Mailman 3 January 2014 - scikit-image

Re: Image filters
by Ronnie Ghose Jan. 6, 2014

Jan. 6, 2014

+ To Juan's Idea.. they look nice ... but I can't see intellectual applications? Maybe have a reference to them or the like, I don't know if we want to spend time maintaining them necessarily On Sun, Jan 5, 2014 at 9:45 PM, Juan Nunez-Iglesias <jni.soma(a)gmail.com>wrote: > I'm ambivalent. They are cool and would be nice for publicity, but let's > not forget that it's *scikit-*image, and these filters have questionable > scientific use (at least that I can think of — I've been shown more than > once to lack imagination! =). In addition, the object-based implementation > wouldn't fit very well with skimage's more functional interface. > > I wouldn't be opposed to including them but I also would not want to spend > my time on them. > > Juan. > > > > On Mon, Jan 6, 2014 at 12:11 PM, Johannes Schönberger <jsch(a)demuc.de>wrote: > >> Hi everyone, >> >> Interesting and those filters could be incorporated into scikit-image in >> my opinion: >> >> http://jason2506.github.io/imfilter/ >> >> What do others think? >> >> -- >> You received this message because you are subscribed to the Google Groups >> "scikit-image" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to scikit-image+unsubscribe(a)googlegroups.com. >> For more options, visit https://groups.google.com/groups/opt_out. >> > > -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image+unsubscribe(a)googlegroups.com. > For more options, visit https://groups.google.com/groups/opt_out. >

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Image filters
by Johannes Schönberger Jan. 6, 2014

Jan. 6, 2014

Hi everyone, Interesting and those filters could be incorporated into scikit-image in my opinion: http://jason2506.github.io/imfilter/ What do others think?

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Is there a bug in polygon?
by Adam Hughes Jan. 2, 2014

Jan. 2, 2014

I'm implementing draw.polygon from this example ( http://scikit-image.org/docs/dev/auto_examples/plot_shapes.html) I connected the dots to the verticies provided in poly and plotted over the imshow result: In [105]: plt.imshow(poly) In [107]: plt.plot(*zip(*poly), ls='--') In [108]: plt.scatter(*zip(*poly)) Which results in the attatched image. This is unexpected, no?

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Job opening in Melbourne
by Juan Nunez-Iglesias Jan. 1, 2014

Jan. 1, 2014

Hi all, Sorry if this is a bit spammy, but I thought some readers of this list might be interested! The Victorian Centre for Functional Genomics (VCFG), part of the Peter MacCallum Cancer Institute, is looking for a bioinformatician to analyse high content imaging screens. This is image analysis on a big scale (millions of images per screen), combined with genetic function and pathway analysis. I've been using scikit-image, scikit-learn, and pandas to analyse two of their screens, so it'd be great to collaborate with another Pythonista on upcoming ones! Here's a link to the job posting: http://petermac.mercury.com.au/ViewPosition.aspx?id=11414 and to the PDF "position description": http://australianbioinformatics.net/storage/VCFG_Bioinformatics_Position_De… You can contact Kaylene Simpson (VCFG Head) at Kaylene.Simpson(a)petermac.orgwith any questions. The application deadline is January 13th (Australia time! ;). Happy New Year everyone! Juan.

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Re: What RGB color is this? (quick Q)
by Adam Hughes Jan. 1, 2014

