From steven.silvester at gmail.com Fri Jan 4 16:02:05 2013 From: steven.silvester at gmail.com (Steven Silvester) Date: Fri, 4 Jan 2013 13:02:05 -0800 (PST) Subject: [OT] markdown in email (and Google Groups) Message-ID: <6a4dd15a-f67a-4453-892b-dade3eb5e777@googlegroups.com> Came across this awesome tool today, and since we're all using markdown for GitHub anyways... https://github.com/adam-p/markdown-here This allows you to write markdown in an e-mail or in Google Groups: import skimage print skimage.__version__ -------------- next part -------------- An HTML attachment was scrubbed... URL: From steven.silvester at gmail.com Fri Jan 4 16:34:38 2013 From: steven.silvester at gmail.com (Steven Silvester) Date: Fri, 4 Jan 2013 13:34:38 -0800 (PST) Subject: [OT] markdown in email (and Google Groups) In-Reply-To: <6a4dd15a-f67a-4453-892b-dade3eb5e777@googlegroups.com> References: <6a4dd15a-f67a-4453-892b-dade3eb5e777@googlegroups.com> Message-ID: <03fbf1e8-6875-4a72-b6fa-5ad1aa337373@googlegroups.com> There is a specific syntax for the browser plugin documented here: https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet On Friday, January 4, 2013 3:02:05 PM UTC-6, Steven Silvester wrote: > > Came across this awesome tool today, and since we're all using markdown > for GitHub anyways... > > https://github.com/adam-p/markdown-here > > This allows you to write markdown in an e-mail or in Google Groups: > > import skimage > print skimage.__version__ > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan at sun.ac.za Fri Jan 4 18:11:21 2013 From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=) Date: Fri, 4 Jan 2013 16:11:21 -0700 Subject: [OT] markdown in email (and Google Groups) In-Reply-To: <6a4dd15a-f67a-4453-892b-dade3eb5e777@googlegroups.com> References: <6a4dd15a-f67a-4453-892b-dade3eb5e777@googlegroups.com> Message-ID: That's really cute! def foo(x): return x + 1 On Fri, Jan 4, 2013 at 2:02 PM, Steven Silvester wrote: > Came across this awesome tool today, and since we're all using markdown > for GitHub anyways... > > https://github.com/adam-p/**markdown-here > > This allows you to write markdown in an e-mail or in Google Groups: > > import skimage > print skimage.__version__ > > -- > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From francois.boulogne at gmail.com Sat Jan 5 16:08:57 2013 From: francois.boulogne at gmail.com (=?UTF-8?Q?Fran=C3=A7ois?=) Date: Sat, 5 Jan 2013 13:08:57 -0800 (PST) Subject: skimage and opencv In-Reply-To: <20121229153649.GA17203@phare.normalesup.org> References: <1c1eacb6-349a-40c8-9058-faae9084e436@googlegroups.com> <20121229153649.GA17203@phare.normalesup.org> Message-ID: <32b67255-3d85-4417-835e-ecc81184a837@googlegroups.com> Le samedi 29 d?cembre 2012 16:36:49 UTC+1, Emmanuelle Gouillart a ?crit : > > > On the skimage home page, there is a 'Related project' box. Don't you > > think that it would be interesting to add these explanations on a > > dedicated page? Even the overview (see > > http://scikit-image.org/docs/dev/overview.html) is very light on the > > topic. > > We welcome pull requests :-D > :) Added in my contrib. todo list. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Mon Jan 7 00:35:14 2013 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Mon, 7 Jan 2013 06:35:14 +0100 Subject: "No definition found" In-Reply-To: References: Message-ID: On Sun, Dec 23, 2012 at 1:39 PM, St?fan van der Walt wrote: > On Thu, Nov 29, 2012 at 6:43 PM, Juan Nunez-Iglesias > wrote: > > I'm getting this message when trying to find the definition header for > > skimage.segmentation.slic: > > > > In [12]: %pdef segmentation.slic > > No definition header found for segmentation.slic > > > > In [15]: %pdef segmentation.join_segmentations > > segmentation.join_segmentations(s1, s2) > > > > Anyone know why this is? Is this a general feature of Cython functions? > > Not sure--but this also shows that IPython does not handle unicode > characters in a docstring correctly! Huh? Are you jumping to conclusions or did you test this? -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Mon Jan 7 00:41:29 2013 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Mon, 7 Jan 2013 06:41:29 +0100 Subject: [OT] markdown in e-mails In-Reply-To: <4bdf9f1c-b02e-489d-bd16-1f67dbecb731@googlegroups.com> References: <3c30be2e-578b-4274-99c9-0651bb3edcd9@googlegroups.com> <4bdf9f1c-b02e-489d-bd16-1f67dbecb731@googlegroups.com> Message-ID: A-mazing! Thanks! On Fri, Jan 4, 2013 at 9:59 PM, Steven Silvester wrote: > Lets try it... > > print 'test' > > > > On Friday, January 4, 2013 2:53:22 PM UTC-6, Steven Silvester wrote: > >> Came across this awesome tool today, and since we're all using markdown >> for GitHub anyways... >> >> https://github.com/adam-p/**markdown-here >> >> This allows you to write markdown in an e-mail and then render into a >> nicely formatted e-mail >> >> Including things like equations. >> >> Now if only it would work in Google Groups... >> > -- > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan at sun.ac.za Mon Jan 7 10:14:01 2013 From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=) Date: Mon, 7 Jan 2013 08:14:01 -0700 Subject: "No definition found" In-Reply-To: References: Message-ID: On Sun, Jan 6, 2013 at 10:35 PM, Juan Nunez-Iglesias wrote: >> Not sure--but this also shows that IPython does not handle unicode >> characters in a docstring correctly! > > Huh? Are you jumping to conclusions or did you test this? I patched the Cython docstring to remove all unicode characters--everything then worked fine. St?fan From stefan at sun.ac.za Tue Jan 8 07:14:37 2013 From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=) Date: Tue, 8 Jan 2013 05:14:37 -0700 Subject: When will 0.8 official be released? In-Reply-To: References: Message-ID: Hi Isaac On Mon, Jan 7, 2013 at 8:14 AM, Isaac Gerg wrote: > I need the entropy function in the 0.8 version of scikit-image. I was > wondering when this version will be officially released so that C Gohlke may > provide a 64 bit package to support python 3.2. I am currently travelling, and was planning on doing a release beginning February when I got back. However, there's no reason I should be the bottleneck, so if any of the other team members feel up to cutting the release earlier I'd encourage them to do so. Tony, Andreas? St?fan From hannesschoenberger at gmail.com Tue Jan 8 06:22:52 2013 From: hannesschoenberger at gmail.com (=?iso-8859-1?Q?Sch=F6nberger_Johannes?