From stefan at sun.ac.za Fri Nov 7 07:18:24 2014 From: stefan at sun.ac.za (Stefan van der Walt) Date: Fri, 07 Nov 2014 14:18:24 +0200 Subject: git: pull PR into new branch Message-ID: <87bnoj431r.fsf@sun.ac.za> Hi everyone I can't remember if I shared this before, but here's a script to pull down a single PR into a new branch: https://gist.github.com/stefanv/daa8fc7bae6dc002ad62 Usage: git pr 1020 which creates a branch `pr/1020`. You can execute it a second time whenever you want to update the branch. St?fan From stefan at sun.ac.za Wed Nov 12 13:32:36 2014 From: stefan at sun.ac.za (Stefan van der Walt) Date: Wed, 12 Nov 2014 20:32:36 +0200 Subject: some broken links in example notebooks In-Reply-To: <03cb4e22-e4b9-48fe-990b-e3a1e033efd6@googlegroups.com> References: <03cb4e22-e4b9-48fe-990b-e3a1e033efd6@googlegroups.com> Message-ID: <87egt8s20r.fsf@sun.ac.za> Hi Michael On 2014-10-09 02:55:54, Michael Aye wrote: > I guess you create the example notebooks somehow automatically with sphinx? > Because the descriptive text is written in html which mostly shows up well > in the notebook, but the links to other skimage functions do show up > weird/broken. I even don't know if it's possible or reasonable to fix that > somehow for a locally downloaded notebook, but I just wanted to inform you > in case you were not aware. Somehow, this email slipped by under the radar! The links should show up correctly on the local browser--if they don't, it's a big. Would you kindly file a bug report? Thanks! St?fan From almar.klein at gmail.com Thu Nov 13 16:03:24 2014 From: almar.klein at gmail.com (Almar Klein) Date: Thu, 13 Nov 2014 22:03:24 +0100 Subject: ANN: imageio v1.0 Message-ID: <54651C9C.2020108@gmail.com> Hi all, I'm pleased to announce version 1.0 of imageio - a library for reading and writing images. This library started as a spin-off of the freeimage plugin in skimage, and is now a fully-fledged library with unit tests and all. Imageio provides an easy interface to read and write a wide range of image data, including animated images, volumetric data, and scientific formats. It is cross-platform, runs on Python 2.x and 3.x, and is easy to install. Imageio is plugin-based, making it easy to extend. It could probably use more scientific formats. I welcome anyone who's interested to contribute! install: pip install imageio website: http://imageio.github.io release notes: http://imageio.readthedocs.org/en/latest/releasenotes.html Regards, Almar From stefan at sun.ac.za Thu Nov 13 16:35:17 2014 From: stefan at sun.ac.za (Stefan van der Walt) Date: Thu, 13 Nov 2014 23:35:17 +0200 Subject: ANN: imageio v1.0 In-Reply-To: <54651C9C.2020108@gmail.com> References: <54651C9C.2020108@gmail.com> Message-ID: <877fyyrdgq.fsf@sun.ac.za> Hi Almar On 2014-11-13 23:03:24, Almar Klein wrote: > I'm pleased to announce version 1.0 of imageio - a library for reading > and writing images. This library started as a spin-off of the freeimage > plugin in skimage, and is now a fully-fledged library with unit tests > and all. Thanks for the announcement! Can you expand on how you see the eco-system of scikit-image, imread and imageio interacting? Regards St?fan From almar.klein at gmail.com Thu Nov 13 17:40:37 2014 From: almar.klein at gmail.com (Almar Klein) Date: Thu, 13 Nov 2014 23:40:37 +0100 Subject: ANN: imageio v1.0 In-Reply-To: <877fyyrdgq.fsf@sun.ac.za> References: <54651C9C.2020108@gmail.com> <877fyyrdgq.fsf@sun.ac.za> Message-ID: <54653365.2020703@gmail.com> > Thanks for the announcement! Can you expand on how you see the > eco-system of scikit-image, imread and imageio interacting? Since imageio has a pretty good plugin system, it could be a good place to implement io for all the weird scientific file formats that exist. Next to imread(), volread(), etc. imageio also provides the read() function, which returns a reader object specific to the plugin. This reader object can have additional methods and may yield other data then just 2D/3D numpy arrays if this makes sense for the format. So I suppose I am hoping for skimage devs to embrace imageio and help move it further. With that, I suppose skimage could focus on the processing rather than the io, since ideally, we'd have one library for processing images, and one for reading/saving images. Developers tend to have a fear for dependencies. I understand this, and I try to minimize dependencies myself, but reading/writing images is a task that warrants a standalone package IMO. It troubles me a bit that different libraries are each rolling their own image io functionalities. As for the imread package: Zach and I considered it when discussing plans for imageio, but imread is based on C++, which is harder to maintain and makes it a harder dependency. imageio is pure Python with ctypes bindings to some libs that are auto-downloaded. - Almar PS: some fancy stuff that imageio can do which might be interesting for skimage users: stream images from webcam, export visualizations to animated gif or mp4. From witzjean at gmail.com Fri Nov 14 10:27:42 2014 From: witzjean at gmail.com (jeff witz) Date: Fri, 14 Nov 2014 07:27:42 -0800 (PST) Subject: regionprops Very slow on centroid identification Message-ID: <00059269-0073-45fe-bcf6-9cb7d10abfce@googlegroups.com> Hello. I'm developing a video extensometer based on the identification of center of mass of circular white mark on a black rubber specimen. In order to deal with data in real time I have to be fast (over 100 fps). So I first identify the Zones Of Interests using this example : http://scikit-image.org/docs/dev/auto_examples/plot_label.html