From silvertrumpet999 at gmail.com Mon Feb 1 01:19:36 2016 From: silvertrumpet999 at gmail.com (Josh Warner) Date: Sun, 31 Jan 2016 22:19:36 -0800 (PST) Subject: dev version installation In-Reply-To: <25621627-8a66-44c8-bac2-47df2b6895ae@googlegroups.com> References: <25621627-8a66-44c8-bac2-47df2b6895ae@googlegroups.com> Message-ID: <2b7816bd-1968-4d0c-9474-c5d0b32e284e@googlegroups.com> It sounds like you're compiling inplace but not informing your preferred Python installation about the package. After compiling, have you run `python setup.py develop`? That might solve everything, assuming `python` maps to your preferred Anaconda environment. It compiles what's needed, then adds the path to your PYTHONPATH so you can develop and use the source install outside Python's site_packages directory. Let us know if that doesn't work, Josh On Sunday, January 31, 2016 at 5:53:54 PM UTC-7, Simone Codeluppi wrote: > > Hi > I tried to install the dev version (0.12x) on anaconda using the command > posted on the website : git clone > https://github.com/scikit-image/scikit-image.git > followed by git pull and compiling of the modified extensions I still get: > 0.11.dev0 > Any idea on what i can be doing wrong? > Thanks a lot for the help! > > Simone > -------------- next part -------------- An HTML attachment was scrubbed... URL: From silvertrumpet999 at gmail.com Mon Feb 1 01:21:13 2016 From: silvertrumpet999 at gmail.com (Josh Warner) Date: Sun, 31 Jan 2016 22:21:13 -0800 (PST) Subject: 0.12 release In-Reply-To: <-6724546148968632515@unknownmsgid> References: <4D387154-865D-4846-B9B6-DFCA10F8C334@demuc.de> <20160131155247.GB819538@phare.normalesup.org> <20160131165818.GC819538@phare.normalesup.org> <20160131195815.GD819538@phare.normalesup.org> <-6724546148968632515@unknownmsgid> Message-ID: <5c343a1e-8ec0-4136-b2d1-7d1202c4ce69@googlegroups.com> I added #1921 to the milestone, but for good reason. Should have minimal fuss and saves us a cycle against this deprecation. Nothing else pending here! On Sunday, January 31, 2016 at 1:35:47 PM UTC-7, Johannes Sch?nberger wrote: > > Agreed and apologies :-) > > No more PRs from my side. > > > On Jan 31, 2016, at 20:58, Emmanuelle Gouillart < > emmanuelle.gouillart at nsup.org> wrote: > > > > One more request, especially to the core team: could we restrain > > ourselves from adding new PRs to the 0.12 milestone, except for bad bug > > fixes? We need to converge at some point :-). > > > > Emma > > > >> On Sun, Jan 31, 2016 at 09:52:25AM -0800, St?fan van der Walt wrote: > >> On 31 January 2016 at 08:58, Emmanuelle Gouillart > >> wrote: > >>>>> St?fan, do you want these PRs to be merged for 0.12? Can you > estimate > >>>>> when they should be ready? > >>> > >>>> I'll make the last changes to those PRs now. If, after that, they > are > >>>> not ready to merge, let us not hold up the whole release. > >> > >> I've made updates to those PRs. Unfortunately, I will be out for most > >> of the rest of the day, but feel free to update those PRs--I've added > >> Emma, Johannes, Josh and Juan as collaborators on my fork. > >> > >> Thanks again! > >> > >> St?fan > >> > >> -- > >> 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. > >> To post to this group, send an email to scikit-image at googlegroups.com. > >> To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/CABDkGQk7emQRwk9W5-sRZ0nq8gS%2Bj5TLJ3GBC7RTcnQ7umzTDQ%40mail.gmail.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. > > To post to this group, send an email to scikit-image at googlegroups.com. > > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/20160131195815.GD819538%40phare.normalesup.org. > > > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simone at codeluppi.org Mon Feb 1 09:11:29 2016 From: simone at codeluppi.org (Simone Codeluppi) Date: Mon, 1 Feb 2016 06:11:29 -0800 (PST) Subject: dev version installation In-Reply-To: <2b7816bd-1968-4d0c-9474-c5d0b32e284e@googlegroups.com> References: <25621627-8a66-44c8-bac2-47df2b6895ae@googlegroups.com> <2b7816bd-1968-4d0c-9474-c5d0b32e284e@googlegroups.com> Message-ID: Hi thanks for the help but it didn't change anything....still 0.11dev Simone On Sunday, January 31, 2016 at 10:19:36 PM UTC-8, Josh Warner wrote: > > It sounds like you're compiling inplace but not informing your preferred > Python installation about the package. > > After compiling, have you run `python setup.py develop`? That might solve > everything, assuming `python` maps to your preferred Anaconda environment. > It compiles what's needed, then adds the path to your PYTHONPATH so you can > develop and use the source install outside Python's site_packages directory. > > Let us know if that doesn't work, > Josh > > On Sunday, January 31, 2016 at 5:53:54 PM UTC-7, Simone Codeluppi wrote: >> >> Hi >> I tried to install the dev version (0.12x) on anaconda using the command >> posted on the website : git clone >> https://github.com/scikit-image/scikit-image.git >> followed by git pull and compiling of the modified extensions I still >> get: 0.11.dev0 >> Any idea on what i can be doing wrong? >> Thanks a lot for the help! >> >> Simone >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From silvertrumpet999 at gmail.com Mon Feb 1 17:55:52 2016 From: silvertrumpet999 at gmail.com (Josh Warner) Date: Mon, 1 Feb 2016 14:55:52 -0800 (PST) Subject: 0.12 release In-Reply-To: <20160201185705.GA3207967@phare.normalesup.org> References: <4D387154-865D-4846-B9B6-DFCA10F8C334@demuc.de> <20160131155247.GB819538@phare.normalesup.org> <20160131165818.GC819538@phare.normalesup.org> <20160131195815.GD819538@phare.normalesup.org> <-6724546148968632515@unknownmsgid> <5c343a1e-8ec0-4136-b2d1-7d1202c4ce69@googlegroups.com> <20160201185705.GA3207967@phare.normalesup.org> Message-ID: Already done, didn't have Wi-Fi over lunch but will push once I get home tonight. From emmanuelle.gouillart at nsup.org Mon Feb 1 13:57:05 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Mon, 1 Feb 2016 19:57:05 +0100 Subject: 0.12 release In-Reply-To: <5c343a1e-8ec0-4136-b2d1-7d1202c4ce69@googlegroups.com> References: <4D387154-865D-4846-B9B6-DFCA10F8C334@demuc.de> <20160131155247.GB819538@phare.normalesup.org> <20160131165818.GC819538@phare.normalesup.org> <20160131195815.GD819538@phare.normalesup.org> <-6724546148968632515@unknownmsgid> <5c343a1e-8ec0-4136-b2d1-7d1202c4ce69@googlegroups.com> Message-ID: <20160201185705.GA3207967@phare.normalesup.org> I completely understand why you added this PR to the milestone, but there are some remaining issues about it (see comments on GitHub: failing tests + gallery examples to update). Will you have time today or tomorrow to work on it, so that we can tag 0.12 very soon :-) ? Thanks! Emma On Sun, Jan 31, 2016 at 10:21:13PM -0800, Josh Warner wrote: > I added #1921??to the milestone, but for good reason. Should have minimal fuss > and saves us a cycle against this deprecation. > Nothing else pending here! > On Sunday, January 31, 2016 at 1:35:47 PM UTC-7, Johannes Sch??nberger wrote: > Agreed and apologies :-) > No more PRs from my side. > > On Jan 31, 2016, at 20:58, Emmanuelle Gouillart < > emmanuelle.gouillart at nsup.org> wrote: > > One more request, especially to the core team: could we restrain > > ourselves from adding new PRs to the 0.12 milestone, except for bad bug > > fixes? We need to converge at some point :-). > > Emma > >> On Sun, Jan 31, 2016 at 09:52:25AM -0800, St??fan van der Walt wrote: > >> On 31 January 2016 at 08:58, Emmanuelle Gouillart > >> wrote: > >>>>> St??fan, do you want these PRs to be merged for 0.12? Can you estimate > >>>>> when they should be ready? > >>>> I'll make the last changes to those PRs now. ??If, after that, they are > >>>> not ready to merge, let us not hold up the whole release. > >> I've made updates to those PRs. ??Unfortunately, I will be out for most > >> of the rest of the day, but feel free to update those PRs--I've added > >> Emma, Johannes, Josh and Juan as collaborators on my fork. > >> Thanks again! > >> St??fan > >> -- > >> 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. > >> To post to this group, send an email to scikit-image at googlegroups.com. > >> To view this discussion on the web, visit https://groups.google.com/d/ > msgid/scikit-image/CABDkGQk7emQRwk9W5-sRZ0nq8gS%2Bj5TLJ3GBC7RTcnQ7umzTDQ% > 40mail.gmail.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. > > To post to this group, send an email to scikit-image at googlegroups.com. > > To view this discussion on the web, visit https://groups.google.com/d/ > msgid/scikit-image/20160131195815.GD819538%40phare.normalesup.org. > > For more options, visit https://groups.google.com/d/optout. From stefanv at berkeley.edu Tue Feb 2 00:08:47 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Mon, 1 Feb 2016 21:08:47 -0800 Subject: dev version installation In-Reply-To: References: <25621627-8a66-44c8-bac2-47df2b6895ae@googlegroups.com> <2b7816bd-1968-4d0c-9474-c5d0b32e284e@googlegroups.com> Message-ID: On 1 February 2016 at 06:11, Simone Codeluppi wrote: > thanks for the help but it didn't change anything....still 0.11dev Can you please send the output of $ git log HEAD^... from the git repo you cloned, as well as $ python -c "import skimage; print(skimage)" from your home directory? Thanks, St?fan From simone at codeluppi.org Tue Feb 2 16:21:26 2016 From: simone at codeluppi.org (Simone Codeluppi) Date: Tue, 2 Feb 2016 13:21:26 -0800 (PST) Subject: dev version installation In-Reply-To: References: <25621627-8a66-44c8-bac2-47df2b6895ae@googlegroups.com> <2b7816bd-1968-4d0c-9474-c5d0b32e284e@googlegroups.com> Message-ID: <64e392f5-f347-4d55-958c-6196b71bde37@googlegroups.com> Hi here are the outputs: from $ python -c "import skimage; print(skimage)" I get (skimage_dev) from $ git log HEAD^... I get: commit 13f9b89023feabe3f7d8b4bc7e4e309a1bca8686 Merge: b6a1bcd 4c781cf Author: Stefan van der Walt Date: Wed Jan 28 13:31:25 2015 -0800 Merge pull request #1319 from ahojnnes/geom-est Improve conditioning of geometric transformations commit 4c781cf5c015ab3d1155d83626a6ec437ac18339 Author: Johannes Sch?nberger Date: Thu Jan 22 07:23:54 2015 -0500 Fix doc string commit ad85dfabd57f55c8cabef5dbfe7e757f96ec677b