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[BUG] - Fix description of time constant estimation #302

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Merged
merged 2 commits into from
Sep 13, 2023
Merged

[BUG] - Fix description of time constant estimation #302

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50f0e70
fix description of time constant estimation
TomDonoghue Sep 12, 2023
bd59f77
add comments on knee convs
TomDonoghue Sep 13, 2023
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2 changes: 1 addition & 1 deletion fooof/tests/utils/test_params.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ def test_compute_knee_frequency():

def test_compute_time_constant():

assert compute_time_constant(100)
assert compute_time_constant(10)

def test_compute_fwhm():

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43 changes: 36 additions & 7 deletions fooof/utils/params.py
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Expand Up @@ -19,26 +19,55 @@ def compute_knee_frequency(knee, exponent):
-------
float
Frequency value, in Hz, of the knee occurs.

Notes
-----
The knee frequency is an estimate of the frequency in spectrum at which the spectrum
moves from the plateau region to the exponential decay.

This approach for estimating the knee frequency comes from [1]_ (see [2]_ for code).

Note that this provides an estimate of the knee frequency, but is not, in the general case,
a precisely defined value. In particular, this conversion is based on the case of a Lorentzian
with exponent = 2, and for other exponent values provides a non-exact approximation.

References
----------
.. [1] Gao, R., van den Brink, R. L., Pfeffer, T., & Voytek, B. (2020). Neuronal timescales
are functionally dynamic and shaped by cortical microarchitecture. Elife, 9, e61277.
https://doi.org/10.7554/eLife.61277
.. [2] https://github.com/rdgao/field-echos/blob/master/echo_utils.py#L64
"""

return knee ** (1./exponent)
return knee ** (1. / exponent)


def compute_time_constant(knee):
"""Compute the characteristic time constant based on the knee value.
def compute_time_constant(knee_freq):
"""Compute the characteristic time constant from the estimated knee frequency.

Parameters
----------
knee : float
Knee parameter value.
knee_freq : float
Estimated knee frequency.

Returns
-------
float
Calculated time constant value, tau, given the knee parameter.
Calculated time constant value, tau, given the knee frequency.

Notes
-----
This approach for estimating the time constant comes from [1]_ (see [2]_ for code).

References
----------
.. [1] Gao, R., van den Brink, R. L., Pfeffer, T., & Voytek, B. (2020). Neuronal timescales
are functionally dynamic and shaped by cortical microarchitecture. Elife, 9, e61277.
https://doi.org/10.7554/eLife.61277
.. [2] https://github.com/rdgao/field-echos/blob/master/echo_utils.py#L65
"""

return 1. / (2*np.pi*knee)
return 1. / (2 * np.pi * knee_freq)


def compute_fwhm(std):
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