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agosztolai committed May 21, 2024
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1,660 changes: 1,660 additions & 0 deletions examples/rat_hippocampus/decoding.ipynb
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108 changes: 41 additions & 67 deletions examples/rat_hippocampus/multianimal_consistency.ipynb
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"name": "stdout",
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"\n",
"\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m A new release of pip is available: \u001b[0m\u001b[31;49m23.3.2\u001b[0m\u001b[39;49m -> \u001b[0m\u001b[32;49m24.0\u001b[0m\n",
"\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m To update, run: \u001b[0m\u001b[32;49mpip install --upgrade pip\u001b[0m\n"
]
},
{
"name": "stderr",
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"text": [
"2024-05-02 08:11:55.834014: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT\n",
"/home/robert/anaconda3/lib/python3.9/site-packages/umap/distances.py:1063: NumbaDeprecationWarning: \u001b[1mThe 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.\u001b[0m\n",
" @numba.jit()\n",
"/home/robert/anaconda3/lib/python3.9/site-packages/umap/distances.py:1071: NumbaDeprecationWarning: \u001b[1mThe 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.\u001b[0m\n",
" @numba.jit()\n",
"/home/robert/anaconda3/lib/python3.9/site-packages/umap/distances.py:1086: NumbaDeprecationWarning: \u001b[1mThe 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.\u001b[0m\n",
" @numba.jit()\n",
"/home/robert/anaconda3/lib/python3.9/site-packages/umap/umap_.py:660: NumbaDeprecationWarning: \u001b[1mThe 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.\u001b[0m\n",
" @numba.jit()\n"
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]
}
],
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"text": [
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"\n",
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]
}
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},
{
"cell_type": "code",
"execution_count": 4,
"execution_count": 3,
"metadata": {},
"outputs": [
{
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3 changes: 1 addition & 2 deletions examples/rat_hippocampus/rat_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,15 +25,14 @@ def prepare_marble(spikes,
frac_geodesic_nb=1,
kernel_width=10,):

s_interval = 1

if spiking_rates:
gk = GaussianKernel(kernel_width * ms)
rates = []
for sp in spikes:
sp_times = np.where(sp)[0]
st = neo.SpikeTrain(sp_times, units="ms", t_stop=len(sp))
r = instantaneous_rate(st, kernel=gk, sampling_period=s_interval * ms).magnitude
r = instantaneous_rate(st, kernel=gk, sampling_period=1. * ms).magnitude
rates.append(r.T)

rates = np.vstack(rates)
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