From nmabhi42 at gmail.com Thu Jan 1 08:51:05 2015 From: nmabhi42 at gmail.com (abhi) Date: Thu, 1 Jan 2015 05:51:05 -0800 (PST) Subject: Hi I'm new, but I'd like to contribute to your organisation, can someone please guide me along? Message-ID: <83b55060-82c6-4808-a627-4696befff576@googlegroups.com> Hi everyone, I am new to opensource contribution.I am familiar with Image processing with Matlab and recently started exploring scikit-image.I would like to contribute to scikit image.Can someone please guide me along ? -------------- next part -------------- An HTML attachment was scrubbed... URL: From steven.silvester at gmail.com Fri Jan 2 21:22:21 2015 From: steven.silvester at gmail.com (Steven Silvester) Date: Fri, 2 Jan 2015 18:22:21 -0800 (PST) Subject: Hi I'm new, but I'd like to contribute to your organisation, can someone please guide me along? In-Reply-To: <83b55060-82c6-4808-a627-4696befff576@googlegroups.com> References: <83b55060-82c6-4808-a627-4696befff576@googlegroups.com> Message-ID: <6363b2ba-f08a-4762-995b-b2afb71031dc@googlegroups.com> Hi abhi, Welcome! You can find a list of requested features here, and see if any spark your interest: https://github.com/scikit-image/scikit-image/wiki/Requested-features. Otherwise, we'd love to a new example for the gallery, if you have anything you've previously done that you'd like to adapt: http://scikit-image.org/docs/dev/auto_examples/. Learning *how* to contribute is described on our website: http://scikit-image.org/docs/dev/contribute.html. Even an issue report for something out of the ordinary you've noticed is helpful. Cheers, Steve On Thursday, January 1, 2015 7:51:05 AM UTC-6, abhi wrote: > > Hi everyone, > I am new to opensource contribution.I am familiar with Image processing > with Matlab and recently started exploring scikit-image.I would like to > contribute to scikit image.Can someone please guide me along ? > -------------- next part -------------- An HTML attachment was scrubbed... URL: From muditjain18011995 at gmail.com Sat Jan 3 00:14:57 2015 From: muditjain18011995 at gmail.com (Mudit Jain) Date: Fri, 2 Jan 2015 21:14:57 -0800 (PST) Subject: Eigen Images Message-ID: <960d7084-c14e-4aac-b0fe-10f59a98a893@googlegroups.com> Hi everyone, I am an undergrad and new to open source. I have developed a good understanding of image processing in python . As suggested in the group I have looked up the requested features also. Recently,I had this idea that could be incorporated in scikit-image. We could have a function that finds the eigen images, given a dataset of images. Finding the Eigen vectors of the co-variance matrix can be written and incorporated in the library. If people can discuss the feasibility of this idea we could then proceed forward with this. Cheers Mudit -------------- next part -------------- An HTML attachment was scrubbed... URL: From mks7.618 at gmail.com Tue Jan 6 14:04:02 2015 From: mks7.618 at gmail.com (muralidhara K S) Date: Tue, 6 Jan 2015 11:04:02 -0800 (PST) Subject: Blind deconvolutioin using radon transfrom Message-ID: hi, with respect to blind deconvolution , there you mentioned about latest state of art. can you please explain about this . -------------- next part -------------- An HTML attachment was scrubbed... URL: From mks7.618 at gmail.com Wed Jan 7 08:23:03 2015 From: mks7.618 at gmail.com (Murali) Date: Wed, 7 Jan 2015 05:23:03 -0800 (PST) Subject: Blind deconvolution Message-ID: <40954f0b-f7a0-40ff-9353-52233a49e416@googlegroups.com> hi, with respect to blind deconvolution , there you mentioned about latest state of art. can you please explain about this . -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan at sun.ac.za Wed Jan 7 10:22:53 2015 From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Wed, 7 Jan 2015 07:22:53 -0800 Subject: Blind deconvolution In-Reply-To: <40954f0b-f7a0-40ff-9353-52233a49e416@googlegroups.com> References: <40954f0b-f7a0-40ff-9353-52233a49e416@googlegroups.com> Message-ID: On Wed, Jan 7, 2015 at 5:23 AM, Murali wrote: > with respect to blind deconvolution , there you mentioned about latest > state of art. > can you please explain about this . The idea is to research the latest methods, figure out which are best established, and implement one or more of those. A reference paper is given as a starting point. Regards St?fan From stefan at sun.ac.za Wed Jan 7 10:53:30 2015 From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Wed, 7 Jan 2015 07:53:30 -0800 Subject: Blind deconvolution In-Reply-To: References: <40954f0b-f7a0-40ff-9353-52233a49e416@googlegroups.com> Message-ID: On Wed, Jan 7, 2015 at 7:45 AM, muralidhara K S wrote: > 1)Is this module have to to be developed are i have to implement it. This is just one method; one would have to establish which method is currently most popular, and see if it viable to implement that instead. However, *any* established method would be a good first experiment. > 2)i wanted work for your community during this Google summer of code-2015 > .So guide me about this In order to participate in GSoC, we ask that you participate in the project beforehand (e.g., by fixing bugs). Once you've established a working relationship with the team, odds are much greater for being selected. Regards St?fan From stefan at sun.ac.za Wed Jan 7 13:35:49 2015 From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Wed, 7 Jan 2015 10:35:49 -0800 Subject: Blind deconvolution In-Reply-To: References: <40954f0b-f7a0-40ff-9353-52233a49e416@googlegroups.com> Message-ID: On Wed, Jan 7, 2015 at 9:47 AM, muralidhara K S wrote: > I have gone through MAT-LAB and scilab (which are interpreter based > languages like python ) till today.So, Can you please suggest me one of such > project which take some 3 weeks to complete which brushes up and increases > proficiency of me . I don't want to discourage you, but I do not think it will be possible to become proficient enough in Python in the time left to participate with skimage in GSoC 2015. That said, we are always happy to help new contributors get involved, and would be glad for any contribution you make. You can start your journey here: http://scipy-lectures.github.io/ Regards St?fan From mks7.618 at gmail.com Wed Jan 7 10:45:38 2015 From: mks7.618 at gmail.com (muralidhara K S) Date: Wed, 7 Jan 2015 21:15:38 +0530 Subject: Blind deconvolution In-Reply-To: References: <40954f0b-f7a0-40ff-9353-52233a49e416@googlegroups.com> Message-ID: yes, i had gone through that paper, but,I have some questions 1)Is this module have to to be developed are i have to implement it. 2)i wanted work for your community during this Google summer of code-2015 .So guide me about this On Wed, Jan 7, 2015 at 8:52 PM, St?fan van der Walt wrote: > On Wed, Jan 7, 2015 at 5:23 AM, Murali wrote: > > with respect to blind deconvolution , there you mentioned about latest > > state of art. > > can you please explain about this . > > The idea is to research the latest methods, figure out which are best > established, and implement one or more of those. A reference paper is > given as a starting point. > > Regards > St?fan > > -- > 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/s88BCppI9jM/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > scikit-image+unsubscribe at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mks7.618 at gmail.com Wed Jan 7 12:47:28 2015 From: mks7.618 at gmail.com (muralidhara K S) Date: Wed, 7 Jan 2015 23:17:28 +0530 Subject: Blind deconvolution In-Reply-To: References: <40954f0b-f7a0-40ff-9353-52233a49e416@googlegroups.com> Message-ID: I have gone through MAT-LAB and scilab (which are interpreter based languages like python ) till today.So, Can you please suggest me one of such project which take some 3 weeks to complete which brushes up and increases proficiency of me . On Wed, Jan 7, 2015 at 9:23 PM, St?fan van der Walt wrote: > On Wed, Jan 7, 2015 at 7:45 AM, muralidhara K S > wrote: > > 1)Is this module have to to be developed are i have to