Then I compute the center of mass on each ZOI. As I have a fast camera the ZOI between two successive images doesn't change much. So if I extend the bounding box of my current ZOI I could be pretty confident in the fact that given circular mark in the next picture will be in the extended ZOI and the recompute an updated extened ZOI for the next image. So this is the big picture. You will find bellow the function I use in order to get it : def barycenter(image_,minx_,miny_,maxx_,maxy_,thresh_,border_): bw_=image_[minx_:maxx_+1,miny_:maxy_+1]>thresh_ [Y,X]=np.meshgrid(range(miny_,maxy_+1),range(minx_,maxx_+1)) region=regionprops(bw_) minx,miny,maxx,maxy=region[0].bbox Px_=(X*bw_).sum().astype(float)/bw_.sum() Py_=(Y*bw_).sum().astype(float)/bw_.sum() minx_=X[minx,miny]-border_ miny_=Y[minx,miny]-border_ maxx_=X[maxx,maxy]+border_ maxy_=Y[maxx,maxy]+border_ return Px_,Py_,minx_,miny_,maxx_,maxy_ As you can see I don't use region[0].centroid. I compute the moment myself if I time my function on a 141x108 ZOI I get 504 ?s If I time this function : def barycenter2(image_,minx_,miny_,maxx_,maxy_,thresh_,border_): bw_=image_[minx_:maxx_+1,miny_:maxy_+1]>thresh_ [Y,X]=np.meshgrid(range(miny_,maxy_+1),range(minx_,maxx_+1)) region=regionprops(bw_) Px_,Py_=region[0].centroid Px_+=minx_ Py_+=miny_ minx,miny,maxx,maxy=region[0].bbox minx_=X[minx,miny]-border_ miny_=Y[minx,miny]-border_ maxx_=X[maxx,maxy]+border_ maxy_=Y[maxx,maxy]+border_ return Px_,Py_,minx_,miny_,maxx_,maxy_ I get 10ms per loop ! What is really strange is if I time : %timeit region[0].centroid I get 58.6 ns per loop ! So I don't really understand why this time explose when I use it in a function ? If someone have some insight it will be very helpfull. Even If I can use my first function, it's a pity to have to use less optimized functions. Best regards. -------------- next part -------------- An HTML attachment was scrubbed... URL: From almar.klein at gmail.com Sat Nov 15 05:03:19 2014 From: almar.klein at gmail.com (Almar Klein) Date: Sat, 15 Nov 2014 11:03:19 +0100 Subject: ANN: imageio v1.0 In-Reply-To: References: <54651C9C.2020108@gmail.com> <877fyyrdgq.fsf@sun.ac.za> <54653365.2020703@gmail.com> Message-ID: <546724E7.4090406@gmail.com> > What I'm looking for in an IO package > is proper treatment of less-common data types that are nonetheless > common in scientific imaging, such as uint16 and 3D tiffs. (Prior to > Steven's PRs, skimage did a poor job with those.) Can you comment on that? Imageio supports TIFF through the freeimage plugin, but this is more the common kind of TIFF, and probably not sufficient for scientific TIFF formats. It will need some testing to see what is supported and what not. The best approach would probably be to refactor existing code that can deal with such Tiffs into an imageio plugin. There's C. Gohlke's tifffile, tiffany, pylibtif. I am not familiar enough with TIFF to say which of these sufficiently covers scientists needs (if any). But if either of them is good enough, it should be relatively easy to include it in imageio. - Almar > > Thanks for the post, and for the library! ? I think it will lead to good > places. =) > > Juan. > > On Fri, Nov 14, 2014 at 9:40 AM, Almar Klein > wrote: > > > Thanks for the announcement! Can you expand on how you see the > eco-system of scikit-image, imread and imageio interacting? > > > Since imageio has a pretty good plugin system, it could be a good > place to implement io for all the weird scientific file formats that > exist. Next to imread(), volread(), etc. imageio also provides the > read() function, which returns a reader object specific to the > plugin. This reader object can have additional methods and may yield > other data then just 2D/3D numpy arrays if this makes sense for the > format. > > So I suppose I am hoping for skimage devs to embrace imageio and > help move it further. > > With that, I suppose skimage could focus on the processing rather > than the io, since ideally, we'd have one library for processing > images, and one for reading/saving images. > > > Developers tend to have a fear for dependencies. I understand this, > and I try to minimize dependencies myself, but reading/writing > images is a task that warrants a standalone package IMO. It troubles > me a bit that different libraries are each rolling their own image > io functionalities. > > > As for the imread package: Zach and I considered it when discussing > plans for imageio, but imread is based on C++, which is harder to > maintain and makes it a harder dependency. imageio is pure Python > with ctypes bindings to some libs that are auto-downloaded. > > - Almar > > PS: some fancy stuff that imageio can do which might be interesting > for skimage users: stream images from webcam, export visualizations > to animated gif or mp4. > > > -- > You received this message because you are subscribed to the Google > Groups "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, > send an email to scikit-image+unsubscribe at __googlegroups.com > . > For more options, visit https://groups.google.com/d/__optout > . > > > -- > You received this message because you are subscribed to the Google > Groups "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send > an email to scikit-image+unsubscribe at googlegroups.com > . > For more options, visit https://groups.google.com/d/optout. From jni.soma at gmail.com Fri Nov 14 22:29:03 2014 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Sat, 15 Nov 2014 14:29:03 +1100 Subject: regionprops Very slow on centroid identification In-Reply-To: <00059269-0073-45fe-bcf6-9cb7d10abfce@googlegroups.com> References: <00059269-0073-45fe-bcf6-9cb7d10abfce@googlegroups.com> Message-ID: Hi Jeff, Firstly, what's with all the trailing underscores? Makes my brain hurt. =) Second, this is *somewhat* of a known issue. See: https://github.com/scikit-image/scikit-image/issues/1092 (Including the notebook link from that issue.) As you can see, PR 1096 made some improvements, but I suspect not enough to solve your problem. Are you on master or on 0.10? Additionally, regionprops works through a "cached-property" pattern, which means that each value is computed once, and then stored for later retrieval. So your second region[0] call is probably hitting the cached value, hence the massive speedup! As to the specific problem of why your calculation is so much faster, my guess right now is that it's because of Python function call overhead: while you are computing everything directly, have a look at the regionprops code : first, you have to go through the cached-property pattern (1 call), check whether the cache is active (2 calls), check whether it's been computed before (3 calls), decide to compute it (4 calls), compute the bbox (another travel through cached-property), then compute the "local" centroid (relative to current bbox), within that compute the moments (another cached-property), and *finally* compute the actual centroid. We're not doing any computations differently, but that is a *heck* of a lot of overhead for such a simple computation. I'd never followed this full path before, so thanks for pointing it out! A PR to improve this situation would be most welcome! (Bonus points for improving 3D support in the process.) Probably not quite the quick fix you were hoping for, but I hope this helps nonetheless! Juan. On Sat, Nov 15, 2014 at 2:27 AM, jeff witz wrote: > Hello. > > I'm developing a video extensometer based on the identification of center > of mass of circular white mark on a black rubber specimen. > > In order to deal with data in real time I have to be fast (over 100 fps). > So I first identify the Zones Of Interests using this example : > http://scikit-image.org/docs/dev/auto_examples/plot_label.html > > Then I compute the center of mass on each ZOI. > > As I have a fast camera the ZOI between two successive images doesn't > change much. So if I extend the bounding box of my current ZOI I could be > pretty confident in the fact that given circular mark in the next picture > will be in the extended ZOI and the recompute an updated extened ZOI for > the next image. > > So this is the big picture. > > You will find bellow the function I use in order to get it : > def barycenter(image_,minx_,miny_,maxx_,maxy_,thresh_,border_): > bw_=image_[minx_:maxx_+1,miny_:maxy_+1]>thresh_ > [Y,X]=np.meshgrid(range(miny_,maxy_+1),range(minx_,maxx_+1)) > region=regionprops(bw_) > minx,miny,maxx,maxy=region[0].bbox > Px_=(X*bw_).sum().astype(float)/bw_.sum() > Py_=(Y*bw_).sum().astype(float)/bw_.sum() > minx_=X[minx,miny]-border_ > miny_=Y[minx,miny]-border_ > maxx_=X[maxx,maxy]+border_ > maxy_=Y[maxx,maxy]+border_ > return Px_,Py_,minx_,miny_,maxx_,maxy_ > > As you can see I don't use region[0].centroid. I compute the moment myself > > if I time my function on a 141x108 ZOI I get 504 ?s > > If I time this function : > > def barycenter2(image_,minx_,miny_,maxx_,maxy_,thresh_,border_): > bw_=image_[minx_:maxx_+1,miny_:maxy_+1]>thresh_ > [Y,X]=np.meshgrid(range(miny_,maxy_+1),range(minx_,maxx_+1)) > region=regionprops(bw_) > Px_,Py_=region[0].centroid > Px_+=minx_ > Py_+=miny_ > minx,miny,maxx,maxy=region[0].bbox > minx_=X[minx,miny]-border_ > miny_=Y[minx,miny]-border_ > maxx_=X[maxx,maxy]+border_ > maxy_=Y[maxx,maxy]+border_ > return Px_,Py_,minx_,miny_,maxx_,maxy_ > > > I get 10ms per loop ! > > What is really strange is if I time : > > %timeit region[0].centroid > I get 58.6 ns per loop ! > > So I don't really understand why this time explose when I use it in a > function ? > > If someone have some insight it will be very helpfull. Even If I can use > my first function, it's a pity to have to use less optimized functions. > > Best regards. > > > > -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image+unsubscribe at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Fri Nov 14 22:48:52 2014 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Sat, 15 Nov 2014 14:48:52 +1100 Subject: ANN: imageio v1.0 In-Reply-To: <54653365.2020703@gmail.com> References: <54651C9C.2020108@gmail.com> <877fyyrdgq.fsf@sun.ac.za> <54653365.2020703@gmail.com> Message-ID: Hi Almar, Thanks for this. Our own IO is much improved thanks to a few PRs by Steven Sylvester, so I care a little bit less than I would have if this had come a few months ago. =P Generally, though, I do agree with you that a dedicated package might be the better spot for this. Part of Steven's improvements was to make PIL a dependency. If imageio is easy enough to install, and complete enough, it might replace that dependency. What I'm looking for in an IO package is proper treatment of less-common data types that are nonetheless common in scientific imaging, such as uint16 and 3D tiffs. (Prior to Steven's PRs, skimage did a poor job with those.) Can you comment on that? Thanks for the post, and for the library! -- I think it will lead to good places. =) Juan. On Fri, Nov 14, 2014 at 9:40 AM, Almar Klein wrote: > > Thanks for the announcement! Can you expand on how you see the >> eco-system of scikit-image, imread and imageio interacting? >> > > Since imageio has a pretty good plugin system, it could be a good place to > implement