Author: Johannes Sch?nberger Date: Thu Jan 22 06:49:16 2015 -0500 Disable catch of all warnings, return nan params instead commit acf68c6d7c0bd49aadc46e86d8082f0b231cc54c Author: Johannes Sch?nberger Date: Fri Dec 26 12:41:03 2014 +0100 Add new parameter to catch exceptions during RANSAC commit 91c697c5f79984b77aae1927a559c1884181c546 Author: Johannes Sch?nberger Date: Wed Dec 24 17:28:44 2014 +0100 Handle special case of 1 pixel image commit 5dbb6e325795aef4c160962f09fe64d8989069a4 Author: Johannes Sch?nberger Date: Wed Dec 24 15:27:10 2014 +0100 Improve conditioning of silimarity transform design matrix commit 983919404f90fdc489f9adfef10d9b04e95bd3b4 Author: Johannes Sch?nberger Date: Wed Dec 24 15:24:34 2014 +0100 Improve conditioning of homography design matrix commit 2f60de736295fccc7f0f360a4f705d1d03f8b1df Author: Johannes Sch?nberger Date: Wed Dec 24 15:19:58 2014 +0100 Create function to center and normalize image points Thanks for the help! Simone On Monday, February 1, 2016 at 9:09:09 PM UTC-8, stefanv wrote: > > On 1 February 2016 at 06:11, Simone Codeluppi > wrote: > > thanks for the help but it didn't change anything....still 0.11dev > > Can you please send the output of > > $ git log HEAD^... > > from the git repo you cloned, as well as > > $ python -c "import skimage; print(skimage)" > > from your home directory? > > Thanks, > St?fan > -------------- next part -------------- An HTML attachment was scrubbed... URL: From simone at codeluppi.org Tue Feb 2 16:58:36 2016 From: simone at codeluppi.org (Simone Codeluppi) Date: Tue, 2 Feb 2016 13:58:36 -0800 (PST) Subject: dev version installation In-Reply-To: References: <25621627-8a66-44c8-bac2-47df2b6895ae@googlegroups.com> <2b7816bd-1968-4d0c-9474-c5d0b32e284e@googlegroups.com> Message-ID: <0e4cd2e0-bb95-4f37-b1c8-3ac804df7255@googlegroups.com> Hi Stefa I re-run the installation and this time the dev 0.12 got installed. Maybe there was something wrong with the installation I did before. Thanks for the help Simone On Monday, February 1, 2016 at 9:09:09 PM UTC-8, stefanv wrote: > > On 1 February 2016 at 06:11, Simone Codeluppi > wrote: > > thanks for the help but it didn't change anything....still 0.11dev > > Can you please send the output of > > $ git log HEAD^... > > from the git repo you cloned, as well as > > $ python -c "import skimage; print(skimage)" > > from your home directory? > > Thanks, > St?fan > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Tue Feb 2 17:11:25 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Tue, 2 Feb 2016 14:11:25 -0800 Subject: dev version installation In-Reply-To: <64e392f5-f347-4d55-958c-6196b71bde37@googlegroups.com> References: <25621627-8a66-44c8-bac2-47df2b6895ae@googlegroups.com> <2b7816bd-1968-4d0c-9474-c5d0b32e284e@googlegroups.com> <64e392f5-f347-4d55-958c-6196b71bde37@googlegroups.com> Message-ID: On 2 February 2016 at 13:21, Simone Codeluppi wrote: > from $ git log HEAD^... I get: This output is a bit strange, so perhaps try: $ git checkout master $ git fetch $ git reset --hard origin/master St?fan From stefanv at berkeley.edu Wed Feb 3 11:21:07 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Wed, 3 Feb 2016 08:21:07 -0800 Subject: 0.12 release In-Reply-To: <20160203075920.GA2389752@phare.normalesup.org> References: <20160131155247.GB819538@phare.normalesup.org> <20160131165818.GC819538@phare.normalesup.org> <20160131195815.GD819538@phare.normalesup.org> <-6724546148968632515@unknownmsgid> <5c343a1e-8ec0-4136-b2d1-7d1202c4ce69@googlegroups.com> <20160201185705.GA3207967@phare.normalesup.org> <6F56AC09-BA2B-43F5-A910-37740BEBEC64@demuc.de> <20160203075920.GA2389752@phare.normalesup.org> Message-ID: Please note that there are still outstanding items on the TODO.txt. I am almost done refactoring the labeling to use zero as background. St?fan On Feb 2, 2016 11:59 PM, "Emmanuelle Gouillart" < emmanuelle.gouillart at nsup.org> wrote: > Yes, I think it's ready now! I've started working on release notes > yesterday and will continue tonight (Paris time), but if someone with > more bandwidth is impatient about releasing, go for it! > > Emma > > On Wed, Feb 03, 2016 at 08:55:45AM +0100, Johannes Sch?nberger wrote: > > Should we release 0.12 now? Seems like all but one PR are merged now. > > > > On Feb 1, 2016, at 11:55 PM, Josh Warner > wrote: > > > > Already done, didn't have Wi-Fi over lunch but will push once I get > home tonight. > > > > -- > > > 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. > > > To post to this group, send an email to scikit-image at googlegroups.com. > > > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/f59e463a-124c-43b7-8272-40bb25925a55%40googlegroups.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. > To post to this group, send an email to scikit-image at googlegroups.com. > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/20160203075920.GA2389752%40phare.normalesup.org > . > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jsch at demuc.de Wed Feb 3 02:55:45 2016 From: jsch at demuc.de (=?utf-8?Q?Johannes_Sch=C3=B6nberger?=) Date: Wed, 3 Feb 2016 08:55:45 +0100 Subject: 0.12 release In-Reply-To: References: <4D387154-865D-4846-B9B6-DFCA10F8C334@demuc.de> <20160131155247.GB819538@phare.normalesup.org> <20160131165818.GC819538@phare.normalesup.org> <20160131195815.GD819538@phare.normalesup.org> <-6724546148968632515@unknownmsgid> <5c343a1e-8ec0-4136-b2d1-7d1202c4ce69@googlegroups.com> <20160201185705.GA3207967@phare.normalesup.org> Message-ID: <6F56AC09-BA2B-43F5-A910-37740BEBEC64@demuc.de> Should we release 0.12 now? Seems like all but one PR are merged now. > On Feb 1, 2016, at 11:55 PM, Josh Warner wrote: > > Already done, didn't have Wi-Fi over lunch but will push once I get home tonight. > > -- > 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. > To post to this group, send an email to scikit-image at googlegroups.com. > To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/f59e463a-124c-43b7-8272-40bb25925a55%40googlegroups.com. > For more options, visit https://groups.google.com/d/optout. From emmanuelle.gouillart at nsup.org Wed Feb 3 02:59:20 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Wed, 3 Feb 2016 08:59:20 +0100 Subject: 0.12 release In-Reply-To: <6F56AC09-BA2B-43F5-A910-37740BEBEC64@demuc.de> References: <20160131155247.GB819538@phare.normalesup.org> <20160131165818.GC819538@phare.normalesup.org> <20160131195815.GD819538@phare.normalesup.org> <-6724546148968632515@unknownmsgid> <5c343a1e-8ec0-4136-b2d1-7d1202c4ce69@googlegroups.com> <20160201185705.GA3207967@phare.normalesup.org> <6F56AC09-BA2B-43F5-A910-37740BEBEC64@demuc.de> Message-ID: <20160203075920.GA2389752@phare.normalesup.org> Yes, I think it's ready now! I've started working on release notes yesterday and will continue tonight (Paris time), but if someone with more bandwidth is impatient about releasing, go for it! Emma On Wed, Feb 03, 2016 at 08:55:45AM +0100, Johannes Sch??nberger wrote: > Should we release 0.12 now? Seems like all but one PR are merged now. > > On Feb 1, 2016, at 11:55 PM, Josh Warner wrote: > > Already done, didn't have Wi-Fi over lunch but will push once I get home tonight. > > -- > > 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. > > To post to this group, send an email to scikit-image at googlegroups.com. > > To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/f59e463a-124c-43b7-8272-40bb25925a55%40googlegroups.com. > > For more options, visit https://groups.google.com/d/optout. From stefanv at berkeley.edu Wed Feb 3 13:29:58 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Wed, 3 Feb 2016 10:29:58 -0800 Subject: 0.12 release In-Reply-To: <20160203172104.GA2977973@phare.normalesup.org> References: <20160131165818.GC819538@phare.normalesup.org> <20160131195815.GD819538@phare.normalesup.org> <-6724546148968632515@unknownmsgid> <5c343a1e-8ec0-4136-b2d1-7d1202c4ce69@googlegroups.com> <20160201185705.GA3207967@phare.normalesup.org> <6F56AC09-BA2B-43F5-A910-37740BEBEC64@demuc.de> <20160203075920.GA2389752@phare.normalesup.org> <20160203172104.GA2977973@phare.normalesup.org> Message-ID: On 3 February 2016 at 09:21, Emmanuelle Gouillart wrote: > Thanks for preventing us from being carried away by the excitement of the > release :-D Let me not stand in the way! I have three months' worth of happiness pent up for the moment that tag gets applied. Onward :) St?fan From emmanuelle.gouillart at nsup.org Wed Feb 3 12:21:04 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Wed, 3 Feb 2016 18:21:04 +0100 Subject: 0.12 release In-Reply-To: References: <20160131165818.GC819538@phare.normalesup.org> <20160131195815.GD819538@phare.normalesup.org> <-6724546148968632515@unknownmsgid> <5c343a1e-8ec0-4136-b2d1-7d1202c4ce69@googlegroups.com> <20160201185705.GA3207967@phare.normalesup.org> <6F56AC09-BA2B-43F5-A910-37740BEBEC64@demuc.de> <20160203075920.GA2389752@phare.normalesup.org> Message-ID: <20160203172104.GA2977973@phare.normalesup.org> Thanks for preventing us from being carried away by the excitement of the release :-D On Wed, Feb 03, 2016 at 08:21:07AM -0800, St??fan van der Walt wrote: > Please note that there are still outstanding items on the TODO.txt.?? I am > almost done refactoring the labeling to use zero as background. > St??fan > On Feb 2, 2016 11:59 PM, "Emmanuelle Gouillart" > wrote: > Yes, I think it's ready now! I've started working on release notes > yesterday and will continue tonight (Paris time), but if someone with > more bandwidth is impatient about releasing, go for it! > Emma > On Wed, Feb 03, 2016 at 08:55:45AM +0100, Johannes Sch??nberger wrote: > > Should we release 0.12 now? Seems like all but one PR are merged now. > > > On Feb 1, 2016, at 11:55 PM, Josh Warner > wrote: > > > Already done, didn't have Wi-Fi over lunch but will push once I get > home tonight. > > > -- > > > 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. > > > To post to this group, send an email to scikit-image at googlegroups.com. > > > To view this discussion on the web, visit https://groups.google.com/d/ > msgid/scikit-image/f59e463a-124c-43b7-8272-40bb25925a55%40googlegroups.com. > > > For more options, visit