Mailman 3 April 2014 - 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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Normalization for optimization in python
by Yuxiang Wang April 27, 2015

April 27, 2015

Dear all, During optimization, it is often helpful to normalize the input parameters to make them on the same order of magnitude, so the convergence can be much better. For example, if we want to minimize f(x), while a reasonable approximation is x0=[1e3, 1e-4], it might be helpful to normalize x0[0] and x0[1] to about the same order of magnitude (often O(1)). My question is, I have been using scipy.optimize and specifically, the L-BFGS-B algorithm. I was wondering that, do I need to normalize that manually by writing a function, or the algorithm already did it for me? Thank you! -Shawn -- Yuxiang "Shawn" Wang Gerling Research Lab University of Virginia yw5aj(a)virginia.edu +1 (434) 284-0836 https://sites.google.com/a/virginia.edu/yw5aj/

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leastsq and multiprocessing
by Frédéric Parrenin May 30, 2014

May 30, 2014

Dear all, Following these posts: http://stackoverflow.com/questions/10489134/multithreaded-calls-to-the-obje… It seems it is possible to make leastsq take part of multiple processors. I was wondering: given that the tendency of processors is to have more and more cores nowadays, why this is not done by default in leastsq? Best regards, Frédéric Parrenin

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question: OLS with sparse design and dense parameter
by josef.pktd＠gmail.com May 1, 2014

May 1, 2014

(sunday night quest for another sparse recipe) This is a sparse algorithm question: scipy.sparse.linalg has a choice of linear system solvers, but I have not much idea about the relative merits. Is there a recommendation for the following case? suppose I want to do estimate a standard linear model by OLS y = x * b, find b = argmin(y - x*b) x is sparse, with blocks, medium large (20000 by 2000) but if it works quite a bit larger, but we don't have a small number of dominant singular values, the solution of the linear system will be dense. the basic parts of my minimum example nobsi, n_groups, k_vars = 10, 2000, 3 #nobsi, n_groups, k_vars = 2, 3, 3 xi = np.arange(nobsi)[:,None]**np.arange(3) #vander x_sp = sparse.kron(sparse.eye(n_groups), xi).tocsr() (balanced kron structure is just to make a quick example) x_sp.shape (20000, 6000) first try xpx = x_sp.T.dot(x_sp) # sparse xpy = x_sp.T.dot(y) # dense p_dense = np.linalg.solve(xpx.toarray(), xpy) p_sp1 = sparse.linalg.spsolve(xpx, xpy) p_sp2 = sparse.linalg.lsmr(x_sp, y)[0] timing: 15.6659998894 0.00500011444092 0.00600004196167 Is this too small to worry, and anything works, or is there a recommendation? definitely don't use dense. Thanks, Josef

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Solving complex and array differential equations with odeint
by Warren Weckesser April 30, 2014

April 30, 2014

Occasionally on the mailing list and stackoverflow, the question of how to solve a system of differential equations in which the dependent variables are complex or an array is raised. `scipy.integrate.ode` (with the `zvode` integrator) and `scipy.integrate.complex_ode` can handle complex equations, but neither `ode` nor `scipy.integrate.odeint` can handle arrays. To solve an array differential equation with either of them, you have to implement the equations with the array flattened to a 1-d vector. I've created a wrapper of `odeint`, cleverly called `odeintw`, that takes care of wrapping complex and array equations so they can be solved with `odeint`. The github repository is here: https://github.com/WarrenWeckesser/odeintw Eventually, I'll work on getting this into scipy itself, but these days the distribution of "eventually" has a fat tail, so it might be a while. Warren

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creating a particular numpy array
by Gabriele Brambilla April 30, 2014

April 30, 2014

Hi, I have a particular array MYMAP = [np.zeros([npha, nobs, nex], dtype=float)] how can I create an array of 210 of MYMAP? thanks Gabriele

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problems handling a numpy array
by Gabriele Brambilla April 30, 2014

April 30, 2014

Hi, I have a 4d numpy array. I want to select an "index" of the fourth dimension to obtain a 3d array. I try to di it in this way: MYMAP = MYMAPS[:, :, :, 1] that is defined in this way: MYMAPS = [np.zeros([npha, nobs, nex, last-first+1], dtype=float)] but I receive an error: TypeError: list indices must be integers, not tuple what am I doing wrong? thanks Gabriele

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DAQmx python wrapper
by Sebastian Berg April 29, 2014

April 29, 2014

Hey, We are thinking about writing some DAQ programs in python, and I was wondering if anyone can recommend a lib for that. There seem to be a bunch of wrappers using ctypes, which seem all good enough, but if there is something more highlevel or very well done, I would be happy to use that :). Regards, Sebastian

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