py-neuromodulation 0.0.4__py3-none-any.whl → 0.0.6__py3-none-any.whl

py_neuromodulation/data/README

@@ -1,6 +1,6 @@
-References
-----------
-Appelhoff, S., Sanderson, M., Brooks, T., Vliet, M., Quentin, R., Holdgraf, C., Chaumon, M., Mikulan, E., Tavabi, K., Höchenberger, R., Welke, D., Brunner, C., Rockhill, A., Larson, E., Gramfort, A. and Jas, M. (2019). MNE-BIDS: Organizing electrophysiological data into the BIDS format and facilitating their analysis. Journal of Open Source Software 4: (1896). https://doi.org/10.21105/joss.01896
-
-Holdgraf, C., Appelhoff, S., Bickel, S., Bouchard, K., D'Ambrosio, S., David, O., … Hermes, D. (2019). iEEG-BIDS, extending the Brain Imaging Data Structure specification to human intracranial electrophysiology. Scientific Data, 6, 102. https://doi.org/10.1038/s41597-019-0105-7
-
+References
+----------
+Appelhoff, S., Sanderson, M., Brooks, T., Vliet, M., Quentin, R., Holdgraf, C., Chaumon, M., Mikulan, E., Tavabi, K., Höchenberger, R., Welke, D., Brunner, C., Rockhill, A., Larson, E., Gramfort, A. and Jas, M. (2019). MNE-BIDS: Organizing electrophysiological data into the BIDS format and facilitating their analysis. Journal of Open Source Software 4: (1896). https://doi.org/10.21105/joss.01896
+
+Holdgraf, C., Appelhoff, S., Bickel, S., Bouchard, K., D'Ambrosio, S., David, O., … Hermes, D. (2019). iEEG-BIDS, extending the Brain Imaging Data Structure specification to human intracranial electrophysiology. Scientific Data, 6, 102. https://doi.org/10.1038/s41597-019-0105-7
+

py_neuromodulation/data/dataset_description.json

@@ -1,8 +1,8 @@
-{
-    "Name": " ",
-    "BIDSVersion": "1.7.0",
-    "DatasetType": "raw",
-    "Authors": [
-        "[Unspecified]"
-    ]
-}
+{
+    "Name": " ",
+    "BIDSVersion": "1.7.0",
+    "DatasetType": "raw",
+    "Authors": [
+        "[Unspecified]"
+    ]
+}

py_neuromodulation/data/participants.json

@@ -1,32 +1,32 @@
-{
-    "participant_id": {
-        "Description": "Unique participant identifier"
-    },
-    "age": {
-        "Description": "Age of the participant at time of testing",
-        "Units": "years"
-    },
-    "sex": {
-        "Description": "Biological sex of the participant",
-        "Levels": {
-            "F": "female",
-            "M": "male"
-        }
-    },
-    "hand": {
-        "Description": "Handedness of the participant",
-        "Levels": {
-            "R": "right",
-            "L": "left",
-            "A": "ambidextrous"
-        }
-    },
-    "weight": {
-        "Description": "Body weight of the participant",
-        "Units": "kg"
-    },
-    "height": {
-        "Description": "Body height of the participant",
-        "Units": "m"
-    }
-}
+{
+    "participant_id": {
+        "Description": "Unique participant identifier"
+    },
+    "age": {
+        "Description": "Age of the participant at time of testing",
+        "Units": "years"
+    },
+    "sex": {
+        "Description": "Biological sex of the participant",
+        "Levels": {
+            "F": "female",
+            "M": "male"
+        }
+    },
+    "hand": {
+        "Description": "Handedness of the participant",
+        "Levels": {
+            "R": "right",
+            "L": "left",
+            "A": "ambidextrous"
+        }
+    },
+    "weight": {
+        "Description": "Body weight of the participant",
+        "Units": "kg"
+    },
+    "height": {
+        "Description": "Body height of the participant",
+        "Units": "m"
+    }
+}

py_neuromodulation/data/participants.tsv

@@ -1,2 +1,2 @@
-participant_id	age	sex	hand	weight	height
-sub-testsub	n/a	n/a	n/a	n/a	n/a
+participant_id	age	sex	hand	weight	height
+sub-testsub	n/a	n/a	n/a	n/a	n/a

py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_space-mni_coordsystem.json