implement it. > > This is just one method; one would have to establish which method is > currently most popular, and see if it viable to implement that > instead. However, *any* established method would be a good first > experiment. > > > 2)i wanted work for your community during this Google summer of code-2015 > > .So guide me about this > > In order to participate in GSoC, we ask that you participate in the > project beforehand (e.g., by fixing bugs). Once you've established a > working relationship with the team, odds are much greater for being > selected. > > Regards > St?fan > > -- > 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/s88BCppI9jM/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > scikit-image+unsubscribe at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From maqianlie at gmail.com Thu Jan 8 08:16:01 2015 From: maqianlie at gmail.com (Ma ChienLi) Date: Thu, 8 Jan 2015 05:16:01 -0800 (PST) Subject: Hi, I would like to offer my help in the next GSoC In-Reply-To: References: Message-ID: <7af30c32-c959-4686-a75b-27b5e4a8e4c6@googlegroups.com> Thank you for your suggestion. Sorry for the late response. I didn't receive update from my email. Maybe I can start solving some issues:) ? 2014?12?30????UTC+8??11?59?06??Ma ChienLi??? > > Hi, everybody~ > > I am Ma Chienli, an undergraduate from China, majoring in electronic and > information engineering. > I have beed using python for scientific computation for a year and now I > am learning cython. > I would like to offer my for your next (possible) GSoC project of writting > the scipy.ndimage in cython :) > So, at first, from where should I start? > > Cheers > Ma > > P.S. I just created another thread which did not show up. If this thread > conflicts with it, please delete one of them . > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mks7.618 at gmail.com Wed Jan 7 21:30:38 2015 From: mks7.618 at gmail.com (muralidhara K S) Date: Thu, 8 Jan 2015 08:00:38 +0530 Subject: Blind deconvolution In-Reply-To: References: <40954f0b-f7a0-40ff-9353-52233a49e416@googlegroups.com> Message-ID: thank you . On Thu, Jan 8, 2015 at 12:05 AM, St?fan van der Walt wrote: > On Wed, Jan 7, 2015 at 9:47 AM, muralidhara K S > wrote: > > I have gone through MAT-LAB and scilab (which are interpreter based > > languages like python ) till today.So, Can you please suggest me one of > such > > project which take some 3 weeks to complete which brushes up and > increases > > proficiency of me . > > I don't want to discourage you, but I do not think it will be possible > to become proficient enough in Python in the time left to participate > with skimage in GSoC 2015. That said, we are always happy to help new > contributors get involved, and would be glad for any contribution you > make. > > You can start your journey here: > > http://scipy-lectures.github.io/ > > Regards > St?fan > > -- > 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/s88BCppI9jM/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > scikit-image+unsubscribe at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mks7.618 at gmail.com Thu Jan 8 11:18:16 2015 From: mks7.618 at gmail.com (muralidhara K S) Date: Thu, 8 Jan 2015 21:48:16 +0530 Subject: Blind deconvolution In-Reply-To: References: <40954f0b-f7a0-40ff-9353-52233a49e416@googlegroups.com> Message-ID: As i am bit well-known to signal processing and is it possible to learn more about python during the course of the project. On Thu, Jan 8, 2015 at 8:00 AM, muralidhara K S wrote: > thank you . > > > On Thu, Jan 8, 2015 at 12:05 AM, St?fan van der Walt > wrote: > >> On Wed, Jan 7, 2015 at 9:47 AM, muralidhara K S >> wrote: >> > I have gone through MAT-LAB and scilab (which are interpreter based >> > languages like python ) till today.So, Can you please suggest me one of >> such >> > project which take some 3 weeks to complete which brushes up and >> increases >> > proficiency of me . >> >> I don't want to discourage you, but I do not think it will be possible >> to become proficient enough in Python in the time left to participate >> with skimage in GSoC 2015. That said, we are always happy to help new >> contributors get involved, and would be glad for any contribution you >> make. >> >> You can start your journey here: >> >> http://scipy-lectures.github.io/ >> >> Regards >> St?fan >> >> -- >> 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/s88BCppI9jM/unsubscribe. >> To unsubscribe from this group and all its topics, send an email to >> scikit-image+unsubscribe at googlegroups.com. >> For more options, visit https://groups.google.com/d/optout. >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From gauravm043 at gmail.com Sun Jan 11 12:01:47 2015 From: gauravm043 at gmail.com (GAURAV MISHRA) Date: Sun, 11 Jan 2015 09:01:47 -0800 (PST) Subject: Gsoc 2015 Aspirant Introduction Message-ID: <8bebef45-1a3e-439f-9f2a-c08b48c167f6@googlegroups.com> Hi everyone, I am Gaurav Mishra, an undergraduate in Computer Science and Engineering .I am doing research in Computer Vision,Machine Learning and have a keen interest in Image Processing. My skills include C/C++/Python/Matlab/Opencv.I would like to contribute to your organisation.Please suggest me as to how should i start contributing.Also is there any irc channel for your organisation? Your guidance will be highly appreciated. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ronnie.ghose at gmail.com Sun Jan 11 17:58:19 2015 From: ronnie.ghose at gmail.com (Ronnie Ghose) Date: Sun, 11 Jan 2015 22:58:19 +0000 Subject: Gsoc 2015 Aspirant Introduction References: <8bebef45-1a3e-439f-9f2a-c08b48c167f6@googlegroups.com> Message-ID: There's a mailing list and a not so frequented IRC. We have a style guide and a bunch of issues in the issue tracker :). Welcome! On Sun, Jan 11, 2015, 5:27 PM GAURAV MISHRA wrote: > Hi everyone, > > I am Gaurav Mishra, an undergraduate in Computer Science and Engineering > .I am doing research in Computer Vision,Machine Learning and have a keen > interest in Image Processing. > > My skills include C/C++/Python/Matlab/Opencv.I would like to contribute to > your organisation.Please suggest me as to how should i start > contributing.Also is there any irc channel for your organisation? > > Your guidance will be highly appreciated. > > -- > 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 at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From emmanuelle.gouillart at nsup.org Mon Jan 12 03:07:05 2015 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Mon, 12 Jan 2015 09:07:05 +0100 Subject: Gsoc 2015 Aspirant Introduction In-Reply-To: <8bebef45-1a3e-439f-9f2a-c08b48c167f6@googlegroups.com> References: <8bebef45-1a3e-439f-9f2a-c08b48c167f6@googlegroups.com> Message-ID: <20150112080705.GA28233@phare.normalesup.org> Hi Gaurav, we have been using https://gitter.im/scikit-image/scikit-image as a chatroom recently. As already mentioned, the list of issues on GitHub is a good place to start. Cheers, Emmanuelle On Sun, Jan 11, 2015 at 09:01:47AM -0800, GAURAV MISHRA wrote: > Hi everyone, > I am Gaurav Mishra, an undergraduate in Computer Science and Engineering .I am > doing research in Computer Vision,Machine Learning and have a keen interest in > Image Processing. > My skills include C/C++/Python/Matlab/Opencv.I would like to contribute to your > organisation.Please suggest me as to how should i start contributing.Also is > there any irc channel for your organisation? > Your guidance will be highly appreciated. From stefan at sun.ac.za Mon Jan 12 19:08:52 2015 From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Mon, 12 Jan 2015 16:08:52 -0800 Subject: Gsoc 2015 Aspirant Introduction In-Reply-To: <20150112080705.GA28233@phare.normalesup.org> References: <8bebef45-1a3e-439f-9f2a-c08b48c167f6@googlegroups.com> <20150112080705.GA28233@phare.normalesup.org> Message-ID: On Mon, Jan 12, 2015 at 12:07 AM, Emmanuelle Gouillart wrote: > we have been using https://gitter.im/scikit-image/scikit-image