py-neuromodulation 0.0.3__py3-none-any.whl → 0.0.5__py3-none-any.whl

tests/test_rereference.py

@@ -1,171 +0,0 @@
-import math
-import os
-import numpy as np
-from numpy.testing import assert_allclose
-import pandas as pd
-import pytest
-
-from py_neuromodulation.nm_rereference import ReReferencer
-from py_neuromodulation import (
-    nm_generator,
-    nm_settings,
-    nm_IO,
-    nm_define_nmchannels,
-)
-
-
-def test_rereference_not_used_channels_no_reref(setup_databatch):
-    ch_names, ch_types, bads, data_batch = setup_databatch
-
-    nm_channels = nm_define_nmchannels.set_channels(
-        ch_names=ch_names,
-        ch_types=ch_types,
-        reference="default",
-        bads=bads,
-        new_names="default",
-        used_types=("ecog", "dbs", "seeg"),
-        target_keywords=("MOV_RIGHT",),
-    )
-
-    re_referencer = ReReferencer(1, nm_channels)
-
-    # select here data that will is selected, this operation takes place in the nm_run_analysis
-    data_used = data_batch[nm_channels["used"] == 1]
-
-    ref_dat = re_referencer.process(data_used)
-
-    for no_ref_idx in np.where(
-        (nm_channels.rereference == "None") & nm_channels.used == 1
-    )[0]:
-        assert_allclose(ref_dat[no_ref_idx, :], data_batch[no_ref_idx, :])
-
-
-def test_rereference_car(setup_databatch):
-    ch_names, ch_types, bads, data_batch = setup_databatch
-
-    nm_channels = nm_define_nmchannels.set_channels(
-        ch_names=ch_names,
-        ch_types=ch_types,
-        reference="default",
-        bads=bads,
-        new_names="default",
-        used_types=("ecog", "dbs", "seeg"),
-        target_keywords=("MOV_RIGHT",),
-    )
-
-    re_referencer = ReReferencer(1, nm_channels)
-
-    data_used = data_batch[nm_channels["used"] == 1]
-
-    ref_dat = re_referencer.process(data_used)
-
-    for ecog_ch_idx in np.where(
-        (nm_channels["type"] == "ecog") & (nm_channels.rereference == "average")
-    )[0]:
-        assert_allclose(
-            ref_dat[ecog_ch_idx, :],
-            data_batch[ecog_ch_idx, :]
-            - data_batch[
-                (nm_channels["type"] == "ecog")
-                & (nm_channels.index != ecog_ch_idx)
-            ].mean(axis=0),
-        )
-
-
-def test_rereference_bp(setup_databatch):
-    ch_names, ch_types, bads, data_batch = setup_databatch
-
-    nm_channels = nm_define_nmchannels.set_channels(
-        ch_names=ch_names,
-        ch_types=ch_types,
-        reference="default",
-        bads=bads,
-        new_names="default",
-        used_types=("ecog", "dbs", "seeg"),
-        target_keywords=("MOV_RIGHT",),
-    )
-
-    re_referencer = ReReferencer(1, nm_channels)
-
-    data_used = data_batch[nm_channels["used"] == 1]
-
-    ref_dat = re_referencer.process(data_used)
-
-    for bp_reref_idx in [
-        ch_idx
-        for ch_idx, ch in enumerate(nm_channels.rereference)
-        if ch in list(nm_channels.name)
-    ]:
-        # bp_reref_idx is the channel index of the rereference anode
-        # referenced_bp_channel is the channel index which is the rereference cathode
-        referenced_bp_channel = np.where(
-            nm_channels.iloc[bp_reref_idx]["rereference"] == nm_channels.name
-        )[0][0]
-        assert_allclose(
-            ref_dat[bp_reref_idx, :],
-            data_batch[bp_reref_idx, :] - data_batch[referenced_bp_channel, :],
-        )
-
-
-def test_rereference_wrong_rererference_column_name(setup_databatch):
-    ch_names, ch_types, bads, data_batch = setup_databatch
-
-    nm_channels = nm_define_nmchannels.set_channels(
-        ch_names=ch_names,
-        ch_types=ch_types,
-        reference="default",
-        bads=bads,
-        new_names="default",
-        used_types=("ecog", "dbs", "seeg"),
-        target_keywords=("SQUARED_ROTATION",),
-    )
-
-    nm_channels.loc[0, "rereference"] = "hallo"
-    with pytest.raises(Exception) as e_info:
-        re_referencer = ReReferencer(1, nm_channels)
-
-
-def test_rereference_muliple_channels(setup_databatch):
-    ch_names, ch_types, bads, data_batch = setup_databatch
-
-    nm_channels = nm_define_nmchannels.set_channels(
-        ch_names=ch_names,
-        ch_types=ch_types,
-        reference="default",
-        bads=bads,
-        new_names="default",
-        used_types=("ecog", "dbs", "seeg"),
-        target_keywords=("MOV_RIGHT",),
-    )
-
-    nm_channels.loc[0, "rereference"] = "LFP_RIGHT_1&LFP_RIGHT_2"
-
-    re_referencer = ReReferencer(1, nm_channels)
-
-    data_used = data_batch[nm_channels["used"] == 1]
-
-    ref_dat = re_referencer.process(data_used)
-
-    assert_allclose(
-        ref_dat[0, :],
-        data_batch[0, :] - (data_batch[1, :] + data_batch[2, :]) / 2,
-    )
-
-
-def test_rereference_same_channel(setup_databatch):
-    ch_names, ch_types, bads, data_batch = setup_databatch
-
-    nm_channels = nm_define_nmchannels.set_channels(
-        ch_names=ch_names,
-        ch_types=ch_types,
-        reference="default",
-        bads=bads,
-        new_names="default",
-        used_types=("ecog", "dbs", "seeg"),
-        target_keywords=("MOV_RIGHT",),
-    )
-
-    nm_channels.loc[0, "rereference"] = nm_channels.loc[0, "name"]
-
-    with pytest.raises(Exception):
-        re_referencer = ReReferencer(1, nm_channels)

