py-neuromodulation 0.0.2__py3-none-any.whl → 0.0.4__py3-none-any.whl

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Files changed (51) hide show
  1. py_neuromodulation/ConnectivityDecoding/Automated Anatomical Labeling 3 (Rolls 2020).nii +0 -0
  2. py_neuromodulation/ConnectivityDecoding/_get_grid_hull.m +34 -0
  3. py_neuromodulation/ConnectivityDecoding/_get_grid_whole_brain.py +106 -0
  4. py_neuromodulation/ConnectivityDecoding/_helper_write_connectome.py +119 -0
  5. py_neuromodulation/ConnectivityDecoding/mni_coords_cortical_surface.mat +0 -0
  6. py_neuromodulation/ConnectivityDecoding/mni_coords_whole_brain.mat +0 -0
  7. py_neuromodulation/ConnectivityDecoding/rmap_func_all.nii +0 -0
  8. py_neuromodulation/ConnectivityDecoding/rmap_struc.nii +0 -0
  9. py_neuromodulation/{helper.py → _write_example_dataset_helper.py} +1 -1
  10. py_neuromodulation/nm_EpochStream.py +2 -3
  11. py_neuromodulation/nm_IO.py +43 -70
  12. py_neuromodulation/nm_RMAP.py +308 -11
  13. py_neuromodulation/nm_analysis.py +1 -1
  14. py_neuromodulation/nm_artifacts.py +25 -0
  15. py_neuromodulation/nm_bispectra.py +64 -29
  16. py_neuromodulation/nm_bursts.py +44 -30
  17. py_neuromodulation/nm_coherence.py +2 -1
  18. py_neuromodulation/nm_features.py +4 -2
  19. py_neuromodulation/nm_filter.py +63 -32
  20. py_neuromodulation/nm_filter_preprocessing.py +91 -0
  21. py_neuromodulation/nm_fooof.py +47 -29
  22. py_neuromodulation/nm_mne_connectivity.py +1 -1
  23. py_neuromodulation/nm_normalization.py +50 -74
  24. py_neuromodulation/nm_oscillatory.py +151 -31
  25. py_neuromodulation/nm_plots.py +13 -10
  26. py_neuromodulation/nm_rereference.py +10 -8
  27. py_neuromodulation/nm_run_analysis.py +28 -13
  28. py_neuromodulation/nm_settings.json +51 -3
  29. py_neuromodulation/nm_sharpwaves.py +103 -136
  30. py_neuromodulation/nm_stats.py +44 -30
  31. py_neuromodulation/nm_stream_abc.py +18 -10
  32. py_neuromodulation/nm_stream_offline.py +188 -46
  33. py_neuromodulation/utils/_logging.py +24 -0
  34. {py_neuromodulation-0.0.2.dist-info → py_neuromodulation-0.0.4.dist-info}/METADATA +72 -32
  35. py_neuromodulation-0.0.4.dist-info/RECORD +72 -0
  36. {py_neuromodulation-0.0.2.dist-info → py_neuromodulation-0.0.4.dist-info}/WHEEL +1 -1
  37. py_neuromodulation/data/derivatives/sub-testsub_ses-EphysMedOff_task-gripforce_run-0/MOV_aligned_features_ch_ECOG_RIGHT_0_all.png +0 -0
  38. py_neuromodulation/data/derivatives/sub-testsub_ses-EphysMedOff_task-gripforce_run-0/all_feature_plt.pdf +0 -0
  39. py_neuromodulation/data/derivatives/sub-testsub_ses-EphysMedOff_task-gripforce_run-0/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_FEATURES.csv +0 -182
  40. py_neuromodulation/data/derivatives/sub-testsub_ses-EphysMedOff_task-gripforce_run-0/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_LM_ML_RES.p +0 -0
  41. py_neuromodulation/data/derivatives/sub-testsub_ses-EphysMedOff_task-gripforce_run-0/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_SETTINGS.json +0 -273
  42. py_neuromodulation/data/derivatives/sub-testsub_ses-EphysMedOff_task-gripforce_run-0/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_SIDECAR.json +0 -6
  43. py_neuromodulation/data/derivatives/sub-testsub_ses-EphysMedOff_task-gripforce_run-0/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_decoding_performance.png +0 -0
  44. py_neuromodulation/data/derivatives/sub-testsub_ses-EphysMedOff_task-gripforce_run-0/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_nm_channels.csv +0 -11
  45. py_neuromodulation/py_neuromodulation.egg-info/PKG-INFO +0 -104
  46. py_neuromodulation/py_neuromodulation.egg-info/dependency_links.txt +0 -1
  47. py_neuromodulation/py_neuromodulation.egg-info/requires.txt +0 -26
  48. py_neuromodulation/py_neuromodulation.egg-info/top_level.txt +0 -1
  49. py_neuromodulation-0.0.2.dist-info/RECORD +0 -73
  50. /py_neuromodulation/{py_neuromodulation.egg-info/SOURCES.txt → utils/__init__.py} +0 -0
  51. {py_neuromodulation-0.0.2.dist-info → py_neuromodulation-0.0.4.dist-info/licenses}/LICENSE +0 -0
@@ -1,273 +0,0 @@
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- {
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- "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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- "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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- ],
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- "features": {
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- "raw_hjorth": false,
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- "return_raw": false,
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- "bandpass_filter": false,
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- "stft": false,
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- "fft": true,
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- "sharpwave_analysis": false,
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- "fooof": false,
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- "bursts": false,
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- "linelength": false,
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- "coherence": false,
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- "nolds": false,
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- "mne_connectivity": 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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- "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": {
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- "normalization_time_s": 30,
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- "normalization_method": "zscore",
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- "clip": 3
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- },
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- "feature_normalization_settings": {
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- "normalization_time_s": 30,
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- "normalization_method": "zscore",
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- "clip": 3
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- },
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- "frequency_ranges_hz": {
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- "theta": [
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- 4,
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- 8
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- ],
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- "alpha": [
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- 8,
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- 12
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- ],
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- "low beta": [
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- 13,
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- 20
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- ],
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- "high beta": [
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- 20,
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- 35
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- ],
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- "low gamma": [
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- 60,
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- 80
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- ],
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- "high gamma": [
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- 90,
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- 200
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- ],
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- "HFA": [
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- 200,
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- 400
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- ]
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- },
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- "fft_settings": {
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- "windowlength_ms": 1000,
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- "log_transform": true,
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- "kalman_filter": false
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- },
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- "stft_settings": {
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- "windowlength_ms": 500,
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- "log_transform": true,
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- "kalman_filter": false
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- },
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- "bandpass_filter_settings": {
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- "segment_lengths_ms": {
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- "theta": 1000,
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- "alpha": 500,
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- "low beta": 333,
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- "high beta": 333,
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- "low gamma": 100,
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- "high gamma": 100,
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- "HFA": 100
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- },
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- "bandpower_features": {
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- "activity": true,
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- "mobility": false,
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- "complexity": false
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- },
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- "log_transform": true,
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- "kalman_filter": false
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- },
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- "kalman_filter_settings": {
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- "Tp": 0.1,
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- "sigma_w": 0.7,
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- "sigma_v": 1,
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- "frequency_bands": [
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- "theta",
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- "alpha",
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- "low beta",
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- "high beta",
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- "low gamma",
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- "high gamma",
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- "HFA"
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- ]
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- },
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- "burst_settings": {
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- "threshold": 75,
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- "time_duration_s": 30,
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- "frequency_bands": [
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- "low beta",
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- "high beta",
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- "low gamma"
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- ],
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- "burst_features": {
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- "duration": true,
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- "amplitude": true,
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- "burst_rate_per_s": true,
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- "in_burst": true
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- }
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- },
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- "sharpwave_analysis_settings": {
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- "sharpwave_features": {
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- "peak_left": true,
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- "peak_right": true,
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- "trough": true,
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- "width": true,
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- "prominence": true,
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- "interval": true,
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- "decay_time": true,
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- "rise_time": true,
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- "sharpness": true,
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- "rise_steepness": true,
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- "decay_steepness": true,
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- "slope_ratio": true
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- },
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- "filter_ranges_hz": [
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- [
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- 5,
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- 80
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- ],
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- [
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- 5,
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- 30
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- ]
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- ],
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- "detect_troughs": {
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- "estimate": true,
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- "distance_troughs_ms": 10,
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- "distance_peaks_ms": 5
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- },
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- "detect_peaks": {
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- "estimate": true,
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- "distance_troughs_ms": 5,
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- "distance_peaks_ms": 10
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- },
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- "estimator": {
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- "mean": [
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- "peak_left",
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- "peak_right",
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- "trough",
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- "width",
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- "prominence",
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- "interval",
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- "decay_time",
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- "rise_time",
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- "sharpness",
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- "rise_steepness",
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- "decay_steepness",
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- "slope_ratio"
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- ],
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- "median": null,
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- "max": [
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- "prominence",
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- "sharpness"
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- ],
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- "min": null,
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- "var": null
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- },
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- "apply_estimator_between_peaks_and_troughs": true
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- },
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- "project_cortex_settings": {
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- "max_dist_mm": 20
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- },
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- "project_subcortex_settings": {
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- "max_dist_mm": 5
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- },
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- "coherence": {
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- "channels": [
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- [
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- "LFP_RIGHT_0",
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- "ECOG_RIGHT_0"
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- ]
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- ],
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- "frequency_bands": [
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- "high beta",
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- "low gamma"
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- ],
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- "features": {
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- "mean_fband": true,
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- "max_fband": true,
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- "max_allfbands": true
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- },
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- "method": {
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- "coh": true,
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- "icoh": true
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- }
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- },
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- "fooof": {
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- "aperiodic": {
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- "exponent": true,
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- "offset": true,
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- "knee": true
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- },
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- "periodic": {
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- "center_frequency": false,
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- "band_width": false,
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- "height_over_ap": false
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- },
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- "windowlength_ms": 800,
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- "peak_width_limits": [
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- 0.5,
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- 12
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- ],
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- "max_n_peaks": 3,
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- "min_peak_height": 0,
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- "peak_threshold": 2,
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- "freq_range_hz": [
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- 2,
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- 40
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- ],
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- "knee": true
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- },
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- "nolds_features": {
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- "sample_entropy": false,
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- "correlation_dimension": false,
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- "lyapunov_exponent": true,
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- "hurst_exponent": false,
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- "detrended_fluctutaion_analysis": false,
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- "data": {
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- "raw": true,
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- "frequency_bands": [
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- "low beta"
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- ]
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- }
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- },
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- "mne_connectiviy": {
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- "method": "plv",
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- "mode": "multitaper"
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- }
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- }
@@ -1,6 +0,0 @@
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- {
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@@ -1,11 +0,0 @@
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- ,name,rereference,used,target,type,status,new_name
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- 0,LFP_RIGHT_0,LFP_RIGHT_2,1,0,dbs,good,LFP_RIGHT_0-LFP_RIGHT_2
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- 1,LFP_RIGHT_1,LFP_RIGHT_0,1,0,dbs,good,LFP_RIGHT_1-LFP_RIGHT_0
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- 2,LFP_RIGHT_2,LFP_RIGHT_1,1,0,dbs,good,LFP_RIGHT_2-LFP_RIGHT_1
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- 3,ECOG_RIGHT_0,average,1,0,ecog,good,ECOG_RIGHT_0-avgref
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- 4,ECOG_RIGHT_1,average,1,0,ecog,good,ECOG_RIGHT_1-avgref
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- 5,ECOG_RIGHT_2,average,1,0,ecog,good,ECOG_RIGHT_2-avgref
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- 6,ECOG_RIGHT_3,average,1,0,ecog,good,ECOG_RIGHT_3-avgref
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- 7,ECOG_RIGHT_4,average,1,0,ecog,good,ECOG_RIGHT_4-avgref
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- 8,ECOG_RIGHT_5,average,1,0,ecog,good,ECOG_RIGHT_5-avgref
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- 9,MOV_RIGHT,None,0,1,misc,good,MOV_RIGHT
@@ -1,104 +0,0 @@
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- Metadata-Version: 2.1
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- Name: py-neuromodulation
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- Version: 0.0.1.dev0
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- Summary: Real-time analysis of intracranial neurophysiology recordings.
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- Author: Timon Merk
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- Maintainer: Timon Merk
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- License: MIT License
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-
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- Copyright (c) 2021 Interventional Cognitive Neuromodulation - Neumann Lab Berlin
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-
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- Permission is hereby granted, free of charge, to any person obtaining a copy
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- of this software and associated documentation files (the "Software"), to deal
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- in the Software without restriction, including without limitation the rights
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- to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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- copies of the Software, and to permit persons to whom the Software is
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- furnished to do so, subject to the following conditions:
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-
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- The above copyright notice and this permission notice shall be included in all
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- copies or substantial portions of the Software.
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-
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- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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- IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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- FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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- AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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- LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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- OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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- SOFTWARE.
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-
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- Project-URL: bugtracker, https://github.com/neuromodulation/py_neuromodulation/issues
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- Project-URL: repository, https://github.com/neuromodulation/py_neuromodulation
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- Keywords: real-time,eeg,ieeg,dbs,ecog,electrocorticography,deep-brain-stimulation,machine-learning
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- Classifier: Development Status :: 2 - Pre-Alpha
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- Classifier: License :: OSI Approved :: MIT License
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- Classifier: Programming Language :: Python
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- Classifier: Topic :: Software Development :: Libraries :: Python Modules
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- Requires-Python: >=3.10
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- Description-Content-Type: text/x-rst
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- Provides-Extra: dev
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- License-File: LICENSE
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-
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- py_neuromodulation
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- ==================
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-
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- .. image:: https://app.travis-ci.com/neuromodulation/py_neuromodulation.svg?branch=main
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- :target: https://app.travis-ci.com/neuromodulation/py_neuromodulation
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-
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- Click this button to run the "example_BIDS.ipynb":
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-
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- .. image:: https://mybinder.org/badge_logo.svg
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- :target: https://mybinder.org/v2/gh/neuromodulation/py_neuromodulation/HEAD
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-
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- The py_neuromodulation toolbox allows for real time capable processing of multimodal electrophysiological data. The primary use is movement prediction for `adaptive deep brain stimulation <https://pubmed.ncbi.nlm.nih.gov/30607748/>`_.
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-
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- Find the documentation here https://neuromodulation.github.io/py_neuromodulation/ for example usage and parametrization.
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-
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- Setup
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- =====
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-
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- For running this toolbox first create a new virtual conda environment and activate it:
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-
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- .. code-block::
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-
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- conda create -n pynm-test python=3.10
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- conda activate pynm-test
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-
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- Then install the packages listed in the `pyproject.toml`.
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-
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- .. code-block::
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-
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- pip install .[dev]
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- pytest -v .
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-
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-
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- Optionally the ipython kernel can be specified to installed for the pynm-test conda environment:
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-
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- .. code-block::
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-
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- ipython kernel install --user --name=pynm-test
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-
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- Then py_neuromodulation can be imported via:
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-
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- .. code-block::
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-
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- import py_neuromodulation as py_nm
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-
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- The main modules include running real time enabled feature preprocessing based on `iEEG BIDS <https://www.nature.com/articles/s41597-019-0105-7>`_ data.
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-
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- Different features can be enabled/disabled and parametrized in the `https://github.com/neuromodulation/py_neuromodulation/blob/main/pyneuromodulation/nm_settings.json>`_.
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-
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- The current implementation mainly focuses band power and `sharpwave <https://www.sciencedirect.com/science/article/abs/pii/S1364661316302182>`_ feature estimation.
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-
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- An example folder with a mock subject and derivate `feature <https://github.com/neuromodulation/py_neuromodulation/tree/main/examples/data>`_ set was estimated.
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-
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- To run feature estimation given the example BIDS data run in root directory.
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-
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- .. code-block::
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-
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- python examples/example_BIDS.py
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-
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-
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- This will write a feature_arr.csv and different sidecar files in the 'examples/data/derivatives' folder.
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-
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- For further documentation view `ParametrizationDefinition <ParametrizationDefinition.html#>`_ for description of necessary parametrization files.
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- `FeatureEstimationDemo <FeatureEstimationDemo.html#>`_ walks through an example feature estimation and explains sharpwave estimation.
@@ -1,26 +0,0 @@
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- mne
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- filterpy>=1.4.5
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- fooof
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- imbalanced-learn
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- matplotlib>=3.3.4
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- mne-bids>=0.8
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- mne-connectivity
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- mrmr-selection
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- nolds
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- numba
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- numpy>=1.21.2
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- pandas>=1.2.2
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- pip
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- pynput
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- pybids
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- scikit-image
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- scikit-learn>=0.24.2
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- scikit-optimize
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- scipy>=1.7.1
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- seaborn>=0.11
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- xgboost
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-
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- [dev]
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- black
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- pytest
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- pytest-cov
@@ -1 +0,0 @@
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- py_neuromodulation
@@ -1,73 +0,0 @@
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- py_neuromodulation/FieldTrip.py,sha256=cq4BIibMvcpyAHd7U8eEK4AhVSOTrRKXcywtgtc-Mg4,18597
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- py_neuromodulation/__init__.py,sha256=3aujkEqF4dzt8WKtK7gaolh782UsR5FFkqcg7fOtze4,296
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- py_neuromodulation/grid_cortex.tsv,sha256=DRnJEBwLBqyzCp3UwBL-Us_9h9GyokCorYl0HLsHSLk,683
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- py_neuromodulation/grid_subcortex.tsv,sha256=oCQDYLDdYSa1DAI9ybwECfuzWulFzXqKHyf7oZ1oDBM,25842
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- py_neuromodulation/helper.py,sha256=MBDMyP-JsqjqpmljCq2sqsLfYpihA-S8MXf_Nc3johs,2510
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- py_neuromodulation/nm_EpochStream.py,sha256=h6qmYfnyBbWwcOqZM3LmJQKPQjDhImxxOSza7kocrdA,2603
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- py_neuromodulation/nm_IO.py,sha256=BrsxpCbcyyxojU3yXJtEDkW1o5ZpxQiU3avaM-CGZPQ,12713
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- py_neuromodulation/nm_RMAP.py,sha256=UEh0vzjTF8UMO4uNgo0CqOeolviBF7zOr6owwdnupHM,7594
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- py_neuromodulation/nm_across_patient_decoding.py,sha256=9Mwu5o5cUAbtSP8BTx4c-BJfJZtk8wsMx_WH0VIegdI,38690
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- py_neuromodulation/nm_analysis.py,sha256=QD7lfi-6VA2v4E1-wCIMNs2GnZK9UvFMsr7slWyZGhA,38509
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- py_neuromodulation/nm_bispectra.py,sha256=DvhRIeq0jpiV34T95gGuj9KH_s5McMD2ctOAaZeIFSU,5617
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