Mailman 3 September 2016 - scikit-image

Line Detection
by KRISHNAMOOORTHY P 02 Oct '16

02 Oct '16

How to get oblique (+45 and 135 degree) of images using scikit-image or with any other packages?

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neighbors contour length
by Jaime Lopez Carvajal 02 Oct '16

02 Oct '16

Hi, I would like to know if someone could help or suggest any idea how to do this: First, I am trying to know how many neighbors (objects) one particular object have using its contour. Second, I need to extract the length of each shared contour with every neighbor, Third, calculate their respective percentage. The last step is the easiest, but I dont know how to get the first and second steps. Example using attached image: Object of interest: red object Neighbors: three neighbors with three shared contours (yellow, green and blue). Total length contour = lengh(yellow) + lengh(yellow) + lengh(yellow) Any suggestion how can I get this? Thanks in advance, Jaime

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Re: GLCM calculation using scikit-learn. Error when using greycomatrix
by ioannisgkan259＠gmail.com 02 Oct '16

02 Oct '16

Thank you very much Juan for your quick reply. That was helpful :) Ioannis On Monday, 19 September 2016 01:03:45 UTC+1, Juan Nunez-Iglesias wrote: > > Hi Ioannis, > > Unfortunately the levels keyword is used as a hint to the function about > the number of levels when the image is uint16, because the possible number > of levels is huge. But if you want to convert the image to those levels, > you have to do it manually. I suggest you look at the "rescale_intensity" > function: > > > http://scikit-image.org/docs/dev/api/skimage.exposure.html#skimage.exposure… > > and process your image before passing it to the glcm function. > > I hope this helps! Keep pinging if you have more questions. =) > > Juan. > > On Sun, Sep 18, 2016 at 4:57 AM, <ioannis...(a)gmail.com <javascript:>> > wrote: > >> Hello everyone, >> >> I am using a SAR image (16-bit) and trying to implement GLCM algorithm >> using sciki-learn. When trying to calculate the GLCM using greycomatrix i >> get the following error: >> >> assert image.max() < levels. It says that the maximum value of the image intensity must be less than the number of grey levels. >> Because the SAR image is really big, i want to reduce the calculation time by reducing the levels to 8. >> Even if i remove the parameter 'level=8' when using greycomatrix, still gives me the same error >> >> My code is the following: >> >> from skimage.feature import greycomatrix, greycoprops >> import numpy as np >> from skimage import data >> import rasterio >> >> path = 'C:\Users\GLCM_implementation\glasgow.tif' >> >> with rasterio.open(path, 'r') as src: >> import_file = src.read() >> img = import_file[0,:,:] #i need only the two dimentions (height, width) >> print img.shape >> >> >> #calculate the GLCM specifying the distance, direction(4 directions) and number of grey levels >> GLCM = greycomatrix(img, [1], [0, np.pi/4, np.pi/2, 3*np.pi/4],levels=8, symmetric=False, normed=True) >> #list(GLCM[:,:,0,2]) >> >> >> #Calculate texture statistics >> contrast = greycoprops(GLCM, 'contrast') >> >> dissimilarity = greycoprops(GLCM, 'dissimilarity') >> >> homogeneity = greycoprops(GLCM, 'homogeneity') >> >> energy = greycoprops(GLCM, 'energy') >> >> correlation = greycoprops(GLCM, 'correlation') >> >> ASM = greycoprops(GLCM, 'ASM') >> >> >> >> Error message: >> >> 101 image = np.ascontiguousarray(image) 102 assert image.min() >= 0--> 103 assert image.max() < levels 104 image = image.astype(np.uint8) 105 distances = np.ascontiguousarray(distances, dtype=np.float64) >> AssertionError: >> >> >> I would appreciate any help. >> Thank you in advance >> >> Ioannis >> >> -- >> 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/520f5f2b-4750-4b56-a40b-28b9… >> <https://groups.google.com/d/msgid/scikit-image/520f5f2b-4750-4b56-a40b-28b9…> >> . >> For more options, visit https://groups.google.com/d/optout. >> > >

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Re: Fwd: PyData Community Cookbook - August Update
by Alexandre Fioravante de Siqueira 30 Sep '16

30 Sep '16

Hi all, Stéfan, thanks for that. I'm working on it. I need your e-mails and institutions for the commit: """ :author: Stéfan van der Walt :email: :institution: :corresponding: :author: Emmanuelle Gouillart :email: :institution: :institution: :equal-contributor: :author: Egor Panfilov :email: :institution: :equal-contributor: :author: Alexandre de Siqueira :email: :institution: University of Campinas :institution: TU Bergakademie Freiberg :equal-contributor: """ We need an abstract too: """ scikit-image is an image processing toolbox for SciPy which provides easy access for segmentation, geometric transformations, color space manipulation, analysis, filtering, morphology, feature detection, and more. It is available free of charge and restriction, and the code is written by an active community of volunteers. (...) """ As you may see I need some ideas for that :) Since this is a cookbook, I think it would be aimed to "recipes" using different functions/objects from the library. Maybe we could specify some examples on the abstract. Do you have any ideas? I'll wait until 10hPM (Berlin time; 8hPM UTC) to submit that, so we can discuss some ideas if you have time. Thanks! I'm here if you need. Kind regards, Alex Em quarta-feira, 31 de agosto de 2016 23:54:06 UTC+2, stefanv escreveu: > > Hi Alex > > On Wed, Aug 31, 2016, at 10:41, Alexandre Fioravante de Siqueira wrote: > > have you figured it out? The deadline is tomorrow, and I would really > > like to participate. > > Would you please submit an initial pull request on the team's behalf? > You can add me, Egor, Emmanuelle, and anyone else who expresses interest > here as co-authors. > > Emmanuelle, I will double check that the chapter is fully open when it > is done so that we can remix parts for the user guide. > > Thanks > Stéfan >

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Generating a dataset of images in RAM
by Jean-Patrick Pommier 28 Sep '16

28 Sep '16

Dear all, I proposed on kagle an image processing/supervised classification problem <https://www.kaggle.com/jeanpat/d/jeanpat/metaphase/generating-overlapping-c…> concerning the resolution of overlapping chromosomes.The aim is to produce a large dataset of examples. A first dataset was produced <https://www.kaggle.com/jeanpat/overlapping-chromosomes>, but it seems to be too small to yield good results for supervised classification with a neural network. As explained in the first notebook, 8Go is not enough to process, mainly to resize/crop, the images. My question how a large batch of images >>100 000 can be resized? Thanks. Jean-Patrick PS I can't hide that It would be great if some would be interrested by the problem itself and give some help on the resolution itself or some advices on the proposed code.

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Re: Implementing Kadir and Brady's saliency detector in skimage?
by Juan Nunez-Iglesias 23 Sep '16

23 Sep '16

Hi Parul, Sorry for the silence! Sometimes we are busy and these PRs fall through the cracks. I'm doing a quick review of your code right now but I don't see any questions regarding parameters on the issue itself? For the gallery example, whatever code you used to apply the method to `data.astronaut` is probably a good choice for the example! Juan. From: Parul Sethi <parul1sethi(a)gmail.com> <parul1sethi(a)gmail.com> Reply: scikit-image(a)googlegroups.com <scikit-image(a)googlegroups.com> <scikit-image(a)googlegroups.com> Date: 23 September 2016 at 3:54:43 PM To: scikit-image(a)googlegroups.com <scikit-image(a)googlegroups.com> <scikit-image(a)googlegroups.com> Subject: Re: Implementing Kadir and Brady's saliency detector in skimage? Hi, I opened a PR regarding this Saliency detection algorithm few days back (#2299). Though the implementation is complete, i required some suggestions regarding parameters(mentioned there). Can any scikit-image maintainer please review it once. Thanks On Thu, Jul 28, 2016 at 11:33 AM, Parul Sethi <parul1sethi(a)gmail.com> wrote: > So sorry for the long pause. > > Thankyou for the response! > I'll soon be done with it. > On 11 Jul 2016 4:11 am, "Stéfan van der Walt" <stefanv(a)berkeley.edu> > wrote: > >> Hi Parul >> >> We are happy to evaluate any PR for inclusion. Saliency detection is >> within scope. >> >> Best regards >> Stéfan >> On Jul 6, 2016 05:54, "parul sethi" <parul1sethi(a)gmail.com> wrote: >> >>> Hi, >>> >>> I required to use Kadir and Brady's saliency detector for feature >>> extraction process, and didn't found it's python implementation. So, i was >>> in process of implementing the same. >>> Will it be of interest to skimage too? I can use some advice from >>> skimage maintainers to build it with specific suitability for skimage >>> module. >>> >>> Thank you. >>> -- >>> 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/7132cb6e-e66f-45be-a71a-327a2e5ff7d9% >>> 40googlegroups.com >>> <https://groups.google.com/d/msgid/scikit-image/7132cb6e-e66f-45be-a71a-327a…> >>> . >>> 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/FzZ1VkJt-Ks/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/CABDkGQ%3D%2BcAy%3DLzc5MOR-CzummOuWiyDWrvoN_mXNX% >> 2BNBh868Ew%40mail.gmail.com >> <https://groups.google.com/d/msgid/scikit-image/CABDkGQ%3D%2BcAy%3DLzc5MOR-C…> >> . >> For more options, visit https://groups.google.com/d/optout. >> > -- Parul Sethi (student) B.Tech (IT & Mathematical innovation) Cluster Innovation Centre Delhi University -- 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/CAFgV4O5DumqYxW-a0zm5vU9bd45… <https://groups.google.com/d/msgid/scikit-image/CAFgV4O5DumqYxW-a0zm5vU9bd45…> . For more options, visit https://groups.google.com/d/optout.

