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')