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A Python package for processing on-line gas chromatography data. ChromStream provides tools to parse, analyze, and visualize chromatographic data from various GC systems, and combine it with data from logfiles such as temperature and pressure.

Features

  • Parse chromatographic data from multiple formats:
    • Chromeleon (exported txt)
    • Agilent .d directories
    • Agilent .dx files
    • ChromStream HDF5 experiment files
  • Access to data at experiment, channel and chromatogram level
  • Quick plotting of chromatograms
  • Small selection of baseline corrections, possibility to use custom ones
  • Integration using a dict of peaks
  • Addition of logfiles
  • Export experiments to a compact HDF5 format

Installation

Installing using pip

pip install ChromStream

Install using uv

If you're using uv for fast Python package management:

uv add ChromStream

Quick Start

Check the Quickstart Notebook to see a full demonstration of the most important features of the package. Here's a simple example of how to set up an experiment, add chromatograms and plot them:

import chromstream as cs

exp = cs.Experiment(name='hello there')
exp.add_chromatogram('path-to-your-chromatogram') #loop over files to add multiple
exp.plot_chromatograms()

To access specific channels: 

exp.channels['channel-name'].plot()

For specific chromatograms:

exp.channels['channel-name'].chromatograms[0].plot()

Supported File Formats

ChromStream currently supports parsing data from:

  • Chromeleon software exports (.txt)
  • Agilent .d directories and .dx files
  • ChromStream HDF5 experiment files (.h5)
  • simple log files (e.g. exported from labview)

ChromStream can also export Experiment objects to HDF5 and load them back again:

import chromstream as cs

exp = cs.Experiment(name="example")
exp.add_mult_chromatograms("path-to-run.dx")
exp.to_hdf5("example.h5")

loaded = cs.parse_experiment_hdf5("example.h5")

Documentation

  • You can find the full documentation of the package here.

Example Notebooks

Check out the example_notebooks/ directory for comprehensive examples:

  • example_calibration.ipynb - GC calibration procedures
  • cracking_example.ipynb - full procedure for analyzing a cracking dataset
  • exporting_hdf5.ipynb - brief example showing HDF5 export and re-loading

Roadmap

  • Support for more files formats
  • Addition of more data sources such as spectroscopy
  • JSON persistence
  • tests

Contributing

This package is in active development. Any help is appreciated. You can submit feature requests or bug reports as issues on the repository. If you have a specific file format which presently is nto supported please provide an example file. PRs are more than welcome.

Authors

Sebastian Rejman - Fritz-Haber-Institute / Utrecht University