Mailman 3 November 2016 - 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

ANN: PyWavelets 0.5.1 Release
by Gregory Lee Nov. 30, 2016

Nov. 30, 2016

Dear all, On behalf of the PyWavelets development team I am pleased to announce the release of PyWavelets 0.5.1. This is a bug-fix only release with no new features as compared to 0.5.0. PyWavelets is a Python toolbox implementing both discrete and continuous wavelet transforms (mathematical time-frequency transforms) with a wide range of built-in wavelets. C/Cython are used for the low-level routines, enabling high performance. Key Features of PyWavelets are: * 1D, 2D and nD Forward and Inverse Discrete Wavelet Transform (DWT and IDWT) * 1D, 2D and nD Multilevel DWT and IDWT * 1D and 2D Forward and Inverse Stationary Wavelet Transform * 1D and 2D Wavelet Packet decomposition and reconstruction * 1D Continuous Wavelet Transform * When multiple valid implementations are available, we have chosen to maintain consistency with MATLAB's Wavelet Toolbox. Bugs Fixed ========== In release 0.5.0 the wrong edge mode was used for the following three deprecated mode names: ``ppd``, ``sp1``, and ``per``. All deprecated edge mode names are now correctly converted to the corresponding new names. One-dimensional discrete wavelet transforms did not properly respect the ``axis`` argument for complex-valued data. Prior to this release, the last axis was always transformed for arrays with complex dtype. This fix affects ``dwt``, ``idwt``, ``wavedec``, ``waverec``.

1 0

Re: [SciPy-User] mailing list migration to scipy-user@python.org
by Ralf Gommers Nov. 14, 2016

Nov. 14, 2016

On Tue, Nov 15, 2016 at 4:01 AM, Didrik Pinte <dpinte(a)enthought.com> wrote: > Hi everyone, > > In order to improve the level of service around the SciPy organisation > mailing lists, we've started migrating to the python.org mailman. > > The scipy-user mailing list has been transferred and now lives here: > > https://mail.python.org/mailman/listinfo/scipy-user > > User subscription and archives have all been transferred. You should only > change your address book and mail filters to use the new e-mail address of > the list: scipy-user(a)python.org. > > The old mailing list (scipy-user(a)scipy.org) will be made read-only . > > Let us know if you have any troubles with the migration. > Thanks Didrik! Ralf

1 0

brentq solver gives a strange bug
by Yuxiang Wang Nov. 12, 2016

Nov. 12, 2016

Dear all, When I run the following code snippet, everything works and x0 is within a and b: --- import numpy as np from scipy.optimize import newton, brentq E = 73000 A = 244.439436713 B = 520.091701874 n = 0.258964804689 strain_pt = 0.00722080901839 # 0.0613590727341 def eqn(stress_pt, strain_pt, A, B, n, E): return stress_pt - A - B * (strain_pt - stress_pt / E) ** n x0, r = brentq(eqn, args=(strain_pt, A, B, n, E), a=A, b=strain_pt * E, full_output=True) --- But when I run the following complete code (actually not that long, and self-contained): --- import numpy as np from scipy.optimize import brentq E = 73000 A = 244.439436713 B = 520.091701874 n = 0.258964804689 def eqn(stress_pt, strain_pt, A, B, n, E): return stress_pt - A - B * (strain_pt - stress_pt / E) ** n strain = np.logspace(0, 4, 100, endpoint=True) / 1e4 stress = np.empty_like(strain) for i in range(strain.shape[0]): if strain[i] <= A / E: stress[i] = E * strain[i] else: stress[i], r = brentq(eqn, args=(strain[i], A, B, n, E), a=A, b=strain[i] * E, full_output=True) --- Some solutions are out of the bracket! If I do: for i in range(strain.shape[0]): if strain[i] <= A / E: stress[i] = E * strain[i] else: stress[i], r = brentq(eqn, args=(strain[i], A, B, n, E), a=A, b=strain[i] * E, full_output=True) if stress[i] < A: print(r) I can see two data points being wrong. Obviously, at i == 46 and i == 69, we have x0 = 0.0 which is out of [a, b]. Could anyone please check whether this is repeatable on your machine? Shawn

2 2

Close this group?
by Denis Akhiyarov Nov. 5, 2016

Nov. 5, 2016

Maybe this group needs to closed? No response for last 6 months. See discussion here: https://mail.scipy.org/pipermail/scipy-user/2016-October/037051.html

1 0

Fwd: using curve_fit with a fixed parameter
by Alexandre Furlan Nov. 4, 2016

Nov. 4, 2016

---------- Forwarded message ---------- From: Alexandre Furlan <alexandrepfurlan(a)gmail.com> Date: 2016-11-04 14:59 GMT-02:00 Subject: using curve_fit with a fixed parameter To: scipy-user(a)scipy.org Hi all, I need to make a least square method of a model function, but a parameter of my model function is fixed (I don't change it). I my case, I have : def func(i,rij,eps,sigma) : where, i is similar "x", rij is a array used to obtain some parameters of the function, and eps and sigma are parameter that I want to optimize. I order to optimize these parameters I'm doing : for i in arange(len(rij)/natoms) : popt,pcov = curve_fit(LJ(i,rij,eps,sigma), x,Ek) where x = x[i] and Ek[i]. When make it, I have : TypeError('{!r} is not a Python function'.format(func)) TypeError: -0.019566048015813797 is not a Python function Do you known how to do this type of optmization using curve_fit ? many thanks for all Best Alexandre

2 1

ANN: pandas v0.19.1 released!
by Joris Van den Bossche Nov. 4, 2016

Nov. 4, 2016

Hi all, I'm pleased to announce the release of pandas 0.19.1. This is a bug-fix release from 0.19.0 and includes some small regression fixes, bug fixes and performance improvements. We recommend that all users upgrade to this version. See the v0.19.1 Whatsnew page <http://pandas.pydata.org/pandas-docs/version/0.19.1/whatsnew.html> for an overview of all bugs that have been fixed in 0.19.1. Thanks to all contributors! Joris --- *How to get it:* Source tarballs and windows/mac/linux wheels are available on PyPI (thanks to Christoph Gohlke for the windows wheels, and to Matthew Brett for setting up the mac/linux wheels). Conda packages are already available via the conda-forge channel (conda install pandas -c conda-forge). It will be available on the main channel shortly. *Issues:* Please report any issues on our issue tracker: https://github.com/pydata/ pandas/issues *Thanks to all the contributors of the 0.19.1 release:* - Adam Chainz - Anthonios Partheniou - Arash Rouhani - Ben Kandel - Brandon M. Burroughs - Chris - chris-b1 - Chris Warth - David Krych - dubourg - gfyoung - Iván Vallés Pérez - Jeff Reback - Joe Jevnik - Jon M. Mease - Joris Van den Bossche - Josh Owen - Keshav Ramaswamy - Larry Ren - mattrijk - Michael Felt - paul-mannino - Piotr Chromiec - Robert Bradshaw - Sinhrks - Thiago Serafim - Tom Bird

1 0

ANN: PyWavelets v0.5.0 release
by Gregory Lee Nov. 3, 2016

Nov. 3, 2016

On behalf of the PyWavelets development team I am pleased to announce the release of PyWavelets 0.5.0. PyWavelets is a Python toolbox implementing both discrete and continuous wavelet transforms (mathematical time-frequency transforms) with a wide range of built-in wavelets. C/Cython are used for the low-level routines, enabling high performance. Key Features of PyWavelets are: * 1D, 2D and nD Forward and Inverse Discrete Wavelet Transform (DWT and IDWT) * 1D, 2D and nD Multilevel DWT and IDWT * 1D and 2D Forward and Inverse Stationary Wavelet Transform * 1D and 2D Wavelet Packet decomposition and reconstruction * 1D Continuous Wavelet Transform * When multiple valid implementations are available, we have chosen to maintain consistency with MATLAB's Wavelet Toolbox. PyWavelets 0.5.0 is the culmination of 1 year of work. In addition to several new features, substantial refactoring of the underlying C and Cython code have been made. Highlights of this release include: - 1D continuous wavelet transforms - new discrete wavelets added (additional Debauchies and Coiflet wavelets) - new 'reflect' extension mode for discrete wavelet transforms - faster performance for multilevel forward stationary wavelet transforms (SWT) - n-dimensional support added to forward SWT - routines to convert multilevel DWT coefficients to and from a single array - axis support for multilevel DWT - substantial refactoring/reorganization of the underlying C and Cython code Full details in the release notes at: http://pywavelets.readthedocs.io/en/latest/release.0.5.0.html This release requires Python 2.6, 2.7 or 3.3-3.5 and Numpy 1.9.1 or greater. Sources can be found on https://pypi.python.org/pypi/PyWavelets and https://github.com/PyWavelets/pywt/releases. As always, new contributors are welcome to join us at https://github.com/PyWavelets/pywt

2 7