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msalign: Signal calibration and alignment by reference peaks

Project description

msalign - signal calibration and alignment

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This package was inspired by MATLAB's msalign function which allows alignment of multiple signals to reference peaks.

Installation

pip install msalign

or

pip install git+https://github.com/lukasz-migas/msalign.git

Usage

Usage is relatively straightforward. Simply import the function msalign from the package and provide xvals, zvals and peaks. Other parameters can be passed-in using kwargs.

import numpy as np
from msalign import msalign


fname = r"./example_data/msalign_test_data.csv"
data = np.genfromtxt(fname, delimiter=",")
xvals = data[1:, 0]
zvals = data[1:, 1:].T

peaks = [3991.4, 4598, 7964, 9160]
kwargs = dict(
    iterations=5,
    weights=[60, 100, 60, 100],
    resolution=100,
    grid_steps=20,
    ratio=2.5,
    shift_range=[-100, 100],
    )

zvals_new = msalign(xvals, zvals, peaks, **kwargs)

Reference

Monchamp, P., Andrade-Cetto, L., Zhang, J.Y., and Henson, R. (2007) Signal Processing Methods for Mass Spectrometry. In Systems Bioinformatics: An Engineering Case-Based Approach, G. Alterovitz and M.F. Ramoni, eds. Artech House Publishers).

MATLAB's msalign

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