imap-processing 0.11.0__py3-none-any.whl → 0.12.0__py3-none-any.whl

imap_processing/idex/idex_l2a.py

@@ -0,0 +1,789 @@
+"""
+Perform IDEX L2a Processing.
+
+Examples
+--------
+.. code-block:: python
+
+    from imap_processing.idex.idex_l1a import PacketParser
+    from imap_processing.idex.idex_l1b import idex_l1b
+    from imap_processing.idex.idex_l2a import idex_l2a
+
+    l0_file = "imap_processing/tests/idex/imap_idex_l0_sci_20231214_v001.pkts"
+    l1a_data = PacketParser(l0_file, data_version)
+    l1b_data = idex_l1b(l1a_data, data_version)
+    l2a_data = idex_l2a(l1b_data, data_version)
+    write_cdf(l2a_data)
+"""
+
+# ruff: noqa: PLR0913
+import logging
+from enum import IntEnum
+from typing import Union
+
+import numpy as np
+import pandas as pd
+import xarray as xr
+from numpy.typing import NDArray
+from scipy.integrate import quad
+from scipy.optimize import curve_fit
+from scipy.signal import butter, detrend, filtfilt, find_peaks
+from scipy.stats import exponnorm
+
+from imap_processing import imap_module_directory
+from imap_processing.idex import idex_constants
+from imap_processing.idex.idex_constants import ConversionFactors
+from imap_processing.idex.idex_l1a import get_idex_attrs
+
+logger = logging.getLogger(__name__)
+
+
+class BaselineNoiseTime(IntEnum):
+    """
+    Time range in microseconds that mark the baseline noise before a Dust impact.
+
+    Attributes
+    ----------
+    START: int
+         Beginning of the baseline noise window.
+    STOP: int
+        End of the baseline noise window.
+    """
+
+    START = -7
+    STOP = -5
+
+
+def idex_l2a(l1b_dataset: xr.Dataset, data_version: str) -> xr.Dataset:
+    """
+    Will process IDEX l1b data to create l2a data products.
+
+    This will use fits to estimate the total impact charge for the Ion Grid and two
+    target signals.
+
+    Calculate mass scales for each event using the TOF high arrays (best quality of the
+    3 gain stages).
+    The TOF peaks are fitted to EMG curves to determine total intensity, max amplitude,
+    and signal quality.
+
+    Parameters
+    ----------
+    l1b_dataset : xarray.Dataset
+        IDEX L1a dataset to process.
+    data_version : str
+        Version of the data product being created.
+
+    Returns
+    -------
+    l1b_dataset : xarray.Dataset
+        The``xarray`` dataset containing the science data and supporting metadata.
+    """
+    logger.info(
+        f"Running IDEX L2A processing on dataset: {l1b_dataset.attrs['Logical_source']}"
+    )
+
+    tof_high = l1b_dataset["TOF_High"]
+    hs_time = l1b_dataset["time_high_sample_rate"]
+    ls_time = l1b_dataset["time_low_sample_rate"]
+
+    # Load an array of known masses of ions
+    atomic_masses_path = f"{imap_module_directory}/idex/atomic_masses.csv"
+    atomic_masses = pd.read_csv(atomic_masses_path)
+    masses = atomic_masses["Mass"]
+    stretches, shifts, mass_scales = time_to_mass(tof_high.data, hs_time.data, masses)
+
+    mass_scales_da = xr.DataArray(
+        name="mass_scale",
+        data=mass_scales,
+        dims=("epoch", "time_high_sample_rate_index"),
+    )
+    snr = calculate_snr(tof_high, hs_time)
+    # Find peaks for each event. The peaks represent a TOF of an ion.
