msalign: Signal calibration and alignment by reference peaks
Project description
msalign - signal calibration and alignment
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).
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