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msalign

Python implementation of MATLAB's msalign function

https://github.com/lukasz-migas/msalign

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.4%) to scientific vocabulary

Keywords from Contributors

geospatial-data transformation hmm md reaction best-practices networking test-automation medical-imaging surrogate
Last synced: 10 months ago · JSON representation

Repository

Python implementation of MATLAB's msalign function

Basic Info
Statistics
  • Stars: 11
  • Watchers: 1
  • Forks: 1
  • Open Issues: 11
  • Releases: 0
Created about 7 years ago · Last pushed 11 months ago
Metadata Files
Readme License

README.md

msalign - signal calibration and alignment

Tests codecov CodeFactor Netlify Status

Wheel PyPI Versions Downloads

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

Installation

Install from PyPi

python pip install msalign

Install directly from GitHub

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

Install in development mode

python python setup.py develop

Usage

Usage 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.

```python import numpy as np from msalign import msalign

filename = r"./exampledata/msaligntest_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) ```

spectrum

Zoom-in on each peak the spectrum was aligned against

peaks

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

Citing msalign

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}, }

Owner

  • Name: Lukasz Migas
  • Login: lukasz-migas
  • Kind: user
  • Location: Delft, NL
  • Company: Delft University of Technology

Postdoctoral Researcher at TU Delft. Interested in native and imaging mass spectrometry.

GitHub Events

Total
  • Watch event: 3
  • Delete event: 2
  • Push event: 13
  • Pull request event: 4
  • Create event: 1
Last Year
  • Watch event: 3
  • Delete event: 2
  • Push event: 13
  • Pull request event: 4
  • Create event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 140
  • Total Committers: 4
  • Avg Commits per committer: 35.0
  • Development Distribution Score (DDS): 0.1
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Lukasz Migas l****s@y****m 126
Renovate Bot b****t@r****m 7
ImgBotApp I****p@g****m 4
pre-commit-ci[bot] 6****] 3
Committer Domains (Top 20 + Academic)
renovateapp.com: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 12
  • Total pull requests: 45
  • Average time to close issues: 3 months
  • Average time to close pull requests: 4 months
  • Total issue authors: 6
  • Total pull request authors: 4
  • Average comments per issue: 0.25
  • Average comments per pull request: 0.73
  • Merged pull requests: 18
  • Bot issues: 1
  • Bot pull requests: 40
Past Year
  • Issues: 0
  • Pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 2
View more stats
Top Authors
Issue Authors
  • lukasz-migas (7)
  • lisemureau (1)
  • ranabanik (1)
  • Shivangi1010 (1)
  • renovate[bot] (1)
  • komodovaran (1)
Pull Request Authors
  • renovate[bot] (37)
  • lukasz-migas (5)
  • imgbot[bot] (4)
  • pre-commit-ci[bot] (3)
Top Labels
Issue Labels
enhancement (6) bug (1)
Pull Request Labels
enhancement (2) bug (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 596 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 16
  • Total maintainers: 1
pypi.org: msalign

msalign: Signal calibration and alignment by reference peaks

  • Versions: 16
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 596 Last month
Rankings
Dependent packages count: 10.1%
Stargazers count: 20.4%
Average: 20.5%
Downloads: 20.5%
Dependent repos count: 21.5%
Forks count: 29.8%
Maintainers (1)
lukasz-migas
Last synced: 11 months ago

Dependencies

requirements.txt pypi
  • markdown-changelog *
  • mkdocs *
  • mkdocs-material *
.github/workflows/ci.yml actions
  • actions/checkout v2 composite
  • actions/checkout master composite
  • actions/setup-python v2 composite
  • actions/setup-python v1 composite
  • codecov/codecov-action v1 composite
  • pypa/gh-action-pypi-publish master composite
pyproject.toml pypi
setup.py pypi