35 lines
1.2 KiB
Python
35 lines
1.2 KiB
Python
import nixio as nix
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import os
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from IPython import embed
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def read_baseline_eod(dataset):
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base = dataset.split(os.path.sep)[-1] + ".nix"
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nix_file = nix.File.open(os.path.join(dataset, base), nix.FileMode.ReadOnly)
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b = nix_file.blocks[0]
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t = b.tags["BaselineActivity_1"]
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eod_da = b.data_arrays["LocalEOD-1"]
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eod = t.retrieve_data("LocalEOD-1")[:]
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time = eod_da.dimensions[0].axis(len(eod))
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nix_file.close()
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return time, eod
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def read_baseline_spikes(dataset):
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base = dataset.split(os.path.sep)[-1] + ".nix"
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nix_file = nix.File.open(os.path.join(dataset, base), nix.FileMode.ReadOnly)
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b = nix_file.blocks[0]
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t = b.tags["BaselineActivity_1"]
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spikes_da = b.data_arrays["Spikes-1"]
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spike_times = spikes_da[:spikes_da.shape[0]-5000]
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baseline_spikes = spike_times[(spike_times > t.position[0]) & (spike_times < (t.position[0] + t.extent[0]))]
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nix_file.close()
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return baseline_spikes
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if __name__ == "__main__":
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data_dir = "../data"
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dataset = "2018-11-09-ad-invivo-1"
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time, eod = read_baseline_eod(os.path.join(data_dir, dataset))
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spike_times = read_baseline_spikes(os.path.join(data_dir, dataset))
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