ramanspy
RamanSPy: An open-source Python package for integrative Raman spectroscopy data analysis
Science Score: 67.0%
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✓DOI references
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○Scientific vocabulary similarity
Low similarity (14.5%) to scientific vocabulary
Keywords
Repository
RamanSPy: An open-source Python package for integrative Raman spectroscopy data analysis
Basic Info
- Host: GitHub
- Owner: barahona-research-group
- License: bsd-3-clause
- Language: Jupyter Notebook
- Default Branch: main
- Homepage: https://ramanspy.readthedocs.io
- Size: 34 MB
Statistics
- Stars: 109
- Watchers: 4
- Forks: 24
- Open Issues: 8
- Releases: 0
Topics
Metadata Files
README.md
RamanSPy: An open-source package for Raman Spectroscopy analytics in Python.
Key features
- Common data format
- Data loaders
- Preprocessing methods
- Preprocessing pipelining
- Preprocessing protocols
- Analysis methods
- AI & ML integration
- Visualisation tools
- Datasets
- Synthetic data generator
- Metrics
Installation
RamanSPy has been published on PyPI and can be installed via pip:
console
pip install ramanspy
Code example
Below is a simple example of how RamanSPy can be used to load, preprocess and analyse Raman spectroscopic data. Here, we load a data file from a commercial Raman instrument; apply a preprocessing pipeline consisting of spectral cropping, cosmic ray removal, denoising, baseline correction and normalisation; perform spectral unmixing; and visualise the results.
``` import ramanspy as rp
load data
image_data = rp.load.witec("
apply a preprocessing pipeline
pipeline = rp.preprocessing.Pipeline([ rp.preprocessing.misc.Cropper(region=(700, 1800)), rp.preprocessing.despike.WhitakerHayes(), rp.preprocessing.denoise.SavGol(windowlength=9, polyorder=3), rp.preprocessing.baseline.ASPLS(), rp.preprocessing.normalise.MinMax() ]) data = pipeline.apply(imagedata)
perform spectral unmixing
nfindr = rp.analysis.unmix.NFINDR(n_endmembers=5) amaps, endmembers = nfindr.apply(data)
plot results
rp.plot.spectra(endmembers) rp.plot.image(amaps) rp.plot.show() ```
Documentation
For more information about the functionalities of the package, refer to the online documentation.
Credits
If you use RamanSPy for your research, please cite our paper:
bibtex
@article{georgiev2024ramanspy,
title={RamanSPy: An open-source Python package for integrative Raman spectroscopy data analysis},
author={Georgiev, Dimitar and Pedersen, Simon Vilms and Xie, Ruoxiao and Fern{\'a}ndez-Galiana, Alvaro and Stevens, Molly M and Barahona, Mauricio},
journal={Analytical Chemistry},
volume={96},
number={21},
pages={8492-8500},
year={2024},
doi={10.1021/acs.analchem.4c00383}
}
Also, if you find RamanSPy useful, please consider leaving a star on GitHub.
Owner
- Name: Barahona Research - Applied Math - Imperial
- Login: barahona-research-group
- Kind: organization
- Email: m.barahona@imperial.ac.uk
- Website: https://scholar.google.co.uk/citations?user=weulBoAAAAAJ&hl=en
- Repositories: 9
- Profile: https://github.com/barahona-research-group
Research codes developed in the Barahona research group - Department of Mathematics - Imperial College London
Citation (CITATION.cff)
cff-version: 1.2.0
message: "If you use this software, please cite it as follows."
authors:
- family-names: Georgiev
given-names: Dimitar
title: "RamanSPy"
repository-code: "https://github.com/barahona-research-group/RamanSPy"
preferred-citation:
type: article
authors:
- family-names: Georgiev
given-names: Dimitar
- family-names: Pedersen
given-names: Simon Vilms
- family-names: Xie
given-names: Ruoxiao
- family-names: Fernández-Galiana
given-names: Álvaro
- family-names: Stevens
given-names: Molly M.
- family-names: Barahona
given-names: Mauricio
doi: "10.26434/chemrxiv-2023-m3xlm"
journal: "ChemRxiv"
title: "RamanSPy: An open-source Python package for integrative Raman spectroscopy data analysis"
url: "https://chemrxiv.org/engage/chemrxiv/article-details/64a53861ba3e99daef8c9c51"
year: 2023
GitHub Events
Total
- Issues event: 6
- Watch event: 50
- Issue comment event: 11
- Push event: 2
- Pull request event: 5
- Fork event: 12
Last Year
- Issues event: 6
- Watch event: 50
- Issue comment event: 11
- Push event: 2
- Pull request event: 5
- Fork event: 12
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 3
- Total pull requests: 4
- Average time to close issues: 7 days
- Average time to close pull requests: 7 months
- Total issue authors: 1
- Total pull request authors: 4
- Average comments per issue: 2.0
- Average comments per pull request: 1.25
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 3
- Pull requests: 2
- Average time to close issues: 7 days
- Average time to close pull requests: 12 minutes
- Issue authors: 1
- Pull request authors: 2
- Average comments per issue: 2.0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- ankit7540 (3)
- RobertASu1 (2)
- InnocenteSimone (1)
- hughhop (1)
- Omnistic (1)
- phoebe-sch (1)
Pull Request Authors
- dgeorgiev21 (4)
- nihauc12 (1)
- gspeed0689 (1)
- Alvaro-FG (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 2,574 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 16
- Total maintainers: 1
pypi.org: ramanspy
RamanSPy: An open-source Python package for integrative Raman spectroscopy data analysis
- Documentation: https://ramanspy.readthedocs.io
- License: BSD 3-Clause License Copyright (c) 2023, Dimitar Georgiev Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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Latest release: 0.2.10
published over 1 year ago
Rankings
Maintainers (1)
Dependencies
- actions/checkout v3 composite
- actions/setup-python v3 composite
- cvxopt *
- matplotlib *
- numpy *
- pandas *
- pybaselines *
- pysptools *
- renishawWiRE *
- scikit-learn *
- scipy *
- wget *