Skip to content
Snippets Groups Projects
Commit d3aad4f8 authored by Simon Oehrl's avatar Simon Oehrl
Browse files

Merge branch 'master' into feature/#9_Copy_python_scripts_during_building

parents 105f2136 c870ba70
Branches
No related tags found
1 merge request!6Copy files during build time
Show whitespace changes
Inline Side-by-side
demos/brunel_simulation/brunel_example.py
+ 70
− 70
View file @ d3aad4f8
......@@ -11,11 +11,10 @@ is not structured spatially.
from copy import deepcopy
from math import sqrt
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
# from mpl_toolkits.mplot3d import Axes3D
# import matplotlib.pyplot as plt
import nest
import nest.raster_plot
import nest.topology as tp
......@@ -23,6 +22,7 @@ class Brunel3D:
def __init__(self):
self.layer_dict = {}
nest.SetKernelStatus({"local_num_threads": 1})
nest.Install("streamingmodule")
# nest.SetKernelStatus({'print_time': True})
......@@ -196,70 +196,70 @@ class Brunel3D:
def simulate(self):
nest.Simulate(1000)
def plot_positions(self):
ex_pos = self.layers[0][1]['positions']
in_pos = self.layers[1][1]['positions']
fig = plt.figure()
ax = Axes3D(fig)
for c, m, positions in [('b', 'o', ex_pos), ('r', '^', in_pos)]:
ax.scatter([x for x, y, z in positions],
[y for x, y, z in positions],
[z for x, y, z in positions],
c=c, marker=m)
def get_results(self):
mm = (self.layer_dict['Multimeter'][0] + 1,)
sd = (self.layer_dict['SpikeDetector'][0] + 1,)
mm_status = nest.GetStatus(mm)[0]
sd_status = nest.GetStatus(sd)[0]
nest.raster_plot.from_device(sd, hist=True)
senders = mm_status['events']['senders']
times = mm_status['events']['times']
v_m = mm_status['events']['V_m']
v_th = mm_status['events']['V_th']
step = int(max(senders)/100 + 1) # Only plot results from some GIDs
mm_events = []
for i in range(1, max(senders) + 1, step):
if i in senders:
indices = np.argwhere(senders == i)
mm_events.append({'GID': i,
'times': [times[n] for n in indices],
'V_m': [v_m[n] for n in indices],
'V_th': [v_th[n] for n in indices]})
return {'multimeter': mm_events,
'spike_detector': nest.GetStatus(sd)[0]}
if __name__ == '__main__':
nest.ResetKernel()
print('Making specifications')
brunel = Brunel3D()
brunel.make_layer_specs()
brunel.make_connection_specs()
print('Making layers')
brunel.make_layers()
nest.topology.DumpLayerNodes([l[0] for l in brunel.layer_dict.values()][:2],
'brunel_nodes.txt')
print('Making connections')
brunel.make_connections()
brunel.simulate()
print('Getting results')
brunel.plot_positions()
results = brunel.get_results()
for value in ['V_m', 'V_th']:
plt.figure()
for n in results['multimeter'][::20]:
plt.plot(n['times'], n[value], label='{}'.format(n['GID']))
plt.legend()
plt.title(value)
plt.show()
# def plot_positions(self):
# ex_pos = self.layers[0][1]['positions']
# in_pos = self.layers[1][1]['positions']
# fig = plt.figure()
# ax = Axes3D(fig)
# for c, m, positions in [('b', 'o', ex_pos), ('r', '^', in_pos)]:
# ax.scatter([x for x, y, z in positions],
# [y for x, y, z in positions],
# [z for x, y, z in positions],
# c=c, marker=m)
# def get_results(self):
# mm = (self.layer_dict['Multimeter'][0] + 1,)
# sd = (self.layer_dict['SpikeDetector'][0] + 1,)
# mm_status = nest.GetStatus(mm)[0]
# sd_status = nest.GetStatus(sd)[0]
# nest.raster_plot.from_device(sd, hist=True)
# senders = mm_status['events']['senders']
# times = mm_status['events']['times']
# v_m = mm_status['events']['V_m']
# v_th = mm_status['events']['V_th']
# step = int(max(senders)/100 + 1) # Only plot results from some GIDs
# mm_events = []
# for i in range(1, max(senders) + 1, step):
# if i in senders:
# indices = np.argwhere(senders == i)
# mm_events.append({'GID': i,
# 'times': [times[n] for n in indices],
# 'V_m': [v_m[n] for n in indices],
# 'V_th': [v_th[n] for n in indices]})
# return {'multimeter': mm_events,
# 'spike_detector': nest.GetStatus(sd)[0]}
# if __name__ == '__main__':
# nest.ResetKernel()
# print('Making specifications')
# brunel = Brunel3D()
# brunel.make_layer_specs()
# brunel.make_connection_specs()
# print('Making layers')
# brunel.make_layers()
# nest.topology.DumpLayerNodes([l[0] for l in brunel.layer_dict.values()][:2],
# 'brunel_nodes.txt')
# print('Making connections')
# brunel.make_connections()
# brunel.simulate()
# print('Getting results')
# brunel.plot_positions()
# results = brunel.get_results()
# for value in ['V_m', 'V_th']:
# plt.figure()
# for n in results['multimeter'][::20]:
# plt.plot(n['times'], n[value], label='{}'.format(n['GID']))
# plt.legend()
# plt.title(value)
# plt.show()
streaming_recording_backend.cpp