=) Date: Tue, 8 Jan 2013 12:22:52 +0100 Subject: When will 0.8 official be released? In-Reply-To: References: Message-ID: <6FEFC4A5-6254-4DD0-814D-687CBE7A3A16@gmail.com> Hi, I would say it is time to release 0.8 as a lot of new features have been added, as well as a lot of bug fixes have been made. What do others think? I personally don't see any PR, which I would merge before 0.8. Regards, Johannes Am 07.01.2013 um 16:14 schrieb Isaac Gerg : > Hi, > I need the entropy function in the 0.8 version of scikit-image. I was wondering when this version will be officially released so that C Gohlke may provide a 64 bit package to support python 3.2. > > Thanks in advance, > Isaac > > -- > > From isaac.gerg at gergltd.com Tue Jan 8 17:06:07 2013 From: isaac.gerg at gergltd.com (Isaac Gerg) Date: Tue, 8 Jan 2013 14:06:07 -0800 (PST) Subject: skimage and opencv In-Reply-To: <1c1eacb6-349a-40c8-9058-faae9084e436@googlegroups.com> References: <1c1eacb6-349a-40c8-9058-faae9084e436@googlegroups.com> Message-ID: Does openCV have Python 3 bindings? Isaac On Thursday, December 27, 2012 5:06:08 PM UTC-5, Fran?ois wrote: > > Hi users and devs, > > It came to my knowledge that another python library (based on C++ and C > codes) for image processing exists too : opencv > I understand that numpy intregrates some basic features and we need some > advanced features but I have the feeling that skimages is redoundant with > opencv in some ways. > What's the position of skimage about that? (Don't read this question as a > troll but like a real question). > I mean that similar features exist in both. Would not be possible to > reuse/integrate opencv or merge? what's the reason for keeping them apart? > > My observation is there is 4 libraries to manipulate images: > * PIL > * numpy > * skimages > * opencv > That's a lot. > > > Cheers, > > -- > Fran?ois Boulogne.http://www.sciunto.org > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From francois.boulogne at gmail.com Wed Jan 9 10:39:18 2013 From: francois.boulogne at gmail.com (=?UTF-8?Q?Fran=C3=A7ois?=) Date: Wed, 9 Jan 2013 07:39:18 -0800 (PST) Subject: skimage and opencv In-Reply-To: References: <1c1eacb6-349a-40c8-9058-faae9084e436@googlegroups.com> Message-ID: Le mardi 8 janvier 2013 23:06:07 UTC+1, Isaac Gerg a ?crit : > > Does openCV have Python 3 bindings? > > Isaac > > AFAIK, no. Not provided with opencv 2.4.3-4 on archlinux. -------------- next part -------------- An HTML attachment was scrubbed... URL: From francois.boulogne at gmail.com Wed Jan 9 11:01:13 2013 From: francois.boulogne at gmail.com (=?UTF-8?Q?Fran=C3=A7ois?=) Date: Wed, 9 Jan 2013 08:01:13 -0800 (PST) Subject: Contribution: circles and hough transform Message-ID: <32b3855a-c23e-4b88-a5d0-e0aea8b6f926@googlegroups.com> Hi, On my spare time, I work on a code to implement a hough transform to detect circles. This is not implemented yet in skimage. Is Skimage interested in this implementation? (I don't want to spend much more time to polish the code if there is no need) If the answer is positive, it can be done in two steps: * add a method to draw circles. The current "circle" method is for disks. We need circles (very easy to write). This is already done, but in pure python. I saw that drawing methods are implemented in cython. I have never used cython before, but it must be easy (I guess). I implemented two methods (Bresenham or midpoint circle and Andres), both are useful I think. * write the hough algorithm for circle. Done for a Quick and dirty usage, but it's not suitable yet for integration (not safe). I would prefer to send one patch per step. Even if I already tackled bugs in some projects, I never done this kind of contribution before ;) Fran?ois. -------------- next part -------------- An HTML attachment was scrubbed... URL: From tsyu80 at gmail.com Wed Jan 9 12:43:42 2013 From: tsyu80 at gmail.com (Tony Yu) Date: Wed, 9 Jan 2013 11:43:42 -0600 Subject: When will 0.8 official be released? In-Reply-To: References: Message-ID: On Tue, Jan 8, 2013 at 6:14 AM, St?fan van der Walt wrote: > Hi Isaac > > On Mon, Jan 7, 2013 at 8:14 AM, Isaac Gerg wrote: > > I need the entropy function in the 0.8 version of scikit-image. I was > > wondering when this version will be officially released so that C Gohlke > may > > provide a 64 bit package to support python 3.2. > > I am currently travelling, and was planning on doing a release > beginning February when I got back. However, there's no reason I > should be the bottleneck, so if any of the other team members feel up > to cutting the release earlier I'd encourage them to do so. Tony, > Andreas? > > St?fan > > I agree that version 0.8 is due. Unfortunately, I just moved half-way across the country, and I'm getting ready to start a new job, so I don't think I'll have much time to work on this release (at least, not in the next couple of weeks). I'll probably have a little more free time starting in February. Cheers, -Tony -------------- next part -------------- An HTML attachment was scrubbed... URL: From steven.silvester at gmail.com Wed Jan 9 21:08:40 2013 From: steven.silvester at gmail.com (Steven Silvester) Date: Wed, 9 Jan 2013 18:08:40 -0800 (PST) Subject: When will 0.8 official be released? In-Reply-To: References: Message-ID: Johannes, RELEASE.txt looks pretty well laid out. Perhaps you could cut a "release candidate", and wait until next month for the final release and the Debian version. Let me know if I can be of service. I maintain a PyPi package. Regards, Steve -------------- next part -------------- An HTML attachment was scrubbed... URL: From hannesschoenberger at gmail.com Wed Jan 9 13:08:45 2013 From: hannesschoenberger at gmail.com (=?UTF-8?Q?Johannes_Sch=C3=B6nberger?