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Re: Implementing Kadir and Brady's saliency detector in skimage?
by Parul Sethi 23 Sep '16

23 Sep '16

Hi, I opened a PR regarding this Saliency detection algorithm few days back (#2299). Though the implementation is complete, i required some suggestions regarding parameters(mentioned there). Can any scikit-image maintainer please review it once. Thanks On Thu, Jul 28, 2016 at 11:33 AM, Parul Sethi <parul1sethi(a)gmail.com> wrote: > So sorry for the long pause. > > Thankyou for the response! > I'll soon be done with it. > On 11 Jul 2016 4:11 am, "Stéfan van der Walt" <stefanv(a)berkeley.edu> > wrote: > >> Hi Parul >> >> We are happy to evaluate any PR for inclusion. Saliency detection is >> within scope. >> >> Best regards >> Stéfan >> On Jul 6, 2016 05:54, "parul sethi" <parul1sethi(a)gmail.com> wrote: >> >>> Hi, >>> >>> I required to use Kadir and Brady's saliency detector for feature >>> extraction process, and didn't found it's python implementation. So, i was >>> in process of implementing the same. >>> Will it be of interest to skimage too? I can use some advice from >>> skimage maintainers to build it with specific suitability for skimage >>> module. >>> >>> Thank you. >>> >>> -- >>> 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/7132cb6e-e66f-45be-a71a-327a2e5ff7d9% >>> 40googlegroups.com >>> <https://groups.google.com/d/msgid/scikit-image/7132cb6e-e66f-45be-a71a-327a…> >>> . >>> 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/FzZ1VkJt-Ks/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/CABDkGQ%3D%2BcAy%3DLzc5MOR-CzummOuWiyDWrvoN_mXNX% >> 2BNBh868Ew%40mail.gmail.com >> <https://groups.google.com/d/msgid/scikit-image/CABDkGQ%3D%2BcAy%3DLzc5MOR-C…> >> . >> For more options, visit https://groups.google.com/d/optout. >> > -- Parul Sethi (student) B.Tech (IT & Mathematical innovation) Cluster Innovation Centre Delhi University

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Re: Dedicated work time from employers
by Emmanuelle Gouillart 23 Sep '16

23 Sep '16

Dear StÃ©fan, thanks for the initiative! My "employer" until December is a 2-week old little boy, and I hope that I'll soon be able to set aside a few hours every week for scikit-image, which will be a welcome change from lullabies and nappies :-). As for my regular employer, I'm afraid that my current position as group leader is not compatible with work on scikit-image during work hours, so I'll try to keep on contributing a little during evenings and week-ends. Best, Emma On Wed, Sep 21, 2016 at 12:28:33PM -0700, Stefan van der Walt wrote: > Dear scikit-image developers > In an effort to make it easier for you to contribute to scikit-image, I > am sending letters to employers asking them to donate a certain amount > of your work time (10 hours a month) to the project. > If you are in a position where this would be helpful, please get in > touch. > The goal, ultimately, is to have have one (or preferably several) > developers active daily in managing the project and reviewing code > contributions. > Best regards > StÃ©fan

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Re: skimage and opencv
by Emmanuelle Gouillart 22 Sep '16

22 Sep '16

Hi FranÃ¯Â¿Â½ois, that's an excellent question, and not a troll :-). Opencv is a very powerful library, but it focuses primarily on computer vision (feature detection and extraction, classification, ...), as opposed to image processing in general (with other tasks such as denoising, segmentation, ...). The other big difference is that skimage builds on numpy ndarrays, and uses the full power of the numpy API (including of course the basic facilities for processing arrays as images that come with numpy), as well as some of scipy functions (you could have added scipy.ndimage to your list -- a few functions in skimage are wrappers around scipy.ndimage, that exist for the sake of completeneness). One important consequence is that algorithms working for 3-d or even n-d images can be easily implemented in 3-d/n-d in skimage, whereas opencv is restricted to 2-D images (as far as I know). Thanks to the use of numpy arrays, the API of skimage is also quite pleasant for a numpy user, more than the API of opencv. A related difference is that skimage is written in python and cython, whereas opencv is a C++ library. The two libraries attract a different crowd of developers, and a Python/Cython toolkit based on numpy arrays is easier to develop and maintain inside the Scientific Python ecosystem. I'm sure that other devs/users will have things to add to this discussion! Cheers, Emmanuelle On Thu, Dec 27, 2012 at 02:06:08PM -0800, FranÃ¯Â¿Â½ois wrote: > Hi users and devs, > It came to my knowledge that another python library (based on C++ and C > codes) for image processing exists too : opencv > I understand that numpy intregrates some basic features and we need some > advanced features but I have the feeling that skimages is redoundant with > opencv in some ways. > What's the position of skimage about that? (Don't read this question as a > troll but like a real question). > I mean that similar features exist in both. Would not be possible to > reuse/integrate opencv or merge? what's the reason for keeping them apart? > My observation is there is 4 libraries to manipulate images: > * PIL > * numpy > * skimages > * opencv > That's a lot. > Cheers,

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Re: Image edge detection
by Dipankar “Dipu” Ganguly 22 Sep '16

22 Sep '16

Thanks for the quick response Juan. Sorry. I DID mean Jython. The real issue is porting this hybrid Scikit-image/openCV/Python 3.5 code on to an Android tablet as an app. I am not an expert on that Android environment but thought Java was the common development platform. If there are other ways to accomplish that, I am all ears! Thanks. Dipu Dipankar “Dipu” Ganguly dipugee(a)gmail.com Cell: 408-203-8814 > On Sep 21, 2016, at 10:49 PM, Juan Nunez-Iglesias <jni.soma(a)gmail.com> wrote: > > Hi Dipu, > > 1. I assume you mean Jython. Most of the SciPy stack is not available for Jython, unless things have changed dramatically since I last looked at it… > > 2. I am not aware of a document translating between scikit-image and openCV. I suspect there is substantial non-overlap. Python bindings for both should operate on numpy arrays, so I think you should use both, wherever it makes sense? Though, as mentioned above, you will have more trouble with this using Jython… > > Juan. > > On 22 September 2016 at 2:34:12 pm, Dipankar “Dipu” Ganguly (dipugee(a)gmail.com <mailto:dipugee@gmail.com>) wrote: > >> Hi Stefan: >> >> I need to bug you again. I have a couple of new questions… >> >> 1 My Python 3.5 code now includes Sci-Image, numpy and matplotlib functions as well some openCV calls. I need too convert this using JPython. How easily will these SciPy and openCV functions convert? >> >> 2. How close are SciImage and openCV in function content? Is there a document where I can find openCV equivalents to Sciimage functions and vice versa? >> >> Thanks. >> >> Dipu >> >> >> Dipankar Ganguly >> Consultant: Strategy/Technology/Commercialization >> Bothell, WA >> Cell: 408-203-8814 >> email: dipugee(a)gmail.com <mailto:dipugee@gmail.com> >> http://www.linkedin.com/in/dipugee <http://www.linkedin.com/in/dipugee> >> >> >> >> >> >> >> >> >> >>> On Aug 9, 2016, at 2:42 PM, Stéfan van der Walt <stefanv(a)berkeley.edu <mailto:stefanv@berkeley.edu>> wrote: >>> >>> Hi Dipu >>> >>> On 9 August 2016 at 14:40, Dipankar “Dipu” Ganguly <dipugee(a)gmail.com <mailto:dipugee@gmail.com>> wrote: >>> Sorry to bother you again. I am having trouble with "from skimage import xyz” commands. I am using Python 3.5 with Jupyter from Navigator. I am wondering if I am running into version mismatches. >>> >>> Yes, I am afraid we don't have an xyz submodule. >>> >>> Perhaps you can share some code with us, along with the error messages you are seeing? >>> >>> 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/7IskXgM-99E/unsubscribe <https://groups.google.com/d/topic/scikit-image/7IskXgM-99E/unsubscribe>. >>> To unsubscribe from this group and all its topics, send an email to scikit-image+unsubscribe(a)googlegroups.com <mailto:scikit-image+unsubscribe@googlegroups.com>. >>> To post to this group, send email to scikit-image(a)googlegroups.com <mailto:scikit-image@googlegroups.com>. >>> To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/CABDkGQnhpOQemWLzN5G2ACwwXgL… <https://groups.google.com/d/msgid/scikit-image/CABDkGQnhpOQemWLzN5G2ACwwXgL…>. >>> For more options, visit https://groups.google.com/d/optout <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 <mailto:scikit-image+unsubscribe@googlegroups.com>. >> To post to this group, send email to scikit-image(a)googlegroups.com <mailto:scikit-image@googlegroups.com>. >> To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/5322EC72-2500-4022-B9EF-1E18… <https://groups.google.com/d/msgid/scikit-image/5322EC72-2500-4022-B9EF-1E18…>. >> For more options, visit https://groups.google.com/d/optout <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/7IskXgM-99E/unsubscribe <https://groups.google.com/d/topic/scikit-image/7IskXgM-99E/unsubscribe>. > To unsubscribe from this group and all its topics, send an email to scikit-image+unsubscribe(a)googlegroups.com <mailto:scikit-image+unsubscribe@googlegroups.com>. > To post to this group, send email to scikit-image(a)googlegroups.com <mailto:scikit-image@googlegroups.com>. > To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/CA%2BJHcKR7UN8QVgN7btj8OyHJT… <https://groups.google.com/d/msgid/scikit-image/CA%2BJHcKR7UN8QVgN7btj8OyHJT…>. > For more options, visit https://groups.google.com/d/optout <https://groups.google.com/d/optout>.

