Python plot_spikes示例

示例#1

文件： components.py 项目： belevtsoff/SpikeSort

 def _plot(self):
     spikes = self.spike_src.spikes
     labels = self.cluster_src.labels
     if self.show_cells =='all':
         show_labels = list(np.unique(labels))
         if 0 in show_labels: show_labels.remove(0)
     else:
         show_labels = self.show_cells
     plotting.plot_spikes(spikes, labels, show_cells=show_labels,
                          fig=self.fig)

示例#2

文件： components.py 项目： nickponvert/SpikeSort

 def _plot(self):
     spikes = self.spike_src.spikes
     labels = self.cluster_src.labels
     if self.show_cells == 'all':
         show_labels = list(np.unique(labels))
         if 0 in show_labels: show_labels.remove(0)
     else:
         show_labels = self.show_cells
     plotting.plot_spikes(spikes,
                          labels,
                          show_cells=show_labels,
                          fig=self.fig)

示例#3

文件： tutorial_spikes.py 项目： belevtsoff/SpikeSort

#!/usr/bin/env python
#coding=utf-8

from spike_sort.io.filters import PyTablesFilter
from spike_sort import extract
from spike_sort import features
from spike_sort import cluster
from spike_sort.ui import plotting
import os

dataset = '/SubjectA/session01/el1'
datapath = '../../../data/tutorial.h5'

io_filter = PyTablesFilter(datapath)
raw = io_filter.read_sp(dataset)
spt = extract.detect_spikes(raw,  contact=3, thresh='auto')

sp_win = [-0.2, 0.8]
spt = extract.align_spikes(raw, spt, sp_win, type="max", resample=10)
sp_waves = extract.extract_spikes(raw, spt, sp_win)
plotting.plot_spikes(sp_waves, n_spikes=200)
plotting.show()
io_filter.close()

示例#4

#!/usr/bin/env python
# -*- coding: utf-8 -*-

from spike_sort.io.filters import PyTablesFilter
from spike_sort import extract
from spike_sort import features
from spike_sort import cluster
from spike_sort.ui import plotting
import os

dataset = '/SubjectA/session01/el1'
datapath = '../../../data/tutorial.h5'

io_filter = PyTablesFilter(datapath)
raw = io_filter.read_sp(dataset)
spt = extract.detect_spikes(raw, contact=3, thresh='auto')

sp_win = [-0.2, 0.8]
spt = extract.align_spikes(raw, spt, sp_win, type="max", resample=10)
sp_waves = extract.extract_spikes(raw, spt, sp_win)
sp_feats = features.combine(
    (features.fetP2P(sp_waves), features.fetPCA(sp_waves)))
clust_idx = cluster.cluster("gmm", sp_feats, 4)
plotting.plot_spikes(sp_waves, clust_idx, n_spikes=200)
plotting.show()
io_filter.close()

示例#5

文件： tutorial_cells.py 项目： belevtsoff/SpikeSort

#!/usr/bin/env python
#coding=utf-8

from spike_sort.io.filters import PyTablesFilter
from spike_sort import extract
from spike_sort import features
from spike_sort import cluster
from spike_sort.ui import plotting
import os 

dataset = '/SubjectA/session01/el1'
datapath = '../../../data/tutorial.h5'

io_filter = PyTablesFilter(datapath)
raw = io_filter.read_sp(dataset)
spt = extract.detect_spikes(raw,  contact=3, thresh='auto')

sp_win = [-0.2, 0.8]
spt = extract.align_spikes(raw, spt, sp_win, type="max", resample=10)
sp_waves = extract.extract_spikes(raw, spt, sp_win)
sp_feats = features.combine(
     (
      features.fetP2P(sp_waves),
      features.fetPCs(sp_waves)
     )
)
clust_idx = cluster.cluster("gmm",sp_feats,4)
plotting.plot_spikes(sp_waves, clust_idx, n_spikes=200)
plotting.show()
io_filter.close()

示例#6

文件： tutorial_spikes.py 项目： nickponvert/SpikeSort

#!/usr/bin/env python
#coding=utf-8

from spike_sort.io.filters import PyTablesFilter
from spike_sort import extract
from spike_sort import features
from spike_sort import cluster
from spike_sort.ui import plotting
import os

dataset = '/SubjectA/session01/el1'
datapath = '../../../data/tutorial.h5'

io_filter = PyTablesFilter(datapath)
raw = io_filter.read_sp(dataset)
spt = extract.detect_spikes(raw, contact=3, thresh='auto')

sp_win = [-0.2, 0.8]
spt = extract.align_spikes(raw, spt, sp_win, type="max", resample=10)
sp_waves = extract.extract_spikes(raw, spt, sp_win)
plotting.plot_spikes(sp_waves, n_spikes=200)
plotting.show()
io_filter.close()