zapit-Python-Bridge

Interface for controlling a running Zapit MATLAB instance from Python. The scanner and sample calibration are performed in MATLAB. The rest of the operations can be performed via Python.

Installing

pip install zapit-Python-Bridge

Example

Then in iPython:

import zapit_python_bridge.bridge as zpb
from importlib import reload

# Create an instance of the bridge object
hZP = zpb.bridge()

# Interact
hZP.is_stimConfig_loaded()
hZP.num_stim_cond()

hZP.send_samples()
hZP.stop_opto_stim


hZP.send_samples(conditionNum=2,laserOn=0)
hZP.stop_opto_stim()

If you need to reload the module for development purposes, you must first delete the running class instance or it will hang when it next tries to connect:

In [1]: hZP.release_matlab()
Disconnecting from MATLAB

In [2]: reload(zpb)
Out[2]: <module 'zapit_python_bridge.bridge' from 'D:zapit-python-bridge\\zapit_python_bridge\\bridge.py'>

In [3]: hZP = zpb.bridge()
Attempting MATLAB connection...
Connected!

Minimal example for running an experiment

See examples directory

python minimal_experiment_example.py

Connecting to the zapit session: minimal example

In MATLAB:

 >> matlab.engine.shareEngine('zapit')

(Note, if this works you can set the openPythonBridgeOnStartup setting in your Zapit config file to true. This will open run the above line each time Zapit starts).

In iPython:

import matlab.engine
eng = matlab.engine.connect_matlab('zapit')

Make sure you have set up and calibrated everything in Zapit. Now in Python you can do:

hZP = eng.workspace['hZP']
hZPview = eng.workspace['hZPview']
eng.eval('hZP.stimConfig.plotChanSamples(2)',nargout=0)

# OR
SC = eng.subsref(hZP, {'type':'.','subs':'stimConfig'})
eng.plotChanSamples(SC, 1, nargout=0)


eng.sendSamples(hZP,  nargout=0)
eng.stopOptoStim(hZP,  nargout=0)