http://www.nowack.lassp.cornell.edu/
Python code package for measurements done in the Nowack lab at Cornell.
Anaconda, Python 3
Download the repository and run python runme.py.
This will install most required packages using pip.
Other packages that require manual installation include:
- ziPython (https://www.zhinst.com/downloads)
- NI DAQmx (http://sine.ni.com/nips/cds/view/p/lang/en/nid/10181)
- PyANC350 (https://github.com/nowacklab/PyANC350)
Installation is non-standard because the package is under constant development.
The normal mode of operation is to make edits to the local GitHub repository containing this package and always run from that version of the code.
runme.py will add this directory to the PYTHONPATH and enable import via import Nowack_Lab.
This import command runs a setup script, which can be tailored to each user.
To allow Anaconda to import the package, we create a github.pth file in the Anaconda site-packages directory (C:\Anaconda3\Lib\site-packages), containing the path to the GitHub directory (e.g. C:\Users\Hemlock\Documents\GitHub).
Adds a some padding to the bottom of the jupyter notebook.
There are two main types of objects used in this package: Instrument and Measurement.
An Instrument is an object with methods (mainly in the form of properties) that handle all communication with the instrument.
For example, to read and to change the time constant on an SR830 lock-in amplifier:
from Nowack_Lab import *
lockin = SR830(3) # 3 == GPIB address
lockin.frequency # property that communicates with SR830 and returns frequency in Hz
>> 123
lockin.frequency = 456 # property that communicates with SR830 and sets frequency in Hz
lockin.frequency
>> 456
A Measurement is an object that accepts a dictionary of many different Instrument objects and, when it is run(), executes a series of commands sent to each Instrument. The Measurement will plot the results using matplotlib and save data using both the JSON and HDF5 formats. Specifically, the JSON file contains all information pertinent to the setup of the Measurement, as well as the status of all Instruments involved in the measurement at the time of saving. The HDF5 compresses large numpy arrays into a compact file size. Loading is nearly instantaneous with the Measurement.load command, restoring the Measurement object to the state it was in at the time of saving, enabling quick and easy replotting of the collected data (but no control over the Instruments).
The basic construction of a Measurement is illustrated below, in which we plot the magnitude of the signal from an SR830 lock-in amplifier versus time:
import Nowack_Lab
import time
class BasicMeasurement(Measurement):
instrument_list = ['lockin']
def __init__(self, instruments={}, t=60, delay=1):
'''
A basic measurement to record lockin signal versus time.
Arguments:
instruments (dict) - dictionary of instrument objects
t (float) - total time to monitor lockin (s)
delay (float) - delay (s)
'''
super().__init__(instruments=instruments) # implicitly adds all instruments as attributes
self.t = t
self.delay = delay
self.V = np.array([])
def do(self):
'''
Do the measurement without saving.
We do not normally call do(); it is called within run().
'''
tstart = time.time()
while time.time()-tstart < self.t:
self.V = np.append(self.V, self.lockin.R)
time.sleep(self.delay)
To run this measurement, we execute the following:
lockin = SR830(3)
instruments = {
'lockin': lockin
}
m = BasicMeasurement(instruments, t=30)
m.run()
Note that we use the run() command, because it contains commands always run before and after the do(), and because it places the do() in a safely-keyboard-interruptable try-except block.
For this basic example, we will see no output for 30 seconds, and then the program will terminate.
The data will be saved locally, and you can now interact with the object (in this example, examine the m.V array).
In most of our Measurements, we have implemented live plotting.
We normally run in a Jupyter kernel, and each Measurement hangs up the kernel.
We are looking into ways to free up the kernel by having the Measurements run in the background.
Under construction...
Will include information and guidelines regarding:
- Save directory structure
- Creating new instruments and measurements
- And more...
- Matt Ferguson - GitHub
- Alex Jarjour - GitHub
- David Low - GitHub
- Katja Nowack - GitHub, External Website
- Guen Prawiroatmodjo - GitHub, External Website
- Rachel Resnick
- Brian Schaefer - GitHub