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Re: Dedicated work time from employers
by Johannes Schönberger 22 Sep '16

22 Sep '16

Hi Stefan, This is a great idea! Unfortunately, such an arrangement will not be possible on my side but I will try to help with reviews as much as time permits. I really hope someone has the option to take this great opportunity. Thanks for your efforts! Johannes > On Sep 21, 2016, at 9:28 PM, Stefan van der Walt <stefanv(a)berkeley.edu> wrote: > > Dear scikit-image developers > > In an effort to make it easier for you to contribute to scikit-image, I > am sending letters to employers asking them to donate a certain amount > of your work time (10 hours a month) to the project. > > If you are in a position where this would be helpful, please get in > touch. > > The goal, ultimately, is to have have one (or preferably several) > developers active daily in managing the project and reviewing code > contributions. > > Best regards > Stéfan > > -- > 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 an email to scikit-image(a)googlegroups.com. > To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/1474486113.2732342.732994105…. > For more options, visit https://groups.google.com/d/optout.

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Re: Image edge detection
by Dipankar “Dipu” Ganguly 22 Sep '16

22 Sep '16

Hi Stefan: I need to bug you again. I have a couple of new questions… 1 My Python 3.5 code now includes Sci-Image, numpy and matplotlib functions as well some openCV calls. I need too convert this using JPython. How easily will these SciPy and openCV functions convert? 2. How close are SciImage and openCV in function content? Is there a document where I can find openCV equivalents to Sciimage functions and vice versa? Thanks. Dipu Dipankar Ganguly Consultant: Strategy/Technology/Commercialization Bothell, WA Cell: 408-203-8814 email: dipugee(a)gmail.com http://www.linkedin.com/in/dipugee > On Aug 9, 2016, at 2:42 PM, Stéfan van der Walt <stefanv(a)berkeley.edu> wrote: > > Hi Dipu > > On 9 August 2016 at 14:40, Dipankar “Dipu” Ganguly <dipugee(a)gmail.com <mailto:dipugee@gmail.com>> wrote: > Sorry to bother you again. I am having trouble with "from skimage import xyz” commands. I am using Python 3.5 with Jupyter from Navigator. I am wondering if I am running into version mismatches. > > Yes, I am afraid we don't have an xyz submodule. > > Perhaps you can share some code with us, along with the error messages you are seeing? > > 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/7IskXgM-99E/unsubscribe <https://groups.google.com/d/topic/scikit-image/7IskXgM-99E/unsubscribe>. > To unsubscribe from this group and all its topics, send an email to scikit-image+unsubscribe(a)googlegroups.com <mailto:scikit-image+unsubscribe@googlegroups.com>. > To post to this group, send email to scikit-image(a)googlegroups.com <mailto:scikit-image@googlegroups.com>. > To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/CABDkGQnhpOQemWLzN5G2ACwwXgL… <https://groups.google.com/d/msgid/scikit-image/CABDkGQnhpOQemWLzN5G2ACwwXgL…>. > For more options, visit https://groups.google.com/d/optout <https://groups.google.com/d/optout>.

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Re: Dedicated work time from employers
by Josh Warner 22 Sep '16

22 Sep '16

Until June, my hands are tied. Surgery residency as an intern will do that. Right now, such a letter wouldn't really go very far. Starting after that point, I will be a Radiology resident. Infinitely superior hours, and my program director has offered 10-12 months of the following four years for research. I will be able to spend a sizeable chunk of that time being much more active. Wish I could do more in the short term, Josh On Wednesday, September 21, 2016 at 2:28:35 PM UTC-5, stefanv wrote: > > Dear scikit-image developers > > In an effort to make it easier for you to contribute to scikit-image, I > am sending letters to employers asking them to donate a certain amount > of your work time (10 hours a month) to the project. > > If you are in a position where this would be helpful, please get in > touch. > > The goal, ultimately, is to have have one (or preferably several) > developers active daily in managing the project and reviewing code > contributions. > > Best regards > Stéfan >

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Dedicated work time from employers
by Stefan van der Walt 21 Sep '16

21 Sep '16

Dear scikit-image developers In an effort to make it easier for you to contribute to scikit-image, I am sending letters to employers asking them to donate a certain amount of your work time (10 hours a month) to the project. If you are in a position where this would be helpful, please get in touch. The goal, ultimately, is to have have one (or preferably several) developers active daily in managing the project and reviewing code contributions. Best regards Stéfan

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Re: Task board
by Johannes Schönberger 20 Sep '16

20 Sep '16

> On 20 Sep 2016, at 19:34, Stefan van der Walt <stefanv(a)berkeley.edu> wrote: > >> On Fri, Sep 16, 2016, at 01:35, François Boulogne wrote: >> I think we need to determine how many boards we want (what github call >> project, I don't like this word... anyway). >> A big one with the progress or small ones, one per submodule? or one per >> core dev? > > I think each board is associated with an outcome. So, e.g., we will > decide on some projects such as "Improve Documentation", or "Add 3D > capability", or "Catch up on review backlog". Each of those will then > have a few standard columns that we have to decide on. > > An initial suggestion would be: > > Inbox (list all relevant PRs) > In Progress (someone is working on it) > Ready for Review (please review this work) > Done > > Would that cover 80% of use cases, or do we need more columns? This sounds good to me and we can add more columns as needed and as we gain some experience with the workflow. Grouping comments into reviews and then having a separate approval status is already a big step forward in my view. > > Stéfan > > -- > 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 an email to scikit-image(a)googlegroups.com. > To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/1474392890.2276972.731679577…. > For more options, visit https://groups.google.com/d/optout.

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Re: Task board
by François Boulogne 20 Sep '16

20 Sep '16

> I think each board is associated with an outcome. So, e.g., we will > decide on some projects such as "Improve Documentation", or "Add 3D > capability", or "Catch up on review backlog". Each of those will then > have a few standard columns that we have to decide on. OK with that. > An initial suggestion would be: > > Inbox (list all relevant PRs) > In Progress (someone is working on it) > Ready for Review (please review this work) > Done > > Would that cover 80% of use cases, or do we need more columns? Maybe we should had Needs Decision. Often, we have tickets stuck on a decision to take, either on new features (names, API...) or on refactoring (change API, dependencies, add new functions, reorganize a code...). These choices are often not straightforward and we need different opinions. -- François Boulogne. http://www.sciunto.org GPG: 32D5F22F

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Re: Task board
by François Boulogne 20 Sep '16

20 Sep '16

I'm just discovering this new feature. It looks like we need to organize ourself because sorting issues in the column of a project is like duplicating the labels "status" we have on issues. I didn't find a way to automatically import issues, but we can search a label and drag the "cards". I think we need to determine how many boards we want (what github call project, I don't like this word... anyway). A big one with the progress or small ones, one per submodule? or one per core dev? Any thoughts?

