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This is an archived project. Repository and other project resources are read-only.
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LuFG VR VIS
VR-Group
In Situ Pipeline
nest-streaming-module
Commits
c5761842
Commit
c5761842
authored
6 years ago
by
Simon Oehrl
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demos/brunel_simulation/brunel_example.py
+70
-70
70 additions, 70 deletions
demos/brunel_simulation/brunel_example.py
with
70 additions
and
70 deletions
demos/brunel_simulation/brunel_example.py
+
70
−
70
View file @
c5761842
...
@@ -11,11 +11,10 @@ is not structured spatially.
...
@@ -11,11 +11,10 @@ is not structured spatially.
from
copy
import
deepcopy
from
copy
import
deepcopy
from
math
import
sqrt
from
math
import
sqrt
import
numpy
as
np
import
numpy
as
np
from
mpl_toolkits.mplot3d
import
Axes3D
#
from mpl_toolkits.mplot3d import Axes3D
import
matplotlib.pyplot
as
plt
#
import matplotlib.pyplot as plt
import
nest
import
nest
import
nest.raster_plot
import
nest.topology
as
tp
import
nest.topology
as
tp
...
@@ -23,6 +22,7 @@ class Brunel3D:
...
@@ -23,6 +22,7 @@ class Brunel3D:
def
__init__
(
self
):
def
__init__
(
self
):
self
.
layer_dict
=
{}
self
.
layer_dict
=
{}
nest
.
SetKernelStatus
({
"
local_num_threads
"
:
1
})
nest
.
Install
(
"
streamingmodule
"
)
nest
.
Install
(
"
streamingmodule
"
)
# nest.SetKernelStatus({'print_time': True})
# nest.SetKernelStatus({'print_time': True})
...
@@ -196,70 +196,70 @@ class Brunel3D:
...
@@ -196,70 +196,70 @@ class Brunel3D:
def
simulate
(
self
):
def
simulate
(
self
):
nest
.
Simulate
(
1000
)
nest
.
Simulate
(
1000
)
def
plot_positions
(
self
):
#
def plot_positions(self):
ex_pos
=
self
.
layers
[
0
][
1
][
'
positions
'
]
#
ex_pos = self.layers[0][1]['positions']
in_pos
=
self
.
layers
[
1
][
1
][
'
positions
'
]
#
in_pos = self.layers[1][1]['positions']
fig
=
plt
.
figure
()
#
fig = plt.figure()
ax
=
Axes3D
(
fig
)
#
ax = Axes3D(fig)
for
c
,
m
,
positions
in
[(
'
b
'
,
'
o
'
,
ex_pos
),
(
'
r
'
,
'
^
'
,
in_pos
)]:
#
for c, m, positions in [('b', 'o', ex_pos), ('r', '^', in_pos)]:
ax
.
scatter
([
x
for
x
,
y
,
z
in
positions
],
#
ax.scatter([x for x, y, z in positions],
[
y
for
x
,
y
,
z
in
positions
],
#
[y for x, y, z in positions],
[
z
for
x
,
y
,
z
in
positions
],
#
[z for x, y, z in positions],
c
=
c
,
marker
=
m
)
#
c=c, marker=m)
def
get_results
(
self
):
#
def get_results(self):
mm
=
(
self
.
layer_dict
[
'
Multimeter
'
][
0
]
+
1
,)
#
mm = (self.layer_dict['Multimeter'][0] + 1,)
sd
=
(
self
.
layer_dict
[
'
SpikeDetector
'
][
0
]
+
1
,)
#
sd = (self.layer_dict['SpikeDetector'][0] + 1,)
mm_status
=
nest
.
GetStatus
(
mm
)[
0
]
#
mm_status = nest.GetStatus(mm)[0]
sd_status
=
nest
.
GetStatus
(
sd
)[
0
]
#
sd_status = nest.GetStatus(sd)[0]
nest
.
raster_plot
.
from_device
(
sd
,
hist
=
True
)
#
nest.raster_plot.from_device(sd, hist=True)
senders
=
mm_status
[
'
events
'
][
'
senders
'
]
#
senders = mm_status['events']['senders']
times
=
mm_status
[
'
events
'
][
'
times
'
]
#
times = mm_status['events']['times']
v_m
=
mm_status
[
'
events
'
][
'
V_m
'
]
#
v_m = mm_status['events']['V_m']
v_th
=
mm_status
[
'
events
'
][
'
V_th
'
]
#
v_th = mm_status['events']['V_th']
step
=
int
(
max
(
senders
)
/
100
+
1
)
# Only plot results from some GIDs
#
step = int(max(senders)/100 + 1) # Only plot results from some GIDs
mm_events
=
[]
#
mm_events = []
for
i
in
range
(
1
,
max
(
senders
)
+
1
,
step
):
#
for i in range(1, max(senders) + 1, step):
if
i
in
senders
:
#
if i in senders:
indices
=
np
.
argwhere
(
senders
==
i
)
#
indices = np.argwhere(senders == i)
mm_events
.
append
({
'
GID
'
:
i
,
#
mm_events.append({'GID': i,
'
times
'
:
[
times
[
n
]
for
n
in
indices
],
#
'times': [times[n] for n in indices],
'
V_m
'
:
[
v_m
[
n
]
for
n
in
indices
],
#
'V_m': [v_m[n] for n in indices],
'
V_th
'
:
[
v_th
[
n
]
for
n
in
indices
]})
#
'V_th': [v_th[n] for n in indices]})
return
{
'
multimeter
'
:
mm_events
,
#
return {'multimeter': mm_events,
'
spike_detector
'
:
nest
.
GetStatus
(
sd
)[
0
]}
#
'spike_detector': nest.GetStatus(sd)[0]}
if
__name__
==
'
__main__
'
:
#
if __name__ == '__main__':
nest
.
ResetKernel
()
#
nest.ResetKernel()
print
(
'
Making specifications
'
)
#
print('Making specifications')
brunel
=
Brunel3D
()
#
brunel = Brunel3D()
brunel
.
make_layer_specs
()
#
brunel.make_layer_specs()
brunel
.
make_connection_specs
()
#
brunel.make_connection_specs()
print
(
'
Making layers
'
)
#
print('Making layers')
brunel
.
make_layers
()
#
brunel.make_layers()
nest
.
topology
.
DumpLayerNodes
([
l
[
0
]
for
l
in
brunel
.
layer_dict
.
values
()][:
2
],
#
nest.topology.DumpLayerNodes([l[0] for l in brunel.layer_dict.values()][:2],
'
brunel_nodes.txt
'
)
#
'brunel_nodes.txt')
print
(
'
Making connections
'
)
#
print('Making connections')
brunel
.
make_connections
()
#
brunel.make_connections()
brunel
.
simulate
()
#
brunel.simulate()
print
(
'
Getting results
'
)
#
print('Getting results')
brunel
.
plot_positions
()
#
brunel.plot_positions()
results
=
brunel
.
get_results
()
#
results = brunel.get_results()
for
value
in
[
'
V_m
'
,
'
V_th
'
]:
#
for value in ['V_m', 'V_th']:
plt
.
figure
()
#
plt.figure()
for
n
in
results
[
'
multimeter
'
][::
20
]:
#
for n in results['multimeter'][::20]:
plt
.
plot
(
n
[
'
times
'
],
n
[
value
],
label
=
'
{}
'
.
format
(
n
[
'
GID
'
]))
#
plt.plot(n['times'], n[value], label='{}'.format(n['GID']))
plt
.
legend
()
#
plt.legend()
plt
.
title
(
value
)
#
plt.title(value)
plt
.
show
()
#
plt.show()
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