Mailman 3 March 2016 - scikit-image

Re: Scipy2016: call for proposals
by Nelle Varoquaux March 21, 2016

March 21, 2016

Dear all, This is a quick reminder that the deadline for submitting talks and posters proposal is next friday. Thanks, Nelle On 22 February 2016 at 10:15, Nelle Varoquaux <nelle.varoquaux(a)gmail.com> wrote: > > Dear all, > > SciPy 2016, the Fifteenth Annual Conference on Python in Science, takes > place in Austin, TX on July, 11th to 17th. The conference features two days > of tutorials by followed by three days of presentations, and concludes with > two days of developer sprints on projects of interest to attendees. . > > The topics presented at SciPy are very diverse, with a focus on advanced > software engineering and original uses of Python and its scientific > libraries, either in theoretical or experimental research, from both > academia and the industry. This year we are happy to announce two > specialized tracks that run in parallel to the general conference (Data > Science , High Performance Computing) and 8 mini-symposia (Earth and Space > Science, Biology and Medicine, Engineering, Social Sciences, Special > Purpose Databases, Case Studies in Industry, Education, Reproducibility) > > Submissions for talks and posters are welcome on our website ( > http://scipy2016.scipy.org). In your abstract, please provide details on > what Python tools are being employed, and how. The talk and poster > submission deadline is March 25th, 2016, while the tutorial submission > deadline is March, 21st, 2016. > > > Important dates: > > Mar 21: Tutorial Proposals Due > Mar 25: Talk and Poster Proposals Due > May 11: Plotting Contest Submissions Due > Apr 22: Tutorials Announced > Apr 22: Financial Aid Submissions Due > May 4: Talk and Posters Announced > May 11: Financial Aid Recipients Notified > May 22: Early Bird Registration Deadline > Jul 11-12: SciPy 2016 Tutorials > Jul 13-15: SciPy 2016 General Conference > Jul 16-17: SciPy 2016 Sprints > > We look forward to an exciting conference and hope to see you in Austin in > July! > > > The Scipy 2016 > http://scipy2016.scipy.org/ > > Conference Chairs: Aric Hagberg, Prabhu Ramachandran > Tutorial Chairs: Justin Vincent, Ben Root > Program Chair: Serge Rey, Nelle Varoquaux > Proceeding Chairs: Sebastian Benthall > >

1 0

filters.entropy
by Paulo Raposo March 18, 2016

March 18, 2016

Hi All, I'm using scikit to run entropy filters on spatial images. I get a message pretty frequently: Bitdepth of 15 may result in bad rank filter performance due to large number of bins. Does this just mean it's slow? Or that there could be errors in the output? Thanks!! Paulo

2 2

Cython + numpy 1.11 -- can you make it work?
by Stéfan van der Walt March 18, 2016

March 18, 2016

Hi all, I'm trying to make skimage work with the latest numpy pre-release, but to no avail. I see failures in the test suite when running this branch: stefanv/int_fixes_np1.11 If you can crack this one, I would be much obliged! Best regards Stéfan

1 0

Re: Saving an image
by Jatin Katyal March 14, 2016

March 14, 2016

Thank you Himanshu, I don't know why I did not see documentation. BTW, it is "imsave". On Sunday, March 13, 2016 at 7:52:03 PM UTC+5:30, Himanshu Mishra wrote: > Hi Jatin, > > Did you try the `io` module of `skimage` ? I believe we can save the > images (numpy ndarray) using `io.save()`. > > Regards, > Himanshu Mishra > > On Sun, Mar 13, 2016 at 7:47 PM, Jatin Katyal <jatink...(a)gmail.com > <javascript:>> wrote: > >> Hi guys, this is Jatin. I was using scikit-image module and was going >> through examples, after some time I realised that in all examples images >> are being opened as numpy.ndarray but nowhere these images were saved as >> .jpg or .png(or any other format). Can you tell me how to save these images >> which I modified? >> >> -- >> 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...(a)googlegroups.com <javascript:>. >> To post to this group, send email to scikit...(a)googlegroups.com >> <javascript:>. >> To view this discussion on the web, visit >> https://groups.google.com/d/msgid/scikit-image/5e40f6a8-1bfc-40f4-bef1-53cb… >> <https://groups.google.com/d/msgid/scikit-image/5e40f6a8-1bfc-40f4-bef1-53cb…> >> . >> For more options, visit https://groups.google.com/d/optout. >> > > > > -- > Himanshu Mishra >

2 2

Saving an image
by Jatin Katyal March 13, 2016

March 13, 2016

Hi guys, this is Jatin. I was using scikit-image module and was going through examples, after some time I realised that in all examples images are being opened as numpy.ndarray but nowhere these images were saved as .jpg or .png(or any other format). Can you tell me how to save these images which I modified?

