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[ENH] Optimization #201

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Merged
merged 3 commits into from
Mar 28, 2021
Merged

[ENH] Optimization #201

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1f436cb
optimization improvements
ryanhammonds Mar 9, 2021
cf721a2
small doc & code notes tweaks
TomDonoghue Mar 28, 2021
c2c8643
extend fit_fooof_3d test
TomDonoghue Mar 28, 2021
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optimization improvements
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@ryanhammonds
ryanhammonds committed Mar 9, 2021
commit 1f436cb10a412360933e9a15fee6ed8517bf391c
6 changes: 5 additions & 1 deletion fooof/core/utils.py
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Expand Up @@ -30,7 +30,11 @@ def group_three(vec):
if len(vec) % 3 != 0:
raise ValueError("Wrong size array to group by three.")

return [list(vec[ii:ii+3]) for ii in range(0, len(vec), 3)]
if isinstance(vec, np.ndarray):
# Reshaping is faster if already an array
return np.reshape(vec, (-1, 3))
else:
return [list(vec[ii:ii+3]) for ii in range(0, len(vec), 3)]


def nearest_ind(array, value):
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14 changes: 6 additions & 8 deletions fooof/objs/fit.py
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Expand Up @@ -1007,18 +1007,16 @@ def _create_peak_params(self, gaus_params):
with `freqs`, `fooofed_spectrum_` and `_ap_fit` all required to be available.
"""

peak_params = np.empty([0, 3])
peak_params = np.empty((len(gaus_params), 3))

for ii, peak in enumerate(gaus_params):

# Gets the index of the power_spectrum at the frequency closest to the CF of the peak
ind = min(range(len(self.freqs)), key=lambda ii: abs(self.freqs[ii] - peak[0]))
ind = np.argmin(np.abs(self.freqs - peak[0]))

# Collect peak parameter data
peak_params = np.vstack((peak_params,
[peak[0],
self.fooofed_spectrum_[ind] - self._ap_fit[ind],
peak[2] * 2]))
peak_params[ii] = [peak[0], self.fooofed_spectrum_[ind] - self._ap_fit[ind],
peak[2] * 2]

return peak_params

Expand All @@ -1037,8 +1035,8 @@ def _drop_peak_cf(self, guess):
Guess parameters for gaussian peak fits. Shape: [n_peaks, 3].
"""

cf_params = [item[0] for item in guess]
bw_params = [item[2] * self._bw_std_edge for item in guess]
cf_params = guess[:, 0]
bw_params = guess[:, 2] * self._bw_std_edge

# Check if peaks within drop threshold from the edge of the frequency range
keep_peak = \
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13 changes: 9 additions & 4 deletions fooof/objs/utils.py
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Expand Up @@ -219,9 +219,14 @@ def fit_fooof_3d(fg, freqs, power_spectra, freq_range=None, n_jobs=1):
>>> fgs = fit_fooof_3d(fg, freqs, power_spectra, freq_range=[3, 30]) # doctest:+SKIP
"""

fgs = []
for cond_spectra in power_spectra:
fg.fit(freqs, cond_spectra, freq_range, n_jobs)
fgs.append(fg.copy())
# Reshape 3d to 2d and fit
shape = np.shape(power_spectra)
powers_2d = np.reshape(power_spectra, (shape[0] * shape[1], shape[2]))

fg.fit(freqs, powers_2d, freq_range, n_jobs)

# Reorganize 2d results
fgs = [fg.get_group(range(dim_a * shape[1], (dim_a + 1) * shape[1])) \
for dim_a in range(shape[0]) ]

return fgs