Menu
▾
▴
Re: [Numpy-discussion] Convolve returning zero array
|
From: <R....@ma...> - 2003-12-16 09:33:43
|
OK, here is the example: [code] from numarray import * import numarray.convolve as conv lx=20 center=10 index=arange(lx,type='Float64') data1=(abs(center-index))<3 print 'The binary pattern:' print data1 PSF=5 xwidth=18 xmid=xwidth/2 sigma=PSF/(sqrt(8*log(2))) index=arange(xwidth,type='Float64') ShortGauss = (1/(sqrt(2*pi)*sigma)) * exp(-0.5*((index-xmid)/sigma)*((index-xmid)/sigma)) print '\nThe short gauss:' print ShortGauss image=conv.convolve(data1,ShortGauss,mode=conv.SAME) print '\nThe convolution of the binary pattern with the short gauss:' print image PSF=5 xwidth=22 xmid=xwidth/2 sigma=PSF/(sqrt(8*log(2))) index=arange(xwidth,type='Float64') LongGauss = (1/(sqrt(2*pi)*sigma)) * exp(-0.5*((index-xmid)/sigma)*((index-xmid)/sigma)) print '\nThe long gauss:' print LongGauss image=conv.convolve(data1,LongGauss,mode=conv.SAME) print '\nThe convolution of the binary pattern with the long gauss:' print image [\code] When I run this code, the first convolution gives an array of zeros, the second convolution is good. I also did a quick try with convolve from nd_image, but this function was slower than the convolve from numarray with a large Gaussian distribution. Remco Jager MAPPER Lithography Lorentzweg 1 2628 CJ Delft, The Netherlands tel.: +31 (0)15 2789439 fax: +31 (0)15-2789473 http://www.mapperlithography.com This e-mail, attachments and (any part of) its content are (i) intended for the named addressee(s) only and (ii) strictly confidential and proprietary. All rights are reserved by MAPPER Lithography. Any unauthorized use, disclosure and/or copying are strictly prohibited, except with prior and express written permission by MAPPER Lithography. Should you have received this e-mail, attachments and its content by mistake, please bring this to our attention and destroy this e-mail and attachments in full. Thank you. |---------+----------------------------> | | Nadav Horesh | | | <nadavh@visionsen| | | se.com> | | | | | | 15/12/2003 14:13 | | | | |---------+----------------------------> >------------------------------------------------------------------------------------------------------------------------------| | | | To: R....@ma... | | cc: Peter Verveer <ve...@em...>, num...@li... | | Subject: Re: [Numpy-discussion] Convolve returning zero array | >------------------------------------------------------------------------------------------------------------------------------| 1. Can you post an example? 2. Whenever convolution runs slow because the arrays are large, use FFT (with a proper padding) --- it can be an order of magnitude (or more) faster. Nadav. R....@ma... wrote: > Hi Peter, > > At first I used numarray 0.6. This morning I have installed 0.8 but the > results are the same. I will try the convolve functions in the nd_image > package. > > Thanks, > > Remco Jager > > MAPPER Lithography > Lorentzweg 1 > 2628 CJ Delft, The Netherlands > tel.: +31 (0)15 2789439 > fax: +31 (0)15-2789473 > http://www.mapperlithography.com > > This e-mail, attachments and (any part of) its content are (i) intended for > the named addressee(s) only and (ii) strictly confidential and proprietary. > All rights are reserved by MAPPER Lithography. Any unauthorized use, > disclosure and/or copying are strictly prohibited, except with prior and > express written permission by MAPPER Lithography. Should you have received > this e-mail, attachments and its content by mistake, please bring this to > our attention and destroy this e-mail and attachments in full. Thank you. > > > |---------+----------------------------> > | | Peter Verveer | > | | <verveer@embl-hei| > | | delberg.de> | > | | | > | | 15/12/2003 12:04 | > | | | > |---------+----------------------------> > >------------------------------------------------------------------------------------------------------------------------------| > | | > | To: R....@ma..., num...@li... | > | cc: | > | Subject: Re: [Numpy-discussion] Convolve returning zero array | > >------------------------------------------------------------------------------------------------------------------------------| > > > > > Hi Remco, > > Sounds like a bug. Which version of numarray do you use? Version 0.8 of > numarray should have appeared on sourceforge now. If the convolve in that > version does still not work, you could try out the convolution function in > the new nd_image package that is part of numarray 0.8. If that does not > work, > let me know since I am the author of that package, and will fix problems > with > it. > > Cheers, Peter > > On Monday 15 December 2003 11:24, R....@ma... wrote: > >>Hi list, >> >>I already posted this on the numarray forum on freshmeat, but Jay T > > Miller > >>advised me to post my problem to this list. OK, now for the problem: I > > try > >>to convolve a Gaussian distribution with a binary pattern. For small > > values > >>of the sigma of the Gaussian distribution the convolution returns an > > array > >>of zeros. For a large value the results are OK. >>I did some more research and found out that the zero array is returned if >>the length of the Gaussian is smaller than the length of the binary >>pattern. In the function call the Gaussian is the kernel and the binary >>pattern is the data. The convolution mode is 'SAME'. I have swapped the >>data and kernel in the convolve function call, but this has no influence > > on > >>the result, as this is swapped again in convolve.py. A quick and dirty >>workaround is to always make the Gaussian distribution longer than the >>binary pattern, but for very large binary patterns this increases the >>calculation time significantly. Does anyone have an idea how to solve > > this > >>properly? >> >>Met vriendelijke groeten, >> >>Remco Jager >> >>MAPPER Lithography >>Lorentzweg 1 >>2628 CJ Delft, The Netherlands >>tel.: +31 (0)15 2789439 >>fax: +31 (0)15-2789473 >>http://www.mapperlithography.com >> >>This e-mail, attachments and (any part of) its content are (i) intended > > for > >>the named addressee(s) only and (ii) strictly confidential and > > proprietary. > >>All rights are reserved by MAPPER Lithography. Any unauthorized use, >>disclosure and/or copying are strictly prohibited, except with prior and >>express written permission by MAPPER Lithography. Should you have > > received > >>this e-mail, attachments and its content by mistake, please bring this to >>our attention and destroy this e-mail and attachments in full. Thank you. >> >> >> >> >> >> >>------------------------------------------------------- >>This SF.net email is sponsored by: SF.net Giveback Program. >>Does SourceForge.net help you be more productive? Does it >>help you create better code? SHARE THE LOVE, and help us help >>YOU! Click Here: http://sourceforge.net/donate/ >>_______________________________________________ >>Numpy-discussion mailing list >>Num...@li... >>https://lists.sourceforge.net/lists/listinfo/numpy-discussion > > > -- > Dr. Peter J. Verveer > Cell Biology and Cell Biophysics Programme > European Molecular Biology Laboratory > Meyerhofstrasse 1 > D-69117 Heidelberg > Germany > Tel. : +49 6221 387245 > Fax : +49 6221 387306 > > > > > > > > > > > ------------------------------------------------------- > This SF.net email is sponsored by: SF.net Giveback Program. > Does SourceForge.net help you be more productive? Does it > help you create better code? SHARE THE LOVE, and help us help > YOU! Click Here: http://sourceforge.net/donate/ > _______________________________________________ > Numpy-discussion mailing list > Num...@li... > https://lists.sourceforge.net/lists/listinfo/numpy-discussion > |
