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

py_neuromodulation-0.0.3.dist-info/RECORD

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+py_neuromodulation-0.0.3.dist-info/METADATA,sha256=YSRxaxhxOF8Mq_1rO67M4I9TMx3ut2Olvd2B-5_y94c,7229
+py_neuromodulation-0.0.3.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+py_neuromodulation-0.0.3.dist-info/top_level.txt,sha256=RAWmR9vjiJ8zRtHRd0SlX4FrBkrgSujkFEJI1wU6GlQ,48
+py_neuromodulation-0.0.3.dist-info/RECORD,,

{py_neuromodulation-0.0.2.dist-info → py_neuromodulation-0.0.3.dist-info}/WHEEL

@@ -1,4 +1,5 @@
 Wheel-Version: 1.0
-Generator: flit 3.9.0
+Generator: bdist_wheel (0.43.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
+

py_neuromodulation-0.0.3.dist-info/top_level.txt

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

tests/conftest.py

@@ -0,0 +1,117 @@
+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

@@ -0,0 +1,10 @@
+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

@@ -0,0 +1,63 @@
+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

@@ -0,0 +1,70 @@
+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

@@ -0,0 +1,105 @@
+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"]
+    )