Mailman 3 February 2015 - 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

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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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Hierarchical clustering query
by rishabh.sharma Feb. 27, 2015

Feb. 27, 2015

hello I have this question,could someone help? I am using scipy.cluster.hiearchical ***I have a distance matrix in squareform 't' as array([[ 0.00000000e+00, 3.44600000e+03, 6.75000000e+02, 2.06000000e+03, 2.24205600e+06], [ 3.44600000e+03, 0.00000000e+00, 2.77300000e+03, 1.75000000e+03, 2.23959500e+06], [ 6.75000000e+02, 2.77300000e+03, 0.00000000e+00, 1.49100000e+03, 2.24154200e+06], [ 2.06000000e+03, 1.75000000e+03, 1.49100000e+03, 0.00000000e+00, 2.24127000e+06], [ 2.24205600e+06, 2.23959500e+06, 2.24154200e+06, 2.24127000e+06, 0.00000000e+00]]) ***I used this cmd z=linkage(t,method='complete') //t is the above matrix z array([[ 0.00000000e+00, 2.00000000e+00, 1.39718861e+03, 2.00000000e+00], [ 1.00000000e+00, 3.00000000e+00, 3.53484724e+03, 2.00000000e+00], [ 5.00000000e+00, 6.00000000e+00, 5.85696654e+03, 4.00000000e+00], [ 4.00000000e+00, 7.00000000e+00, 5.00927065e+06, 5.00000000e+00]]) **Question: why in the first row of z where objects 0,2 are merged the distance is shown as 1.397e+3[3rd element of 1st row] whereas it should the distance given by t[0][2] as in distance matrix(these objects are original objects/leaf nodes) Thanks

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ANN: SfePy 2015.1
by Robert Cimrman Feb. 26, 2015

Feb. 26, 2015

I am pleased to announce release 2015.1 of SfePy. Description ----------- SfePy (simple finite elements in Python) is a software for solving systems of coupled partial differential equations by the finite element method or by the isogeometric analysis (preliminary support). It is distributed under the new BSD license. Home page: http://sfepy.org Mailing list: http://groups.google.com/group/sfepy-devel Git (source) repository, issue tracker, wiki: http://github.com/sfepy Highlights of this release -------------------------- - support for multiple fields in isogeometric analysis - redesigned handling of solver parameters - new modal analysis example For full release notes see http://docs.sfepy.org/doc/release_notes.html#id1 (rather long and technical). Best regards, Robert Cimrman and Contributors (*) (*) Contributors to this release (alphabetical order): Lubos Kejzlar, Vladimir Lukes

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Scipy with pip compliation problems on Centos 6.6
by Robinson, Roger Feb. 25, 2015

Feb. 25, 2015

Hi, I am on CentOS 6.6. I have compiled BLAS+ATLAS+LAPACK separately on a network drive. I have python 2.7.9 compiled. Im using this command to install + complie scipy pip install --target=/apps_shared/python/scipy/scipy-0.15.1 scipy I get this error Python 2.7.9 (default, Feb 16 2015, 11:29:23) [GCC 4.4.7 20120313 (Red Hat 4.4.7-11)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from scipy.stats import genextreme Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/apps_shared/python/scipy/current/scipy/stats/__init__.py", line 338, in <module> from .stats import * File "/apps_shared/python/scipy/current/scipy/stats/stats.py", line 184, in <module> import scipy.special as special File "/apps_shared/python/scipy/current/scipy/special/__init__.py", line 586, in <module> from ._ufuncs import * ImportError: /apps_shared/python/scipy/current/scipy/special/_ufuncs.so: undefined symbol: dstevr_ Any advice ? Thanks Roger [EvotecLogoMail.png] Dr Roger Robinson My Linkedin Profile<https://www.linkedin.com/profile/view?id=40177586&trk=nav_responsive_tab_pr…> Systems Developer Computational Chemistry & Cheminformatics +44 (0)1235 441424 (direct) roger.robinson(a)evotec.com<mailto:roger.robinson@evotec.com> www.evotec.com<blocked::http://www.evotec.com> Evotec(UK) Ltd 114 Innovation Drive Milton Park Abingdon Oxfordshire OX14 4RZ United Kingdom Evotec (UK) Ltd is a limited company registered in England and Wales. Registration number:2674265. Registered office: 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, United Kingdom.