io for all the weird scientific file formats that exist. Next to > imread(), volread(), etc. imageio also provides the read() function, which > returns a reader object specific to the plugin. This reader object can have > additional methods and may yield other data then just 2D/3D numpy arrays if > this makes sense for the format. > > So I suppose I am hoping for skimage devs to embrace imageio and help move > it further. > > With that, I suppose skimage could focus on the processing rather than the > io, since ideally, we'd have one library for processing images, and one for > reading/saving images. > > > Developers tend to have a fear for dependencies. I understand this, and I > try to minimize dependencies myself, but reading/writing images is a task > that warrants a standalone package IMO. It troubles me a bit that different > libraries are each rolling their own image io functionalities. > > > As for the imread package: Zach and I considered it when discussing plans > for imageio, but imread is based on C++, which is harder to maintain and > makes it a harder dependency. imageio is pure Python with ctypes bindings > to some libs that are auto-downloaded. > > - Almar > > PS: some fancy stuff that imageio can do which might be interesting for > skimage users: stream images from webcam, export visualizations to animated > gif or mp4. > > > -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image+unsubscribe at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From steven.silvester at gmail.com Sat Nov 15 19:41:06 2014 From: steven.silvester at gmail.com (Steven Silvester) Date: Sat, 15 Nov 2014 16:41:06 -0800 (PST) Subject: ANN: imageio v1.0 In-Reply-To: <54651C9C.2020108@gmail.com> References: <54651C9C.2020108@gmail.com> Message-ID: Almar, This is a very interesting project indeed. We included a copy of Christophe's `tifffile.py` in our repo and are using that within our PIL plugin for loading TIFF files. We have an interest in minimizing our dependencies, especially when considering our Debian packaging. I could see perhaps *vendoring* ImageIO to replace `skimage.io` and requiring FreeImage as the only external dependency. St?fan would have to weigh in on that. Regards, Steve On Thursday, November 13, 2014 3:03:27 PM UTC-6, Almar Klein wrote: > > Hi all, > > I'm pleased to announce version 1.0 of imageio - a library for reading > and writing images. This library started as a spin-off of the freeimage > plugin in skimage, and is now a fully-fledged library with unit tests > and all. > > Imageio provides an easy interface to read and write a wide range of > image data, including animated images, volumetric data, and scientific > formats. It is cross-platform, runs on Python 2.x and 3.x, and is easy > to install. > > Imageio is plugin-based, making it easy to extend. It could probably use > more scientific formats. I welcome anyone who's interested to contribute! > > install: pip install imageio > website: http://imageio.github.io > release notes: http://imageio.readthedocs.org/en/latest/releasenotes.html > > Regards, > Almar > -------------- next part -------------- An HTML attachment was scrubbed... URL: From almar.klein at gmail.com Mon Nov 17 03:15:18 2014 From: almar.klein at gmail.com (Almar Klein) Date: Mon, 17 Nov 2014 09:15:18 +0100 Subject: ANN: imageio v1.0 In-Reply-To: References: <54651C9C.2020108@gmail.com> Message-ID: <5469AE96.5090403@gmail.com> > We included a copy of Christophe's `tifffile.py` in our repo and are > using that within our PIL plugin for loading TIFF files. Ah great, in that case I suspect making an imageio plugin would be easy. > I could see perhaps *vendoring* ImageIO to replace `skimage.io` and > requiring FreeImage as the only external dependency. What do you mean by "vendoring"? BTW: the freeimage lib is auto-downloaded. Imageio also has its own version of that lib for Linux, since I found some Linux's have a rather old version of FreeImage, which was causing bugs. Also good to know: Ghislain Vaillant is currently making a debian package for imageio. Regards, Almar > > St?fan would have to weigh in on that. > > > Regards, > > Steve > > > > > > On Thursday, November 13, 2014 3:03:27 PM UTC-6, Almar Klein wrote: > > Hi all, > > I'm pleased to announce version 1.0 of imageio - a library for reading > and writing images. This library started as a spin-off of the freeimage > plugin in skimage, and is now a fully-fledged library with unit tests > and all. > > Imageio provides an easy interface to read and write a wide range of > image data, including animated images, volumetric data, and scientific > formats. It is cross-platform, runs on Python 2.x and 3.x, and is easy > to install. > > Imageio is plugin-based, making it easy to extend. It could probably > use > more scientific formats. I welcome anyone who's interested to > contribute! > > install: pip install imageio > website: http://imageio.github.io > release notes: > http://imageio.readthedocs.org/en/latest/releasenotes.html > > > Regards, > Almar > > -- > You received this message because you are subscribed to the Google > Groups "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send > an email to scikit-image+unsubscribe at googlegroups.com > . > For more options, visit https://groups.google.com/d/optout. From steven.silvester at gmail.com Mon Nov 17 21:57:34 2014 From: steven.silvester at gmail.com (Steven Silvester) Date: Mon, 17 Nov 2014 18:57:34 -0800 (PST) Subject: ANN: imageio v1.0 In-Reply-To: <54651C9C.2020108@gmail.com> References: <54651C9C.2020108@gmail.com> Message-ID: Almar, By vendoring I