tests/test_sampling.py

@@ -1,57 +0,0 @@
-import py_neuromodulation as nm
-import numpy as np
-
-
-def get_fast_compute_settings():
-    settings = nm.nm_settings.get_default_settings()
-    settings = nm.nm_settings.reset_settings(settings)
-    settings = nm.nm_settings.set_settings_fast_compute(settings)
-    settings["preprocessing"] = ["re_referencing", "notch_filter"]
-    settings["features"]["fft"] = True
-    settings["postprocessing"]["feature_normalization"] = True
-    return settings
-
-
-def get_features(time_end_ms: int, segment_length_features_ms: int):
-    data = np.random.random([2, time_end_ms])
-    settings = get_fast_compute_settings()
-    settings["segment_length_features_ms"] = segment_length_features_ms
-    settings["fft_settings"]["windowlength_ms"] = segment_length_features_ms
-
-    settings["frequency_ranges_hz"] = {
-        # "high beta" : [20, 35],
-        "low gamma": [60, 80],
-        "high gamma": [90, 200],
-    }
-    stream = nm.Stream(
-        sfreq=1000,
-        data=data,
-        sampling_rate_features_hz=10,
-        verbose=False,
-        settings=settings,
-    )
-
-    features = stream.run(data)
-    return features
-
-
-def test_feature_timing_5s_start_800ms():
-    """Test if the features timing duration are computed correctly for a 5s signal with 800ms segment length"""
-    time_end_ms = 5000
-    segment_length_features_ms = 800
-    features = get_features(time_end_ms, segment_length_features_ms)
-
-    assert int(features["time"].iloc[0]) == segment_length_features_ms
-
-    assert int(features["time"].iloc[-1]) == time_end_ms
-
-
-def test_feature_timing_1s_start_500ms():
-    """Test if the features timing duration are computed correctly for a 1s signal with 500ms segment length"""
-    time_end_ms = 1000
-    segment_length_features_ms = 500
-    features = get_features(time_end_ms, segment_length_features_ms)
-
-    assert int(features["time"].iloc[0]) == segment_length_features_ms
-
-    assert int(features["time"].iloc[-1]) == time_end_ms

