Mailman 3 July 2013 - SciPy-User

How to display a RGB image (MFISH)?
by jp April 3, 2023

April 3, 2023

Hi, I have written a script to try to combine five images into a three channels RGB images<http://dip4fish.blogspot.com/2011/05/trying-to-combine-mfish-images-into-rg…> . The resulting RGB image looks like a grey scale image instead of a color one. I have three np.array Rnorm, Gnorm, Bnorm which are copied into a rgb array: *rgb = np.zeros((shape[0],shape[1],3),dtype=float) mxr=np.max(R) mxg=np.max(G) mxb=np.max(B) Rnorm=np.uint8((255*(R/mxr)))Gnorm=np.uint8((255*(R/mxg)))Bnorm=np.uint8((255*(R/mxb)))#copy each RGB component in an RGB array rgb[:,:,0]=Rnorm rgb[:,:,1]=Gnorm rgb[:,:,2]=Bnorm* *pylab.subplot(224, aspect='equal',frameon=False, xticks=[], yticks=[]) pylab.imshow(rgb) pylab.show()* Any advice? Thank you Jean-Patrick

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Invitation to connect on LinkedIn
by Jelle Feringa via LinkedIn July 28, 2022

July 28, 2022

LinkedIn ------------ Jelle Feringa requested to add you as a connection on LinkedIn: ------------------------------------------ Jose, I'd like to add you to my professional network on LinkedIn. - Jelle Accept invitation from Jelle Feringa http://www.linkedin.com/e/-3wy1w2-gpkzwpgn-5n/Q6WKH0LACopGJkAw_6fSqajo6R7VM… View invitation from Jelle Feringa http://www.linkedin.com/e/-3wy1w2-gpkzwpgn-5n/Q6WKH0LACopGJkAw_6fSqajo6R7VM… ------------------------------------------ DID YOU KNOW your LinkedIn profile helps you control your public image when people search for you? Setting your profile as public means your LinkedIn profile will come up when people enter your name in leading search engines. Take control of your image! http://www.linkedin.com/e/-3wy1w2-gpkzwpgn-5n/ewp/inv-22/ -- (c) 2011, LinkedIn Corporation

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Help required regding Eigenvectors
by Sudheer Phani March 14, 2022

March 14, 2022

Hello All, I have been encountering some strange problems with the calculation of eigen vectors using python. The problem is with the sign of the eigen vectors calculated. On Very few occasions the eigen vectors calculated using python have an opposite sign than the actual eigenvectors, though the magnitude is correct. Can any one of you plz help me in this regard and suggest me some solution if you have encoutered similar problems . Any help in this regd is appreciated Thanks in Advace regds Sudheer

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Allan Variance
by Daniele Nicolodi Feb. 4, 2014

Feb. 4, 2014

Hello, does anyone know or have written and is willing to share some code to compute the Allan variance, modified Allan variance and friends, ideally both from frequency than from phase data? I'm writing my own code, it is not that difficult, but I would prefer the time required for testing and validation doing something more fun. If there is no available code implementing Allan variance, would it be interesting to include in in SciPy? Thank you so much. Best, Daniele

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At.: question about refresh numpy array in a for-cycle
by Josè Luis Mietta Aug. 19, 2013

Aug. 19, 2013

Hi experts! Im writing a code with a numpy array L, the numpy matrix M and the next script: for x in L: for l in srange(N): z= l in L if z is False and M[x,l] != 0: L=np.append(L,l) here, in the end of the cycle, new elements are incorporated to the array 'L'. I want these new elements be considered as 'x' index in the cycle. When I execute the script I see that only the 'originals' elements of L are considered as 'x'. How can i fix it? Waiting for your answers. Thanks a lot!

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Read file with comma decimal separator
by Florian Lindner Aug. 14, 2013

Aug. 14, 2013

Hello, I have a file that used comma as a decimal separator. How can I read a file like that using loadtxt or genfromtxt ? Thanks, Florian

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RFE: dictionnary of figures in Matplotlib
by Frédéric Parrenin July 29, 2013

July 29, 2013

Currently, one call figures with their number in matplotlib. If you have a code which draw a lot a different figures at different places with some of them being optional, this is not very convenient. One convenient way to call figure would be to use a dictionnary of figures. Of course I could create some wrapper around matplotlib.figure function but it would be far more convenient if such feature would be standard in matplotlib. Is there any plan to implement such a feature? Best regards, Frédéric Parrenin

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fitting with convolution?
by Petro July 21, 2013