https://groups.google.com/d/optout. From kunalgrover05 at gmail.com Sat Feb 6 07:17:12 2016 From: kunalgrover05 at gmail.com (Kunal Grover) Date: Sat, 6 Feb 2016 04:17:12 -0800 (PST) Subject: DTW implementation Message-ID: Hi, I am interested to be a part of this community. I went through the last year's proposed projects at GSoC and DTW was one of them. Was it taken up? Otherwise, I would like to take it up as my GSoC project for this year. Regards. -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Sun Feb 7 04:12:40 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Sun, 7 Feb 2016 01:12:40 -0800 Subject: DTW implementation In-Reply-To: References: Message-ID: Hi Kunal On 6 February 2016 at 04:17, Kunal Grover wrote: > I am interested to be a part of this community. I went through the last > year's proposed projects at GSoC and DTW was one of them. Was it taken up? > Otherwise, I would like to take it up as my GSoC project for this year. Thank you for your interest in improving scikit-image! I cannot speak for the rest of the team, but due to other scikit-image related commitments I will not take part in GSoC this year. Best regards St?fan From emmanuelle.gouillart at nsup.org Sun Feb 7 10:32:32 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Sun, 7 Feb 2016 16:32:32 +0100 Subject: 0.12 release In-Reply-To: References: <20160131195815.GD819538@phare.normalesup.org> <-6724546148968632515@unknownmsgid> <5c343a1e-8ec0-4136-b2d1-7d1202c4ce69@googlegroups.com> <20160201185705.GA3207967@phare.normalesup.org> <6F56AC09-BA2B-43F5-A910-37740BEBEC64@demuc.de> <20160203075920.GA2389752@phare.normalesup.org> <20160203172104.GA2977973@phare.normalesup.org> Message-ID: <20160207153232.GA2920916@phare.normalesup.org> Dear all, after having pressed everyone to finish pull requests and promised to take care of the release, I'm having a few busy days during which I can't find time to work on the release. It's going to be much better starting from Tuesday evening, so please bear with me and be patient: the release is (still) coming! And it means that there are still a few days to complete outstanding items on TODO.txt :-) Cheers, Emmanuelle On Wed, Feb 03, 2016 at 10:29:58AM -0800, St??fan van der Walt wrote: > On 3 February 2016 at 09:21, Emmanuelle Gouillart > wrote: > > Thanks for preventing us from being carried away by the excitement of the > > release :-D > Let me not stand in the way! I have three months' worth of happiness > pent up for the moment that tag gets applied. > Onward :) > St??fan From himanshu2014iit at gmail.com Sun Feb 7 08:30:00 2016 From: himanshu2014iit at gmail.com (Himanshu Mishra) Date: Sun, 7 Feb 2016 19:00:00 +0530 Subject: DTW implementation In-Reply-To: References: Message-ID: Hey St?fan, The last date for applying under PSF umbrella is March 7, exactly one month from now. I guess we have good time to take a decision regarding GSoC participation. -- Himanshu Mishra -------------- next part -------------- An HTML attachment was scrubbed... URL: From kunalgrover05 at gmail.com Sun Feb 7 08:37:34 2016 From: kunalgrover05 at gmail.com (Kunal Grover) Date: Sun, 7 Feb 2016 19:07:34 +0530 Subject: DTW implementation In-Reply-To: References: Message-ID: Hi Himanshu and St?fan*,* Thank you for your replies. Could you suggest some other person who would be interested to mentor this project. *Kunal Grover* about.me/kunalgrover05 On Sun, Feb 7, 2016 at 7:00 PM, Himanshu Mishra wrote: > Hey St?fan, > > The last date for applying under PSF umbrella is March 7, exactly one > month from now. I guess we have good time to take a decision regarding GSoC > participation. > > -- > Himanshu Mishra > > -- > 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/8QrEgYpcbZ8/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > scikit-image+unsubscribe at googlegroups.com. > To post to this group, send email to scikit-image at googlegroups.com. > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/CANpJW-XB6p-V%3DvEJT3o1POwPJWtqqZwJ0yBM_ipzOT%2BDgYd99g%40mail.gmail.com > > . > > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From spagodo at gmail.com Mon Feb 8 20:38:14 2016 From: spagodo at gmail.com (Christopher) Date: Mon, 8 Feb 2016 17:38:14 -0800 (PST) Subject: ValueError: Images of type float must be between -1 and 1. Message-ID: <96935606-9924-4b1b-a29f-ffb3b0ffa176@googlegroups.com> Hi, I am having a problem trying to create an image object from an array. The problem is the array extends beyond -1 and 1. The pixel values are raw 32bit float values from a detector. array.dtype float32 summary(array) Mean: 0.00656827 Min: -6.1125 Median: 1.09516e-08 Max: 3.69815 image = skimage.img_as_float(array) File "/home/user/anaconda2/lib/python2.7/site-packages/skimage/util/dtype.py", line 291, in img_as_float return convert(image, np.float64, force_copy) File "/home/user/anaconda2/lib/python2.7/site-packages/skimage/util/dtype.py", line 195, in convert raise ValueError("Images of type float must be between -1 and 1.") ValueError: Images of type float must be between -1 and 1 I am using version 0.11.3 via anaconda on fedora 23 Sometimes I can get img_as_float to work if I use astype on the array first, but then it doesn't seem to change the values, and then skimage.io.Image() will fail with a similar error Thanks in advance for any help. -------------- next part -------------- An HTML attachment was scrubbed... URL: From spagodo at gmail.com Mon Feb 8 20:40:14 2016 From: spagodo at gmail.com (Christopher) Date: Mon, 8 Feb 2016 17:40:14 -0800 (PST) Subject: ValueError: Images of type float must be between -1 and 1. In-Reply-To: <96935606-9924-4b1b-a29f-ffb3b0ffa176@googlegroups.com> References: <96935606-9924-4b1b-a29f-ffb3b0ffa176@googlegroups.com> Message-ID: An update, the values are not 32 bit from the detector, the detector is 16bit. But the images have been aligned by a previous program, so they are interpolated to 32 bit precision. On Monday, February 8, 2016 at 8:38:14 PM UTC-5, Christopher wrote: > > Hi, I am having a problem trying to create an image object from an array. > The problem is the array extends beyond -1 and 1. The pixel values are raw > 32bit float values from a detector. > > > array.dtype > float32 > > > summary(array) > Mean: 0.00656827 > > Min: -6.1125 > Median: 1.09516e-08 > Max: 3.69815 > > > > image = skimage.img_as_float(array) > > > > File > "/home/user/anaconda2/lib/python2.7/site-packages/skimage/util/dtype.py", > line 291, in img_as_float > return convert(image, np.float64, force_copy) > File > "/home/user/anaconda2/lib/python2.7/site-packages/skimage/util/dtype.py", > line 195, in convert > raise ValueError("Images of type float must be between -1 and 1.") > ValueError: Images of type float must be between -1 and 1 > > > I am using version 0.11.3 via anaconda on fedora 23 > > > Sometimes I can get img_as_float to work if I use astype on the array > first, but then it doesn't seem to change the values, and then > skimage.io.Image() will fail with a similar error > > Thanks in advance for any help. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From spagodo at gmail.com Tue Feb 9 14:23:41 2016 From: spagodo at gmail.com (Christopher) Date: Tue, 9 Feb 2016 11:23:41 -0800 (PST) Subject: ValueError: Images of type float must be between -1 and 1. In-Reply-To: References: <96935606-9924-4b1b-a29f-ffb3b0ffa176@googlegroups.com> Message-ID: Hi! Thanks for the reply The reason I wanted to use img_as_float is because I eventually plan to use many functions and I thought I should get the image into a format that scikit-image likes before proceeding. However, as you suggested, the function I want to use immediately is transform.rotate() which does have a preserve scale option, and that did fix my problem. Should I just use this on every function? -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Tue Feb 9 16:34:08 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Tue, 9 Feb 2016 13:34:08 -0800 Subject: ValueError: Images of type float must be between -1 and 1. In-Reply-To: References: <96935606-9924-4b1b-a29f-ffb3b0ffa176@googlegroups.com> Message-ID: Hi Christopher On 9 February 2016 at 11:23, Christopher wrote: > The reason I wanted to use img_as_float is because I eventually plan to use > many functions and I thought I should get the image into a format that > scikit-image likes before proceeding. However, as you suggested, the > function I want to use immediately is transform.rotate() which does have a > preserve scale option, and that did fix my problem. Should I just use this > on every function? If you know the range of your input data, then you could rescale the image to be between -1 and 1: exposure.rescale_intensity(data, in_range=(-10, 10)) >From there on, you should have no problems. If, however, you need to preserve your original scale, you can either use `preserve_range` or rescale your image afterwards. The latter approach is dangerous, though, since you don't know how the range of values get influenced by the operations you performed on your image. Regards St?fan From jni.soma at gmail.com Tue Feb 9 01:32:22 2016 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Tue, 9 Feb 2016 17:32:22 +1100 Subject: ValueError: Images of type float must be between -1 and 1. In-Reply-To: References: <96935606-9924-4b1b-a29f-ffb3b0ffa176@googlegroups.com> Message-ID: Hi Christopher! In some cases, skimage has to assume a certain input range for images, so that things like display brightness and type conversions are consistent between images. In cases like yours, this can get in the way. A few questions: - why are you using img_as_float at all, if your image is already float? - if img_as_float is being called by a particular function that you need, what is that function? - Does it have a `preserve_range` keyword argument? If so, try setting it to True. If it turns out that you're using a valid function for input of arbitrary ranges and still getting an error, that's a bug and we should raise an issue on github. Let us know! Juan. PS: If at all possible, you should think about switching to Python 3 for your main environment. =) On Tue, Feb 9, 2016 at 12:40 PM, Christopher wrote: > An update, the values