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.