Mailman 3 February 2013 - 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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Linear interpolation in 3D
by Hardock, Andreas June 13, 2013

June 13, 2013

Hi, I'm trying to interpolate a 3D data (from the pic attached) with the interp2d command. What I have, are three vectors f, z, A (x, y, z respectively, A is the percentage data given on the isolines). I first put the f and z in a meshgrid and afterwards in the griddata to get a 3D-grid then started the interpolateion. I plotted the the data after gridding, and I observed that almost all nodes are ignored. Do you have any idea how to prepare data to the interp2d command? Don't hesitate to suggest any other solution. my code so far is: import numpy as np from mpl_toolkits.mplot3d import axes3d from scipy.interpolate import interp2d import matplotlib.pyplot as plt from matplotlib import mlab plt.clf() fig = plt.figure(1) ax = axes3d.Axes3D(fig) #read data (ff,ZZ,A,a) = np.loadtxt("accuracy-map.txt", unpack=True) f=np.log10(ff) z=np.log10(ZZ) ##grid everything fgrid, zgrid=np.meshgrid(f,z) #define grid ef=np.linspace(min(f), max(f), len(f)) ez=np.linspace(min(z), max(z), len(f)) Agrid=mlab.griddata(f,z,A, ef,ez) int2d=interp2d(fgrid, zgrid, Agrid, kind='linear') ax.plot(f, z, A, 'ok', markerfacecolor='w') ax.plot_surface(fgrid, zgrid, Agrid) ax.set_xlim3d((min(f), max(f))) ax.set_ylim3d(min(z), max(z)) ax.set_zlim3d(0,100) plt.show()

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efficiency of the simplex routine: R (optim) vs scipy.optimize.fmin
by servant mathieu May 10, 2013

May 10, 2013

Dear scipy users, Again a question about optimization. I've just compared the efficiency of the simplex routine in R (optim) vs scipy (fmin), when minimizing a chi-square. fmin is faster than optim, but appears to be less efficient. In R, the value of the function is always minimized step by step (there are of course some exceptions) while there is lot of fluctuations in python. Given that the underlying simplex algorithm is supposed to be the same, which mechanism is responsible for this difference? Is it possible to constrain fmin so it could be more rigorous? Cheers, Mathieu

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scipy sprint @ EuroSciPy '12?
by Ralf Gommers May 1, 2013

May 1, 2013

Hi all, Would people be interested in having a scipy sprint at EuroSciPy this year? Last year we tried to do a last minute mini-sprint and ended up hunting for wifi access for half the time, so it would be good to organize things better this time around. I'm thinking a one-day sprint on Wed Aug 22nd would be good. If there's interest, I'm happy to organize (contact the conference organizers for a room, create a wiki page, etc.). Ralf

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Re: [SciPy-User] cobyla
by The Helmbolds March 26, 2013

March 26, 2013

On my system (Windows 7, Python 2.7.x and IDLE, latest SciPy), I observe the following behavior with fmin_cobyla and minimize's COBYLA method. Case 1: When run either in the IDLE interactive shell or within an enclosing Python program: 1.1. The fmin_cobyla function never returns the Results dictionary, and never displays it to Python's stdout. This is true regardless of the function call's disp setting. 1.2. The 'minimize' function always returns the Results dictionary but never displays it to Python's stdout. Again, this is true regardless of the function call's disp setting. Case 2: When run interactively in Window's Command Prompt box: 2.1 The fmin_cobyla function never returns the Result dictionary, regardless of the function call's disp setting. Setting disp to True or False either displays the Results dictionary in the command box or not (respectively). I don't think the Results dictionary gets to the command box via stdout. 2.2 The 'minimize' function always returns the Result dictionary, regardless of the function call's disp setting. Setting disp to True or False either displays the Results dictionary in the command box or not (respectively). I don't think the Results dictionary gets to the command box via stdout. My thanks to all who helped clarify this situation. Bob H

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Installing Polymode
by Manders, Mark March 14, 2013

March 14, 2013

I was trying to install polymode into my Python 2.7 (32bit), for some reason the following errors come up. It can't seem to find the numpy 'lapack' libraries even though I have numpy & scipy installed. I also have boost_python installed but it can't find anything from that either. Z:\polymode>setup.py install W: Using scipy hankel ratio - this may be inaccurate! lapack_opt_info: lapack_mkl_info: mkl_info: libraries mkl,vml,guide not found in C:\Python27\lib libraries mkl,vml,guide not found in C:\ libraries mkl,vml,guide not found in C:\Python27\libs NOT AVAILABLE NOT AVAILABLE atlas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in C:\Python27\lib libraries lapack_atlas not found in C:\Python27\lib libraries ptf77blas,ptcblas,atlas not found in C:\ libraries lapack_atlas not found in C:\ libraries ptf77blas,ptcblas,atlas not found in C:\Python27\libs libraries lapack_atlas not found in C:\Python27\libs numpy.distutils.system_info.atlas_threads_info NOT AVAILABLE atlas_info: libraries f77blas,cblas,atlas not found in C:\Python27\lib libraries lapack_atlas not found in C:\Python27\lib libraries f77blas,cblas,atlas not found in C:\ libraries lapack_atlas not found in C:\ libraries f77blas,cblas,atlas not found in C:\Python27\libs libraries lapack_atlas not found in C:\Python27\libs numpy.distutils.system_info.atlas_info NOT AVAILABLE C:\Python27\lib\site-packages\numpy\distutils\system_info.py:1340: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) lapack_info: libraries lapack not found in C:\Python27\lib libraries lapack not found in C:\ libraries lapack not found in C:\Python27\libs NOT AVAILABLE C:\Python27\lib\site-packages\numpy\distutils\system_info.py:1351: UserWarning: Lapack (http://www.netlib.org/lapack/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [lapack]) or by setting the LAPACK environment variable. warnings.warn(LapackNotFoundError.__doc__) lapack_src_info: NOT AVAILABLE C:\Python27\lib\site-packages\numpy\distutils\system_info.py:1354: UserWarning: Lapack (http://www.netlib.org/lapack/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [lapack_src]) or by setting the LAPACK_SRC environment variable. warnings.warn(LapackSrcNotFoundError.__doc__) NOT AVAILABLE boost_python_info: NOT AVAILABLE Traceback (most recent call last): File "Z:\polymode\setup.py", line 69, in <module> setup_package() File "Z:\polymode\setup.py", line 63, in setup_package cmdclass = {'doc' : generate_api_docs} File "C:\Python27\lib\site-packages\numpy\distutils\core.py", line 152, in set up config = configuration() File "Z:\polymode\setup.py", line 44, in configuration config.add_subpackage(package_name) File "C:\Python27\lib\site-packages\numpy\distutils\misc_util.py", line 1002, in add_subpackage caller_level = 2) File "C:\Python27\lib\site-packages\numpy\distutils\misc_util.py", line 971, i n get_subpackage caller_level = caller_level + 1) File "C:\Python27\lib\site-packages\numpy\distutils\misc_util.py", line 908, i n _get_configuration_from_setup_py config = setup_module.configuration(*args) File "Polymode\setup.py", line 10, in configuration config.add_subpackage('mathlink') File "C:\Python27\lib\site-packages\numpy\distutils\misc_util.py", line 1002, in add_subpackage caller_level = 2) File "C:\Python27\lib\site-packages\numpy\distutils\misc_util.py", line 971, i n get_subpackage caller_level = caller_level + 1) File "C:\Python27\lib\site-packages\numpy\distutils\misc_util.py", line 908, i n _get_configuration_from_setup_py config = setup_module.configuration(*args) File "Polymode\mathlink\setup.py", line 71, in configuration raise NotFoundError,'no lapack/blas resources found' numpy.distutils.system_info.NotFoundError: no lapack/blas resources found

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pupynere/scipy.io.netcdf
by Ryan May March 6, 2013

March 6, 2013

Hi, Anyone know if pupynere (a version of which is in scipy.io.netcdf) supports writing files with 64-bit offsets? This allows writing files larger than 2GB. Ryan -- Ryan May Graduate Research Assistant School of Meteorology University of Oklahoma

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_dop.error: failed in processing argument list for call-back fcn.
by SHIHUI GUO March 1, 2013

March 1, 2013

HI all, I want to use scipy to implement an oscillator, ie. solving a secod-order ordinary differential equation, my code is: =================================== from scipy.integrate import ode y0,t0 = [0, 1], 0 def fun(t, y, params): rou = 1 omega = 10 sigma = 1 # convergence rate, ie, lambda conrate = 10 temp = -conrate*((y[0]^2+y[1]^2)/rou^2-sigma) dy = temp*y[0] - omega*y[1] ddy = omega*y[0] + temp*y[1] return [dy, ddy] test = ode(fun).set_integrator('dopri5') test.set_initial_value(y0, t0) t1 = 10 dt = 0.1 while test.successful() and test.t<t1: test.integrate(test.t+dt) print test.t, test.yy =================================== =================================== The error says: _dop.error: failed in processing argument list for call-back fcn. File "/home/shepherd/python/research/testode.py", line 23, in <module> test.integrate(test.t+dt) File "/home/shepherd/epd/epd_free-7.3-2-rh5-x86/lib/python2.7/site-packages/scipy/integrate/_ode.py", line 333, in integrate self.f_params, self.jac_params) File "/home/shepherd/epd/epd_free-7.3-2-rh5-x86/lib/python2.7/site-packages/scipy/integrate/_ode.py", line 827, in run tuple(self.call_args) + (f_params,))) =================================== Previously I use the ubuntu default python, and scipy is 0.9.0. Some thread says it is a bug and has been fixed in 0.10.0, so I switched to enthought, now the scipy is newest version, but the error remains. Thanks for any help. Shihui -- * --------------------------------------------------------------------------------------- * SHIHUI GUO National Center for Computer Animation Bournemouth University United Kingdom BU is a Disability Two Ticks Employer and has signed up to the Mindful Employer charter. Information about the accessibility of University buildings can be found on the BU DisabledGo webpages [ http://www.disabledgo.com/en/org/bournemouth-university ] This email is intended only for the person to whom it is addressed and may contain confidential information. If you have received this email in error, please notify the sender and delete this email, which must not be copied, distributed or disclosed to any other person. Any views or opinions presented are solely those of the author and do not necessarily represent those of Bournemouth University or its subsidiary companies. Nor can any contract be formed on behalf of the University or its subsidiary companies via email.

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