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[reproclasses/baseline] add function to get the raw membrane voltage

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Jan Grewe 2019-10-18 16:39:07 +02:00
parent ade9b62c54
commit 1a1dabf955
1 changed files with 24 additions and 0 deletions
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fishbook/reproclasses.py
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@ -166,6 +166,30 @@ class BaselineData:
def spikes(self, index: int=0): def spikes(self, index: int=0):
return self.__spike_data[index] if len(self.__spike_data) >= index else None return self.__spike_data[index] if len(self.__spike_data) >= index else None
def membrane_voltage(self, index: int=0):
if index >= self.size:
raise IndexError("Index %i out of bounds for size %i!" % (index, self.size))
if not self.__dataset.has_nix:
print('Sorry, this is not supported for non-nixed datasets. Implement it at '
'fishbook.reproclasses.BaselineData.membrane_voltage and send a pull request!')
return None, None
else:
rp = self.__repros[index]
data_source = os.path.join(self.__dataset.data_source, self.__dataset.id + ".nix")
f = nix.File.open(data_source, nix.FileMode.ReadOnly)
b = f.blocks[0]
t = b.tags[rp.id]
if not t:
print("Tag not found!")
try:
data = t.retrieve_data("V-1")[:]
time = np.asarray(t.references["V-1"].dimensions[0].axis(len(data)))
except:
data = np.empty()
time = np.empty()
f.close()
return time, data
def eod(self, index: int=0): def eod(self, index: int=0):
eod = self.__eod_data[index] if len(self.__eod_data) >= index else None eod = self.__eod_data[index] if len(self.__eod_data) >= index else None
time = np.arange(len(eod)) / self.__dataset.samplerate time = np.arange(len(eod)) / self.__dataset.samplerate