are not 32 bit from the detector, the detector is > 16bit. But the images have been aligned by a previous program, so they are > interpolated to 32 bit precision. > > On Monday, February 8, 2016 at 8:38:14 PM UTC-5, Christopher wrote: >> >> Hi, I am having a problem trying to create an image object from an array. >> The problem is the array extends beyond -1 and 1. The pixel values are raw >> 32bit float values from a detector. >> >> >> array.dtype >> float32 >> >> >> summary(array) >> Mean: 0.00656827 >> >> Min: -6.1125 >> Median: 1.09516e-08 >> Max: 3.69815 >> >> >> >> image = skimage.img_as_float(array) >> >> >> >> File >> "/home/user/anaconda2/lib/python2.7/site-packages/skimage/util/dtype.py", >> line 291, in img_as_float >> return convert(image, np.float64, force_copy) >> File >> "/home/user/anaconda2/lib/python2.7/site-packages/skimage/util/dtype.py", >> line 195, in convert >> raise ValueError("Images of type float must be between -1 and 1.") >> ValueError: Images of type float must be between -1 and 1 >> >> >> I am using version 0.11.3 via anaconda on fedora 23 >> >> >> Sometimes I can get img_as_float to work if I use astype on the array >> first, but then it doesn't seem to change the values, and then >> skimage.io.Image() will fail with a similar error >> >> Thanks in advance for any help. >> > -- > 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. > To post to this group, send email to scikit-image at googlegroups.com. > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/d8581def-a4fd-4b4c-bcab-71abfc8fabca%40googlegroups.com > > . > > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From spagodo at gmail.com Wed Feb 10 14:15:45 2016 From: spagodo at gmail.com (Christopher) Date: Wed, 10 Feb 2016 11:15:45 -0800 (PST) Subject: ValueError: Images of type float must be between -1 and 1. In-Reply-To: References: <96935606-9924-4b1b-a29f-ffb3b0ffa176@googlegroups.com> Message-ID: <42c9f415-7482-476e-adea-a70241c46d1b@googlegroups.com> Ok thanks, exposure.rescale_intensity(data, in_range=(-1, 1)) seems to do the trick. Was -10,10 a typo? Is there any concern for loss of information when doing a rescale? -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Wed Feb 10 17:06:19 2016 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Thu, 11 Feb 2016 09:06:19 +1100 Subject: ValueError: Images of type float must be between -1 and 1. In-Reply-To: <42c9f415-7482-476e-adea-a70241c46d1b@googlegroups.com> References: <96935606-9924-4b1b-a29f-ffb3b0ffa176@googlegroups.com> <42c9f415-7482-476e-adea-a70241c46d1b@googlegroups.com> Message-ID: Um, yeah, I think you're probably clipping your data by doing `in_range=(-1, 1)`. That means that the function will consider any values under -1 as -1 and any values above 1 as 1. Probably not what you want! The input range should cover the entire range of possible values in your data. On Thu, Feb 11, 2016 at 6:15 AM, Christopher wrote: > > Ok thanks, exposure.rescale_intensity(data, in_range=(-1, 1)) seems to do > the trick. Was -10,10 a typo? Is there any concern for loss of information > when doing a rescale? > > -- > 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. > To post to this group, send email to scikit-image at googlegroups.com. > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/42c9f415-7482-476e-adea-a70241c46d1b%40googlegroups.com > > . > > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From saxenauts at gmail.com Sat Feb 13 03:16:18 2016 From: saxenauts at gmail.com (Utkarsh Saxena) Date: Sat, 13 Feb 2016 00:16:18 -0800 (PST) Subject: Participating in GSoC 2016? Project Ideas ? Message-ID: Hi, I wanted to know if scikit-image will be participating in GSoC 2016? If yes, then we(less experienced contributors) would greatly benefit if a list of project ideas is released, so that we can do our homework before application period begins. Thanks, Utkarsh -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Sat Feb 13 23:35:20 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Sat, 13 Feb 2016 20:35:20 -0800 Subject: Participating in GSoC 2016? Project Ideas ? In-Reply-To: References: Message-ID: Hi Utkarsh I do not plan to take part this year myself; perhaps some other members of the team are interested, but I haven't seen any such mentions. Regards St?fan On 13 February 2016 at 00:16, Utkarsh Saxena wrote: > Hi, > > I wanted to know if scikit-image will be participating in GSoC 2016? If yes, > then we(less experienced contributors) would greatly benefit if a list of > project ideas is released, so that we can do our homework before application > period begins. > > Thanks, > Utkarsh > > -- > 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. > To post to this group, send email to scikit-image at googlegroups.com. > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/a6181673-26a5-485f-a837-19a9d796cf04%40googlegroups.com. > For more options, visit https://groups.google.com/d/optout. From jalopcar at gmail.com Mon Feb 15 14:44:23 2016 From: jalopcar at gmail.com (Jaime Lopez Carvajal) Date: Mon, 15 Feb 2016 11:44:23 -0800 (PST) Subject: linear texture Message-ID: Hi all, I want to know if there exist some method to calculate texture using image lines from different sizes. I know that usually texture use square kernels (3x3, 5x5, etc), but I guess some years ago, I read about a method to obtain texture from lines. Any suggestion? Thanks, Jaime -------------- next part -------------- An HTML attachment was scrubbed... URL: From jalopcar at gmail.com Mon Feb 15 14:49:56 2016 From: jalopcar at gmail.com (Jaime Lopez Carvajal) Date: Mon, 15 Feb 2016 11:49:56 -0800 (PST) Subject: Boundary/outline of objects in an Image In-Reply-To: References: Message-ID: <27bba460-0078-4f87-8a0d-46572421364c@googlegroups.com> Hi, Do you check out skimage.measure?, there is a function called find_contours, that maybe is what you need. Jaime On Friday, October 23, 2015 at 3:33:38 AM UTC-4, as... at walla.co.il wrote: > > Hi, > > I try to focus on scikit-image instead of other non-open source software. > Therefore, is there an example how to boundary/outline of objects in an > Image? Something like this tutorial: > http://www.mathworks.com/help/images/boundary-tracing-in-images.html > > Thanks > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From chandragirivinay7 at gmail.com Wed Feb 17 08:31:09 2016 From: chandragirivinay7 at gmail.com (Vinay Chandragiri) Date: Wed, 17 Feb 2016 05:31:09 -0800 (PST) Subject: Gsoc 2016 - Project Ideas Message-ID: <38efbf8a-7902-4264-8946-688153a463a5@googlegroups.com> Hi All, This is Vinay. I am a senior undergrad majoring computer science from Indian Institute of Technology Guwahati and also a Computer Vision and Machine Learning enthusiast. I would like to contribute to scikit - image as a part of GSOC 2016. I faced the problem of Image Segmentation during one of my projects for neural images and I ended up using the below link, which was the best one available so far, in theory and in practice. http://fiji.sc/Morphological_Segmentation I personally think this plugin for scikit-image will be helpful to the community as most of them aren't aware of this as per my knowledge. What do you suggest ? I would like to hear your thoughts. Thanks, Vinay. -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Wed Feb 17 14:36:47 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Wed, 17 Feb 2016 11:36:47 -0800 Subject: Gsoc 2016 - Project Ideas In-Reply-To: <38efbf8a-7902-4264-8946-688153a463a5@googlegroups.com> References: <38efbf8a-7902-4264-8946-688153a463a5@googlegroups.com> Message-ID: Hi Vinay On 17 February 2016 at 05:31, Vinay Chandragiri wrote: > I personally think this plugin for scikit-image will be helpful to the > community as most of them aren't aware of this as per my knowledge. What do > you suggest ? I would like to hear your thoughts. Thank you for your interest in scikit-image. It does not look as though we will be taking part in GSoC this year, though, so you may want to look at what scipy and numpy are offering. Best regards St?fan From r.t.wilson.bak at googlemail.com Wed Feb 17 17:30:29 2016 From: r.t.wilson.bak at googlemail.com (Robin Wilson) Date: Wed, 17 Feb 2016 14:30:29 -0800 (PST) Subject: img_as_float In-Reply-To: <12E733D0-B357-4C02-8980-05218ADEBD19@demuc.de> References: <12E733D0-B357-4C02-8980-05218ADEBD19@demuc.de> Message-ID: Hi, For what it's worth, I agree with you entirely. I process satellite imagery with scikit-image, and usually want to keep the values exactly how they are (as they represent actual physical measurements in SI units) - and so converting to an arbitrary range always causes me problems. (I'm probably not representative of the typical skimage user though - so don't take my opinion too seriously!) Robin On Wednesday, 17 February 2016 21:21:12 UTC, Johannes Sch?nberger wrote: > > Hi everyone, > > There has been a little discussion in #1945 about our range conversion and > I think that we should try to avoid `img_as_float` in our functions as much > as possible, unless really necessary for the correctness of the algorithm. > In most cases, there is no reason to tinker around with the range of values > of the input image. Some examples: > > skimage.filter.gaussian_filter > skimage.transform.warp et al. > skimage.filter.sobel et al. > skimage.restoration.denoise_tv_chambolle > > What is your opinion? > > Best, Johannes -------------- next part -------------- An HTML attachment was scrubbed... URL: From kmichael.aye at gmail.com Wed Feb 17 18:36:56 2016 From: kmichael.aye at gmail.com (Michael Aye) Date: Wed, 17 Feb 2016 15:36:56 -0800 (PST) Subject: img_as_float In-Reply-To: <75C45B40-769F-4CEA-920E-811476E2E77C@demuc.de> References: <12E733D0-B357-4C02-8980-05218ADEBD19@demuc.de> <75C45B40-769F-4CEA-920E-811476E2E77C@demuc.de> Message-ID: <30071aab-6083-4943-98b8-26edff888071@googlegroups.com> I agree with Robin that changing the range of values silently (if that's still the case) is a problem for users like us where the pixel values are actually some kind of physical measures and not just a RGB value of a photograph. One quick fix would be to be 'quite loud' about it and provide user