spectral

This module offers utilities for processing data cubes and related operations.

Module Overview

wizard._processing.spectral.smooth_savgol(spectrum, window_length=11, polyorder=2)[source]

Apply a Savitzky-Golay filter to smooth a given spectrum.

Parameters:

  • spectrum (numpy.ndarray) – Input spectrum to be smoothed.

  • window_length (int, optional) – Length of the filter window, must be a positive odd integer.

  • polyorder (int, optional) – Order of the polynomial used to fit the samples.

Returns:

Smoothed spectrum.

Return type:

numpy.ndarray

wizard._processing.spectral.smooth_moving_average(spectrum, window_size=5)[source]

Apply a moving average filter to smooth a given spectrum.

Parameters:

  • spectrum (numpy.ndarray) – Input spectrum to be smoothed.

  • window_size (int, optional) – Size of the moving window.

Returns:

Smoothed spectrum.

Return type:

numpy.ndarray

wizard._processing.spectral.smooth_butter_lowpass(spectrum, cutoff=0.1, fs=1.0, order=5)[source]

Apply a Butterworth low-pass filter to the input spectrum.

Parameters:

  • spectrum (numpy.ndarray) – Input spectrum to be filtered.

  • cutoff (float, optional) – Cutoff frequency of the filter.

  • fs (float, optional) – Sampling frequency of the input signal.

  • order (int, optional) – Order of the filter.

Returns:

Filtered spectrum.

Return type:

numpy.ndarray

wizard._processing.spectral.spec_baseline_als(spectrum, lam, p, niter=10)[source]

Perform baseline correction using Asymmetric Least Squares Smoothing.

Parameters:

  • spectrum (numpy.ndarray) – Input spectrum to be smoothed.

  • lam (float) – Smoothness parameter, typically between 10^2 and 10^9.

  • p (float) – Asymmetry parameter, usually between 0.001 and 0.1.

  • niter (int, optional) – Number of iterations.

Returns:

Smoothed baseline.

Return type:

numpy.ndarray

wizard._processing.spectral.calculate_modified_z_score(spectrum)[source]

Calculate the modified z-score of a data cube by computing the difference in intensity along the first axis.

Parameters:

spectrum (numpy.ndarray) – spectrum

Returns:

Modified z-score representing the difference in intensity along the first axis.

Return type:

numpy.ndarray

wizard._processing.spectral.get_ratio_two_specs(spectrum, waves, wave_1, wave_2)[source]

Calculate the ratio between two selected wavelengths in the spectrum.

Parameters:

  • spectrum (numpy.ndarray) – Main spectrum from which the wavelengths will be selected.

  • waves (numpy.ndarray) – Array of wavelengths for the given spectrum.

  • wave_1 (int) – First selected wavelength.

  • wave_2 (int) – Second selected wavelength.

Returns:

Ratio of the two selected wavelengths.

Return type:

numpy.ndarray

wizard._processing.spectral.get_sub_tow_specs(spectrum, waves, wave_1, wave_2)[source]

Subtract two selected wavelengths from a spectrum.

Parameters:

  • spectrum (numpy.ndarray) – Main spectrum from which the wavelengths will be selected.

  • waves (numpy.ndarray) – Array of wavelengths for the given spectrum.

  • wave_1 (int) – First selected wavelength.

  • wave_2 (int) – Second selected wavelength.

Returns:

Difference of the two selected wavelengths.

Return type:

numpy.ndarray

wizard._processing.spectral.signal_to_noise(spectrum)[source]

Calculate the signal-to-noise ratio (SNR) of a given spectrum.

Parameters:

spectrum (numpy.ndarray) – 1D array representing the intensity values of the spectrum.

Returns:

Signal-to-noise ratio (SNR) value in decibels (dB).

Return type:

float

wizard._processing.spectral.del_leading_zeros(spectrum, idx=-1, auto_offset=5)[source]

Remove leading zeros from a spectrum array.

Parameters:

  • spectrum (numpy.ndarray) – Input spectrum array.

  • idx (int, optional) – Index value for cutting.

  • auto_offset (int, optional) – Number of values to be deleted in auto mode (idx + auto_offset).

Returns:

Spectrum array with leading zeros removed.

Return type:

numpy.ndarray

wizard._processing.spectral.del_last_zeros(spectrum, idx=-1, auto_offset=5)[source]

Remove trailing zeros from a spectrum array.

Parameters:

  • spectrum (numpy.ndarray) – Input spectrum array.

  • idx (int, optional) – Index value for cutting.

  • auto_offset (int, optional) – Number of values to be deleted in auto mode (idx + auto_offset).

Returns:

Spectrum array with trailing zeros removed.

Return type:

numpy.ndarray