Mailman 3 December 2014 - scikit-image

Re: Travis-wheels fix?
by Olivier Grisel 12 Dec '14

12 Dec '14

Please use `pip install --timeout=60 -f http://wheels.scipy.org packagename` to increase the default timeout when connecting to the rackspace container. pip uses a default of 15s which is apparently sometimes not enough. For scikit-learn the stability of the build has greatly improved since I switched to 60s timeout. -- Olivier

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Re: How do you keep documentation so nice?
by Adam Hughes 12 Dec '14

12 Dec '14

Wait, so github is hosting scikitimage.org? To my (outdated) understanding, one had to use a gh-pages branch for github to find the documentations. If I were to put the docs in the package master branch as you've done, how can github find a hook to host the site? On Thu, Dec 11, 2014 at 7:13 PM, Stéfan van der Walt <stefan(a)sun.ac.za> wrote: > > On Dec 11, 2014 7:58 PM, "Thomas Caswell" <tcaswell(a)gmail.com> wrote: > > > > matplotlib uses the organization-level gh-pages to host the > documentation which seems to work pretty well. > > We do the same thing, in fact. No go-pages branch needed. > > 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/k5K6_vanZVI/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > scikit-image+unsubscribe(a)googlegroups.com. > For more options, visit https://groups.google.com/d/optout. >

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Re: How do you keep documentation so nice?
by Stéfan van der Walt 11 Dec '14

11 Dec '14

On Dec 11, 2014 7:58 PM, "Thomas Caswell" <tcaswell(a)gmail.com> wrote: > > matplotlib uses the organization-level gh-pages to host the documentation which seems to work pretty well. We do the same thing, in fact. No go-pages branch needed. Stéfan

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Re: How do you keep documentation so nice?
by Thomas Caswell 11 Dec '14

11 Dec '14

matplotlib uses the organization-level gh-pages to host the documentation which seems to work pretty well. On Thu Dec 11 2014 at 12:45:30 PM Adam Hughes <hughesadam87(a)gmail.com> wrote: > Thanks, that's great advice. Also, do you guys pay to host your site? > Can you recommend a low-cost, or free, static-website hosting vendor? We > are currently using gh-pages branch on github to host our site, and I > really hate having this secondary branch. Especially when I need the > documentation to have access to the source code modules or setup.py file > (as it's on a second branch). > > On Thu, Dec 11, 2014 at 6:56 AM, Juan Nunez-Iglesias <jni.soma(a)gmail.com> > wrote: >> >> Adam, just fyi, we are considering moving away from GoogleGroups... (See >> a separate discussion on this list). Since you are on the ground floor, you >> might want to reconsider your choice. I've been using Nabble for my (very >> low volume!) gala list and it's been really good. >> >> >> >> >> On Thu, Dec 11, 2014 at 12:01 PM, Adam Hughes <hughesadam87(a)gmail.com> >> wrote: >> >>> Thanks Michael. >>> >>> Be warned, only about 3 people are using the library at the moment, so >>> it's quite likely that you'll encounter some bugs just by virtue of using a >>> new dataset that probably will bring to light some considerations that we >>> overlooked. In addition, I only support pandas 0.14 right now (0.15 has a >>> lot of private API changes that directly affect us). But we did feel like >>> the library was close enough to ready to share it, and I hope you can try >>> it out. If you do want to give it a whirl sometime soon, please feel free >>> to contact us at skspec(a)googlegroups.com (or me personally) and we will >>> at least make sure to help get you up and running. Let us know what kind >>> of data you're working on and what type of analysis you're doing. We've >>> spend a lot of time putting out datastructures together, but we haven't put >>> a great deal of thought into the actual spectral utilitiles, workflows and >>> analysis that we should host, other than correlation spectroscopy and base >>> things like dynamic baseline fitting. >>> >>> >>> >>> On Wed, Dec 10, 2014 at 6:14 PM, Michael Aye <kmichael.aye(a)gmail.com> >>> wrote: >>> >>>> On 2014-12-10 02:43:46, Adam Hughes <hughes...(a)gmail.com> wrote: >>>> >>>>> > http://hugadams.github.io/scikit-spectra/ >>>>>>> >>>>>>> That is a very impressive notebook widget shown in the video! I love >>>>>>> how it interacts with mpl3d. >>>>>>> >>>>>>> >>>>>>> Ditto! Man, can't wait to play with this! Very happy that there's >>>> finally a package focusing on spectral analysis! It also just comes at the >>>> right time, just started in my new job working on data from an imaging >>>> spectrometer for the first time. ;) >>>> >>>> Michael >>>> >>>> >>>> -- >>>> 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/k5K6_vanZVI/unsubscribe. >>>> To unsubscribe from this group and all its topics, send an email to >>>> scikit-image+unsubscribe(a)googlegroups.com. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> -- >>> 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/d/optout. >>> >> >> -- >> 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/k5K6_vanZVI/unsubscribe. >> To unsubscribe from this group and all its topics, send an email to >> scikit-image+unsubscribe(a)googlegroups.com. >> For more options, visit https://groups.google.com/d/optout. >> > -- > 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/d/optout. >

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Re: How do you keep documentation so nice?
by Juan Nunez-Iglesias 11 Dec '14

11 Dec '14

Adam, just fyi, we are considering moving away from GoogleGroups... (See a separate discussion on this list). Since you are on the ground floor, you might want to reconsider your choice. I've been using Nabble for my (very low volume!) gala list and it's been really good. On Thu, Dec 11, 2014 at 12:01 PM, Adam Hughes <hughesadam87(a)gmail.com> wrote: > Thanks Michael. > Be warned, only about 3 people are using the library at the moment, so it's > quite likely that you'll encounter some bugs just by virtue of using a new > dataset that probably will bring to light some considerations that we > overlooked. In addition, I only support pandas 0.14 right now (0.15 has a > lot of private API changes that directly affect us). But we did feel like > the library was close enough to ready to share it, and I hope you can try > it out. If you do want to give it a whirl sometime soon, please feel free > to contact us at skspec(a)googlegroups.com (or me personally) and we will at > least make sure to help get you up and running. Let us know what kind of > data you're working on and what type of analysis you're doing. We've spend > a lot of time putting out datastructures together, but we haven't put a > great deal of thought into the actual spectral utilitiles, workflows and > analysis that we should host, other than correlation spectroscopy and base > things like dynamic baseline fitting. > On Wed, Dec 10, 2014 at 6:14 PM, Michael Aye <kmichael.aye(a)gmail.com> wrote: >> On 2014-12-10 02:43:46, Adam Hughes <hughes...(a)gmail.com> wrote: >> >>> > http://hugadams.github.io/scikit-spectra/ >>>>> >>>>> That is a very impressive notebook widget shown in the video! I love >>>>> how it interacts with mpl3d. >>>>> >>>>> >>>>> Ditto! Man, can't wait to play with this! Very happy that there's >> finally a package focusing on spectral analysis! It also just comes at the >> right time, just started in my new job working on data from an imaging >> spectrometer for the first time. ;) >> >> Michael >> >> >> -- >> 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/k5K6_vanZVI/unsubscribe. >> To unsubscribe from this group and all its topics, send an email to >> scikit-image+unsubscribe(a)googlegroups.com. >> For more options, visit https://groups.google.com/d/optout. >> > -- > 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/d/optout.

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Re: How do you keep documentation so nice?
by Michael Aye 10 Dec '14

10 Dec '14

On 2014-12-10 02:43:46, Adam Hughes <hughes...(a)gmail.com <javascript:>> wrote: > > http://hugadams.github.io/scikit-spectra/ >>> >>> That is a very impressive notebook widget shown in the video! I love >>> how it interacts with mpl3d. >>> >>> >>> Ditto! Man, can't wait to play with this! Very happy that there's finally a package focusing on spectral analysis! It also just comes at the right time, just started in my new job working on data from an imaging spectrometer for the first time. ;) Michael

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Re: How do you keep documentation so nice?
by Adam Hughes 10 Dec '14

10 Dec '14

*model On Dec 10, 2014 10:09 AM, "Adam Hughes" <hughesadam87(a)gmail.com> wrote: > Thanks Stefan. Ya we were pretty surprised when dumping the mpld3 html > back into midel just happened to work and not break anything > On Dec 10, 2014 6:24 AM, "Stefan van der Walt" <stefan(a)sun.ac.za> wrote: > >> Hi Adam >> >> On 2014-12-10 02:43:46, Adam Hughes <hughesadam87(a)gmail.com> wrote: >> > http://hugadams.github.io/scikit-spectra/ >> >> That is a very impressive notebook widget shown in the video! I love >> how it interacts with mpl3d. >> >> 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/k5K6_vanZVI/unsubscribe. >> To unsubscribe from this group and all its topics, send an email to >> scikit-image+unsubscribe(a)googlegroups.com. >> For more options, visit https://groups.google.com/d/optout. >> >

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Re: How do you keep documentation so nice?
by Stefan van der Walt 10 Dec '14

10 Dec '14

Hi Adam On 2014-12-10 02:43:46, Adam Hughes <hughesadam87(a)gmail.com> wrote: > http://hugadams.github.io/scikit-spectra/ That is a very impressive notebook widget shown in the video! I love how it interacts with mpl3d. Stéfan

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Number of bins in Entropy and Enhance_contrast for uint16
by Pål Gunnar Ellingsen 10 Dec '14

10 Dec '14

Hi I'm new to using the scikit-image library, so if this question is silly please excuse me. I'm trying to run contrast enhancement on thousands of 1000x1000 images of "numpy.uint16" type. I'm expecting this to be very computationally expensive, something confirmed when running either entropy or enhance_contrast (from "skimage.filter.rank") with the warning: "Bitdepth of 15 may result in bad rank filter performance due to large number of bins". I'm wondering if it is possible to reduce the number of bins via an option? I've tried to find such a keyword in the documentation and source code, but I haven't been able to find it. Kind regards Pål

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Help with shape descriptors
by Claiborne Morton 10 Dec '14

10 Dec '14

Hello Scikit community, I'm looking for help using particle descriptors to identify sickle cells in the attached image. As you can see the sickle cells are the long, thin cells. I have two issues, the first is that in some cases the sickle cells are in contact with other healthy cells. I am trying to find a way of separating (or water-shedding) the cells so that each "particle" is actually one cell. The second issue is that I am dealing with is trying to find shape descriptors that will allow me to accurately distinguish the sickle cells from the healthy cells. I used an eccentricity filter on the original image to remove all of the cells with eccentricity less than 0.6. Making this any higher results in removal of sickle cells. What other descriptors might be used for further differentiation? Thanks, Clay

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