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Splits binary object to approximated ellipses using scikit-image
by l.roca＠gmx.us 19 Sep '16

19 Sep '16

Hi, Can scikit-image do ellipse splitting like in an imageJ plugin (http://imagej.net/Ellipse_split) that splits binary object to approximated ellipses? Thanks, Lluis

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GLCM calculation using scikit-learn. Error when using greycomatrix
by ioannisgkan259＠gmail.com 19 Sep '16

19 Sep '16

Hello everyone, I am using a SAR image (16-bit) and trying to implement GLCM algorithm using sciki-learn. When trying to calculate the GLCM using greycomatrix i get the following error: assert image.max() < levels. It says that the maximum value of the image intensity must be less than the number of grey levels. Because the SAR image is really big, i want to reduce the calculation time by reducing the levels to 8. Even if i remove the parameter 'level=8' when using greycomatrix, still gives me the same error My code is the following: from skimage.feature import greycomatrix, greycoprops import numpy as np from skimage import data import rasterio path = 'C:\Users\GLCM_implementation\glasgow.tif' with rasterio.open(path, 'r') as src: import_file = src.read() img = import_file[0,:,:] #i need only the two dimentions (height, width) print img.shape #calculate the GLCM specifying the distance, direction(4 directions) and number of grey levels GLCM = greycomatrix(img, [1], [0, np.pi/4, np.pi/2, 3*np.pi/4],levels=8, symmetric=False, normed=True) #list(GLCM[:,:,0,2]) #Calculate texture statistics contrast = greycoprops(GLCM, 'contrast') dissimilarity = greycoprops(GLCM, 'dissimilarity') homogeneity = greycoprops(GLCM, 'homogeneity') energy = greycoprops(GLCM, 'energy') correlation = greycoprops(GLCM, 'correlation') ASM = greycoprops(GLCM, 'ASM') Error message: 101 image = np.ascontiguousarray(image) 102 assert image.min() >= 0--> 103 assert image.max() < levels 104 image = image.astype(np.uint8) 105 distances = np.ascontiguousarray(distances, dtype=np.float64) AssertionError: I would appreciate any help. Thank you in advance Ioannis

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Re: Task board
by Juan Nunez-Iglesias 15 Sep '16

15 Sep '16

Yes, crazy timing! =D On 15 September 2016 at 9:08:59 AM, Stefan van der Walt ( stefanv(a)berkeley.edu) wrote: On Mon, Aug 29, 2016, at 13:17, Stefan van der Walt wrote: > I have some ideas around (1) that need fleshing out, but in the mean > time I was looking at http://zube.io to address part of (2). Take a look at this! https://github.com/blog/2256-a-whole-new-github-universe-announcing-new-too… E.g., here's an empty project to play around with: https://github.com/scikit-image/scikit-image/projects/1 Stéfan -- 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 an email to scikit-image(a)googlegroups.com. To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/1473894533.1455710.726083169…. For more options, visit https://groups.google.com/d/optout.

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how to find the intersection point of two objects
by LC 15 Sep '16

15 Sep '16

Dear All, I am new to image processing and using OpenCV on python for implementing a part of research work. The aim is : - To identify the predecessor and successor of an object (shape) and - To calculate the Indegree(edges coming on shape) and outdegree(edges going out from shape) of object. Or is thr anyway to find digraph for given image? Can anybody help to find the intersection point of two object called rectangle and edges(directed line) in the attached img? your guidance /pointers will be appriciated. thanks & regards

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Re: Management of PRs, issues, and threads
by Stefan van der Walt 14 Sep '16

14 Sep '16

On Sun, Sep 11, 2016, at 23:13, Juan Nunez-Iglesias wrote: > > This way your PRs are always checked against the latest master, not > > whatever was around when they were first made > > I thought Travis did this already? > > https://docs.travis-ci.com/user/pull-requests > > "Rather than test the commits that have been pushed to the branch the > pull request is from, we test the merge between the origin and the > upstream branch." This happens the moment you make the PR, or push new commits. Ideally, you want to run the tests just before merging. Stéfan

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Task board
by Stefan van der Walt 14 Sep '16

14 Sep '16

Hi, everyone As Juan mentioned recently, it's becoming harder to keep track of the motion of the project as a whole. Sometimes, tickets lounge unattended for an unacceptable long time. I can think of two main routes for improving the situation: 1) Improve our team structure, so that individuals take responsibility for moving certain aspects of the project forward. 2) Processes / systems to help us get a grasp on the current state of things I have some ideas around (1) that need fleshing out, but in the mean time I was looking at http://zube.io to address part of (2). Do you have any experience with this system? Zube can be compared against HuBoard, gh-board, and ZenHub. A test scikit-image board is here: https://zube.io/projects/4670/kanban (it's vanilla, I haven't done anything with it yet) Let me hear your thoughts. Stéfan

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Re: Management of PRs, issues, and threads
by Johannes Schönberger 14 Sep '16

14 Sep '16

This should very be interesting in this regard: https://github.com/blog/2256-a-whole-new-github-universe-announcing-new-too… > On 12 Sep 2016, at 18:35, Nelle Varoquaux <nelle.varoquaux(a)gmail.com> wrote: > > Hi scikit-image folks! > > >> We've had a couple of community fails on GitHub recently: >> https://github.com/scikit-image/scikit-image/pull/1474#issuecomment-2412830… >> https://github.com/scikit-image/scikit-image/issues/2080 >> (The last one is missing a presumably-deleted comment where someone outside >> the project recommended to a potential contributor to just fork the >> project!). > > Being the person that reported one of those community fails, I'd like > to say that I've had great experience with the scikit-image community > overall. Contributors are (usually) very well welcomed, feedback is > friendly, and we can have discussion and debates about "hot" topics > (like dropping python2.7) in a friendly and nice environment. I've > recently contributed to another scientific python project where many > members of the community were aggressive in their reviews, without > giving valuable feedback on PRs, so I value scikit-image's (& > scikit-learn) community even more. > >> That's just the couple I've noticed, I'm sure there are lots more. We >> definitely have many, many abandoned PRs from >1y, >2y ago. >> >> Obviously, something in our process isn't working. I don't have immediate >> solutions, but here's a couple of suggestions: >> >> - we need a system to assign core devs to PRs/issues. Currently, it's too >> easy for all of us to go, "someone else on the team will handle this". We >> need a fair way to assign a manager to each issue/PR. The assigned dev >> wouldn't necessarily be responsible for review, but they would be >> responsible for chasing up other reviewers. >> >> - NEVER close a PR without the explicit consent of the contributor, OR after >> the contributor has been non-responsive for e.g. 1mo and two pings. In this >> last situation I would even suggest that we need two core devs to sign off. > > I would not close old PR, for the sake of closing them. If the > contributor is not interested in finishing the contribution and the > patch is almost ready, it might be a good way to introduce new > contributors (/students) to the PR. This can probably be done by an > "Need contributor" tag + "Easy fix", though I haven't thought more > about this > >> Other suggestions welcome in this thread. We should try to get a new process >> hammered out very soon. >> >> I also want to acknowledge @soupault for his triage/labelling work, which is >> a massive step in the right direction. But we need to follow up his triage >> with some actual process. >> >> Juan. >> >> -- >> 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/CA%2BJHcKSh-k%2ByM0yBTRzTy%3…. >> 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 an email to scikit-image(a)googlegroups.com. > To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/CAE-UAvSnKid2zn9bM4%3DdU2mvG…. > For more options, visit https://groups.google.com/d/optout.

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Re: Management of PRs, issues, and threads
by Nelle Varoquaux 12 Sep '16

12 Sep '16

Hi scikit-image folks! > We've had a couple of community fails on GitHub recently: > https://github.com/scikit-image/scikit-image/pull/1474#issuecomment-2412830… > https://github.com/scikit-image/scikit-image/issues/2080 > (The last one is missing a presumably-deleted comment where someone outside > the project recommended to a potential contributor to just fork the > project!). Being the person that reported one of those community fails, I'd like to say that I've had great experience with the scikit-image community overall. Contributors are (usually) very well welcomed, feedback is friendly, and we can have discussion and debates about "hot" topics (like dropping python2.7) in a friendly and nice environment. I've recently contributed to another scientific python project where many members of the community were aggressive in their reviews, without giving valuable feedback on PRs, so I value scikit-image's (& scikit-learn) community even more. > That's just the couple I've noticed, I'm sure there are lots more. We > definitely have many, many abandoned PRs from >1y, >2y ago. > > Obviously, something in our process isn't working. I don't have immediate > solutions, but here's a couple of suggestions: > > - we need a system to assign core devs to PRs/issues. Currently, it's too > easy for all of us to go, "someone else on the team will handle this". We > need a fair way to assign a manager to each issue/PR. The assigned dev > wouldn't necessarily be responsible for review, but they would be > responsible for chasing up other reviewers. > > - NEVER close a PR without the explicit consent of the contributor, OR after > the contributor has been non-responsive for e.g. 1mo and two pings. In this > last situation I would even suggest that we need two core devs to sign off. I would not close old PR, for the sake of closing them. If the contributor is not interested in finishing the contribution and the patch is almost ready, it might be a good way to introduce new contributors (/students) to the PR. This can probably be done by an "Need contributor" tag + "Easy fix", though I haven't thought more about this > Other suggestions welcome in this thread. We should try to get a new process > hammered out very soon. > > I also want to acknowledge @soupault for his triage/labelling work, which is > a massive step in the right direction. But we need to follow up his triage > with some actual process. > > Juan. > > -- > 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/CA%2BJHcKSh-k%2ByM0yBTRzTy%3…. > For more options, visit https://groups.google.com/d/optout.

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Re: Management of PRs, issues, and threads
by Juan Nunez-Iglesias 12 Sep '16

12 Sep '16

> This way your PRs are always checked against the latest master, not whatever was around when they were first made I thought Travis did this already? https://docs.travis-ci.com/user/pull-requests "Rather than test the commits that have been pushed to the branch the pull request is from, we test the merge between the origin and the upstream branch." However this would imply that Travis wouldn't do anything when you can't automatically merge. I don't remember whether this is True... On 10 September 2016 at 5:33:04 PM, Matthew Brett (matthew.brett(a)gmail.com) wrote: Hi, On Sat, Sep 10, 2016 at 12:21 AM, Stefan van der Walt <stefanv(a)berkeley.edu> wrote: > On Thu, Sep 8, 2016, at 07:22, Egor Panfilov wrote: > > Remember me hyping around with the GitHub bot idea? > Here it is: > - in the source code: https://github.com/facebook/mention-bot > - in action: > https://github.com/tensorflow/tensorflow/pull/4239#issuecomment-245180925 > > > This is cute. Although I think what could be even more useful is a feature > I saw elsewhere: instead of clicking the merge button, you instruct it to > re-run the test suite and merge upon successful completion. This way your > PRs are always checked against latest master, not whatever was around when > they were first made. Yes, this was the homu bot - we have a copy of that running on the nipy server in Berkeley. Matthias B of IPython fame was talking about sharing some work to refactor the homu code into something more general to extend the range of github tasks it could do - maybe including mention-automation like the face-book-bot. Matthew -- 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 an email to scikit-image(a)googlegroups.com. To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/CAH6Pt5phve%3DS1t1haAVT%3D3%…. For more options, visit https://groups.google.com/d/optout.

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Re: Management of PRs, issues, and threads
by Egor Panfilov 10 Sep '16

10 Sep '16

Dears, I believe there might be a generic solution already: see my comment ( https://github.com/scikit-image/scikit-image/issues/2269#issuecomment-24335…) and, particularly, "rust-lang" reference. Regards, Egor 2016-09-10 10:32 GMT+03:00 Matthew Brett <matthew.brett(a)gmail.com>: > Hi, > > On Sat, Sep 10, 2016 at 12:21 AM, Stefan van der Walt > <stefanv(a)berkeley.edu> wrote: > > On Thu, Sep 8, 2016, at 07:22, Egor Panfilov wrote: > > > > Remember me hyping around with the GitHub bot idea? > > Here it is: > > - in the source code: https://github.com/facebook/mention-bot > > - in action: > > https://github.com/tensorflow/tensorflow/pull/4239# > issuecomment-245180925 > > > > > > This is cute. Although I think what could be even more useful is a > feature > > I saw elsewhere: instead of clicking the merge button, you instruct it to > > re-run the test suite and merge upon successful completion. This way > your > > PRs are always checked against latest master, not whatever was around > when > > they were first made. > > Yes, this was the homu bot - we have a copy of that running on the > nipy server in Berkeley. Matthias B of IPython fame was talking > about sharing some work to refactor the homu code into something more > general to extend the range of github tasks it could do - maybe > including mention-automation like the face-book-bot. > > Matthew > > -- > 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 an email to scikit-image(a)googlegroups.com. > To view this discussion on the web, visit https://groups.google.com/d/ > msgid/scikit-image/CAH6Pt5phve%3DS1t1haAVT%3D3% > 3DRhwwDBdZzO9Mqh1ED4_cDx2B-Pw%40mail.gmail.com. > For more options, visit https://groups.google.com/d/optout. >

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Re: Management of PRs, issues, and threads
by Matthew Brett 10 Sep '16

10 Sep '16

Hi, On Sat, Sep 10, 2016 at 12:21 AM, Stefan van der Walt <stefanv(a)berkeley.edu> wrote: > On Thu, Sep 8, 2016, at 07:22, Egor Panfilov wrote: > > Remember me hyping around with the GitHub bot idea? > Here it is: > - in the source code: https://github.com/facebook/mention-bot > - in action: > https://github.com/tensorflow/tensorflow/pull/4239#issuecomment-245180925 > > > This is cute. Although I think what could be even more useful is a feature > I saw elsewhere: instead of clicking the merge button, you instruct it to > re-run the test suite and merge upon successful completion. This way your > PRs are always checked against latest master, not whatever was around when > they were first made. Yes, this was the homu bot - we have a copy of that running on the nipy server in Berkeley. Matthias B of IPython fame was talking about sharing some work to refactor the homu code into something more general to extend the range of github tasks it could do - maybe including mention-automation like the face-book-bot. Matthew

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Re: Management of PRs, issues, and threads
by Emmanuelle Gouillart 10 Sep '16

10 Sep '16

Hi Juan, thanks for bringing these issues to light. How about we tackle the queue of open PRs from its two ends? That is, for the new PRs we have this manager system (we still need to decide how to assign them), and at the same time we go through old PRs to try to unblock or (worst case) close them? Best, Emma On Mon, Aug 22, 2016 at 02:47:16PM +1000, Juan Nunez-Iglesias wrote: > Hi everyone, > We've had a couple of community fails on GitHub recently: > https://github.com/scikit-image/scikit-image/pull/1474#issuecomment-2412830… > https://github.com/scikit-image/scikit-image/issues/2080 > (The last one is missing a presumably-deleted comment where someone outside the > project recommended to a potential contributor to just fork the project!). > That's just the couple I've noticed, I'm sure there are lots more. We > definitely have many, many abandoned PRs from >1y, >2y ago. > Obviously, something in our process isn't working. I don't have immediate > solutions, but here's a couple of suggestions: > - we need a system to assign core devs to PRs/issues. Currently, it's too easy > for all of us to go, "someone else on the team will handle this". We need a > fair way to assign a manager to each issue/PR. The assigned dev wouldn't > necessarily be responsible for review, but they would be responsible for > chasing up other reviewers. > - NEVER close a PR without the explicit consent of the contributor, OR after > the contributor has been non-responsive for e.g. 1mo and two pings. In this > last situation I would even suggest that we need two core devs to sign off. > Other suggestions welcome in this thread. We should try to get a new process > hammered out very soon. > I also want to acknowledge @soupault for his triage/labelling work, which is a > massive step in the right direction. But we need to follow up his triage with > some actual process. > Juan.

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Re: Task board
by Ralf Gommers 05 Sep '16

05 Sep '16

On Mon, Sep 5, 2016 at 10:42 PM, Stefan van der Walt <stefanv(a)berkeley.edu> wrote: > On Sun, Sep 4, 2016, at 01:32, Egor Panfilov wrote: > > You mean RFCs like PEPs? > > > Exactly. I think, this format would help to accumulate our opinions on > different matters (e.g. how to we treat and depend on `matplotlib`) > > > We should chat to Ralf Gommers to find out how successful the Enhancement > Proposal approach has been for SciPy, which is similar to this project in > many ways. > Since we don't have those for SciPy, I'd say not very:) You're thinking about NumPy probably: http://docs.scipy.org/doc/numpy/neps/index.html https://github.com/numpy/numpy/tree/master/doc/neps We don't use them often, but when we do they've been valuable. For example the .npy version format is a good reference with rationale, and for complex discussions like datetime and NA it helps to summarize the issues and outlike solution directions (emails really don't work well for that). Cheers, Ralf

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Re: Task board
by Stefan van der Walt 05 Sep '16

05 Sep '16

On Sun, Sep 4, 2016, at 01:32, Egor Panfilov wrote: >> You mean RFCs like PEPs? > > Exactly. I think, this format would help to accumulate our opinions on > different matters (e.g. how to we treat and depend on `matplotlib`) We should chat to Ralf Gommers to find out how successful the Enhancement Proposal approach has been for SciPy, which is similar to this project in many ways. > Well, I'm just saying that we as a core team should drive the > evolution of backend and make life easier for contributors and users. > Like, try to imagine some new contributor making a PR introducing > Sphinx Gallery. Can't see this happenning. Of course, all of us are > working on this kind of features already, I just want to highlight > this (maybe trivial) point. > As a "practical guide", perhaps we should dedicate more time to the > _complex_ issues/requests/PRs we have. Still, I'm unclear how we can make it easier for newcomers to contribute to the backend. Do you have any practical suggestions? Best regards Stefan

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Re: Fwd: PyData Community Cookbook - August Update
by Josh Warner 05 Sep '16

05 Sep '16

I would also contribute - Joshua D. Warner, email joshua dot dale dot warner at Gmail, institution Mayo Clinic.

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Re: Task board
by Johannes Schönberger 04 Sep '16

04 Sep '16

To better keep track of PR/issues, I suggest core developers assign themselves to some of the issues in their field of expertise. There are so many PRs that are >90% finished but it seems we forgot to continue reviewing them. > On Sep 4, 2016, at 10:32 AM, Egor Panfilov <multicolor.mood(a)gmail.com> wrote: > > Hi Stefan! > >> As for issues/PRs management system, I think that GitHub tags pretty much do the deal. We've recently added "status: xxx" tags to facilitate tracking of active/abandoned/WIP/review+1 issues/PRs. > The issue I wanted to address was getting a good "bird's eye view" on issues. I don't think tags are that useful in that regard. > > Yes, I see. I think, this could be helpful for project owners to make strategic decisions. On the other hand, I personally don't find a great benefit of using these tools for triaging, cross-linking issues/PRs and other cases I care about. Maybe we should just give it a try. >> From the pricing perspective, Zube is not the best choice as it offers Free plans for teams up to 4 people. I think > No, Zube is free for open source, for unlimited users. > > Indeed, sorry, I see this now. >> (I'd __love__ to have RFCs, not just random discussions in issues/mailing list), Trello (trello.com) could be also a nice choice. > You mean RFCs like PEPs? > > Exactly. I think, this format would help to accumulate our opinions on different matters (e.g. how to we treat and depend on `matplotlib`), for which website (deeply buried pages of it) is not the best place. At the moment, discussions on many sensitive topics appear again and again in the different PRs, making them hard to align and to be referenced. > As for technical side of this, we probably could reuse GitHub issues (by creating exclusive tag "SkimageEP" or something similar). `matplotlib` people, as far as I know, use GitHub Wiki to post "xEP"s, but I'm not sure where do they held the discusssions. GitHub does also support protecting different pages from modifcation, that could also be useful. >> From this section, actually, one more pragmatic topic arises. Even if we keep image processing part up to the community, I think that we have to put more our (core team) efforts on the backend part of the project (not just testing and documentation part, but also e.g. make easier function chaining - https://github.com/scikit-image/scikit-image/issues/1529). I'd not expect from anyone outside the core team to have enough knowledge, experience and confidence to implement this and some other features. I.e. I believe that we have to make some necessary contributions to stay competitive. > Can you explain what you mean? > > Well, I'm just saying that we as a core team should drive the evolution of backend and make life easier for contributors and users. Like, try to imagine some new contributor making a PR introducing Sphinx Gallery. Can't see this happenning. Of course, all of us are working on this kind of features already, I just want to highlight this (maybe trivial) point. > As a "practical guide", perhaps we should dedicate more time to the _complex_ issues/requests/PRs we have. > > > Thanks for all your comments on Theano/GPU/whatever part (/cc Emmanuelle, Johannes), they're very informative and insightful. I'd prefer to raise this discussion again (as I have more food to bring to the table) or maybe just collect your opinions in one place when (and if) we decipe on SkimageEPs. > > Regards, > Egor > > -- > 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/CAP0v5tm5C4%3Df9c9u1juf37yYp…. > For more options, visit https://groups.google.com/d/optout.

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Re: Task board
by Egor Panfilov 04 Sep '16

04 Sep '16

Hi Stefan! As for issues/PRs management system, I think that GitHub tags pretty much > do the deal. We've recently added "status: xxx" tags to facilitate tracking > of active/abandoned/WIP/review+1 issues/PRs. > > The issue I wanted to address was getting a good "bird's eye view" on > issues. I don't think tags are that useful in that regard. > Yes, I see. I think, this could be helpful for project owners to make strategic decisions. On the other hand, I personally don't find a great benefit of using these tools for triaging, cross-linking issues/PRs and other cases I care about. Maybe we should just give it a try. > From the pricing perspective, Zube is not the best choice as it offers > Free plans for teams up to 4 people. I think > > No, Zube is free for open source, for unlimited users. > Indeed, sorry, I see this now. > (I'd __love__ to have RFCs, not just random discussions in issues/mailing > list), Trello (trello.com) could be also a nice choice. > > You mean RFCs like PEPs? > Exactly. I think, this format would help to accumulate our opinions on different matters (e.g. how to we treat and depend on `matplotlib`), for which website (deeply buried pages of it) is not the best place. At the moment, discussions on many sensitive topics appear again and again in the different PRs, making them hard to align and to be referenced. As for technical side of this, we probably could reuse GitHub issues (by creating exclusive tag "SkimageEP" or something similar). `matplotlib` people, as far as I know, use GitHub Wiki to post "xEP"s, but I'm not sure where do they held the discusssions. GitHub does also support protecting different pages from modifcation, that could also be useful. > From this section, actually, one more pragmatic topic arises. Even if we > keep image processing part up to the community, I think that we have to put > more our (core team) efforts on the backend part of the project (not just > testing and documentation part, but also e.g. make easier function chaining > - https://github.com/scikit-image/scikit-image/issues/1529). I'd not > expect from anyone outside the core team to have enough knowledge, > experience and confidence to implement this and some other features. I.e. I > believe that we have to make some necessary contributions to stay > competitive. > > Can you explain what you mean? > > Well, I'm just saying that we as a core team should drive the evolution of backend and make life easier for contributors and users. Like, try to imagine some new contributor making a PR introducing Sphinx Gallery. Can't see this happenning. Of course, all of us are working on this kind of features already, I just want to highlight this (maybe trivial) point. As a "practical guide", perhaps we should dedicate more time to the _complex_ issues/requests/PRs we have. Thanks for all your comments on Theano/GPU/whatever part (/cc Emmanuelle, Johannes), they're very informative and insightful. I'd prefer to raise this discussion again (as I have more food to bring to the table) or maybe just collect your opinions in one place when (and if) we decipe on SkimageEPs. Regards, Egor

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Re: Task board
by Johannes Schönberger 03 Sep '16

03 Sep '16

Hi, >> I understand that everyone in the core team has a lot of matters to deal with outside the project, but the activity from our (maintainers) side is far less compared to the activity of the contributors. In my opinion, people tend to quit contributing > > This is true, unfortunately. How do we increase the number of hours available? I can see two ways: grow the contributor community (in such a way that contributors know to review as well) or hire someone to work on the project full time. I'd be interested in exploring the latter avenue. We can also reach out to employers of existing contributors and try and negotiated dedicated working time on the project. The latter would be a great step forward! >> Pt.2 - "issues/PRs management tool for stronger management, not just for its own sake". >> P.S. I like the practice of `scikit-learn` guys to rename PRs as "[MRG] some awesome contribution" -> [MRG + 1] some awesome contribution". Pretty simple and cheap solution to track LGTM :+1: entities. > > I'd be fine with that. +1 >> outines just to have a common ground for their functionality. I believe we could still catch the train. So, I propose to consider moving `skimage` infrastructure onto `theano`. That is a hell lot of work, of course, but I'm asking just for a discussion yet. > > We do evaluate these things from time to time. When GPUs came into fashion, we looked at those, at a recent conference I spoke to folks about using DSLs like Halide for speed optimization, and with our GSoC student Daniil we've spoken a lot about integrating neural nets. Adopting theano may be quite tricky, so perhaps a proof of concept (or an RFC ;) would be the easiest way to kick off that conversation. I'd argue that scikit-image wouldn't gain any more traction by transitioning to Theano. The big advantage of theano in the deep learning setting is its automatic differentiation functionality. This will only be useful for a very small subset of functions in scikit-image. The input/output variables to any Python-based deep learning framework are still numpy arrays. >> From this section, actually, one more pragmatic topic arises. Even if we keep image processing part up to the community, I think that we have to put more our (core team) efforts on the backend part of the project (not just testing and documentation part, but also e.g. make easier function chaining - https://github.com/scikit-image/scikit-image/issues/1529). I'd not expect from anyone outside the core team to have enough knowledge, experience and confidence to implement this and some other features. I.e. I believe that we have to make some necessary contributions to stay competitive. It would be good, if you could elaborate a little more on this point. Most of skimage's API was designed with exactly that in mind. Best, Johannes

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Re: Task board
by Stefan van der Walt 02 Sep '16

02 Sep '16

Hi Egor On Fri, Sep 2, 2016, at 01:54, Egor Panfilov wrote: > Regarding the points raised by Stefan, I think that the main issue we > have is a lack of resources and reviews (just a casual bump of > https://github.com/scikit-image/scikit-image/pull/2040 here ;) ). I still don't see any explanation of what the term 'l2hys' means! > I understand that everyone in the core team has a lot of matters to > deal with outside the project, but the activity from our > (maintainers) side is far less compared to the activity of the > contributors. In my opinion, people tend to quit contributing This is true, unfortunately. How do we increase the number of hours available? I can see two ways: grow the contributor community (in such a way that contributors know to review as well) or hire someone to work on the project full time. I'd be interested in exploring the latter avenue. We can also reach out to employers of existing contributors and try and negotiated dedicated working time on the project. > As for issues/PRs management system, I think that GitHub tags pretty > much do the deal. We've recently added "status: xxx" tags to > facilitate tracking of active/abandoned/WIP/review+1 issues/PRs. The issue I wanted to address was getting a good "bird's eye view" on issues. I don't think tags are that useful in that regard. > From the pricing perspective, Zube is not the best choice as it offers > Free plans for teams up to 4 people. I think No, Zube is free for open source, for unlimited users. > (I'd __love__ to have RFCs, not just random discussions in > issues/mailing list), Trello (trello.com) could be also a nice choice. You mean RFCs like PEPs? > Pt.2 - "issues/PRs management tool for stronger management, not just > for its own sake". > P.S. I like the practice of `scikit-learn` guys to rename PRs as > "[MRG] some awesome contribution" -> [MRG + 1] some awesome > contribution". Pretty simple and cheap solution to track LGTM > :+1: entities. I'd be fine with that. > outines just to have a common ground for their functionality. I > believe we could still catch the train. So, I propose to consider > moving `skimage` infrastructure onto `theano`. That is a hell lot of > work, of course, but I'm asking just for a discussion yet. We do evaluate these things from time to time. When GPUs came into fashion, we looked at those, at a recent conference I spoke to folks about using DSLs like Halide for speed optimization, and with our GSoC student Daniil we've spoken a lot about integrating neural nets. Adopting theano may be quite tricky, so perhaps a proof of concept (or an RFC ;) would be the easiest way to kick off that conversation. > From this section, actually, one more pragmatic topic arises. Even if > we keep image processing part up to the community, I think that we > have to put more our (core team) efforts on the backend part of the > project (not just testing and documentation part, but also e.g. make > easier function chaining - > https://github.com/scikit-image/scikit-image/issues/1529). I'd not > expect from anyone outside the core team to have enough knowledge, > experience and confidence to implement this and some other features. > I.e. I believe that we have to make some necessary contributions to > stay competitive. Can you explain what you mean? Thanks for all your comments, Stéfan

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Re: deep learning
by Emmanuelle Gouillart 02 Sep '16

02 Sep '16

[changing the title of the thread since one of your comments deviated quite a lot from the topic of "task board"] > One more point (yet it is better to start a discussion in a RFC :) ) I'd like > to bring to the discussion. I remember a short discussion with Stefan, that > there was a decision upon that `skimage` is a community driven-project. I > understand, that it is probably mostly used for educational purposes, but we > shouldn't as a project fall behind the progress in Image Processing and > Computer Vision. I see that many modern Deep Learning frameworks start to > implement their own image processing routines just to have a common ground for > their functionality. I believe we could still catch the train. So, I propose to > consider moving `skimage` infrastructure onto `theano`. That is a hell lot of > work, of course, but I'm asking just for a discussion yet. > From this section, actually, one more pragmatic topic arises. Even if we keep > image processing part up to the community, I think that we have to put more our > (core team) efforts on the backend part of the project (not just testing and > documentation part, but also e.g. make easier function chaining - https:// > github.com/scikit-image/scikit-image/issues/1529). I'd not expect from anyone > outside the core team to have enough knowledge, experience and confidence to > implement this and some other features. I.e. I believe that we have to make > some necessary contributions to stay competitive. I have to say that I disagree a lot with this analysis. 1. First of all, I don't think that scikit-image is used primarily for educational purposes. If you browse through the research articles that cite the scikit-image paper, you'll find that people have used scikit-image as a building block for scientific software and applications or for research in various fields such as medical science, materials science, plant research, etc. I know several industrial groups which are using scikit-image for their daily R&D workflow. Tens of thousands of people are browsing every month through the examples of the gallery to discover how to perform specific image processing operations. That said, you're totally right to raise the question of "staying competitive". But it's a tricky issue, since in my opinion, being competitive is a subtle mixture of usability, features, performance (probably in this order, but it's a matter of debate). 2. About Deep Learning: deep learning is very cool, trendy and powerful, it can blow your mind for some operations, yet it cannot do everything in image processing. Labeling images with kittens is not the sole purpose that our users have :-). Furthermore, deep learning require intensive computations, that are best done on the GPU. Some packages like keras provide elegant solutions for deep learning and are compatible with scikit-image, thanks to the common use of numpy arrays. Can some scikit-image contributors work on a deep learning package for image processing using theano, tensorflow, keras and some of the knowledge/features of scikit-image? Probably. Does it have to be in scikit-image? I don't think so (although it could be a project of the scikit-image organization). Let's try not to build a monster package with everything and the kitchen sink, that quickly becomes uninstallable and unusable. Using theano instead of NumPy arrays would be to favor one image processing workflow at the expense of many others, so I don't think it's wise. To quote David Waley-Farley: "Yep. Theano, Numba, numexpr, Cython and PyPy shall one day all merge to form Numtron, defender of sanity, runner of fast numerics.". But before we're there, NumPy is the common denominator for the scientific packages. It would be interesting to know which are the deep learning frameworks that you're mentioning, to see how they tackle image processing. I'd be interested in knowing more about this. 3. For function chaining, it might be interesting to take a look at scikit-learn's pipeline http://scikit-learn.org/stable/modules/generated/sklearn.pipeline.Pipeline.… My 2 cents, Emma

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Re: Task board
by Egor Panfilov 02 Sep '16

