py-neuromodulation 0.0.3__py3-none-any.whl → 0.0.4__py3-none-any.whl

py_neuromodulation-0.0.3.dist-info/RECORD

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py_neuromodulation-0.0.3.dist-info/top_level.txt

@@ -1,5 +0,0 @@
-docs
-examples
-packages
-py_neuromodulation
-tests

tests/conftest.py

@@ -1,117 +0,0 @@
-import pytest
-import numpy as np
-
-from py_neuromodulation import (
-    nm_generator,
-    nm_stream_offline,
-    nm_settings,
-    nm_IO,
-    nm_define_nmchannels,
-)
-
-
-@pytest.fixture
-def setup_default_stream_fast_compute():
-    """This test function sets a data batch and automatic initialized M1 datafram
-
-    Args:
-        PATH_PYNEUROMODULATION (string): Path to py_neuromodulation repository
-
-    Returns:
-        ieeg_batch (np.ndarray): (channels, samples)
-        df_M1 (pd Dataframe): auto intialized table for rereferencing
-        settings_wrapper (settings.py): settings.json
-        fs (float): example sampling frequency
-    """
-
-    (
-        RUN_NAME,
-        PATH_RUN,
-        PATH_BIDS,
-        PATH_OUT,
-        datatype,
-    ) = nm_IO.get_paths_example_data()
-
-    (
-        raw,
-        data,
-        sfreq,
-        line_noise,
-        coord_list,
-        coord_names,
-    ) = nm_IO.read_BIDS_data(
-        PATH_RUN=PATH_RUN, BIDS_PATH=PATH_BIDS, datatype=datatype
-    )
-
-    nm_channels = nm_define_nmchannels.set_channels(
-        ch_names=raw.ch_names,
-        ch_types=raw.get_channel_types(),
-        reference="default",
-        bads=raw.info["bads"],
-        new_names="default",
-        used_types=("ecog", "dbs", "seeg"),
-        target_keywords=("MOV_RIGHT_CLEAN",),
-    )
-
-    settings = nm_settings.get_default_settings()
-    settings = nm_settings.reset_settings(settings)
-    settings["fooof"]["aperiodic"]["exponent"] = True
-    settings["fooof"]["aperiodic"]["offset"] = True
-    settings["features"]["fooof"] = True
-
-    stream = nm_stream_offline.Stream(
-        settings=settings,
-        nm_channels=nm_channels,
-        path_grids=None,
-        verbose=True,
-        sfreq=sfreq,
-        line_noise=line_noise,
-        coord_list=coord_list,
-        coord_names=coord_names,
-    )
-
-    return data, stream
-
-
-@pytest.fixture
-def setup_databatch():
-    """This test function sets a data batch and automatic initialized M1 datafram
-
-    Args:
-        PATH_PYNEUROMODULATION (string): Path to py_neuromodulation repository
-
-    Returns:
-        ieeg_batch (np.ndarray): (channels, samples)
-        df_M1 (pd Dataframe): auto intialized table for rereferencing
-        settings_wrapper (settings.py): settings.json
-        fs (float): example sampling frequency
-    """
-
-    (
-        RUN_NAME,
-        PATH_RUN,
-        PATH_BIDS,
-        PATH_OUT,
-        datatype,
-    ) = nm_IO.get_paths_example_data()
-
-    (
-        raw,
-        data,
-        sfreq,
-        line_noise,
-        coord_list,
-        coord_names,
-    ) = nm_IO.read_BIDS_data(
-        PATH_RUN=PATH_RUN, BIDS_PATH=PATH_BIDS, datatype=datatype
-    )
-
-    settings = nm_settings.get_default_settings()
-    settings = nm_settings.set_settings_fast_compute(settings)
-
-    generator = nm_generator.raw_data_generator(
-        data, settings, int(np.floor(sfreq))
-    )
-    data_batch = next(generator, None)
-
-    return [raw.ch_names, raw.get_channel_types(), raw.info["bads"], data_batch]

tests/test_all_examples.py

@@ -1,10 +0,0 @@
-from pathlib import Path
-import pytest
-import subprocess
-import runpy
-
-
-@pytest.mark.parametrize("example_filename", Path("examples").glob("*.py"))
-def test_run_through_all_test(example_filename):
-    print(f"Running {example_filename}")
-    runpy.run_path(example_filename)

tests/test_all_features.py

@@ -1,63 +0,0 @@
-import numpy as np
-import pandas as pd
-import pytest
-
-from py_neuromodulation import (
-    nm_settings,
-    nm_stream_offline,
-    nm_define_nmchannels,
-    nm_stream_abc,
-)
-
-
-def get_example_stream(test_arr: np.array) -> nm_stream_abc.PNStream:
-    settings = nm_settings.get_default_settings()
-    settings["features"]["raw_hjorth"] = True
-    settings["features"]["return_raw"] = True
-    settings["features"]["bandpass_filter"] = True
-    settings["features"]["stft"] = True
-    settings["features"]["fft"] = True
-    settings["features"]["sharpwave_analysis"] = True
-    settings["features"]["fooof"] = True
-    settings["features"]["bursts"] = True
-    settings["features"]["linelength"] = True
-    settings["features"]["nolds"] = False
-    settings["features"]["mne_connectivity"] = False
-    settings["features"]["coherence"] = False
-
-    nm_channels = nm_define_nmchannels.get_default_channels_from_data(test_arr)
-
-    stream = nm_stream_offline.Stream(
-        sfreq=1000, nm_channels=nm_channels, settings=settings, verbose=True
-    )
-    return stream
-
-
-def test_all_features_random_array():
-    """This test runs's through all enabled features, and check's if they break
-    """
-    np.random.seed(0)
-    arr = np.random.random([2, 2000])
-    stream = get_example_stream(arr)
-
-    df = stream.run(arr)
-
-    assert df.shape[0] != 0  # terrible test
-
-
-def test_all_features_zero_array():
-
-    arr = np.zeros([2, 2000])
-    stream = get_example_stream(arr)
-
-    df = stream.run(arr)
-
-
-def test_all_features_NaN_array():
-
-    arr = np.empty([2, 2000])
-    arr[:] = np.nan
-
-    stream = get_example_stream(arr)
-
-    df = stream.run(arr)