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library for GF(2) Galois Fields
by Jason Sachs Feb. 24, 2015

Feb. 24, 2015

Is there any Python library that can deal with Galois fields, specifically the binary GF(2)? This comes up a lot in communications theory and for linear-feedback shift registers. I would really like to use a library that has things like arithmetic and matrix operations. MATLAB offers this in their Communications Toolbox http://www.mathworks.com/help/comm/galois-field-computations.html I have a rudimentary library for some arithmetic that I've open-sourced (https://bitbucket.org/jason_s/libgf2), but it's not vectorized and it's really not up to the standard of numpy/scipy I think.

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Bug in interpolate.splrep() or am I doing something wrong?
by Daniele Nicolodi Feb. 20, 2015

Feb. 20, 2015

Hello, reading the documentation, I would expect this to work: > x = np.linspace(0, 2.0 * np.pi, 1000) > y = np.sin(x) + np.random.randn(x.shape[0]) * 0.2 > tck0 = interpolate.splrep(x, y, task=0, w=np.ones(x.shape[0])/0.2) > tck1 = interpolate.splrep(x, y, task=1, w=np.ones(x.shape[0])/0.1) however, the second splrep() call fails: > Traceback (most recent call last): > File "test-splrep.py", line 17, in <module> > main() > File "test-splrep.py", line 9, in main > tck1 = interpolate.splrep(x, y, task=1, w=np.ones(x.shape[0])/0.1) > File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/interpolate/fitpack.py", line 495, in splrep > t = _curfit_cache['t'] > UnboundLocalError: local variable '_curfit_cache' referenced before assignment This is with scipy 0.15.1. Cheers, Daniele

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Re: [SciPy-User] [Numpy-discussion] Google Summer of Code and NumFOCUS
by Ralf Gommers Feb. 20, 2015

Feb. 20, 2015

Hi Raniere, On Thu, Feb 19, 2015 at 1:03 PM, Raniere Silva <raniere(a)ime.unicamp.br> wrote: > Hi, > > NumFOCUS has promotes and supports the ongoing research and development of > open-source computing tools including NumPy. > > This year NumFOCUS want to try be a Google Summer of Code > "umbrella" mentoring organization, > > Umbrella organizations are mentoring organizations accepted into the > Google > Summer of Code program that have other open source organizations > working > "under" them. Sometime organizations that work very closely or have > very > similar goals or communities may get put together under an "umbrella." > Google stills expects all organizations under the umbrella, whether > accepted > into the program under their title or not, to adhere to all the rules > and > regulations of the program. > > From > https://www.google-melange.com/gsoc/document/show/gsoc_program/google/gsoc2… > > To help promote and support NumPy. > > We encourage NumPy to apply to Google Summer of Code under your own title > and will be very happy if you can also do with us. > If you are interested, please check > https://github.com/swcarpentry/gsoc2015 > and https://github.com/swcarpentry/gsoc2015/blob/master/CONTRIBUTING.md. > > If you have any question, please email me directly. > Thanks for the enthusiasm in getting Numfocus set up as a new mentoring org - I'm sure that this will be useful for the long term. I'm not sure if you're aware that Numpy, Scipy and many other scientific Python projects have been participating under the umbrella of the PSF for a number of years already (see https://wiki.python.org/moin/SummerOfCode/2014). For this year we'd like to keep it that way. I'll email you privately with more details and to see if I can help you in any way. Cheers, Ralf

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