=) Date: Wed, 9 Jan 2013 19:08:45 +0100 Subject: When will 0.8 official be released? In-Reply-To: References: Message-ID: I could do it in the coming weeks, but I have never done it before. Is there any step by step guide? To be honest I'd rather wait to avoid an invalid release... Am Mittwoch, 9. Januar 2013 schrieb Tony Yu : > > > On Tue, Jan 8, 2013 at 6:14 AM, St?fan van der Walt > > wrote: > >> Hi Isaac >> >> On Mon, Jan 7, 2013 at 8:14 AM, Isaac Gerg > >> wrote: >> > I need the entropy function in the 0.8 version of scikit-image. I was >> > wondering when this version will be officially released so that C >> Gohlke may >> > provide a 64 bit package to support python 3.2. >> >> I am currently travelling, and was planning on doing a release >> beginning February when I got back. However, there's no reason I >> should be the bottleneck, so if any of the other team members feel up >> to cutting the release earlier I'd encourage them to do so. Tony, >> Andreas? >> >> St?fan >> >> > I agree that version 0.8 is due. Unfortunately, I just moved half-way > across the country, and I'm getting ready to start a new job, so I don't > think I'll have much time to work on this release (at least, not in the > next couple of weeks). I'll probably have a little more free time starting > in February. > > Cheers, > -Tony > > -- > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From google at terre-adelie.org Wed Jan 9 13:40:22 2013 From: google at terre-adelie.org (=?ISO-8859-1?Q?J=E9r=F4me?= Kieffer) Date: Wed, 9 Jan 2013 19:40:22 +0100 Subject: Contribution: circles and hough transform In-Reply-To: <32b3855a-c23e-4b88-a5d0-e0aea8b6f926@googlegroups.com> References: <32b3855a-c23e-4b88-a5d0-e0aea8b6f926@googlegroups.com> Message-ID: <20130109194022.e8c505a2354de0bf87aa73ce@terre-adelie.org> On Wed, 9 Jan 2013 08:01:13 -0800 (PST) Fran?ois wrote: > Is Skimage interested in this implementation? (I don't want to spend much > more time to polish the code if there is no need) Yes I am personally interested for my research... > If the answer is positive, it can be done in two steps: > * add a method to draw circles. The current "circle" method is for disks. > We need circles (very easy to write). Yes I am working only on circles (and other conics but this is another story). Cheers, -- J?r?me Kieffer From stefan at sun.ac.za Wed Jan 9 11:05:53 2013 From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=) Date: Wed, 9 Jan 2013 23:05:53 +0700 Subject: Contribution: circles and hough transform In-Reply-To: <32b3855a-c23e-4b88-a5d0-e0aea8b6f926@googlegroups.com> References: <32b3855a-c23e-4b88-a5d0-e0aea8b6f926@googlegroups.com> Message-ID: Hi Fran?ois On Wed, Jan 9, 2013 at 11:01 PM, Fran?ois wrote: > Is Skimage interested in this implementation? (I don't want to spend much > more time to polish the code if there is no need) Definitely! I've also been thinking about a more general hough transform that uses the Ax + By + Cxy + D definition of certain curves, but never got around to it (there's an earlier mail about it on the list). > If the answer is positive, it can be done in two steps: > * add a method to draw circles. The current "circle" method is for disks. We > need circles (very easy to write). This is already done, but in pure python. > I saw that drawing methods are implemented in cython. I have never used > cython before, but it must be easy (I guess). I implemented two methods > (Bresenham or midpoint circle and Andres), both are useful I think. > * write the hough algorithm for circle. Done for a Quick and dirty usage, > but it's not suitable yet for integration (not safe). Both patches would be very welcome! Let us know if you need any help getting started. Regards St?fan From hannesschoenberger at gmail.com Thu Jan 10 07:12:10 2013 From: hannesschoenberger at gmail.com (=?UTF-8?Q?Johannes_Sch=C3=B6nberger?=) Date: Thu, 10 Jan 2013 13:12:10 +0100 Subject: Master branch fails tests? In-Reply-To: References: Message-ID: I think this is only necessary if new have been added or removed. Am Donnerstag, 10. Januar 2013 schrieb Juan Nunez-Iglesias : > That did the trick! Any guidelines on when I should do a full working tree > cleanup? Every build? > > On Thu, Jan 10, 2013 at 9:12 PM, St?fan van der Walt > > wrote: > >> Hi Juan >> >> On Thu, Jan 10, 2013 at 11:46 AM, Juan Nunez-Iglesias >> > >> wrote: >> > Am I doing something wrong? I can't get master to work on OSX; 6 tests >> fail >> > with the following import error: >> >> Could you try: >> >> git checkout master >> git reset --hard origin/master >> git clean -xdf >> make >> >> And then try again? The tests run fine over here. >> >> Thanks! >> St?fan >> >> -- >> >> >> > -- > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Wed Jan 9 23:35:58 2013 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Thu, 10 Jan 2013 15:35:58 +1100 Subject: "No definition found" In-Reply-To: References: Message-ID: Hmm. Well IPython seems to work fine with unicode docstrings in when you specify the encoding, in Python files at least... def foo(x): """A?adir 1 al n?mero deseado.""" return x + 1 gives In [1]: import foo File "foo.py", line 2 SyntaxError: Non-ASCII character '\xc3' in file foo.py on line 2, but no encoding declared; see http://www.python.org/peps/pep-0263.html for details but placing the line `# coding=utf-8` at the start of the file gives: In [2]: import foo In [3]: %pdoc foo.foo Class Docstring: A?adir 1 al n?mero deseado. Calling Docstring: x.__call__(...) <==> x(...) So maybe it's a Cython thing? Science is tricky... ;) On Tue, Jan 8, 2013 at 2:14 AM, St?fan van der Walt wrote: > On Sun, Jan 6, 2013 at 10:35 PM, Juan Nunez-Iglesias > wrote: > >> Not sure--but this also shows that IPython does not handle unicode > >> characters in a docstring correctly! > > > > Huh? Are you jumping to conclusions or did you test this? > > I patched the Cython docstring to remove all unicode > characters--everything then worked fine. > > St?fan > > -- > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Wed Jan 9 23:46:52 2013 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Thu, 10 Jan 2013 15:46:52 +1100 Subject: Master branch fails tests? Message-ID: Hi everyone, Am I doing something wrong? I can't get master to work on OSX; 6 tests fail with the following import error: ====================================================================== ERROR: Failure: ImportError (cannot import name denoise_tv_chambolle) ---------------------------------------------------------------------- Traceback (most recent call last): File "/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/loader.py", line 390, in loadTestsFromName addr.filename, addr.module) File "/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/importer.py", line 39, in importFromPath return self.importFromDir(dir_path, fqname) File "/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/site-packages/nose-1.1.2-py2.7.egg/nose/importer.py", line 86, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/Volumes/Projects/skimage/skimage/feature/__init__.py", line 4, in from .peak import peak_local_max File "/Volumes/Projects/skimage/skimage/feature/peak.py", line 3, in from ..filter import rank_order File "/Volumes/Projects/skimage/skimage/filter/__init__.py", line 6, in from ._denoise import denoise_tv_chambolle, tv_denoise ImportError: cannot import name denoise_tv_chambolle This is after running make all. If I do `git co ec3f3`, i.e. before implementation of `tv_denoise`, it runs fine. nuneziglesiasj at jni-lscc-mbp Thu Jan 10 15:45 ~/projects/skimage ((no branch))$ make test nosetests skimage Exception AttributeError: "'UmfpackContext' object has no attribute '_symbolic'" in > ignored ...........................................................................................................................................................................................................................................................SSSSS.....SSSS.....................S......................SSS.....................................................S....................................................................................................................................................................................................... ---------------------------------------------------------------------- Ran 565 tests in 22.690s OK (SKIP=14) Any ideas? -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan at sun.ac.za Thu Jan 10 05:12:28 2013 From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=) Date: Thu, 10 Jan 2013 17:12:28 +0700 Subject: Master branch fails tests? In-Reply-To: References: Message-ID: Hi Juan On Thu, Jan 10, 2013 at 11:46 AM, Juan Nunez-Iglesias wrote: > Am I doing something wrong? I can't get master to work on OSX; 6 tests fail > with the following import error: Could you try: git checkout master git reset --hard origin/master git clean -xdf make And then try again? The tests run fine over here. Thanks! St?fan From jni.soma at gmail.com Thu Jan 10 06:27:09 2013 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Thu, 10 Jan 2013 22:27:09 +1100 Subject: Master branch fails tests? In-Reply-To: References: Message-ID: That did the trick! Any guidelines on when I should do a full working tree cleanup? Every build? On Thu, Jan 10, 2013 at 9:12 PM, St?fan van der Walt wrote: > Hi Juan > > On Thu, Jan 10, 2013 at 11:46 AM, Juan Nunez-Iglesias > wrote: > > Am I doing something wrong? I can't get master to work on OSX; 6 tests > fail > > with the following import error: > > Could you try: > > git checkout master > git reset --hard origin/master > git clean -xdf > make > > And then try again? The tests run fine over here. > > Thanks! > St?fan > > -- > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From francois.boulogne at gmail.com Sat Jan 12 05:54:07 2013 From: francois.boulogne at gmail.com (=?UTF-8?Q?Fran=C3=A7ois?=) Date: Sat, 12 Jan 2013 02:54:07 -0800 (PST) Subject: Contribution: circles and hough transform In-Reply-To: References: <32b3855a-c23e-4b88-a5d0-e0aea8b6f926@googlegroups.com> Message-ID: Le mercredi 9 janvier 2013 17:05:53 UTC+1, Stefan van der Walt a ?crit : > > > Both patches would be very welcome! Let us know if you need any help > getting started. > > Thank. I discovered in master circle_perimeter(). This is actually the bresenham method. This PR is for Andres method. https://github.com/scikit-image/scikit-image/pull/410 Since bresenham in already in master, I'm working on the hough transform. :) Fran?ois. -------------- next part -------------- An HTML attachment was scrubbed... URL: From tsyu80 at gmail.com Mon Jan 14 21:41:06 2013 From: tsyu80 at gmail.com (Tony Yu) Date: Mon, 14 Jan 2013 20:41:06 -0600 Subject: When will 0.8 official be released? In-Reply-To: References: Message-ID: On Wed, Jan 9, 2013 at 8:08 PM, Steven Silvester wrote: > Johannes, > > RELEASE.txt looks pretty well laid out. Perhaps you could cut a "release > candidate", and wait until next month for the final release and the Debian > version. > > Let me know if I can be of service. I maintain a PyPi package. > > > Regards, > Steve > Sorry, I meant to respond sooner, but I've been busy. I think it's a great idea to get an early start on the release. In particular, there's some grace period where we should announce a pending release. Any bug fixes or *small* enhancements that people want to get in before the release should be added at this time (~week). Then, there should be another week or so for testing. (I don't think we've done release branches in the past, but it might be a good idea.) So, to summarize, Johannes: I think it'd be great if you could get the ball rolling by setting the timeline. You may want to take a look at my email preparing for the 0.7 release . Also, as Steve suggests, RELEASE.txt is pretty thorough. The previous release was the first release not handled by St?fan, and I more or less followed that document for the release. (Well, I probably also sent numerous emails to St?fan, too.) So if you're up for it, Johannes, it might be a good idea to give it a go. (And any improvements you can make to RELEASE.txt would be great.) Just a reminder: We may want to revisit the docs version linked on the websiteafter this release. Cheers, -Tony -------------- next part -------------- An HTML attachment was scrubbed... URL: From hannesschoenberger at gmail.com Tue Jan 15 01:45:59 2013 From: hannesschoenberger at gmail.com (=?UTF-8?Q?Johannes_Sch=C3=B6nberger?