Re: [Tutor] Fitting data to error function
Hi Danny,
Thanks for the help! As you mentioned, using scipy.special.erfc was a much
better idea. Below is a copy of my program and the stack trace, showing a
new error. It seems that the first auto correlation works, however the
second fails.
###
# Autocorrelation program
###
import numpy as np
from numpy import ma, logical_or
import pylab
from pylab import *
import matplotlib.pyplot as plt
from matplotlib.ticker import AutoMinorLocator
import math
from math import exp
import scipy
from scipy.integrate import quad,fixed_quad
import sys
from scipy.optimize import curve_fit
from scipy.fftpack import fft, ifft, fftfreq
##
#fitting function (gaussian)
##
def fit(x,a,b,c):
return a*np.exp(-(x-b)**2/c)
#(1.0/(np.sqrt(2*np.pi)*sigma))*np.exp(-(x-mu)**2 / (2*sigma**2))
##
# Load data from .txt file
##
data1 = np.loadtxt('TL_pulseC.txt',skiprows = 2 ,usecols = (0,1))
data2 = np.loadtxt('cos_pulseC.txt',skiprows = 2 ,usecols = (0,1))
#print \n Stage Position (um) Amplitude (V)
#print data
# Create data arrays
pos = np.array(data1[:,0]) # micrometers
pos_m = pos*1.0*10**(-6) # meters
print pos_m
amp = np.array(data1[:,1]) # V
amp_auto = np.array(data2[:,1])
#
# Finding the index of the maximum amplitude where the pulse delay is zero.
Then calculating the
# mean to shift the curve accordingly.
#
peak_id = np.where(amp == np.max(amp))[0][0]
mean = pos_m[peak_id]
print mean
dif = pos_m - mean
t_d =(2.*dif)/(2.99*10**8)*10**(12.) # ps
print t_d
t = np.arange(0.,0.5,1/float(2*len(t_d)))# picoseconds (ps)
# Define constants
c = 2.99*10**8 # m/s
alpha = np.pi # rad
gamma = 200.0*10**(-15.)
lamb_o = 1160.00*10**(-9.) # m
omega_o = ((2.*np.pi*c)/lamb_o)*1.*10**(-12.) # ps^-1
delta = np.pi/2.# rad
FWHM = 32.53*10**(-6) # m
t_p = ((FWHM)/c)*10**(12.) # ps
print t_p
E_norm = 1. # normalized
# Define functions
# Electric field
def E_o(x):
return E_norm*(cosh(1.76*x/t_p))**(-1.)
# Real part of electric field
def E_rin(x):
return (1./2.)*E_o(x)*cos(omega_o*x)
# Imaginary part of electric field
def E_iin(x):
return (1./2.)*E_o(x)*sin(omega_o*x)
# Total electric field
def E_(x):
return (1./2.)*E_o(x)*np.exp(-1j*omega_o*x)
# Autocorrelation
'''
def integrand(t,t_d):
return abs(E_rin(t))**2.*abs(E_rin(t - t_d))**2.
'''
def integrand(x,y):
return abs(E_(x))**2.*abs(E_(x - y))**2.
#integrand = abs(E_(t))**2.*abs(E_(t - t_d))**2.
def G(y):
return quad(integrand, -np.infty, np.infty, args=(y))
G_plot = []
for tau in t_d:
integral,error = G(tau)
G_plot.append(integral)
#fit data
params = curve_fit(fit,pos[174-100:174+100],amp[174-100:174+100],p0=[0.003,
8550,350]) #function, xdata, ydata, initial guess (from plot)
#parameters
[a,b,d] = params[0]
#error
[da,db,dd] = np.sqrt(np.diag(params[1]))
#
# Shaped electric field
#
alpha = np.pi
delta = np.pi/2.
gamma = 200.*10**(-15) # sec
dt = (t[1]-t[0])*(1*10**(-12))
def phi(x):
return alpha*np.cos(gamma*(x - omega_o) - delta)
def M(x):
return np.exp(1j*phi(x))
def E_out(x):
E_in_w = fft(E_(x))
omega = fftfreq(len(x),dt)*2*np.pi
E_out_w = E_in_w*M(omega)
return ifft(E_out_w)
#
# Second autocorrelation
#
def integrand1(x,y):
return abs(E_out(x))**2.*abs(E_out(x - y))**2.