2 1

Extracting attributes from images using Scikit-image
by Ahmed Dassouki March 11, 2016

March 11, 2016

Hi folks, I posted this question <http://stackoverflow.com/questions/35938740/extracting-attributes-from-imag…> on stackoverflow on how to extract images using scikit-image. I am using the following code to generate the images: plt.rcParams['image.cmap'] = 'spectral' labels = seg.slic(color_image, n_segments=6, compactness=4). The end goal is to build an attribute table of the images dataset.

1 0

Re: Problem with using sp.ndimage.label to get largest object in a binary image
by Matteo Niccoli March 11, 2016

March 11, 2016

Hello Juan I've cleaned up the notebook and moved things around a bit. But mainly, I modified the *ndimaged.label* part (thanks to you for my better understanding of how it works), and also replaced the masking with *remove_small_objects*. here's my new notebook: https://github.com/mycarta/rainbowbot/blob/master/crop_image_reduce_colors_… The one part that puzzled me for a bit is that things did not work when I used skimage.io.imread to import the image, but then I figured out it was because of the alpha channel... :-) [image: Inline image 1] Cheers, Matteo On Tue, Mar 8, 2016 at 3:44 PM, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: > Hi Matteo, > > ndimage.label keeps 0 as 0 (background) and then labels every nonzero blob > as 1, 2, ... n. Then, numpy.bincount is completely agnostic as to whether > you are looking at images or any other kind of array, and is just going to > count the values, including 0. > > As I mentioned, remove_small_objects does what you want but you need to > find out the size of the largest blob and pass that in as the min_size > parameter. > > Juan. > > On Wed, Mar 9, 2016 at 1:59 AM, Matteo <matteo.niccoli(a)gmail.com> wrote: > >> Hello Juan >> >> Thanks for your reply. >> Here is a second notebook with the problem image to look at. >> https://github.com/mycarta/rainbowbot/blob/master/crop_image_reduce_colors_… >> >> I have not had time to change anything except for running it, and won't >> be able until tonight. When I do, I will look into your suggestions, and >> recommendations, and any other comments you may have from seeing the >> notebook. >> But, so, the background counts when it comes to labeling/size? I had >> assumed the operations would only apply to bright elements, that's the >> misunderstanding. >> >> Also, being here, the way, is there a better way, or a dedicated >> operation, to get the largest object/blob in a binary image? >> >> Cheers, >> Matteo >> >> On Monday, March 7, 2016 at 11:18:25 PM UTC-7, Juan Nunez-Iglesias wrote: >>> >>> Hi Matteo, >>> >>> It would be useful if you showed us the notebook being run with the >>> problematic image, as well as the original. >>> >>> Having said that, it looks like perhaps you should replace this line: >>> mask_sizes[0] = 0 >>> >>> with >>> >>> sizes[0] = 0 >>> >>> higher up. Perhaps your background is bigger than your foreground in the >>> problem image. =) >>> >>> Juan. >>> >>> PS: Incidentally, have a look at skimage.morphology.remove_small_objects >>> and skimage.morphology.remove_small_holes (this last one is in the >>> just-released 0.12 version). >>> >>> PPS: Also incidentally, for ndimage we often use the convention "from >>> scipy import ndimage as ndi" >>> >>> PPPS: Also, skimage.io.imread can directly load images from URLs. =) >>> >>> On Tue, Mar 8, 2016 at 3:06 AM, Matteo <matteo....(a)gmail.com> wrote: >>> >>>> Hello there >>>> >>>> I'm putting together some code to grab an image with a map, colorbar, >>>> and possibly text and other elements, guess what the largest object in the >>>> image is -assuming it is the map - crop the image to the map extent, then >>>> reduce the number of colors in the map. >>>> My Jupiter notebook is at this location on GitHub: >>>> >>>> https://github.com/mycarta/rainbowbot/blob/master/crop_image_reduce_colors.… >>>> >>>> The issue I have with this code is that: >>>> If I run it with the current test image ( >>>> https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_noteb…) >>>> or even a nimage with map touching the border( >>>> https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_noteb…) >>>> the code seems to work. >>>> >>>> However, in the case of an image with larger blocks of text ( >>>> https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_noteb… >>>> ) >>>> the output of [9] is an array that is all zeroes, although as far as I >>>> know it should not. Can anyone suggest why this is happening? >>>> >>>> I am sure it is something I am overlooking in my code/understanding of >>>> image processing. >>>> >>>> Thanks >>>> Matteo >>>> >>>> -- >>>> 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...(a)googlegroups.com. >>>> To post to this group, send email to scikit...(a)googlegroups.com. >>>> To view this discussion on the web, visit >>>> https://groups.google.com/d/msgid/scikit-image/b5e56392-b181-4f70-a090-115a… >>>> <https://groups.google.com/d/msgid/scikit-image/b5e56392-b181-4f70-a090-115a…> >>>> . >>>> 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. >> To post to this group, send email to scikit-image(a)googlegroups.com. >> To view this discussion on the web, visit >> https://groups.google.com/d/msgid/scikit-image/057d7338-f94a-4151-8200-0bf3… >> <https://groups.google.com/d/msgid/scikit-image/057d7338-f94a-4151-8200-0bf3…> >> . >> >> 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/2_OZaXf2xEs/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > scikit-image+unsubscribe(a)googlegroups.com. > To post to this group, send email to scikit-image(a)googlegroups.com. > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/CA%2BJHcKSGywM5%2BLKA-fniCeb… > <https://groups.google.com/d/msgid/scikit-image/CA%2BJHcKSGywM5%2BLKA-fniCeb…> > . > > For more options, visit https://groups.google.com/d/optout. >

