Convert to rferences bib

Signed-off-by: Adam Li <[email protected]>
mne-tools · Sep 21, 2023 · c80a8e7 · c80a8e7
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diff --git a/doc/conf.py b/doc/conf.py
@@ -38,6 +38,7 @@
     'sphinx.ext.doctest',
     'sphinx.ext.intersphinx',
     'sphinx_gallery.gen_gallery',
+    "sphinxcontrib.bibtex",
     'numpydoc',
     'nbsphinx',  # to render jupyter notebooks
     'sphinx_copybutton',

diff --git a/doc/references.bib b/doc/references.bib
@@ -0,0 +1,57 @@
+@article{dumpelmann2012automatic,
+  title     = {Automatic 80--250 Hz “ripple” high frequency oscillation detection in invasive subdural grid and strip recordings in epilepsy by a radial basis function neural network},
+  author    = {D{\"u}mpelmann, Matthias and Jacobs, Julia and Kerber, Karolin and Schulze-Bonhage, Andreas},
+  journal   = {Clinical Neurophysiology},
+  volume    = {123},
+  number    = {9},
+  pages     = {1721--1731},
+  year      = {2012},
+  publisher = {Elsevier},
+  doi       = {10.1016/j.clinph.2012.02.072}
+}
+
+@inproceedings{esteller2001line,
+  title        = {Line length: an efficient feature for seizure onset detection},
+  author       = {Esteller, Rosana and Echauz, Javier and Tcheng, T and Litt, Brian and Pless, Benjamin},
+  booktitle    = {2001 Conference Proceedings of the 23rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society},
+  volume       = {2},
+  pages        = {1707--1710},
+  year         = {2001},
+  organization = {IEEE}
+}
+
+@article{gardner2007human,
+  title     = {Human and automated detection of high-frequency oscillations in clinical intracranial EEG recordings},
+  author    = {Gardner, Andrew B and Worrell, Greg A and Marsh, Eric and Dlugos, Dennis and Litt, Brian},
+  journal   = {Clinical neurophysiology},
+  volume    = {118},
+  number    = {5},
+  pages     = {1134--1143},
+  year      = {2007},
+  publisher = {Elsevier},
+  doi       = {10.1016/j.clinph.2006.12.019}
+}
+
+@article{kucewicz2014high,
+  title     = {High frequency oscillations are associated with cognitive processing in human recognition memory},
+  author    = {Kucewicz, Michal T and Cimbalnik, Jan and Matsumoto, Joseph Y and Brinkmann, Benjamin H and Bower, Mark R and Vasoli, Vincent and Sulc, Vlastimil and Meyer, Fred and Marsh, WR and Stead, SM and others},
+  journal   = {Brain},
+  volume    = {137},
+  number    = {8},
+  pages     = {2231--2244},
+  year      = {2014},
+  publisher = {Oxford University Press},
+  doi       = {10.1093/brain/awu149}
+}
+
+@article{staba2002quantitative,
+  title     = {Quantitative analysis of high-frequency oscillations (80--500 Hz) recorded in human epileptic hippocampus and entorhinal cortex},
+  author    = {Staba, Richard J and Wilson, Charles L and Bragin, Anatol and Fried, Itzhak and Engel Jr, Jerome},
+  journal   = {Journal of neurophysiology},
+  volume    = {88},
+  number    = {4},
+  pages     = {1743--1752},
+  year      = {2002},
+  publisher = {American Physiological Society Bethesda, MD},
+  doi       = {10.1152/jn.2002.88.4.1743}
+}
diff --git a/mne_hfo/detect.py b/mne_hfo/detect.py
@@ -12,6 +12,7 @@ class HilbertDetector(Detector):  # noqa
 
     A multi-taper method with: 4 Hz bandwidth, 1 sec sliding window,
     stepsize 100 ms, for the 1-500 Hz range, no padding, 2 tapers.
+    For full details, see :footcite:`kucewicz2014high`.
 
     Parameters
     ----------
@@ -46,11 +47,7 @@ class HilbertDetector(Detector):  # noqa
 
     References
     ----------
-    [1] M. T. Kucewicz, J. Cimbalnik, J. Y. Matsumoto, B. H. Brinkmann,
-    M. Bower, V. Vasoli, V. Sulc, F. Meyer, W. R. Marsh, S. M. Stead, and
-    G. A. Worrell, “High frequency oscillations are associated with
-    cognitive processing in human recognition memory.,” Brain, pp. 1–14,
-    Jun. 2014.
+    .. footbibliography::
     """
 
     def __init__(
@@ -165,15 +162,16 @@ class LineLengthDetector(Detector):
     "(HFOs), which we collectively term as all activity >40 Hz
     (including gamma, high-gamma, ripple, and fast ripple oscillations),
     may have a fundamental role in the generation and spread of focal
-    seizures."
+    seizures." See :footcite:`gardner2007human`.
 
     In the paper, data were sampled at 200 Hz and bandpass-filtered (0.1 – 100
     Hz) during acquisition. Data were further digitally bandpass-filtered
     (4th-order Butterworth, forward-backward filtering, ``0.1 – 85 Hz``)
     to minimize potential artifacts due to aliasing. (IIR for forward-backward
     pass).
 
-    Compared to RMS detector, they utilize line-length metric.
+    Compared to RMS detector, they utilize line-length metric
+    :footcite:`esteller2001line`.
 
     Parameters
     ----------
@@ -207,14 +205,7 @@ class LineLengthDetector(Detector):
 
     References
     ----------
-    .. [1] A. B. Gardner, G. A. Worrell, E. Marsh, D. Dlugos, and B. Litt,
-           “Human and automated detection of high-frequency oscillations in
-           clinical intracranial EEG recordings,” Clin. Neurophysiol.,
-           vol. 118, no. 5, pp. 1134–1143, May 2007.
-    .. [2] Esteller, R. et al. (2001). Line length: an efficient feature for
-           seizure onset detection. In Engineering in Medicine and Biology
-           Society, 2001. Proceedings of the 23rd Annual International
-           Conference of the IEEE (Vol. 2, pp. 1707-1710). IEEE.
+    .. footbibliography::
     """
 
     def __init__(
@@ -300,7 +291,7 @@ class RMSDetector(Detector):
     Then events not having a minimum of 6 peaks (i.e. band-pass signal
     rectified above 0 V) with greater then 3 std above mean baseline
     were removed. A finite impulse response (FIR) filter with a
-    Hamming window was used.
+    Hamming window was used. See :footcite:`staba2002quantitative`.
 
     Parameters
     ----------
@@ -328,10 +319,7 @@ class RMSDetector(Detector):
 
     References
     ----------
-    [1] R. J. Staba, C. L. Wilson, A. Bragin, I. Fried, and J. Engel,
-    “Quantitative Analysis of High-Frequency Oscillations (80 − 500 Hz)
-    Recorded in Human Epileptic Hippocampus and Entorhinal Cortex,”
-    J. Neurophysiol., vol. 88, pp. 1743–1752, 2002.
+    .. footbibliography::
     """
 
     def __init__(

diff --git a/mne_hfo/utils.py b/mne_hfo/utils.py
@@ -226,6 +226,8 @@ def compute_rms(signal, win_size=6):
 def compute_line_length(signal, win_size=6):
     """Calculate line length.
 
+    See :footcite:`esteller2001line` and :footcite:`dumpelmann2012automatic`.
+
     Parameters
     ----------
     signal : numpy array
@@ -246,12 +248,7 @@ def compute_line_length(signal, win_size=6):
 
     References
     ----------
-    .. [1] Esteller, R. et al. (2001). Line length: an efficient feature for
-           seizure onset detection. In Engineering in Medicine and Biology
-           Society, 2001. Proceedings of the 23rd Annual International
-           Conference of the IEEE (Vol. 2, pp. 1707-1710). IEEE.
-
-    .. [2] Dümpelmann et al, 2012.  Clinical Neurophysiology: 123 (9): 1721-31.
+    .. footbibliography::
     """
     aux = np.abs(np.subtract(signal[1:], signal[:-1]))
     window = np.ones(win_size) / float(win_size)