meant including a snapshot of the imageio project in the scikit-image repo, and using it if there is not a system version available (which is how we handle `tifffile.py`). As someone who has worked in a lab with no internet connection, I am wary of requiring an external library to be downloaded upon install, and I agree with St?fan that we should include imageio as an optional plugin in the short term and then once an imageio Debian package and conda mainline package are available, more toward making it a requirement instead of PIL. I will implement the imageio scikit-image plugin (unless you'd rather), but I've got a few other commitments lined up prior to getting more involved in the short term. Regards, Steve On Thursday, November 13, 2014 3:03:27 PM UTC-6, Almar Klein wrote: > > Hi all, > > I'm pleased to announce version 1.0 of imageio - a library for reading > and writing images. This library started as a spin-off of the freeimage > plugin in skimage, and is now a fully-fledged library with unit tests > and all. > > Imageio provides an easy interface to read and write a wide range of > image data, including animated images, volumetric data, and scientific > formats. It is cross-platform, runs on Python 2.x and 3.x, and is easy > to install. > > Imageio is plugin-based, making it easy to extend. It could probably use > more scientific formats. I welcome anyone who's interested to contribute! > > install: pip install imageio > website: http://imageio.github.io > release notes: http://imageio.readthedocs.org/en/latest/releasenotes.html > > Regards, > Almar > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan at sun.ac.za Mon Nov 17 14:04:31 2014 From: stefan at sun.ac.za (Stefan van der Walt) Date: Mon, 17 Nov 2014 21:04:31 +0200 Subject: ANN: imageio v1.0 In-Reply-To: <54653365.2020703@gmail.com> References: <54651C9C.2020108@gmail.com> <877fyyrdgq.fsf@sun.ac.za> <54653365.2020703@gmail.com> Message-ID: <87egt1ps1s.fsf@sun.ac.za> Hi Almar On 2014-11-14 00:40:37, Almar Klein wrote: > With that, I suppose skimage could focus on the processing rather than > the io, since ideally, we'd have one library for processing images, and > one for reading/saving images. That is certainly the direction we're aiming for. At the moment, we try to have a minimal setup that works in 80% of use-cases. Once imageio is distributed widely in the main distributions, we can even make it a default dependency. In the mean time, let's talk about integrating it as a plugin, or perhaps add a page to the skimage docs on how to read more exotic formats (especially cross-platform video would be a big win!). St?fan From stefan at sun.ac.za Mon Nov 17 18:38:15 2014 From: stefan at sun.ac.za (Stefan van der Walt) Date: Tue, 18 Nov 2014 01:38:15 +0200 Subject: regionprops Very slow on centroid identification In-Reply-To: <00059269-0073-45fe-bcf6-9cb7d10abfce@googlegroups.com> References: <00059269-0073-45fe-bcf6-9cb7d10abfce@googlegroups.com> Message-ID: <8761edpfdk.fsf@sun.ac.za> Hi Jeff On 2014-11-14 17:27:42, jeff witz wrote: > In order to deal with data in real time I have to be fast (over 100 fps). > So I first identify the Zones Of Interests using this example : > http://scikit-image.org/docs/dev/auto_examples/plot_label.html I'm afraid that for a 100 fps applications, you'll currently have to look at OpenCV. We'd love to get those kinds of execution times, but it's not easily achievable with our current stack. That said, we are working on improving regionprops calculations. Regards St?fan From georgeshattab at gmail.com Tue Nov 18 05:10:36 2014 From: georgeshattab at gmail.com (Georges H) Date: Tue, 18 Nov 2014 02:10:36 -0800 (PST) Subject: Error with importing canny (filter/feature) Message-ID: <212a546b-5e70-4111-8ddc-428433c9681e@googlegroups.com> Hi everyone, So the problem is that canny is not working under feature while i see all the tutorials online using the feature module if i look at the directory, it s just not there >>> print dir(skimage.feature) ['BRIEF', 'CENSURE', 'ORB', '__all__', '__builtins__', '__doc__', '__file__' , '__name__', '__package__', '__path__', '_daisy', '_hessian_det_appx', '_hog', '_texture', 'blob', 'blob_dog', 'blob_doh', 'blob_log', 'brief', 'brief_cy', 'censure', 'censure_cy', 'corner', 'corner_cy', 'corner_fast', 'corner_foerstner', 'corner_harris', 'corner_kitchen_rosenfeld', 'corner_moravec', 'corner_orientations', 'corner_peaks', 'corner_shi_tomasi' , 'corner_subpix', 'daisy', 'greycomatrix', 'greycoprops', 'hessian_matrix', 'hessian_matrix_det', 'hessian_matrix_eigvals', 'hog', 'local_binary_pattern', 'match', 'match_descriptors', 'match_template', 'orb', 'orb_cy', 'peak', 'peak_local_max', 'plot_matches', 'structure_tensor', 'structure_tensor_eigvals', 'template', 'texture', 'util'] looked up a bit on the web this issue, found that it s in feature, proven by : >>> print dir(skimage.filter) ['LPIFilter2D', '__all__', '__builtins__', '__doc__', '__file__', '__name__' , '__package__', '__path__', '_canny', '_gabor', '_gaussian', '_rank_order', 'canny', 'denoise_bilateral', 'denoise_tv_bregman', 'denoise_tv_chambolle', 'deprecated', 'edges', 'gabor_filter', 'gabor_kernel', 'gaussian_filter', 'hprewitt', 'hscharr', 'hsobel', 'inverse', 'lpi_filter', 'prewitt', 'rank', 'rank_order', 'restoration', 'roberts', 'roberts_negative_diagonal', 'roberts_positive_diagonal', 'scharr', 'sobel', 'threshold_adaptive', 'threshold_isodata', 'threshold_otsu', 'threshold_yen', 'thresholding', 'vprewitt', 'vscharr', 'vsobel', 'wiener'] now the thing is can i fix this and why is it there ? Appreciate any help