+ 27
− 20
View file @ d3aad4f8
......@@ -38,6 +38,19 @@ void StreamingRecordingBackend::initialize() {
std::cout << "initialize()" << std::endl;
}
void StreamingRecordingBackend::prepare() {
std::cout << "prepare()" << std::endl;
std::cout << "Get the number of nodes" << nest::kernel().node_manager.size() << std::endl;
}
void StreamingRecordingBackend::cleanup() {
std::cout << "cleanup()" << std::endl;
}
void StreamingRecordingBackend::post_run_cleanup() {
std::cout << "post_run_cleanup()" << std::endl;
}
void StreamingRecordingBackend::enroll(
const nest::RecordingDevice &device,
const std::vector<Name> &double_value_names,
......@@ -80,32 +93,16 @@ void StreamingRecordingBackend::write(const nest::RecordingDevice &device,
const nest::Event &event,
const std::vector<double> &double_values,
const std::vector<long> &long_values) {
// Called per thread
// std::lock_guard<std::mutex> lock_guard(write_mutex_);
// std::cout << std::this_thread::get_id() << ' ';
// std::cout << device.get_name() << ' ';
// std::cout << event.get_sender_gid() << ' ';
// std::cout << event.get_stamp() << ' ';
// for (const auto value : double_values) {
// std::cout << value << ' ';
// }
// std::cout << ' ';
// for (const auto value : long_values) {
// std::cout << value << ' ';
// }
// std::cout << std::endl;
const auto thread_devices = devices_.find(std::this_thread::get_id());
if (thread_devices == devices_.end()) {
// std::cout << "Error: no devices assigned to this thread!" << std::endl;
std::cerr << "Error: no devices assigned to this thread!" << std::endl;
return;
}
const auto thread_device = thread_devices->second.find(device.get_name());
if (thread_device == thread_devices->second.end()) {
// std::cout << "Error: device not found in this thread (device = "
// << device.get_name() << ")" << std::endl;
std::cerr << "Error: device not found in this thread (device = "
<< device.get_name() << ")" << std::endl;
return;
}
......@@ -121,7 +118,13 @@ void StreamingRecordingBackend::write(const nest::RecordingDevice &device,
void StreamingRecordingBackend::synchronize() {
// Called per thread
for (const auto &device : devices_.at(std::this_thread::get_id())) {
const auto thread_devices = devices_.find(std::this_thread::get_id());
if (thread_devices == devices_.end()) {
return;
}
for (const auto &device : thread_devices->second) {
{
std::lock_guard<std::mutex> lock_guard(relay_mutex_);
relay_.Send(device.second->node(), false);
......@@ -131,6 +134,10 @@ void StreamingRecordingBackend::synchronize() {
}
}
void StreamingRecordingBackend::clear(const nest::RecordingDevice& device) {
std::cout << "clear(" << device.get_name() << ")" << std::endl;
}
void StreamingRecordingBackend::finalize() {
// Called once
std::cout << "finalize()" << std::endl;
......
streaming_recording_backend.h
+ 7
− 0
View file @ d3aad4f8
......@@ -27,6 +27,7 @@
#include <memory>
#include <mutex>
#include <string>
#include <thread>
#include <vector>
#include "nest_types.h"
......@@ -49,9 +50,15 @@ class StreamingRecordingBackend : public nest::RecordingBackend {
void initialize() override;
void prepare() override;
void cleanup() override;
void post_run_cleanup() override;
void finalize() override;
void synchronize() override;
void clear(const nest::RecordingDevice&) override;
void write(const nest::RecordingDevice &, const nest::Event &,
const std::vector<double> &, const std::vector<long> &) override;
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment