Python for Scientists

A. DewesQuantronics Group Seminar

Python: Qu'est-ce que c'est?

A high-level programming

language …… with a simple &

easy to learn syntax… … a huge

standard library … … and packages for

mathematics, data processing, UI

design …

print “Easy as…“for i in [1,2,3]: print i

Matplotlib,SciPy,NumPy,PyQT,…

ctypes,sockets,files,regex,…

Multi-paradigm (object oriented, functional…)

Why to use it: A Scientific Workflow

Experiment(Re-)Design

DataAcquisition

DataAnalysis

Presentation & Visualization

Software makes life easier…

Experiment(Re-)Design

Data Acquisition

Labview, TestPoint, C++

Data Analysis

Mathlab, Mathematica

Presentation & Visualization

Origin, …

Experiment(Re-)Design

Data Acquisition

PyVisa, ctypes, …

Data Analysis

NumPy, SciPy, …

Presentation & Visualization

Mathplotlib, PyQt, …

Using Python…

Data Acquisition

PyVisa•Wrapper library for NI-Visa

interface•Allows to easily control

instruments via GPIB, VXI, TCP/IP...

ctypes•Library for calling C DLL

functions•Allows to control all kinds of

external libraries (e.g. Acqiris card)

http://pyvisa.sourceforge.net http://docs.python.org/library/ctypes.html

PyVisa Example: MWG & VNA

Keypoints•Clear, object-oriented interface•Directly process & analyze measured data•Fast, flexible programming•Not too much worrying about technical details…•VNA example uses PyQt for the user interface

from visa import *#Open a connection to an Anritsu MWGanritsu = instrument(“GPIB0::12“)#Ask for the output frequencyprint anritsu.ask(“OF1“)#Set the output poweranritsu.write(“L15DM“)#Turn on the microwaveanritsu.write(“RF0“)

VNA Frontpanel

vna = instrument(„GPIB0::15“)x = vna.ask_for_values(“fma;ofv;“)y = vna.ask_for_values(“fma;ofd;“)

ctypes Example: Taming an Acqiris card

from pylab import *;from ctypes import *

vi_session = c_uint32()temperature = c_int32() time_us = c_int32() timestamp = c_int32() nsegments_returned = c_int32()npoints_returned = c_int32()

acqiris = windll.LoadLibrary(r‘C:\projects\python\pylab\instruments\dllAcqiris.dll‘)acqiris.FindDevicesV1(byref(vi_session),byref(temperature))

#Configuration...

acqiris.AcquireV1(vi_session,1,byref(time_us))

waveforms = zeros((4,250 *100))

acqiris.DMATransferV1(vi_session,15,100,250,0,1,4e-9, byref(timestamp),waveforms[0,:].ctypes.data,waveforms[1,:].ctypes.data,waveforms[2,:].ctypes.data,waveforms[3,:].ctypes.data,byref(time_us),byref(nsegments_returned),byref(npoints_returned))

#Waveform data now is stored in „waveforms“ array and can be processed, e.g. apply FFT & plot:plot(range(len(waveforms[0,:])),fft(waveforms[0,:]))

Objective: Load the external DLL, transfer some measurement data and process it on the fly.

Data Analysis

SciPy•Free collection of algorithms

and tools•Tools for optimization, (fast)

linear algebra, signal processing, …

NumPy•High-level interface for

handling large arrays & matrices

•Based on highly optimized & fast C code

http://www.scipy.org http://numpy.scipy.org

SciPy & NumPy Exampleimport scipy.optimize

#Define the model to be fittedfitfunc = lambda p, x: p[0]+p[1]*

exp(-x*abs(p[2]))*cos(p[3]+p[4]*x)

#Define the error functionerrfunc = lambda p, x, y: fitfunc(p, x) – y

#Make a fit by minimizing the error functionp1 = scipy.optimize.fmin(lambda p,x,y: norm(errfunc(p,x,y)), p0, args=(data [:,0], data[:,1]))

#Print the returned parametersprint p1

#Plot the data and the fit…plot(data[:,0], data[:,1], "ro", data[:,0],

fitfunc(p1, data[:,0]), "b-")

#Add a legendlegend(("data","fit"))

#Add a titletitle("Ramsey - $V_{fluxline}= %d mV$,

$T_2 = %d$ ns, $A = %f$ " % (int(voltage) , abs(int(1.0/p1[2])),p1[1]))

Presentation & VisualizationMathplotlib•Easy to use, powerful

plotting library•Generates publication quality

output•Mathlab-like interface

PyQT•Free-to-use, cross-platform

user interface development kit

•Easy to learn, flexible and versatile

http://matplotlib.sourceforge.net/ http://qt.nokia.com/

Matplotlib Examplesgrid() #Add grid lines to the plot#Plot 4 datasetsplot(x1,y1,x2,y2,x3,y3,x4,y4)#Add a legend

legend((“Amplification …“,“…“))

#Set the axis labelsxlabel(“frequency [GHz]“)ylabel(“attenuation [dB]“)

#Save the figure as a PDFsavefig(“attenuation.pdf“)

jet() #Select a color sheme

#Plot the matriximshow(dataMatrix ,aspect = 'auto',origin = 'lower',extent = (xmin,xmax,ymin,ymax))

xlabel("$A$ [V]")ylabel("$f$ [GHz]")

#Use Latex for text…title("Qubit 1 – Modulated by $V_{flux2} = A \cdot \sin{(20 MHz \cdot 2\pi t)}$")

Some more examples…

PyQT Example: Instrument frontpanelstitle = QLabel(„Qubit 1") splitter = QSplitter(Qt.Horizontal)

SetButton = QPushButton("Set") splitter.addWidget(SetButton)

#... grid = QGridLayout(self)grid.addWidget(title,0,0)grid.addWidget(QLabel("Voltage"),1,0)#...self.connect(SetButton,SIGNAL("clicked()"),self.changeVoltage) self.setLayout(grid)

Or useQt Designer:

How To Get Started1. Download it…

http://www.python.org http://docs.python.org/tutorial/ http://wiki-quantro.extra.cea.fr

2. Check out the documentation & tutorial (online)3. Go &contribute to the Wiki

4. Ask your colleagues…

That‘s it.

Object Hirarchy Example

Instrument

RemoteInstrument VisaInstrument

VNA AgilentMWG YokogawaAcqiris

Dispatcher SubjectReloadable

ThreadedDispatcher