beads.cpp File Reference

Baseline estimation and subtraction using Baseline Estimation And Denoising using Sparsity(BEADS)(implementation). More...

#include <algorithm>
#include <cmath>
#include <functional>
#include "../misc/convolve.h"
#include "../misc/diff.h"
#include "../misc/spdiags.h"
#include "beads.h"

Go to the source code of this file.

Functions
const std::tuple< std::vector< double >, std::vector< double > >	sablib::BaselineBeads (const std::vector< double > &y, const unsigned int s, const double frequency, const double r, const double lambda0, const double lambda1, const double lambda2, const unsigned int loop=30, const double eps=1e-3, const BeadsPenalty penalty=BeadsPenalty::L1_v2)
	Performs baseline estimation and denoising using Sparsity (BEADS).
const std::vector< double >	sablib::BeadsExpandBoundaries (const std::vector< double > &y, const unsigned int n=400)
	Expands the signal boundaries by padding with a tapered sequence.
const std::vector< double >	sablib::BeadsTrimBoundaries (const std::vector< double > &y, const unsigned int n=400)
	Trims the expanded signal boundaries.

Detailed Description

Baseline estimation and subtraction using Baseline Estimation And Denoising using Sparsity(BEADS)(implementation).

Author

Izadori

Note

This file includes code derived from Duval's MATLAB implemetation. Original MATLAB code is licensed under BSD 3-Clause License.

Definition in file beads.cpp.

Macro Definition Documentation

_USE_MATH_DEFINES

#define _USE_MATH_DEFINES

Definition at line 38 of file beads.cpp.

Function Documentation

BaselineBeads()

const std::tuple< std::vector< double >, std::vector< double > > sablib::BaselineBeads	(	const std::vector< double > &	y,
		const unsigned int	s,
		const double	frequency,
		const double	r,
		const double	lambda0,
		const double	lambda1,
		const double	lambda2,
		const unsigned int	loop = 30,
		const double	eps = 1e-3,
		const BeadsPenalty	penalty = BeadsPenalty::L1_v2 )

Performs baseline estimation and denoising using Sparsity (BEADS).

Parameters

y	The input data.
s	Order of the derivative for baseline sparsity (typically 1 or 2).
frequency	Sampling frequency of the signal.
r	High-pass filter parameter (cut-off frequency relative to sampling frequency).
lambda0	Sparsity parameter for the baseline.
lambda1	Sparsity parameter for the first-order derivative of the signal.
lambda2	Sparsity parameter for the second-order derivative of the signal.
loop	Maximum number of iterations.
eps	Convergence threshold.
penalty	Penalty type (L1_v1 or L1_v2).

Returns

A tuple containing (baseline, denoised signal).

Exceptions

std::invalid_argument

One or more parameters are wrong.

Definition at line 101 of file beads.cpp.

BeadsExpandBoundaries()

const std::vector< double > sablib::BeadsExpandBoundaries	(	const std::vector< double > &	y,
		const unsigned int	n = 400 )

Expands the signal boundaries by padding with a tapered sequence.

Parameters

y	The input data vector.
n	The number of elements to add at each end.

Returns

A expanded vector.

Exceptions

std::invalid_argument

The length of y is zero.

Definition at line 257 of file beads.cpp.

BeadsTrimBoundaries()

const std::vector< double > sablib::BeadsTrimBoundaries	(	const std::vector< double > &	y,
		const unsigned int	n = 400 )

Trims the expanded signal boundaries.

Parameters

y	The input data vector (expanded signal).
n	The number of elements to trim from each end.

Returns

A trimmed vector.

Exceptions

std::invalid_argument

The length of y is zero or less than `2 * n`.

Definition at line 282 of file beads.cpp.