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Order Statistic Constant False Alarm Rate detector package

Project description

oscfar

OSCFAR (Order Statistic Constant False Alarm Rate) is a radar signal processing technique used for target detection. It adaptively estimates the noise or clutter power in the vicinity of a potential target and sets a detection threshold accordingly, maintaining a constant false alarm rate regardless of the background noise characteristics.

Getting Started

To get started with the OSCFAR implementation, you'll need to set up your environment. We recommend using Conda for managing dependencies.

1. Create a Conda Environment:

conda create -n myenv python=3.9  # Or your preferred Python version above 3.9
conda activate myenv

2. Install OSCFAR Package:

pip install oscfar

You may need to manually install some packages like fitburst. For fitburst follow installation instructions on GitHub.

Documentation:

Table of Contents

šŸ…¼ oscfar

Functions

šŸ…µ oscfar.do_os_cfar

def do_os_cfar(data: np.array, guard_cells, train_cells, rank_k, threshold_factor, averaging, min_dist, min_snr, baseline):

Performs OS-CFAR detection on a 2D data array (e.g., spectrogram) by summing

along the frequency axis to create a 1D time series. Applies filtering, peak refinement, and baseline removal.

Parameters:

  • data (np.ndarray): 2D array of input data (frequency vs. time).
  • guard_cells (int): Number of guard cells on each side of the CUT.
  • train_cells (int): Number of training cells on each side of the CUT.
  • rank_k (float): Rank (as a fraction of total training cells) for OS.
  • threshold_factor (float): Scaling factor for the threshold.
  • averaging (int): Window size for moving average smoothing.
  • min_dist (int): Minimum distance between peaks (in samples).
  • min_snr (float): Minimum SNR for peak verification.
  • baseline (float): Factor for removing baseline peaks.

Returns:

  • utils.Peaks: An object containing the refined peak indices and the threshold array from OS-CFAR.

šŸ…¼ oscfar.cfar

Functions

šŸ…µ oscfar.cfar.os_cfar_1d

def os_cfar_1d(data, guard_cells, train_cells, rank_k, threshold_factor):

Performs 1D Ordered Statistic Constant False Alarm Rate (OS-CFAR) detection.

Parameters:

  • data (np.ndarray): 1D array of input data (must be in linear power, not dB).
  • guard_cells (int): Number of guard cells on EACH side of the CUT.
  • train_cells (int): Number of training cells on EACH side of the CUT.
  • rank_k (int): The rank (1-based index) of the sorted training cell values to use for noise estimation (1 <= rank_k <= N). N = 2 * train_cells is the total number of training cells. A common choice is around 0.75 * N.
  • threshold_factor (float): The scaling factor (alpha) to multiply the noise estimate by to get the threshold.

Returns:

  • tuple: A tuple containing:
  • detected_peaks_indices (np.ndarray): Indices where peaks were detected.
  • threshold (np.ndarray): The calculated threshold for each cell. (Same size as input data, padded with NaNs at edges where CFAR wasn't computed).

šŸ…µ oscfar.cfar.variable_window_cfar

def variable_window_cfar(data, guard_cells, min_window, max_window, homogeneity_threshold):

A basic implementation of a Variable Window CFAR detector using a split-window approach.

Parameters:

  • data (np.ndarray): The input signal data (1D).
  • guard_cells (int): The number of guard cells on each side of the CUT.
  • min_window (int): The minimum number of reference cells on each side.
  • max_window (int): The maximum number of reference cells on each side.
  • homogeneity_threshold (float): A threshold to determine if the reference windows are considered homogeneous.

Returns:

  • np.ndarray: A boolean array indicating detections (True) and non-detections (False).

šŸ…µ oscfar.cfar.variable_window_os_cfar_indices

def variable_window_os_cfar_indices(data, guard_cells, min_window, max_window, k_rank, homogeneity_threshold, threshold_factor):

A basic implementation of a Variable Window OS-CFAR detector returning detection indices.

Parameters:

  • data (np.ndarray): The input signal data (1D).
  • guard_cells (int): The number of guard cells on each side of the CUT.
  • min_window (int): The minimum number of reference cells on each side.
  • max_window (int): The maximum number of reference cells on each side.
  • k_rank (int): The rank of the order statistic to use for noise estimation.
  • homogeneity_threshold (float): A threshold to determine if the reference windows are considered homogeneous.
  • threshold_factor (float): Factor multiplied by the noise estimate for the threshold.

Returns:

  • np.ndarray: An array of indices where detections occurred.

šŸ…¼ oscfar.cluster

Functions

šŸ…µ oscfar.cluster.cluster_peaks

def cluster_peaks(peak_positions, peak_heights, n, max_e = 0.7):

Clusters peaks based on their positions and heights using DBSCAN.

Parameters:

  • peak_positions (list or np.ndarray): Positions of the peaks.
  • peak_heights (list or np.ndarray): Heights of the peaks.
  • n (int): Minimum number of samples in a cluster.
  • max_e (float): The maximum distance between two samples for one to be considered as in the neighborhood of the other. Defaults to 0.7.

Returns:

  • list: A list of representative peak positions, one from each cluster.

šŸ…¼ oscfar.filters

Functions

šŸ…µ oscfar.filters.remove_baseline_peaks

def remove_baseline_peaks(data, detection_indices, noise_estimates, secondary_threshold_factor = 2.0):

Removes detected peaks that are too close to the baseline using a secondary amplitude threshold.

Parameters:

  • data (np.ndarray): The original signal data.
  • detection_indices (np.ndarray): Indices of peaks detected by OS-CFAR.
  • noise_estimates (np.ndarray): Array of noise estimates corresponding to each detection.
  • secondary_threshold_factor (float): Factor multiplied by the noise estimate to set the secondary threshold.

Returns:

  • np.ndarray: Indices of the filtered detections.

šŸ…µ oscfar.filters.median_filter

def median_filter(data, kernel_size):

Applies a median filter to the 1D data.

Parameters:

  • data (np.ndarray): 1D array of input data.
  • kernel_size (int): The size of the median filter kernel. Must be a positive integer. If even, it will be incremented by 1 to ensure an odd size.

Returns:

  • np.ndarray: The median-filtered data array, same shape as input.

Raises:

  • ValueError: If input data is not a 1D numpy array, or if kernel_size is not a positive integer.

šŸ…µ oscfar.filters.lowpass_filter

def lowpass_filter(data, cutoff_freq, sampling_rate, order = 5):

Applies a low-pass Butterworth filter to the 1D data.

This uses a zero-phase filter ('filtfilt') to avoid introducing phase shifts in the filtered signal.

Parameters:

  • data (np.ndarray): 1D array of input data (e.g., time series).
  • cutoff_freq (float): The desired cutoff frequency in Hz. Frequencies above this value will be attenuated.
  • sampling_rate (float): The sampling rate of the input data in Hz. This is crucial for digital filter design.
  • order (int): The order of the Butterworth filter. Higher orders provide a steeper rolloff but can be less stable. Defaults to 5.

Returns:

  • np.ndarray: The low-pass filtered data array, same shape as input.

Raises:

  • ValueError: If input data is not a 1D numpy array, or if cutoff_freq or sampling_rate are invalid.

šŸ…µ oscfar.filters.highpass_filter

def highpass_filter(data, cutoff_freq, sampling_rate, order = 5):

Applies a high-pass Butterworth filter to the 1D data.

This uses a zero-phase filter ('filtfilt') to avoid introducing phase shifts in the filtered signal.

Parameters:

  • data (np.ndarray): 1D array of input data (e.g., time series).
  • cutoff_freq (float): The desired cutoff frequency in Hz. Frequencies below this value will be attenuated.
  • sampling_rate (float): The sampling rate of the input data in Hz. This is crucial for digital filter design.
  • order (int): The order of the Butterworth filter. Higher orders provide a steeper rolloff but can be less stable. Defaults to 5.

Returns:

  • np.ndarray: The high-pass filtered data array, same shape as input.

Raises:

  • ValueError: If input data is not a 1D numpy array, or if cutoff_freq or sampling_rate are invalid.

šŸ…µ oscfar.filters.group_close_peaks

def group_close_peaks(peak_indices, min_distance):

Groups peak indices that are close to each other.

Iterates through sorted peak indices and groups any peaks that are separated by less than or equal to 'min_distance' samples.