tests/test_settings_change_after_init.py

@@ -1,76 +0,0 @@
-import numpy as np
-
-import py_neuromodulation as nm
-from py_neuromodulation import nm_settings
-
-
-def test_post_init_nm_channels_change():
-    """Test if post initialization of nm_channels will also be ported to the feature computation."""
-
-    data = np.random.random((10, 1000))
-    fs = 1000
-
-    stream = nm.Stream(fs, data)
-
-    # default channel names are "ch{i}"
-    # every time the name changes, the "new_name" should also changes
-    # this is however only done during initialization
-    stream.nm_channels["new_name"] = [f"new_ch_name_{i}" for i in range(10)]
-
-    features = stream.run()
-
-    assert len([f for f in features.columns if "new_ch_name_0" in f]) != 0
-
-
-def test_post_init_nm_channels_used_channels_change_single_channel():
-    """Test if post initialization of nm_settings will also be ported to the feature computation."""
-
-    np.random.seed(0)
-    data = np.random.random((3, 1000))
-    sfreq = 1000
-    stream = nm.Stream(sfreq=sfreq, data=data, sampling_rate_features_hz=11)
-    stream.nm_channels["used"] = 0
-    stream.nm_channels.loc[1, "used"] = 1
-
-    features = stream.run(data)
-
-    chs_not_used = stream.nm_channels[stream.nm_channels["used"] == 0][
-        "new_name"
-    ]
-
-    assert (
-        np.sum(
-            [
-                len([c for c in features.columns if c.startswith(ch_not_used)])
-                for ch_not_used in chs_not_used
-            ]
-        )
-        == 0
-    )
-
-
-def test_post_init_nm_channels_used_channels_change_multiple_channel():
-    """Test if post initialization of nm_settings will also be ported to the feature computation."""
-
-    np.random.seed(0)
-    data = np.random.random((3, 1000))
-    sfreq = 1000
-    stream = nm.Stream(sfreq=sfreq, data=data, sampling_rate_features_hz=11)
-    stream.nm_channels["used"] = 0
-    stream.nm_channels.loc[[0, 2], "used"] = 1
-
-    features = stream.run(data)
-
-    chs_not_used = stream.nm_channels[stream.nm_channels["used"] == 0][
-        "new_name"
-    ]
-
-    assert (
-        np.sum(
-            [
-                len([c for c in features.columns if c.startswith(ch_not_used)])
-                for ch_not_used in chs_not_used
-            ]
-        )
-        == 0
-    )

