<filename>mne_nirs/simulation/_simulation.py
# Authors: <NAME> <<EMAIL>>
#
# License: BSD (3-clause)

import numpy as np
from mne import Annotations, create_info
from mne.io import RawArray


def simulate_nirs_raw(sfreq=3.,
                      amplitude=1.,
                      annot_desc='A',
                      sig_dur=300.,
                      stim_dur=5.,
                      isi_min=15.,
                      isi_max=45.,
                      ch_name='Simulated',
                      hrf_model='glover'):
    """
    Create simulated fNIRS data.

    The returned data is of type `hbo`.
    One or more conditions can be simulated.
    To simulate multiple conditions pass in a description and amplitude
    for each
    `amplitude=[0., 2., 4.], annot_desc=['Control', 'Cond_A', 'Cond_B']`.

    Parameters
    ----------
    sfreq : Number
        The sample rate.
    amplitude : Number, Array of numbers
        The amplitude of the signal to simulate in uM.
        Pass in an array to simulate multiple conditions.
    annot_desc : str, Array of str
        The name of the annotations for simulated amplitudes.
        Pass in an array to simulate multiple conditions,
        must be the same length as amplitude.
    sig_dur : Number
        The length of the boxcar signal to generate in seconds that will
        be convolved with the HRF.
    stim_dur : Number, Array of numbers
        The length of the stimulus to generate in seconds.
    isi_min : Number
        The minimum duration of the inter stimulus interval in seconds.
    isi_max : Number
        The maximum duration of the inter stimulus interval in seconds.
    ch_name : str
        Channel name to be used in returned raw instance.
    hrf_model : str
        Specifies the hemodynamic response function. See nilearn docs.

    Returns
    -------
    raw : instance of Raw
        The generated raw instance.
    """
    from nilearn.glm.first_level import make_first_level_design_matrix
    from pandas import DataFrame

    if type(amplitude) is not list:
        amplitude = [amplitude]
    if type(annot_desc) is not list:
        annot_desc = [annot_desc]
    if type(stim_dur) is not list:
        stim_dur = [stim_dur]

    frame_times = np.arange(sig_dur * sfreq) / sfreq

    assert len(amplitude) == len(annot_desc), "Same number of amplitudes as " \
                                              "annotations required."
    assert len(amplitude) == len(stim_dur), "Same number of amplitudes as " \
                                            "durations required."

    onset = 0.
    onsets = []
    conditions = []
    durations = []
    while onset < sig_dur - 60:
        c_idx = np.random.randint(0, len(amplitude))
        onset += np.random.uniform(isi_min, isi_max) + stim_dur[c_idx]
        onsets.append(onset)
        conditions.append(annot_desc[c_idx])
        durations.append(stim_dur[c_idx])

    events = DataFrame({'trial_type': conditions,
                        'onset': onsets,
                        'duration': durations})

    dm = make_first_level_design_matrix(frame_times, events,
                                        hrf_model=hrf_model,
                                        drift_model='polynomial',
                                        drift_order=0)
    dm = dm.drop(columns='constant')

    annotations = Annotations(onsets, durations, conditions)

    info = create_info(ch_names=[ch_name], sfreq=sfreq, ch_types=['hbo'])

    for idx, annot in enumerate(annot_desc):
        if annot in dm.columns:
            dm[annot] *= amplitude[idx]

    a = np.sum(dm.to_numpy(), axis=1) * 1.e-6
    a = a.reshape(-1, 1).T

    raw = RawArray(a, info, verbose=False)
    raw.set_annotations(annotations)

    return raw

<filename>mne_nirs/simulation/_simulation.py
# Authors: <NAME> <<EMAIL>>
#
# License: BSD (3-clause)

import numpy as np
from mne import Annotations, create_info
from mne.io import RawArray


def simulate_nirs_raw(sfreq=3.,
                      amplitude=1.,
                      annot_desc='A',
                      sig_dur=300.,
                      stim_dur=5.,
                      isi_min=15.,
                      isi_max=45.,
                      ch_name='Simulated',
                      hrf_model='glover'):
    """
    Create simulated fNIRS data.