02 Sep '16

Hello everyone! Here are some of mine reflections on the topic: Regarding the points raised by Stefan, I think that the main issue we have is a lack of resources and reviews (just a casual bump of https://github.com/scikit-image/scikit-image/pull/2040 here ;) ). I understand that everyone in the core team has a lot of matters to deal with outside the project, but the activity from our (maintainers) side is far less compared to the activity of the contributors. In my opinion, people tend to quit contributing and even stop using OSS if they don't have enough treatment. Of course, many of the PRs we currently have are quite poor in terms of quiality and/or abandoned (we have to be more aggressive managing them), but those which are pretty good, maybe not perfect, totally deserve to get much more attention (e.g. https://github.com/scikit-image/scikit-image/pull/1957, https://github.com/scikit-image/scikit-image/pull/1570, etc). I'd prefer to have slow (pure Python) implementations of established image processing algorithms and make more people involved in the project rather then asking them to write an extremely fast and ideal code and losing them in process. So, pt.1 - "we should do more and grow the active community". As for issues/PRs management system, I think that GitHub tags pretty much do the deal. We've recently added "status: xxx" tags to facilitate tracking of active/abandoned/WIP/review+1 issues/PRs. The only _extra_ feature I'd personally prefer to have is issues/PRs aging, so to easily observe which of them haven't gotten any activity recently. If the management system offers this kind of functionality, I'd be glad to give a shot testing it, otherwise I'm neutral about this. >From the pricing perspective, Zube is not the best choice as it offers Free plans for teams up to 4 people. I think that https://waffle.io/ could be a better alternative. Here you can see a preview https://waffle.io/scikit-image/scikit-image . From my knowledge, Waffle is one of the first services of this kind, so should be well-designed from the UI perspective. If we'd like not just to manage open GitHub issues/PRs, but have a more structured backlog for our discussions and RFCs (I'd __love__ to have RFCs, not just random discussions in issues/mailing list), Trello (trello.com) could be also a nice choice. It has awesome GitHub integration and many more features. Although, I'm not sure that devs would like to get acquainted with this heavy system just for a single project management. Pt.2 - "issues/PRs management tool for stronger management, not just for its own sake". P.S. I like the practice of `scikit-learn` guys to rename PRs as "[MRG] some awesome contribution" -> [MRG + 1] some awesome contribution". Pretty simple and cheap solution to track LGTM :+1: entities. One more point (yet it is better to start a discussion in a RFC :) ) I'd like to bring to the discussion. I remember a short discussion with Stefan, that there was a decision upon that `skimage` is a community driven-project. I understand, that it is probably mostly used for educational purposes, but we shouldn't as a project fall behind the progress in Image Processing and Computer Vision. I see that many modern Deep Learning frameworks start to implement their own image processing routines just to have a common ground for their functionality. I believe we could still catch the train. So, I propose to consider moving `skimage` infrastructure onto `theano`. That is a hell lot of work, of course, but I'm asking just for a discussion yet. >From this section, actually, one more pragmatic topic arises. Even if we keep image processing part up to the community, I think that we have to put more our (core team) efforts on the backend part of the project (not just testing and documentation part, but also e.g. make easier function chaining - https://github.com/scikit-image/scikit-image/issues/1529). I'd not expect from anyone outside the core team to have enough knowledge, experience and confidence to implement this and some other features. I.e. I believe that we have to make some necessary contributions to stay competitive. +1, In my opinion, reviewing is almost more important than writing the > code. With the current system, Github only "rewards" people who contribute > code and, I think, this is part of the problem. With every commit, people > get credit in the form of # commits or # lines of code and Github shows the > stats nicely in the profile or the project graphs. Maybe there is a way to > create an equivalent for the reviewing process, e.g., # comments and # > merged PRs. I fully agree with you, Johannes, but have not a single idea on how to implement this. Well, we still can set up a GitHub bot (sorry, I'm being unreasonably hyped by this tech these days) and track who participated in the review process for each PR, but I'm definitely not sure how fair it could be (what if I just comment something like "LOL" in 1e6 lines of code PR and got credited for that) and what kind of appreciation one might expect (like, "this person has reviewed a lot"). Ofc, we can track who put "LGTM" or "+1" on the PR page, but this isn't a fair solution either. We are already publishing "list of fame" with every new release, and an organization badge in GitHub account is self-speaking. I guess that's the most safe option we could have at the moment. Sorry for the long read. :) Have a nice we. Regards, Egor Panfilov 2016-08-31 2:54 GMT+03:00 Stefan van der Walt <stefanv(a)berkeley.edu>: > Hi Johannes > > On Tue, Aug 30, 2016, at 12:58, Johannes Schönberger wrote: > > I agree that Github does not provide a good overview of active/passive > > issues. I am overwhelmed by the amount of issues and, usually, after a > > week of scikit-image "abstinence" :-), I have to start from scratch to > > find the relevant issues. Tags don't really help me in this regard > > either... > > Did you look at the proposed Zube (or the alternatives)? I'd be curious > to hear what you think. > > > > We have a document (http://scikit-image.org/docs/ > stable/contribute.html) > > > that invites users to contribute, but we can simplify those > instructions > > > for newcomers, and also add a "Please help us review some code" button > > > on the front page? > > > > +1, In my opinion, reviewing is almost more important than writing the > > code. With the current system, Github only "rewards" people who > > contribute code and, I think, this is part of the problem. With every > > commit, people get credit in the form of # commits or # lines of code and > > Github shows the stats nicely in the profile or the project graphs. Maybe > > there is a way to create an equivalent for the reviewing process, e.g., # > > comments and # merged PRs. > > > > What do people think about this idea? > > We can extend our release script to pull that information from GitHub. > Would it be helpful to credit with new releases, or should this come as > more continuous feedback, e.g. a weekly mail to the list with > statistics? > > Stéfan > > -- > 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 an email to scikit-image(a)googlegroups.com. > To view this discussion on the web, visit https://groups.google.com/d/ > msgid/scikit-image/1472601249.1617176.710940585.4C1ED035% > 40webmail.messagingengine.com. > For more options, visit https://groups.google.com/d/optout. >

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Re: Distance Estimation
by Emmanuelle Gouillart 01 Sep '16

01 Sep '16

Hi Chris, the short version is no, there is no function in scikit-image that can do what the Stanford paper does. However, you can find some useful building blocks in scikit-image and scikit-learn, that you can put together to build your own version of the algorithm (from what I figured out after a quick reading of http://www.cs.cornell.edu/~asaxena/reconstruction3d/saxena_iccv_3drr07_lear…) - Felzenswalb superpixels are available in skimage.segmentation (http://scikit-image.org/docs/dev/auto_examples/segmentation/plot_segmentati…) - Local features can be computed using several functions of scikit-image, such as color transforms (color.ycbcr) and edge filters (filters.sobel_h, filters.sobel_v, ...) - A logistic regression algorithm is available in scikit-learn (http://scikit-learn.org/stable/modules/generated/sklearn.linear_model.Logis…) The trickiest part to code would be the MAP inference on the MRF, where I guess you would have to code it yourself (I think). So, it is feasible to assemble these different blocks, but it's not a small project either. As for other libraries, I'm afraid nothing comes to my mind. OpenCV does have a depth estimation function, but only from stereo images. Hope this helps, Emma On Wed, Aug 31, 2016 at 09:30:20PM -0400, Chris Spencer wrote: > Essentially, what's described here: > http://www.cs.cornell.edu/~asaxena/learningdepth/ > On Wed, Aug 31, 2016 at 9:29 PM, Chris Spencer <chrisspen(a)gmail.com> wrote: > Given a JPG image of a scene, convert that into a depth map, where each > pixel is associated with a discrete distance estimate. > On Wed, Aug 31, 2016 at 7:12 PM, Stefan van der Walt <stefanv(a)berkeley.edu> > wrote: > Hi Chris > On Sun, Aug 28, 2016, at 17:31, Chris Spencer wrote: > > Is there any algorithm in scikit-image that I could use to train a > predictor that could estimate the distance at each pixel in an image? > > I've gone through all the examples, and none of them seemed to > directly apply. The image segmentation example seemed to be the > closest, but that didn't use supervised learning, so I wasn't sure how > I could adapt it's code. > Could you explain what you mean by "estimate the distance"? > StÃ©fan

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Re: Distance Estimation
by Chris Spencer 01 Sep '16

01 Sep '16

Essentially, what's described here: http://www.cs.cornell.edu/~asaxena/learningdepth/ On Wed, Aug 31, 2016 at 9:29 PM, Chris Spencer <chrisspen(a)gmail.com> wrote: > Given a JPG image of a scene, convert that into a depth map, where each > pixel is associated with a discrete distance estimate. > > On Wed, Aug 31, 2016 at 7:12 PM, Stefan van der Walt <stefanv(a)berkeley.edu > > wrote: > >> Hi Chris >> >> On Sun, Aug 28, 2016, at 17:31, Chris Spencer wrote: >> > Is there any algorithm in scikit-image that I could use to train a >> predictor that could estimate the distance at each pixel in an image? >> >> > I've gone through all the examples, and none of them seemed to directly >> apply. The image segmentation example seemed to be the closest, but that >> didn't use supervised learning, so I wasn't sure how I could adapt it's >> code. >> >> Could you explain what you mean by "estimate the distance"? >> >> 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/to >> pic/scikit-image/qvGm0zOv2rc/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 an email to scikit-image(a)googlegroups.com. >> To view this discussion on the web, visit https://groups.google.com/d/ms >> gid/scikit-image/1472685144.113590.712117217.1B48040B%40webm >> ail.messagingengine.com. >> For more options, visit https://groups.google.com/d/optout. >> > >

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Distance Estimation
by Chris Spencer 01 Sep '16

01 Sep '16

Hi, Can scikit-image be used for supervised learning? I have training data, where each sample is composed of a raw RGB image, a black-and-white image mask showing the laser projection onto the image, and the laser range finder distance measurements in millimetres. Is there any algorithm in scikit-image that I could use to train a predictor that could estimate the distance at each pixel in an image? I've gone through all the examples, and none of them seemed to directly apply. The image segmentation example seemed to be the closest, but that didn't use supervised learning, so I wasn't sure how I could adapt it's code. Can this goal be accomplished with sckit-image? If not, is there another library and algorithm you could recommend? Regards, Chris

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