rainbow-api 1.0.16

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

Agilent .dx (OpenLab CDS)

• .UV - DAD spectrum
• .CH - single-wavelength UV/DAD signals
• .IT - instrument telemetry, as analog data (parse with telemetry=True)

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

Prebuilt wheels include an optional compiled accelerator (see Performance); installation never requires a compiler, and rainbow works the same with or without it.

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.

Performance

Decoding Agilent diode-array (DAD) .uv files is the one hot spot in the library: each file holds a large retention-time × wavelength grid of delta-encoded absorbances, and the decoding is inherently sequential, so it cannot be vectorized with NumPy. rainbow ships an optional compiled extension (rainbow/agilent/_uvdelta.pyx, built with Cython) that runs this inner loop in C, decoding large DAD files roughly 100× faster while producing bit-identical results.

The accelerator is entirely optional:

• Prebuilt wheels on PyPI already include it, so pip install rainbow-api gives you the fast path with no compiler needed.
• If you install from source without a compiler (or without Cython), the build simply skips the extension and rainbow falls back to a pure-Python decoder with identical output. You can check which path is active with rainbow.agilent.chemstation._uvdelta_fast is not None.

Other formats (.ch channels, .ms, MassHunter) are already fast and do not use the accelerator.

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.

For development, an editable install (pip install -e .) compiles the optional accelerator in place if a C compiler and Cython are available; otherwise the pure-Python fallback is used. The parity between the two paths is checked by tests/test_accelerator.py.