July 21, 2013

Hi all, I try to fir a time-resolved dataset with multiple exponents convoluted with a Gaussian instrument response function (IRF). I had a look how it is done in Origin http://wiki.originlab.com/~originla/howto/index.php?title=Tutorial:Fitting_… There fft_fft_convolution calculates the circular convolution of an exponent with IRF. I have found a similar function for python here: http://stackoverflow.com/questions/6855169/convolution-computations-in-nump… This convolution also can be calculated analytically as, for example, in this package: http://www.photonfactory.auckland.ac.nz/uoa/home/photon-factory/pytra def convolutedexp(tau,mu,fwhm,x): d = (fwhm/(2*sqrt(2*log(2)))) return 0.5*exp(-x/tau)*exp((mu+(d**2.)/(2.*tau))/tau)* (1.+erf((x-(mu+(d**2.)/tau))/(sqrt(2.)*d))) def gaussian(mu,fwhm,x): d = (fwhm/(2.*sqrt(2.*log(2.)))) return exp(-((x-mu)**2.)/(2.*d**2.)) My problem is if I compare analytical and circular convolution they do not match: _____source_________ import numpy from scipy.special import erf def cconv(a, b): ''' Computes the circular convolution of the (real-valued) vectors a and b. ''' return fft.ifft(fft.fft(a) * fft.fft(b)).real def convolutedexp(tau,mu,fwhm,x): d = (fwhm/(2*sqrt(2*log(2)))) return 0.5*exp(-x/tau)*exp((mu+(d**2.)/(2.*tau))/tau)*(1.+erf((x-(mu+(d**2.)/tau))/(sqrt(2.)*d))) def gaussian(mu,fwhm,x): d = (fwhm/(2.*sqrt(2.*log(2.)))) return exp(-((x-mu)**2.)/(2.*d**2.)) t = array(linspace(-10.0,1000.0,2040.0))[:-1] mu = 0 fwhm = 4.0 tau = 20.0 uf = gaussian(mu,fwhm,t) vf = exp(-t/tau) figure(figsize=[12,12]) plot(t,uf) #plot(t,vf) uvf1 = cconv(uf,vf) plot(tuv,uvf1/14.5) uvf2 = convolutedexp(tau,mu,fwhm,t) plot(t,uvf2) xlim([-10,20]) ____source_end___ My feeling is that I miss something about convolution? Can anybody give me a hint? Thanks. Petro

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scipy 0.11.0 to 0.12.0 changes scipy.interpolate.interp1d, breaks constantly updated interpolator
by Benjamin Evans July 20, 2013

July 20, 2013

Hello all, I have been playing around with a package that uses a linear scipy.interpolate.interp1d to create a history function for the ode solver in scipy, described here<http://zulko.wordpress.com/2013/03/01/delay-differential-equations-easy-wit…> . The relevant bit of code goes something like def update(self, ti, Y): """ Add one new (ti, yi) to the interpolator """ self.itpr.x = np.hstack([self.itpr.x, [ti]]) yi = np.array([Y]).T self.itpr.y = np.hstack([self.itpr.y, yi]) self.itpr.fill_value = Y Where "self.itpr" is initialized in __init__: def __init__(self, g, tc=0): """ g(t) = expression of Y(t) for t<tc """ self.g = g self.tc = tc # We must fill the interpolator with 2 points minimum self.itpr = scipy.interpolate.interp1d( np.array([tc-1, tc]), # X np.array([self.g(tc), self.g(tc)]).T, # Y kind='linear', bounds_error=False, fill_value = self.g(tc)) Where g is some function that returns an array of values that are solutions to a set of differential equations and tc is the current time. This seems nice to me because a new interpolator object doesn't have to be re-created every time I want to update the ranges of values (which happens at each explicit time step during a simulation). This method of updating the interpolator works well under scipy v 0.11.0. However, after updating to v 0.12.0 I ran into issues. I see that the new interpolator now includes an array _y<https://github.com/scipy/scipy/blob/master/scipy/interpolate/interpolate.py…>. Is it safe and/or sane to just update _y as outlined above as well? Is there a simpler, more pythonic way to address this that would hopefully be more robust to future updates in scipy? Again, in v 0.11 everything works well and expected results are produced, and in v 0.12 I get an IndexError when _y is referenced<https://github.com/scipy/scipy/blob/master/scipy/interpolate/interpolate.py…>as it isn't updated in my function while y itself is. Any help/pointers would be appreciated! Thanks! Ben Evans

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Fwd: Submissão de palestras científicas na Pythonbrasil 2014
by Marcel Caraciolo July 18, 2013

July 18, 2013

Hi all, My name is Marcel and I am from Brazil. I'd like to invite you all to submit talks or projects related to scientific computing with Python at our IX Python Brazilian Conference (PythonBrasil). It is one of the largest events at Brazil related to development and it happens once a year. This year we will have a special track for science. So if you have any work with python, libraries, or even representants interested to submit a talk and meet the Brazilian churrasco food :) You're all invited! :) To submit, follow the links: http://2013.pythonbrasil.org.br/pythonbrasil http://2013.pythonbrasil.org.br/pythonbrasil/sobre-o-evento/noticias/chamad… Submissions are open until July'26! Regards, -- Marcel Pinheiro Caraciolo M.S.C. Candidate at CIN/UFPE http://www.mobideia.com http://aimotion.blogspot.com/ -- Marcel Pinheiro Caraciolo M.S.C. Candidate at CIN/UFPE http://www.mobideia.com http://aimotion.blogspot.com/

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