(r['seg_name']),
id=str(r['seg_id']))
if r['x_prox']:
loop_prox = neuroml.Point3DWithDiam(
*(r[x] for x in ['x_prox', 'y_prox', 'z_prox', 'd_prox']))
s.proximal = loop_prox
loop = neuroml.Point3DWithDiam(*(r[x]
for x in ['x', 'y', 'z', 'd']))
s.distal = loop
morph.segments.append(s)
# Query for segment groups
query = segment_group_query.substitute(morph_name=morph_name)
qres = self['semantic_net'].query(query, initNs=ns)
for r in qres:
s = neuroml.SegmentGroup(id=r['gid'])
if r['member']:
m = neuroml.Member()
m.segments = str(r['member'])
s.members.append(m)
elif r['include']:
i = neuroml.Include()
i.segment_groups = str(r['include'])
s.includes.append(i)
morph.segment_groups.append(s)
return morph
def convert_morphology(root, positions='auto'):
"""Convert moose neuron morphology contained under `root` into a
NeuroML object. The id of the return object is
{root.name}_morphology. Each segment object gets the numeric value
of the moose id of the object. The name of the segments are same
as the corresponding moose compartment.
Parameters
----------
root : a moose element containing a single cell model.
positions : string
flag to indicate if the positions of the end points of the
compartments are explicitly available in the compartments or
should be automatically generated. Possible values:
`auto` - automatically generate z coordinates using length of the
compartments.
`explicit` - model has explicit coordinates for all compartments.
Return
------
a neuroml.Morphology instance.
"""
if positions == 'auto':
queue = deque([autoposition(root)])
elif positions == 'explicit':
compartments = moose.wildcardFind('%s/##[TYPE=Compartment]' % (root.path))
queue = deque([compartment for compartment in map(moose.element, compartments)
if len(compartment.neighbours['axial']) == 0])
if len(queue) != 1:
raise Exception('There must be one and only one top level compartment. Found %d' % (len(topcomp_list)))
else:
raise Exception('allowed values for keyword argument positions=`auto` or `explicit`')
comp_seg = {}
parent = None
while len(queue) > 0:
compartment = queue.popleft()
proximal = neuroml.Point3DWithDiam(x=compartment.x0,
y=compartment.y0,
z=compartment.z0,
diameter=compartment.diameter)
distal = neuroml.Point3DWithDiam(x=compartment.x,
y=compartment.y,
z=compartment.z,
diameter=compartment.diameter)
plist = list(map(moose.element, compartment.neighbours['axial']))
try:
parent = neuroml.SegmentParent(segments=comp_seg[moose.element(plist[0])].id)
except (KeyError, IndexError) as e:
parent = None
segment = neuroml.Segment(id=compartment.id_.value,
proximal=proximal,
distal=distal,
parent=parent)
# TODO: For the time being using numerical value of the moose
# id for neuroml id.This needs to be updated for handling
# array elements
segment.name = compartment.name
comp_seg[compartment] = segment
queue.extend([comp for comp in map(moose.element, compartment.neighbours['raxial'])])
morph = neuroml.Morphology(id='%s_morphology' % (root.name))
morph.segments.extend(comp_seg.values())
return morph
In this example an axon is built, a morphology is loaded, the axon is
then connected to the loadeed morphology.
"""
import neuroml
import neuroml.loaders as loaders
import neuroml.writers as writers
fn = './test_files/Purk2M9s.nml'
doc = loaders.NeuroMLLoader.load(fn)
print("Loaded morphology file from: " + fn)
#get the parent segment:
parent_segment = doc.cells[0].morphology.segments[0]
parent = neuroml.SegmentParent(segments=parent_segment.id)
#make an axon:
seg_id = 5000 # need a way to get a unique id from a morphology
axon_segments = []
for i in range(10):
p = neuroml.Point3DWithDiam(x=parent_segment.distal.x,
y=parent_segment.distal.y,
z=parent_segment.distal.z,
diameter=0.1)
d = neuroml.Point3DWithDiam(x=parent_segment.distal.x + 10,
y=parent_segment.distal.y,
z=parent_segment.distal.z,
diameter=0.1)
def to_neuroml(self, filename, resolution=10, write=True):
'''
Save the neuron as a NeuroML (.nml) object.
Parameters
----------
filename : str
Name of the MNL file to write.
resolution : int, optional (default: 10)
Coarse-graining factor of the structure: only one point every
`resolution` will be kept.
write : bool, optional (default: True)
Write the file.
Returns
-------
neuroml.Cell object.