=) Date: Tue, 15 Jan 2013 07:45:59 +0100 Subject: When will 0.8 official be released? In-Reply-To: References: Message-ID: Hi Tony, OK, I'll give it a try! There is one small PR (https://github.com/scikit-image/scikit-image/pull/413) I would like to merge before I would set the timeline. I will get in touch with you if I encounter any problems. Regards, Johannes 2013/1/15 Tony Yu : > On Wed, Jan 9, 2013 at 8:08 PM, Steven Silvester > wrote: >> >> Johannes, >> >> RELEASE.txt looks pretty well laid out. Perhaps you could cut a "release >> candidate", and wait until next month for the final release and the Debian >> version. >> >> Let me know if I can be of service. I maintain a PyPi package. >> >> >> Regards, >> Steve > > > > Sorry, I meant to respond sooner, but I've been busy. I think it's a great > idea to get an early start on the release. > > In particular, there's some grace period where we should announce a pending > release. Any bug fixes or *small* enhancements that people want to get in > before the release should be added at this time (~week). Then, there should > be another week or so for testing. (I don't think we've done release > branches in the past, but it might be a good idea.) > > So, to summarize, Johannes: I think it'd be great if you could get the ball > rolling by setting the timeline. You may want to take a look at my email > preparing for the 0.7 release. > > Also, as Steve suggests, RELEASE.txt is pretty thorough. The previous > release was the first release not handled by St?fan, and I more or less > followed that document for the release. (Well, I probably also sent numerous > emails to St?fan, too.) So if you're up for it, Johannes, it might be a good > idea to give it a go. (And any improvements you can make to RELEASE.txt > would be great.) > > Just a reminder: We may want to revisit the docs version linked on the > website after this release. > > Cheers, > -Tony > > -- > > From hannesschoenberger at gmail.com Wed Jan 16 14:42:43 2013 From: hannesschoenberger at gmail.com (=?UTF-8?Q?Johannes_Sch=C3=B6nberger?=) Date: Wed, 16 Jan 2013 11:42:43 -0800 (PST) Subject: Release plan for 0.8 Message-ID: <5ab3b898-02f6-42f5-9205-cec42b9cc9c5@googlegroups.com> Hi everybody, a lot of features have been added since we released version 0.7 about 4 months ago. I therefore suggest to make a feature freeze for the next week until January 23rd and only merge bugfixes in this time frame. Are there any changes you want to see in 0.8? It would be great if we could test the current development version on all common system environments to ensure we don't release a broken version. For me it works on OSX 10.8, Python 2.7 and Ubuntu 12.10 32bit, Python 2.7. Regards, Johannes -------------- next part -------------- An HTML attachment was scrubbed... URL: From silvertrumpet999 at gmail.com Wed Jan 16 19:51:58 2013 From: silvertrumpet999 at gmail.com (Josh Warner) Date: Wed, 16 Jan 2013 16:51:58 -0800 (PST) Subject: Release plan for 0.8 In-Reply-To: <5ab3b898-02f6-42f5-9205-cec42b9cc9c5@googlegroups.com> References: <5ab3b898-02f6-42f5-9205-cec42b9cc9c5@googlegroups.com> Message-ID: I'm getting a single test failure on Windows 7 x64 running Python 2.7.2 32bit: FAIL: test_rank.test_otsu ---------------------------------------------------------------------- Traceback (most recent call last): File "C:\Python27\lib\site-packages\nose\case.py", line 187, in runTest self.test(*self.arg) File "S:\src\scikit-image\skimage\filter\rank\tests\test_rank.py", line 337, in test_otsu assert_array_equal(th, res) File "C:\Python27\lib\site-packages\numpy\testing\utils.py", line 707, in assert_array_equal verbose=verbose, header='Arrays are not equal') File "C:\Python27\lib\site-packages\numpy\testing\utils.py", line 636, in assert_array_compare raise AssertionError(msg) AssertionError: Arrays are not equal (mismatch 31.25%) x: array([[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1],... y: array([[1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1], [1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1], [1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1],... On Wednesday, January 16, 2013 1:42:43 PM UTC-6, Johannes Sch?nberger wrote: > > Hi everybody, > > a lot of features have been added since we released version 0.7 about 4 > months ago. > > I therefore suggest to make a feature freeze for the next week until > January 23rd and only merge bugfixes in this time frame. Are there any > changes you want to see in 0.8? > > It would be great if we could test the current development version on all > common system environments to ensure we don't release a broken version. For > me it works on OSX 10.8, Python 2.7 and Ubuntu 12.10 32bit, Python 2.7. > > Regards, Johannes > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjgohlke at gmail.com Wed Jan 16 21:06:03 2013 From: cjgohlke at gmail.com (Christoph Gohlke) Date: Wed, 16 Jan 2013 18:06:03 -0800 Subject: Release plan for 0.8 In-Reply-To: <5ab3b898-02f6-42f5-9205-cec42b9cc9c5@googlegroups.com> References: <5ab3b898-02f6-42f5-9205-cec42b9cc9c5@googlegroups.com> Message-ID: <50F75C8B.7040702@gmail.com> On 1/16/2013 11:42 AM, Johannes Sch??????nberger wrote: > Hi everybody, > > a lot of features have been added since we released version 0.7 about 4 > months ago. > > I therefore suggest to make a feature freeze for the next week until > January 23rd and only merge bugfixes in this time frame. Are there any > changes you want to see in 0.8? > > It would be great if we could test the current development version on > all common system environments to ensure we don't release a broken > version. For me it works on OSX 10.8, Python 2.7 and Ubuntu 12.10 32bit, > Python 2.7. > > Regards, Johannes > Please consider the attached patch to fix build failures on Windows with msvc compilers. The quickshift extension segfaults. Will check later. Christoph -------------- next part -------------- diff --git a/skimage/draw/setup.py b/skimage/draw/setup.py index 5b8e237..1414fca 100644 --- a/skimage/draw/setup.py +++ b/skimage/draw/setup.py @@ -15,7 +15,7 @@ def configuration(parent_package='', top_path=None): cython(['_draw.pyx'], working_path=base_path) config.add_extension('_draw', sources=['_draw.c'], - include_dirs=[get_numpy_include_dirs(), '../shared']) + include_dirs=[get_numpy_include_dirs(), '../_shared']) return config diff --git a/skimage/filter/rank/_crank16.pyx b/skimage/filter/rank/_crank16.pyx index e81bf81..b7aca48 100644 --- a/skimage/filter/rank/_crank16.pyx +++ b/skimage/filter/rank/_crank16.pyx @@ -5,7 +5,7 @@ import numpy as np cimport numpy as np -from libc.math cimport log2 +from libc.math cimport log from skimage.filter.rank._core16 cimport _core16 @@ -274,7 +274,7 @@ cdef inline np.uint16_t kernel_entropy(Py_ssize_t * histo, float pop, for i in