as a > chatroom recently. > > As already mentioned, the list of issues on GitHub is a good place to > start. I've updated the Wiki with an introduction for prospective GSoC students: https://github.com/scikit-image/scikit-image/wiki/GSoC-2015 St?fan From gauravm043 at gmail.com Tue Jan 13 11:36:01 2015 From: gauravm043 at gmail.com (GAURAV MISHRA) Date: Tue, 13 Jan 2015 08:36:01 -0800 (PST) Subject: Gsoc 2015 Aspirant Introduction In-Reply-To: <20150112080705.GA28233@phare.normalesup.org> References: <8bebef45-1a3e-439f-9f2a-c08b48c167f6@googlegroups.com> <20150112080705.GA28233@phare.normalesup.org> Message-ID: <3894dde1-4011-4320-b351-9ad89de26cb5@googlegroups.com> Thanks Emmanuelle Gouillart and *Ronnie Ghose* i will look forward to it :) . On Tuesday, 13 January 2015 03:48:13 UTC+5:30, Emmanuelle Gouillart wrote: > > Hi Gaurav, > > we have been using https://gitter.im/scikit-image/scikit-image as a > chatroom recently. > > As already mentioned, the list of issues on GitHub is a good place to > start. > > Cheers, > Emmanuelle > > On Sun, Jan 11, 2015 at 09:01:47AM -0800, GAURAV MISHRA wrote: > > Hi everyone, > > > I am Gaurav Mishra, an undergraduate in Computer Science and Engineering > .I am > > doing research in Computer Vision,Machine Learning and have a keen > interest in > > Image Processing. > > > My skills include C/C++/Python/Matlab/Opencv.I would like to contribute > to your > > organisation.Please suggest me as to how should i start > contributing.Also is > > there any irc channel for your organisation? > > > Your guidance will be highly appreciated. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From aaaagrawal at gmail.com Thu Jan 15 05:44:53 2015 From: aaaagrawal at gmail.com (Ankit Agrawal) Date: Thu, 15 Jan 2015 02:44:53 -0800 (PST) Subject: Segmentation of multi-channel(>3) images Message-ID: <6da040a2-f58a-4b88-849d-e3381e8bf1dd@googlegroups.com> Hi everyone, I am working on a problem a small step of which requires me to perform segmentation of a multi-channel/multi-band image. That is, like RGB images which are 2D images with 3 channels, I have 2D images with 5 channels. I looked at the segmentation API and it seems to me that all the current implement algorithms work on 2D single channel(grayscale) or/and 2D three channel(RGB). I don't have a thorough knowledge of the implemented segmentation algorithms, so I would like to know if any of them can be extended to multi-channel(>3) images. Thanks. Regards, Ankit. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Thu Jan 15 05:56:28 2015 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Thu, 15 Jan 2015 02:56:28 -0800 (PST) Subject: Segmentation of multi-channel(>3) images In-Reply-To: <6da040a2-f58a-4b88-849d-e3381e8bf1dd@googlegroups.com> References: <6da040a2-f58a-4b88-849d-e3381e8bf1dd@googlegroups.com> Message-ID: <1421319388137.c7f721bd@Nodemailer> Hi Ankit, iirc SLIC was updated to work for any number of channels with `multichannel=True`! Looks like the docstring needs updating! Feel free to submit a PR but in the meantime, give it a shot! =) Juan. On Thu, Jan 15, 2015 at 9:44 PM, Ankit Agrawal wrote: > Hi everyone, > I am working on a problem a small step of which requires me to > perform segmentation of a multi-channel/multi-band image. That is, like RGB > images which are 2D images with 3 channels, I have 2D images with 5 > channels. I looked at the segmentation API > and it > seems to me that all the current implement algorithms work on 2D single > channel(grayscale) or/and 2D three channel(RGB). I don't have a thorough > knowledge of the implemented segmentation algorithms, so I would like to > know if any of them can be extended to multi-channel(>3) images. Thanks. > Regards, > Ankit. > -- > 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 at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Thu Jan 15 06:03:13 2015 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Thu, 15 Jan 2015 03:03:13 -0800 (PST) Subject: Segmentation of multi-channel(>3) images In-Reply-To: References: Message-ID: <1421319793324.d91402b3@Nodemailer> So... pass convert2lab=False! ;) On Thu, Jan 15, 2015 at 10:00 PM, Ankit Agrawal wrote: > Hi Juan, > Apparently the docs of slic are updated with `multi-channel = True`, > but when I tried it for my case, it returned this error - > In [24]: ps = seg.slic(pn, n_segments=100, multichannel=True) > --------------------------------------------------------------------------- > ValueError Traceback (most recent call last) > in () > ----> 1 ps = seg.slic(pn, n_segments=100, multichannel=True) > /usr/local/lib/python2.7/dist-packages/skimage/segmentation/slic_superpixels.pyc > in slic(image, n_segments, compactness, max_iter, sigma, spacing, > multichannel, convert2lab, enforce_connectivity, min_size_factor, > max_size_factor, slic_zero) > 142 if convert2lab and multichannel: > 143 if image.shape[3] != 3: > --> 144 raise ValueError("Lab colorspace conversion requires a > RGB image.") > 145 image = rgb2lab(image) > 146 > ValueError: Lab colorspace conversion requires a RGB image. > Ankit Agrawal, > IIT Bombay. > On Thu, Jan 15, 2015 at 4:26 PM, Juan Nunez-Iglesias > wrote: >> Hi Ankit, >> >> iirc SLIC was updated to work for any number of channels with >> `multichannel=True`! Looks like the docstring needs updating! Feel free to >> submit a PR but in the meantime, give it a shot! =) >> >> Juan. >> >> >> >> >> On Thu, Jan 15, 2015 at 9:44 PM, Ankit Agrawal >> wrote: >> >>> Hi everyone, >>> >>> I am working on a problem a small step of which requires me to >>> perform segmentation of a multi-channel/multi-band image. That is, like RGB >>> images which are 2D images with 3 channels, I have 2D images with 5 >>> channels. I looked at the segmentation API >>> and it >>> seems to me that all the current implement algorithms work on 2D single >>> channel(grayscale) or/and 2D three channel(RGB). I don't have a thorough >>> knowledge of the implemented segmentation algorithms, so I would like to >>> know if any of them can be extended to multi-channel(>3) images. Thanks. >>> >>> Regards, >>> Ankit. >>> >>> -- >>> 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 at googlegroups.com. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> -- >> You received this message because you are subscribed to a topic in the >> Google Groups "scikit-image" group. >> To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/scikit-image/_WIES8XQrN8/unsubscribe. >> To unsubscribe from this group and all its topics, send an email to >> scikit-image+unsubscribe at googlegroups.com. >> For more options, visit https://groups.google.com/d/optout. >> > -- > You received this message because you are subscribed to the Google Groups "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan at sun.ac.za Thu Jan 15 14:25:16 2015 From: stefan at sun.ac.za (Stefan van der Walt) Date: Thu, 15 Jan 2015 11:25:16 -0800 Subject: Segmentation of multi-channel(>3) images In-Reply-To: <1421319388137.c7f721bd@Nodemailer> References: <6da040a2-f58a-4b88-849d-e3381e8bf1dd@googlegroups.com> <1421319388137.c7f721bd@Nodemailer> Message-ID: <87sifbyhgj.fsf@sun.ac.za> Hi Juan On 2015-01-15 02:56:28, Juan Nunez-Iglesias wrote: > iirc SLIC was updated to work for any number of channels with > `multichannel=True`! Looks like the docstring needs updating! Feel > free to submit a PR but in the meantime, give it a shot! =) This reminds me--I used SLIC recently to answer a StackOverflow question, and noticed that not all the parameters are well described. For example, what is SLIC-0? Would you be willing to review that docstring for us, especially given that we're using SLIC quite heavily in our tutorials? Thanks! St?fan From jsch at demuc.de Thu Jan 15 07:15:22 2015 From: jsch at demuc.de (Johannes Schoenberger) Date: Thu, 15 Jan 2015 13:15:22 +0100 Subject: Matching images with rotation/scaling invariant match In-Reply-To: References: Message-ID: Number of matched features would be a good