'''
import neuroml
import neuroml.writers as writers
x = self.position[0].to('micrometer').m
y = self.position[1].to('micrometer').m
z = 0.
p = neuroml.Point3DWithDiam(x=x,
y=y,
z=z,
diameter=2. * self.soma_radius.m)
soma = neuroml.Segment(proximal=p, distal=p)
soma.name = 'Soma'
soma.id = 0
seg_id = 0
morpho = neuroml.Morphology()
morpho.id = "Morphology neuron {}".format(int(self))
morpho.segments.append(soma)
neurites_segments = []
neurites = list(self.dendrites.values())
if self.axon is not None:
neurites.append(self.axon)
# set dendrites
for neurite in neurites:
p_segment = soma
parent = neuroml.SegmentParent(segments=soma.id)
branch_seen = {}
todo = _deque([branch for branch in neurite.branches])
indices = _deque([i for i in range(len(todo))])
while todo:
branch = todo.popleft()
idx = indices.popleft()
if branch.parent in (-1, 0, None):
p_segment = soma
parent = neuroml.SegmentParent(segments=soma.id)
elif branch.parent in branch_seen:
p_segment = branch_seen[branch.parent]
parent = neuroml.SegmentParent(segments=p_segment.id)
else:
parent = None
if parent is not None:
diameter = branch.diameter
if neurite.taper_rate is not None:
dist_to_tip = _np.cumsum(branch.r[::-1])[::-1]
diameter = diameter + neurite.taper_rate * dist_to_tip
else:
diameter = (diameter for _ in range(len(branch.xy)))
# subsample positions and diameters
subnodes = branch.xy[::resolution].m
subdiam = diameter[::resolution].m
for pos, diam in zip(subnodes, subdiam):
p = neuroml.Point3DWithDiam(
x=p_segment.distal.x,
y=p_segment.distal.y,
z=p_segment.distal.z,
diameter=p_segment.distal.diameter)
d = neuroml.Point3DWithDiam(x=pos[0],
y=pos[1],
z=p_segment.distal.z,
diameter=diam)
n_segment = neuroml.Segment(proximal=p,
distal=d,
parent=parent)
n_segment.id = seg_id
n_segment.name = '{}_segment_{}'.format(
neurite, seg_id)
# set as next parent
p_segment = n_segment
parent = neuroml.SegmentParent(segments=p_segment.id)
seg_id += 1
neurites_segments.append(n_segment)
# store the last point as future parent for child branches
branch_seen[branch.node_id] = p_segment
else:
todo.append(branch)
indices.append(idx)
morpho.segments += neurites_segments
# make the neuroml cell
cell = neuroml.Cell()
cell.name = "Neuron {}".format(int(self))
cell.id = int(self)
cell.morphology = morpho
# write
if write:
doc = neuroml.NeuroMLDocument(id=filename)
doc.cells.append(cell)
writers.NeuroMLWriter.write(doc, filename)
return cell
def parse_templates_json(templates_json="templates.json",
ignore_chans = [],
save_example_files=False,
verbose=False):
with open(templates_json, "r") as templates_json_file:
json_cells = json.load(templates_json_file)
concentrationModels = ''
for firing_type_u in json_cells:
if verbose: print("\n --------------- %s "%(firing_type_u))
firing_type = str(firing_type_u)
cell_dict = json_cells[firing_type]
nml_doc = neuroml.NeuroMLDocument(id=firing_type)
# Membrane properties
#
included_channels[firing_type] = []
channel_densities = []
channel_density_nernsts = []
channel_density_non_uniform_nernsts = []
channel_density_non_uniforms = []
species = []
for section_list in cell_dict['forsecs']:
for parameter_name in cell_dict['forsecs'][section_list]:
value = cell_dict['forsecs'][section_list][parameter_name]
if verbose: print(" --- %s, %s: %s "%(section_list,parameter_name,value))
if parameter_name == 'g_pas':
channel = 'pas'
arguments = {}
cond_density = "%s S_per_cm2" % value
if verbose: print(' - Adding %s with %s'%(channel, cond_density))
channel_nml2_file = "%s.channel.nml"%channel
if channel_nml2_file not in included_channels[firing_type]:
nml_doc.includes.append(
neuroml.IncludeType(
href="../../NeuroML2/%s" %
channel_nml2_file))
included_channels[firing_type].append(channel_nml2_file)
erev = cell_dict['forsecs'][section_list]['e_pas']
erev = "%s mV" % erev
arguments["cond_density"] = cond_density
arguments['ion_channel'] = channel
arguments["ion"] = "non_specific"
arguments["erev"] = erev
arguments["id"] = "%s_%s" % (section_list, parameter_name)
channel_class = 'ChannelDensity'
density = getattr(neuroml, channel_class)(**arguments)
channel_densities.append(density)
for section_list in cell_dict['parameters']:
for parameter_name in cell_dict['parameters'][section_list]:
