Mailman 3 November 2019 - 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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numpy.longdouble and scipy status?
by Iyán Méndez Veiga Nov. 13, 2019

Nov. 13, 2019

Hi, How is the current status of SciPy when using np.longdouble (np.float128)? I am doing some calculations where I would like to get a resolution of 1e-18. np.float128 in my computer would be ok for that, at least based on the output of numpy.finfo(numpy.float128). However, some scipy functions always output numpy.float64 even though the input is numpy.float128. For example, try the following code: import numpy as np from scipy.linalg import expm I = np.eye(3, dtype=np.float128) A = expm(I) print(A.dtype) >> float128 >> float64 Is this behavious expected? I couldn't find anything on scipy docs, sorry if I overlooked. Thanks, Iyán

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NumPy 1.17.4 release.
by Charles R Harris Nov. 11, 2019

Nov. 11, 2019

Hi All, On behalf of the NumPy team I am pleased to announce that NumPy 1.17.4 has been released. This is a bugfix release. The Python versions supported in this release are 3.5-3.8. Downstream developers should use Cython >= 0.29.13 for Python 3.8 support and OpenBLAS >= 3.7 to avoid wrong results on the Skylake architecture. The NumPy Wheels for this release can be downloaded from PyPI <https://pypi.org/project/numpy/1.17.4/>, source archives and release notes are available from Github <https://github.com/numpy/numpy/releases/tag/v1.17.4>. *Highlights* - Fixed `random.random_integers` biased generation of 8 and 16 bit integers. - Fixed `np.einsum` regression on Power9 and z/Linux. - Fixed histogram problem with signed integer arrays *Contributors* A total of 5 people contributed to this release. People with a "+" by their names contributed a patch for the first time. - Charles Harris - Chris Burr + - Matti Picus - Qiming Sun + - Warren Weckesser *Pull requests merged* A total of 8 pull requests were merged for this release. - gh-14758: BLD: Declare support for python 3.8 - gh-14781: BUG: Random: biased samples from integers() with 8 or 16 bit... - gh-14851: BUG: Fix `_ctypes` class circular reference. (gh-13808) - gh-14852: BLD: Add 'apt update' to shippable - gh-14855: BUG: Fix `np.einsum` errors on Power9 Linux and z/Linux - gh-14857: BUG: Fix histogram problem with signed integer arrays. - gh-14858: BLD: Prevent -flto from optimising long double representation... - gh-14866: MAINT: move buffer.h -> npy_buffer.h to avoid conflicts Cheers, Charles Harris

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Re: [SciPy-User] Scipy and information theory
by Robert Lucente - Pipeline.Com Nov. 11, 2019

Nov. 11, 2019

> interested in using log2 instead of natural logarithm. I was expecting > to be able to choose the base with this functions but it is not > possible Why not use Python's built in fcn? https://docs.python.org/3/library/math.html#math.log2 math.log2(x) Return the base-2 logarithm of x. This is usually more accurate than log(x, 2). New in version 3.3. -----Original Message----- From: Robert Lucente - Pipeline.Com <rlucente(a)pipeline.com> Sent: Friday, November 8, 2019 12:11 PM To: 'scipy-user(a)python.org' <scipy-user(a)python.org> Cc: Robert Gmail Backup 2 Lucente (robert.backup.2.lucente(a)gmail.com) <robert.backup.2.lucente(a)gmail.com> Subject: Re: Scipy and information theory > interested in using log2 instead of natural logarithm. I was expecting > to be able to choose the base with this functions but it is not > possible Why not use Python's built in fcn? https://docs.python.org/3/library/math.html#math.log math.log(x[, base]) With one argument, return the natural logarithm of x (to base e). With two arguments, return the logarithm of x to the given base, calculated as log(x)/log(base). -----Original Message----- From: SciPy-User <scipy-user-bounces+rlucente=pipeline.com(a)python.org> On Behalf Of scipy-user-request(a)python.org Sent: Friday, November 8, 2019 12:00 PM To: scipy-user(a)python.org Subject: SciPy-User Digest, Vol 195, Issue 2 Send SciPy-User mailing list submissions to scipy-user(a)python.org To subscribe or unsubscribe via the World Wide Web, visit https://mail.python.org/mailman/listinfo/scipy-user or, via email, send a message with subject or body 'help' to scipy-user-request(a)python.org You can reach the person managing the list at scipy-user-owner(a)python.org When replying, please edit your Subject line so it is more specific than "Re: Contents of SciPy-User digest..." Today's Topics: 1. Scipy and information theory (Iy?n M?ndez Veiga) 2. Re: Scipy and information theory (Ralf Gommers) ---------------------------------------------------------------------- Message: 1 Date: Thu, 07 Nov 2019 13:11:55 +0100 From: Iy?n M?ndez Veiga <me(a)iyanmv.com> To: scipy-user(a)python.org Subject: [SciPy-User] Scipy and information theory Message-ID: <20976252.W2eyRVhfPJ@theotp40> Content-Type: text/plain; charset="iso-8859-1" Hi, I discovered recently some interesting functions in scipy that are useful in the context of information theory. In particular, xlogy, entr and rel_entr. However, for the calculations I want to do I am interested in using log2 instead of natural logarithm. I was expecting to be able to choose the base with this functions but it is not possible. Do you think it would be a nice feature to add to scipy? Maybe not for a general base, but at least the bases that are available in numpy (log2, log10). The workaround I am using with xlogy(x,y) (and similar functions) is multiplying x array by log2(e). Best wishes, Iy?n ------------------------------ Message: 2 Date: Fri, 8 Nov 2019 10:54:32 -0500 From: Ralf Gommers <ralf.gommers(a)gmail.com> To: SciPy Users List <scipy-user(a)python.org> Subject: Re: [SciPy-User] Scipy and information theory Message-ID: <CABL7CQh=LDNJfH+P7tJQz2wB8SyeY3uRKRK5NFYs4eWHxYnYTg(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Iy?n, On Thu, Nov 7, 2019 at 12:21 PM Iy?n M?ndez Veiga <me(a)iyanmv.com> wrote: > Hi, > > I discovered recently some interesting functions in scipy that are > useful in the context of information theory. In particular, xlogy, > entr and rel_entr. > However, for the calculations I want to do I am interested in using > log2 instead of natural logarithm. I was expecting to be able to > choose the base with this functions but it is not possible. > > Do you think it would be a nice feature to add to scipy? Maybe not for > a general base, but at least the bases that are available in numpy > (log2, log10). > This does sound like a useful feature to add to these functions. I'm not sure how easy it is to add a keyword to those functions though, since the ufunc machinery may be limited in flexibility. Maybe someone else can say straight away. If you want to start looking into implementing this, here are some notes of where to start: http://scipy.github.io/devdocs/dev/core-dev/index.html#scipy-special Cheers, Ralf > The workaround I am using with xlogy(x,y) (and similar functions) is > multiplying x array by log2(e). > > Best wishes, > Iy?n > > > _______________________________________________ > SciPy-User mailing list > SciPy-User(a)python.org > https://mail.python.org/mailman/listinfo/scipy-user >

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best way to get minimum and maximum support for generic random variable
by Ben Avrahami Nov. 10, 2019

Nov. 10, 2019

Hello, I'm trying to come up with a simple universal method to get the minimum and maximum values for any random variable (both rv_continuous and rv_discrete). The best I came up with was rv.interval(1) but that is both more obtuse than I'd like and error prone (as seen in the issue I opened: https://github.com/scipy/scipy/issues/11026), also, it's not exactly was the method is made for which makes me uneasy. Is there any better way to get the smallest and largest possible values for any rv? regards, Ben.

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Re: [SciPy-User] Scipy and information theory
by Robert Lucente - Pipeline.Com Nov. 8, 2019

