This package was inspired by MATLAB's msalign function which allows alignment of multiple signals to reference peaks.
Install from PyPi
pip install msalignInstall directly from GitHub
pip install -e git+https://github.com/lukasz-migas/msalign.gitInstall in development mode
python setup.py developUsage is relatively straightforward. Simply import msalign from the package and provide x, array
and peaks values. msalign accepts a lot of other parameters that might improve your alignment - simply provide them
as keyword parameters.
import numpy as np
from msalign import msalign
filename = r"./example_data/msalign_test_data.csv"
data = np.genfromtxt(filename, delimiter=",")
x = data[1:, 0]
array = data[1:, 1:].T
peaks = [3991.4, 4598, 7964, 9160]
aligned = msalign(x, array, peaks, weights=[60, 100, 60, 100], only_shift=False)
Zoom-in on each peak the spectrum was aligned against
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).
If you find msalign useful in your research and wish to cite it, please use the following BibTex entry:
@software{msalign2024,
author = {Lukasz G. Migas},
title = {{msalign}: Spectral alignment based on MATLAB's `msalign` function.},
url = {https://github.com/lukasz-migas/msalign},
version = {0.2.0},
year = {2024},
}