tests/test_bispectra.py

@@ -1,70 +0,0 @@
-import pytest
-import mne
-import numpy as np
-
-from py_neuromodulation import (
-    nm_analysis,
-    nm_decode,
-    nm_define_nmchannels,
-    nm_IO,
-    nm_plots,
-    nm_settings,
-    nm_stream_offline,
-)
-
-
-def test_bispectrum():
-    (
-        RUN_NAME,
-        PATH_RUN,
-        PATH_BIDS,
-        PATH_OUT,
-        datatype,
-    ) = nm_IO.get_paths_example_data()
-
-    (
-        raw,
-        data,
-        sfreq,
-        line_noise,
-        coord_list,
-        coord_names,
-    ) = nm_IO.read_BIDS_data(
-        PATH_RUN=PATH_RUN, BIDS_PATH=PATH_BIDS, datatype=datatype
-    )
-
-    ch_names = raw.ch_names[4]
-    ch_types = raw.get_channel_types()[4]
-
-    nm_channels = nm_define_nmchannels.set_channels(
-        ch_names=[ch_names],
-        ch_types=[ch_types],
-        reference="default",
-        bads=None,
-        new_names="default",
-        used_types=("ecog", "dbs", "seeg"),
-        target_keywords=("MOV_RIGHT_CLEAN",),
-    )
-
-    settings = nm_settings.get_default_settings()
-    settings = nm_settings.reset_settings(settings)
-
-    settings["features"]["bispectrum"] = True
-
-    stream = nm_stream_offline.Stream(
-        settings=settings,
-        nm_channels=nm_channels,
-        path_grids=None,
-        verbose=True,
-        sfreq=sfreq,
-        line_noise=line_noise,
-        coord_list=coord_list,
-        coord_names=coord_names,
-    )
-
-    features = stream.run(np.expand_dims(data[3, :], axis=0))
-
-    assert (
-        features["ECOG_RIGHT_1_Bispectrum_phase_mean_whole_fband_range"].sum()
-        != 0
-    )

tests/test_bursts.py

@@ -1,105 +0,0 @@
-import pytest
-import numpy as np
-from py_neuromodulation import (
-    nm_bursts,
-    nm_settings,
-    nm_stream_offline,
-    nm_define_nmchannels,
-)
-
-
-def test_init_wrong_fband():
-    settings = nm_settings.get_default_settings()
-    settings["burst_settings"]["frequency_bands"] = ["wrong_band"]
-    with pytest.raises(Exception):
-        nm_bursts.Burst.test_settings(
-            settings,
-            [
-                "ch1",
-                "ch2",
-            ],
-            1000,
-        )
-
-
-def test_init_wrong_treshold():
-    settings = nm_settings.get_default_settings()
-    settings["burst_settings"]["threshold"] = -1
-    with pytest.raises(Exception):
-        nm_bursts.Burst.test_settings(
-            settings,
-            [
-                "ch1",
-                "ch2",
-            ],
-            1000,
-        )
-
-
-def test_init_wrong_timeduration():
-    settings = nm_settings.get_default_settings()
-    settings["burst_settings"]["time_duration_s"] = -1
-    with pytest.raises(Exception):
-        nm_bursts.Burst.test_settings(
-            settings,
-            [
-                "ch1",
-                "ch2",
-            ],
-            1000,
-        )
-
-
-def test_init_wrong_burst_feature_init():
-    settings = nm_settings.get_default_settings()
-    settings["burst_settings"]["burst_features"]["duration"] = -1
-    with pytest.raises(Exception):
-        nm_bursts.Burst.test_settings(
-            settings,
-            [
-                "ch1",
-                "ch2",
-            ],
-            1000,
-        )
-
-
-def test_bursting_duration():
-    np.random.seed(0)
-    settings = nm_settings.get_default_settings()
-    settings["features"]["bursts"] = True
-    settings["postprocessing"]["feature_normalization"] = False
-    TIME_DURATION = 10
-    sfreq = 1000
-    NUM_CH = 1
-    time_points_beta = np.arange(0, 1, 1 / sfreq)
-    beta_freq = 18
-
-    beta_wave = np.sin(2 * np.pi * beta_freq * time_points_beta)
-
-    ch_names = ["ch0"]
-
-    bursts = nm_bursts.Burst(settings, ch_names, sfreq)
-
-    for _ in range(10):
-        np.random.seed(0)
-        data = np.random.random([NUM_CH, 1 * sfreq])
-        f = bursts.calc_feature(data, {})
-
-    np.random.seed(0)
-    # the percentile of the hilbert transform of a continuous oscillation will be high
-    # select better max amplitude
-    bursts = nm_bursts.Burst(settings, ch_names, sfreq)
-    f_burst = bursts.calc_feature(
-        beta_wave + np.random.random([NUM_CH, 1 * sfreq]), {}
-    )
-
-    assert (
-        f["ch0_bursts_low beta_amplitude_max"]
-        < f_burst["ch0_bursts_low beta_amplitude_max"]
-    )
-
-    assert (
-        f["ch0_bursts_low beta_duration_max"]
-        < f_burst["ch0_bursts_low beta_duration_max"]
-    )