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

py_neuromodulation/nm_settings.json

@@ -1,338 +0,0 @@
-{
-    "sampling_rate_features_hz": 10,
-    "segment_length_features_ms": 1000,
-    "preprocessing": [
-        "raw_resampling",
-        "notch_filter",
-        "re_referencing"
-    ],
-    "documentation_preprocessing_options": [
-        "raw_resampling",
-        "notch_filter",
-        "re_referencing",
-        "raw_normalization",
-        "preprocessing_filter"
-    ],
-    "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
-    },
-    "postprocessing": {
-        "feature_normalization": true,
-        "project_cortex": false,
-        "project_subcortex": false
-    },
-    "raw_resampling_settings": {
-        "resample_freq_hz": 1000
-    },
-    "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
-        },
-        "lowpass_filter_settings": {
-            "frequency_cutoff_hz": 200
-        },
-        "highpass_filter_settings": {
-            "frequency_cutoff_hz": 3
-        },
-        "bandpass_filter_settings": {
-            "frequency_low_hz": 3,
-            "frequency_high_hz": 200
-        }
-    },
-    "re_referencing_settings": {
-        "reference": "common"
-    },
-    "documentation_normalization_options": [
-        "mean",
-        "median",
-        "zscore",
-        "zscore-median",
-        "quantile",
-        "power",
-        "robust",
-        "minmax"
-    ],
-    "raw_normalization_settings": {
-        "normalization_time_s": 30,
-        "normalization_method": "zscore",
-        "clip": 3
-    },
-    "feature_normalization_settings": {
-        "normalization_time_s": 30,
-        "normalization_method": "zscore",
-        "clip": 3
-    },
-    "frequency_ranges_hz": {
-        "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
-        ]
-    },
-    "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,
-            "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": [
-            [
-                5,
-                80
-            ],
-            [
-                5,
-                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": null,
-            "max": [
-                "prominence",
-                "sharpness"
-            ],
-            "min": null,
-            "var": null
-        },
-        "apply_estimator_between_peaks_and_troughs": true
-    },
-    "project_cortex_settings": {
-        "max_dist_mm": 20
-    },
-    "project_subcortex_settings": {
-        "max_dist_mm": 5
-    },
-    "coherence": {
-        "channels": [
-            [
-                "STN_RIGHT_0",
-                "ECOG_RIGHT_0"
-            ]
-        ],
-        "frequency_bands": [
-            "high beta"
-        ],
-        "features": {
-            "mean_fband": true,
-            "max_fband": true,
-            "max_allfbands": true
-        },
-        "method": {
-            "coh": true,
-            "icoh": true
-        }
-    },
-    "fooof": {
-        "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_features": {
-        "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": {
-        "method": "plv",
-        "mode": "multitaper"
-    },
-    "bispectrum": {
-        "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/nm_settings.py

@@ -1,68 +0,0 @@
-"""Module for handling settings."""
-import pathlib
-
-import pandas as pd
-
-from py_neuromodulation import nm_IO
-
-
-def get_default_settings() -> dict:
-    """Read default settings from nm_settings.json"""
-    settings_path = str(
-        pathlib.Path(__file__).parent.resolve() / "nm_settings.json"
-    )
-    return nm_IO.read_settings(settings_path)
-
-
-def reset_settings(
-    settings: dict,
-) -> dict:
-    for f in settings["features"]:
-        settings["features"][f] = False
-    settings["preprocessing"] = []
-    for f in settings["postprocessing"]:
-        settings["postprocessing"][f] = False
-    return settings
-
-
-def set_settings_fast_compute(
-    settings: dict,
-) -> dict:
-    settings = reset_settings(settings)
-    settings["features"]["fft"] = True
-    settings["preprocessing"] = [
-        "raw_resampling",
-        "notch_filter",
-        "re_referencing",
-    ]
-    settings["postprocessing"]["feature_normalization"] = True
-    settings["postprocessing"]["project_cortex"] = False
-    settings["postprocessing"]["project_subcortex"] = False
-    return settings
-
-
-def test_settings(
-    settings: dict,
-) -> None:
-    """Test if settings are specified correctly in nm_settings.json
-    Parameters
-    ----------
-    settings: dict
-        settings to tests
-    verbose: boolean
-        set to True if feedback is desired.
-    Returns
-    -------
-    None
-    """
-    s = settings
-
-    assert isinstance(s["sampling_rate_features_hz"], (float, int))
-
-    assert (
-        isinstance(value, bool) for value in s["features"].values()
-    ), "features must be a boolean value."
-
-    assert any(
-        value is True for value in s["features"].values()
-    ), "Set at least one feature to True."