measure. Number of matched features is the number of rows of the match matrix. Depending on what you do, I would also suggest some geometric verification of the matches. From siggin at gmail.com Thu Jan 15 18:48:45 2015 From: siggin at gmail.com (Sigmund) Date: Thu, 15 Jan 2015 15:48:45 -0800 (PST) Subject: skimage.feature.peak_local_max behaviour Message-ID: Hi, My first post a few hours ago somehow didn't appear. It was with examples but I trink I can make my paint without. If two peaks with the same value are within the min_distance range they are not detectes as too closer and reduced to one. Just use the provided examples in the doc and change the peaks to the same value. From aaaagrawal at gmail.com Thu Jan 15 06:00:19 2015 From: aaaagrawal at gmail.com (Ankit Agrawal) Date: Thu, 15 Jan 2015 16:30:19 +0530 Subject: Segmentation of multi-channel(>3) images In-Reply-To: <1421319388137.c7f721bd@Nodemailer> References: <6da040a2-f58a-4b88-849d-e3381e8bf1dd@googlegroups.com> <1421319388137.c7f721bd@Nodemailer> Message-ID: Hi Juan, Apparently the docs of slic are updated with `multi-channel = True`, but when I tried it for my case, it returned this error - In [24]: ps = seg.slic(pn, n_segments=100, multichannel=True) --------------------------------------------------------------------------- ValueError Traceback (most recent call last) in () ----> 1 ps = seg.slic(pn, n_segments=100, multichannel=True) /usr/local/lib/python2.7/dist-packages/skimage/segmentation/slic_superpixels.pyc in slic(image, n_segments, compactness, max_iter, sigma, spacing, multichannel, convert2lab, enforce_connectivity, min_size_factor, max_size_factor, slic_zero) 142 if convert2lab and multichannel: 143 if image.shape[3] != 3: --> 144 raise ValueError("Lab colorspace conversion requires a RGB image.") 145 image = rgb2lab(image) 146 ValueError: Lab colorspace conversion requires a RGB image. Ankit Agrawal, IIT Bombay. On Thu, Jan 15, 2015 at 4:26 PM, Juan Nunez-Iglesias wrote: > Hi Ankit, > > iirc SLIC was updated to work for any number of channels with > `multichannel=True`! Looks like the docstring needs updating! Feel free to > submit a PR but in the meantime, give it a shot! =) > > Juan. > > > > > On Thu, Jan 15, 2015 at 9:44 PM, Ankit Agrawal > wrote: > >> Hi everyone, >> >> I am working on a problem a small step of which requires me to >> perform segmentation of a multi-channel/multi-band image. That is, like RGB >> images which are 2D images with 3 channels, I have 2D images with 5 >> channels. I looked at the segmentation API >> and it >> seems to me that all the current implement algorithms work on 2D single >> channel(grayscale) or/and 2D three channel(RGB). I don't have a thorough >> knowledge of the implemented segmentation algorithms, so I would like to >> know if any of them can be extended to multi-channel(>3) images. Thanks. >> >> Regards, >> Ankit. >> >> -- >> 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 at googlegroups.com. >> For more options, visit https://groups.google.com/d/optout. >> > > -- > You received this message because you are subscribed to a topic in the > Google Groups "scikit-image" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/scikit-image/_WIES8XQrN8/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > scikit-image+unsubscribe at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hrishikeshvganu at gmail.com Thu Jan 15 06:28:54 2015 From: hrishikeshvganu at gmail.com (Hrishi Ganu) Date: Thu, 15 Jan 2015 16:58:54 +0530 Subject: Matching images with rotation/scaling invariant match Message-ID: I have a template image and want to match it with a set of images. Since the template could be in a rotated position or scaled in the image I want to use ORB. I have extracted the ORB descriptor for the template image and for each of the images to be matched. Question-how should I assess the degree of match between the template's ORB descriptor and that for the image? Can I use len() ndarray returned by match_descriptors since I'm specifying the same # keypoints for both the templete and the images? Hrishi -------------- next part -------------- An HTML attachment was scrubbed... URL: From aaaagrawal at gmail.com Thu Jan 15 09:41:19 2015 From: aaaagrawal at gmail.com (Ankit Agrawal) Date: Thu, 15 Jan 2015 20:11:19 +0530 Subject: Segmentation of multi-channel(>3) images In-Reply-To: <1421319793324.d91402b3@Nodemailer> References: <1421319793324.d91402b3@Nodemailer> Message-ID: Oops...missed it! Thanks. Ankit Agrawal, IIT Bombay. On Thu, Jan 15, 2015 at 4:33 PM, Juan Nunez-Iglesias wrote: > So... pass convert2lab=False! ;) > > > > > On Thu, Jan 15, 2015 at 10:00 PM, Ankit Agrawal > wrote: > >> Hi Juan, >> >> Apparently the docs of slic are updated with `multi-channel = True`, >> but when I tried it for my case, it returned this error - >> >> In [24]: ps = seg.slic(pn, n_segments=100, multichannel=True) >> >> --------------------------------------------------------------------------- >> ValueError Traceback (most recent call >> last) >> in () >> ----> 1 ps = seg.slic(pn, n_segments=100, multichannel=True) >> >> /usr/local/lib/python2.7/dist-packages/skimage/segmentation/slic_superpixels.pyc >> in slic(image, n_segments, compactness, max_iter, sigma, spacing, >> multichannel, convert2lab, enforce_connectivity, min_size_factor, >> max_size_factor, slic_zero) >> 142 if convert2lab and multichannel: >> 143 if image.shape[3] != 3: >> --> 144 raise ValueError("Lab colorspace conversion requires >> a RGB image.") >> 145 image = rgb2lab(image) >> 146 >> >> ValueError: Lab colorspace conversion requires a RGB image. >> >> >> >> >> Ankit Agrawal, >> IIT Bombay. >> >> On Thu, Jan 15, 2015 at 4:26 PM, Juan Nunez-Iglesias >> wrote: >> >>> Hi Ankit, >>> >>> iirc SLIC was updated to work for any number of channels with >>> `multichannel=True`! Looks like the docstring needs updating! Feel free to >>> submit a PR but in the meantime, give it a shot! =) >>> >>> Juan. >>> >>> >>> >>> >>> On Thu, Jan 15, 2015 at 9:44 PM, Ankit Agrawal >>> wrote: >>> >>>> Hi everyone, >>>> >>>> I am working on a problem a small step of which requires me to >>>> perform segmentation of a multi-channel/multi-band image. That is, like RGB >>>> images which are 2D images with 3 channels, I have 2D images with 5 >>>> channels. I looked at the segmentation API >>>> and >>>> it seems to me that all the current implement algorithms work on 2D single >>>> channel(grayscale) or/and 2D three channel(RGB). I don't have a thorough >>>> knowledge of the implemented segmentation algorithms, so I would like to >>>> know if any of them can be extended to multi-channel(>3) images. Thanks. >>>> >>>> Regards, >>>> Ankit. >>>> >>>> -- >>>> 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 at googlegroups.com. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> -- >>> You received this message because you are subscribed to a topic in the >>> Google Groups "scikit-image" group. >>> To unsubscribe from this topic, visit >>> https://groups.google.com/d/topic/scikit-image/_WIES8XQrN8/unsubscribe. >>> To unsubscribe from this group and all its topics, send an email to >>> scikit-image+unsubscribe at googlegroups.com. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "scikit-image" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to scikit-image+unsubscribe at googlegroups.com. >> For more options, visit https://groups.google.com/d/optout. >> > > -- > You received this message because you are subscribed to a topic in the > Google Groups "scikit-image" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/scikit-image/_WIES8XQrN8/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > scikit-image+unsubscribe at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From siggin at gmail.com Thu Jan 15 18:52:37 2015 From: siggin at gmail.com (Sigmund Neher) Date: Fri, 16 Jan 2015 00:52:37 +0100 Subject: skimage.feature.peak_local_max behaviour In-Reply-To: References: Message-ID: Sorry! I realy suck at writing with my cellphone. Am 16.01.2015 00:48 schrieb "Sigmund" : > Hi, > My first post a few hours ago somehow didn't appear. It was with examples > but I trink I can make my paint without. > If two peaks with the same value are within the min_distance range they > are not detectes as too closer and reduced to one. Just use the provided > examples in the doc and change the peaks to the same value. > > -- > 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/HksA6QBButU/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > scikit-image+unsubscribe at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From siggin at gmail.com Fri Jan 16 04:59:36 2015 From: siggin at gmail.com (Sigmund) Date: Fri, 16 Jan 2015 01:59:36 -0800 (PST) Subject: skimage.feature.peak_local_max behaviour In-Reply-To: References: Message-ID: <224de330-7ef0-483d-8211-828824bfb737@googlegroups.com> Since nothing has happened here and I'm back at my office some examples: *normal behavior:* >>> img1 = np.zeros((7, 7))>>> img1[3, 4] = 1>>> img1[3, 2] = 1.5>>> img1array([[ 0. , 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 1.5, 0. , 1. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. , 0. ]]) >>> peak_local_max(img1, min_distance=1)array([[3, 2], [3, 4]]) >>> peak_local_max(img1, min_distance=2)array([[3, 2]]) *now the, in my opinion, not normal behavior: * >>> img1 = np.zeros((7, 7))>>> img1[3, 4] = 1>>> img1[3, 2] = 1>>> img1array([[ 0. , 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 1. , 0. , 1. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. , 0. ], [ 0. , 0. , 0. , 0. , 0. , 0. , 0. ]]) >>> peak_local_max(img1, min_distance=1)array([[3, 2], [3, 4]]) >>> peak_local_max(img1, min_distance=2) array([[3, 2], [3, 4]]) *Thanks again!Siggi* Am Freitag, 16. Januar 2015 00:48:45 UTC+1 schrieb Sigmund: > > Hi, > My first post a few hours ago somehow didn't appear. It was with examples > but I trink I can make my paint without. > If two peaks with the same value are within the min_distance range they > are not detectes as too closer and reduced to one. Just use the provided > examples in the doc and change the peaks to the same value. -------------- next part -------------- An HTML attachment was scrubbed... URL: From siggin at gmail.com Fri Jan 16 08:53:25 2015 From: siggin at gmail.com (Sigmund) Date: Fri, 16 Jan 2015 05:53:25 -0800 (PST) Subject: skimage.feature.peak_local_max behaviour In-Reply-To: References: <224de330-7ef0-483d-8211-828824bfb737@googlegroups.com> Message-ID: <54d071d0-b016-46cf-bb0c-7b51aafc73fa@googlegroups.com> Thanks! skimage.feature.corner_peaks is working like I expect peak_local_max to do. Siggi On Friday, January 16, 2015 at 11:11:15 AM UTC+1, Johannes Sch?nberger wrote: > > This is not ideal, but please try `skimage.feature.corner_peaks`. It > should work with this function (untested). -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan at sun.ac.za Fri Jan 16 10:01:17 2015 From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Fri, 16 Jan 2015 07:01:17 -0800 Subject: skimage.feature.peak_local_max behaviour In-Reply-To: <54d071d0-b016-46cf-bb0c-7b51aafc73fa@googlegroups.com> References: <224de330-7ef0-483d-8211-828824bfb737@googlegroups.com> <54d071d0-b016-46cf-bb0c-7b51aafc73fa@googlegroups.com> Message-ID: On Fri, Jan 16, 2015 at 5:53 AM, Sigmund wrote: > skimage.feature.corner_peaks is working like I expect peak_local_max to do. Thanks for the feedback, Sigmund. We've been discussing a rewrite of this functionality exactly because it yields unexpected results like those you mentioned. St?fan From jsch at demuc.de Fri Jan 16 05:11:11 2015 From: jsch at demuc.de (Johannes Schoenberger) Date: Fri, 16 Jan 2015 11:11:11 +0100 Subject: skimage.feature.peak_local_max behaviour In-Reply-To: <224de330-7ef0-483d-8211-828824bfb737@googlegroups.com> References: <224de330-7ef0-483d-8211-828824bfb737@googlegroups.com> Message-ID: This is not ideal, but please try `skimage.feature.corner_peaks`. It should work with this function (untested). From omer.ozak at gmail.com Mon Jan 19 16:16:31 2015 From: omer.ozak at gmail.com (OOM) Date: Mon, 19 Jan 2015 13:16:31 -0800 (PST) Subject: minimum cost MCP with IPython Parallel Message-ID: <7d57e12c-e78d-402d-b26f-73d122891abd@googlegroups.com> Hi, I am trying to use graph.MCP_Geometric(costs) on a cluster. The script and methods I use work on my personal computer which has 64GB memory. I am now trying to implement the same code on a cluster using IPython parallel. Here's the problem, each node/task only has about 20GB memory so they cannot even complete the mcp=graph.MCP_Geometric(costs) command. My cost data has shape (12837, 43345). I am trying IPython parallel since I think it should allow me to overcome the lack of memory in each node. E.g. If I define a parallel function like @dview.parallel(block=True) def costsnx(costs): mcp=graph.MCP_Geometric(costs) return mcp and run it mcpp=costsnx(costs) I get a list with mcp objects like , one for each process I created. So in principle this would solve the memory problem, but the individual mcp objects do not seem to work e.g. executing mcpp[30].find_costs([[0,0]]) generates TypeError: object of type 'NoneType' has no len() Also, there is no way to join them to recreate the real graph. I tried also including the mcp.find_costs(location) command in the parallel function, but it cannot find the location. I was thinking that perhaps there would be a way to use the intermediate steps of the graph.MCP_Geometric function to get the indices or something that could be constructed in parallel and then joined back into a unique element to compute minimum_costs. Any ideas on how this could be implemented? Or any idea on how to tackle the problem at all? I appreciate any help or pointers. Thanks OOM -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan at sun.ac.za Wed Jan 21 16:49:27 2015 From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Wed, 21 Jan 2015 13:49:27 -0800 Subject: Release timeline, v0.11 Message-ID: Hi everyone We didn't quite hit New Year for the 0.11 release, but I'd like to get it out the door as soon as possible. I've triaged most of the milestone tickets, so please help wherever you can with reviewing and closing up any remaining PRs. Thanks! St?fan From kwiechen1 at gmail.com Sat Jan 24 06:46:23 2015 From: kwiechen1 at gmail.com (Kai Wiechen) Date: Sat, 24 Jan 2015 03:46:23 -0800 (PST) Subject: border artefacts with skimage.exposure.equalize_adapthist Message-ID: Hello, I am new to scikit-image (and python too), but found the combination of scikit-image implementation of algorithms together with ndarrays extremely powerful. For now, I am trying to find nuclei in microscopic images (color deconvolution, find seeds with blob_log) This works fairly well but due to low contrast some nuclei are not detected. nuclei_clahe = equalize_adapthist(nuclei) gives much better local contrast but introduces linear artefacts at the test image borders. Is it possible to avoid/reduce this? Best regards, Kai -------------- next part -------------- An HTML attachment was scrubbed... URL: From steven.silvester at gmail.com Sat Jan 24 17:54:29 2015 From: steven.silvester at gmail.com (Steven Silvester) Date: Sat, 24 Jan 2015 14:54:29 -0800 (PST) Subject: border artefacts with skimage.exposure.equalize_adapthist In-Reply-To: References: Message-ID: <9e91b640-f732-47c3-b4ab-fbfc48c0a3bc@googlegroups.com> Hi Kai, Yes, this is a known bug, and the fix will be in the next release (coming soon!). Regards, Steve From silvertrumpet999 at gmail.com Sat Jan 24 18:41:25 2015 From: silvertrumpet999 at gmail.com (Josh Warner) Date: Sat, 24 Jan 2015 15:41:25 -0800 (PST) Subject: border artefacts with skimage.exposure.equalize_adapthist In-Reply-To: References: Message-ID: <287dcc05-6464-4912-9626-c2b6805e96fb@googlegroups.com> Just to confirm what Steven said, building from current master and applying your command to your `nuclei.jpg` image I obtain the attached image without artifacts. 