Mailman 3 August 2014 - 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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Fwd: ANN: Vispy 0.3, high-performance visualization in Python
by Cyrille Rossant Aug. 30, 2014

Aug. 30, 2014

Hi, We are pleased to announce the release of Vispy version 0.3! This release provides new graphics API (including a scene graph), a basic OpenGL backend for matplotlib, and experimental integration in the IPython notebook. Further, we have improved the existing modules and added several application backends (e.g. wx and sdl2). We are now focusing our efforts on: * Consolidating the higher-level graphics APIs: visuals, transforms, scene graph. * Improving the performance of the scene graph, notably through batch rendering (Collections system). * Adding more features to the matplotlib backend. * Improving the integration in the IPython notebook: better performance, improved event loop integration, client-side backend with WebGL. Eventually, scientists with no knowledge of OpenGL will be able to easily create fast and scalable interactive visualizations. We will greatly appreciate any feedback, bug reports, and feature requests. See http://vispy.org for downloads and more information. The Vispy team

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Re: [SciPy-User] ANN: NumPy 1.9.0 release candidate 1 available
by Neal Becker Aug. 29, 2014

Aug. 29, 2014

OK, it's fixed by doing: rm -rf ~/.local/lib/python2.7/site-packages/numpy* python setup.py install --user I guess something was not cleaned out from previous packages

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loadmat: Unknown mat file type, version 49
by Florian Lindner Aug. 27, 2014

Aug. 27, 2014

Hello, when trying to read a matlab file, writen bei petSC, I get this error: Traceback (most recent call last): File "petsc_plot.py", line 9, in <module> rbf_results = scipy.io.loadmat("rbf_results") File "/usr/lib/python3.4/site-packages/scipy/io/matlab/mio.py", line 131, in loadmat MR = mat_reader_factory(file_name, appendmat, **kwargs) File "/usr/lib/python3.4/site-packages/scipy/io/matlab/mio.py", line 55, in mat_reader_factory mjv, mnv = get_matfile_version(byte_stream) File "/usr/lib/python3.4/site-packages/scipy/io/matlab/miobase.py", line 237, in get_matfile_version % ret) ValueError: Unknown mat file type, version 49, 49 The file contains a matrix and a vector and looks like that: %Mat Object:Nodes 1 MPI processes % type: seqdense % Size = 10 2 Nodes = zeros(10,2); Nodes = [ 7.2003197397953400e-01 4.0114727059134836e-01 6.1793966542126100e-02 5.2764865382548720e-01 1.0022337819588500e-02 1.4405427480322786e-01 1.4463931936456476e-01 9.9650445216117589e-01 3.9777780919128602e-01 1.0677308875937896e-01 7.3036588248200474e-02 9.8905332488367748e-01 1.0386628927366459e-01 7.3131275919223881e-01 2.5078039364333193e-01 3.0846024921541471e-01 9.8405227390177075e-01 1.8055644102282642e-01 7.3851607000756303e-01 9.8604536855510361e-01 ]; %Vec Object:Coefficients 1 MPI processes % type: seq Coefficients = [ 5.0245251254608746e+04 2.3659864438721524e+04 -1.4592196188522011e+05 1.4189477757354762e+04 7.8494387129370181e+04 2.5176418131682707e+05 -4.3384330330706594e+04 -1.7567379893104360e+05 6.5349663489607065e+02 -5.4052285933927575e+04 ]; The petsc C code: PetscViewer viewer; PetscViewerASCIIOpen(PETSC_COMM_WORLD, "rbf_results", &viewer); PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_MATLAB); MatView(Nodes, viewer); VecView(c, viewer); PetscViewerDestroy(&viewer); Any idea what could be the problem here? System is ArchLinux, SciPy 0.14, NumPy 1.8.2, Python 3.4.1 Thanks, Florian

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Convert 3d NumPy array into 2d
by phinn stuart Aug. 27, 2014

Aug. 27, 2014

Hi everyone, how can I convert (1L, 480L, 1440L) shaped numpy array into (480L, 1440L)? Thanks in the advance. phinn

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time-frequency diagram with wavelet transform
by Frédéric Parrenin Aug. 22, 2014

Aug. 22, 2014

Dear all, I have a irregularly sampled time series and I would like to plot its time-frequency diagram using wavelet transform. (I am relatively new in wavelets, especially in python) Is there any example on how to do this? (I could not find any clear example on the internet) Thanks in advance, best regards, Frédéric

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ANN: BayesPy 0.2
by Jaakko Luttinen Aug. 21, 2014

Aug. 21, 2014

Dear all, I am pleased to announce the release of BayesPy version 0.2. BayesPy provides tools for Bayesian inference in Python. In particular, it implements variational message passing framework, which enables modular and efficient way to construct models and perform approximate posterior inference. Download: https://pypi.python.org/pypi/bayespy/ Documentation: http://www.bayespy.org Repository: https://github.com/bayespy/bayespy Comments, feedback and contributions are welcome. Best regards, Jaakko

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