tests/test_sharpwave.py

@@ -1,165 +0,0 @@
-import pytest
-import numpy as np
-
-from py_neuromodulation import nm_sharpwaves, nm_settings
-
-
-def init_sw_settings() -> dict:
-    settings = nm_settings.get_default_settings()
-    settings["sharpwave_analysis"] = True
-    return settings
-
-
-def test_sharpwaveinit_wrong_peak_param():
-
-    settings = init_sw_settings()
-    with pytest.raises(Exception) as e_info:
-
-        settings["sharpwave_analysis_settings"]["sharpwave_features"][
-            "peak_left"
-        ] = 5
-        nm_sharpwaves.SharpwaveAnalyzer.test_settings(
-            settings, ch_names=[], sfreq=1000
-        )
-
-
-def test_sharpwaveinit_wrong_filter_range():
-    settings = init_sw_settings()
-    with pytest.raises(Exception) as e_info:
-        settings["sharpwave_analysis_settings"]["filter_ranges_hz"] = [
-            [5, 1200]
-        ]
-        nm_sharpwaves.SharpwaveAnalyzer.test_settings(
-            settings, ch_names=[], sfreq=1000
-        )
-
-
-def test_sharpwaveinit_missing_estimator():
-    settings = init_sw_settings()
-    with pytest.raises(Exception) as e_info:
-
-        settings["sharpwave_analysis_settings"]["sharpwave_features"][
-            "prominence"
-        ] = True
-        settings["sharpwave_analysis_settings"]["estimator"]["mean"] = []
-        settings["sharpwave_analysis_settings"]["estimator"]["median"] = []
-        settings["sharpwave_analysis_settings"]["estimator"]["max"] = []
-        settings["sharpwave_analysis_settings"]["estimator"]["min"] = []
-        settings["sharpwave_analysis_settings"]["estimator"]["var"] = []
-
-        nm_sharpwaves.SharpwaveAnalyzer.test_settings(
-            settings, ch_names=[], sfreq=1000
-        )
-
-
-def test_sharpwaveinit_correct_featurelist():
-    settings = init_sw_settings()
-    settings["sharpwave_analysis_settings"]["sharpwave_features"][
-        "prominence"
-    ] = True
-    settings["sharpwave_analysis_settings"]["sharpwave_features"][
-        "interval"
-    ] = True
-    settings["sharpwave_analysis_settings"]["sharpwave_features"][
-        "sharpness"
-    ] = True
-    settings["sharpwave_analysis_settings"]["estimator"]["mean"] = [
-        "prominence",
-        "interval",
-    ]
-    settings["sharpwave_analysis_settings"]["estimator"]["median"] = [
-        "sharpness"
-    ]
-    settings["sharpwave_analysis_settings"]["estimator"]["max"] = []
-    settings["sharpwave_analysis_settings"]["estimator"]["min"] = []
-    settings["sharpwave_analysis_settings"]["estimator"]["var"] = []
-
-    assert (
-        nm_sharpwaves.SharpwaveAnalyzer.test_settings(
-            settings, ch_names=[], sfreq=1000
-        )
-        == None
-    )
-
-
-def test_prominence_features():
-
-    settings = init_sw_settings()
-    sfreq = 1000
-    ch_names = ["ch1", "ch2", "ch3", "ch4"]
-
-    # Reset feataures
-    for f in settings["sharpwave_analysis_settings"][
-        "sharpwave_features"
-    ].keys():
-        settings["sharpwave_analysis_settings"]["sharpwave_features"][f] = False
-    for est in settings["sharpwave_analysis_settings"]["estimator"].keys():
-        settings["sharpwave_analysis_settings"]["estimator"][est] = []
-
-    settings["sharpwave_analysis_settings"]["sharpwave_features"][
-        "prominence"
-    ] = True
-    settings["sharpwave_analysis_settings"]["estimator"]["max"] = ["prominence"]
-
-    settings["sharpwave_analysis_settings"]["filter_ranges_hz"] = [[5, 80]]
-
-    sw = nm_sharpwaves.SharpwaveAnalyzer(settings, ch_names, sfreq)
-
-    data = np.zeros([len(ch_names), sfreq])
-    data[0, 500] = 1
-    data[1, 500] = 2
-    data[2, 500] = 3
-    data[3, 500] = 4
-
-    features = sw.calc_feature(data, {})
-
-    assert (
-        features["ch4_Sharpwave_Max_prominence_range_5_80"]
-        > features["ch3_Sharpwave_Max_prominence_range_5_80"]
-        > features["ch2_Sharpwave_Max_prominence_range_5_80"]
-        > features["ch1_Sharpwave_Max_prominence_range_5_80"]
-    ), "prominence features were not calculated correctly"
-
-
-def test_interval_feature():
-
-    settings = init_sw_settings()
-    sfreq = 1000
-    ch_names = ["ch1", "ch2", "ch3", "ch4"]
-
-    # Reset feataures
-    for f in settings["sharpwave_analysis_settings"][
-        "sharpwave_features"
-    ].keys():
-        settings["sharpwave_analysis_settings"]["sharpwave_features"][f] = False
-    for est in settings["sharpwave_analysis_settings"]["estimator"].keys():
-        settings["sharpwave_analysis_settings"]["estimator"][est] = []
-
-    settings["sharpwave_analysis_settings"]["sharpwave_features"][
-        "interval"
-    ] = True
-    settings["sharpwave_analysis_settings"]["estimator"]["max"] = ["interval"]
-
-    # the filter cannot be too high, since adjacent ripples will be detected as peaks
-    settings["sharpwave_analysis_settings"]["filter_ranges_hz"] = [[5, 200]]
-
-    sw = nm_sharpwaves.SharpwaveAnalyzer(settings, ch_names, sfreq)
-
-    data = np.zeros([len(ch_names), sfreq])
-    for i in np.arange(0, 1000, 100):
-        data[0, i] = 1
-    for i in np.arange(0, 1000, 200):
-        data[1, i] = 1
-    for i in np.arange(0, 1000, 300):
-        data[2, i] = 1
-    for i in np.arange(0, 1000, 400):
-        data[3, i] = 1
-
-    features = sw.calc_feature(data, {})
-
-    assert (
-        features["ch1_Sharpwave_Max_interval_range_5_200"]
-        < features["ch2_Sharpwave_Max_interval_range_5_200"]
-        < features["ch3_Sharpwave_Max_interval_range_5_200"]
-        < features["ch4_Sharpwave_Max_interval_range_5_200"]
-    ), "interval features were not calculated correctly"