0.11 should be released fairly soon, but if you need this sooner you can build from source. We'd be happy to help if you run into problems. Josh On Saturday, January 24, 2015 at 4:46:23 AM UTC-7, Kai Wiechen wrote: > > > > > Hello, > > I am new to scikit-image (and python too), but found the combination of > scikit-image implementation of algorithms together with ndarrays extremely > powerful. > > For now, I am trying to find nuclei in microscopic images (color > deconvolution, find seeds with blob_log) This works fairly well but due to > low contrast some nuclei are not detected. > > nuclei_clahe = equalize_adapthist(nuclei) > > gives much better local contrast but introduces linear artefacts at the > test image borders. Is it possible to avoid/reduce this? > > Best regards, > > > Kai > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: nuclei_dev.png Type: image/png Size: 67053 bytes Desc: not available URL: From kevin.keraudren at googlemail.com Sat Jan 24 19:14:02 2015 From: kevin.keraudren at googlemail.com (Kevin Keraudren) Date: Sun, 25 Jan 2015 00:14:02 +0000 Subject: Question on tests Message-ID: <54C4354A.9040305@googlemail.com> Hi, I have two questions related to tests in scikit-image: 1) is there a way to run just a specific test file, as "make test" runs all tests? I tried: python skimage/feature/tests/test_peak.py but it dies with "NameError: name 'version' is not defined" 2) What about using conditional skips for tests in skimage/viewer/tests otherwise these tests fail with "cannot connect to X server" if we are using ssh without -X? StackOverflow suggests checking os.environ['DISPLAY'] (http://stackoverflow.com/questions/12122671/how-to-determine-from-a-python-application-if-x-server-x-forwarding-is-running) Kind regards, Kevin From emmanuelle.gouillart at nsup.org Sun Jan 25 09:27:13 2015 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Sun, 25 Jan 2015 15:27:13 +0100 Subject: Question on tests In-Reply-To: <54C4354A.9040305@googlemail.com> References: <54C4354A.9040305@googlemail.com> Message-ID: <20150125142713.GA23589@phare.normalesup.org> Hi Kevin, regarding your first question, you can use nose: nosetests skimage/feature/tests/test_peak.py Cheers, Emmanuelle On Sun, Jan 25, 2015 at 12:14:02AM +0000, Kevin Keraudren wrote: > Hi, > I have two questions related to tests in scikit-image: > 1) is there a way to run just a specific test file, as "make test" > runs all tests? > I tried: > python skimage/feature/tests/test_peak.py > but it dies with "NameError: name 'version' is not defined" > 2) What about using conditional skips for tests in > skimage/viewer/tests otherwise these tests fail with "cannot connect > to X server" if we are using ssh without -X? > StackOverflow suggests checking os.environ['DISPLAY'] (http://stackoverflow.com/questions/12122671/how-to-determine-from-a-python-application-if-x-server-x-forwarding-is-running) > Kind regards, > Kevin From kevin.keraudren at googlemail.com Sun Jan 25 11:14:32 2015 From: kevin.keraudren at googlemail.com (Kevin Keraudren) Date: Sun, 25 Jan 2015 16:14:32 +0000 Subject: Question on tests In-Reply-To: <20150125142713.GA23589@phare.normalesup.org> References: <54C4354A.9040305@googlemail.com> <20150125142713.GA23589@phare.normalesup.org> Message-ID: <54C51668.3060300@googlemail.com> Thanks, it will save me some time the next time I need to focus on a specific test! Cheers, Kevin Le 25/01/2015 14:27, Emmanuelle Gouillart a ?crit : > Hi Kevin, > > regarding your first question, you can use nose: > > nosetests skimage/feature/tests/test_peak.py > > Cheers, > Emmanuelle > > On Sun, Jan 25, 2015 at 12:14:02AM +0000, Kevin Keraudren wrote: >> Hi, >> I have two questions related to tests in scikit-image: >> 1) is there a way to run just a specific test file, as "make test" >> runs all tests? >> I tried: >> python skimage/feature/tests/test_peak.py >> but it dies with "NameError: name 'version' is not defined" >> 2) What about using conditional skips for tests in >> skimage/viewer/tests otherwise these tests fail with "cannot connect >> to X server" if we are using ssh without -X? >> StackOverflow suggests checking os.environ['DISPLAY'] (http://stackoverflow.com/questions/12122671/how-to-determine-from-a-python-application-if-x-server-x-forwarding-is-running) >> Kind regards, >> Kevin From martin.savc at gmail.com Tue Jan 27 14:18:34 2015 From: martin.savc at gmail.com (Martin Savc) Date: Tue, 27 Jan 2015 11:18:34 -0800 (PST) Subject: Improving HoG Message-ID: I've been implementing my own HoG transform looking at different sources. While the implementation in scikit-image seems to lack certain features (multiple normalization schemes, general block overlap, Gaussian block window, trillinear interpolation/weighting of bin assignments,...) these don't seem to be that important, at least when applied to my current problem (eye blink analysis). Most of these would increase complexity, giving the implementation a complicated look, with little gain. I've also been looking into some practical improvements - integral histogram, separating the cell-block histogram feature to use it with other dense feature transforms such as LBP, a HoG visualization function that would render the visualization at higher resolutions that the original image. Would any of these be welcomed additions to scikit-image? Regards, Martin Savc PuppySaturation -------------- next part -------------- An HTML attachment was scrubbed... URL: From marcel.gutsche at gmail.com Wed Jan 28 05:58:35 2015 From: marcel.gutsche at gmail.com (Marcel Gutsche) Date: Wed, 28 Jan 2015 02:58:35 -0800 (PST) Subject: Viewer Plugins -> Passing precalculated arguments Message-ID: Hi everyone, I'm working on an image processing project involving several consecutive steps. For parameter optimization I would like to create a viewer plugin which is capable to take these previous outputs into account. So basically the introductory example found in the docs of denoise_plugin = Plugin(image_filter=denoise_tv_bregman) would be sufficient, if I could pass additional fixed arguments (like an additional numpy array). I hope I made myself clear, and someone can give me hint at where to look at. Best regards, Marcel -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Wed Jan 28 06:10:02 2015 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Wed, 28 Jan 2015 03:10:02 -0800 (PST) Subject: Viewer Plugins -> Passing precalculated arguments In-Reply-To: References: Message-ID: <1422443401677.95428a1c@Nodemailer> Hi Marcel, Check out functools.partial, which is a standard function in Python. It allows you to create functions with pre-evaluated arguments: from skimage.restoration import denoise_tv_bregman import functools denoise = functools.partial(denoise_tv_bregman, weight=5, max_iter=10) # use denoise_tv_bregman with weight and max_iter set: denoise_plugin = Plugin(image_filter=denoise) hth! On Wed, Jan 28, 2015 at 9:59 PM, Marcel Gutsche wrote: > Hi everyone, > I'm working on an image processing project involving several consecutive > steps. For parameter optimization I would like to create a viewer plugin > which is capable to take these previous outputs into account. > So basically the introductory example found in the docs of > denoise_plugin = Plugin(image_filter=denoise_tv_bregman) > would be sufficient, if I could pass additional fixed arguments (like an > additional numpy array). > I hope I made myself clear, and someone can give me hint at where to look > at. > Best regards, > Marcel > -- > 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 at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -------------- next part -------------- An HTML attachment was scrubbed... URL: From marcel.gutsche at gmail.com Wed Jan 28 08:18:12 2015 From: marcel.gutsche at gmail.com (Marcel Gutsche) Date: Wed, 28 Jan 2015 05:18:12 -0800 (PST) Subject: Viewer Plugins -> Passing precalculated arguments In-Reply-To: <1422443401677.95428a1c@Nodemailer> References: <1422443401677.95428a1c@Nodemailer> Message-ID: <64fe9fe2-adb0-46ec-b008-ea9c4d02f812@googlegroups.com> > > Hi Juan, thanks, that worked perfectly. -------------- next part -------------- An HTML attachment was scrubbed... URL: From marcel.gutsche at gmail.com Thu Jan 29 03:57:33 2015 From: marcel.gutsche at gmail.com (Marcel Gutsche) Date: Thu, 29 Jan 2015 00:57:33 -0800 (PST) Subject: Image viewer plugins - multiple parameters from different functions Message-ID: Hi folks, kind of a follow up question of my last one (see here ). I still have a chain of image processing tasks, which I want to visualize with the image viewer. Certain parameters should be changed on the fly, where i can see the results in the image viwer immediately by the use of plugins. Something like this basically: a, b = previous_function(image, parameter1 = 0.002 parameter = 0.02) new_image = next_function(image, a, b, another_parameter = 3) I managed to pass the values a and b, generated by a previous function using Juan's hint with functools. next_function which was fine as long as I don't want to change parameter1 and parameter2 interactively. What do I do now, when I want to change them? Using functools here won't get me far, since now I want to be able to change parameter1 and parameter2 with a slider, as well as another_parameter. Maybe there is still a way to achive this, I saw something like a callback argument for the widgets, but I am not sure how to use them or whether they are related to my problem at all. I would also be fine with writing my own Plugin class, but could not get my head around the given examples. I feel that something like this is quite common, so I hope there are already ways to achieve this. Thanks a lot for the great work, Marcel -------------- next part -------------- An HTML attachment was scrubbed... URL: From fars.rg at gmail.com Thu Jan 29 04:20:22 2015 From: fars.rg at gmail.com (FARS Research Group) Date: Thu, 29 Jan 2015 01:20:22 -0800 (PST) Subject: Starting with Scikit-Image Message-ID: Hello everyone, As you'll see the dumb questions I'll make, I'm starting with scikit-image. I started studying but I wanted to run the tests with my own images. But I tried to import them and there was no way to do it. Is there any documentation or tutorial that could help me with this issue? All I want is to run the algorithms in my own image. Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Thu Jan 29 05:55:14 2015 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Thu, 29 Jan 2015 02:55:14 -0800 (PST) Subject: Starting with Scikit-Image In-Reply-To: References: Message-ID: <1422528914538.3f56e333@Nodemailer> Hey, um, FARS? =) Have you seen our gallery? http://scikit-image.org/docs/0.10.x/auto_examples/ If you have any code that is failing, please feel free to ask for help ? but provide as much code as possible as well as error messages you're seeing to help us diagnose the problem! Juan. On Thu, Jan 29, 2015 at 9:03 PM, FARS Research Group wrote: > Hello everyone, > As you'll see the dumb questions I'll make, I'm starting with scikit-image. > I started studying but I wanted to run the tests with my own images. But I > tried to import them and there was no way to do it. > Is there any documentation or tutorial that could help me with this issue? > All I want is to run the algorithms in my own image. > Thanks > -- > 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 at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Thu Jan 29 06:01:07 2015 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Thu, 29 Jan 2015 03:01:07 -0800 (PST) Subject: Image viewer plugins - multiple parameters from different functions In-Reply-To: References: Message-ID: <1422529267175.500a6e6b@Nodemailer> Hi Marcel, I'm guessing you only need to see the final output of the pipeline? Why not define your own function? def piped(image, parameter1, parameter, another_parameter): ? ? a, b = previous_function(image, parameter1, parameter) ? ? new_image = next_function(image, a, b, another_parameter) ? ? return new_image Then use that in your plugin? Juan. On Thu, Jan 29, 2015 at 7:58 PM, Marcel Gutsche wrote: > Hi folks, > kind of a follow up question of my last one (see here > ). > I > still have a chain of image processing tasks, which I want to visualize > with the image viewer. Certain parameters should be changed on the fly, > where i can see the results in the image viwer immediately by the use of > plugins. Something like this basically: > a, b = previous_function(image, parameter1 = 0.002 > parameter = 0.02) > new_image = next_function(image, a, b, another_parameter = 3) > I managed to pass the values a and b, generated by a previous function > using Juan's hint with functools. > next_function > which was fine as long as I don't want to change parameter1 and parameter2 > interactively. What do I do now, when I want to change them? > Using functools here won't get me far, since now I want to be able to > change parameter1 and parameter2 with a slider, as well as > another_parameter. > Maybe there is still a way to achive this, I saw something like a callback > argument for the widgets, but I am not sure how to use them or whether they > are related to my problem at all. I would also be fine with writing my own > Plugin class, but could not get my head around the given examples. I feel > that something like this is quite common, so I hope there are already ways > to achieve this. > Thanks a lot for the great work, > Marcel > -- > 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 at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -------------- next part -------------- An HTML attachment was scrubbed... URL: From fars.rg at gmail.com Thu Jan 29 06:05:01 2015 From: fars.rg at gmail.com (FARS Research Group) Date: Thu, 29 Jan 2015 03:05:01 -0800 (PST) Subject: Starting with Scikit-Image In-Reply-To: References: Message-ID: Hi Juan Forest Applied Remote Sensing research group. (I know its weird...=)...) Yes, I checked some examples, but it worked with scikit-image data. Trying to put my own images, didn't work. But now I added the line im = plt.imread('image.png') and it worked. Just a suggestion, I know it is basic stuff, but perhaps you could show how to import other data, not just the data that comes with scikit-image. Thanks for the answer. Regards, Em quinta-feira, 29 de janeiro de 2015 10:20:22 UTC+1, FARS Research Group escreveu: > > Hello everyone, > > As you'll see the dumb questions I'll make, I'm starting with scikit-image. > I started studying but I wanted to run the tests with my own images. But I > tried to import them and there was no way to do it. > > Is there any documentation or tutorial that could help me with this issue? > All I want is to run the algorithms in my own image. > > Thanks > -------------- next part -------------- An HTML attachment was scrubbed... URL: From fars.rg at gmail.com Thu Jan 29 07:29:25 2015 From: fars.rg at gmail.com (Forest Applied Remote Sensing RG (FARS)) Date: Thu, 29 Jan 2015 04:29:25 -0800 (PST) Subject: Starting with Scikit-Image In-Reply-To: References: Message-ID: Hi Emmanuelle Thank you very much for the information. I'll be waiting. Regards, Em quinta-feira, 29 de janeiro de 2015 10:20:22 UTC+1, Forest Applied Remote Sensing RG (FARS) escreveu: > > Hello everyone, > > As you'll see the dumb questions I'll make, I'm starting with scikit-image. > I started studying but I wanted to run the tests with my own images. But I > tried to import them and there was no way to do it. > > Is there any documentation or tutorial that could help me with this issue? > All I want is to run the algorithms in my own image. > > Thanks > -------------- next part -------------- An HTML attachment was scrubbed... URL: From marcel.gutsche at gmail.com Thu Jan 29 09:35:21 2015 From: marcel.gutsche at gmail.com (Marcel Gutsche) Date: Thu, 29 Jan 2015 06:35:21 -0800 (PST) Subject: Image viewer