@@ -1,5 +1,5 @@
-{
-    "iEEGCoordinateSystem": "Other",
-    "iEEGCoordinateSystemDescription": "n/a",
-    "iEEGCoordinateUnits": "m"
-}
+{
+    "iEEGCoordinateSystem": "Other",
+    "iEEGCoordinateSystemDescription": "n/a",
+    "iEEGCoordinateUnits": "m"
+}

py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_space-mni_electrodes.tsv

@@ -1,11 +1,11 @@
-name	x	y	z	size	impedance
-LFP_RIGHT_0	0.0118280802308701	-0.0151597482742092	-0.00776909845640809	n/a	n/a
-LFP_RIGHT_1	0.0123908351968705	-0.0142925082817827	-0.0059367986990887	n/a	n/a
-LFP_RIGHT_2	0.012930849148285701	-0.0134128499400548	-0.00409165661961333	n/a	n/a
-ECOG_RIGHT_0	0.037318173999999996	-0.048610126639999994	0.06179765474	n/a	n/a
-ECOG_RIGHT_1	0.0401598943	-0.037315929830000004	0.06431171618	n/a	n/a
-ECOG_RIGHT_2	0.040943035780000005	-0.02721778456	0.06409518407999999	n/a	n/a
-ECOG_RIGHT_3	0.03978395522	-0.01700523081	0.06386618136	n/a	n/a
-ECOG_RIGHT_4	0.03968813641	-0.005528024572	0.06168254254	n/a	n/a
-ECOG_RIGHT_5	0.03751915924	0.004304913414	0.060541263549999995	n/a	n/a
-MOV_RIGHT	n/a	n/a	n/a	n/a	n/a
+name	x	y	z	size	impedance
+LFP_RIGHT_0	0.0118280802308701	-0.0151597482742092	-0.00776909845640809	n/a	n/a
+LFP_RIGHT_1	0.0123908351968705	-0.0142925082817827	-0.0059367986990887	n/a	n/a
+LFP_RIGHT_2	0.012930849148285701	-0.0134128499400548	-0.00409165661961333	n/a	n/a
+ECOG_RIGHT_0	0.037318173999999996	-0.048610126639999994	0.06179765474	n/a	n/a
+ECOG_RIGHT_1	0.0401598943	-0.037315929830000004	0.06431171618	n/a	n/a
+ECOG_RIGHT_2	0.040943035780000005	-0.02721778456	0.06409518407999999	n/a	n/a
+ECOG_RIGHT_3	0.03978395522	-0.01700523081	0.06386618136	n/a	n/a
+ECOG_RIGHT_4	0.03968813641	-0.005528024572	0.06168254254	n/a	n/a
+ECOG_RIGHT_5	0.03751915924	0.004304913414	0.060541263549999995	n/a	n/a
+MOV_RIGHT	n/a	n/a	n/a	n/a	n/a