tests/test_target_channel_add.py

@@ -1,100 +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_settings(test_arr: np.array) -> nm_stream_abc.PNStream:
-    settings = nm_settings.set_settings_fast_compute(
-        nm_settings.get_default_settings()
-    )
-
-    nm_channels = nm_define_nmchannels.get_default_channels_from_data(test_arr)
-
-    return settings, nm_channels
-
-
-def test_label_add_single_target():
-    sampling_rate_features = 10
-    arr_test = np.random.random([2, 5000])
-    target_arr = np.arange(0, 5000, 1)
-    arr_test[1, :] = target_arr
-
-    settings, nm_channels = get_example_settings(arr_test)
-
-    nm_channels["target"] = [0, 1]
-    nm_channels["used"] = [1, 0]
-    nm_channels.loc[1, "name"] = "target_ch"
-
-    settings["sampling_rate_features_hz"] = sampling_rate_features
-
-    stream = nm_stream_offline.Stream(
-        sfreq=1000, nm_channels=nm_channels, settings=settings, verbose=True
-    )
-
-    df = stream.run(arr_test)
-
-    assert df[
-        "target_ch"
-    ].is_monotonic_increasing, "Not all target values are ascending"
-
-    # check if all "target_ch" values are in the target_arr
-    assert all(
-        [i in target_arr for i in df["target_ch"]]
-    ), "Not all target values are were estimated correctly from the simulated target array"
-
-
-def test_label_add_multidimensional_target():
-    sampling_rate_features = 10
-    arr_test = np.random.random([4, 5000])
-    target_arr = np.arange(0, 5000, 1)
-    target_arr = np.tile(target_arr, (2, 1))
-    arr_test[[0, 2], :] = target_arr
-
-    settings, nm_channels = get_example_settings(arr_test)
-
-    nm_channels["target"] = [1, 0, 1, 0]
-    nm_channels["used"] = [0, 1, 0, 1]
-    nm_channels.loc[0, "name"] = "target_ch_0"
-    nm_channels.loc[2, "name"] = "target_ch_1"
-
-    settings["sampling_rate_features_hz"] = sampling_rate_features
-
-    stream = nm_stream_offline.Stream(
-        sfreq=1000, nm_channels=nm_channels, settings=settings, verbose=True
-    )
-
-    df = stream.run(arr_test)
-
-    for target_ch in ["target_ch_0", "target_ch_1"]:
-        assert df[
-            target_ch
-        ].is_monotonic_increasing, "Not all target values are ascending"
-
-        # check if all "target_ch" values are in the target_arr
-        assert all(
-            [i in target_arr for i in df[target_ch]]
-        ), "Not all target values are were estimated correctly from the simulated target array"
-
-
-def test_label_add_no_target():
-    sampling_rate_features = 10
-    arr_test = np.random.random([4, 5000])
-
-    settings, nm_channels = get_example_settings(arr_test)
-
-    settings["sampling_rate_features_hz"] = sampling_rate_features
-
-    stream = nm_stream_offline.Stream(
-        sfreq=1000, nm_channels=nm_channels, settings=settings, verbose=True
-    )
-
-    df = stream.run(arr_test)
-
-    assert all([col.startswith("ch") or col.startswith("time") for col in df])