def G1(y):
return quad(integrand1, -np.infty, np.infty, args=(y))
G_plot_1 = []
for tau in t_d:
integral,error = G1(tau)
G_plot_1.append(integral)
#
# Plotting data
#
# Defining x and y minorlocator
xminorLocator = AutoMinorLocator()
yminorLocator = AutoMinorLocator()
# Setting minor ticks
ax = plt.subplot(111)
ax.xaxis.set_minor_locator(xminorLocator)
ax.yaxis.set_minor_locator(yminorLocator)
sample_pos = np.linspace(min(pos),max(pos),1000)
[Tutor] print method in Python2.7 problem
Stat = {'Vbatt': 51.24, 'Ichrg': 6.75}
print ' td style=text-align: center;SOLAR PANEL VOLTAGE/td'
print('DSB HI; %s') % (str(Stat['Vbatt']))
print(' td style=width: 50%; text-align: center;%s/td') %
(str(Stat['Vbatt']))
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Re: [Tutor] print method in Python2.7 problem
On 15/03/2015 17:40, Mark Lawrence wrote:
On 15/03/2015 16:46, Doug Basberg wrote:
Nothing because it was in a completely unnecessary attachment (some
people won't even receive it), so here's the code.
Stat = {'Vbatt': 51.24, 'Ichrg': 6.75}
print ' td style=text-align: center;SOLAR PANEL VOLTAGE/td'
print('DSB HI; %s') % (str(Stat['Vbatt']))
print(' td style=width: 50%; text-align: center;%s/td') %
(str(Stat['Vbatt']))
He also didn't bother specifying the actual problem,but like others here
we just love guessing games. So I'll go for:-
TypeError: unsupported operand type(s) for %: 'NoneType' and 'str'
Print in 2.7 is a statement so the first one is fine. The second (and
third) you're trying to apply the % operator to the print statememt
which by definition is None, hence the error. You also don't need the
call to str so put it all together it simply becomes.
print 'DSB HI; %s' % Stat['Vbatt']
I'll leave you to come back with the next problem as I haven't worked
out what the solution is yet :)
Having read Steven D'Aprano's reply I have now, I was mixing Python 2
and 3, whoops, sorry about that!!!
--
My fellow Pythonistas, ask not what our language can do for you, ask
what you can do for our language.
Mark Lawrence
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Re: [Tutor] print method in Python2.7 problem
To be fair to Doug his mails aren't cp,ing through to the list fully.
I susp3ect because he is using an Outlook message format with lots of
fancy formatting and a background all of which are being sent as
attachments...
Here is his text (with a lot of extraneous whitespace removed):
-
For some reason my e-mails to this forum seem to have a problem,
I may sign up again to see if something is wrong with my account.
Mean while can the moderator cut and paste so members can see my post?
Thank you. Do you know what my account problem is? Thank you, Doug
Basberg dbasb...@comcast.net
I am attempting to write web pages in Python and inserting
numbers from a dictionary read in this program and populated
in another using a classes methods for read and write.
In this process, I found that in Python 2.7 on my Raspberry Pi,
I have a problem with a print statement. I have attached a
very small test program exhibiting the same problem. The
error message tells me that the semicolon is a problem.
It is in a single quoted string, so it should not be interpreted ??
I know that %xxx is interpreted inside strings of print
statements. Are there other special characters (like %) that
I am not aware of?
I can sure use some help with this. Thanks, Doug
File attached and shown as text below:
Stat = {'Vbatt': 51.24, 'Ichrg': 6.75}
print ' td style=text-align: center;SOLAR PANEL VOLTAGE/td'
print('DSB HI; %s') % (str(Stat['Vbatt']))
print(' td style=width: 50%; text-align: center;%s/td') %
(str(Stat['Vbatt']))
Running the program:
$ python dsbtest02.py
td style=text-align: center;SOLAR PANEL VOLTAGE/td
DSB HI; 51.24
Traceback (most recent call last):
File dsbtest02.py, line 5, in module
print(' td style=width: 50%; text-align: center;%s/td') %
(str(Stat['Vbatt']))
ValueError: unsupported format character ';' (0x3b) at index 24
-
The solution (to the messaging issue) is if Doug uses plain text
for posts to the list in future.
