hybridizer_python

This Python package (hybridizer) creates a class named Hybridizer to communcate with and control the Janelia Hybridizer. The hybridizer uses two hardware control devices, the mixed_signal_controller modular_device, and the bioshake_device. The mixed_signal_controller both switches the valves and reads the analog signals from the cylinder hall effect sensors. The bioshake_device controls the heater/shaker.

Authors:

Peter Polidoro <[email protected]>

License:

BSD

##Example Usage

Example Config File

Open a terminal and enter:

source ~/virtualenvs/hybridizer/bin/activate
hybridzer example_calibration.yaml example_config.yaml

##Installation

Setup Python

####Debian-based Linux Install Dependencies

Open a terminal and enter:

sudo apt-get install git python-pip python-virtualenv python-dev build-essential -y

###Linux and Mac OS X

Open a terminal and enter:

mkdir ~/git
cd ~/git
git clone https://github.com/janelia-idf/hybridizer_config.git
git clone https://github.com/janelia-idf/hybridizer.git
cd hybridizer
git submodule init
git submodule update
cd ~
mkdir ~/virtualenvs
cd ~/virtualenvs
virtualenv hybridizer
source ~/virtualenvs/hybridizer/bin/activate
pip install hybridizer

On linux, you may need to add yourself to the group 'dialout' in order to have write permissions on the USB port:

Open a terminal and enter:

sudo usermod -aG dialout $USER
sudo reboot

###Windows

Open a terminal and enter:

virtualenv C:\virtualenvs\hybridizer
C:\virtualenvs\hybridizer\Scripts\activate
pip install ipython
pip install hybridizier