+    # Peaks_2d is a list of variable-length arrays
+    peaks_2d = [find_peaks(tof, prominence=0.01)[0] for tof in tof_high]
+    kappa = calculate_kappa(mass_scales, peaks_2d)
+
+    # Analyze peaks for estimating dust composition
+    peak_fits, area_under_fits = xr.apply_ufunc(
+        analyze_peaks,
+        tof_high,
+        hs_time,
+        mass_scales_da,
+        np.arange(len(peaks_2d)),
+        kwargs={"peaks_2d": peaks_2d},
+        input_core_dims=[
+            ["time_high_sample_rate_index"],
+            ["time_high_sample_rate_index"],
+            ["time_high_sample_rate_index"],
+            [],
+        ],
+        # TODO: Determine dimension name
+        output_core_dims=[
+            ["time_of_flight", "peak_fit_parameters"],
+            ["time_of_flight"],
+        ],
+        vectorize=True,
+    )
+
+    l2a_dataset = l1b_dataset.copy()
+
+    for waveform in ["Target_Low", "Target_High", "Ion_Grid"]:
+        # Convert back to raw DNs for more accurate fits
+        waveform_dn = l1b_dataset[waveform] / ConversionFactors[waveform]
+        # Get the dust mass estimates and fit results
+        fit_results = xr.apply_ufunc(
+            estimate_dust_mass,
+            ls_time,
+            waveform_dn,
+            input_core_dims=[
+                ["time_low_sample_rate_index"],
+                ["time_low_sample_rate_index"],
+            ],
+            output_core_dims=[
+                ["fit_parameters"],
+                [],
+                [],
+                [],
+                ["time_low_sample_rate_index"],
+            ],
+            vectorize=True,
+            output_dtypes=[np.float64] * 6,
+        )
+        waveform_name = waveform.lower()
+        # Add variables
+        l2a_dataset[f"{waveform_name}_fit_parameters"] = fit_results[0]
+        l2a_dataset[f"{waveform_name}_fit_imapct_charge"] = fit_results[1]
+        # TODO: convert charge to mass
+        l2a_dataset[f"{waveform_name}_fit_imapct_mass_estimate"] = fit_results[1]
+        l2a_dataset[f"{waveform_name}_chi_squared"] = fit_results[2]
+        l2a_dataset[f"{waveform_name}_reduced_chi_squared"] = fit_results[3]
+        l2a_dataset[f"{waveform_name}_fit_results"] = fit_results[4]
+
+    l2a_dataset["tof_peak_fit_parameters"] = peak_fits
+    l2a_dataset["tof_peak_area_under_fit"] = area_under_fits
+    l2a_dataset["tof_peak_kappa"] = xr.DataArray(kappa, dims=["epoch"])
+    l2a_dataset["tof_snr"] = xr.DataArray(snr, dims=["epoch"])
+    l2a_dataset["mass"] = mass_scales_da
+    # Update global attributes
+    idex_attrs = get_idex_attrs(data_version)
+    l2a_dataset.attrs = idex_attrs.get_global_attributes("imap_idex_l2a_sci")
+
+    logger.info("IDEX L2A science data processing completed.")
+    return l2a_dataset
+
+
+def time_to_mass(
+    tof_high: np.ndarray, high_sampling_time: np.ndarray, masses: np.ndarray
+) -> tuple[NDArray, NDArray, NDArray]:
+    """
+    Calculate a mass scale for each TOF array in 'TOF_high'.
+
+    1) Make a vector with all zeros and a length of 8189, same as the TOF length: t_i
+    2) Calculate the times when each input mass should appear in the TOF data: t_calc
+        for each mass, calculate a time using this formula:
+
+            t_calc = t_offset + stretch_factor*sqrt(mass)
+
+            t_offset is the time offset (ns)
+            stretch factor (ns)
+
+        Then and set the value at the index of t_i that is closest to each of the
+        t_calcs to 1, the rest stay zero.
+    3) Calculate the cross-correlation with the original TOF.
+        The max will give you the best lag (t_offset) for a given stretch_factor.
+    4) Choose the stretch_factor that has the highest correlation
+
+    Parameters
+    ----------
+    tof_high : numpy.ndarray
+        The time of flight array for one dust event. Shape is
+        (epoch, high_time_sample_rate).
+    high_sampling_time : numpy.ndarray
+        The high sampling time array for one dust event. Shape is
+        (epoch, high_time_sample_rate).
+    masses : np.ndarray
+        Array of known masses of ions. Shape is (21,).
+
+    Returns
+    -------
+    numpy.ndarray
+        Best stretch value per event(adjusts scale).
+    numpy.ndarray
+        Best shift value per event (shifts scale left or right).
+    numpy.ndarray
+        Estimated mass for each time per event (after the time has been aligned using
+        the best t_offset and stretch_factor).