if parameter_name != 'e_pas' and 'CaDynamics_E2' not in parameter_name:
parameter_dict = cell_dict['parameters'][section_list][parameter_name]
if verbose: print(" --- %s, %s: %s "%(section_list,parameter_name,parameter_dict))
channel = parameter_dict['channel']
if channel not in ignore_chans:
arguments = {}
cond_density = None
variable_parameters = None
if parameter_dict['distribution']['disttype'] == "uniform":
value = float(parameter_dict['distribution']['value'])
if channel in density_scales:
value = value * density_scales[channel]
cond_density = "%s S_per_cm2" % value
else:
new_expr = '1e4 * (%s)'%parameter_dict['distribution']['value'].replace('x','p').replace('epp','exp')
iv = neuroml.InhomogeneousValue(inhomogeneous_parameters="PathLengthOver_%s"%section_list,
value=new_expr)
variable_parameters = [
neuroml.VariableParameter(
segment_groups=section_list,
parameter='condDensity',
inhomogeneous_value=iv)]
channel_name = channel
if channel_substitutes.has_key(channel):
channel_name = channel_substitutes[channel]
channel_nml2_file = "%s.channel.nml"%channel_name
if channel_nml2_file not in included_channels[firing_type]:
nml_doc.includes.append(
neuroml.IncludeType(
href="../../NeuroML2/%s" %
channel_nml2_file))
included_channels[firing_type].append(channel_nml2_file)
arguments['ion'] = channel_ions[channel]
erev = ion_erevs[arguments["ion"]]
channel_class = 'ChannelDensity'
if erev == "nernst":
erev = None
channel_class = 'ChannelDensityNernst'
elif erev == "pas":
erev = cell_dict['parameters'] \
[section_list]['e_pas']['distribution']\
['value']
erev = "%s mV" % erev
arguments["ion"] = "non_specific"
if variable_parameters is not None:
channel_class += 'NonUniform'
else:
arguments["segment_groups"] = section_list
if erev is not None:
arguments["erev"] = erev
arguments["id"] = "%s_%s" % (section_list, parameter_name)
if cond_density is not None:
arguments["cond_density"] = cond_density
arguments['ion_channel'] = channel_name
if variable_parameters is not None:
arguments['variable_parameters'] = variable_parameters
density = getattr(neuroml, channel_class)(**arguments)
if channel_class == "ChannelDensityNernst":
channel_density_nernsts.append(density)
elif channel_class == "ChannelDensityNernstNonUniform":
channel_density_non_uniform_nernsts.append(density)
elif channel_class == "ChannelDensityNonUniform":
channel_density_non_uniforms.append(density)
else:
channel_densities.append(density)
elif 'gamma_CaDynamics_E2' in parameter_name:
parameter_dict = cell_dict['parameters'][section_list][parameter_name]
model = 'CaDynamics_E2_NML2__%s_%s'%(firing_type,section_list)
value = parameter_dict['distribution']['value']
concentrationModels+='<concentrationModel id="%s" ion="ca" '%model +\
'type="concentrationModelHayEtAl" minCai="1e-4 mM" ' +\
'gamma="%s" '%value
elif 'decay_CaDynamics_E2' in parameter_name:
# calcium_model = \
# neuroml.DecayingPoolConcentrationModel(ion='ca')
model = 'CaDynamics_E2_NML2__%s_%s'%(firing_type,section_list)
species.append(neuroml.Species(
id='ca',
ion='ca',
initial_concentration='5.0E-11 mol_per_cm3',
initial_ext_concentration='2.0E-6 mol_per_cm3',
concentration_model=model,
segment_groups=section_list))
channel_nml2_file = 'CaDynamics_E2_NML2.nml'
if channel_nml2_file not in included_channels[firing_type]:
included_channels[firing_type].append(channel_nml2_file)
parameter_dict = cell_dict['parameters'][section_list][parameter_name]
value = parameter_dict['distribution']['value']
concentrationModels+='decay="%s ms" depth="0.1 um"/> <!-- For group %s in %s-->\n\n'%(value,section_list,firing_type)
capacitance_overwrites = {}
for section_list in cell_dict['forsecs']:
for parameter_name in cell_dict['forsecs'][section_list]:
if parameter_name == "cm" and section_list != 'all':
value = cell_dict['forsecs'][section_list][parameter_name]
capacitance_overwrites[
section_list] = "%s uF_per_cm2" % value
specific_capacitances = []
for section_list in default_capacitances:
if section_list in capacitance_overwrites:
capacitance = capacitance_overwrites[section_list]
else:
capacitance = default_capacitances[section_list]
specific_capacitances.append(
neuroml.SpecificCapacitance(value=capacitance,
segment_groups=section_list))
