def get_morphology_exemplars(blue_config, random_selection=False):
"""Returns a list of exemplars where each one represent a category of the different
morphologies. If the random selection flag is set, then they will be picked up randomly,
otherwise, the first one of each selected type will be picked.
:param blue_config:
A circuit configuration file.
:param random_selection:
Randomly selected cells.
:return:
A list of exemplars to all the mtypes that exist in the circuit.
"""
# Import bbp
try:
import bbp
except ImportError:
print('ERROR: Cannot import brain')
return None
# Create an experiment
bbp_experiment = bbp.Experiment()
# Open the blue config
bbp_experiment.open(blue_config)
# Load the entire mc2_Column in the micro-circuit
bbp_microcircuit = bbp_experiment.microcircuit()
bbp_cell_target = bbp_experiment.cell_target('mc2_Column')
bbp_microcircuit.load(bbp_cell_target, bbp.Loading_Flags.NEURONS)
# retrieve a list of all the neurons in the circuit
bbp_neurons = bbp_microcircuit.neurons()
# create a list of selected exemplars
exemplars_list = []
for m_type in nmv.consts.MTYPES:
# All the cells with that specific m-type
m_type_cells = []
# Get all the cells with that specific m-type
for neuron in bbp_neurons:
# Get BBP neuron data from the BBP-SDK
neuron_gid = neuron.gid()
neuron_m_type = neuron.morphology_type().name()
if neuron_m_type == m_type:
m_type_cells.append([neuron_gid, neuron_m_type])
# Select a random cell and add it to the exemplars list, otherwise, use the first m-type
if random_selection:
exemplars_list.append(random.choice(m_type_cells))
else:
exemplars_list.append(m_type_cells[0])
# Return the exemplars list
return exemplars_list
def get_neuron_from_gid(blue_config, gid):
"""Return a BBP neuron structure from its input GID.
:param blue_config:
Input circuit configuration file.
:param gid:
Input neuron GID.
:return:
A reference to the BBP neuron
"""
# Import BBP-SDK module inside the function to avoid the BBP tree complexity for non-BBP
# morphologies.
import bbp
# Create a new experiment
bbp_experiment = bbp.Experiment()
# Open the blue-config file
bbp_experiment.open(blue_config)
# Create a micro-circuit
bbp_microcircuit = bbp_experiment.microcircuit()
# Set the cell target to the given gid
bbp_cell_target = bbp.Cell_Target()
bbp_cell_target.insert(int(gid))
# Load the circuit
bbp_microcircuit.load(bbp_cell_target, bbp.Loading_Flags.NEURONS)
# Get the neuron from the microcircuit
bbp_neuron = bbp_microcircuit.neurons()
# Return a reference to the BBP neuron
return bbp_neuron