The solution for the code issue is, as Steven says,
to use %% to escape the percent sign.
--
Alan G
Author of the Learn to Program web site
http://www.alan-g.me.uk/
http://www.amazon.com/author/alan_gauld
Follow my photo-blog on Flickr at:
http://www.flickr.com/photos/alangauldphotos
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Re: [Tutor] Ipython Queries
Thank you All. I forgot to update you guys , i use ubuntu 14.10 . I believe/was under assumption that we cannot used ipython both for python 2.x and python 3.x. So ipython is for python 2.x and ipython3 is for python 3.x Thanks, santosh On Sun, Mar 15, 2015 at 3:47 AM, Oscar Benjamin oscar.j.benja...@gmail.com wrote: On 14 March 2015 at 09:53, Steven D'Aprano st...@pearwood.info wrote: On Fri, Mar 13, 2015 at 10:39:50PM +0530, Santosh Kumar wrote: Hi All, I have installed both python2 and python3 in my system . When i used ipython it by default goes to python2 base. How/what is the easy way to swith between python2 and python3 ? I don't think there is an easy way on Windows, but I could be wrong. You could try asking on a dedicated iPython mailing list. If you get an answer, please come back and tell us here so we can learn too. When you install ipython (or any Python package) you install it for a particular Python version. You haven't said how you installed either of the Python versions or ipython or which version of Python you installed ipython for. Assuming that you have installed ipython for Python 3 then you may be able to run ipython for Python 3 by typing one of the following in a terminal: $ ipython3 $ python3 -m IPython $ py -3 -m IPython (Note carefully that the I and P at the start of IPython in the last two examples are capitalised - the first example is all lower case). You may find that ipython is in the programs menu on Windows. I'm not really sure how that stuff works on newer versions of Windows though. Without knowing more about your setup it's hard to be specific about what you should do. What OS are you using (e.g. Windows 8?)? How did you install Python 2 and Python 3 and which versions (e.g. 2.7 and 3.4?). How did you install ipython? Which version of Python did you install it for? Do you know what folder the Python installations are in (e.g. C:\Python34)? Oscar ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor -- D. Santosh Kumar RHCE | SCSA +91-9703206361 Every task has a unpleasant side .. But you must focus on the end result you are producing. ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] print method in Python2.7 problem
On 15/03/2015 16:46, Doug Basberg wrote:
Nothing because it was in a completely unnecessary attachment (some
people won't even receive it), so here's the code.
Stat = {'Vbatt': 51.24, 'Ichrg': 6.75}
print ' td style=text-align: center;SOLAR PANEL VOLTAGE/td'
print('DSB HI; %s') % (str(Stat['Vbatt']))
print(' td style=width: 50%; text-align: center;%s/td') %
(str(Stat['Vbatt']))
He also didn't bother specifying the actual problem,but like others here
we just love guessing games. So I'll go for:-
TypeError: unsupported operand type(s) for %: 'NoneType' and 'str'
Print in 2.7 is a statement so the first one is fine. The second (and
third) you're trying to apply the % operator to the print statememt
which by definition is None, hence the error. You also don't need the
call to str so put it all together it simply becomes.
print 'DSB HI; %s' % Stat['Vbatt']
I'll leave you to come back with the next problem as I haven't worked
out what the solution is yet :)
--
My fellow Pythonistas, ask not what our language can do for you, ask
what you can do for our language.
Mark Lawrence
___
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Re: [Tutor] print method in Python2.7 problem
On Sun, Mar 15, 2015 at 12:46:04PM -0400, Doug Basberg wrote:
Stat = {'Vbatt': 51.24, 'Ichrg': 6.75}
print ' td style=text-align: center;SOLAR PANEL VOLTAGE/td'
print('DSB HI; %s') % (str(Stat['Vbatt']))
print(' td style=width: 50%; text-align: center;%s/td') %
(str(Stat['Vbatt']))
Yes? What about it? Do you have a question or do you expect us to read
your mind?
If the second, this is your lucky day, because in fact I am a powerful
psychic, and by reading your mind I can see that you are getting a
ValueError exception from the last line:
ValueError: unsupported format character ';' (0x3b) at index 24
By using another of my superpowers, called reading the error message,
I can work out the nature of the problem: you have a format command %;
which isn't supported.
When using string interpolation with the % operator, it looks for %
formatting characters in the string. %s you already know. %d needs an
integer value, %f a float. And %; isn't supported at all -- it is an
error.
What you need to do is escape the percent sign, so it will be turned
into a percent sign in the output, not treated as a format command in
the input:
print(' td style=width: 50%%; text-align: center;%s/td') %
(str(Stat['Vbatt']))
--
Steve
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Re: [Tutor] Fitting data to error function
Thanks for the help! As you mentioned, using scipy.special.erfc was a much better idea. Below is a copy of my program and the stack trace, showing a new error. It seems that the first auto correlation works, however the second fails. At this point, the program is large enough that we need to apply alternative techniques besides reading the entire program and trying to keep it in our head at once. One approach that is often successful is to check the _user functions_ in isolation, because they should be separable and independently testable. You've written a few functions in your program. In particular: ## def fit(x,a,b,c): ... def E_o(x): ... def E_rin(x): ... def E_iin(x): ... def E_(x): ... def integrand(t,t_d): ... def integrand(x,y): ...## why is this being defined twice?! def G(y): ... def phi(x): ... def M(x): ... def E_out(x): ... def integrand1(x,y): ... def G1(y): ... ## A function-based perspective will ask the following questions: 1. What is the documented purpose of each of these functions? 2. What are the expected inputs and output types for each of these functions? 3. Which of these functions have unit tests to spot-check their quality? I can say for certain, without looking at any significant code, that something is strange with regards to integrand. Your program has defined this twice, and that's almost certainly not right. The strategy here is to pinpoint where the problem is: we can't possibly say that the whole program is broken, so we try to scope the problem down to a manageable size. You mention that the first auto-correlation is producing good results. What functions are involved in the computation of the first auto-correlation? Another technique to try to scope is to look at the stack trace and the involved functions. The stack trace says that the following functions are involved at the point of the program breakage: G1 quad integrand1 E_out E_ In particular, note the tail end of the stack trace: 7 def E_out(x): 8 E_in_w = fft(E_(x)) It is on the call to: fft(E_(x)) that things break with the IndexError. Note that fft() is provided by the scipy library. For the purposes of debugging, let us assume that all external third-party libraries are bug-free. What does fft expect to receive as an argument? We can read the following: http://docs.scipy.org/doc/scipy/reference/generated/scipy.fftpack.fft.html#scipy.fftpack.fft Since fft is erroring out: there's only one possibility: E_(x) is not providing a value that's appropriate to fft(). Why would it do that? Two possibilities: 1. E_ is buggy and needs investigation. 2. E_ is fine, but the inputted value of x is one that E_x is not defined to handle. And so we start the investigation by considering those two possibilities. Start with #1. Do you know if E_ is fine? What is it supposed to do? What is the shape of its input? What is the shape of its output? Is its output something that fft() is designed to handle? ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
Re: [Tutor] Fitting data to error function
What does fft expect to receive as an argument? We can read the following: http://docs.scipy.org/doc/scipy/reference/generated/scipy.fftpack.fft.html#scipy.fftpack.fft Since fft is erroring out: there's only one possibility: E_(x) is not providing a value that's appropriate to fft(). Why would it do that? Two possibilities: 1. E_ is buggy and needs investigation. 2. E_ is fine, but the inputted value of x is one that E_x is not defined to handle. And so we start the investigation by considering those two possibilities. Start with #1. Do you know if E_ is fine? What is it supposed to do? What is the shape of its input? What is the shape of its output? Is its output something that fft() is designed to handle? Just to add: this is not to say that E_() is buggy. We just have to start investigation somewhere, and it seemed as good a place as any, since I don't know if _any_ of the functions are behaving. :P This is very much the reason why programmers like to do unit testing: we want to know what functions at least do something that we know is useful. We know all too well that whole programs break, and we want to have some confidence on what components of our program are likely ok. If #2 is the actual issue, then the question becomes: why is the program producing an invalid input 'x'? And that's where we need to start reasoning backwards, to discover how that value was constructed. ___ Tutor maillist - Tutor@python.org To unsubscribe or change subscription options: https://mail.python.org/mailman/listinfo/tutor