on the matter. Note : "from skimage import filter" works perfectly -------------- next part -------------- An HTML attachment was scrubbed... URL: From hervebouy at gmail.com Tue Nov 18 06:21:34 2014 From: hervebouy at gmail.com (Herve Bouy) Date: Tue, 18 Nov 2014 03:21:34 -0800 (PST) Subject: Image warping using transform.PolynomialTransform: crazy results Message-ID: <133fea57-5306-428a-8812-350eefdcd5e0@googlegroups.com> Hi, I found very few examples for transform.PolynomialTransform on the internet so I hope someone in this group can help me understand what I am doing wrong. If it's not the right place to ask for help, please forgive me! Here is my problem. I have a greyscale image with some curved lines. I want to transform it so the lines become straight. So I measure the position of the lines at regular intervals (in the attached file source_test2.csv) And compute the desired positions after transformation (in the attached file destination_test2.csv) So i have a nice set of input points and their correspondences as in the figure below (red = input points, and blue = desired positions after transformation): Next I compute the transformation using skimage.transform.PolynomialTransform and a polynomial of order 2, and apply the transformation to get the warped image using skimage.transform.warp But the warped image is completely crazy! See below: It seems the transformation found by PolynomialTransform is completely wrong... *Note that I managed to get a good transformation in some cases for sub-images (e.g using the first 400 columns only).* What am I doing wrong? Are PolynomialTransform too unstable? Do I need a regular grid? I attach the code I use (warp.py) Thanks for your help! Herv? -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: destination_test2.csv Type: text/csv Size: 74260 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: source_test2.csv Type: text/csv Size: 117277 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: warp.py Type: text/x-python Size: 1326 bytes Desc: not available URL: From jni.soma at gmail.com Tue Nov 18 06:43:29 2014 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Tue, 18 Nov 2014 03:43:29 -0800 (PST) Subject: Error with importing canny (filter/feature) In-Reply-To: <212a546b-5e70-4111-8ddc-428433c9681e@googlegroups.com> References: <212a546b-5e70-4111-8ddc-428433c9681e@googlegroups.com> Message-ID: <1416311009594.b95fc455@Nodemailer> Hi Georges, I believe this is because you are using a tagged version of skimage (probably even the most recent, 0.10.1), but looking at the dev documentation, which reflects a recent move of Canny from filter to feature: https://github.com/scikit-image/scikit-image/pull/1113 Which tutorials are you finding? Anyway, your options are: * Carry on using filter for now, know that this is the expected behaviour * Download the latest `master` branch from github and install that, and use the new feature syntax for Canny. Hope this helps! Juan. On Tue, Nov 18, 2014 at 9:10 PM, Georges H wrote: > Hi everyone, > So the problem is that canny is not working under feature while i see all > the tutorials online using the feature module > if i look at the directory, it s just not there >>>> print dir(skimage.feature) > ['BRIEF', 'CENSURE', 'ORB', '__all__', '__builtins__', '__doc__', '__file__' > , '__name__', '__package__', '__path__', '_daisy', '_hessian_det_appx', > '_hog', '_texture', 'blob', 'blob_dog', 'blob_doh', 'blob_log', 'brief', > 'brief_cy', 'censure', 'censure_cy', 'corner', 'corner_cy', 'corner_fast', > 'corner_foerstner', 'corner_harris', 'corner_kitchen_rosenfeld', > 'corner_moravec', 'corner_orientations', 'corner_peaks', 'corner_shi_tomasi' > , 'corner_subpix', 'daisy', 'greycomatrix', 'greycoprops', 'hessian_matrix', > 'hessian_matrix_det', 'hessian_matrix_eigvals', 'hog', > 'local_binary_pattern', 'match', 'match_descriptors', 'match_template', > 'orb', 'orb_cy', 'peak', 'peak_local_max', 'plot_matches', > 'structure_tensor', 'structure_tensor_eigvals', 'template', 'texture', > 'util'] > looked up a bit on the web this issue, found that it s in feature, proven > by : >>>> print dir(skimage.filter) > ['LPIFilter2D', '__all__', '__builtins__', '__doc__', '__file__', '__name__' > , '__package__', '__path__', '_canny', '_gabor', '_gaussian', '_rank_order', > 'canny', 'denoise_bilateral', 'denoise_tv_bregman', 'denoise_tv_chambolle', > 'deprecated', 'edges', 'gabor_filter', 'gabor_kernel', 'gaussian_filter', > 'hprewitt', 'hscharr', 'hsobel', 'inverse', 'lpi_filter', 'prewitt', 'rank', > 'rank_order', 'restoration', 'roberts', 'roberts_negative_diagonal', > 'roberts_positive_diagonal', 'scharr', 'sobel', 'threshold_adaptive', > 'threshold_isodata', 'threshold_otsu', 'threshold_yen', 'thresholding', > 'vprewitt', 'vscharr', 'vsobel', 'wiener'] > now the thing is can i fix this and why is it there ? > Appreciate any help on the matter. > Note : "from skimage import filter" works perfectly > -- > You received this message because you are subscribed to the Google Groups "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -------------- next part -------------- An HTML attachment was scrubbed... URL: From georgeshattab at gmail.com Tue Nov 18 10:06:00 2014 From: georgeshattab at gmail.com (Georges H) Date: Tue, 18 Nov 2014 07:06:00 -0800 (PST) Subject: Error with importing canny (filter/feature) In-Reply-To: <1416311009594.b95fc455@Nodemailer> References: <212a546b-5e70-4111-8ddc-428433c9681e@googlegroups.com> <1416311009594.b95fc455@Nodemailer> Message-ID: <9c03555c-197f-4d2e-b015-913088bccea7@googlegroups.com> Hi Juan, thanks