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[reproclasses/FICurve] fixed time alignment of spikes, create time arrays

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Jan Grewe 2019-10-09 11:38:05 +02:00
parent ecdd29da79
commit fe2457d85f
1 changed files with 28 additions and 17 deletions
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45
fishbook/reproclasses.py
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@ -435,10 +435,7 @@ class FIData:
start_time = stimulus.start_time - delay
end_time = stimulus.start_time + stimulus.duration
spikes_da = mtag.references["Spikes-1"]
eod_da = mtag.references["LocalEOD-1"]
start_index_spikes = spikes_da.dimensions[0].index_of(start_time)
end_index_spikes = spikes_da.dimensions[0].index_of(end_time)
start_index_eod = eod_da.dimensions[0].index_of(start_time)
end_index_eod = eod_da.dimensions[0].index_of(end_time)
@ -479,37 +476,51 @@ class FIData:
def __do_read_data_block(self, f, l):
spikes = []
while len(l.strip()) > 0 and "#" not in l:
spikes.append(float(l.strip()))
spikes.append(float(l.strip())/1000)
l = f.readline()
return spikes, l
def __read_spikes_from_directory(self, repro: RePro):
spikes = []
contrasts = []
times = []
print("Warning! Exact reconstruction of stimulus order not possible for old relacs files!")
data_source = os.path.join(self.__dataset.data_source, "fispikes1.dat")
delay = 0.0
pause = 0.0
for s in repro.settings.split(", "):
if "pause" in s:
s = s.split(":")[-1].strip()
pause = float(s[:-2])/1000 if "ms" in s else float(s[:-1])
if "delay" in s:
s = s.split(":")[-1].strip()
delay = float(s[:-2])/1000 if "ms" in s else float(s[:-1])
t_start = -delay
t_end = pause + delay
time = np.arange(t_start, t_end, 1./repro.dataset.samplerate)
if os.path.exists(data_source):
with open(data_source, 'r') as f:
l = f.readline()
line = f.readline()
fish_intensity = None
stim_intensity = None
while l:
l = l.strip().lower()
if "index" in l:
while line:
line = line.strip().lower()
if "index" in line:
fish_intensity = None
stim_intensity = None
if "intensity = " in l:
if "true intensity = " in l:
fish_intensity = float(l.split("=")[-1].strip()[:-2])
elif "pre" not in l:
stim_intensity = float(l.split("=")[-1].strip()[:-2])
if len(l) > 0 and "#" not in l: # data line
sp, l = self.__do_read_data_block(f, l)
if "intensity = " in line:
if "true intensity = " in line:
fish_intensity = float(line.split("=")[-1].strip()[:-2])
elif "pre" not in line:
stim_intensity = float(line.split("=")[-1].strip()[:-2])
if len(line) > 0 and "#" not in line: # data line
sp, line = self.__do_read_data_block(f, line)
spikes.append(sp)
times.append(time)
contrasts.append((stim_intensity/fish_intensity-1)*100)
continue
l = f.readline()
return spikes, contrasts, None, None
line = f.readline()
return spikes, contrasts, None, times
@property
def size(self) -> int: