py-neuromodulation 0.0.2__py3-none-any.whl → 0.0.3__py3-none-any.whl

py_neuromodulation/nm_settings.json

@@ -1,290 +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"
-    ],
-    "features": {
-        "raw_hjorth": true,
-        "return_raw": true,
-        "bandpass_filter": false,
-        "stft": false,
-        "fft": 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
-    },
-    "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,
-        "kalman_filter": false
-    },
-    "stft_settings": {
-        "windowlength_ms": 500,
-        "log_transform": true,
-        "kalman_filter": 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/py_neuromodulation.egg-info/PKG-INFO

@@ -1,104 +0,0 @@
-Metadata-Version: 2.1
-Name: py-neuromodulation
-Version: 0.0.1.dev0
-Summary: Real-time analysis of intracranial neurophysiology recordings.
-Author: Timon Merk
-Maintainer: Timon Merk
-License: MIT License
-        
-        Copyright (c) 2021 Interventional Cognitive Neuromodulation - Neumann Lab Berlin
-        
-        Permission is hereby granted, free of charge, to any person obtaining a copy
-        of this software and associated documentation files (the "Software"), to deal
-        in the Software without restriction, including without limitation the rights
-        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-        copies of the Software, and to permit persons to whom the Software is
-        furnished to do so, subject to the following conditions:
-        
-        The above copyright notice and this permission notice shall be included in all
-        copies or substantial portions of the Software.
-        
-        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-        SOFTWARE.
-        
-Project-URL: bugtracker, https://github.com/neuromodulation/py_neuromodulation/issues
-Project-URL: repository, https://github.com/neuromodulation/py_neuromodulation
-Keywords: real-time,eeg,ieeg,dbs,ecog,electrocorticography,deep-brain-stimulation,machine-learning
-Classifier: Development Status :: 2 - Pre-Alpha
-Classifier: License :: OSI Approved :: MIT License 
-Classifier: Programming Language :: Python
-Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Requires-Python: >=3.10
-Description-Content-Type: text/x-rst
-Provides-Extra: dev
-License-File: LICENSE
-
-py_neuromodulation
-==================
-
-.. image:: https://app.travis-ci.com/neuromodulation/py_neuromodulation.svg?branch=main
-    :target: https://app.travis-ci.com/neuromodulation/py_neuromodulation
-
-Click this button to run the "example_BIDS.ipynb":
-
-.. image:: https://mybinder.org/badge_logo.svg
- :target: https://mybinder.org/v2/gh/neuromodulation/py_neuromodulation/HEAD
-
-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/>`_.
-
-Find the documentation here https://neuromodulation.github.io/py_neuromodulation/ for example usage and parametrization.
-
-Setup
-=====
-
-For running this toolbox first create a new virtual conda environment and activate it:
-
-.. code-block::
-
-    conda create -n pynm-test python=3.10
-    conda activate pynm-test
-
-Then install the packages listed in the `pyproject.toml`.
-
-.. code-block::
-
-    pip install .[dev]
-    pytest -v .
-
-
-Optionally the ipython kernel can be specified to installed for the pynm-test conda environment:
-
-.. code-block::
-
-    ipython kernel install --user --name=pynm-test
-
-Then py_neuromodulation can be imported via:
-
-.. code-block::
-
-    import py_neuromodulation as py_nm
-
-The main modules include running real time enabled feature preprocessing based on `iEEG BIDS <https://www.nature.com/articles/s41597-019-0105-7>`_ data.
-
-Different features can be enabled/disabled and parametrized in the `https://github.com/neuromodulation/py_neuromodulation/blob/main/pyneuromodulation/nm_settings.json>`_.
-
-The current implementation mainly focuses band power and `sharpwave <https://www.sciencedirect.com/science/article/abs/pii/S1364661316302182>`_ feature estimation.
-
-An example folder with a mock subject and derivate `feature <https://github.com/neuromodulation/py_neuromodulation/tree/main/examples/data>`_ set was estimated.
-
-To run feature estimation given the example BIDS data run in root directory.
-
-.. code-block::
-
-    python examples/example_BIDS.py
-
-
-This will write a feature_arr.csv and different sidecar files in the 'examples/data/derivatives' folder.
-
-For further documentation view `ParametrizationDefinition <ParametrizationDefinition.html#>`_ for description of necessary parametrization files.
-`FeatureEstimationDemo <FeatureEstimationDemo.html#>`_ walks through an example feature estimation and explains sharpwave estimation.

py_neuromodulation/py_neuromodulation.egg-info/dependency_links.txt

@@ -1 +0,0 @@
-

py_neuromodulation/py_neuromodulation.egg-info/requires.txt

@@ -1,26 +0,0 @@
-mne
-filterpy>=1.4.5
-fooof
-imbalanced-learn
-matplotlib>=3.3.4
-mne-bids>=0.8
-mne-connectivity
-mrmr-selection
-nolds
-numba
-numpy>=1.21.2
-pandas>=1.2.2
-pip
-pynput
-pybids
-scikit-image
-scikit-learn>=0.24.2
-scikit-optimize
-scipy>=1.7.1
-seaborn>=0.11
-xgboost
-
-[dev]
-black
-pytest
-pytest-cov

py_neuromodulation/py_neuromodulation.egg-info/top_level.txt

@@ -1 +0,0 @@
-py_neuromodulation

py_neuromodulation-0.0.2.dist-info/RECORD

@@ -1,73 +0,0 @@
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