1 0

Fused data types
by Stéfan van der Walt March 10, 2016

March 10, 2016

Hi everyone There is a PR asking for comments on how we wish to proceed with Fused Datatypes: https://github.com/scikit-image/scikit-image/pull/1977 What input & output types should be supported in which combinations? Stéfan

1 0

Re: Problem with using sp.ndimage.label to get largest object in a binary image
by Matteo Niccoli March 9, 2016

March 9, 2016

Thanks again Juan Once I've had a chance to experiment with these options and get a polished, working notebook running, I will re-post it. Matteo On Tue, Mar 8, 2016 at 3:44 PM, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: > Hi Matteo, > > ndimage.label keeps 0 as 0 (background) and then labels every nonzero blob > as 1, 2, ... n. Then, numpy.bincount is completely agnostic as to whether > you are looking at images or any other kind of array, and is just going to > count the values, including 0. > > As I mentioned, remove_small_objects does what you want but you need to > find out the size of the largest blob and pass that in as the min_size > parameter. > > Juan. > > On Wed, Mar 9, 2016 at 1:59 AM, Matteo <matteo.niccoli(a)gmail.com> wrote: > >> Hello Juan >> >> Thanks for your reply. >> Here is a second notebook with the problem image to look at. >> https://github.com/mycarta/rainbowbot/blob/master/crop_image_reduce_colors_… >> >> I have not had time to change anything except for running it, and won't >> be able until tonight. When I do, I will look into your suggestions, and >> recommendations, and any other comments you may have from seeing the >> notebook. >> But, so, the background counts when it comes to labeling/size? I had >> assumed the operations would only apply to bright elements, that's the >> misunderstanding. >> >> Also, being here, the way, is there a better way, or a dedicated >> operation, to get the largest object/blob in a binary image? >> >> Cheers, >> Matteo >> >> On Monday, March 7, 2016 at 11:18:25 PM UTC-7, Juan Nunez-Iglesias wrote: >>> >>> Hi Matteo, >>> >>> It would be useful if you showed us the notebook being run with the >>> problematic image, as well as the original. >>> >>> Having said that, it looks like perhaps you should replace this line: >>> mask_sizes[0] = 0 >>> >>> with >>> >>> sizes[0] = 0 >>> >>> higher up. Perhaps your background is bigger than your foreground in the >>> problem image. =) >>> >>> Juan. >>> >>> PS: Incidentally, have a look at skimage.morphology.remove_small_objects >>> and skimage.morphology.remove_small_holes (this last one is in the >>> just-released 0.12 version). >>> >>> PPS: Also incidentally, for ndimage we often use the convention "from >>> scipy import ndimage as ndi" >>> >>> PPPS: Also, skimage.io.imread can directly load images from URLs. =) >>> >>> On Tue, Mar 8, 2016 at 3:06 AM, Matteo <matteo....(a)gmail.com> wrote: >>> >>>> Hello there >>>> >>>> I'm putting together some code to grab an image with a map, colorbar, >>>> and possibly text and other elements, guess what the largest object in the >>>> image is -assuming it is the map - crop the image to the map extent, then >>>> reduce the number of colors in the map. >>>> My Jupiter notebook is at this location on GitHub: >>>> >>>> https://github.com/mycarta/rainbowbot/blob/master/crop_image_reduce_colors.… >>>> >>>> The issue I have with this code is that: >>>> If I run it with the current test image ( >>>> https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_noteb…) >>>> or even a nimage with map touching the border( >>>> https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_noteb…) >>>> the code seems to work. >>>> >>>> However, in the case of an image with larger blocks of text ( >>>> https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_noteb… >>>> ) >>>> the output of [9] is an array that is all zeroes, although as far as I >>>> know it should not. Can anyone suggest why this is happening? >>>> >>>> I am sure it is something I am overlooking in my code/understanding of >>>> image processing. >>>> >>>> Thanks >>>> Matteo >>>> >>>> -- >>>> 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...(a)googlegroups.com. >>>> To post to this group, send email to scikit...(a)googlegroups.com. >>>> To view this discussion on the web, visit >>>> https://groups.google.com/d/msgid/scikit-image/b5e56392-b181-4f70-a090-115a… >>>> <https://groups.google.com/d/msgid/scikit-image/b5e56392-b181-4f70-a090-115a…> >>>> . >>>> 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. >> To post to this group, send email to scikit-image(a)googlegroups.com. >> To view this discussion on the web, visit >> https://groups.google.com/d/msgid/scikit-image/057d7338-f94a-4151-8200-0bf3… >> <https://groups.google.com/d/msgid/scikit-image/057d7338-f94a-4151-8200-0bf3…> >> . >> >> 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/2_OZaXf2xEs/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > scikit-image+unsubscribe(a)googlegroups.com. > To post to this group, send email to scikit-image(a)googlegroups.com. > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/CA%2BJHcKSGywM5%2BLKA-fniCeb… > <https://groups.google.com/d/msgid/scikit-image/CA%2BJHcKSGywM5%2BLKA-fniCeb…> > . > > For more options, visit https://groups.google.com/d/optout. >

1 0

Re: Problem with using sp.ndimage.label to get largest object in a binary image
by Matteo March 8, 2016

March 8, 2016

Hello Juan Thanks for your reply. Here is a second notebook with the problem image to look at. https://github.com/mycarta/rainbowbot/blob/master/crop_image_reduce_colors_… I have not had time to change anything except for running it, and won't be able until tonight. When I do, I will look into your suggestions, and recommendations, and any other comments you may have from seeing the notebook. But, so, the background counts when it comes to labeling/size? I had assumed the operations would only apply to bright elements, that's the misunderstanding. Also, being here, the way, is there a better way, or a dedicated operation, to get the largest object/blob in a binary image? Cheers, Matteo On Monday, March 7, 2016 at 11:18:25 PM UTC-7, Juan Nunez-Iglesias wrote: > > Hi Matteo, > > It would be useful if you showed us the notebook being run with the > problematic image, as well as the original. > > Having said that, it looks like perhaps you should replace this line: > mask_sizes[0] = 0 > > with > > sizes[0] = 0 > > higher up. Perhaps your background is bigger than your foreground in the > problem image. =) > > Juan. > > PS: Incidentally, have a look at skimage.morphology.remove_small_objects > and skimage.morphology.remove_small_holes (this last one is in the > just-released 0.12 version). > > PPS: Also incidentally, for ndimage we often use the convention "from > scipy import ndimage as ndi" > > PPPS: Also, skimage.io.imread can directly load images from URLs. =) > > On Tue, Mar 8, 2016 at 3:06 AM, Matteo <matteo....(a)gmail.com <javascript:> > > wrote: > >> Hello there >> >> I'm putting together some code to grab an image with a map, colorbar, and >> possibly text and other elements, guess what the largest object in the >> image is -assuming it is the map - crop the image to the map extent, then >> reduce the number of colors in the map. >> My Jupiter notebook is at this location on GitHub: >> >> https://github.com/mycarta/rainbowbot/blob/master/crop_image_reduce_colors.… >> >> The issue I have with this code is that: >> If I run it with the current test image ( >> https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_noteb…) >> or even a nimage with map touching the border( >> https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_noteb…) >> the code seems to work. >> >> However, in the case of an image with larger blocks of text ( >> https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_noteb… >> ) >> the output of [9] is an array that is all zeroes, although as far as I >> know it should not. Can anyone suggest why this is happening? >> >> I am sure it is something I am overlooking in my code/understanding of >> image processing. >> >> Thanks >> Matteo >> >> -- >> 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...(a)googlegroups.com <javascript:>. >> To post to this group, send email to scikit...(a)googlegroups.com >> <javascript:>. >> To view this discussion on the web, visit >> https://groups.google.com/d/msgid/scikit-image/b5e56392-b181-4f70-a090-115a… >> <https://groups.google.com/d/msgid/scikit-image/b5e56392-b181-4f70-a090-115a…> >> . >> For more options, visit https://groups.google.com/d/optout. >> > >

2 1