def main(config_file):
configure = pointnet.Config.from_json(config_file)
configure.build_env()
network = pointnet.PointNetwork.from_config(configure)
sim = pointnet.PointSimulator.from_config(configure, network)
sim.run()
plot_spikes('network/V1_nodes.h5', 'network/V1_node_types.csv',
'output/spikes.h5')
def raster(config=None,title=None,population=None,group_key='pop_name'):
conf = util.load_config(config)
cells_file = conf["networks"]["nodes"][0]["nodes_file"]
cell_types_file = conf["networks"]["nodes"][0]["node_types_file"]
spikes_path = os.path.join(conf["output"]["output_dir"],conf["output"]["spikes_file"])
from bmtk.analyzer.visualization import spikes
spikes.plot_spikes(cells_file,cell_types_file,spikes_path,population=population,group_key=group_key)
return
def run(config_file):
conf = bionet.Config.from_json(config_file, validate=True)
conf.build_env()
net = bionet.BioNetwork.from_config(conf)
sim = bionet.BioSimulator.from_config(conf, network=net)
sim.run()
bionet.nrn.quit_execution()
from bmtk.analyzer.visualization.spikes import plot_spikes, plot_rates
plot_spikes('network/nodes.h5',
'network/node_types.csv',
'output/spikes.h5',
save_as='rasters/plot.png',
group_key='model_name')
from bmtk.analyzer.visualization.spikes import plot_spikes
plot_spikes('network/cortex_nodes.h5', 'network/cortex_node_types.csv',
'output/spikes.h5')
from bmtk.analyzer.visualization.spikes import plot_spikes
plot_spikes('network/internal_nodes.h5', 'network/internal_node_types.csv', 'output/spikes.h5', group_key='model_name')
from bmtk.analyzer.visualization.spikes import plot_spikes
import sys
title = None
if len(sys.argv)>1:
title = 'Simulator: %s'%sys.argv[1]
# Note: depends on https://github.com/AllenInstitute/bmtk/pull/73
plot_spikes('network/internal_nodes.h5',
'network/internal_node_types.csv',
'output/spikes.h5',
group_key='model_name',
legend=False,
title=title,
font_size=13)
from bmtk.analyzer.visualization.spikes import plot_spikes
plot_spikes('network/internal_nodes.h5', 'network/internal_node_types.csv',
'output/spikes.h5')
import sys
from bmtk.analyzer.visualization.spikes import plot_spikes
sys.path.append("../../../shared_components/scripts")
from analyze_output_utils import plot_data
if __name__ == '__main__':
plot_data('output/membrane_potential.h5',
'mV',
'Membrane Potential',
show_already=True)
plot_spikes('../input/network/ten_cells_iclamp_nodes.h5',
'../input/network/ten_cells_iclamp_node_types.csv',
'output/spikes.h5')
from bmtk.analyzer.visualization.spikes import plot_spikes
plot_spikes('network/v1_nodes.h5',
'network/v1_node_types.csv',
'output/spikes.h5',
group_key='pop_name')
import sys
from bmtk.analyzer.visualization.spikes import plot_spikes
sys.path.append("../../../shared_components/scripts")
from analyze_output_utils import plot_data
if __name__ == '__main__':
#plot_data('output/membrane_potential.h5', 'mV', 'Membrane Potential', show_already=True)
plot_spikes('../input/network/pre_nodes.h5',
'../input/network/pre_node_types.csv', 'output/spikes.h5')
plot_spikes('../input/network/post_nodes.h5',
'../input/network/post_node_types.csv', 'output/spikes.h5')