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FIX: utils.find_cells using cell coordinate #45

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FIX: utils.find_cells using cell coordinate #45

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ed2ead7
first approach, should later add include_dim kwarg for example:
mmagnuski Jun 4, 2025
fdbb63b
give more detail to the part of spike density when values below noise…
mmagnuski Jun 5, 2025
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9 changes: 7 additions & 2 deletions pylabianca/spike_rate.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,6 @@


# TODO: add n_jobs?
# CONSIDER wintype 'rectangular' vs 'gaussian'
# TODO: refactor (DRY: merge both loops into one?)
# TODO: consider adding `return_type` with `Epochs` option (mne object)
def compute_spike_rate(spk, picks=None, winlen=0.25, step=0.01, tmin=None,
Expand Down Expand Up @@ -229,8 +228,14 @@ def _spike_density(spk, picks=None, winlen=0.3, gauss_sd=None, fwhm=None,
# numerical errors, that do not seem to be present if we do one
# cell-trial at a time, this needs to be investigated a bit more
# but now we just set them to zero
# (this is likely related to numerical precision in computing the
# correlations via FFT)
# using oaconvolve (overlap-add convolution) instead of correlate
# helps, but does not solve the problem completely, so we still remove
# activity below a certain "noise level" threshold
# - [ ] CHECK if this is still an issue and whether the kernel is to
# blame
noise_level = 1e-14

mask = np.abs(cnt) < noise_level
cnt[mask] = 0.

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2 changes: 2 additions & 0 deletions pylabianca/utils/xarr.py
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Expand Up @@ -126,6 +126,8 @@ def df_from_xarray_coords(xarr, dim):
'''
import pandas as pd
use_dims = find_nested_dims(xarr, dim)
if dim not in use_dims:
use_dims = [dim] + use_dims

if len(use_dims) > 1:
df = {dim: xarr.coords[dim].values for dim in use_dims}
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