Python generate_fake_probeの例

コード例 #1

import scipy
import cPickle
from circusort.io.utils import generate_fake_probe
from circusort.obj import TemplateStore

host = '127.0.0.1'  # to run the test locally

director = circusort.create_director(host=host)
manager = director.create_manager(host=host)
manager2 = director.create_manager(host=host)

nb_channels = 10
sampling_rate = 20000
two_components = True
nb_clustering = 2
probe_file = generate_fake_probe(nb_channels, radius=5)

noise = manager.create_block('fake_spike_generator', nb_channels=nb_channels)
filter = manager.create_block('filter')
whitening = manager.create_block('whitening')
mad_estimator = manager.create_block('mad_estimator')
peak_detector = manager.create_block('peak_detector', threshold=6)
pca = manager.create_block('pca', nb_waveforms=5000)

clusters = []

for i in xrange(nb_clustering):
    clusters += [
        manager2.create_block('density_clustering',
                              probe=probe_file,
                              nb_waveforms=500,

コード例 #2

ファイル: test_scaling.py プロジェクト: spyking-circus/spyking-circus-ort

data_path = '/tmp/output.dat'
peak_path = '/tmp/peaks.dat'
thres_path = '/tmp/thresholds.dat'
temp_path = '/tmp/templates'

director = circusort.create_director(host=master)

manager = {}
for computer in slaves + [master]:
    manager[computer] = director.create_manager(host=computer)

sampling_rate = 20000
two_components = True
nb_channels = 4

probe_file = generate_fake_probe(nb_channels, radius=2, prb_file='test.prb')

generator = manager[master].create_block('fake_spike_generator',
                                         nb_channels=nb_channels)
filter = manager[master].create_block('filter', cut_off=100)
whitening = manager[master].create_block('whitening')
mad_estimator = manager[master].create_block('mad_estimator')
peak_detector = manager[master].create_block('peak_detector', threshold=5)
pca = manager[master].create_block('pca', nb_waveforms=500)

cluster_1 = manager[slaves[0]].create_block('density_clustering',
                                            probe=probe_file,
                                            nb_waveforms=100,
                                            two_components=two_components,
                                            channels=range(0, nb_channels, 2))
cluster_2 = manager[slaves[1]].create_block('density_clustering',

コード例 #3

ファイル: test_clustering.py プロジェクト: spyking-circus/spyking-circus-ort

# Test to measure the computational efficiency of two operations in one block
# associated to one manager.

import circusort
import logging
from circusort.io.utils import generate_fake_probe

host = '127.0.0.1' # to run the test locally

director      = circusort.create_director(host=host)
manager       = director.create_manager(host=host)
manager2      = director.create_manager(host=host)

nb_channels   = 10
probe_file    = generate_fake_probe(nb_channels)

noise         = manager.create_block('fake_spike_generator', nb_channels=nb_channels)
filter        = manager.create_block('filter')
whitening     = manager.create_block('whitening')
mad_estimator = manager.create_block('mad_estimator')
peak_detector = manager.create_block('peak_detector', threshold=6, sign_peaks='both')
pca           = manager.create_block('pca', nb_waveforms=5000)
cluster       = manager2.create_block('density_clustering', probe=probe_file, nb_waveforms=1000, two_components=False, log_level=logging.DEBUG)

director.initialize()

director.connect(noise.output, filter.input)
director.connect(filter.output, whitening.input)
director.connect(whitening.output, [mad_estimator.input, peak_detector.get_input('data'), pca.get_input('data'), cluster.get_input('data')])
director.connect(mad_estimator.output, [peak_detector.get_input('mads'), cluster.get_input('mads')])
director.connect(peak_detector.get_output('peaks'), [pca.get_input('peaks'), cluster.get_input('peaks')])