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tested and corrected sam_data function

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mbergmann 2024-10-22 15:12:28 +02:00
parent c7436ad6b6
commit c995ed7a3b
1 changed files with 46 additions and 43 deletions
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code/test.py
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@ -5,6 +5,7 @@ import matplotlib.pyplot as plt
import rlxnix as rlx import rlxnix as rlx
from IPython import embed from IPython import embed
from scipy.signal import welch from scipy.signal import welch
import useful_functions as f
def binary_spikes(spike_times, duration, dt): def binary_spikes(spike_times, duration, dt):
""" """
@ -68,10 +69,10 @@ def extract_stim_data(stimulus):
''' '''
# extract metadata # extract metadata
# the stim.name adjusts the first key as it changes with every stimulus # the stim.name adjusts the first key as it changes with every stimulus
amplitude = stim.metadata[stim.name]['Contrast'][0][0] amplitude = stimulus.metadata[stimulus.name]['Contrast'][0][0]
df = stim.metadata[stim.name]['DeltaF'][0][0] df = stimulus.metadata[stimulus.name]['DeltaF'][0][0]
eodf = round(stim.metadata[stim.name]['EODf'][0][0]) eodf = round(stimulus.metadata[stimulus.name]['EODf'][0][0])
stim_freq = round(stim.metadata[stim.name]['Frequency'][0][0]) stim_freq = round(stimulus.metadata[stimulus.name]['Frequency'][0][0])
# calculates the amplitude modulation # calculates the amplitude modulation
amp_mod, ny_freq = AM(eodf, stim_freq) amp_mod, ny_freq = AM(eodf, stim_freq)
return amplitude, df, eodf, stim_freq, amp_mod, ny_freq return amplitude, df, eodf, stim_freq, amp_mod, ny_freq
@ -187,7 +188,7 @@ def sam_data(sam):
#find example data #find example data
datafolder = "../../data" datafolder = "../../data"
example_file = datafolder + "/" + "2024-10-16-ah-invivo-1.nix" example_file = datafolder + "/" + "2024-10-16-ad-invivo-1.nix"
data_files = glob.glob("../../data/*.nix") data_files = glob.glob("../../data/*.nix")
@ -209,41 +210,43 @@ ax.scatter(spike_times[spike_times < 0.1],
np.ones_like(spike_times[spike_times < 0.1]) * np.max(potential)) #plot teh spike times on top np.ones_like(spike_times[spike_times < 0.1]) * np.max(potential)) #plot teh spike times on top
plt.show() plt.show()
plt.close() plt.close()
# get all the stimuli
stims = sam.stimuli sam_amp, sam_am,sam_df, sam_eodf, sam_nyquist, sam_stim = f.sam_data(sam)
# empty list for the spike times # # get all the stimuli
spikes = [] # stims = sam.stimuli
#spikes2 = np.array(range(len(stims))) # # empty list for the spike times
# loop over the stimuli # spikes = []
for stim in stims: # #spikes2 = np.array(range(len(stims)))
# get the spike times # # loop over the stimuli
spike, _ = stim.trace_data('Spikes-1') # for stim in stims:
# append the first 100ms to spikes # # get the spike times
spikes.append(spike[spike < 0.1]) # spike, _ = stim.trace_data('Spikes-1')
# get stimulus duration # # append the first 100ms to spikes
duration = stim.duration # spikes.append(spike[spike < 0.1])
ti = stim.trace_info("V-1") # # get stimulus duration
dt = ti.sampling_interval # get the stimulus interval # duration = stim.duration
bin_spikes = binary_spikes(spike, duration, dt) #binarize the spike_times # ti = stim.trace_info("V-1")
print(len(bin_spikes)) # dt = ti.sampling_interval # get the stimulus interval
pot,tim= stim.trace_data("V-1") #membrane potential # bin_spikes = binary_spikes(spike, duration, dt) #binarize the spike_times
rate = firing_rate(bin_spikes, dt = dt) # print(len(bin_spikes))
print(np.mean(rate)) # pot,tim= stim.trace_data("V-1") #membrane potential
fig, [ax1, ax2] = plt.subplots(1, 2,layout = 'constrained') # rate = firing_rate(bin_spikes, dt = dt)
ax1.plot(tim,rate) # print(np.mean(rate))
ax1.set_ylim(0,600) # fig, [ax1, ax2] = plt.subplots(1, 2,layout = 'constrained')
ax1.set_xlim(0, 0.04) # ax1.plot(tim,rate)
freq, power = power_spectrum(rate, dt) # ax1.set_ylim(0,600)
ax2.plot(freq,power) # ax1.set_xlim(0, 0.04)
ax2.set_xlim(0,1000) # freq, power = power_spectrum(rate, dt)
plt.close() # ax2.plot(freq,power)
if stim == stims[-1]: # ax2.set_xlim(0,1000)
amplitude, df, eodf, stim_freq = extract_stim_data(stim) # plt.close()
print(amplitude, df, eodf, stim_freq) # if stim == stims[-1]:
# amplitude, df, eodf, stim_freq = extract_stim_data(stim)
# make an eventplot # print(amplitude, df, eodf, stim_freq)
fig = plt.figure(figsize = (5, 3), layout = 'constrained')
ax = fig.add_subplot() # # make an eventplot
ax.eventplot(spikes, linelength = 0.8) # fig = plt.figure(figsize = (5, 3), layout = 'constrained')
ax.set_xlabel('time [ms]') # ax = fig.add_subplot()
ax.set_ylabel('loop no.') # ax.eventplot(spikes, linelength = 0.8)
# ax.set_xlabel('time [ms]')
# ax.set_ylabel('loop no.')