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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scikit-image September 2016