plugins - multiple parameters from different functions In-Reply-To: <1422529267175.500a6e6b@Nodemailer> References: <1422529267175.500a6e6b@Nodemailer> Message-ID: <5ef40657-c186-4dc2-bf6d-3c23ef065ee1@googlegroups.com> Hi Juan, thanks for the hint. That could work, but i forgot to mention, that the previous function is quite expensive to compute, so I would like to update the first one only, if the slider for its parameter is touched. Right now i try to reduce the amount of recomputations with memoization using the joblib module, but I think I need a while to figure out when exactly values are cached. Marcel Am Donnerstag, 29. Januar 2015 12:01:14 UTC+1 schrieb Juan Nunez-Iglesias: > > Hi Marcel, > > I'm guessing you only need to see the final output of the pipeline? Why > not define your own function? > > def piped(image, parameter1, parameter, another_parameter): > a, b = previous_function(image, parameter1, parameter) > new_image = next_function(image, a, b, another_parameter) > return new_image > > Then use that in your plugin? > > Juan. > > > > > On Thu, Jan 29, 2015 at 7:58 PM, Marcel Gutsche > wrote: > >> Hi folks, >> >> kind of a follow up question of my last one (see here >> ). >> I >> still have a chain of image processing tasks, which I want to visualize >> with the image viewer. Certain parameters should be changed on the fly, >> where i can see the results in the image viwer immediately by the use of >> plugins. Something like this basically: >> >> >> a, b = previous_function(image, parameter1 = 0.002 >> parameter = 0.02) >> new_image = next_function(image, a, b, another_parameter = 3) >> >> >> I managed to pass the values a and b, generated by a previous function >> using Juan's hint with functools. >> >> next_function >> >> which was fine as long as I don't want to change parameter1 and >> parameter2 interactively. What do I do now, when I want to change them? >> >> Using functools here won't get me far, since now I want to be able to >> change parameter1 and parameter2 with a slider, as well as >> another_parameter. >> >> Maybe there is still a way to achive this, I saw something like a >> callback argument for the widgets, but I am not sure how to use them or >> whether they are related to my problem at all. I would also be fine with >> writing my own Plugin class, but could not get my head around the given >> examples. I feel that something like this is quite common, so I hope there >> are already ways to achieve this. >> >> Thanks a lot for the great work, >> Marcel >> >> -- >> 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... at googlegroups.com . >> For more options, visit https://groups.google.com/d/optout. >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From emmanuelle.gouillart at nsup.org Thu Jan 29 06:13:00 2015 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Thu, 29 Jan 2015 12:13:00 +0100 Subject: Starting with Scikit-Image In-Reply-To: References: Message-ID: <20150129111300.GB14531@phare.normalesup.org> Hi, a "getting started" section for the user guide has been merged in the development version (master branch) and mentions how to open image files (https://github.com/scikit-image/scikit-image/blob/master/doc/source/user_guide/getting_started.txt). It's not online yet, but it should be, soon. Cheers, Emmanuelle On Thu, Jan 29, 2015 at 03:05:01AM -0800, FARS Research Group wrote: > Hi Juan > Forest Applied Remote Sensing research group. (I know its weird...=)...) > Yes, I checked some examples, but it worked with scikit-image data. Trying to > put my own images, didn't work. > But now I added the line im = plt.imread('image.png') and it worked. > Just a suggestion, I know it is basic stuff, but perhaps you could show how to > import other data, not just the data that comes with scikit-image. > Thanks for the answer. > Regards, > Em quinta-feira, 29 de janeiro de 2015 10:20:22 UTC+1, FARS Research Group > escreveu: > Hello everyone, > As you'll see the dumb questions I'll make, I'm starting with scikit-image. > I started studying but I wanted to run the tests with my own images. But I > tried to import them and there was no way to do it. > Is there any documentation or tutorial that could help me with this issue? > All I want is to run the algorithms in my own image. > Thanks From steven.silvester at gmail.com Thu Jan 29 21:20:44 2015 From: steven.silvester at gmail.com (Steven Silvester) Date: Thu, 29 Jan 2015 18:20:44 -0800 (PST) Subject: Image viewer plugins - multiple parameters from different functions In-Reply-To: <5ef40657-c186-4dc2-bf6d-3c23ef065ee1@googlegroups.com> References: <1422529267175.500a6e6b@Nodemailer> <5ef40657-c186-4dc2-bf6d-3c23ef065ee1@googlegroups.com> Message-ID: <4905c246-846f-46ef-b849-e64d57e317af@googlegroups.com> Marcel, It sounds like you want use IPython traitlets , something like: from IPython.utils.traitlets import HasTraits, Float, on_trait_change, Anyfrom skimage.viewer import ImageViewer class Pipeline(HasTraits): param1 = Float(0.1) param2 = Float(0.2) param3 = Float(0.3) viewer = Any @on_trait_change('param1, param2') def use_previous_function(self): # do something with previous function @on_trait_change(''param3') def use_next_function(self): # do something with next function v =ImageViewer(...) p = Pipeline(viewer=v) On Thursday, January 29, 2015 at 8:35:21 AM UTC-6, Marcel Gutsche wrote: Hi Juan, > > thanks for the hint. That could work, but i forgot to mention, that the > previous function is quite expensive to compute, so I would like to update > the first one only, if the slider for its parameter is touched. Right now i > try to reduce the amount of recomputations with memoization using the > joblib module, but I think I need a while to figure out when exactly values > are cached. > > Marcel > > Am Donnerstag, 29. Januar 2015 12:01:14 UTC+1 schrieb Juan Nunez-Iglesias: >> >> Hi Marcel, >> >> I'm guessing you only need to see the final output of the pipeline? Why >> not define your own function? >> >> def piped(image, parameter1, parameter, another_parameter): >> a, b = previous_function(image, parameter1, parameter) >> new_image = next_function(image, a, b, another_parameter) >> return new_image >> >> Then use that in your plugin? >> >> Juan. >> >> >> >> >> On Thu, Jan 29, 2015 at 7:58 PM, Marcel Gutsche >> wrote: >> >>> Hi folks, >>> >>> kind of a follow up question of my last one (see here >>> ). >>> I >>> still have a chain of image processing tasks, which I want to visualize >>> with the image viewer. Certain parameters should be changed on the fly, >>> where i can see the results in the image viwer immediately by the use of >>> plugins. Something like this basically: >>> >>> >>> a, b = previous_function(image, parameter1 = 0.002 >>> parameter = 0.02) >>> new_image = next_function(image, a, b, another_parameter = 3) >>> >>> >>> I managed to pass the values a and b, generated by a previous function >>> using Juan's hint with functools. >>> >>> next_function >>> >>> which was fine as long as I don't want to change parameter1 and >>> parameter2 interactively. What do I do now, when I want to change them? >>> >>> Using functools here won't get me far, since now I want to be able to >>> change parameter1 and parameter2 with a slider, as well as >>> another_parameter. >>> >>> Maybe there is still a way to achive this, I saw something like a >>> callback argument for the widgets, but I am not sure how to use them or >>> whether they are related to my problem at all. I would also be fine with >>> writing my own Plugin class, but could not get my head around the given >>> examples. I feel that something like this is quite common, so I hope there >>> are already ways to achieve this. >>> >>> Thanks a lot for the great work, >>> Marcel >>> >>> -- >>> 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... at googlegroups.com. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> ? -------------- next part -------------- An HTML attachment was scrubbed... URL: