py-neuromodulation 0.0.4__py3-none-any.whl → 0.0.5__py3-none-any.whl

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Files changed (80) hide show
  1. py_neuromodulation/ConnectivityDecoding/_get_grid_hull.m +34 -34
  2. py_neuromodulation/ConnectivityDecoding/_get_grid_whole_brain.py +95 -106
  3. py_neuromodulation/ConnectivityDecoding/_helper_write_connectome.py +107 -119
  4. py_neuromodulation/FieldTrip.py +589 -589
  5. py_neuromodulation/__init__.py +74 -13
  6. py_neuromodulation/_write_example_dataset_helper.py +83 -65
  7. py_neuromodulation/data/README +6 -6
  8. py_neuromodulation/data/dataset_description.json +8 -8
  9. py_neuromodulation/data/participants.json +32 -32
  10. py_neuromodulation/data/participants.tsv +2 -2
  11. py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_space-mni_coordsystem.json +5 -5
  12. py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_space-mni_electrodes.tsv +11 -11
  13. py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_channels.tsv +11 -11
  14. py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.json +18 -18
  15. py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.vhdr +35 -35
  16. py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.vmrk +13 -13
  17. py_neuromodulation/data/sub-testsub/ses-EphysMedOff/sub-testsub_ses-EphysMedOff_scans.tsv +2 -2
  18. py_neuromodulation/grid_cortex.tsv +40 -40
  19. py_neuromodulation/liblsl/libpugixml.so.1.12 +0 -0
  20. py_neuromodulation/liblsl/linux/bionic_amd64/liblsl.1.16.2.so +0 -0
  21. py_neuromodulation/liblsl/linux/bookworm_amd64/liblsl.1.16.2.so +0 -0
  22. py_neuromodulation/liblsl/linux/focal_amd46/liblsl.1.16.2.so +0 -0
  23. py_neuromodulation/liblsl/linux/jammy_amd64/liblsl.1.16.2.so +0 -0
  24. py_neuromodulation/liblsl/linux/jammy_x86/liblsl.1.16.2.so +0 -0
  25. py_neuromodulation/liblsl/linux/noble_amd64/liblsl.1.16.2.so +0 -0
  26. py_neuromodulation/liblsl/macos/amd64/liblsl.1.16.2.dylib +0 -0
  27. py_neuromodulation/liblsl/macos/arm64/liblsl.1.16.0.dylib +0 -0
  28. py_neuromodulation/liblsl/windows/amd64/liblsl.1.16.2.dll +0 -0
  29. py_neuromodulation/liblsl/windows/x86/liblsl.1.16.2.dll +0 -0
  30. py_neuromodulation/nm_IO.py +413 -417
  31. py_neuromodulation/nm_RMAP.py +496 -531
  32. py_neuromodulation/nm_analysis.py +993 -1074
  33. py_neuromodulation/nm_artifacts.py +30 -25
  34. py_neuromodulation/nm_bispectra.py +154 -168
  35. py_neuromodulation/nm_bursts.py +292 -198
  36. py_neuromodulation/nm_coherence.py +251 -205
  37. py_neuromodulation/nm_database.py +149 -0
  38. py_neuromodulation/nm_decode.py +918 -992
  39. py_neuromodulation/nm_define_nmchannels.py +300 -302
  40. py_neuromodulation/nm_features.py +144 -116
  41. py_neuromodulation/nm_filter.py +219 -219
  42. py_neuromodulation/nm_filter_preprocessing.py +79 -91
  43. py_neuromodulation/nm_fooof.py +139 -159
  44. py_neuromodulation/nm_generator.py +45 -37
  45. py_neuromodulation/nm_hjorth_raw.py +52 -73
  46. py_neuromodulation/nm_kalmanfilter.py +71 -58
  47. py_neuromodulation/nm_linelength.py +21 -33
  48. py_neuromodulation/nm_logger.py +66 -0
  49. py_neuromodulation/nm_mne_connectivity.py +149 -112
  50. py_neuromodulation/nm_mnelsl_generator.py +90 -0
  51. py_neuromodulation/nm_mnelsl_stream.py +116 -0
  52. py_neuromodulation/nm_nolds.py +96 -93
  53. py_neuromodulation/nm_normalization.py +173 -214
  54. py_neuromodulation/nm_oscillatory.py +423 -448
  55. py_neuromodulation/nm_plots.py +585 -612
  56. py_neuromodulation/nm_preprocessing.py +83 -0
  57. py_neuromodulation/nm_projection.py +370 -394
  58. py_neuromodulation/nm_rereference.py +97 -95
  59. py_neuromodulation/nm_resample.py +59 -50
  60. py_neuromodulation/nm_run_analysis.py +325 -435
  61. py_neuromodulation/nm_settings.py +289 -68
  62. py_neuromodulation/nm_settings.yaml +244 -0
  63. py_neuromodulation/nm_sharpwaves.py +423 -401
  64. py_neuromodulation/nm_stats.py +464 -480
  65. py_neuromodulation/nm_stream.py +398 -0
  66. py_neuromodulation/nm_stream_abc.py +166 -218
  67. py_neuromodulation/nm_types.py +193 -0
  68. {py_neuromodulation-0.0.4.dist-info → py_neuromodulation-0.0.5.dist-info}/METADATA +29 -26
  69. py_neuromodulation-0.0.5.dist-info/RECORD +83 -0
  70. {py_neuromodulation-0.0.4.dist-info → py_neuromodulation-0.0.5.dist-info}/WHEEL +1 -1
  71. {py_neuromodulation-0.0.4.dist-info → py_neuromodulation-0.0.5.dist-info}/licenses/LICENSE +21 -21
  72. py_neuromodulation/nm_EpochStream.py +0 -92
  73. py_neuromodulation/nm_across_patient_decoding.py +0 -927
  74. py_neuromodulation/nm_cohortwrapper.py +0 -435
  75. py_neuromodulation/nm_eval_timing.py +0 -239
  76. py_neuromodulation/nm_features_abc.py +0 -39
  77. py_neuromodulation/nm_settings.json +0 -338
  78. py_neuromodulation/nm_stream_offline.py +0 -359
  79. py_neuromodulation/utils/_logging.py +0 -24
  80. py_neuromodulation-0.0.4.dist-info/RECORD +0 -72
py_neuromodulation/nm_features_abc.py DELETED
@@ -1,39 +0,0 @@
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- from abc import ABC, abstractmethod
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- import numpy as np
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- from typing import Iterable
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-
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-
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- class Feature(ABC):
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- @abstractmethod
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- def __init__(
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- self, settings: dict, ch_names: Iterable[str], sfreq: int | float
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- ) -> None:
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- pass
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-
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- @staticmethod
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- @abstractmethod
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- def test_settings(
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- settings: dict,
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- ch_names: Iterable[str],
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- sfreq: int | float,
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- ):
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- """Method to check passed settings"""
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- pass
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-
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- @abstractmethod
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- def calc_feature(self, data: np.array, features_compute: dict) -> dict:
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- """
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- Feature calculation method. Each method needs to loop through all channels
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-
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- Parameters
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- ----------
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- data : np.array
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- (channels, time)
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- features_compute : dict
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- ch_names : Iterable[str]
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-
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- Returns
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- -------
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- dict
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- """
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- pass
py_neuromodulation/nm_settings.json DELETED
@@ -1,338 +0,0 @@
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- {
2
- "sampling_rate_features_hz": 10,
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- "segment_length_features_ms": 1000,
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- "preprocessing": [
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- "raw_resampling",
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- "notch_filter",
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- "re_referencing"
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- ],
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- "documentation_preprocessing_options": [
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- "raw_resampling",
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- "notch_filter",
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- "re_referencing",
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- "raw_normalization",
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- "preprocessing_filter"
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- ],
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- "features": {
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- "raw_hjorth": true,
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- "return_raw": true,
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- "bandpass_filter": false,
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- "stft": false,
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- "fft": true,
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- "welch": true,
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- "sharpwave_analysis": true,
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- "fooof": false,
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- "bursts": true,
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- "linelength": true,
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- "coherence": false,
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- "nolds": false,
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- "mne_connectivity": false,
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- "bispectrum": false
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- },
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- "postprocessing": {
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- "feature_normalization": true,
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- "project_cortex": false,
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- "project_subcortex": false
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- },
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- "raw_resampling_settings": {
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- "resample_freq_hz": 1000
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- },
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- "preprocessing_filter": {
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- "bandstop_filter": true,
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- "lowpass_filter": true,
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- "highpass_filter": true,
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- "bandpass_filter": true,
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- "bandstop_filter_settings": {
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- "frequency_low_hz": 100,
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- "frequency_high_hz": 160
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- },
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- "lowpass_filter_settings": {
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- "frequency_cutoff_hz": 200
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- },
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- "highpass_filter_settings": {
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- "frequency_cutoff_hz": 3
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- },
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- "bandpass_filter_settings": {
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- "frequency_low_hz": 3,
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- "frequency_high_hz": 200
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- }
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- },
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- "re_referencing_settings": {
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- "reference": "common"
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- },
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- "documentation_normalization_options": [
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- "mean",
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- "median",
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- "zscore",
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- "zscore-median",
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- "quantile",
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- "power",
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- "robust",
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- "minmax"
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- ],
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- "raw_normalization_settings": {
74
- "normalization_time_s": 30,
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- "normalization_method": "zscore",
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- "clip": 3
77
- },
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- "feature_normalization_settings": {
79
- "normalization_time_s": 30,
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- "normalization_method": "zscore",
81
- "clip": 3
82
- },
83
- "frequency_ranges_hz": {
84
- "theta": [
85
- 4,
86
- 8
87
- ],
88
- "alpha": [
89
- 8,
90
- 12
91
- ],
92
- "low beta": [
93
- 13,
94
- 20
95
- ],
96
- "high beta": [
97
- 20,
98
- 35
99
- ],
100
- "low gamma": [
101
- 60,
102
- 80
103
- ],
104
