def setup_network(self, neurons_path, num_replicas=10, neuron_types=None):
# TODO: num_replicas should be set by a parameter, it affects how many duplicates of each neuron
# and thus how many steps we have between n_min and n_max number of inputs specified.
config_def = self.create_network_config(neurons_path=neurons_path,
num_replicas=num_replicas,
neuron_types=neuron_types)
print(
f"Writing network config file to {self.network_config_file_name}")
with open(self.network_config_file_name, "w") as f:
json.dump(config_def, f, indent=2, cls=NumpyEncoder)
create_cube_mesh(os.path.join("data", "mesh", "InputTestMesh.obj"),
[0, 0, 0],
1e-3,
description="Mesh file used for Input Scaling")
# Write the neurons path to file
self.write_tuning_info()
from snudda.place.place import SnuddaPlace
from snudda.detect.detect import SnuddaDetect
from snudda.detect.prune import SnuddaPrune
sp = SnuddaPlace(network_path=self.network_path)
sp.parse_config()
sp.write_data()
sd = SnuddaDetect(network_path=self.network_path)
sd.detect()
sp = SnuddaPrune(network_path=self.network_path)
sp.prune()
def setUp(self):
if os.path.dirname(__file__):
os.chdir(os.path.dirname(__file__))
network_path = os.path.join(os.path.dirname(__file__), "networks", "network_testing_detect")
create_cube_mesh(file_name=os.path.join(network_path, "mesh", "simple_mesh.obj"),
centre_point=(0, 0, 0),
side_len=500e-6)
config_file = os.path.join(network_path, "network-config.json")
position_file = os.path.join(network_path, "network-neuron-positions.hdf5")
save_file = os.path.join(network_path, "voxels", "network-putative-synapses.hdf5")
# TODO: If d_view is None code run sin serial, add test parallel
sp = SnuddaPlace(config_file=config_file, d_view=None, verbose=True)
sp.parse_config()
sp.write_data(position_file)
# We want to load in the ball and stick neuron that has 20 micrometer soma diameter, and axon (along y-axis),
# and dendrite along (x-axis) out to 100 micrometer distance from centre of soma.
self.sd = SnuddaDetect(config_file=config_file, position_file=position_file,
save_file=save_file, rc=None,
hyper_voxel_size=130, verbose=True)
def __init__(self):
if os.path.dirname(__file__):
os.chdir(os.path.dirname(__file__))
self.network_path = "touch_detection_illustration_network"
self.config_file = os.path.join(self.network_path, "network-config.json")
self.position_file = os.path.join(self.network_path, "network-neuron-positions.hdf5")
self.save_file = os.path.join(self.network_path, "voxels", "network-putative-synapses.hdf5")
create_cube_mesh(file_name=os.path.join(self.network_path, "mesh", "simple_mesh.obj"),
centre_point=(0, 0, 0),
side_len=500e-6)
sp = SnuddaPlace(config_file=self.config_file, d_view=None)
sp.parse_config()
sp.write_data(self.position_file)
self.sd = SnuddaDetect(config_file=self.config_file, position_file=self.position_file,
save_file=self.save_file, rc=None,
hyper_voxel_size=150)
# Reposition the neurons so we know how many synapses and where they will be located before pruning
neuron_positions = np.array([[0, 59, 0], # Postsynaptiska
[0, 89, 0],
[0, 119, 0],
[0, 149, 0],
[0, 179, 0],
[0, 209, 0],
[0, 239, 0],
[0, 269, 0],
[0, 299, 0],
[0, 329, 0],
[59, 0, 0], # Presynaptiska
[89, 0, 0],
[119, 0, 0],
[149, 0, 0],
[179, 0, 0],
[209, 0, 0],
[239, 0, 0],
[269, 0, 0],
[299, 0, 0],
[329, 0, 0],
]) * 1e-6
for idx, pos in enumerate(neuron_positions):
self.sd.neurons[idx]["position"] = pos
ang = -np.pi / 2
R_x = np.array([[1, 0, 0],
[0, np.cos(ang), -np.sin(ang)],
[0, np.sin(ang), np.cos(ang)]])
ang = np.pi / 2
R_y = np.array([[np.cos(ang), 0, np.sin(ang)],
[0, 1, 0],
[-np.sin(ang), 0, np.cos(ang)]])
for idx in range(0, 10): # Post synaptic neurons
self.sd.neurons[idx]["rotation"] = R_x
for idx in range(10, 20): # Presynaptic neurons
self.sd.neurons[idx]["rotation"] = R_y
self.sd.detect(restart_detection_flag=True)
# Also update so that the new positions are saved in the place file
rn = RepositionNeurons(self.position_file)
for neuron_info in self.sd.neurons:
rn.place(neuron_info["neuronID"], position=neuron_info["position"], rotation=neuron_info["rotation"],
verbose=False)
rn.close()
sp = SnuddaPrune(network_path=self.network_path) # Use default config file
sp.prune()
sp = []
def setUp(self):
from snudda.place.create_cube_mesh import create_cube_mesh
# Create cube meshes
self.network_path = os.path.join("networks", "network_testing_project")
mesh_file_a = os.path.join(self.network_path, "mesh", "volume_A.obj")
mesh_file_b = os.path.join(self.network_path, "mesh", "volume_B.obj")
create_cube_mesh(mesh_file_a, [5e-3, 0, 0], 300e-6,
"Volume A - connect structures example")
create_cube_mesh(mesh_file_b, [-5e-3, 0, 0], 300e-6,
"Volume B - connect structures example")
# Define network
from snudda.init.init import SnuddaInit
cnc = SnuddaInit(network_path=self.network_path, random_seed=123)
cnc.define_structure(struct_name="VolumeA",
struct_mesh=mesh_file_a,
d_min=15e-6,
mesh_bin_width=50e-6)
cnc.define_structure(struct_name="VolumeB",
struct_mesh=mesh_file_b,
d_min=15e-6,
mesh_bin_width=50e-6)
cnc.add_neurons(name="dSPN",
num_neurons=20,
volume_id="VolumeA",
neuron_dir=os.path.join("$DATA", "neurons", "striatum",
"dspn"))
cnc.add_neurons(name="iSPN",
num_neurons=20,
volume_id="VolumeB",
neuron_dir=os.path.join("$DATA", "neurons", "striatum",
"ispn"))
# Add the projection we want to test dSPN->iSPN
proj_file = os.path.join("data", "ExampleProjection.json")
cnc.neuron_projection(neuron_name="dSPN",
target_name="iSPN",
projection_name="ExampleProjection",
projection_file=proj_file,
source_volume="VolumeA",
dest_volume="VolumeB",
projection_radius=100e-6,
number_of_targets=[10, 5],
number_of_synapses=[10, 5],
dendrite_synapse_density="1",
connection_type="GABA",
dist_pruning=None,
f1=0.9,
soft_max=None,
mu2=None,
a3=None)
# Also add dSPN-dSPN and iSPN-iSPN synapses
# Note we do NOT add dSPN-iSPN again this way, as that would overwrite the above connections
# (The above neuron_projection will also do normal touch detection)
SPN2SPNdistDepPruning = "1-exp(-(0.4*d/60e-6)**2)"
MSD1gGABA = [0.24e-9, 0.1e-9]
MSD2gGABA = [0.24e-9, 0.1e-9]
MSD1GABAfailRate = 0.7 # Taverna 2008, figure 2
MSD2GABAfailRate = 0.4 # Taverna 2008, 2mM
pfdSPNdSPN = os.path.join("$DATA", "synapses", "striatum",
"PlanertFitting-DD-tmgaba-fit.json")
pfdSPNiSPN = os.path.join("$DATA", "synapses", "striatum",
"PlanertFitting-DI-tmgaba-fit.json")
pfiSPNdSPN = os.path.join("$DATA", "synapses", "striatum",
"PlanertFitting-ID-tmgaba-fit.json")
pfiSPNiSPN = os.path.join("$DATA", "synapses", "striatum",
"PlanertFitting-II-tmgaba-fit.json")
cnc.add_neuron_target(neuron_name="dSPN",
target_name="dSPN",
connection_type="GABA",
dist_pruning=SPN2SPNdistDepPruning,
f1=0.38,
soft_max=3,
mu2=2.4,
a3=1.0,
conductance=MSD1gGABA,
parameter_file=pfdSPNdSPN,
mod_file="tmGabaA",
channel_param_dictionary={
"tau1": (1.3e-3, 1e3),
"tau2": (12.4e-3, 1e3),
"failRate": MSD1GABAfailRate
})
cnc.add_neuron_target(neuron_name="iSPN",
target_name="iSPN",
connection_type="GABA",
dist_pruning=SPN2SPNdistDepPruning,
f1=0.55,
soft_max=4,
mu2=2.4,
a3=1.0,
conductance=MSD2gGABA,
parameter_file=pfiSPNiSPN,
mod_file="tmGabaA",
channel_param_dictionary={
"tau1": (1.3e-3, 1e3),
"tau2": (12.4e-3, 1e3),
"failRate": MSD2GABAfailRate
})
cnc.write_json()
# Place neurons, then detect, project and prune
from snudda.place.place import SnuddaPlace
sp = SnuddaPlace(network_path=self.network_path, verbose=True)
sp.parse_config()
sp.write_data()
from snudda.detect.detect import SnuddaDetect
sd = SnuddaDetect(network_path=self.network_path,
hyper_voxel_size=100,
verbose=True)
sd.detect()
from snudda.detect.project import SnuddaProject
sp = SnuddaProject(network_path=self.network_path)
sp.project()
sp.write()
from snudda.detect.prune import SnuddaPrune
sp = SnuddaPrune(network_path=self.network_path, verbose=True)
sp.prune()
def __init__(self):
if os.path.dirname(__file__):
os.chdir(os.path.dirname(__file__))
self.network_path = "pruning_illustration_network"
self.config_file = os.path.join(self.network_path, "network-config.json")
self.position_file = os.path.join(self.network_path, "network-neuron-positions.hdf5")
self.save_file = os.path.join(self.network_path, "voxels", "network-synapses.hdf5")
create_cube_mesh(file_name=os.path.join(self.network_path, "mesh", "simple_mesh.obj"),
centre_point=(0, 0, 0),
side_len=500e-6)
sp = SnuddaPlace(config_file=self.config_file, d_view=None)
print("Calling read_config")
sp.parse_config()
print("Read done")
sp.write_data(self.position_file)
# We want to load in the ball and stick neuron that has 20 micrometer soma diameter, and axon (along y-axis),
# and dendrite along (x-axis) out to 200 micrometer distance from centre of soma.
self.sd = SnuddaDetect(config_file=self.config_file, position_file=self.position_file,
save_file=self.save_file, rc=None,
hyper_voxel_size=150)
# Reposition the neurons so we know how many synapses and where they will be located before pruning
neuron_positions = np.array([[0, 59, 0], # Postsynaptiska
[0, 89, 0],
[0, 119, 0],
[0, 149, 0],
[0, 179, 0],
[0, 209, 0],
[0, 239, 0],
[0, 269, 0],
[0, 299, 0],
[0, 329, 0],
[59, 0, 0], # Presynaptiska
[89, 0, 0],
[119, 0, 0],
[149, 0, 0],
[179, 0, 0],
[209, 0, 0],
[239, 0, 0],
[269, 0, 0],
[299, 0, 0],
[329, 0, 0],
]) * 1e-6
# TODO: Add potential for gap junctions also by having 5 + 5 neurons in other grid
for idx, pos in enumerate(neuron_positions):
self.sd.neurons[idx]["position"] = pos
ang = -np.pi / 2
R_x = np.array([[1, 0, 0],
[0, np.cos(ang), -np.sin(ang)],
[0, np.sin(ang), np.cos(ang)]])
ang = np.pi / 2
R_y = np.array([[np.cos(ang), 0, np.sin(ang)],
[0, 1, 0],
[-np.sin(ang), 0, np.cos(ang)]])
for idx in range(0, 10): # Post synaptic neurons
self.sd.neurons[idx]["rotation"] = R_x
for idx in range(10, 20): # Presynaptic neurons
self.sd.neurons[idx]["rotation"] = R_y
self.sd.detect(restart_detection_flag=True)
# Also update so that the new positions are saved in the place file
rn = RepositionNeurons(self.position_file)
for neuron_info in self.sd.neurons:
rn.place(neuron_info["neuronID"], position=neuron_info["position"], rotation=neuron_info["rotation"],
verbose=False)
rn.close()
if False:
self.sd.process_hyper_voxel(1)
plt, ax = self.sd.plot_hyper_voxel(plot_neurons=True, elev_azim=(90, 0),
draw_axon_voxels=False, draw_dendrite_voxels=False,
draw_axons=True, draw_dendrites=True,
show_axis=False, title="No pruning",
fig_file_name="Pruning-fig-1-no-pruning")
import pdb
pdb.set_trace()
def setUp(self):
if os.path.dirname(__file__):
os.chdir(os.path.dirname(__file__))
self.network_path = os.path.join(os.path.dirname(__file__), "networks",
"network_testing_prune3")
create_cube_mesh(file_name=os.path.join(self.network_path, "mesh",
"simple_mesh.obj"),
centre_point=(0, 0, 0),
side_len=500e-6)
config_file = os.path.join(self.network_path, "network-config.json")
position_file = os.path.join(self.network_path,
"network-neuron-positions.hdf5")
save_file = os.path.join(self.network_path, "voxels",
"network-putative-synapses.hdf5")
sp = SnuddaPlace(config_file=config_file, d_view=None, verbose=True)
sp.parse_config()
sp.write_data(position_file)
# We want to load in the ball and stick neuron that has 20 micrometer soma diameter, and axon (along y-axis),
# and dendrite along (x-axis) out to 100 micrometer distance from centre of soma.
self.sd = SnuddaDetect(config_file=config_file,
position_file=position_file,
save_file=save_file,
rc=None,
hyper_voxel_size=120,
verbose=True)
# Reposition the neurons so we know how many synapses and where they will be located before pruning
neuron_positions = np.array([
[0, 20, 0], # Postsynaptiska
[0, 40, 0],
[0, 60, 0],
[0, 80, 0],
[0, 100, 0],
[0, 120, 0],
[0, 140, 0],
[0, 160, 0],
[0, 180, 0],
[0, 200, 0],
[20, 0, 0], # Presynaptiska
[40, 0, 0],
[60, 0, 0],
[80, 0, 0],
[100, 0, 0],
[120, 0, 0],
[140, 0, 0],
[160, 0, 0],
[180, 0, 0],
[200, 0, 0],
[70, 0, 500], # For gap junction check
[110, 0, 500],
[150, 0, 500],
[190, 0, 500],
[0, 70, 500],
[0, 110, 500],
[0, 150, 500],
[0, 190, 500],
]) * 1e-6
# TODO: Add potential for gap junctions also by having 5 + 5 neurons in other grid
for idx, pos in enumerate(neuron_positions):
self.sd.neurons[idx]["position"] = pos
ang = -np.pi / 2
R_x = np.array([[1, 0, 0], [0, np.cos(ang), -np.sin(ang)],
[0, np.sin(ang), np.cos(ang)]])
ang = np.pi / 2
R_y = np.array([[np.cos(ang), 0, np.sin(ang)], [0, 1, 0],
[-np.sin(ang), 0, np.cos(ang)]])
for idx in range(0, 10): # Post synaptic neurons
self.sd.neurons[idx]["rotation"] = R_x
for idx in range(10, 20): # Presynaptic neurons
self.sd.neurons[idx]["rotation"] = R_y
for idx in range(24, 28): # GJ neurons
self.sd.neurons[idx]["rotation"] = R_x
ang = np.pi / 2
R_z = np.array([[np.cos(ang), -np.sin(ang), 0],
[np.sin(ang), np.cos(ang), 0], [0, 0, 1]])
for idx in range(20, 24): # GJ neurons
self.sd.neurons[idx]["rotation"] = np.matmul(R_z, R_x)
self.sd.detect(restart_detection_flag=True)
if False:
self.sd.process_hyper_voxel(1)
self.sd.plot_hyper_voxel(plot_neurons=True)
def __init__(self):
if os.path.dirname(__file__):
os.chdir(os.path.dirname(__file__))
self.network_path = "touch_detection_hypervoxel_illustration_network"
self.config_file = os.path.join(self.network_path, "network-config.json")
self.position_file = os.path.join(self.network_path, "network-neuron-positions.hdf5")
self.save_file = os.path.join(self.network_path, "voxels", "network-putative-synapses.hdf5")
create_cube_mesh(file_name=os.path.join(self.network_path, "mesh", "simple_mesh.obj"),
centre_point=(0, 0, 0),
side_len=500e-6)
sp = SnuddaPlace(config_file=self.config_file, d_view=None)
sp.parse_config()
sp.write_data(self.position_file)
self.sd = SnuddaDetect(config_file=self.config_file, position_file=self.position_file,
save_file=self.save_file, rc=None,
hyper_voxel_size=60)
neuron_positions = np.array([[10, 30, 70], # Postsynaptiska
[50, 60, 70], # Presynaptiska
]) * 1e-6
for idx, pos in enumerate(neuron_positions):
self.sd.neurons[idx]["position"] = pos
ang = -np.pi / 2
R_x = np.array([[1, 0, 0],
[0, np.cos(ang), -np.sin(ang)],
[0, np.sin(ang), np.cos(ang)]])
ang = np.pi * 0.2
R_y = np.array([[np.cos(ang), 0, np.sin(ang)],
[0, 1, 0],
[-np.sin(ang), 0, np.cos(ang)]])
ang = np.pi * (0.5 + 0.2)
R_z0 = np.array([[np.cos(ang), -np.sin(ang), 0],
[np.sin(ang), np.cos(ang), 0],
[0, 0, 1]])
ang = np.pi*0.4
R_z1 = np.array([[np.cos(ang), -np.sin(ang), 0],
[np.sin(ang), np.cos(ang), 0],
[0, 0, 1]])
# Post synaptic
self.sd.neurons[0]["rotation"] = R_z0
# Presynaptic neuron
self.sd.neurons[1]["rotation"] = np.matmul(R_z1, R_y)
self.sd.detect(restart_detection_flag=True)
self.sd.process_hyper_voxel(0)
plt, ax = self.sd.plot_hyper_voxel(plot_neurons=False,
draw_axon_voxels=True,
draw_dendrite_voxels=True,
elev_azim=(50, -22),
title="",
fig_file_name="touch_detection_illustration-voxels.pdf",
dpi=300)
plt, ax = self.sd.plot_hyper_voxel(plot_neurons=True,
draw_axon_voxels=False,
draw_dendrite_voxels=False,
elev_azim=(50, -22),
title="",
fig_file_name="touch_detection_illustration-morph.pdf",
dpi=300)
print(f"\n--> Figures written to {self.sd.network_path}/figures")