def test_sp_shape(self):
with open(self.conf_file, "r+") as fid:
file_desc = json.load(fid)
file_desc["n_contacts"] = 4
fid.seek(0)
json.dump(file_desc, fid)
filter = BakerlabFilter(self.conf_file)
sp = filter.read_sp(self.el_node)
data = sp["data"]
ok_(data.shape == (4, len(self.data)))
def test_sp_shape(self):
with open(self.conf_file, 'r+') as fid:
file_desc = json.load(fid)
file_desc['n_contacts'] = 4
fid.seek(0)
json.dump(file_desc, fid)
filter = BakerlabFilter(self.conf_file)
sp = filter.read_sp(self.el_node)
data = sp['data']
ok_(data.shape == (4, len(self.data)))
DATAPATH = "../data"
if __name__ == "__main__":
dataset = "/Gollum/s39gollum01/el1"
cell_templ = "/Gollum/s39gollum01/el1/cell{cell_id}"
stim_node = "/".join(dataset.split("/")[:3] + ["stim"])
sp_win = [-0.2, 0.8]
start = time.time()
io_filter = BakerlabFilter("../data/gollum.inf")
export_filter = PyTablesFilter("../data/exported.h5")
sp = io_filter.read_sp(dataset, memmap="none")
spt = sort.extract.detect_spikes(sp, contact=3, thresh="auto")
spt = sort.extract.align_spikes(sp, spt, sp_win, type="max", contact=3, resample=10)
sp_waves = sort.extract.extract_spikes(sp, spt, sp_win)
features = sort.features.combine(
(sort.features.fetP2P(sp_waves, contacts=[0, 1, 2, 3]), sort.features.fetPCs(sp_waves, ncomps=1)),
normalize=True,
)
clust_idx = sort.cluster.cluster("gmm", features, 5)
features = sort.features.combine((sort.features.fetSpIdx(sp_waves), features))
spike_sort.ui.plotting.plot_features(features, clust_idx)
spike_sort.ui.plotting.figure()
spike_sort.ui.plotting.plot_spikes(sp_waves, clust_idx, n_spikes=200)
def test_read_sp(self):
filter = BakerlabFilter(self.conf_file)
sp = filter.read_sp(self.el_node)
read_data = sp["data"][0, :]
print read_data.shape
ok_((np.abs(read_data - self.data) <= 1 / 200.0).all())
def test_read_sp(self):
filter = BakerlabFilter(self.conf_file)
sp = filter.read_sp(self.el_node)
read_data = sp['data'][0, :]
print read_data.shape
ok_((np.abs(read_data - self.data) <= 1 / 200.).all())
#!/usr/bin/env python
#coding=utf-8
from spike_sort.io.filters import PyTablesFilter, BakerlabFilter
in_dataset = "/Gollum/s5gollum01/el3"
out_dataset = "/SubjectA/session01/el1/raw"
in_filter = BakerlabFilter("gollum.inf")
out_filter = PyTablesFilter("tutorial.h5")
sp = in_filter.read_sp(in_dataset)
out_filter.write_sp(sp, out_dataset)
in_filter.close()
out_filter.close()
