eden-kramer-lab/rate_adjustment_for_spike_coherence

An implementation of the spike-rate adjustment method from Aoi et al. (2015) for comparing spike-field and spike-spike coherences.

Eden-Kramer-Lab

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rate_adjustment_for_spike_coherence's Issues

MemoryError after changing sampling frequency

Hi,
I would like to use your code to determine the spike-field coherence of my data. My sampling rate is 20 kHz, I have 200 trials, and I would like to examine a 300 ms time interval. I initially tried the example using the surrogate LFPs and spikes based on the Aoi et al., 2015 publication. This worked great. After I converted my spike data and LFP data into the correct format I ran it and I obtained a MemoryError.
To try to determine what was causing the error I used the surrogate data example again and there I changed the n_time to 10000, the sampling_frequency to 10000 and ran the code. Again I obtained the same MemoryError:

Connected to pydev debugger (build 202.8194.22)
INFO:spectral_connectivity.transforms:Multitaper(sampling_frequency=10000, time_halfbandwidth_product=5,
time_window_duration=1.0, time_window_step=1.0,
detrend_type='constant', start_time=0, n_tapers=9)
INFO:spectral_connectivity.transforms:Multitaper(sampling_frequency=10000, time_halfbandwidth_product=25,
time_window_duration=1.0, time_window_step=1.0,
detrend_type='constant', start_time=0, n_tapers=49)
Traceback (most recent call last):
File "C:\Program Files\JetBrains\PyCharm Community Edition 2019.1.1\plugins\python-ce\helpers\pydev\pydevd.py", line 1448, in _exec
pydev_imports.execfile(file, globals, locals) # execute the script
File "C:\Program Files\JetBrains\PyCharm Community Edition 2019.1.1\plugins\python-ce\helpers\pydev_pydev_imps_pydev_execfile.py", line 18, in execfile
exec(compile(contents+"\n", file, 'exec'), glob, loc)
File "C:/Users/dsuchane/PycharmProjects/iCSD/Test_coherence.py", line 78, in
c = Connectivity.from_multitaper(m)
File "C:\Users\dsuchane\PycharmProjects\untitled\venv\lib\site-packages\spectral_connectivity\connectivity.py", line 108, in from_multitaper
fourier_coefficients=multitaper_instance.fft(),
File "C:\Users\dsuchane\PycharmProjects\untitled\venv\lib\site-packages\spectral_connectivity\transforms.py", line 217, in fft
self.sampling_frequency).swapaxes(2, -1)
File "C:\Users\dsuchane\PycharmProjects\untitled\venv\lib\site-packages\spectral_connectivity\transforms.py", line 315, in _multitaper_fft
tapers[np.newaxis, np.newaxis, ...])
MemoryError
python-BaseException
Backend TkAgg is interactive backend. Turning interactive mode on.

If I run only 20 trials at a time it works, so what I thought I'd do is run a set of 20 trials at a time and then average the 20 resulting coherence spectra. I'm not sure if that is even allowed, I'm not a mathematician. Any help on this would be greatly appreciated.

Thanks.