py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_channels.tsv

@@ -1,11 +1,11 @@
-name	type	units	low_cutoff	high_cutoff	description	sampling_frequency	status	status_description
-LFP_RIGHT_0	DBS	µV	0.0	500.0	Deep Brain Stimulation	1000.0	good	n/a
-LFP_RIGHT_1	DBS	µV	0.0	500.0	Deep Brain Stimulation	1000.0	good	n/a
-LFP_RIGHT_2	DBS	µV	0.0	500.0	Deep Brain Stimulation	1000.0	good	n/a
-ECOG_RIGHT_0	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
-ECOG_RIGHT_1	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
-ECOG_RIGHT_2	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
-ECOG_RIGHT_3	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
-ECOG_RIGHT_4	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
-ECOG_RIGHT_5	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
-MOV_RIGHT	MISC	µV	0.0	500.0	Miscellaneous	1000.0	good	n/a
+name	type	units	low_cutoff	high_cutoff	description	sampling_frequency	status	status_description
+LFP_RIGHT_0	DBS	µV	0.0	500.0	Deep Brain Stimulation	1000.0	good	n/a
+LFP_RIGHT_1	DBS	µV	0.0	500.0	Deep Brain Stimulation	1000.0	good	n/a
+LFP_RIGHT_2	DBS	µV	0.0	500.0	Deep Brain Stimulation	1000.0	good	n/a
+ECOG_RIGHT_0	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
+ECOG_RIGHT_1	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
+ECOG_RIGHT_2	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
+ECOG_RIGHT_3	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
+ECOG_RIGHT_4	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
+ECOG_RIGHT_5	ECOG	µV	0.0	500.0	Electrocorticography	1000.0	good	n/a
+MOV_RIGHT	MISC	µV	0.0	500.0	Miscellaneous	1000.0	good	n/a

py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.json

@@ -1,18 +1,18 @@
-{
-    "TaskName": "gripforce",
-    "Manufacturer": "Brain Products",
-    "PowerLineFrequency": 60.0,
-    "SamplingFrequency": 1000.0,
-    "SoftwareFilters": "n/a",
-    "RecordingDuration": 19.0,
-    "RecordingType": "continuous",
-    "iEEGReference": "n/a",
-    "ECOGChannelCount": 6,
-    "SEEGChannelCount": 3,
-    "EEGChannelCount": 0,
-    "EOGChannelCount": 0,
-    "ECGChannelCount": 0,
-    "EMGChannelCount": 0,
-    "MiscChannelCount": 1,
-    "TriggerChannelCount": 0
-}
+{
+    "TaskName": "gripforce",
+    "Manufacturer": "Brain Products",
+    "PowerLineFrequency": 60.0,
+    "SamplingFrequency": 1000.0,
+    "SoftwareFilters": "n/a",
+    "RecordingDuration": 19.0,
+    "RecordingType": "continuous",
+    "iEEGReference": "n/a",
+    "ECOGChannelCount": 6,
+    "SEEGChannelCount": 3,
+    "EEGChannelCount": 0,
+    "EOGChannelCount": 0,
+    "ECGChannelCount": 0,
+    "EMGChannelCount": 0,
+    "MiscChannelCount": 1,
+    "TriggerChannelCount": 0
+}