Nov. 8, 2019

> interested in using log2 instead of natural logarithm. I was expecting to be able to choose the base with this functions but it is not possible Why not use Python's built in fcn? https://docs.python.org/3/library/math.html#math.log math.log(x[, base]) With one argument, return the natural logarithm of x (to base e). With two arguments, return the logarithm of x to the given base, calculated as log(x)/log(base). -----Original Message----- From: SciPy-User <scipy-user-bounces+rlucente=pipeline.com(a)python.org> On Behalf Of scipy-user-request(a)python.org Sent: Friday, November 8, 2019 12:00 PM To: scipy-user(a)python.org Subject: SciPy-User Digest, Vol 195, Issue 2 Send SciPy-User mailing list submissions to scipy-user(a)python.org To subscribe or unsubscribe via the World Wide Web, visit https://mail.python.org/mailman/listinfo/scipy-user or, via email, send a message with subject or body 'help' to scipy-user-request(a)python.org You can reach the person managing the list at scipy-user-owner(a)python.org When replying, please edit your Subject line so it is more specific than "Re: Contents of SciPy-User digest..." Today's Topics: 1. Scipy and information theory (Iy?n M?ndez Veiga) 2. Re: Scipy and information theory (Ralf Gommers) ---------------------------------------------------------------------- Message: 1 Date: Thu, 07 Nov 2019 13:11:55 +0100 From: Iy?n M?ndez Veiga <me(a)iyanmv.com> To: scipy-user(a)python.org Subject: [SciPy-User] Scipy and information theory Message-ID: <20976252.W2eyRVhfPJ@theotp40> Content-Type: text/plain; charset="iso-8859-1" Hi, I discovered recently some interesting functions in scipy that are useful in the context of information theory. In particular, xlogy, entr and rel_entr. However, for the calculations I want to do I am interested in using log2 instead of natural logarithm. I was expecting to be able to choose the base with this functions but it is not possible. Do you think it would be a nice feature to add to scipy? Maybe not for a general base, but at least the bases that are available in numpy (log2, log10). The workaround I am using with xlogy(x,y) (and similar functions) is multiplying x array by log2(e). Best wishes, Iy?n ------------------------------ Message: 2 Date: Fri, 8 Nov 2019 10:54:32 -0500 From: Ralf Gommers <ralf.gommers(a)gmail.com> To: SciPy Users List <scipy-user(a)python.org> Subject: Re: [SciPy-User] Scipy and information theory Message-ID: <CABL7CQh=LDNJfH+P7tJQz2wB8SyeY3uRKRK5NFYs4eWHxYnYTg(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Iy?n, On Thu, Nov 7, 2019 at 12:21 PM Iy?n M?ndez Veiga <me(a)iyanmv.com> wrote: > Hi, > > I discovered recently some interesting functions in scipy that are > useful in the context of information theory. In particular, xlogy, > entr and rel_entr. > However, for the calculations I want to do I am interested in using > log2 instead of natural logarithm. I was expecting to be able to > choose the base with this functions but it is not possible. > > Do you think it would be a nice feature to add to scipy? Maybe not for > a general base, but at least the bases that are available in numpy > (log2, log10). > This does sound like a useful feature to add to these functions. I'm not sure how easy it is to add a keyword to those functions though, since the ufunc machinery may be limited in flexibility. Maybe someone else can say straight away. If you want to start looking into implementing this, here are some notes of where to start: http://scipy.github.io/devdocs/dev/core-dev/index.html#scipy-special Cheers, Ralf > The workaround I am using with xlogy(x,y) (and similar functions) is > multiplying x array by log2(e). > > Best wishes, > Iy?n > > > _______________________________________________ > SciPy-User mailing list > SciPy-User(a)python.org > https://mail.python.org/mailman/listinfo/scipy-user >

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Scipy and information theory
by Iyán Méndez Veiga Nov. 8, 2019

Nov. 8, 2019

Hi, I discovered recently some interesting functions in scipy that are useful in the context of information theory. In particular, xlogy, entr and rel_entr. However, for the calculations I want to do I am interested in using log2 instead of natural logarithm. I was expecting to be able to choose the base with this functions but it is not possible. Do you think it would be a nice feature to add to scipy? Maybe not for a general base, but at least the bases that are available in numpy (log2, log10). The workaround I am using with xlogy(x,y) (and similar functions) is multiplying x array by log2(e). Best wishes, Iyán

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[ANN] pvfactors: a view-factor network model for bifacial PV by SunPower
by Dr. Mark Alexander Mikofski PhD Nov. 6, 2019

Nov. 6, 2019

SunPower has just released the latest version of pvfactors (v1.3.0), a Python package for modeling the incident irradiance on bifacial photovoltaic (PV) using the network radiosity model. Bifacial PV are solar panels that can generate energy from both the front and back surfaces. PyPI: https://pypi.org/project/pvfactors/ GitHub: https://github.com/SunPower/pvfactors/releases Thanks SunPower! -- Mark Mikofski, PhD (2005) *Fiat Lux*

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