Mailman 3 July 2018 - 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

3 4

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

2 1

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

5 5

NumPy 1.15.0 released.
by Charles R Harris July 23, 2018

July 23, 2018

Hi All, On behalf of the NumPy team I'm pleased to announce the release of NumPy 1.15.0rc2. This release has an unusual number of cleanups, many deprecations of old functions, and improvements to many existing functions. A total of 438 pull reguests were merged for this release, please look at the release notes <https://github.com/numpy/numpy/releases/tag/v1.15.0>for details. Some highlights are: - NumPy has switched to pytest for testing. - A new `numpy.printoptions` context manager. - Many improvements to the histogram functions. - Support for unicode field names in python 2.7. - Improved support for PyPy. - Fixes and improvements to `numpy.einsum`. The Python versions supported by this release are 2.7, 3.4-3.7. The wheels are linked with OpenBLAS v0.3.0, which should fix some of the linalg problems reported for NumPy 1.14. Wheels for this release can be downloaded from PyPI <https://pypi.org/project/numpy/1.15.0/>, source archives are available from Github <https://github.com/numpy/numpy/releases/tag/v1.15.0>. *Contributors* A total of 133 people contributed to this release. People with a "+" by their names contributed a patch for the first time. * Aaron Critchley + * Aarthi + * Aarthi Agurusa + * Alex Thomas + * Alexander Belopolsky * Allan Haldane * Anas Khan + * Andras Deak * Andrey Portnoy + * Anna Chiara * Aurelien Jarno + * Baurzhan Muftakhidinov * Berend Kapelle + * Bernhard M. Wiedemann * Bjoern Thiel + * Bob Eldering * Cenny Wenner + * Charles Harris * ChloeColeongco + * Chris Billington + * Christopher + * Chun-Wei Yuan + * Claudio Freire + * Daniel Smith * Darcy Meyer + * David Abdurachmanov + * David Freese * Deepak Kumar Gouda + * Dennis Weyland + * Derrick Williams + * Dmitriy Shalyga + * Eric Cousineau + * Eric Larson * Eric Wieser * Evgeni Burovski * Frederick Lefebvre + * Gaspar Karm + * Geoffrey Irving * Gerhard Hobler + * Gerrit Holl * Guo Ci + * Hameer Abbasi + * Han Shen * Hiroyuki V. Yamazaki + * Hong Xu * Ihor Melnyk + * Jaime Fernandez * Jake VanderPlas + * James Tocknell + * Jarrod Millman * Jeff VanOss + * John Kirkham * Jonas Rauber + * Jonathan March + * Joseph Fox-Rabinovitz * Julian Taylor * Junjie Bai + * Juris Bogusevs + * Jörg Döpfert * Kenichi Maehashi + * Kevin Sheppard * Kimikazu Kato + * Kirit Thadaka + * Kritika Jalan + * Kyle Sunden + * Lakshay Garg + * Lars G + * Licht Takeuchi * Louis Potok + * Luke Zoltan Kelley * MSeifert04 + * Mads R. B. Kristensen + * Malcolm Smith + * Mark Harfouche + * Marten H. van Kerkwijk + * Marten van Kerkwijk * Matheus Vieira Portela + * Mathieu Lamarre * Mathieu Sornay + * Matthew Brett * Matthew Rocklin + * Matthias Bussonnier * Matti Picus * Michael Droettboom * Miguel Sánchez de León Peque + * Mike Toews + * Milo + * Nathaniel J. Smith * Nelle Varoquaux * Nicholas Nadeau, P.Eng., AVS + * Nick Minkyu Lee + * Nikita + * Nikita Kartashov + * Nils Becker + * Oleg Zabluda * Orestis Floros + * Pat Gunn + * Paul van Mulbregt + * Pauli Virtanen * Pierre Chanial + * Ralf Gommers * Raunak Shah + * Robert Kern * Russell Keith-Magee + * Ryan Soklaski + * Samuel Jackson + * Sebastian Berg * Siavash Eliasi + * Simon Conseil * Simon Gibbons * Stefan Krah + * Stefan van der Walt * Stephan Hoyer * Subhendu + * Subhendu Ranjan Mishra + * Tai-Lin Wu + * Tobias Fischer + * Toshiki Kataoka + * Tyler Reddy + * Unknown + * Varun Nayyar * Victor Rodriguez + * Warren Weckesser * William D. Irons + * Zane Bradley + * cclauss + * fo40225 + * lapack_lite code generator + * lumbric + * luzpaz + * mamrehn + * tynn + * xoviat Cheers, Charles Harris

1 1

scipy.optimize.minimize changes values at low decimal place
by jan-hendrik.berlin July 23, 2018