for the fast reply ! I was mentioning tutorials such as this one : hough_transform that uses the canny from feature, and many others out there even if canny is actually in filter Got the master and 0.10.x. Canny is not in the feature module unless i did something wrong.. On Tuesday, 18 November 2014 12:43:31 UTC+1, Juan Nunez-Iglesias wrote: > > Hi Georges, > > I believe this is because you are using a tagged version of skimage > (probably even the most recent, 0.10.1), but looking at the dev > documentation, which reflects a recent move of Canny from filter to feature: > https://github.com/scikit-image/scikit-image/pull/1113 > > Which tutorials are you finding? > > Anyway, your options are: > > * Carry on using filter for now, know that this is the expected behaviour > * Download the latest `master` branch from github and install that, and > use the new feature syntax for Canny. > > Hope this helps! > > Juan. > > > > > On Tue, Nov 18, 2014 at 9:10 PM, Georges H > wrote: > >> Hi everyone, >> >> So the problem is that canny is not working under feature while i see all >> the tutorials online using the feature module >> if i look at the directory, it s just not there >> >> >>> print dir(skimage.feature) >> ['BRIEF', 'CENSURE', 'ORB', '__all__', '__builtins__', '__doc__', >> '__file__', '__name__', '__package__', '__path__', '_daisy', >> '_hessian_det_appx', '_hog', '_texture', 'blob', 'blob_dog', 'blob_doh', >> 'blob_log', 'brief', 'brief_cy', 'censure', 'censure_cy', 'corner', >> 'corner_cy', 'corner_fast', 'corner_foerstner', 'corner_harris', >> 'corner_kitchen_rosenfeld', 'corner_moravec', 'corner_orientations', >> 'corner_peaks', 'corner_shi_tomasi', 'corner_subpix', 'daisy', >> 'greycomatrix', 'greycoprops', 'hessian_matrix', 'hessian_matrix_det', >> 'hessian_matrix_eigvals', 'hog', 'local_binary_pattern', 'match', >> 'match_descriptors', 'match_template', 'orb', 'orb_cy', 'peak', >> 'peak_local_max', 'plot_matches', 'structure_tensor', >> 'structure_tensor_eigvals', 'template', 'texture', 'util'] >> >> >> looked up a bit on the web this issue, found that it s in feature, proven >> by : >> >> >>> print dir(skimage.filter) >> ['LPIFilter2D', '__all__', '__builtins__', '__doc__', '__file__', >> '__name__', '__package__', '__path__', '_canny', '_gabor', '_gaussian', >> '_rank_order', 'canny', 'denoise_bilateral', 'denoise_tv_bregman', >> 'denoise_tv_chambolle', 'deprecated', 'edges', 'gabor_filter', >> 'gabor_kernel', 'gaussian_filter', 'hprewitt', 'hscharr', 'hsobel', >> 'inverse', 'lpi_filter', 'prewitt', 'rank', 'rank_order', 'restoration', >> 'roberts', 'roberts_negative_diagonal', 'roberts_positive_diagonal', >> 'scharr', 'sobel', 'threshold_adaptive', 'threshold_isodata', >> 'threshold_otsu', 'threshold_yen', 'thresholding', 'vprewitt', 'vscharr', >> 'vsobel', 'wiener'] >> >> >> now the thing is can i fix this and why is it there ? >> >> Appreciate any help on the matter. >> >> Note : "from skimage import filter" works perfectly >> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "scikit-image" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to scikit-image... at googlegroups.com . >> For more options, visit https://groups.google.com/d/optout. >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Tue Nov 18 17:16:53 2014 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Tue, 18 Nov 2014 14:16:53 -0800 (PST) Subject: Error with importing canny (filter/feature) In-Reply-To: <9c03555c-197f-4d2e-b015-913088bccea7@googlegroups.com> References: <9c03555c-197f-4d2e-b015-913088bccea7@googlegroups.com> Message-ID: <1416349013023.e40630db@Nodemailer> What do you mean by "*and* 0.10.x"? My guess is you are running everything from 0.10. On master, from "skimage.feature import canny" should work. Easy way to check: "import skimage; print(skimage.__version__)". You can tell from the URL in that link, which contains "dev", that it is for the master version. You can find links for the release APIs on the right hand side. Mind if I ask how you got there? Going to the API reference from scikit-image.org takes me to 0.10.x. On Wed, Nov 19, 2014 at 2:06 AM, Georges H wrote: > Hi Juan, thanks for the fast reply ! > I was mentioning tutorials such as this one : hough_transform > that > uses the canny from feature, and many others out there even if canny is > actually in filter > Got the master and 0.10.x. Canny is not in the feature module unless i did > something wrong.. > On Tuesday, 18 November 2014 12:43:31 UTC+1, Juan Nunez-Iglesias wrote: >> >> Hi Georges, >> >> I believe this is because you are using a tagged version of skimage >> (probably even the most recent, 0.10.1), but looking at the dev >> documentation, which reflects a recent move of Canny from filter to feature: >> https://github.com/scikit-image/scikit-image/pull/1113 >> >> Which tutorials are you finding? >> >> Anyway, your options are: >> >> * Carry on using filter for now, know that this is the expected behaviour >> * Download the latest `master` branch from github and install that, and >> use the new feature syntax for Canny. >> >> Hope this helps! >> >> Juan. >> >> >> >> >> On Tue, Nov 18, 2014 at 9:10 PM, Georges H > > wrote: >> >>> Hi everyone, >>> >>> So the problem is that canny is not working under feature while i see all >>> the tutorials online using the feature module >>> if i look at the directory, it s just not there >>> >>> >>> print dir(skimage.feature) >>> ['BRIEF', 'CENSURE', 'ORB', '__all__', '__builtins__', '__doc__', >>> '__file__', '__name__', '__package__', '__path__', '_daisy', >>> '_hessian_det_appx', '_hog', '_texture', 