+    """
+    # Create an array of random stretches
+    # eventually, the stretch_factor used to create the highest correlation is used to
+    # align the time
+    min_stretch = 1400
+    random_stretches = np.linspace(min_stretch, min_stretch + 100, 10)
+
+    # Normalize time so start time is zero.
+    # This is necessary to find the correct time offset
+    time = high_sampling_time - high_sampling_time[:, 0:1]
+
+    # Start with a time offset of 0
+    t_offset = 0
+    shift = np.zeros((len(random_stretches), len(tof_high)))
+    correlation = np.zeros_like(shift)
+    # Step 1
+    t_i = np.zeros((len(random_stretches), len(tof_high[0])))
+    # Step 2
+    t_calc = t_offset + random_stretches[:, np.newaxis] * np.sqrt(np.array(masses))
+    for i in range(len(random_stretches)):
+        # Round every calculated time to the nearest int
+        t_calc_int = np.round(t_calc[i]).astype(int)
+        # Set values of t_i to 1 at the rounded calculated times if the time is less
+        # than the length of t_i
+        # E.g., if t_calc_int[0] = 5 then t_i[5] = 1.
+        t_i[i, t_calc_int[t_calc_int < len(t_i[0])]] = 1
+        # Step 3
+        # Cross-correlate t_i with TOF
+        # T_i simulates peaks at the times expected from the formula above,
+        # when this is cross correlated with the actual time of flight array with
+        # The measured peaks, we can measure the lags between them.
+        for j in range(len(tof_high)):
+            cross_correlation = np.correlate(t_i[i], tof_high[j], mode="full")
+            if np.all(cross_correlation == 0):
+                logger.warning(
+                    "There are no correlations found between the TOF array "
+                    "and the expected mass times array. The resulting mass scale "
+                    "may be inaccurate."
+                )
+            # Find the lag corresponding to the maximum correlation
+            # Represents the time lag from where the arrays are most correlated
+
+            # When np.correlate mode is 'full', it returns the convolution at each
+            # point of overlap, with an output shape of (N+M-1,) where N and M are the
+            # lengths of the input arrays. The center point or zero lag is at index
+            # len(M) - 1. Positions before this are negative lags, and
+            # positions after are positive lags.
+            middle = len(t_i[0]) - 1
+            shift[i, j] = np.argmax(cross_correlation) - middle
+            correlation[i, j] = np.max(cross_correlation)
+
+    # Calculate the estimated mass for each time (after the time has been aligned using
+    # the best t_offset and stretch_factor and converted to seconds).
+    # Step 4
+    # Gets the best shift in seconds (shift is currently in number of samples)
+    best_shift = (
+        idex_constants.FM_SAMPLING_RATE
+        * shift[np.argmax(correlation, axis=0), np.arange(len(shift[0]))]
+    )
+    # Get the best stretch in seconds
+    best_stretch = (
+        idex_constants.NS_TO_S * random_stretches[np.argmax(correlation, axis=0)]
+    )
+
+    mass_scale = (
+        (time * idex_constants.US_TO_S - best_shift[:, np.newaxis])
+        / best_stretch[:, np.newaxis]
+    ) ** 2
+
+    return best_stretch, best_shift, mass_scale
+
+
+def calculate_kappa(mass_scales: np.ndarray, peaks_2d: list) -> NDArray:
+    """
+    Calculate the kappa value for each mass scale.
+
+    Kappa represents the difference between the observed mass peaks and their
+    expected integer values in the calculated mass scale. The value ranges between zero
+    and one. A kappa value closer to zero indicates a better accuracy of the mass scale.
+
+    Parameters
+    ----------
+    mass_scales : xarray.DataArray
+        Array containing the masses at each time value for each dust event.
+    peaks_2d : list
+        A Nested list of tof peak indices.
+
+    Returns
+    -------
+    numpy.ndarray
+        Average distance from the assigned peak to the nearest integer value.
+    """
+    #  Find the average deviation between each TOF peak's assigned mass value and its
+    #  nearest decimal value per spectrum.
+    kappas = np.asarray(
+        [
+            np.mean(mass_scale[peaks] - np.round(mass_scale[peaks]))
+            for mass_scale, peaks in zip(mass_scales, peaks_2d)
+        ]
+    )
+    return kappas
+
+
+def calculate_snr(tof_high: xr.DataArray, hs_time: xr.DataArray) -> NDArray:
+    """
+    Calculate the signal-to-noise ratio.
+
+    Parameters
+    ----------
+    tof_high : xarray.DataArray
+        The time of flight array.
+    hs_time : xarray.DataArray
+        The high sampling time array.
+
+    Returns
+    -------
+    numpy.ndarray
+        Signal-to-noise ratio at each event.
+    """
+    # Find indices where Time (High Sampling) is between -7 and -5 ns (no signal yet)
+    # To determine the baseline noise
+    baseline_noise = np.where(
+        np.logical_and(
+            hs_time >= BaselineNoiseTime.START, hs_time <= BaselineNoiseTime.STOP
+        ),
+        tof_high,
+        np.nan,
+    )
+    if np.all(np.isnan(baseline_noise)):
+        logger.warning(
+            "Unable to find baseline noise. "
+            f"There is no signal from {BaselineNoiseTime.START} to "
+            f"{BaselineNoiseTime.STOP} ns. Returning np.nan SNR values"
+        )
+        return np.full(len(hs_time), fill_value=np.nan)
+    # Get the max signal without baseline noise
+    tof_max = np.max(tof_high, axis=1) - np.nanmean(baseline_noise, axis=1)
+    tof_sigma = np.nanstd(baseline_noise, axis=1, ddof=1)
+    # Return snr ratio
+    return tof_max / tof_sigma
+
+
+def analyze_peaks(
+    tof_high: xr.DataArray,
+    high_sampling_time: xr.DataArray,
+    mass_scale: xr.DataArray,
+    event_num: int,
+    peaks_2d: np.ndarray,
+) -> tuple[NDArray, NDArray]:
+    """
+    Fit an EMG curve to the Time of Flight data around each peak.
+
+    Parameters
+    ----------
+    tof_high : xarray.DataArray
+        The time of flight array.
+    high_sampling_time : xarray.DataArray
+        The high sampling time array.
+    mass_scale : xarray.DataArray
+        Time to mass scale.
+    event_num : int
+        Dust event number (for debugging purposes).
+    peaks_2d : numpy.ndarray
+        Nested list of peak indices.
+
+    Returns
+    -------
+    params: numpy.ndarray
+        Array of the EMG fit parameters (mu, sigma, lambda) at the corresponding mass.
+        Empty mass slots contain zeros.
+
+    area_under_emg : numpy.ndarray
+        Array of the area under the EMG curve at that mass. Empty mass slots
+        contain zeros.
+    """
+    # Initialize arrays to store EMG fit results
+    # fit_params: (500, 3) array where the first dimension is the estimated ion mass (
+    # 0-499)
+    # and the second is EMG fit parameters (mu, sigma, lambda) for peaks at that mass
+    # area_under_emg: (500) array storing the area under each EMG peak at
+    # corresponding mass.
+    fit_params = np.zeros((500, 3))
+    area_under_emg = np.zeros(500)
+    for peak in peaks_2d[event_num]:
+        # Take a slice of 5 samples on either side of the peak
+        start = max(0, peak - 5)
+        end = min(len(tof_high), peak + 6)
+
+        time_slice = high_sampling_time[start:end]
+        tof_slice = tof_high[start:end]
+
+        param = fit_emg(time_slice, tof_slice, event_num)
+        if param is None:
+            continue
+
+        area = calculate_area_under_emg(time_slice, param)
+        # extract the variables
+        k, mu, sigma = param
+        # Calculate lambda
+        lam = 1 / (k * sigma)
+        # Find the index where time is closest to mu
+        time_idx = np.argmin(np.abs(high_sampling_time.data - mu))
+        mass = mass_scale[time_idx]
+        # Round calculated mass to get the index
+        # If that index is already taken, keep increasing the index by one
+        # until we find an empty slot.
+        # This ensures we don't overwrite existing data when we have multiple peaks
+        # close to the same mass number
+        if mass < 0:
+            logger.warning(f"Warning: Calculated a negative mass: {mass}.")
+
+        mass = max(0, round(mass))
+        # Find the first index with non-zero fit parameters, starting from current mass
+        non_zero_idxs = np.nonzero(np.all(fit_params[mass:] != 0, axis=-1))[0]
+
+        # Determine index to use
+        # If no non-zero parameters found, use current mass index
+        # Otherwise, use the current mass plus offset to first non-zero index
+        idx = mass if not non_zero_idxs.size else mass + non_zero_idxs[0]
+
+        if idx < 500:
+            fit_params[idx] = np.array([mu, sigma, lam])
+            area_under_emg[idx] = area
+        else:
+            logger.warning(
+                f"Unable to find a slot for mass: {mass}. Discarding " f"value."
+            )
+
+    return fit_params, area_under_emg
+
+
+def fit_emg(
+    peak_time: np.ndarray, peak_signal: np.ndarray, event_num: int
+) -> Union[NDArray, None]:
+    """
+    Fit an exponentially modified gaussian function to the peak signal.
+
+    Scipy.stats.exponnorm.pdf uses parameters shape (k),
+    location (mu), and scale (sigma) where k = 1/(sigma*lambda)
+    with lambda being the exponential decay rate.
+
+    Parameters
+    ----------
+    peak_time : numpy.ndarray
+        TOF high +5 and -5 samples around peak.
+    peak_signal : numpy.ndarray
+        High sampling time array at +5 and -5 samples around peak.
+    event_num : int
+        Dust event number (for debugging purposes).
+
+    Returns
+    -------
+    param : numpy.ndarray or None
+        Fitted EMG optimal values for the parameters (popt) [k (shape parameter), mu,
+        sigma] if fit successful, None otherwise.
+    """
+    # Initial Guess for the parameters of the emg fit:
+    # center of gaussian
+    mu = peak_time[np.argmax(peak_signal)]
+    sigma = np.std(peak_time) / 10
+    # Decay rate
+    lam = 1 / (peak_time[-1] - peak_time[0])
+    # Calculate shape parameter K from lambda and sigma
+    k = 1 / (lam * sigma)
+    p0 = [k, mu, sigma]
+
+    try:
+        param, _ = curve_fit(
+            exponnorm.pdf, peak_time, peak_signal, p0=p0, maxfev=100_000
+        )
+
+    except RuntimeError as e:
+        logger.warning(
+            f"Failed to fit EMG curve: {e}\n"
+            f"Time range: {peak_time[0]:.2f} to {peak_time[-1]:.2f}\n"
+            f"Signal range: {min(peak_signal):.2f} to {max(peak_signal):.2f}\n"
+            f"Event number: {event_num}\n"
+            "Returning None."
+        )
+        return None
+
+    return param
+
+
+def calculate_area_under_emg(time_slice: np.ndarray, param: np.ndarray) -> float:
+    """
+    Calculate the area under the emg fit which is equal to the impact charge.
+
+    Parameters
+    ----------
+    time_slice : numpy.ndarray
+        Time values around the peak.
+    param : numpy.ndarray
+        Optimal parameters (k, mu, sigma) for the emg curve fit.
+
+    Returns
+    -------
+    float
+        Total area under the emg curve.
+    """
+    # Extract EMG fit parameters: k, mu, sigma
+    k, mu, sigma = param
+    # Compute integral
+    area, _ = quad(exponnorm.pdf, time_slice[0], time_slice[-1], args=(k, mu, sigma))
+
+    return float(area)
+
+
+def estimate_dust_mass(
+    low_sampling_time: xr.DataArray,
+    target_signal: xr.DataArray,
+    remove_noise: bool = True,
+) -> tuple[NDArray, float, float, float, NDArray]:
+    """
+    Filter and fit the target or ion grid signals to get the total dust impact charge.
+
+    Parameters
+    ----------
+    low_sampling_time : xarray.DataArray
+        The low sampling time array.
+    target_signal : xarray.DataArray
+        Target signal data.
+    remove_noise : bool
+        If true, attempt to remove background noise, otherwise fit on the unfiltered
+        signal.
+
+    Returns
+    -------
+    param : numpy.ndarray
+        Optimal target signal fit values for the parameters (popt)
+        [time_of_impact, constant_offset, amplitude, rise_time, discharge_time]
+        if fit successful. None otherwise.
+    sig_amp : float
+        Signal amplitude, calculated as difference between fitted maximum signal
+        and baseline mean if fit successful. None otherwise.
+    chi_squared : float
+        Sum of squared residuals from the fit.
+    reduced_chi_squared : float
+        Chi-squared per degree of freedom.
+    result : numpy.ndarray
+        The model values evaluated at each time point.
+    """
+    # TODO: The IDEX team is iterating on this Function and will provide more
+    #         information soon.
+    signal = np.array(target_signal.data)
+    time = np.array(low_sampling_time.data)
+    good_mask = np.logical_and(
+        time >= BaselineNoiseTime.START,
+        time <= BaselineNoiseTime.STOP,
+    )
+    if not np.any(good_mask):
+        logger.warning(
+            "Unable to find baseline noise. "
+            f"There is no signal from {BaselineNoiseTime.START} to "
+            f"{BaselineNoiseTime.STOP} ns."
+        )
+    if remove_noise:
+        # Remove noise due to "microphonics"
+        signal = remove_signal_noise(time, signal, good_mask)
+    # Time before image charge
+    pre = -2.0
+    # Get signal values where the time is before the image charge
+    signal_before_imapact = signal[time < pre]
+    # Center the baseline signal around zero
+    signal_baseline = signal_before_imapact - np.mean(signal_before_imapact)
+
+    # Initial Guess for the parameters of the ion grid signal
+    time_of_impact = 0.0  # Time of dust hit
+    constant_offset = 0.0  # Initial baseline
+    amplitude: float = np.max(signal)  # Signal height
+    rise_time = 0.371  # How fast the signal rises (s)
+    discharge_time = 0.371  # How fast signal decays (s)
+
+    p0 = [time_of_impact, constant_offset, amplitude, rise_time, discharge_time]
+
+    try:
+        with np.errstate(invalid="ignore", over="ignore"):
+            param, _ = curve_fit(
+                fit_impact,
+                time,
+                signal,
+                p0=p0,
+                maxfev=100_000,  # , epsfcn=1e-10
+            )
+    except RuntimeError as e:
+        logger.warning(
+            f"Failed to fit curve: {e}\n"
+            f"Time range: {time[0]:.2f} to {time[-1]:.2f}\n"
+            f"Signal range: {min(signal):.2f} to {max(signal):.2f}\n"
+            "Returning None."
+        )
+        return (
+            np.full(len(p0), np.nan),
+            np.nan,
+            np.nan,
+            np.nan,
+            np.full_like(time, np.nan),
+        )
+
+    impact_fit = fit_impact(time, *param)
+    # Calculate the resulting signal amplitude after removing baseline noise
+    sig_amp = max(impact_fit) - np.mean(signal_baseline)
+
+    # Calculate chi square and reduced chi square
+    chisqr = float(np.sum((signal - impact_fit) ** 2))
+    # To get reduced chi square divide by dof (number of points - number of params)
+    redchi = chisqr / (len(signal) - len(p0))
+
+    return param, float(sig_amp), chisqr, redchi, impact_fit
+
+
+def fit_impact(
+    time: np.ndarray,
+    time_of_impact: float,
+    constant_offset: float,
+    amplitude: float,
+    rise_time: float,
+    discharge_time: float,
+) -> NDArray:
+    """
+    Fit function for the Ion Grid and two target signals.
+
+    Parameters
+    ----------
+    time : np.ndarray
+        Time values for the signal.
+    time_of_impact : float
+        Time of dust impact.
+    constant_offset : float
+        Initial baseline noise.
+    amplitude : float
+        Signal height.
+    rise_time : float
+        How fast the signal rises (s).
+    discharge_time : float
+        How fast the signal decays (s).
+
+    Returns
+    -------
+    np.ndarray
+        Function values calculated at the input time points.
+
+    Notes
+    -----
+    Impact charge fit function [1]_:
+    Y(t) = C₀ + H(t - t₀)[C₂(1 - e^(-(t-t₀)/τ₁))e^(-(t-t₀)/τ₂) - C₁]
+
+    References
+    ----------
+    .. [1] Horányi, M., et al. (2014), The Lunar Dust Experiment (LDEX) Onboard the
+       Lunar Atmosphere and Dust Environment Explorer (LADEE) mission, Space Sci. Rev.,
+       185(1–4), 93–113, doi:10.1007/s11214-014-0118-7.
+    """
+    exponent_1 = 1.0 - np.exp(-(time - time_of_impact) / rise_time)
+    exponent_2 = np.exp(-(time - time_of_impact) / discharge_time)
+    return constant_offset + np.heaviside(time - time_of_impact, 0) * (
+        amplitude * exponent_1 * exponent_2
+    )
+
+
+def remove_signal_noise(
+    time: np.ndarray, signal: np.ndarray, good_mask: np.ndarray
+) -> NDArray:
+    """
+    Remove linear, sine wave, and high frequency background noise from the input signal.
+
+    Parameters
+    ----------
+    time : np.ndarray
+        Time values for the signal.
+    signal : numpy.ndarray
+        Target or Ion Grid signal.
+    good_mask : numpy.ndarray
+        Boolean mask for the signal array to determine where the baseline noise is.
+
+    Returns
+    -------
+    numpy.ndarray
+        Signal with linear, sine wave, and high frequency background noise filtered out.
+    """
+    # Remove linear noise
+    signal = detrend(signal, type="linear")
+    # Remove sine wave Background
+    baseline_detrended = signal[good_mask]
+    # Approximate initial values for the fit
+    amplitude: float = max(baseline_detrended)
+    frequency = idex_constants.TARGET_NOISE_FREQUENCY
+    # Horizontal wave shift
+    phase_shift = 45
+    # Minimize function
+    p0 = [amplitude, frequency, phase_shift]
+    # Fit a sign wave to the baseline noise with initial best guesses of
+    # amplitude, period, and phase shift
+    try:
+        # Set epsfcn to 1e-10 to mimic what lmfit minimize does
+        param, _ = curve_fit(
+            sine_fit,
+            time[good_mask],
+            baseline_detrended,
+            p0=p0,
+            maxfev=100_000,
+            epsfcn=1e-10,
+        )
+        # Remove the sine wave background from the signal
+        signal -= sine_fit(time, *param)
+    except RuntimeError as e:
+        logger.warning(f"Failed to fit background noise sine wave : {e}\n")
+
+    # Use the butterworth filter to smooth remaining noise and remove noise above
+    # desired cutoff
+    signal = butter_lowpass_filter(time, signal)
+    return signal
+
+
+def sine_fit(time: np.ndarray, a: float, f: float, p: float) -> NDArray:
+    """
+    Generate a sine wave with given amplitude, frequency, and phase.
+
+    Parameters
+    ----------
+    time : numpy.ndarray
+        Time points at which to evaluate the sine wave, in seconds.
+    a : float
+        Amplitude of the sine wave.
+    f : float
+        Frequency of the sine wave in Hz.
+    p : float
+        Phase shift of the sine wave in radians.
+
+    Returns
+    -------
+    numpy.ndarray
+        Sine wave values calculated at the input time points.
+    """
+    return a * np.sin(2 * np.pi * f * time + p)
+
+
+def butter_lowpass_filter(
+    time: np.ndarray,
+    signal: np.ndarray,
+    cutoff: float = idex_constants.TARGET_HIGH_FREQUENCY_CUTOFF,
+) -> NDArray:
+    """
+    Apply a Butterworth low-pass filter to remove high frequency noise from the signal.
+
+    Parameters
+    ----------
+    time : numpy.ndarray
+        Time values for the signal.
+    signal : numpy.ndarray
+        Target or Ion Grid signal.
+    cutoff : float
+        Frequency cutoff in Mhz (time is in microseconds).
+
+    Returns
+    -------
+    numpy.ndarray
+        Filtered signal.
+    """
+    # TODO: The IDEX team might be switching this function out for a different filter.
+    sample_period = time[1] - time[0]
+    # sampling frequency
+    fs = (time[-1] - time[0]) / sample_period  # Hz
+    # Calculate nyquist frequency
+    # It is the highest frequency for the sampling frequency
+    nyq = 0.5 * fs
+    # sine wave can be approx represented as quadratic
+    order = 2
+    # Normalize the nyquist frequency. It is expected to be between 0 and 1
+    normal_cutoff = cutoff / nyq
+    # Get the filter coefficients
+    b, a = butter(order, normal_cutoff, btype="low", analog=False)
+    y = filtfilt(b, a, signal)
+    return y