July 23, 2018

Hey guys, this is my code for the optimisation. initialGuess = D.Matrix[:,D.menge] bnds = D.Matrix[:,(D.mengenMin,D.mengenMax)] con1 = {'type': 'eq', 'fun': PercentSum} con2 = {'type': 'eq', 'fun': MinMaxProportion} cons = ([con1,con2]) solution = minimize(rootfunc,initialGuess,method='SLSQP',\ bounds=bnds,constraints=cons) The Problem is, the algorithm changes values at low decimal place. e.g. this is my initial guess. I already tried to change from float to integers, to have a work around. [ 0. 0. 123. 0. 0. 622. 245. 0. 0. 0.] The first try of the of the optimizer looks like this: [1.49011612e-08 0.00000000e+00 1.23000000e+02 0.00000000e+00 0.00000000e+00 6.22000000e+02 2.45000000e+02 0.00000000e+00 0.00000000e+00 0.00000000e+00] Another is this: [ 0. 0. 123.00000001 0. 0. 622. 245. 0. 0. 0. ] And finally the optimization finishes with this error: status 6 message Singular matrix C in LSQ subproblem I think the problem is the tiny difference. Is there a possibility to tell the SLSQP algorithm only to try changes on the first two decimal places or higher? kind regards jan

1 0

NumPy 1.15.0rc2 released.
by Charles R Harris July 9, 2018

July 9, 2018

Hi All, On behalf of the NumPy team I'm pleased to announce the release of NumPy 1.15.0rc2. This release has an unusual number of cleanups, many deprecations of old functions, and improvements to many existing functions. A total of 435 pull reguests were merged for this release, please look at the release notes <https://github.com/numpy/numpy/releases/tag/v1.15.0rc2>for details. Some highlights are: - NumPy has switched to pytest for testing. - A new `numpy.printoptions` context manager. - Many improvements to the histogram functions. - Support for unicode field names in python 2.7. - Improved support for PyPy. - Fixes and improvements to `numpy.einsum`. The Python versions supported by this release are 2.7, 3.4-3.7. The wheels are linked with OpenBLAS v0.3.0, which should fix some of the linalg problems reported for NumPy 1.14. Wheels for this release can be downloaded from PyPI <https://pypi.org/project/numpy/1.15.0rc2/>, source archives are available from Github <https://github.com/numpy/numpy/releases/tag/v1.15.0rc2>. A total of 131 people contributed to this release. People with a "+" by their names contributed a patch for the first time. - Aaron Critchley + - Aarthi + - Aarthi Agurusa + - Alex Thomas + - Alexander Belopolsky - Allan Haldane - Anas Khan + - Andras Deak - Andrey Portnoy + - Anna Chiara - Aurelien Jarno + - Baurzhan Muftakhidinov - Berend Kapelle + - Bernhard M. Wiedemann - Bjoern Thiel + - Bob Eldering - Cenny Wenner + - Charles Harris - ChloeColeongco + - Chris Billington + - Christopher + - Chun-Wei Yuan + - Claudio Freire + - Daniel Smith - Darcy Meyer + - David Abdurachmanov + - David Freese - Deepak Kumar Gouda + - Dennis Weyland + - Derrick Williams + - Dmitriy Shalyga + - Eric Cousineau + - Eric Larson - Eric Wieser - Evgeni Burovski - Frederick Lefebvre + - Gaspar Karm + - Geoffrey Irving - Gerhard Hobler + - Gerrit Holl - Guo Ci + - Hameer Abbasi + - Han Shen - Hiroyuki V. Yamazaki + - Hong Xu - Ihor Melnyk + - Jaime Fernandez - Jake VanderPlas + - James Tocknell + - Jarrod Millman - Jeff VanOss + - John Kirkham - Jonas Rauber + - Jonathan March + - Joseph Fox-Rabinovitz - Julian Taylor - Junjie Bai + - Juris Bogusevs + - Jörg Döpfert - Kenichi Maehashi + - Kevin Sheppard - Kimikazu Kato + - Kirit Thadaka + - Kritika Jalan + - Lakshay Garg + - Lars G + - Licht Takeuchi - Louis Potok + - Luke Zoltan Kelley - MSeifert04 + - Mads R. B. Kristensen + - Malcolm Smith + - Mark Harfouche + - Marten H. van Kerkwijk + - Marten van Kerkwijk - Matheus Vieira Portela + - Mathieu Lamarre - Mathieu Sornay + - Matthew Brett - Matthew Rocklin + - Matthias Bussonnier - Matti Picus - Michael Droettboom - Miguel Sánchez de León Peque + - Mike Toews + - Milo + - Nathaniel J. Smith - Nelle Varoquaux - Nicholas Nadeau, P.Eng., AVS + - Nick Minkyu Lee + - Nikita + - Nikita Kartashov + - Nils Becker + - Oleg Zabluda - Orestis Floros + - Pat Gunn + - Paul van Mulbregt + - Pauli Virtanen - Pierre Chanial + - Ralf Gommers - Raunak Shah + - Robert Kern - Russell Keith-Magee + - Ryan Soklaski + - Samuel Jackson + - Sebastian Berg - Siavash Eliasi + - Simon Conseil - Simon Gibbons - Stefan Krah + - Stefan van der Walt - Stephan Hoyer - Subhendu + - Subhendu Ranjan Mishra + - Tai-Lin Wu + - Tobias Fischer + - Toshiki Kataoka + - Tyler Reddy + - Unknown + - Varun Nayyar - Victor Rodriguez + - Warren Weckesser - William D. Irons + - Zane Bradley + - fo40225 + - lapack_lite code generator + - lumbric + - luzpaz + - mamrehn + - tynn + - xoviat Cheers Chuck

1 0

Re: [SciPy-User] Q: on scipy probplot user defined distribution function (solution)
by Sergio Rojas July 9, 2018

July 9, 2018

> From: Paul Hobson <pmhobson(a)gmail.com> > Hmm. I don't think scipy needs to know about your distribution per se. You > Thanks for sharing your thoughts, Paul. I finally found the way to go. As you mention, the parameter "dist" is wher one needs to specify our own distribution. The key is to give it without quotes. Here is a working example: import matplotlib.pyplot as plt #prefer this import numpy as np from scipy import stats class mydist(object): def pdf(x): "define and return the pdf" return stats.norm.pdf(x) def cdf(x): "define and return the cdf" return stats.norm.cdf(x) def ppf(x): "define and return the ppf" return stats.norm.ppf(x) mymean = 1.0 myvar = 1.0 n = 5000 colData = np.random.normal(mymean, myvar, n) """ It took me a while to realize that the quotes surrounding the distribution should not be there when using a user defined one """ print(' ProbPlot using system norm ') res = stats.probplot(colData, dist="norm", plot=plt, rvalue=True) plt.show() # To use our own defined distribution remove the quotes around the name: print(' ProbPlot using my redefined system norm ') res = stats.probplot(colData, dist=mydist, plot=plt, rvalue=True) plt.show() Sergio ------------------------------ Message: 2 Date: Thu, 5 Jul 2018 00:11:52 -0700 From: Paul Hobson <pmhobson(a)gmail.com> To: SciPy Users List <scipy-user(a)python.org> Subject: Re: [SciPy-User] Q: on scipy probplot user defined distribution function Message-ID: <CADT3MEANHqw+w_+acbp9U6H1QqdhLOY9Ei1LK430we5+Wo1eyA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hmm. I don't think scipy needs to know about your distribution per se. You just need to be able to pass it to the probplot function via the `dist` parameter. Per the docs ( https://docs.scipy.org/doc/scipy-0.14.0/reference/generated/scipy.stats.pro… ): scipy.stats.probplot(*x*, *sparams=()*, *dist='norm'*, *fit=True*, *plot=None*)[source] <http://github.com/scipy/scipy/blob/v0.14.0/scipy/stats/morestats.py#L296[ht…> [snip] *dist* : str or stats.distributions instance, optional Distribution or distribution function name. The default is ?norm? for a normal probability plot. Objects that look enough like a stats.distributions instance (i.e. they have a ppf method) are also accepted. [snip] On Wed, Jul 4, 2018 at 12:19 PM Sergio Rojas <sergio_r(a)mail.com> wrote: > > > Here's an example of using different distributions with the mpl-probscale > > package: > > > https://matplotlib.org/mpl-probscale/tutorial/closer_look_at_viz.html#using… > > > -Paul > > Thanks, Paul. I guess I might need to build a <dist>.pdf, .cdf, and .ppf > files for my distribution. What is not clear is how to specify the > alternative > directory to make them available to scipy > > On Mon, Jul 2, 2018 at 11:40 AM Sergio Rojas <sergio_r(a)mail.com> wrote: > > > Hello folks, > > > > How can one specify our own (user made) probability distribution > > function to scipy.stats.probplot ? > > > > Can it be done is the pdf used is not in a closed form function > > (meaning that the random drawings comes from a numerical > > procedure)? > > > > Salut, > > > > > > Sergio > > _______________________________________________ > > SciPy-User mailing list > > SciPy-User(a)python.org > > > https://mail.python.org/mailman/listinfo/scipy-user[https://mail.python.org… > > >

1 0

Re: [SciPy-User] Q: on scipy probplot user defined distribution function
by Sergio Rojas July 5, 2018

July 5, 2018

> Here's an example of using different distributions with the mpl-probscale > package: > https://matplotlib.org/mpl-probscale/tutorial/closer_look_at_viz.html#using… > -Paul Thanks, Paul. I guess I might need to build a <dist>.pdf, .cdf, and .ppf files for my distribution. What is not clear is how to specify the alternative directory to make them available to scipy On Mon, Jul 2, 2018 at 11:40 AM Sergio Rojas <sergio_r(a)mail.com> wrote: > Hello folks, > > How can one specify our own (user made) probability distribution > function to scipy.stats.probplot ? > > Can it be done is the pdf used is not in a closed form function > (meaning that the random drawings comes from a numerical > procedure)? > > Salut, > > > Sergio > _______________________________________________ > SciPy-User mailing list > SciPy-User(a)python.org > https://mail.python.org/mailman/listinfo/scipy-user[https://mail.python.org… >

2 1

Q: on scipy probplot user defined distribution function
by Sergio Rojas July 2, 2018

July 2, 2018

Hello folks, How can one specify our own (user made) probability distribution function to scipy.stats.probplot ? Can it be done is the pdf used is not in a closed form function (meaning that the random drawings comes from a numerical procedure)? Salut, Sergio

2 1