range(maxbin): p = histo[i] / pop if p > 0: - e -= p * log2(p) + e -= p * log(p) / 0.30102999566398119521373889472449 return < np.uint16_t > e * 1000 else: diff --git a/skimage/filter/rank/_crank8.pyx b/skimage/filter/rank/_crank8.pyx index 8bff970..d7ece4d 100644 --- a/skimage/filter/rank/_crank8.pyx +++ b/skimage/filter/rank/_crank8.pyx @@ -5,7 +5,7 @@ import numpy as np cimport numpy as np -from libc.math cimport log2 +from libc.math cimport log from skimage.filter.rank._core8 cimport _core8 @@ -279,7 +279,7 @@ cdef inline np.uint8_t kernel_entropy(Py_ssize_t * histo, float pop, for i in range(256): p = histo[i] / pop if p > 0: - e -= p * log2(p) + e -= p * log(p) / 0.30102999566398119521373889472449 return < np.uint8_t > e * 10 else: diff --git a/skimage/filter/setup.py b/skimage/filter/setup.py index 650a26a..934d3f2 100644 --- a/skimage/filter/setup.py +++ b/skimage/filter/setup.py @@ -29,31 +29,31 @@ def configuration(parent_package='', top_path=None): include_dirs=[get_numpy_include_dirs()]) config.add_extension('_denoise_cy', sources=['_denoise_cy.c'], include_dirs=[get_numpy_include_dirs(), '../_shared']) - config.add_extension('rank/_core8', sources=['rank/_core8.c'], + config.add_extension('rank._core8', sources=['rank/_core8.c'], include_dirs=[get_numpy_include_dirs()]) - config.add_extension('rank/_core16', sources=['rank/_core16.c'], + config.add_extension('rank._core16', sources=['rank/_core16.c'], include_dirs=[get_numpy_include_dirs()]) - config.add_extension('rank/_crank8', sources=['rank/_crank8.c'], + config.add_extension('rank._crank8', sources=['rank/_crank8.c'], include_dirs=[get_numpy_include_dirs()]) config.add_extension( - 'rank/_crank8_percentiles', sources=['rank/_crank8_percentiles.c'], + 'rank._crank8_percentiles', sources=['rank/_crank8_percentiles.c'], include_dirs=[get_numpy_include_dirs()]) - config.add_extension('rank/_crank16', sources=['rank/_crank16.c'], + config.add_extension('rank._crank16', sources=['rank/_crank16.c'], include_dirs=[get_numpy_include_dirs()]) config.add_extension( - 'rank/_crank16_percentiles', sources=['rank/_crank16_percentiles.c'], + 'rank._crank16_percentiles', sources=['rank/_crank16_percentiles.c'], include_dirs=[get_numpy_include_dirs()]) config.add_extension( - 'rank/_crank16_bilateral', sources=['rank/_crank16_bilateral.c'], + 'rank._crank16_bilateral', sources=['rank/_crank16_bilateral.c'], include_dirs=[get_numpy_include_dirs()]) config.add_extension( - 'rank/rank', sources=['rank/rank.c'], + 'rank.rank', sources=['rank/rank.c'], include_dirs=[get_numpy_include_dirs()]) config.add_extension( - 'rank/percentile_rank', sources=['rank/percentile_rank.c'], + 'rank.percentile_rank', sources=['rank/percentile_rank.c'], include_dirs=[get_numpy_include_dirs()]) config.add_extension( - 'rank/bilateral_rank', sources=['rank/bilateral_rank.c'], + 'rank.bilateral_rank', sources=['rank/bilateral_rank.c'], include_dirs=[get_numpy_include_dirs()]) return config From steven.silvester at gmail.com Wed Jan 16 21:14:17 2013 From: steven.silvester at gmail.com (Steven Silvester) Date: Wed, 16 Jan 2013 18:14:17 -0800 (PST) Subject: Release plan for 0.8 In-Reply-To: <5ab3b898-02f6-42f5-9205-cec42b9cc9c5@googlegroups.com> References: <5ab3b898-02f6-42f5-9205-cec42b9cc9c5@googlegroups.com> Message-ID: <4ab77029-647e-40b0-add0-f3a4f96c3703@googlegroups.com> I tested it on Ubuntu 12.10, 64 bit, Python 2.7, and all tests pass. I created an issue on GitHub for the Windows 7 failure before I saw Josh's post here. -------------- next part -------------- An HTML attachment was scrubbed... URL: From tsyu80 at gmail.com Wed Jan 16 20:46:33 2013 From: tsyu80 at gmail.com (Tony Yu) Date: Wed, 16 Jan 2013 19:46:33 -0600 Subject: Release plan for 0.8 In-Reply-To: <5ab3b898-02f6-42f5-9205-cec42b9cc9c5@googlegroups.com> References: <5ab3b898-02f6-42f5-9205-cec42b9cc9c5@googlegroups.com> Message-ID: On Wed, Jan 16, 2013 at 1:42 PM, Johannes Sch?nberger < hannesschoenberger at gmail.com> wrote: > Hi everybody, > > a lot of features have been added since we released version 0.7 about 4 > months ago. > > I therefore suggest to make a feature freeze for the next week until > January 23rd and only merge bugfixes in this time frame. Are there any > changes you want to see in 0.8? > > It would be great if we could test the current development version on all > common system environments to ensure we don't release a broken version. For > me it works on OSX 10.8, Python 2.7 and Ubuntu 12.10 32bit, Python 2.7. > > Regards, Johannes > > -- > The Bento build is a bit out of date (fixed in PR 415). The tests run fine on my end (OSX 10.6, Python 2.6). -Tony P.S. Thanks for taking charge of this release! -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan at sun.ac.za Wed Jan 16 23:14:38 2013 From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=) Date: Wed, 16 Jan 2013 21:14:38 -0700 Subject: Release plan for 0.8 In-Reply-To: <50F75C8B.7040702@gmail.com> References: <5ab3b898-02f6-42f5-9205-cec42b9cc9c5@googlegroups.com> <50F75C8B.7040702@gmail.com> Message-ID: On Wed, Jan 16, 2013 at 7:06 PM, Christoph Gohlke wrote: > Please consider the attached patch to fix build failures on Windows with > msvc compilers. The quickshift extension segfaults. Will check later. Thanks, Christoph. This is now available for review as https://github.com/scikit-image/scikit-image/pull/417 St?fan From hannesschoenberger at gmail.com Mon Jan 21 13:58:50 2013 From: hannesschoenberger at gmail.com (=?iso-8859-1?Q?Sch=F6nberger_Johannes?=) Date: Mon, 21 Jan 2013 19:58:50 +0100 Subject: Release plan for 0.8 In-Reply-To: References: <5ab3b898-02f6-42f5-9205-cec42b9cc9c5@googlegroups.com> <50F75C8B.7040702@gmail.com> Message-ID: Hi, some bugs have been fixed so far, thanks to everyone. This mail serves as a reminder for everyone who encountered any remaining problems with the current development version, since I plan to push out 0.8 in two days. Regards, Johannes From stefan at sun.ac.za Mon Jan 21 22:13:54 2013 From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=) Date: Mon, 21 Jan 2013 20:13:54 -0700 Subject: Release plan for 0.8 In-Reply-To: References: <5ab3b898-02f6-42f5-9205-cec42b9cc9c5@googlegroups.com> <50F75C8B.7040702@gmail.com> Message-ID: Hi all, There are some easy issues we can look at before the release: https://github.com/scikit-image/scikit-image/issues/318 https://github.com/scikit-image/scikit-image/issues/209 (for someone with access to SPARC) https://github.com/scikit-image/scikit-image/issues/212 (debian package) https://github.com/scikit-image/scikit-image/issues/336 (search and replace) https://github.com/scikit-image/scikit-image/issues/341 (figure out how to do parallel loops on all systems) https://github.com/scikit-image/scikit-image/issues/416 (review patches and apply) https://github.com/scikit-image/scikit-image/pull/417 (review patch and apply) https://github.com/scikit-image/scikit-image/issues/418 (check relevance) Thanks for everyone's help, and to Johannes for taking the lead on this release! St?fan On Mon, Jan 21, 2013 at 11:58 AM, Sch?nberger Johannes wrote: > Hi, > > some bugs have been fixed so far, thanks to everyone. > > This mail serves as a reminder for everyone who encountered any remaining problems with the current development version, since I plan to push out 0.8 in two days. > > Regards, Johannes = From hannesschoenberger at gmail.com Tue Jan 22 17:06:20 2013 From: hannesschoenberger at gmail.com (=?iso-8859-1?Q?Sch=F6nberger_Johannes?=) Date: Tue, 22 Jan 2013 23:06:20 +0100 Subject: Release plan for 0.8 In-Reply-To: References: <5ab3b898-02f6-42f5-9205-cec42b9cc9c5@googlegroups.com> <50F75C8B.7040702@gmail.com> Message-ID: <3AE50060-766D-4CC1-8657-94289FDCF873@gmail.com> I think we should push the release some days back to fix the majority of these issues. > https://github.com/scikit-image/scikit-image/issues/318 I'll take on this tomorrow. > https://github.com/scikit-image/scikit-image/issues/336 Made the necessary changes today as part of a new PR. > https://github.com/scikit-image/scikit-image/issues/341 I commented on this topic on github. > https://github.com/scikit-image/scikit-image/issues/418 (check relevance) Has been fixed before, so closed. From tsyu80 at gmail.com Thu Jan 24 22:55:15 2013 From: tsyu80 at gmail.com (Tony Yu) Date: Thu, 24 Jan 2013 21:55:15 -0600 Subject: canvastools subpackage for scikit-image viewer In-Reply-To: References: <3d65b13b-c793-4337-a1fa-764e4210b264@googlegroups.com> Message-ID: On Thu, Dec 27, 2012 at 11:56 PM, St?fan van der Walt wrote: > Hi Tony > > On Wed, Dec 26, 2012 at 10:41 PM, Tony Yu wrote: > > I just added another tool: A canvas painter. It's a bit less responsive > than > > I'd like, but I think it's as fast as it'll get (it's limited by > > matplotlib's blitting support for images). Check out the watershed demo > in > > the `viewer_examples/plugins` folder, which uses the paint tool to > generate > > markers for watershed segmentation. > > Finally, a path to that FFT filter painter I've had in mind! This is > very exciting. > > By the way, it took me a while to figure out to press "enter" to run > the segmentation, so how about printing some instructions to the > terminal? > > Thanks again, > St?fan > > Sorry for the really late reply on this. Actually, the demo should have printed instructions to the terminal in that version. In any case, getting the user to press enter wasn't great for usability. I just changed this demo so that you press a button to display the watershed segmentation. -T -------------- next part -------------- An HTML attachment was scrubbed... URL: From tsyu80 at gmail.com Tue Jan 29 23:42:37 2013 From: tsyu80 at gmail.com (Tony Yu) Date: Tue, 29 Jan 2013 22:42:37 -0600 Subject: Policy for import of submodules In-Reply-To: References: Message-ID: On Tue, Jan 29, 2013 at 10:05 PM, Juan Nunez-Iglesias wrote: > Hi, > > Does scikit-image have a specific policy for how imports should work? For > example, as far as I know, numpy currently imports everything into the np > namespace with: > > import numpy as np > > > However, the following raises an error, even though the import statement > works fine: > > import skimage as skim > coins = skim.data.coins() > > giving the error: > > --------------------------------------------------------------------------- > AttributeError Traceback (most recent call last) > in () > ----> 1 coins = skim.data.coins() > > AttributeError: 'module' object has no attribute 'data' > > > But some things *are* in the top-level namespace. The following works > fine: > > import skimage as skimfrom skimage import data > coins = data.coins() > coins = skim.img_as_float(coins) > > > So my question is, is this behaviour by design, or should there be nothing > at all in the top-level, or should everything be imported? > > I tend to agree that it should be one or the other (with the exception of the standard metadata at the top-level). The argument against importing everything is that it can lead to slow import times (see, numpy for example), even when you're only using a small subset of the package. While this time may not be too severe now, the hope is that scikit-image will grow ever-more functionality, which would slow import times. I'm in favor of moving the functionality out of the top level. I think the only thing that would need to be moved out would be the converters in `skimage.util.dtype`. There should be a shorter path to access those functions, though. Side note: I'm not a huge fan of `util` (I would have thought `utils`), but that's a minor point. And of course, if others agree, this would need to be phased in over time---probably with a couple of releases raising deprecation warnings when trying to access those functions at the top level. Also, this would wait until after the release of 0.8. -Tony -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan at sun.ac.za Wed Jan 30 01:13:27 2013 From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=) Date: Wed, 30 Jan 2013 13:13:27 +0700 Subject: Policy for import of submodules In-Reply-To: References: Message-ID: On Wed, Jan 30, 2013 at 11:42 AM, Tony Yu wrote: >> So my question is, is this behaviour by design, or should there be nothing >> at all in the top-level, or should everything be imported? > > I tend to agree that it should be one or the other (with the exception of > the standard metadata at the top-level). As Tony mentioned, it's by design from the lessons learnt in NumPy, aimed at limiting the import time of the library. Because ``img_as_float``, ``test`` etc. are used so often, we put