feedback when it happens. I would welcome an effort to remove this where possible. Michael On Wednesday, February 17, 2016 at 3:39:57 PM UTC-7, Johannes Sch?nberger wrote: > > Thanks for your feedback! > > > (I'm probably not representative of the typical skimage user though - so > don't take my opinion too seriously!) > > I am not sure if there is a typical skimage user... at least we don't have > a good picture of what people are using the library at this point. Maybe we > should do a survey at some point... -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Wed Feb 17 20:06:52 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Wed, 17 Feb 2016 17:06:52 -0800 Subject: img_as_float In-Reply-To: <30071aab-6083-4943-98b8-26edff888071@googlegroups.com> References: <12E733D0-B357-4C02-8980-05218ADEBD19@demuc.de> <75C45B40-769F-4CEA-920E-811476E2E77C@demuc.de> <30071aab-6083-4943-98b8-26edff888071@googlegroups.com> Message-ID: On 17 February 2016 at 15:36, Michael Aye wrote: > I agree with Robin that changing the range of values silently (if that's > still the case) is a problem for users like us where the pixel values are > actually some kind of physical measures and not just a RGB value of a > photograph. > One quick fix would be to be 'quite loud' about it and provide user feedback > when it happens. > I would welcome an effort to remove this where possible. I am not opposed to supporting range preservation, but we do have to think a bit about the implications: - what do you do when the data-type of values change? - what do you do when your operation due to, e.g., rounding issues push values outside the input range? - what do you do when you need to know the full potential range of the data? The ``preserve_range`` flag has allowed us to do whatever we do normally, unless the user gave explicit permission to change data types, ranges, etc. It also serves as a nice tag for "I, the developer, thought about this issue". St?fan From jsch at demuc.de Wed Feb 17 16:21:09 2016 From: jsch at demuc.de (=?utf-8?Q?Johannes_Sch=C3=B6nberger?=) Date: Wed, 17 Feb 2016 22:21:09 +0100 Subject: img_as_float Message-ID: <12E733D0-B357-4C02-8980-05218ADEBD19@demuc.de> Hi everyone, There has been a little discussion in #1945 about our range conversion and I think that we should try to avoid `img_as_float` in our functions as much as possible, unless really necessary for the correctness of the algorithm. In most cases, there is no reason to tinker around with the range of values of the input image. Some examples: skimage.filter.gaussian_filter skimage.transform.warp et al. skimage.filter.sobel et al. skimage.restoration.denoise_tv_chambolle What is your opinion? Best, Johannes From jsch at demuc.de Wed Feb 17 17:39:56 2016 From: jsch at demuc.de (=?utf-8?Q?Johannes_Sch=C3=B6nberger?=) Date: Wed, 17 Feb 2016 23:39:56 +0100 Subject: img_as_float In-Reply-To: References: <12E733D0-B357-4C02-8980-05218ADEBD19@demuc.de> Message-ID: <75C45B40-769F-4CEA-920E-811476E2E77C@demuc.de> Thanks for your feedback! > (I'm probably not representative of the typical skimage user though - so don't take my opinion too seriously!) I am not sure if there is a typical skimage user... at least we don't have a good picture of what people are using the library at this point. Maybe we should do a survey at some point... From godber at gmail.com Thu Feb 18 08:54:21 2016 From: godber at gmail.com (Austin Godber) Date: Thu, 18 Feb 2016 06:54:21 -0700 Subject: Simple Docstring Improvements Message-ID: Hi All, I've just submitted the following simple pull request: https://github.com/scikit-image/scikit-image/pull/1948 It's a one line change to an example in the recttool docstring. I have found a few other like this, basically forgotten imports. I suppose it's possible these are deliberately omitted for some reason since some tend to fall into the category of "I didn't bother to show the import of the module this docstring documents". The question is, would you guys like me to fix these as I find them and if so would you prefer I batch them together in pull requests? Nice work with scikit image BTW. I am going through and learning more about the image viewer. Austin -------------- next part -------------- An HTML attachment was scrubbed... URL: From kmichael.aye at gmail.com Thu Feb 18 18:00:04 2016 From: kmichael.aye at gmail.com (Michael Aye) Date: Thu, 18 Feb 2016 15:00:04 -0800 (PST) Subject: img_as_float In-Reply-To: References: <12E733D0-B357-4C02-8980-05218ADEBD19@demuc.de> <75C45B40-769F-4CEA-920E-811476E2E77C@demuc.de> <30071aab-6083-4943-98b8-26edff888071@googlegroups.com> Message-ID: <2533ca46-2701-4178-9560-28a9a6ed84b7@googlegroups.com> I am not opposed to supporting range preservation, but we do have to > think a bit about the implications: > > - what do you do when the data-type of values change? > What are the situations where they *have* to change? > - what do you do when your operation due to, e.g., rounding issues > push values outside the input range? > Return a new object instead of changing the original, maybe? > - what do you do when you need to know the full potential range of the > data? > > don't understand, do you mean the full potential range per data-type? isn't that defined by the data-type the input image has? The ``preserve_range`` flag has allowed us to do whatever we do > normally, unless the user gave explicit permission to change data > types, ranges, etc. It also serves as a nice tag for "I, the > developer, thought about this issue". > > And that's quite cool that that's offered, but the question is, I guess, which default is best and why? Which default setting would confuse the least new (and old) users? Michael -------------- next part -------------- An HTML attachment was scrubbed... URL: From silvertrumpet999 at gmail.com Thu Feb 18 19:10:07 2016 From: silvertrumpet999 at gmail.com (Josh Warner) Date: Thu, 18 Feb 2016 16:10:07 -0800 (PST) Subject: img_as_float In-Reply-To: <2533ca46-2701-4178-9560-28a9a6ed84b7@googlegroups.com> References: <12E733D0-B357-4C02-8980-05218ADEBD19@demuc.de> <75C45B40-769F-4CEA-920E-811476E2E77C@demuc.de> <30071aab-6083-4943-98b8-26edff888071@googlegroups.com> <2533ca46-2701-4178-9560-28a9a6ed84b7@googlegroups.com> Message-ID: <455ac4c1-d145-4b30-93da-217adb817538@googlegroups.com> Sometimes the input dtype needs to change, at least along the way. As just one example: - uint8 or uint16 inputs with a chain of calculations, including transformations or exposure tweaks. In this instance, all intermediate calculations should be carried out with full floating-point precision. If forced back into their originating dtype at each step, the result would have terrible compounded error. Returning to the original dtype at the end would be reasonable, but you only want to do this once. Because of our functional approach (vs. VTK's pipelining or similar), there is no way for us to know which step is the final one. So - if desired - the user needs to handle this, because from such functions we'll always return the higher precision. We always return a new object, unless the function explicitly operates on the input. When this is possible it is enabled by a standard `out=None` kwarg like in numpy/scipy. One of the biggest things the "float images are on range [0, 1]" saves us from is worrying about aliasing. At all. We just do calculations, it doesn't matter if the input image gets squared a few times along the way. Try to do a few simple numpy operations on a uint8 array and see how fast the results aren't what you expect. Now, we can relax this and still be mostly OK because float64 is big. But concerns like this are a huge potential maintenance headache. I think what Stefan means by "full potential range" is that you have to plan calculations in advance, examining every intermediate step for its maximum potential range, against your dtype. Certain exposure calculations are explicitly defined with normalized images on the range [0, 1], because they heavily use exponential functions. An input with a greater range must be handled carefully by any such function. This is the greatest danger in simply removing the normalization step from the package, IMO. A lot of things will break, and depending on the algorithm the fix may vary. Perhaps that helps pull back the curtain a little... Josh On Thursday, February 18, 2016 at 4:00:04 PM UTC-7, Michael Aye wrote: > > I am not opposed to supporting range preservation, but we do have to > >> think a bit about the implications: >> >> - what do you do when the data-type of values change? >> > > What are the situations where they *have* to change? > > >> - what do you do when your operation due to, e.g., rounding issues >> push values outside the input range? >> > > Return a new object instead of changing the original, maybe? > > >> - what do you do when you need to know the full potential range of the >> data? >> >> don't understand, do you mean the full potential range per data-type? > isn't that defined by the data-type the input image has? > > The ``preserve_range`` flag has allowed us to do whatever we do >> normally, unless the user gave explicit permission to change data >> types, ranges, etc. It also serves as a nice tag for "I, the >> developer, thought about this issue". >> >> And that's quite cool that that's offered, but the question is, I guess, > which default is best and why? > Which default setting would confuse the least new (and old) users? > > Michael > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nelle.varoquaux at gmail.com Mon Feb 22 04:15:51 2016 From: nelle.varoquaux at gmail.com (Nelle Varoquaux) Date: Mon, 22 Feb 2016 10:15:51 +0100 Subject: Scipy2016: call for proposals Message-ID: Dear all, SciPy 2016, the Fifteenth Annual Conference on Python in Science, takes place in Austin, TX on July, 11th to 17th. The conference features two days of tutorials by followed by three days of presentations, and concludes with two days of developer sprints on projects of interest to attendees. . The topics presented at SciPy are very diverse, with a focus on advanced software engineering and original uses of Python and its scientific libraries, either in theoretical or experimental research, from both academia and the industry. This year we are happy to announce two specialized tracks that run in parallel to the general conference (Data Science , High Performance Computing) and 8 mini-symposia (Earth and Space Science, Biology and Medicine, Engineering, Social Sciences, Special Purpose Databases, Case Studies in Industry, Education, Reproducibility) Submissions for talks and posters are welcome on our website ( http://scipy2016.scipy.org). In your abstract, please provide details on what Python tools are being employed, and how. The talk and poster submission deadline is March 25th, 2016, while the tutorial submission deadline is March, 21st, 2016. Important dates: Mar 21: Tutorial Proposals Due Mar 25: Talk and Poster Proposals Due May 11: Plotting Contest Submissions Due Apr 22: Tutorials Announced Apr 22: Financial Aid Submissions Due May 4: Talk and Posters Announced May 11: Financial Aid Recipients Notified May 22: Early Bird Registration Deadline Jul 11-12: SciPy 2016 Tutorials Jul 13-15: SciPy 2016 General Conference Jul 16-17: SciPy 2016 Sprints We look forward to an exciting conference and hope to see you in Austin in July! The Scipy 2016 http://scipy2016.scipy.org/ Conference Chairs: Aric Hagberg, Prabhu Ramachandran Tutorial Chairs: Justin Vincent, Ben Root Program Chair: Serge Rey, Nelle Varoquaux Proceeding Chairs: Sebastian Benthall -------------- next part -------------- An HTML attachment was scrubbed... URL: From pdyban at gmail.com Mon Feb 22 16:43:09 2016 From: pdyban at gmail.com (Pavlo Dyban) Date: Mon, 22 Feb 2016 13:43:09 -0800 (PST) Subject: Livewire segmentation in scikit-image Message-ID: <53412d16-841c-4269-a1c7-b7a80d099ecd@googlegroups.com> Hello! I am a great fan of scikit-learn and have used it in a number of various projects so far. This time, I want to contribute to the project. I have implemented Livewire segmentation algorithm for image segmentation and would like to bring it into the main package. My code is hosted on github, it is documented with sphinx and tested. Livewire segmentation technique deduces object boundaries in the image by converting the image to a weighted graph where edges' weights are computed from the gradient image. The shortest path algorithm minimises the total cost function, thus avoiding steep gradients (i.e. object boundaries in the original image). An example of how the algorithm works you will find in my repository: https://github.com/pdyban/livewire. The API is straightforward: from livewire import LiveWireSegmentationalgorithm = LiveWireSegmentation(image)path = algorithm.compute_shortest_path((0, 0), (10, 25)) Do you think this algorithm would be needed inside scikit-image? If yes, would that belong inside segmentation module? Could someone assist me in my first open source contribution? It would be great if I could contribute to your project! Thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Mon Feb 22 21:56:08 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Mon, 22 Feb 2016 18:56:08 -0800 Subject: Livewire segmentation in scikit-image In-Reply-To: <53412d16-841c-4269-a1c7-b7a80d099ecd@googlegroups.com> References: <53412d16-841c-4269-a1c7-b7a80d099ecd@googlegroups.com> Message-ID: Hi Pavlo On 22 February 2016 at 13:43, Pavlo Dyban wrote: > Hello! I am a great fan of scikit-learn and have used it in a number of > various projects so far. This time, I want to contribute to the project. I > have implemented Livewire segmentation algorithm for image segmentation and > would like to bring it into the main package. My code is hosted on github, > it is documented with sphinx and tested. Thanks for your interest in contributing to scikit-image! > Livewire segmentation technique deduces object boundaries in the image by > converting the image to a weighted graph where edges' weights are computed > from the gradient image. The shortest path algorithm minimises the total > cost function, thus avoiding steep gradients (i.e. object boundaries in the > original image). An example of how the algorithm works you will find in my > repository: https://github.com/pdyban/livewire. I've only heard of livewire in terms of interactive work. Is it commonly used as a stand-alone technique? > Do you think this algorithm would be needed inside scikit-image? If yes, > would that belong inside segmentation module? Could someone assist me in my > first open source contribution? It would be great if I could contribute to > your project! Thanks! It may well be--I will rely on our segmentation specialists Emmanuelle and Juan to take a look. Do you perhaps have a citation for this method? We're happy to help you get pull requests off the ground. In the mean time, take a look at: http://scikit-image.org/docs/stable/contribute.html Thanks! St?fan From jalopcar at gmail.com Tue Feb 23 09:33:33 2016 From: jalopcar at gmail.com (Jaime Lopez Carvajal) Date: Tue, 23 Feb 2016 06:33:33 -0800 (PST) Subject: profile_line function Message-ID: Hi, I would like to know why the function profile_line from profile.py in module skimage.measure, always return an additional value (zero value) at the end for horizontal and vertical lines, and two extra values (2 zeros) for diagonal lines. I mean, if I have an image 10x10, and I want the profile line > a = profile_line(img, (0, 0), (0, 10)) > array([ 83., 82., 81., 88., 95., 88., 93., 107., 121., 146., * 0.*]) and with diagonal lines it returns two additional values (2 zeros), like this: > a = profile_line(img, (0, 0), (10, 10)) > array([ 83., 92., 105., 123., 100., 69., 46., 46., 48., 52., 62., 70., 77., 84., *0., 0.*]) Thanks in advance for your comments, Jaime -------------- next part -------------- An HTML attachment was scrubbed... URL: From pdyban at gmail.com Tue Feb 23 12:38:30 2016 From: pdyban at gmail.com (Pavlo Dyban) Date: Tue, 23 Feb 2016 09:38:30 -0800 (PST) Subject: Livewire segmentation in scikit-image In-Reply-To: References: <53412d16-841c-4269-a1c7-b7a80d099ecd@googlegroups.com> Message-ID: <2d25b2a6-4b6a-44c3-bb2e-3b5dcea48d16@googlegroups.com> Hello St?fan! You are right. Livewire segmentation approach is often used for interactive segmentation when the contour is updated and displayed while user is moving the mouse. However, the approach itself is not limited to interactive segmentations, but can just as well be used as a semi-automatic segmentation approach. This is the functionality that the iPython ntebook in my repository on Github demonstrates (https://github.com/pdyban/livewire/blob/master/notebooks/Livewire.ipynb). Even though scikit-image is majorilly used as a static tool (wihtout on-the-fly user interaction), it can nonetheless be used in the latter case. In both cases I imagine that Liewire segmentation would enrich the segmentation arsenal in scikit-image. The algorithm is simple and follows along this article: https://en.wikipedia.org/wiki/Livewire_Segmentation_Technique. An enhanced search for the shortest path has been implemented based on a thread here: http://code.activestate.com/recipes/119466-dijkstras-algorithm-for-shortest-paths/, see comment 1. Please let me know if you have any concerns. Thanks! On Tuesday, 23 February 2016 03:56:30 UTC+1, stefanv wrote: > > Hi Pavlo > > On 22 February 2016 at 13:43, Pavlo Dyban > > wrote: > > Hello! I am a great fan of scikit-learn and have used it in a number of > > various projects so far. This time, I want to contribute to the project. > I > > have implemented Livewire segmentation algorithm for image segmentation > and > > would like to bring it into the main package. My code is hosted on > github, > > it is documented with sphinx and tested. > > Thanks for your interest in contributing to scikit-image! > > > Livewire segmentation technique deduces object boundaries in the image > by > > converting the image to a weighted graph where edges' weights are > computed > > from the gradient image. The shortest path algorithm minimises the total > > cost function, thus avoiding steep gradients (i.e. object boundaries in > the > > original image). An example of how the algorithm works you will find in > my > > repository: https://github.com/pdyban/livewire. > > I've only heard of livewire in terms of interactive work. Is it > commonly used as a stand-alone technique? > > > Do you think this algorithm would be needed inside scikit-image? If yes, > > would that belong inside segmentation module? Could someone assist me in > my > > first open source contribution? It would be great if I could contribute > to > > your project! Thanks! > > It may well be--I will rely on our segmentation specialists Emmanuelle > and Juan to take a look. Do you perhaps have a citation for this > method? > > We're happy to help you get pull requests off the ground. In the mean > time, take a look at: > > http://scikit-image.org/docs/stable/contribute.html > > Thanks! > St?fan > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Tue Feb 23 12:40:56 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Tue, 23 Feb 2016 09:40:56 -0800 Subject: 0.12 release In-Reply-To: <20160223153821.GB1829563@phare.normalesup.org> References: <-6724546148968632515@unknownmsgid> <5c343a1e-8ec0-4136-b2d1-7d1202c4ce69@googlegroups.com> <20160201185705.GA3207967@phare.normalesup.org> <6F56AC09-BA2B-43F5-A910-37740BEBEC64@demuc.de> <20160203075920.GA2389752@phare.normalesup.org> <20160203172104.GA2977973@phare.normalesup.org> <20160207153232.GA2920916@phare.normalesup.org> <20160223153821.GB1829563@phare.normalesup.org> Message-ID: Hi Emma On 23 February 2016 at 07:38, Emmanuelle Gouillart wrote: > TODO.txt is now empty as far as 0.12 is concerned, release notes are > ready, shall we tag now? St?fan, no regrets about #1937 or #1905? Thanks for your hard work in moving the release forward! #1937 highlights a bug in our tests (and failing tests, that aren't currently showing up), so I would consider that the last blocker. I'll try to get around to #1905, but if I don't that's also OK. > - Update the version number in ``skimage/__init__.py`` and ``bento.info`` > and commit All of this can be done on a 0.12.x branch. > - Edit ``doc/source/_static/docversions.js`` and commit This change needs to be done on / merged onto master. > - Add the version number as a tag in git:: > > git tag -s v0.X.0 This again can happen on the 0.12.x branch. > St?fan, if I tag, can you publish on PyPi? I'd be happy to! Thanks! St?fan From jalopcar at gmail.com Tue Feb 23 18:40:25 2016 From: jalopcar at gmail.com (Jaime Lopez Carvajal) Date: Tue, 23 Feb 2016 15:40:25 -0800 (PST) Subject: profile_line function In-Reply-To: References: Message-ID: <29d306ff-5856-4acf-a1e9-5decb71f8e76@googlegroups.com> Hi Juan, I see your point, I read about the difference with Numpy indexing, but I did understand at that time. Your explanation is very clear, as well your suggestion about to use the shorter range. Thanks for your time. Jaime On Tuesday, February 23, 2016 at 6:15:31 PM UTC-5, Juan Nunez-Iglesias wrote: > > Hi Jaime, > > It's a bit confusing, but, because profile_line is used in interactive > tools, *the final point is included in the line*, unlike normal > Python/NumPy indexing. It would be unintuitive in interactive tools *not* > to include the final point. (This is in the "Notes" section in the > docstring.) So, your final point, (0, 10), is actually outside your image, > and the constant value of 0 is returned. I suspect that for your use case > you want to call profile_line(img, (0, 0), (0, 9)) and profile_line(img, > (0, 0), (9, 9)). I think it should work as expected in those cases. > > I hope that helps! > > Juan. > > On Wed, Feb 24, 2016 at 1:33 AM, Jaime Lopez Carvajal > wrote: > >> Hi, >> >> I would like to know why the function profile_line from profile.py in >> module skimage.measure, always return an additional value (zero value) at >> the end for horizontal and vertical lines, and two extra values (2 zeros) >> for diagonal lines. >> I mean, if I have an image 10x10, and I want the profile line >> >> > a = profile_line(img, (0, 0), (0, 10)) >> > array([ 83., 82., 81., 88., 95., 88., 93., 107., 121., >> 146., * 0.*]) >> >> and with diagonal lines it returns two additional values (2 zeros), like >> this: >> >> > a = profile_line(img, (0, 0), (10, 10)) >> > array([ 83., 92., 105., 123., 100., 69., 46., 46., 48., >> 52., 62., 70., 77., 84., *0., 0.*]) >> >> Thanks in advance for your comments, >> >> Jaime >> >> -- >> 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 . >> To post to this group, send email to scikit... at googlegroups.com >> . >> To view this discussion on the web, visit >> https://groups.google.com/d/msgid/scikit-image/d4e6af4a-b4de-49b1-9e57-6391e17dcb9b%40googlegroups.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 Tue Feb 23 10:38:21 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Tue, 23 Feb 2016 16:38:21 +0100 Subject: 0.12 release In-Reply-To: <20160207153232.GA2920916@phare.normalesup.org> References: <-6724546148968632515@unknownmsgid> <5c343a1e-8ec0-4136-b2d1-7d1202c4ce69@googlegroups.com> <20160201185705.GA3207967@phare.normalesup.org> <6F56AC09-BA2B-43F5-A910-37740BEBEC64@demuc.de> <20160203075920.GA2389752@phare.normalesup.org> <20160203172104.GA2977973@phare.normalesup.org> <20160207153232.GA2920916@phare.normalesup.org> Message-ID: <20160223153821.GB1829563@phare.normalesup.org> Dear all, TODO.txt is now empty as far as 0.12 is concerned, release notes are ready, shall we tag now? St??fan, no regrets about #1937 or #1905? I'm not used to "pushing origin master" (instead of pull requests), so I prefer asking before: are instructions such as - Update the version number in ``skimage/__init__.py`` and ``bento.info`` and commit - Edit ``doc/source/_static/docversions.js`` and commit - Add the version number as a tag in git:: git tag -s v0.X.0 git push --tags origin master etc... meant to be done in master and pushed directly to origin? St??fan, if I tag, can you publish on PyPi? Cheers, Emma > On Wed, Feb 03, 2016 at 10:29:58AM -0800, St??fan van der Walt wrote: > > On 3 February 2016 at 09:21, Emmanuelle Gouillart > > wrote: > > > Thanks for preventing us from being carried away by the excitement of the > > > release :-D > > Let me not stand in the way! I have three months' worth of happiness > > pent up for the moment that tag gets applied. > > Onward :) > > St??fan From jni.soma at gmail.com Tue Feb 23 18:15:11 2016 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Wed, 24 Feb 2016 10:15:11 +1100 Subject: profile_line function In-Reply-To: References: Message-ID: Hi Jaime, It's a bit confusing, but, because profile_line is used in interactive tools, *the final point is included in the line*, unlike normal Python/NumPy indexing. It would be unintuitive in interactive tools *not* to include the final point. (This is in the "Notes" section in the docstring.) So, your final point, (0, 10), is actually outside your image, and the constant value of 0 is returned. I suspect that for your use case you want to call profile_line(img, (0, 0), (0, 9)) and profile_line(img, (0, 0), (9, 9)). I think it should work as expected in those cases. I hope that helps! Juan. On Wed, Feb 24, 2016 at 1:33 AM, Jaime Lopez Carvajal wrote: > Hi, > > I would like to know why the function profile_line from profile.py in > module skimage.measure, always return an additional value (zero value) at > the end for horizontal and vertical lines, and two extra values (2 zeros) > for diagonal lines. > I mean, if I have an image 10x10, and I want the profile line > > > a = profile_line(img, (0, 0), (0, 10)) > > array([ 83., 82., 81., 88., 95., 88., 93., 107., 121., > 146., * 0.*]) > > and with diagonal lines it returns two additional values (2 zeros), like > this: > > > a = profile_line(img, (0, 0), (10, 10)) > > array([ 83., 92., 105., 123., 100., 69., 46., 46., 48., > 52., 62., 70., 77., 84., *0., 0.*]) > > Thanks in advance for your comments, > > Jaime > > -- > 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. > To post to this group, send email to scikit-image at googlegroups.com. > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/d4e6af4a-b4de-49b1-9e57-6391e17dcb9b%40googlegroups.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 Wed Feb 24 16:57:44 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Wed, 24 Feb 2016 22:57:44 +0100 Subject: 0.12 release In-Reply-To: References: <20160201185705.GA3207967@phare.normalesup.org> <6F56AC09-BA2B-43F5-A910-37740BEBEC64@demuc.de> <20160203075920.GA2389752@phare.normalesup.org> <20160203172104.GA2977973@phare.normalesup.org> <20160207153232.GA2920916@phare.normalesup.org> <20160223153821.GB1829563@phare.normalesup.org> Message-ID: <20160224215744.GA1087205@phare.normalesup.org> Hi St??fan, > #1937 highlights a bug in our tests (and failing tests, that aren't > currently showing up), so I would consider that the last blocker. > I'll try to get around to #1905, but if I don't that's also OK. OK ! For #1937, I think the bug highlighted by test_orb.test_keypoints_orb_desired_no_of_keypoints should be fixed before the PR can be merged. Otherwise we'll have Travis failing all the time, for all new PRs. Am I wrong? And many thanks for all the explanations! Cheers, Emma From himanshu2014iit at gmail.com Thu Feb 25 11:30:07 2016 From: himanshu2014iit at gmail.com (Himanshu Mishra) Date: Thu, 25 Feb 2016 08:30:07 -0800 (PST) Subject: Extracting data from an image of plots Message-ID: <23c90105-72ea-4e68-abd2-2e567edf5358@googlegroups.com> Hello everyone, We have a pdf page which contains one or more figures which are two-dimensional plots of experimental results. The figures may or may not be embedded in text. Each plot has the x and y axis with their labels and unit measurements marked in the plot. Inside each figure are one or more plots, each with a different color. How can we convert the plot into a table of corresponding x and y values (say for 100 points) ? Looking forward to a solution, Thank you, Himanshu Mishra -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Thu Feb 25 14:29:12 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Thu, 25 Feb 2016 11:29:12 -0800 Subject: Undergraduate team Message-ID: Hi, everyone Thanks to Berkeley's Undergraduate Research Assistants Program (URAP), you may be seeing a few new faces active on GitHub. Some of the URAP team members are new to open source development, so I'd like to thank you in advance for your patience and time in giving them a helping hand. The URAP team members are: Seth Park Emily Pedersen Jenny Dai Ben Gee Shaun Singh Anand Kuchibotla Thanks! St?fan From fboulogne at sciunto.org Thu Feb 25 11:35:36 2016 From: fboulogne at sciunto.org (=?UTF-8?Q?Fran=c3=a7ois_Boulogne?=) Date: Thu, 25 Feb 2016 11:35:36 -0500 Subject: Extracting data from an image of plots In-Reply-To: <23c90105-72ea-4e68-abd2-2e567edf5358@googlegroups.com> References: <23c90105-72ea-4e68-abd2-2e567edf5358@googlegroups.com> Message-ID: <56CF2D58.40104@sciunto.org> > How can we convert the plot into a table of corresponding x and y > values (say for 100 points) ? > http://arohatgi.info/WebPlotDigitizer/ It's released under GPLv3. There is an instance hosted by the dev. Best, -- Fran?ois Boulogne. http://www.sciunto.org GPG: 32D5F22F From stefanv at berkeley.edu Thu Feb 25 14:38:52 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Thu, 25 Feb 2016 11:38:52 -0800 Subject: 0.12 release In-Reply-To: <20160224215744.GA1087205@phare.normalesup.org> References: <20160201185705.GA3207967@phare.normalesup.org> <6F56AC09-BA2B-43F5-A910-37740BEBEC64@demuc.de> <20160203075920.GA2389752@phare.normalesup.org> <20160203172104.GA2977973@phare.normalesup.org> <20160207153232.GA2920916@phare.normalesup.org> <20160223153821.GB1829563@phare.normalesup.org> <20160224215744.GA1087205@phare.normalesup.org> Message-ID: On 24 February 2016 at 13:57, Emmanuelle Gouillart wrote: > OK ! For #1937, I think the bug highlighted by > test_orb.test_keypoints_orb_desired_no_of_keypoints should be fixed > before the PR can be merged. Otherwise we'll have Travis failing all the > time, for all new PRs. Am I wrong? That's correct, yes! St?fan From pradyumnanpk at gmail.com Thu Feb 25 15:14:24 2016 From: pradyumnanpk at gmail.com (Pradyumna Kumar N) Date: Thu, 25 Feb 2016 12:14:24 -0800 (PST) Subject: New Contributor - Want to work on #1875 - Walker fails if a