seabreeze-opentrons 0.1.1

Python interface module for Ocean Optics spectrometers. This software is not associated with Ocean Optics. Use it at your own risk. Modified by Michael Carter for use with Amassian Research Group Opentrons.

Python module for Ocean Optics spectrometers

Python-seabreeze is the easy way to access your Ocean Optics spectrometers from python. It wraps the SeaBreeze library provided by Ocean Optics to communicate with the spectrometer. It also provides a pyUSB based reimplementation of SeaBreeze for easy extension. This software is not associated with Ocean Optics. Use it at your own risk.

DOCUMENTATION ON RTD

You'll find the documentation and more detailed information here https://python-seabreeze.readthedocs.io/en/latest/

Changes

The changelog can be found here CHANGELOG.md

Install

# via pypi
pip install seabreeze-opentrons
seabreeze_os_setup

Usage

The following example shows how simple it is to acquire a spectrum with python-seabreeze through the model independent Spectrometer class. For a more detailed description read the documentation:

>>> from seabreeze.spectrometers import Spectrometer
>>> spec = Spectrometer.from_first_available()
>>> spec.integration_time_micros(20000)
>>> spec.wavelengths()
array([  340.32581   ,   340.70321186,   341.08058305, ...,  1024.84940994,
        1025.1300678 ,  1025.4106617 ])
>>> spec.intensities()
array([  1.58187931e+01,   2.66704852e+04,   6.80208103e+02, ...,
         6.53090172e+02,   6.35011552e+02,   6.71168793e+02])

To use the pyseabreeze backend (requires pyusb) simply run this before importing seabreeze.spectrometers.

>>> import seabreeze
>>> seabreeze.use('pyseabreeze')
>>> import seabreeze.spectrometers as sb

Supported Devices

Spectrometer	cseabreeze	pyseabreeze
HR2000	x	x
HR2000PLUS	x	x
HR4000	x	x
JAZ	x	x
MAYA2000	x	x
MAYA2000PRO	x	x
MAYALSL	x	x
NIRQUEST256	x	x
NIRQUEST512	x	x
QE65000	x	x
QE-PRO	x	x
STS	x	x
TORUS	x	x
USB2000	x	x
USB2000PLUS	x	x
USB4000	x	x
USB650		Issue #47
SPARK	x	x

Known Issues

• USB2000 spectrometers cause Data transfer error due to old firmware Issue #48
• USB650 not supported Issue #47
• No conda packages for armv6 (RPI version 1) Issue #46

Contributing Guidelines

If you run into any problems, file an issue and be sure to include the following in your report:

• Operating system (Linux distribution, Windows version, OSX version) and archictecture (32bit, 64bit, arm)
• Python version and arch (i.e. Python 2.7.10 64bit)
• python-seabreeze version

If you want a feature implemented, please file an issue, or create a pull request when you implement it yourself. And if you would like to support me via paypal, click on the paypal donate button on top of this README.

License

Files in this repository are released under the MIT license.

Related Repositories

If you want me to add your project here, let me know. Happy to add it.

• python-seatease by @jonathanvanschenck - a software emulator of python-seabreeze. Emulates seabreeze's behavior so for testing my code without access to a spectrometer.
• python-seabreeze-server by @jonathanvanschenck - a TCP-based server to host the seabreeze.cseabreeze backend, allowing multiple clients (potentially offsite) to interact with a single spectrometer.
• SeaBreeze - Ocean Optics' SeaBreeze C library.
• libseabreeze - github clone of the C library. internal use only (has pre-built libraries if you know what you're doing)
• python-seabreeze-feedstock - anaconda feedstock for automated package deployment. internal use only
• yaqd-seabreaeze - A seabreeze interface for the yaq instrument control framework