init_memb_potentials = [neuroml.InitMembPotential(
value="-80 mV", segment_groups='all')]
membrane_properties = neuroml.MembraneProperties(
channel_densities=channel_densities,
channel_density_nernsts=channel_density_nernsts,
channel_density_non_uniform_nernsts=channel_density_non_uniform_nernsts,
channel_density_non_uniforms=channel_density_non_uniforms,
specific_capacitances=specific_capacitances,
init_memb_potentials=init_memb_potentials)
# Intracellular Properties
#
resistivities = []
resistivities.append(neuroml.Resistivity(
value="100 ohm_cm", segment_groups='all'))
intracellular_properties = neuroml.IntracellularProperties(
resistivities=resistivities,
species=species)
# Cell construction
#
biophysical_properties = \
neuroml.BiophysicalProperties(id="biophys",
intracellular_properties=
intracellular_properties,
membrane_properties=
membrane_properties)
biophysical_properties_vs_types[firing_type] = biophysical_properties
if save_example_files:
cell = neuroml.Cell(id=firing_type,
notes="\n*************************\nThis is not a physiologically constrained cell model!!\n"+\
"It is only for testing formatting of the biophysicalProperties extracted from templates.json\n*************************\n",
biophysical_properties=biophysical_properties)
nml_doc.cells.append(cell)
cell.morphology = neuroml.Morphology(id="morph")
cell.morphology.segments.append(neuroml.Segment(id='0',
name='soma',
proximal=neuroml.Point3DWithDiam(x=0,y=0,z=0,diameter=10),
distal=neuroml.Point3DWithDiam(x=0,y=20,z=0,diameter=10)))
cell.morphology.segment_groups.append(neuroml.SegmentGroup(id="soma",
neuro_lex_id="sao864921383",
members=[neuroml.Member("0")]))
cell.morphology.segments.append(neuroml.Segment(id='1',
name='axon',
parent=neuroml.SegmentParent(segments='0',fraction_along="0"),
proximal=neuroml.Point3DWithDiam(x=0,y=0,z=0,diameter=2),
distal=neuroml.Point3DWithDiam(x=0,y=-50,z=0,diameter=2)))
cell.morphology.segment_groups.append(neuroml.SegmentGroup(id="axon",
neuro_lex_id="sao864921383",
members=[neuroml.Member("1")]))
cell.morphology.segments.append(neuroml.Segment(id='2',
name='basal_dend',
parent=neuroml.SegmentParent(segments='0'),
proximal=neuroml.Point3DWithDiam(x=0,y=20,z=0,diameter=3),
distal=neuroml.Point3DWithDiam(x=50,y=20,z=0,diameter=3)))
cell.morphology.segment_groups.append(neuroml.SegmentGroup(id="basal_dend",
neuro_lex_id="sao864921383",
members=[neuroml.Member("2")]))
cell.morphology.segments.append(neuroml.Segment(id='3',
name='apical_dend1',
parent=neuroml.SegmentParent(segments='0'),
proximal=neuroml.Point3DWithDiam(x=0,y=20,z=0,diameter=3),
distal=neuroml.Point3DWithDiam(x=0,y=120,z=0,diameter=3)))
cell.morphology.segments.append(neuroml.Segment(id='4',
name='apical_dend2',
parent=neuroml.SegmentParent(segments='0'),
proximal=neuroml.Point3DWithDiam(x=0,y=120,z=0,diameter=3),
distal=neuroml.Point3DWithDiam(x=0,y=220,z=0,diameter=3)))
cell.morphology.segment_groups.append(neuroml.SegmentGroup(id="apical_dend",
neuro_lex_id="sao864921383",
members=[neuroml.Member("3"),neuroml.Member("4")]))
cell.morphology.segment_groups.append(neuroml.SegmentGroup(id="somatic",includes=[neuroml.Include("soma")]))
cell.morphology.segment_groups.append(neuroml.SegmentGroup(id="axonal", includes=[neuroml.Include("axon")]))
sg = neuroml.SegmentGroup(id="basal", includes=[neuroml.Include("basal_dend")])
sg.inhomogeneous_parameters.append(neuroml.InhomogeneousParameter(id="PathLengthOver_"+"basal",
variable="x",
metric="Path Length from root",
proximal=neuroml.ProximalDetails(translation_start="0")))
cell.morphology.segment_groups.append(sg)
sg = neuroml.SegmentGroup(id="apical", includes=[neuroml.Include("apical_dend")])
sg.inhomogeneous_parameters.append(neuroml.InhomogeneousParameter(id="PathLengthOver_"+"apical",
variable="x",
metric="Path Length from root",
proximal=neuroml.ProximalDetails(translation_start="0")))
cell.morphology.segment_groups.append(sg)
nml_filename = 'test/%s.cell.nml' % firing_type
neuroml.writers.NeuroMLWriter.write(nml_doc, nml_filename)
logging.debug("Written cell file to: %s", nml_filename)
neuroml.utils.validate_neuroml2(nml_filename)
conc_mod_file = open('test/concentrationModel.txt','w')
conc_mod_file.write(concentrationModels)
conc_mod_file.close()