    The returned data is of type `hbo`.
    One or more conditions can be simulated.
    To simulate multiple conditions pass in a description and amplitude
    for each
    `amplitude=[0., 2., 4.], annot_desc=['Control', 'Cond_A', 'Cond_B']`.

    Parameters
    ----------
    sfreq : Number
        The sample rate.
    amplitude : Number, Array of numbers
        The amplitude of the signal to simulate in uM.
        Pass in an array to simulate multiple conditions.
    annot_desc : str, Array of str
        The name of the annotations for simulated amplitudes.
        Pass in an array to simulate multiple conditions,
        must be the same length as amplitude.
    sig_dur : Number
        The length of the boxcar signal to generate in seconds that will
        be convolved with the HRF.
    stim_dur : Number, Array of numbers
        The length of the stimulus to generate in seconds.
    isi_min : Number
        The minimum duration of the inter stimulus interval in seconds.
    isi_max : Number
        The maximum duration of the inter stimulus interval in seconds.
    ch_name : str
        Channel name to be used in returned raw instance.
    hrf_model : str
        Specifies the hemodynamic response function. See nilearn docs.

    Returns
    -------
    raw : instance of Raw
        The generated raw instance.
    """
    from nilearn.glm.first_level import make_first_level_design_matrix
    from pandas import DataFrame

    if type(amplitude) is not list:
        amplitude = [amplitude]
    if type(annot_desc) is not list:
        annot_desc = [annot_desc]
    if type(stim_dur) is not list:
        stim_dur = [stim_dur]

    frame_times = np.arange(sig_dur * sfreq) / sfreq

    assert len(amplitude) == len(annot_desc), "Same number of amplitudes as " \
                                              "annotations required."
    assert len(amplitude) == len(stim_dur), "Same number of amplitudes as " \
                                            "durations required."

    onset = 0.
    onsets = []
    conditions = []
    durations = []
    while onset < sig_dur - 60:
        c_idx = np.random.randint(0, len(amplitude))
        onset += np.random.uniform(isi_min, isi_max) + stim_dur[c_idx]
        onsets.append(onset)
        conditions.append(annot_desc[c_idx])
        durations.append(stim_dur[c_idx])

    events = DataFrame({'trial_type': conditions,
                        'onset': onsets,
                        'duration': durations})

    dm = make_first_level_design_matrix(frame_times, events,
                                        hrf_model=hrf_model,
                                        drift_model='polynomial',
                                        drift_order=0)
    dm = dm.drop(columns='constant')

    annotations = Annotations(onsets, durations, conditions)

    info = create_info(ch_names=[ch_name], sfreq=sfreq, ch_types=['hbo'])

    for idx, annot in enumerate(annot_desc):
        if annot in dm.columns:
            dm[annot] *= amplitude[idx]

    a = np.sum(dm.to_numpy(), axis=1) * 1.e-6
    a = a.reshape(-1, 1).T

    raw = RawArray(a, info, verbose=False)
    raw.set_annotations(annotations)

    return raw

# Authors: <NAME> <<EMAIL>> # # License: BSD (3-clause) Create simulated fNIRS data.      The returned data is of type `hbo`.     One or more conditions can be simulated.     To simulate multiple conditions pass in a description and amplitude     for each     `amplitude=[0., 2., 4.], annot_desc=['Control', 'Cond_A', 'Cond_B']`.      Parameters     ----------     sfreq : Number         The sample rate.     amplitude : Number, Array of numbers         The amplitude of the signal to simulate in uM.         Pass in an array to simulate multiple conditions.     annot_desc : str, Array of str         The name of the annotations for simulated amplitudes.         Pass in an array to simulate multiple conditions,         must be the same length as amplitude.     sig_dur : Number         The length of the boxcar signal to generate in seconds that will         be convolved with the HRF.     stim_dur : Number, Array of numbers         The length of the stimulus to generate in seconds.     isi_min : Number         The minimum duration of the inter stimulus interval in seconds.     isi_max : Number         The maximum duration of the inter stimulus interval in seconds.     ch_name : str         Channel name to be used in returned raw instance.     hrf_model : str         Specifies the hemodynamic response function. See nilearn docs.      Returns     -------     raw : instance of Raw         The generated raw instance.