jgrewe/gp_neurobio
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Merge branch 'master' of https://whale.am28.uni-tuebingen.de/git/jgrewe/gp_neurobio

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Ramona 2018-11-21 13:49:41 +01:00
commit f67d95961d
1 changed files with 34 additions and 5 deletions
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39
code/read_chirp_data.py
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@ -1,5 +1,7 @@
import numpy as np
import os
import nixio as nix
from IPython import embed
def read_chirp_spikes(dataset):
@ -85,10 +87,37 @@ def read_chirp_times(dataset):
return chirp_times
def read_chirp_stimulus(dataset):
base = dataset.split(os.path.sep)[-1] + ".nix"
nix_file = nix.File.open(os.path.join(dataset, base), nix.FileMode.ReadOnly)
b = nix_file.blocks[0]
data = {}
for t in b.tags:
if "Chirps" in t.name:
stims = []
index = int(t.name.split("_")[-1])
df = t.metadata["RePro-Info"]["settings"]["deltaf"]
cs = t.metadata["RePro-Info"]["settings"]["chirpsize"]
stim_da = t.references["GlobalEFieldStimulus"]
si = stim_da.dimensions[0].sampling_interval
for mt in b.multi_tags:
if mt.positions[0] >= t.position[0] and \
mt.positions[0] < (t.position[0] + t.extent[0]):
break
for i in range(len(mt.positions)):
start_index = int(mt.positions[i] / si)
end_index = int((mt.positions[i] + mt.extents[i]) / si) - 1
stim = stim_da[start_index:end_index]
time = stim_da.dimensions[0].axis(len(stim)) + mt.positions[i]
stims.append((time, stim))
data[(index, df, cs)] = stims
nix_file.close()
return data
if __name__ == "__main__":
data_dir = "../data"
dataset = "2018-11-09-ad-invivo-1"
spikes = load_chirp_spikes(os.path.join(data_dir, dataset))
chirp_times = load_chirp_times(os.path.join(data_dir, dataset))
chirp_eod = load_chirp_eod(os.path.join(data_dir, dataset))
dataset = "2018-11-20-ad-invivo-1"
#spikes = load_chirp_spikes(os.path.join(data_dir, dataset))
#chirp_times = load_chirp_times(os.path.join(data_dir, dataset))
#chirp_eod = load_chirp_eod(os.path.join(data_dir, dataset))
stim = read_chirp_stimulus(os.path.join(data_dir, dataset))