def _try_arb_morpho(path):
import arbor
try:
morfo = arbor.load_swc_arbor(path)
labels = arbor.label_dict({})
except:
try:
m = arbor.load_asc(path)
except:
raise IOError(f"Can't load '{path}' as an SWC or ASC morphology.")
morfo, labels = m.morphology, m.labels
return morfo, labels
import sys
from arbor import mechanism as mech
#(1) Creat a cell.
# Create the morphology
# Read the SWC filename from input
# Example from docs: single_cell_detailed.swc
if len(sys.argv) < 2:
print("No SWC file passed to the program")
sys.exit(0)
filename = sys.argv[1]
morph = arbor.load_swc_arbor(filename)
# Create and populate the label dictionary.
labels = arbor.label_dict()
# Regions:
labels['soma'] = '(tag 1)'
labels['axon'] = '(tag 2)'
labels['dend'] = '(tag 3)'
labels['last'] = '(tag 4)'
labels['all'] = '(all)'
labels['gt_1.5'] = '(radius-ge (region "all") 1.5)'
tree = arbor.segment_tree()
tree.append(mnpos, mpoint(-3.0, 0.0, 0.0, 3.0), mpoint( 3.0, 0.0, 0.0, 3.0), tag=1)
tree.append(0, mpoint( 3.0, 0.0, 0.0, 0.6), mpoint(9.0,-1.0, 0.0, 0.5), tag=3)
tree.append(1, mpoint(14.0, 0.0, 0.0, 0.5), tag= 3)
tree.append(2, mpoint(17.0, -4.0, 0.0, 0.3), tag= 3)
tree.append(2, mpoint(19.0, 3.0, 0.0, 0.3), tag= 3)
tree.append(0, mpoint( 3.0, 0.0, 0.0, 0.6), mpoint(13.0, 3.0, 0.0, 0.5), tag=3)
tree.append(5, mpoint(19.0, 3.0, 0.0, 0.3), tag= 3)
tree.append(5, mpoint(17.0, 8.0, 0.0, 0.1), tag= 3)
tree.append(mnpos, mpoint(-3.0, 0.0, 0.0, 1.5), mpoint(-5.5,-0.2, 0.0, 0.5), tag=2)
tree.append(8, mpoint(-14.5,-0.1, 0.0, 0.5), tag=2)
ysoma_morph3 = arbor.morphology(tree)
fn = os.path.realpath(os.path.join(os.getcwd(), os.path.dirname(__file__), "../concepts/example.swc"))
swc_morph = arbor.load_swc_arbor(fn)
regions = {
'empty': '(nil)',
'all': '(all)',
'tag1': '(tag 1)',
'tag2': '(tag 2)',
'tag3': '(tag 3)',
'tag4': '(tag 4)',
'soma': '(region "tag1")',
'axon': '(region "tag2")',
'dend': '(join (region "tag3") (region "tag4"))',
'radlt5': '(radius-lt (all) 0.5)',
'radle5': '(radius-le (all) 0.5)',
'radgt5': '(radius-gt (all) 0.5)',
'radge5': '(radius-ge (all) 0.5)',
arbor.cable_probe_membrane_voltage_cell(),
arbor.cable_probe_total_current_cell(),
arbor.cable_probe_stimulus_current_cell()
]
# Read the SWC filename from input
# Example from docs: single_cell_detailed.swc
if len(sys.argv) < 2:
print("No SWC file passed to the program")
sys.exit(0)
filename = sys.argv[1]
# define morphology (needed for arbor.place_pwlin)
morphology = arbor.load_swc_arbor(filename)
# number of CVs per branch
nseg = 3
# Label dictionary
defs = {}
labels = arbor.label_dict(defs)
# decor
decor = arbor.decor()
# set initial voltage, temperature, axial resistivity, membrane capacitance
decor.set_property(
Vm=-65, # Initial membrane voltage [mV]
tempK=300, # Temperature [Kelvin]