Parameters:

  • peak_indices (list or np.ndarray): A list or array of peak indices, assumed to be sorted or will be sorted.
  • min_distance (int): The maximum distance (in samples) between two consecutive peaks for them to be considered part of the same group.

Returns:

  • list[list[int]]: A list where each element is a list representing a group of close peak indices. Returns an empty list if no peaks are provided.

šŸ…µ oscfar.filters.find_representative_peaks

def find_representative_peaks(data, peak_indices, min_distance):

Groups close peaks and returns the index of the maximum peak from each group.

First, groups peaks that are within 'min_distance' of each other using group_close_peaks. Then, for each group, identifies the index corresponding to the highest value in the 'data' array.

Parameters:

  • data (np.ndarray): The 1D data array (e.g., time series) where peak values are found. Used to determine the max peak.
  • peak_indices (list or np.ndarray): A list or array of peak indices to be grouped and processed.
  • min_distance (int): The maximum distance (in samples) between two consecutive peaks for them to be considered part of the same group.

Returns:

  • list[int]: A list containing the index of the maximum peak from each identified group. Returns an empty list if no peaks are provided.

šŸ…µ oscfar.filters.verify_peaks_snr

def verify_peaks_snr(data, peak_indices, noise_window_factor = 3, min_snr = 3.0):

Verifies peaks based on their local Signal-to-Noise Ratio (SNR).

Calculates SNR for each peak relative to the noise estimated in adjacent windows.

Parameters:

  • data (np.ndarray): The 1D data array (e.g., time series) where peaks were detected.
  • peak_indices (list or np.ndarray): Indices of the detected peaks.
  • noise_window_factor (int): Determines the size and offset of the noise estimation windows relative to a conceptual 'peak width'. A simple proxy for peak width (e.g., 5 samples) is used internally. The noise windows will be roughly this size and offset by this amount from the peak center. Defaults to 3.
  • min_snr (float): The minimum acceptable local SNR for a peak to be considered verified. Defaults to 3.0.

Returns:

  • list: A list of indices corresponding to the verified peaks.

Raises:

  • ValueError: If input data is not a 1D numpy array.

šŸ…µ oscfar.filters.enforce_min_distance

def enforce_min_distance(raw_peak_indices, data_values, min_distance):

Refines CFAR detections to enforce a minimum distance between peaks.

Parameters:

  • raw_peak_indices: List of indices where CFAR detected a peak.
  • data_values: The original data array (or SNR array) used for sorting.
  • min_distance: The minimum allowed separation between final peaks (in indices).

Returns:

  • List of indices of the final, refined peaks.

šŸ…µ oscfar.filters.filter_peaks_by_extent_1d

def filter_peaks_by_extent_1d(peak_indices, min_extent, max_extent):

Filters a list of 1D peak indices, removing peaks that belong to consecutive groups larger than max_extent.

Parameters:

  • peak_indices (list or np.ndarray): A list or array of integer indices where peaks were detected by CFAR. Assumed to be along a single dimension.
  • max_extent (int): The maximum allowed number of consecutive indices for a valid peak group. Groups larger than this are considered extended clutter/scattering and removed.

Returns:

  • list: A list of filtered peak indices, keeping only those belonging to groups with extent <= max_extent.

šŸ…µ oscfar.filters.moving_average_filter

def moving_average_filter(data, window_size):

Applies a simple moving average filter to the 1D data.

Each point in the output is the average of the 'window_size' neighboring points in the input data (including the point itself). Uses 'same' mode for convolution, meaning the output array has the same size as the input, but edge effects might be present where the window doesn't fully overlap.

Parameters:

  • data (np.ndarray): 1D array of input data.
  • window_size (int): The number of points to include in the averaging window. Should be an odd number for a centered average, but works with even numbers too. Must be positive.

Returns:

  • np.ndarray: The smoothed data array, same shape as input.

Raises:

  • ValueError: If input data is not a 1D numpy array or if window_size is not a positive integer.

šŸ…¼ oscfar.gaussian_fit

Functions

šŸ…µ oscfar.gaussian_fit.sum_of_gaussians

def sum_of_gaussians(x, *params):

Calculates the sum of multiple Gaussian functions.

Each Gaussian is defined by its amplitude, mean, and standard deviation. The parameters for the Gaussians are provided in a flat list: [amp1, mean1, stddev1, amp2, mean2, stddev2, ..., ampN, meanN, stddevN]

Parameters:

  • x (np.array): The independent variable where the functions are calculated.
  • *params (list or np.array): A variable number of arguments representing the parameters. The total number of parameters must be a multiple of 3.
  • amp: Amplitude of the Gaussian.
  • mean: Mean (center) of the Gaussian.
  • stddev: Standard deviation (width) of the Gaussian.

Returns:

  • y (np.array): The sum of the Gaussian functions evaluated at x.

Raises:

  • ValueError: If the number of parameters in `params` is not a multiple of 3.

šŸ…µ oscfar.gaussian_fit.sum_of_scattered_gaussians

def sum_of_scattered_gaussians(x, *params):

Calculates the sum of multiple scattered Gaussian functions.

Each scattered Gaussian is defined by its amplitude, mean, standard deviation, and scattering timescale. The parameters for the scattered Gaussians are provided in a flat list: [amp1, mean1, sigma1, tau1, amp2, mean2, sigma2, tau2, ..., ampN, meanN, sigmaN, tauN]

Parameters:

  • x (np.array): The independent variable where the functions are calculated.
  • *params (list or np.array): A variable number of arguments representing the parameters. The total number of parameters must be a multiple of 4.
  • amp: Amplitude of the scattered Gaussian.
  • mean: Mean (center) of the scattered Gaussian.
  • sigma: Standard deviation (width) of the Gaussian before scattering.
  • tau: Scattering timescale.

Returns:

  • y (np.array): The sum of the scattered Gaussian functions evaluated at x.

Raises:

  • ValueError: If the number of parameters in `params` is not a multiple of 4.

šŸ…µ oscfar.gaussian_fit.find_best_multi_gaussian_fit

def find_best_multi_gaussian_fit(x_data, y_data, initial_flat_params, max_n_gaussians = None, y_err = None):

Finds the best fit to the data using a sum of Gaussian functions.

This function attempts to fit the data with a varying number of Gaussian components, up to a specified maximum. The best fit is determined by comparing the Bayesian Information Criterion (BIC) for each fit.

Parameters:

  • x_data (np.array): The independent variable where the data is measured.
  • y_data (np.array): The dependent data to be fitted.
  • initial_flat_params (list or np.array): A flat list of initial parameters for Gaussian components, ordered as [amp1, mean1, sigma1, amp2, mean2, sigma2, ...]. Amplitudes can be positive or negative.
  • max_n_gaussians (int): The maximum number of Gaussian components to try. If None, it defaults to the number of components implied by `initial_flat_params`.
  • y_err (list or np.array): Error on y_data. If provided, it's used in `curve_fit` for weighted least squares.

Returns:

  • dict: A dictionary containing the results of the fitting process. The dictionary has two keys:
  • 'best_fit': A dictionary containing the results of the best fit found (lowest BIC). It includes: - 'n_components': The number of Gaussian components in the best fit. - 'popt': The optimized parameters for the best fit. - 'pcov': The estimated covariance of popt. - 'bic': The Bayesian Information Criterion (BIC) for the best fit. - 'rss': The Residual Sum of Squares for the best fit.
  • 'all_fits': A list of dictionaries, each containing the results for a fit with a specific number of components. Each dictionary in the list has the same structure as 'best_fit', but for a different number of components.

Raises:

  • ValueError: If `initial_flat_params` is invalid (empty or not a multiple of 3), if `x_data` and `y_data` are empty or have different lengths.

šŸ…µ oscfar.gaussian_fit.find_best_multi_gaussian_fit_combinatorial

def find_best_multi_gaussian_fit_combinatorial(x_data, y_data, initial_flat_params, max_n_gaussians = None, y_err = None, max_initial_components_for_pool = None, model_to_test = 'gaussian', default_initial_tau = 0.0001, max_tau_bound_factor = 1.0, use_multiprocessing = True, num_processes = None):

Performs a grid search to find the best multi-component fit by trying

different numbers of components, different combinations of initial peak guesses, and optionally different model types (Gaussian or Scattered Gaussian).

This version supports multiprocessing to speed up the fitting process.

Args: (Same as the single-process version, plus the following:) use_multiprocessing (bool, optional): Whether to use multiprocessing. Defaults to True. num_processes (int, optional): The number of processes to use. If None, uses the number of CPU cores.

Returns: (Same as the single-process version)

Raises: (Same as the single-process version)

šŸ…¼ oscfar.reload

Functions

šŸ…µ oscfar.reload.update_version

def update_version(version):

Updates the version number in __init__.py and setup.py.

šŸ…µ oscfar.reload.update_init_version

def update_init_version(version):

Updates the version number in __init__.py.

šŸ…µ oscfar.reload.update_setup_version

def update_setup_version(version):

Updates the version number in setup.py.

šŸ…¼ oscfar.setup

šŸ…¼ oscfar.utils

Classes

šŸ…² oscfar.utils.NpzReader

class NpzReader(DataReader):

Class for reading .npz files containing spectrogram data.

Inherits from fitburst.backend.generic.DataReader.

Attributes:

  • metadata (dict): Metadata associated with the data.
  • downsampling_factor (int): Factor by which the data has been downsampled.

Functions:

šŸ…µ oscfar.utils.NpzReader.__init__

def __init__(self, fname, factor):

Initializes the NpzReader with the given file and downsampling factor.

Parameters:

  • fname (str): Path to the .npz file.
  • factor (int): Downsampling factor applied to the data.

šŸ…µ oscfar.utils.NpzReader.__repr__

def __repr__(self):

Returns a string representation of the NpzReader object.

šŸ…µ oscfar.utils.NpzReader.__str__

def __str__(self):

Returns a string representation of the NpzReader object.

šŸ…² oscfar.utils.NpzWriter

class NpzWriter:

Class for writing data to .npz files, typically after processing.

Attributes:

  • reader (NpzReader): An instance of NpzReader containing the original data.
  • burst_parameters (dict): Dictionary of burst parameters to be saved.

Functions:

šŸ…µ oscfar.utils.NpzWriter.__init__

def __init__(self, original_data: NpzReader):

Initializes the NpzWriter with the given NpzReader instance.

Parameters:

  • original_data (NpzReader): An instance of NpzReader containing the original data to be processed and saved.

šŸ…µ oscfar.utils.NpzWriter.update_burst_parameters

def update_burst_parameters(self, **kwargs):

Updates the burst parameters with the provided keyword arguments.

Parameters:

  • **kwargs: Keyword arguments representing burst parameters to update. Possible keys include:
  • 'amplitude': Amplitude of the burst.
  • 'dm': Dispersion measure of the burst.
  • 'scattering_timescale': Scattering timescale of the burst.
  • 'arrival_time': Arrival time of the burst.
  • 'burst_width': Intrinsic width of the burst.
  • 'spectral_running': Spectral index of the burst.

šŸ…µ oscfar.utils.NpzWriter.save

def save(self, new_filepath: str):

Saves the processed data and burst parameters to a new .npz file.

Parameters:

  • new_filepath (str): Path to the new .npz file where the data will be saved.

šŸ…² oscfar.utils.Peaks

class Peaks:

Class to hold results from OS-CFAR.

Attributes:

  • peaks (np.array): First half of the OS-CFAR results containing the peaks resulting from the algorithm.
  • threshold (np.array): Second half of the OS-CFAR results containing the threshold used by the algorithm.

Functions:

šŸ…µ oscfar.utils.Peaks.__init__

def __init__(self, oscfar_result):

Initializes the Peaks object with the result from OS-CFAR.

Parameters:

  • oscfar_result (tuple): A tuple containing the detected peak indices and the threshold array.

šŸ…² oscfar.utils.WaterFallAxes

class WaterFallAxes:

Class to create axes for waterfall plots (spectrograms).

Attributes:

  • _data (DataReader): DataReader object containing the spectrogram data.
  • show_ts (bool): Whether to show the time series plot.
  • show_spec (bool): Whether to show the spectrum plot.
  • im (matplotlib.axes._subplots.AxesSubplot): Axes for the spectrogram.
  • ts (matplotlib.axes._subplots.AxesSubplot): Axes for the time series plot.
  • spec (matplotlib.axes._subplots.AxesSubplot): Axes for the spectrum plot.
  • time_series (np.ndarray): Time series data (sum over frequencies).
  • freq_series (np.ndarray): Frequency series data (sum over time).

Functions:

šŸ…µ oscfar.utils.WaterFallAxes.__init__

def __init__(self, data: DataReader, width: float, height: float, bottom: float, left: float = None, hratio: float = 1, vratio: float = 1, show_ts = True, show_spec = True, labels_on = [True, True], title = '', readjust_title = 0):

Initializes the WaterFallAxes object.

Parameters:

  • data (DataReader): DataReader object containing the spectrogram data.
  • width (float): Width of the main spectrogram plot.
  • height (float): Height of the main spectrogram plot.
  • bottom (float): Bottom position of the main spectrogram plot.
  • left (float): Left position of the main spectrogram plot. Defaults to the value of 'bottom'.
  • hratio (float) (default: 1): Horizontal ratio for plot dimensions. Defaults to 1.
  • vratio (float) (default: 1): Vertical ratio for plot dimensions. Defaults to 1.
  • show_ts (bool) (default: True): Whether to show the time series plot. Defaults to True.
  • show_spec (bool) (default: True): Whether to show the spectrum plot. Defaults to True.
  • labels_on (list): List of two booleans indicating whether to show labels on the x and y axes, respectively. Defaults to [True, True].
  • title (str) (default: ""): Title of the plot. Defaults to "".
  • readjust_title (int) (default: 0): Vertical adjustment for the title position. Defaults to 0.

šŸ…µ oscfar.utils.WaterFallAxes.plot

def plot(self):

Plots the spectrogram.

šŸ…µ oscfar.utils.WaterFallAxes.plot_time_peaks

def plot_time_peaks(self, peaks: Peaks, color, show_thres = False):

Plots vertical lines on the spectrogram at the time indices of the detected peaks.

Also plots the peaks on the time series plot if it is shown.

Parameters:

  • peaks (Peaks): An object containing the peak indices and threshold.
  • color (str): Color for the vertical lines and scatter points.
  • show_thres (bool): Whether to show the threshold on the time series plot.

šŸ…² oscfar.utils.WaterFallGrid

class WaterFallGrid:

Class to create a grid of waterfall plots (spectrograms).

Attributes:

  • nrows (int): Number of rows in the grid.
  • ncols (int): Number of columns in the grid.
  • axes (np.ndarray): 2D array of WaterFallAxes objects representing the grid.
  • vs (float): Vertical spacing between plots.
  • hs (float): Horizontal spacing between plots.

Functions:

šŸ…µ oscfar.utils.WaterFallGrid.__init__

def __init__(self, nrows: int, ncols: int, vspacing = 0.1, hspacing = 0.1):

Initializes the WaterFallGrid object.

Parameters:

  • nrows (int): Number of rows in the grid.
  • ncols (int): Number of columns in the grid.
  • vspacing (float) (default: 0.1): Vertical spacing between plots. Defaults to 0.1.
  • hspacing (float) (default: 0.1): Horizontal spacing between plots. Defaults to 0.1.

šŸ…µ oscfar.utils.WaterFallGrid.plot

def plot(self, data: list, peaks: list, titles: list, color, labels = [True, False], adjust_t = 0, show_thres = False):

Plots the waterfall grid with the provided data, peaks, and titles.

Parameters:

  • data (list): List of DataReader objects, one for each subplot.
  • peaks (list): List of Peaks objects, one for each subplot.
  • titles (list): List of titles for each subplot.
  • color (str): Color for the peak markers.
  • labels (list): List of two booleans indicating whether to show labels on the x and y axes, respectively. Defaults to [True, False].
  • adjust_t (int) (default: 0): Vertical adjustment for the title position. Defaults to 0.
  • show_thres (bool): Whether to show the threshold on the time series plot.

šŸ…µ oscfar.utils.WaterFallGrid.add_info

def add_info(self, info: pd.DataFrame):

Adds a table with additional information below the grid.

Parameters:

  • info (pd.DataFrame): DataFrame containing the information to be displayed.

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BLAKE2b-256 ed2ba9ceb9a7cde516f0d8b9fe5ae7ab8aafbc32bd78355745aeb8a820f3741d

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