them in the root namespace. We have: skimage.data_dir skimage.img_as_int skimage.test skimage.get_log skimage.img_as_ubyte skimage.test_verbose skimage.img_as_bool skimage.img_as_uint skimage.util skimage.img_as_float skimage.pkg_dir skimage.version Of these, I would keep at least skimage.version, skimage.test, skimage.test_verbose and skimage.get_log, because they provide overarching functionality. St?fan From stefan at sun.ac.za Wed Jan 30 01:51:08 2013 From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=) Date: Wed, 30 Jan 2013 13:51:08 +0700 Subject: Policy for import of submodules In-Reply-To: References: Message-ID: On Wed, Jan 30, 2013 at 1:37 PM, Juan Nunez-Iglesias wrote: > Ok so I'm hearing consensus about what you guys want to do, which is great. > For future reference though, is the intent that second-level packages do > import everything underneath? Currently there don't appear to be more than > two levels, but will that always be true? Yes, we don't want to stack anything more deeply than that. It really is just a means of ensuring that you can import a selected portion of scikit-image without waiting too long, or without loading unnecessary dependencies (e.g., importing the io module will also import gstreamer if available). Also, in the most severe case where one sub-module can't import, you can at least continue working with the rest. St?fan From jni.soma at gmail.com Tue Jan 29 23:05:41 2013 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Wed, 30 Jan 2013 15:05:41 +1100 Subject: Policy for import of submodules Message-ID: Hi, Does scikit-image have a specific policy for how imports should work? For example, as far as I know, numpy currently imports everything into the np namespace with: import numpy as np However, the following raises an error, even though the import statement works fine: import skimage as skim coins = skim.data.coins() giving the error: --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) in () ----> 1 coins = skim.data.coins() AttributeError: 'module' object has no attribute 'data' But some things *are* in the top-level namespace. The following works fine: import skimage as skimfrom skimage import data coins = data.coins() coins = skim.img_as_float(coins) So my question is, is this behaviour by design, or should there be nothing at all in the top-level, or should everything be imported? -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Wed Jan 30 01:37:16 2013 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Wed, 30 Jan 2013 17:37:16 +1100 Subject: Policy for import of submodules In-Reply-To: References: Message-ID: Ok so I'm hearing consensus about what you guys want to do, which is great. For future reference though, is the intent that second-level packages *do* import everything underneath? Currently there don't appear to be more than two levels, but will that always be true? On Wed, Jan 30, 2013 at 5:13 PM, St?fan van der Walt wrote: > On Wed, Jan 30, 2013 at 11:42 AM, Tony Yu wrote: > >> So my question is, is this behaviour by design, or should there be > nothing > >> at all in the top-level, or should everything be imported? > > > > I tend to agree that it should be one or the other (with the exception of > > the standard metadata at the top-level). > > As Tony mentioned, it's by design from the lessons learnt in NumPy, > aimed at limiting the import time of the library. Because > ``img_as_float``, ``test`` etc. are used so often, we put them in the > root namespace. We have: > > skimage.data_dir skimage.img_as_int skimage.test > skimage.get_log skimage.img_as_ubyte skimage.test_verbose > skimage.img_as_bool skimage.img_as_uint skimage.util > skimage.img_as_float skimage.pkg_dir skimage.version > > Of these, I would keep at least skimage.version, skimage.test, > skimage.test_verbose and skimage.get_log, because they provide > overarching functionality. > > 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. > For more options, visit https://groups.google.com/groups/opt_out. > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Wed Jan 30 22:19:02 2013 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Thu, 31 Jan 2013 14:19:02 +1100 Subject: removing small connected components Message-ID: Hi guys, For my own segmentation package, I wrote a small function to remove small connected components in an ndarray. You can see it here: https://github.com/janelia-flyem/gala/blob/master/gala/morpho.py#L72 I've been looking at things that could be moved from there to skimage and I thought that was a prime candidate (I think you actually do the same thing in one of the examples, but without making it into a function). Any interest in a PR? There's other nd operations in there: morphological reconstruction, h-minima, regional (aka local) minima, and impose minima. Let me know if you would like any of these for inclusion in skimage... Thanks, Juan. -------------- next part -------------- An HTML attachment was scrubbed... URL: From almar.klein at gmail.com Thu Jan 31 18:24:12 2013 From: almar.klein at gmail.com (Almar Klein) Date: Fri, 1 Feb 2013 00:24:12 +0100 Subject: Displaying video In-Reply-To: References: Message-ID: You could do it with OpenGl, although it wouldn't be straightforward. You can also do it in visvis (which uses OpenGl). Here's some untested code that would do this: import visvis as vv vv.clf() # Clear figure (or create a new figure) tex = vv.imshow(first_frame) while video_not_ended: tex.SetData(next_frame) time.sleep(1.0/framerate) vv.processEvents() - Almar On 30 January 2013 22:07, Colin Lea wrote: > For a long time now I've kept OpenCV in my vision stack primarily for > displaying videos. I'm trying to get rid of it as a dependence for use on a > secure remote server which I don't have unfettered access to. > > So I'm wondering, how do other people display videos? I see that PyGame is > another option. Does anyone use that? By displaying videos essentially I > just mean showing streams of images (not necessary from a video file). > > If nobody else has a solution other than to use OpenCV, would it be of > interest to implement something (either using PyGame or otherwise) for > skimage? > > > -- > 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/groups/opt_out. > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: