Mailman 3 June 2015 - 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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Playing numpy array over speakers
by Todd Oct. 17, 2015

Oct. 17, 2015

Is anyone aware of a well-maintained, simple, cross-platform python package that can play a numpy array as sound over speakers? I am aware of https://wiki.python.org/moin/Audio/. However, in all the cases there, as far as I can find they either do not support numpy arrays, are not cross-platform, cannot playback sound at all, or are unmaintained. There is also PySoundCard, which would do what I need but also appears to be unmaintained (no release in over a year, and no commits in 5 months, no release with serious bugfixes mentioned in commits).

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Thinking in HDF5
by nitin chandra June 30, 2015

June 30, 2015

Hello All, I have been on this for a long time and have done a lot of research / reading on this topic, HDF5. To use it for development of in-house software for design calculation of various alignments. A lot many time the basic alignment information is picked from a map / satellite imageries. Kilometre, ground level, geographic feature on the proposed route, etc. , in a csv file. Any where between 7-9 files are generated for each alignment. 1. How to read / write data into the HDF5 file ? What after creating root ? 2. In a regular situation, I have 2 input file with 3 column csv data, and 2 output files. How to do that within the same root ? Will be working in Python and c / c++. This is just the basic. If I can do this much, I can do the rest, hopefully :) Thanks to All Nitin PS :- Will post in boost-user list too.

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Re: [SciPy-User] Quick Implementation of Matrix via a Sum
by Lorenzo Isella June 29, 2015

June 29, 2015

>Hi Lorenzo: > >Is this what you want? > >https://github.com/guziy/PyNotebooks/blob/master/np_demo1.ipynb > >Cheers > >2015-06-29 11:03 GMT-04:00 Lorenzo Isella <lorenzo.isella(a)gmail.com>: > >> Dear All, >> My scipy is unbelievably rusty and I am struggling with a simple >> problem. >> Please consider the following quantity (which I write a la LaTex) >> >> D_{n,r}=\frac{1}{n} \sum_{j=1}^r frac{1}{n-j+1} for r=1,2,...n >> >> How can I implement this efficiently as a numpy array? >> I am struggling with newaxis, but I am not going very far. >> Any suggestion is welcome. >> Cheers >> >> Lorenzo >> Perfect! Thanks. Lorenzo

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Quick Implementation of Matrix via a Sum
by Lorenzo Isella June 29, 2015

June 29, 2015

Dear All, My scipy is unbelievably rusty and I am struggling with a simple problem. Please consider the following quantity (which I write a la LaTex) D_{n,r}=\frac{1}{n} \sum_{j=1}^r frac{1}{n-j+1} for r=1,2,...n How can I implement this efficiently as a numpy array? I am struggling with newaxis, but I am not going very far. Any suggestion is welcome. Cheers Lorenzo

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Why is Ward limited to Euclidean/full data matrix?
by Juan Nunez-Iglesias June 29, 2015

June 29, 2015

The Wikipedia page seems to suggest that Ward's method can be implemented just from the distance matrix. Why is it restricted to using the full dataset and only Euclidean distance? https://en.wikipedia.org/wiki/Ward's_method#Lance.E2.80.93Williams_algorithms

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notebook crash with fmin_lbfgsb
by josef.pktd＠gmail.com June 27, 2015

June 27, 2015

Just a general question: Has anybody experience ipython notebook crashes with fmin_lbfgsb? Is it just my setup or is this more general? When I ran an estimation that uses fmin_lbfgsb for the optimization, then the notebook kernel shuts down and restarts. (Windows 8.1, winpython 3.4, previous release of ipython, I think) 2015-06-27 09:39:42.956 [NotebookApp] Saving notebook at /Untitled0.ipynb RUNNING THE L-BFGS-B CODE * * * Machine precision = 2.220D-16 N = 5 M = 12 forrtl: severe (47): write to READONLY file, unit 8, file M:\josef_new\eclipse_w s\statsmodels\statsmodels_py34\examples\notebooks\iterate.dat Image PC Routine Line Source libifcoremd.dll 0000000009154E2C Unknown Unknown Unknown _lbfgsb.pyd 00007FFC31529C01 Unknown Unknown Unknown _lbfgsb.pyd 00007FFC31524AD3 Unknown Unknown Unknown _lbfgsb.pyd 00007FFC3152465C Unknown Unknown Unknown _lbfgsb.pyd 00007FFC315224BF Unknown Unknown Unknown python34.dll 0000000073C28771 Unknown Unknown Unknown python34.dll 0000000073CE4074 Unknown Unknown Unknown ... python34.dll 0000000073BCD4D3 Unknown Unknown Unknown python.exe 000000001C1911AE Unknown Unknown Unknown KERNEL32.DLL 00007FFC56E313D2 Unknown Unknown Unknown ntdll.dll 00007FFC59335444 Unknown Unknown Unknown 2015-06-27 09:40:04.227 [NotebookApp] KernelRestarter: restarting kernel (1/5) WARNING:root:kernel a46450ce-69fe-4034-9869-4f1f3c543390 restarted AFAIR, I didn't have problems with spyder AFAIR, setting iprint=0 avoided the crash in the previous example, but doens't seem to fix it in my current example. I switched to bfgs, which works well in my example (aside: example is statsmodels ARIMA which uses fmin_lbfgsb by default) Josef

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Increasing the maximum number of points in the spatial.Delaunay triangulation
by Cantwell Carson June 22, 2015

June 22, 2015

I am working on an image processing algorithm that relies on the Delaunay triangulation of a 3d image. Unfortunately, I need to work on images with more than 2**24 points that go into the Delaunay triangulation. This is problematic because the Qhull routine labels the input vertices with a 24-bit label. I have tried editing the source code for qhull here in libqhull.h, lines 352, 380 and 663 - 664: unsigned id:32; /* unique identifier, =>room for 8 flags, bit field matches qh.ridge_id */ ... unsigned id:32; /* unique identifier, bit field matches qh.vertex_id */ ... unsigned ridge_id:32; /* ID of next, new ridge from newridge() */ unsigned vertex_id:32; /* ID of next, new vertex from newvertex() */ poly.c, lines 569, 1019 - 1023: long ridgeid; ... if (qh ridge_id == 0xFFFFFFFF) { qh_fprintf(qh ferr, 7074, "\ qhull warning: more than %d ridges. ID field overflows and two ridges\n\ may have the same identifier. Otherwise output ok.\n", 0xFFFFFFFF); and poly2.c, lines 2277 - 2279: if (qh vertex_id == 0xFFFFFFFF) { qh_fprintf(qh ferr, 6159, "qhull error: more than %d vertices. ID field overflows and two vertices\n\ may have the same identifier. Vertices will not be sorted correctly.\n", 0xFFFFFFFF); This compiles fine, but so far, this produces a memory leak (as far as I can tell) when I put more than 2**24 points into the algorithm. I have emailed Brad Barber, who indicated that this changing the ridgeid field was possible. I am also working on a divide and conquer approach, but am having trouble deleting the old Delaunay object before instantiating the next one. I can send that code along if there is no good way to increase the number of points in the algorithm. I think it would be useful to have an algorithm that can accept more points, given the increased speed and processing power of modern computers. Thanks for your help.

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