fujitsu-systems-europe-fse / rainbow

Read chromatography and mass spectrometry binary files.

rainbow

rainbow provides programmatic access to the raw data encoded in chromatography and mass spectrometry binary files. This library supports the following vendors and detectors:

Agilent .D

• .uv - UV spectrum (supports incomplete files)
• .ch - UV, FID, CAD, and ELSD channels
• .ms - MS (supports incomplete files)
• MSProfile.bin - HRMS

Waters .raw

• CHRO - CAD and ELSD, as well as miscellaneous analog data
• FUNC - UV and MS

There is documentation for rainbow that also details the structure of each binary file format.

Installation

pip install rainbow-api

Usage

The easiest way to get started is to give rainbow a directory path. Assume that we have a directory mydata.D that contains a binary file DAD1.uv with UV data.

import rainbow as rb
datadir = rb.read("mydata.D")
datafile = datadir.get_file("DAD1A.uv")

Here, the datadir DataDirectory object contains a DataFile object for DAD1A.uv. The raw UV data is contained in numpy arrays that are attributes of datafile. Users may find the following particularly useful:

• datafile.xlabels - 1D numpy array with retention times
• datafile.ylabels - 1D numpy array with wavelengths
• datafile.data - 2D numpy array with absorbances

There is a tutorial available. There are also example snippets for basic tasks. Or just check out the full API.

Contents

• rainbow/ contains the code of the Python library.
• docs/ contains code for generating documentation. To build documentation locally, you will need to install the sphinx and sphinx-rtd-theme packages. Then, move to the docs/ directory and run make html. The docpages will be generated under docs/_build.
• tests/ contains unit tests for the library. These can be run with python -m unittest.