Mailman 3 May 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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Allan Variance
by Daniele Nicolodi Feb. 4, 2014

Feb. 4, 2014

Hello, does anyone know or have written and is willing to share some code to compute the Allan variance, modified Allan variance and friends, ideally both from frequency than from phase data? I'm writing my own code, it is not that difficult, but I would prefer the time required for testing and validation doing something more fun. If there is no available code implementing Allan variance, would it be interesting to include in in SciPy? Thank you so much. Best, Daniele

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noob question: numpy copy vs standard lib copy
by psoriasis June 28, 2013

June 28, 2013

I'm new to python. As I understand it, assignment copies by reference and to do otherwise requires a function like the standard library's copy or deepcopy functions. However, from what I see numpy has it's own copy function and using it on a random object (instance of a test class I made up not an array etc) doesn't seem to return the expected copy object. I did try importing the copy module and that worked but then the numpy copy module was "shadowed" but I don't know if that's a problem. Still, I'm sure numpy users need to copy regular objects so what's the standard solution to this? Note: I'm using the latest pythonxy (==> spyder, numpy, etc) Thanks

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problem with scipy.io.wavfile (urgent)
by rohan wadnerkar June 16, 2013

June 16, 2013

Hello all, I am trying to read .wav file using scipy.io.wavfile.read(). It reads some file properly. For some files its giving following error... Warning (from warnings module): File "D:\project\cardiocare-1.0\src\scipy\io\wavfile.py", line 121 warnings.warn("chunk not understood", WavFileWarning)WavFileWarning: chunk not understoodTraceback (most recent call last): File "D:\project\cardiocare-1.0\src\ccare\plot.py", line 37, in plot input_data = read(p.bitfile) File "D:\project\cardiocare-1.0\src\scipy\io\wavfile.py", line 119, in read data = _read_data_chunk(fid, noc, bits) File "D:\project\cardiocare-1.0\src\scipy\io\wavfile.py", line 56, in _read_data_chunk data = data.reshape(-1,noc)ValueError: total size of new array must be unchanged Can any one suggest me any solution? -- -- -- -- -- -- -- -- -- -- Rohan Wadnerkar 09590686578

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Sparse Matricies and NNLS
by Calvin Morrison June 14, 2013

June 14, 2013

Hi! I have a very large matrix that I am using with the scipy.optimize.nnls function, however the matrix is so large that it takes 30Gb of memory to load with python! I was thinking about using a sparse matrix since it is relatively sparse, but the problem is that even if I was to use the sparse matricies, the nnls function only accepts a ndarray, not a sparse matrix. (when I try and throw a sparse matrix at it I get an error.) So of course I'd need to convert it to a dense array before passing it into nnls, but that would totally void the whole point of a sparse array, because then python would still have to allocate the full dense matrix. Does anyone have an idea about how to efficiently pass a matrix and store it without blowing up the memory usage? Thank you, Calvin

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Storing return values of optimize.fmin()
by Jeroen Meidam June 14, 2013

June 14, 2013

Hi, I am using optimize.fmin to minimize a function over 2 parameters. In the documentation it says that the output is: (xopt, {fopt, iter, funcalls, warnflag}) I have no problem putting xopt into a variable, because this is simply done by writing: xopt = fmin(function,x0) After which I can use xopt for anything I need it for. What I want however, is to store "fopt" into a variable, like I did with xopt. In the standard case, fopt is only returned as text in the output stream: " Optimization terminated successfully. Current function value: -0.995801 <--- This is what I'm interested in Iterations: 35 Function evaluations: 71 " How can I store it into a variable? Is it possible? Thanks, Jeroen

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sqrtm is too slow for matrices of size 1000
by Vivek Kulkarni June 14, 2013

June 14, 2013

Hi, I am implementing spectral clustering for my course work and am using the sqrtm function to find the square root of a matrix . But its far too slow, my matrix is of size (1258,1258). Any suggestions on how I can speed things up or some other function that scipy supports which can be used. I am implementing the algorithm as described here: http://books.nips.cc/papers/files/nips14/AA35.pdf Finding the square root of D^(-1) is way too slow for D^-1 of size (1258,1258). Thanks. Vivek.

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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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