Jan. 1, 2014

Thanks Thomas. Yes, I'm starting to see all the headaches that come with flexibility in dtypes and colors. Thanks for linking, that clears some stuff up for me. On Tue, Dec 31, 2013 at 7:59 PM, Thomas A Caswell <tcaswell(a)uchicago.edu>wrote: > There is no canonical mapping between scalar values (1d) and RGB (3d) > which is why matplotlib has so many color maps. > > If you pass in to imshow a NxMx3 or NxMx4 array it is interpreted as RGB > or RGBA values respectively (see > http://matplotlib.org/api/axes_api.html#matplotlib.axes.Axes.imshow) and > not color mapped. If the arrays are float they are assumed to be in the > range [0-1], if they are integers they should be uint8. There was some > discussion recently on github abut tweaking the validation a bit (issues > 2499 and 2632). > > Tom > On Dec 31, 2013 1:01 PM, "Adam Hughes" <hughesadam87(a)gmail.com> wrote: > >> Thanks Stefan. That helps clarify some of the dtypes to me; however I >> still have a few confusions in regard to color data. I should have >> specified this more in my OP. >> >> I am trying to create a program where all color data is stored as RGB. >> This requires a validator that does flexible *to_rgb()* conversion. I >> want the users to have flexibility, so it should accept names like "aqua" >> as well as RGB tuples. I realize now that imshow() will do its own >> conversions, but still don't quite understand exactly what constraints I >> need to impose on users for all the various use cases. For example, if a >> user enters a single integer (say 239), is there a de-facto way to >> rgb-convert this? I've tried to exhause the scenarious below; any case >> with question marks is still unclear to me. >> >> INPUT TYPE INPUT EXAMPLE HANDLER DESIRED OUTPUT >> >> ----------------------------------------------------------------------------------------------------- >> >> hex string '#0FF000' ColorConverter.to_rgb() (.2, .4, .5) >> name string 'purple ' ColorConverter.to_rgb() (.1, .8, .3) >> < 1 float tuple ' (.5, .2, .4) PASS (.5, >> .2, .4) >> > 1 float/int tuple (30, 28, 90) ???? >> ???? >> int 140 (Digital channel?) >> (140, 140, 140)??? >> float 39.5 (Error??) >> ??? >> >> I read on wiki that a RGB tuple with elements > 1 can be interpreted as a >> "Digital Channel", so perhaps just leave these as is. The tough cases for >> me are really when a user enters a single Int or Float. Of course, I could >> just raise an exception if there's no de-facto way to handle this... >> >> >> On Tue, Dec 31, 2013 at 6:15 AM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: >> >>> Hi Adam >>> >>> On Mon, 30 Dec 2013 22:37:43 -0800, Adam Hughes wrote: >>> > I noticed recently that matplotlib.colors limits RGB values to a range >>> (0 - >>> > 1), while in scikit image, RGB values can be much larger. For example: >>> > >>> > *test = np.zeros( (500,500,3) )* >>> > >>> > *test[:,:,0]=50* >>> > *test[:,:,1]=19* >>> > *test[:,:,2]=25* >>> > >>> > *imshow(test); * >>> > >>> > Produces a teal background. I was curious how the color teal is >>> derived >>> > from this? I tried normalizing to 255 and and 50 but neither seemed to >>> > produce the same teal color. >>> >>> Here's a write-up of the data-type and range representation that >>> scikit-image >>> uses: >>> >>> http://scikit-image.org/docs/0.9.x/user_guide/data_types.html >>> >>> When visualizing data with Matplotlib, note that data is normalized by >>> default, so you have to specify "vmin" and "vmax" to correctly display >>> your >>> generated background. >>> >>> Regards >>> Stéfan >>> >>> -- >>> You received this message because you are subscribed to a topic in the >>> Google Groups "scikit-image" group. >>> To unsubscribe from this topic, visit >>> https://groups.google.com/d/topic/scikit-image/a54ehbd1fLk/unsubscribe. >>> To unsubscribe from this group and all of its topics, send an email to >>> scikit-image+unsubscribe(a)googlegroups.com. >>> For more options, visit https://groups.google.com/groups/opt_out. >>> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "scikit-image" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to scikit-image+unsubscribe(a)googlegroups.com. >> >> For more options, visit https://groups.google.com/groups/opt_out. >> > -- > You received this message because you are subscribed to a topic in the > Google Groups "scikit-image" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/scikit-image/a54ehbd1fLk/unsubscribe. > To unsubscribe from this group and all of its topics, send an email to > scikit-image+unsubscribe(a)googlegroups.com. > For more options, visit https://groups.google.com/groups/opt_out. >