seed is surrounded by masked pixels In-Reply-To: References: <9a4820a9-87d1-4bde-a05a-49b8d2579e36@googlegroups.com> Message-ID: <87a32cae-f9e0-47ad-9586-5e50665a16e6@googlegroups.com> Hi St?fan, If you have some bandwidth, can you mentor me so that I can start contributing to scikit-image. On Friday, 22 January 2016 12:43:19 UTC-7, stefanv wrote: > > Hi Pradyumna > > On Fri, Jan 22, 2016 at 11:39 AM, Pradyumna Kumar N > > wrote: > > I am Pradyumna, pursuing my PhD at Colorado State University in the > field of > > Computer Vision. I would like to contribute to scikit-image project. I > > already forked the project and I would like to work on #1875. I am in > the > > process of reading the random walk paper. In the mean time, any pointers > or > > help on #1875 would be appreciated. > > > > In the long run I would like to implement DTW routine if it is not > already > > implemented. > > Welcome, and thanks for working on these issues! At the moment we're > in release mode, but if all goes well that should be done soon and > have a bit more bandwidth to spend on mentoring. > > Regards > St?fan > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Thu Feb 25 15:40:51 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Thu, 25 Feb 2016 12:40:51 -0800 Subject: New Contributor - Want to work on #1875 - Walker fails if a seed is surrounded by masked pixels In-Reply-To: <87a32cae-f9e0-47ad-9586-5e50665a16e6@googlegroups.com> References: <9a4820a9-87d1-4bde-a05a-49b8d2579e36@googlegroups.com> <87a32cae-f9e0-47ad-9586-5e50665a16e6@googlegroups.com> Message-ID: On 25 February 2016 at 12:14, Pradyumna Kumar N wrote: > If you have some bandwidth, can you mentor me so that I can start > contributing to scikit-image. Certainly. Go ahead and read: http://scikit-image.org/docs/stable/contribute.html When you make your first pull request, the team will happily give you feedback. Thanks! St?fan From stefanv at berkeley.edu Thu Feb 25 16:04:55 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Thu, 25 Feb 2016 13:04:55 -0800 Subject: Livewire segmentation in scikit-image In-Reply-To: <2d25b2a6-4b6a-44c3-bb2e-3b5dcea48d16@googlegroups.com> References: <53412d16-841c-4269-a1c7-b7a80d099ecd@googlegroups.com> <2d25b2a6-4b6a-44c3-bb2e-3b5dcea48d16@googlegroups.com> Message-ID: Hi Pavlo On 23 February 2016 at 09:38, Pavlo Dyban wrote: > You are right. Livewire segmentation approach is often used for interactive > segmentation when the contour is updated and displayed while user is moving > the mouse. However, the approach itself is not limited to interactive > segmentations, but can just as well be used as a semi-automatic segmentation > approach. This is the functionality that the iPython ntebook in my > repository on Github demonstrates > (https://github.com/pdyban/livewire/blob/master/notebooks/Livewire.ipynb). I've managed to get your notebook running under Python 3, but I don't know how to use the Matplotlib popup GUI--can you explain? Clicking around yields no results. > The algorithm is simple and follows along this article: > https://en.wikipedia.org/wiki/Livewire_Segmentation_Technique. An enhanced > search for the shortest path has been implemented based on a thread here: > http://code.activestate.com/recipes/119466-dijkstras-algorithm-for-shortest-paths/, > see comment 1. Could you use the shortest path implementation already implemented in scikit-image? St?fan From pradyumnanpk at gmail.com Fri Feb 26 16:08:01 2016 From: pradyumnanpk at gmail.com (Pradyumna Kumar N) Date: Fri, 26 Feb 2016 13:08:01 -0800 (PST) Subject: HOG enhancement to accept color images #1963 Message-ID: Hi all, I implemented the HOG for color images based on the excerpt from the original paper "For colour images, we calculate separate gradients for each colour channel, and take the one with the largest norm as the pixel?s gradient vector"[Dalal and Triggs] and the CVPR presentation "For color image, pick the color channel with the highest gradient magnitude for each pixel"[Dalal and Triggs]. To allow this change, I refactored the code so that image gradients are computed in a separate method. If the image has more than 1 channels, this method is called on each channel. Gradient magnitude is calculated for each channel and for each pixel, the gradient vector with maximum magnitude is considered. This is my first open source contribution and I implemented the change based on my understanding. I pushed my changes to Github. Please review my code and let me know if I implemented the functionality correctly. Please comment on coding style too. -------------- next part -------------- An HTML attachment was scrubbed... URL: From silvertrumpet999 at gmail.com Fri Feb 26 18:15:05 2016 From: silvertrumpet999 at gmail.com (Josh Warner) Date: Fri, 26 Feb 2016 15:15:05 -0800 (PST) Subject: Extracting data from an image of plots In-Reply-To: References: <23c90105-72ea-4e68-abd2-2e567edf5358@googlegroups.com> <56CF2D58.40104@sciunto.org> Message-ID: You may want to look into the work of Matt Terry (@mrterry) from SciPy 2013 and earlier. There are a number of tools he created, using what may now be outdated matplotlib interfaces but which could save you time. One of which is yoink (https://github.com/mrterry/yoink), which is particularly good with rastered data behind a color map. Using tools like Inkscape and/or the GIMP you should be able to crop any arbitrary figure out of a scanned paper/image and transform it so it's at least relatively rectilinear. Save that out as an image and these tools start to be useful - though there may be some customization left to go depending on what type of figure you're digitizing. Matt gave a lightning talk at SciPy 2013 about yoink: https://youtu.be/ywHqIEv3xXg?t=1890 Josh On Friday, February 26, 2016 at 9:12:07 AM UTC-7, Himanshu Mishra wrote: > > WebPlotDigitizer works very well for an image with single plot. But when I > try it with a research paper with text on it and more than one plot, it > works miserably. I don't know if such tool is available online, but I would > love to hear suggestions on how to make one. > > Thank you, > Himanshu Mishra > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Fri Feb 26 19:00:05 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Fri, 26 Feb 2016 16:00:05 -0800 Subject: Extracting data from an image of plots In-Reply-To: References: <23c90105-72ea-4e68-abd2-2e567edf5358@googlegroups.com> <56CF2D58.40104@sciunto.org> Message-ID: On 26 February 2016 at 15:15, Josh Warner wrote: > Using tools like Inkscape and/or the GIMP you should be able to crop any > arbitrary figure out of a scanned paper/image and transform it so it's at > least relatively rectilinear. Save that out as an image and these tools > start to be useful - though there may be some customization left to go > depending on what type of figure you're digitizing. > If you have a PDF that wasn't scanned (i.e., straight out of LaTeX), you can export the figures directly. St?fan -------------- next part -------------- An HTML attachment was scrubbed... URL: From himanshu2014iit at gmail.com Fri Feb 26 11:11:26 2016 From: himanshu2014iit at gmail.com (Himanshu Mishra) Date: Fri, 26 Feb 2016 21:41:26 +0530 Subject: Extracting data from an image of plots In-Reply-To: <56CF2D58.40104@sciunto.org> References: <23c90105-72ea-4e68-abd2-2e567edf5358@googlegroups.com> <56CF2D58.40104@sciunto.org> Message-ID: WebPlotDigitizer works very well for an image with single plot. But when I try it with a research paper with text on it and more than one plot, it works miserably. I don't know if such tool is available online, but I would love to hear suggestions on how to make one. Thank you, Himanshu Mishra -------------- next part -------------- An HTML attachment was scrubbed... URL: From rylanlzc at gmail.com Sun Feb 28 23:34:52 2016 From: rylanlzc at gmail.com (Zichao Li) Date: Sun, 28 Feb 2016 20:34:52 -0800 (PST) Subject: Feature extraction for 3D model Message-ID: <30db04dd-0c2e-45df-a69f-16eb49bdee50@googlegroups.com> I have about 1Gb 3d models contained in .obj file and now I'd like to do some feature extraction: color, texture, shape etc. I wonder how can i do it with scikit-image? I can't find relative explanation in documents. Thanks a lot! -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Sun Feb 28 23:50:40 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Sun, 28 Feb 2016 20:50:40 -0800 Subject: Feature extraction for 3D model In-Reply-To: <30db04dd-0c2e-45df-a69f-16eb49bdee50@googlegroups.com> References: <30db04dd-0c2e-45df-a69f-16eb49bdee50@googlegroups.com> Message-ID: Hi, Zichao In what format is your obj file? The ones I've dealt with in the past didn't store color or texture! St?fan On 28 February 2016 at 20:34, Zichao Li wrote: > I have about 1Gb 3d models contained in .obj file and now I'd like to do > some feature extraction: color, texture, shape etc. I wonder how can i do it > with scikit-image? I can't find relative explanation in documents. Thanks a > lot! > > -- > 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. > To post to this group, send email to scikit-image at googlegroups.com. > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/30db04dd-0c2e-45df-a69f-16eb49bdee50%40googlegroups.com. > For more options, visit https://groups.google.com/d/optout. From rylanlzc at gmail.com Mon Feb 29 03:30:54 2016 From: rylanlzc at gmail.com (Zichao Li) Date: Mon, 29 Feb 2016 00:30:54 -0800 (PST) Subject: Feature extraction for 3D model In-Reply-To: <30db04dd-0c2e-45df-a69f-16eb49bdee50@googlegroups.com> References: <30db04dd-0c2e-45df-a69f-16eb49bdee50@googlegroups.com> Message-ID: <45772dd8-3a9e-40ae-934e-eb6a2021cf8d@googlegroups.com> Dear Stefanv, Here is one of my .obj files. Please take a look. Best, Zichao ? 2016?2?29???? UTC+8??12:34:52?Zichao Li??? > > I have about 1Gb 3d models contained in .obj file and now I'd like to do > some feature extraction: color, texture, shape etc. I wonder how can i do > it with scikit-image? I can't find relative explanation in documents. > Thanks a lot! > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 4_13.obj.zip Type: application/zip Size: 3406004 bytes Desc: not available URL: