Mailman 3 March 2012 - scikit-image

Re: euroscipy 2012
by Emmanuelle Gouillart 22 Mar '12

22 Mar '12

> I'll be at the conference, but I hadn't considered giving a talk. Do > you have any suggestions? Either you could give a general talk on scikits-image (like the one at PyData), if you feel like to, or (and/or) Vincent and I could prepare a talk on scikits-image and how to use the package for our applications, that is tomography datasets in materials science. There is possibly room for two talks on scikits-image (or one talk and a poster), if one is more general and the other one focusses more on applications. Emmanuelle

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Re: PyData scikits-image overview video
by Guillaume CALMETTES 22 Mar '12

22 Mar '12

Hi Stéfan, Le Mar 21, 2012 à 10:25 PM, Stéfan van der Walt a écrit : > Hi Guillaume > > On Wed, Mar 21, 2012 at 3:09 PM, Guillaume CALMETTES > <guillaume.calmettes(a)gmail.com> wrote: >> Did you make the ipython notebook you are using in the video >> somewhere? > > The material is available here: > > http://mentat.za.net/refer/skimage_py4science.tar.gz Thanks, it works like a charm ! > > You may need a fairly new version of IPython to open the notebook > (otherwise, just open up the notebook in a text editor and change the > version number from "2" to "3"). > > Stéfan

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euroscipy 2012
by Emmanuelle Gouillart 22 Mar '12

22 Mar '12

Hello, is anyone planning to submit an abstract on scikits-image at Euroscipy 2012 (Brussels, August 23-27)? Cheers, Emmanuelle

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Re: PyData scikits-image overview video
by Stéfan van der Walt 22 Mar '12

22 Mar '12

Hi Guillaume On Wed, Mar 21, 2012 at 3:09 PM, Guillaume CALMETTES <guillaume.calmettes(a)gmail.com> wrote: > Did you make the ipython notebook you are using in the video somewhere? The material is available here: http://mentat.za.net/refer/skimage_py4science.tar.gz You may need a fairly new version of IPython to open the notebook (otherwise, just open up the notebook in a text editor and change the version number from "2" to "3"). Stéfan

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Re: PyData scikits-image overview video
by Guillaume CALMETTES 21 Mar '12

21 Mar '12

Thanks Stéfan ! Great presentation of the scikit ! Did you make the ipython notebook you are using in the video somewhere? Guillaume 2012/3/21 Stéfan van der Walt <stefan(a)sun.ac.za> > Hi all, > > Max Walker and co. from Marakana did a fantastic job with the videos > from PyData. The scikits-image lecture is now available online: > > > http://marakana.com/s/image_processing_in_python_with_scikits-image_pydata_… > > I find it pretty annoying listening to my own voice, so what I like to > do is to go to: > > http://youtube.com/html5 > > and enable the HTML5 trial. Then, if you watch on YouTube, there's an > icon at the bottom to adjust the playback speed to 1.5x (ah, the > relief!). > > Stéfan >

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PyData scikits-image overview video
by Stéfan van der Walt 21 Mar '12

21 Mar '12

Hi all, Max Walker and co. from Marakana did a fantastic job with the videos from PyData. The scikits-image lecture is now available online: http://marakana.com/s/image_processing_in_python_with_scikits-image_pydata_… I find it pretty annoying listening to my own voice, so what I like to do is to go to: http://youtube.com/html5 and enable the HTML5 trial. Then, if you watch on YouTube, there's an icon at the bottom to adjust the playback speed to 1.5x (ah, the relief!). Stéfan

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Fwd: Platform for filters development
by Nadav Horesh 21 Mar '12

21 Mar '12

(I think I missed the attachment) Attached here a concept code showing my attempt to produce in improved (over ndimage.generic_filter) platform for filters development. The code is very preliminary and needs a lot of extension as well as rewrite. My main questions are: 1. Is there is already a mature package for this purpose? 2. Is there is need for such a module inside scikits? Any comment is welcome. Nadav

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(no subject)
by Nadav Horesh 21 Mar '12

21 Mar '12

(I think I missed the attachment) Attached here a concept code showing my attempt to produce in improved (over ndimage.generic_filter) platform for filters development. The code is very preliminary and needs a lot of extension as well as rewrite. My main questions are: 1. Is there is already a mature package for this purpose? 2. Is there is need for such a module inside scikits? Any comment is welcome. Nadav

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Re: Normalised cross correlation
by Tony Yu 20 Mar '12

20 Mar '12

On Tue, Mar 20, 2012 at 12:12 PM, Malcolm Reynolds < malcolm.reynolds(a)gmail.com> wrote: > >> Wow, those results are incredibly different. Yes, please put together a >> small script to reproduce the different behaviors (ideally, with the matlab >> result saved as .npy---or if it's easier .mat---file; also, if you can >> reproduce with a smaller image, that would be great). >> >> It'll be easy to check for switched arguments, but the rest might >> take some time for me to get to. In your original email, it sounded like >> you have some expertise in template matching; feel free to dig into the >> code and see if you can spot any errors in the code. >> >> Cheers, >> -Tony >> > > I've quickly whipped up some scripts in both matlab (if you have access to > that) and python and put them here: > https://github.com/malcolmreynolds/NCC-test-program - if you don't have > access to matlab, then the .mat file included should contain the inputs and > outputs from matlab's normxcorr2. To run it you just need to put any image > called 'lena.png' in the directory and then I ran 'ipython --pylab -i > run_ncc.py' at the shell on OS X. You may have your plotting set up a > different way, or not use pylab, but if all else fails the result images > are written out as pngs (also included in the repository). With matlab just > get to the matlab prompt and do "run_ncc". > > For reference, this is what I see when using a 256x256 downsampled version > of the lena image: > http://img843.imageshack.us/img843/2729/screenshot20120320at155.png (matlab on left, middle and right are python with and without the > pad_output flag). > > I'm afraid I'm definitely not an expert on template matching, but I reckon > it's pretty crucial to have a good free (&fast!) implementation available > in numpy/scipy/skimage in order to compete.. I will take a dig through your > code sometime but unfortunately deadlines are always looming for me.. I'll > hopefully get a chance this coming weekend. > > Thanks for your quick response, let me know if you have any problems with > the stuff on github. > > Malcolm > Great. Thanks for putting this together and for the original bug report. I'll take a look at this soon.... I hope. :) -Tony

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Re: Normalised cross correlation
by Malcolm Reynolds 20 Mar '12

20 Mar '12

> > > Wow, those results are incredibly different. Yes, please put together a > small script to reproduce the different behaviors (ideally, with the matlab > result saved as .npy---or if it's easier .mat---file; also, if you can > reproduce with a smaller image, that would be great). > > It'll be easy to check for switched arguments, but the rest might > take some time for me to get to. In your original email, it sounded like > you have some expertise in template matching; feel free to dig into the > code and see if you can spot any errors in the code. > > Cheers, > -Tony > I've quickly whipped up some scripts in both matlab (if you have access to that) and python and put them here: https://github.com/malcolmreynolds/NCC-test-program - if you don't have access to matlab, then the .mat file included should contain the inputs and outputs from matlab's normxcorr2. To run it you just need to put any image called 'lena.png' in the directory and then I ran 'ipython --pylab -i run_ncc.py' at the shell on OS X. You may have your plotting set up a different way, or not use pylab, but if all else fails the result images are written out as pngs (also included in the repository). With matlab just get to the matlab prompt and do "run_ncc". For reference, this is what I see when using a 256x256 downsampled version of the lena image: http://img843.imageshack.us/img843/2729/screenshot20120320at155.png (matlab on left, middle and right are python with and without the pad_output flag). I'm afraid I'm definitely not an expert on template matching, but I reckon it's pretty crucial to have a good free (&fast!) implementation available in numpy/scipy/skimage in order to compete.. I will take a dig through your code sometime but unfortunately deadlines are always looming for me.. I'll hopefully get a chance this coming weekend. Thanks for your quick response, let me know if you have any problems with the stuff on github. Malcolm

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