- "high gamma": [
105
- 90,
106
- 200
107
- ],
108
- "HFA": [
109
- 200,
110
- 400
111
- ]
112
- },
113
- "fft_settings": {
114
- "windowlength_ms": 1000,
115
- "log_transform": true,
116
- "features": {
117
- "mean": true,
118
- "median": false,
119
- "std": false,
120
- "max": false
121
- },
122
- "return_spectrum": false
123
- },
124
- "welch_settings": {
125
- "windowlength_ms": 1000,
126
- "log_transform": true,
127
- "features": {
128
- "mean": true,
129
- "median": false,
130
- "std": false,
131
- "max": false
132
- },
133
- "return_spectrum": false
134
- },
135
- "stft_settings": {
136
- "windowlength_ms": 500,
137
- "log_transform": true,
138
- "features": {
139
- "mean": true,
140
- "median": false,
141
- "std": false,
142
- "max": false
143
- },
144
- "return_spectrum": false
145
- },
146
- "bandpass_filter_settings": {
147
- "segment_lengths_ms": {
148
- "theta": 1000,
149
- "alpha": 500,
150
- "low beta": 333,
151
- "high beta": 333,
152
- "low gamma": 100,
153
- "high gamma": 100,
154
- "HFA": 100
155
- },
156
- "bandpower_features": {
157
- "activity": true,
158
- "mobility": false,
159
- "complexity": false
160
- },
161
- "log_transform": true,
162
- "kalman_filter": false
163
- },
164
- "kalman_filter_settings": {
165
- "Tp": 0.1,
166
- "sigma_w": 0.7,
167
- "sigma_v": 1,
168
- "frequency_bands": [
169
- "theta",
170
- "alpha",
171
- "low beta",
172
- "high beta",
173
- "low gamma",
174
- "high gamma",
175
- "HFA"
176
- ]
177
- },
178
- "burst_settings": {
179
- "threshold": 75,
180
- "time_duration_s": 30,
181
- "frequency_bands": [
182
- "low beta",
183
- "high beta",
184
- "low gamma"
185
- ],
186
- "burst_features": {
187
- "duration": true,
188
- "amplitude": true,
189
- "burst_rate_per_s": true,
190
- "in_burst": true
191
- }
192
- },
193
- "sharpwave_analysis_settings": {
194
- "sharpwave_features": {
195
- "peak_left": false,
196
- "peak_right": false,
197
- "trough": false,
198
- "width": false,
199
- "prominence": true,
200
- "interval": true,
201
- "decay_time": false,
202
- "rise_time": false,
203
- "sharpness": true,
204
- "rise_steepness": false,
205
- "decay_steepness": false,
206
- "slope_ratio": false
207
- },
208
- "filter_ranges_hz": [
209
- [
210
- 5,
211
- 80
212
- ],
213
- [
214
- 5,
215
- 30
216
- ]
217
- ],
218
- "detect_troughs": {
219
- "estimate": true,
220
- "distance_troughs_ms": 10,
221
- "distance_peaks_ms": 5
222
- },
223
- "detect_peaks": {
224
- "estimate": true,
225
- "distance_troughs_ms": 5,
226
- "distance_peaks_ms": 10
227
- },
228
- "estimator": {
229
- "mean": [
230
- "interval"
231
- ],
232
- "median": null,
233
- "max": [
234
- "prominence",
235
- "sharpness"
236
- ],
237
- "min": null,
238
- "var": null
239
- },
240
- "apply_estimator_between_peaks_and_troughs": true
241
- },
242
- "project_cortex_settings": {
243
- "max_dist_mm": 20
244
- },
245
- "project_subcortex_settings": {
246
- "max_dist_mm": 5
247
- },
248
- "coherence": {
249
- "channels": [
250
- [
251
- "STN_RIGHT_0",
252
- "ECOG_RIGHT_0"
253
- ]
254
- ],
255
- "frequency_bands": [
256
- "high beta"
257
- ],
258
- "features": {
259
- "mean_fband": true,
260
- "max_fband": true,
261
- "max_allfbands": true
262
- },
263
- "method": {
264
- "coh": true,
265
- "icoh": true
266
- }
267
- },
268
- "fooof": {
269
- "aperiodic": {
270
- "exponent": true,
271
- "offset": true,
272
- "knee": true
273
- },
274
- "periodic": {
275
- "center_frequency": false,
276
- "band_width": false,
277
- "height_over_ap": false
278
- },
279
- "windowlength_ms": 800,
280
- "peak_width_limits": [
281
- 0.5,
282
- 12
283
- ],
284
- "max_n_peaks": 3,
285
- "min_peak_height": 0,
286
- "peak_threshold": 2,
287
- "freq_range_hz": [
288
- 2,
289
- 40
290
- ],
291
- "knee": true
292
- },
293
- "nolds_features": {
294
- "sample_entropy": false,
295
- "correlation_dimension": false,
296
- "lyapunov_exponent": true,
297
- "hurst_exponent": false,
298
- "detrended_fluctutaion_analysis": false,
299
- "data": {
300
- "raw": true,
301
- "frequency_bands": [
302
- "low beta"
303
- ]
304
- }
305
- },
306
- "mne_connectiviy": {
307
- "method": "plv",
308
- "mode": "multitaper"
309
- },
310
- "bispectrum": {
311
- "f1s": [
312
- 5,
313
- 35
314
- ],
315
- "f2s": [
316
- 5,
317
- 35
318
- ],
319
- "compute_features_for_whole_fband_range": true,
320
- "frequency_bands": [
321
- "theta",
322
- "alpha",
323
- "low beta",
324
- "high beta"
325
- ],
326
- "components": {
327
- "absolute": true,
328
- "real": true,
329
- "imag": true,
330
- "phase": true
331
- },
332
- "bispectrum_features": {
333
- "mean": true,
334
- "sum": true,
335
- "var": true
336
- }
337
- }
338
- }