py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.vhdr

@@ -1,35 +1,35 @@
-Brain Vision Data Exchange Header File Version 1.0
-; Written using pybv 0.7.5
-
-[Common Infos]
-Codepage=UTF-8
-DataFile=sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.eeg
-MarkerFile=sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.vmrk
-DataFormat=BINARY
-; Data orientation: MULTIPLEXED=ch1,pt1, ch2,pt1 ...
-DataOrientation=MULTIPLEXED
-NumberOfChannels=10
-; Sampling interval in microseconds
-SamplingInterval=1000.0
-
-[Binary Infos]
-BinaryFormat=IEEE_FLOAT_32
-
-[Channel Infos]
-; Each entry: Ch<Channel number>=<Name>,<Reference channel name>,
-; <Resolution in "Unit">,<Unit>, Future extensions..
-; Fields are delimited by commas, some fields might be omitted (empty).
-; Commas in channel names are coded as "\1".
-Ch1=LFP_RIGHT_0,,0.1,µV
-Ch2=LFP_RIGHT_1,,0.1,µV
-Ch3=LFP_RIGHT_2,,0.1,µV
-Ch4=ECOG_RIGHT_0,,0.1,µV
-Ch5=ECOG_RIGHT_1,,0.1,µV
-Ch6=ECOG_RIGHT_2,,0.1,µV
-Ch7=ECOG_RIGHT_3,,0.1,µV
-Ch8=ECOG_RIGHT_4,,0.1,µV
-Ch9=ECOG_RIGHT_5,,0.1,µV
-Ch10=MOV_RIGHT,,0.1,µV
-
-[Comment]
-
+Brain Vision Data Exchange Header File Version 1.0
+; Written using pybv 0.7.5
+
+[Common Infos]
+Codepage=UTF-8
+DataFile=sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.eeg
+MarkerFile=sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.vmrk
+DataFormat=BINARY
+; Data orientation: MULTIPLEXED=ch1,pt1, ch2,pt1 ...
+DataOrientation=MULTIPLEXED
+NumberOfChannels=10
+; Sampling interval in microseconds
+SamplingInterval=1000.0
+
+[Binary Infos]
+BinaryFormat=IEEE_FLOAT_32
+
+[Channel Infos]
+; Each entry: Ch<Channel number>=<Name>,<Reference channel name>,
+; <Resolution in "Unit">,<Unit>, Future extensions..
+; Fields are delimited by commas, some fields might be omitted (empty).
+; Commas in channel names are coded as "\1".
+Ch1=LFP_RIGHT_0,,0.1,µV
+Ch2=LFP_RIGHT_1,,0.1,µV
+Ch3=LFP_RIGHT_2,,0.1,µV
+Ch4=ECOG_RIGHT_0,,0.1,µV
+Ch5=ECOG_RIGHT_1,,0.1,µV
+Ch6=ECOG_RIGHT_2,,0.1,µV
+Ch7=ECOG_RIGHT_3,,0.1,µV
+Ch8=ECOG_RIGHT_4,,0.1,µV
+Ch9=ECOG_RIGHT_5,,0.1,µV
+Ch10=MOV_RIGHT,,0.1,µV
+
+[Comment]
+

py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.vmrk

@@ -1,13 +1,13 @@
-Brain Vision Data Exchange Marker File, Version 1.0
-; Exported using pybv 0.7.5
-
-[Common Infos]
-Codepage=UTF-8
-DataFile=sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.eeg
-
-[Marker Infos]
-; Each entry: Mk<Marker number>=<Type>,<Description>,<Position in data points>,
-;             <Size in data points>, <Channel number (0 = marker is related to all channels)>
-;             <Date (YYYYMMDDhhmmssuuuuuu)>
-; Fields are delimited by commas, some fields might be omitted (empty).
-; Commas in type or description text are coded as "\1".
+Brain Vision Data Exchange Marker File, Version 1.0
+; Exported using pybv 0.7.5
+
+[Common Infos]
+Codepage=UTF-8
+DataFile=sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.eeg
+
+[Marker Infos]
+; Each entry: Mk<Marker number>=<Type>,<Description>,<Position in data points>,
+;             <Size in data points>, <Channel number (0 = marker is related to all channels)>
+;             <Date (YYYYMMDDhhmmssuuuuuu)>
+; Fields are delimited by commas, some fields might be omitted (empty).
+; Commas in type or description text are coded as "\1".

py_neuromodulation/data/sub-testsub/ses-EphysMedOff/sub-testsub_ses-EphysMedOff_scans.tsv

@@ -1,2 +1,2 @@
-filename	acq_time
-ieeg/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.vhdr	n/a
+filename	acq_time
+ieeg/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.vhdr	n/a

py_neuromodulation/default_settings.yaml

@@ -0,0 +1,241 @@
+---
+########################
+### General settings ###
+########################
+sampling_rate_features_hz: 10
+segment_length_features_ms: 1000
+
+frequency_ranges_hz: # frequency band ranges can be added, removed and altered
+  theta: [4, 8]
+  alpha: [8, 12]
+  low_beta: [13, 20]
+  high_beta: [20, 35]
+  low_gamma: [60, 80]
+  high_gamma: [90, 200]
+  HFA: [200, 400]
+
+# Enabled features
+features:
+  raw_hjorth: true
+  return_raw: true
+  bandpass_filter: false
+  stft: false
+  fft: true
+  welch: true
+  sharpwave_analysis: true
+  fooof: false
+  bursts: true
+  linelength: true
+  coherence: false
+  nolds: false
+  mne_connectivity: false
+  bispectrum: false
+
+##############################
+### Preprocessing settings ###
+##############################
+# preprocessing options: raw_resampling, notch_filter, re_referencing, preprocessing_filter, raw_normalization
+# note: the list order specifies also the order of execution
+preprocessing: [raw_resampling, notch_filter, re_referencing]
+
+raw_resampling_settings:
+  resample_freq_hz: 1000
+
+raw_normalization_settings:
+  normalization_time_s: 30
+  normalization_method: zscore # supported methods: mean, median, zscore, zscore-median, quantile, power, robust, minmax
+  clip: 3
+
+preprocessing_filter:
+  bandstop_filter: true
+  lowpass_filter: true
+  highpass_filter: true
+  bandpass_filter: true
+  bandstop_filter_settings:
+    frequency_low_hz: 100
+    frequency_high_hz: 160
+  bandpass_filter_settings:
+    frequency_low_hz: 3
+    frequency_high_hz: 200
+  lowpass_filter_cutoff_hz: 200
+  highpass_filter_cutoff_hz: 3
+
+################################
+### Postprocessing settings ####
+################################
+postprocessing:
+  feature_normalization: true
+  project_cortex: false
+  project_subcortex: false
+
+feature_normalization_settings:
+  normalization_time_s: 30
+  normalization_method: zscore # supported methods: mean, median, zscore, zscore-median, quantile, power, robust, minmax
+  clip: 3
+
+project_cortex_settings:
+  max_dist_mm: 20
+
+project_subcortex_settings:
+  max_dist_mm: 5
+
+#################################
+### Feature specific settings ###
+#################################
+
+fft_settings:
+  windowlength_ms: 1000
+  log_transform: true
+  features:
+    mean: true
+    median: false
+    std: false
+    max: false
+  return_spectrum: false
+
+welch_settings:
+  windowlength_ms: 1000
+  log_transform: true
+  features:
+    mean: true
+    median: false
+    std: false
+    max: false
+  return_spectrum: false
+
+stft_settings:
+  windowlength_ms: 500
+  log_transform: true
+  features:
+    mean: true
+    median: false
+    std: false
+    max: false
+  return_spectrum: false
+
+bandpass_filter_settings:
+  segment_lengths_ms:
+    theta: 1000
+    alpha: 500
+    low_beta: 333
+    high_beta: 333
+    low_gamma: 100
+    high_gamma: 100
+    HFA: 100
+  bandpower_features:
+    activity: true
+    mobility: false
+    complexity: false
+  log_transform: true
+  kalman_filter: false
+
+kalman_filter_settings:
+  Tp: 0.1
+  sigma_w: 0.7
+  sigma_v: 1
+  frequency_bands:
+    [theta, alpha, low_beta, high_beta, low_gamma, high_gamma, HFA]
+
+burst_settings:
+  threshold: 75
+  time_duration_s: 30
+  frequency_bands: [low_beta, high_beta, low_gamma]
+  burst_features:
+    duration: true
+    amplitude: true
+    burst_rate_per_s: true
+    in_burst: true
+
+sharpwave_analysis_settings:
+  sharpwave_features:
+    peak_left: false
+    peak_right: false
+    num_peaks: false
+    trough: false
+    width: false
+    prominence: true
+    interval: true
+    decay_time: false
+    rise_time: false
+    sharpness: true
+    rise_steepness: false
+    decay_steepness: false
+    slope_ratio: false
+  filter_ranges_hz:
+    - frequency_low_hz: 5
+      frequency_high_hz: 80
+    - frequency_low_hz: 5
+      frequency_high_hz: 30
+  detect_troughs:
+    estimate: true
+    distance_troughs_ms: 10
+    distance_peaks_ms: 5
+  detect_peaks:
+    estimate: true
+    distance_troughs_ms: 5
+    distance_peaks_ms: 10
+  estimator:
+    mean: [interval]
+    median: []
+    max: [prominence, sharpness]
+    min: []
+    var: []
+  apply_estimator_between_peaks_and_troughs: true
+
+coherence_settings:
+  channels: [] # List of channel pairs, empty by default. Each pair is a list of two channels.
+  # Example channels: [[STN_RIGHT_0, ECOG_RIGHT_0], [STN_RIGHT_1, ECOG_RIGHT_1]]
+  frequency_bands: [high_beta]
+  features:
+    mean_fband: true
+    max_fband: true
+    max_allfbands: true
+  method:
+    coh: true
+    icoh: true
+
+fooof_settings:
+  aperiodic:
+    exponent: true
+    offset: true
+    knee: true
+  periodic:
+    center_frequency: false
+    band_width: false
+    height_over_ap: false
+  windowlength_ms: 800
+  peak_width_limits: [0.5, 12]
+  max_n_peaks: 3
+  min_peak_height: 0
+  peak_threshold: 2
+  freq_range_hz: [2, 40]
+  knee: true
+
+nolds_settings:
+  sample_entropy: false
+  correlation_dimension: false
+  lyapunov_exponent: true
+  hurst_exponent: false
+  detrended_fluctutaion_analysis: false
+  data:
+    raw: true
+    frequency_bands: [low_beta]
+
+mne_connectiviy_settings:
+  method: plv
+  mode: multitaper
+
+bispectrum_settings:
+  f1s: [5, 35]
+  f2s: [5, 35]
+  compute_features_for_whole_fband_range: true
+  frequency_bands: [theta, alpha, low_beta, high_beta]
+  components:
+    absolute: true
+    real: true
+    imag: true
+    phase: true
+  bispectrum_features:
+    mean: true
+    sum: true
+    var: true

py_neuromodulation/features/__init__.py

@@ -0,0 +1,31 @@
+# Expose feature settings
+from py_neuromodulation.features.bispectra import BispectraSettings
+from py_neuromodulation.features.coherence import CoherenceSettings
+from py_neuromodulation.features.fooof import FooofSettings
+from py_neuromodulation.features.mne_connectivity import MNEConnectivitySettings
+from py_neuromodulation.features.nolds import NoldsSettings
+from py_neuromodulation.features.sharpwaves import SharpwaveSettings
+from py_neuromodulation.features.bursts import BurstsSettings
+from py_neuromodulation.features.oscillatory import OscillatorySettings
+from py_neuromodulation.features.bandpower import BandPowerSettings
+
+
+# Expose feature classes
+from py_neuromodulation.features.linelength import LineLength
+from py_neuromodulation.features.hjorth_raw import Hjorth, Raw
+from py_neuromodulation.features.bispectra import Bispectra
+from py_neuromodulation.features.coherence import Coherence
+from py_neuromodulation.features.fooof import FooofAnalyzer
+from py_neuromodulation.features.mne_connectivity import MNEConnectivity
+from py_neuromodulation.features.nolds import Nolds
+from py_neuromodulation.features.sharpwaves import SharpwaveAnalyzer
+from py_neuromodulation.features.bursts import Bursts
+from py_neuromodulation.features.oscillatory import FFT, STFT, Welch
+from py_neuromodulation.features.bandpower import BandPower
+
+# Expose feature processor and custom feature functions
+from py_neuromodulation.features.feature_processor import (
+    FeatureProcessors,
+    add_custom_feature,
+    remove_custom_feature,
+)