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Re: What RGB color is this? (quick Q)
by Thomas A Caswell Jan. 1, 2014

Jan. 1, 2014

There is no canonical mapping between scalar values (1d) and RGB (3d) which is why matplotlib has so many color maps. If you pass in to imshow a NxMx3 or NxMx4 array it is interpreted as RGB or RGBA values respectively (see http://matplotlib.org/api/axes_api.html#matplotlib.axes.Axes.imshow) and not color mapped. If the arrays are float they are assumed to be in the range [0-1], if they are integers they should be uint8. There was some discussion recently on github abut tweaking the validation a bit (issues 2499 and 2632). Tom On Dec 31, 2013 1:01 PM, "Adam Hughes" <hughesadam87(a)gmail.com> wrote: > Thanks Stefan. That helps clarify some of the dtypes to me; however I > still have a few confusions in regard to color data. I should have > specified this more in my OP. > > I am trying to create a program where all color data is stored as RGB. > This requires a validator that does flexible *to_rgb()* conversion. I > want the users to have flexibility, so it should accept names like "aqua" > as well as RGB tuples. I realize now that imshow() will do its own > conversions, but still don't quite understand exactly what constraints I > need to impose on users for all the various use cases. For example, if a > user enters a single integer (say 239), is there a de-facto way to > rgb-convert this? I've tried to exhause the scenarious below; any case > with question marks is still unclear to me. > > INPUT TYPE INPUT EXAMPLE HANDLER DESIRED OUTPUT > > ----------------------------------------------------------------------------------------------------- > > hex string '#0FF000' ColorConverter.to_rgb() (.2, .4, .5) > name string 'purple ' ColorConverter.to_rgb() (.1, .8, .3) > < 1 float tuple ' (.5, .2, .4) PASS (.5, > .2, .4) > > 1 float/int tuple (30, 28, 90) ???? ???? > int 140 (Digital channel?) > (140, 140, 140)??? > float 39.5 (Error??) > ??? > > I read on wiki that a RGB tuple with elements > 1 can be interpreted as a > "Digital Channel", so perhaps just leave these as is. The tough cases for > me are really when a user enters a single Int or Float. Of course, I could > just raise an exception if there's no de-facto way to handle this... > > > On Tue, Dec 31, 2013 at 6:15 AM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > >> Hi Adam >> >> On Mon, 30 Dec 2013 22:37:43 -0800, Adam Hughes wrote: >> > I noticed recently that matplotlib.colors limits RGB values to a range >> (0 - >> > 1), while in scikit image, RGB values can be much larger. For example: >> > >> > *test = np.zeros( (500,500,3) )* >> > >> > *test[:,:,0]=50* >> > *test[:,:,1]=19* >> > *test[:,:,2]=25* >> > >> > *imshow(test); * >> > >> > Produces a teal background. I was curious how the color teal is derived >> > from this? I tried normalizing to 255 and and 50 but neither seemed to >> > produce the same teal color. >> >> Here's a write-up of the data-type and range representation that >> scikit-image >> uses: >> >> http://scikit-image.org/docs/0.9.x/user_guide/data_types.html >> >> When visualizing data with Matplotlib, note that data is normalized by >> default, so you have to specify "vmin" and "vmax" to correctly display >> your >> generated background. >> >> Regards >> Stéfan >> >> -- >> You received this message because you are subscribed to a topic in the >> Google Groups "scikit-image" group. >> To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/scikit-image/a54ehbd1fLk/unsubscribe. >> To unsubscribe from this group and all of its topics, send an email to >> scikit-image+unsubscribe(a)googlegroups.com. >> For more options, visit https://groups.google.com/groups/opt_out. >> > > -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image+unsubscribe(a)googlegroups.com. > For more options, visit https://groups.google.com/groups/opt_out. >

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