tests/test_timing.py

@@ -1,80 +0,0 @@
-import py_neuromodulation as nm
-from py_neuromodulation import (
-    nm_settings,
-)
-
-import numpy as np
-
-
-def test_setting_computation_time():
-    """Intantiate test for feature computation with fixed time duration.
-    The number of output features should match the ratio of the sampling rate of the data and raw signal sampling rate.
-    """
-
-    data_duration_s = 5
-    sampling_rate_features_hz = 200
-    fs = 1000
-    data = np.random.random((1, int(data_duration_s * fs)))
-
-    settings = nm_settings.get_default_settings()
-    settings = nm_settings.set_settings_fast_compute(settings)
-    settings["segment_length_features_ms"] = 1000  # start afte 1 second
-    settings["features"]["fft"] = False
-    settings["features"]["raw_hjorth"] = True
-    stream = nm.Stream(
-        sfreq=fs,
-        data=data,
-        sampling_rate_features_hz=sampling_rate_features_hz,
-        settings=settings,
-    )
-
-    features = stream.run()
-
-    # test if features up till the last sample was computed
-    assert (
-        data_duration_s * 1000 - features["time"].iloc[-1]
-    ) < 1000 / sampling_rate_features_hz
-
-    # test that the time difference between two samples is the feature sampling rate
-    assert (
-        features["time"].iloc[1] - features["time"].iloc[0]
-    ) == 1000 / sampling_rate_features_hz
-
-    assert features["time"].iloc[0] == settings["segment_length_features_ms"]
-
-
-def test_float_fs():
-    """Change sampling rate here to be float, s.t. rounding issues are not affecting overall number of
-    computed features.
-    """
-
-    data_duration_s = 5
-    sampling_rate_features_hz = 200
-    fs = 1111.111
-    data = np.random.random((1, int(data_duration_s * fs)))
-
-    settings = nm_settings.get_default_settings()
-    settings = nm_settings.set_settings_fast_compute(settings)
-    settings["segment_length_features_ms"] = 333  # start afte 1 second
-
-    settings["features"]["fft"] = False
-    settings["features"]["raw_hjorth"] = True
-    stream = nm.Stream(
-        sfreq=fs,
-        data=data,
-        sampling_rate_features_hz=sampling_rate_features_hz,
-        settings=settings,
-    )
-
-    features = stream.run()
-
-    # test if features up till the last sample was computed
-    assert (
-        data_duration_s * 1000 - features["time"].iloc[-1]
-    ) < 1000 / sampling_rate_features_hz
-
-    assert (
-        features["time"].iloc[1] - features["time"].iloc[0]
-    ) == 1000 / sampling_rate_features_hz
-
-    assert features["time"].iloc[0] == settings["segment_length_features_ms"]