'blob', 'blob_dog', 'blob_doh', >>> 'blob_log', 'brief', 'brief_cy', 'censure', 'censure_cy', 'corner', >>> 'corner_cy', 'corner_fast', 'corner_foerstner', 'corner_harris', >>> 'corner_kitchen_rosenfeld', 'corner_moravec', 'corner_orientations', >>> 'corner_peaks', 'corner_shi_tomasi', 'corner_subpix', 'daisy', >>> 'greycomatrix', 'greycoprops', 'hessian_matrix', 'hessian_matrix_det', >>> 'hessian_matrix_eigvals', 'hog', 'local_binary_pattern', 'match', >>> 'match_descriptors', 'match_template', 'orb', 'orb_cy', 'peak', >>> 'peak_local_max', 'plot_matches', 'structure_tensor', >>> 'structure_tensor_eigvals', 'template', 'texture', 'util'] >>> >>> >>> looked up a bit on the web this issue, found that it s in feature, proven >>> by : >>> >>> >>> print dir(skimage.filter) >>> ['LPIFilter2D', '__all__', '__builtins__', '__doc__', '__file__', >>> '__name__', '__package__', '__path__', '_canny', '_gabor', '_gaussian', >>> '_rank_order', 'canny', 'denoise_bilateral', 'denoise_tv_bregman', >>> 'denoise_tv_chambolle', 'deprecated', 'edges', 'gabor_filter', >>> 'gabor_kernel', 'gaussian_filter', 'hprewitt', 'hscharr', 'hsobel', >>> 'inverse', 'lpi_filter', 'prewitt', 'rank', 'rank_order', 'restoration', >>> 'roberts', 'roberts_negative_diagonal', 'roberts_positive_diagonal', >>> 'scharr', 'sobel', 'threshold_adaptive', 'threshold_isodata', >>> 'threshold_otsu', 'threshold_yen', 'thresholding', 'vprewitt', 'vscharr', >>> 'vsobel', 'wiener'] >>> >>> >>> now the thing is can i fix this and why is it there ? >>> >>> Appreciate any help on the matter. >>> >>> Note : "from skimage import filter" works perfectly >>> >>> >>> -- >>> You received this message because you are subscribed to the Google Groups >>> "scikit-image" group. >>> To unsubscribe from this group and stop receiving emails from it, send an >>> email to scikit-image... at googlegroups.com . >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> > -- > You received this message because you are subscribed to the Google Groups "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -------------- next part -------------- An HTML attachment was scrubbed... URL: From hughesadam87 at gmail.com Tue Nov 18 17:01:06 2014 From: hughesadam87 at gmail.com (Adam Hughes) Date: Tue, 18 Nov 2014 17:01:06 -0500 Subject: Easy masking of RGB images Message-ID: Hi, I often find myself wanting to mask two overlay two color images, where the second image will replace values on the first image rather than adding. IE: img1 + img 2 --> adds values img1 U img2 --> replaces values Essentially, overlay all the pixels that are not black. Is there a library or set of functions somewhere that makes this easy? I remember a while back thinking I would have to write my own overlay/masking utilities to get this behavior, but I hope that's not true. Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From almar.klein at gmail.com Tue Nov 18 11:13:08 2014 From: almar.klein at gmail.com (Almar Klein) Date: Tue, 18 Nov 2014 17:13:08 +0100 Subject: ANN: imageio v1.0 In-Reply-To: References: <54651C9C.2020108@gmail.com> Message-ID: <546B7014.40008@gmail.com> > By vendoring I meant including a snapshot of the imageio project in the > scikit-image repo, and > using it if there is not a system version available (which is how we > handle `tifffile.py`). I suppose you'd like imageio to use relative imports throughout for this to work? It does not yet, but that's easy enough to fix from my end. > I agree with St?fan that we should include > imageio as an optional plugin in the short term and then once an imageio > Debian package > and conda mainline package are available, more toward making it a > requirement instead of PIL. That sounds like a reasonable plan. > I will implement the imageio scikit-image plugin (unless you'd rather), > but I've got a few other commitments > lined up prior to getting more involved in the short term. Great. I am involved in a few other things now as well, so I was hoping someone would pick this up. > As someone who has worked in a lab with no internet connection, I am > wary of requiring an external library to be downloaded upon install Actually, it's downloaded at runtime. Which is even worse, I guess :) The motivation for this is that a) it made the code simpler; 2) some dependencies like the ffmpeg exe are rather large, and installing these by default (or shipping them along in the dist package) seemed like something that might irritate users who just want to read a png image. I'd be happy to work towards a solution for that. At least to get freeimage working. Perhaps you can help find a solution, as having been in such a situation, you might have a good idea of what could work and what not. See: https://github.com/imageio/imageio/issues/42 Regards, Almar > > On Thursday, November 13, 2014 3:03:27 PM UTC-6, Almar Klein wrote: > > Hi all, > > I'm pleased to announce version 1.0 of imageio - a library for reading > and writing images. This library started as a spin-off of the freeimage > plugin in skimage, and is now a fully-fledged library with unit tests > and all. > > Imageio provides an easy interface to read and write a wide range of > image data, including animated images, volumetric data, and scientific > formats. It is cross-platform, runs on Python 2.x and 3.x, and is easy > to install. > > Imageio is plugin-based, making it easy to extend. It could probably > use > more scientific formats. I welcome anyone who's interested to > contribute! > > install: pip install imageio > website: http://imageio.github.io > release notes: > http://imageio.readthedocs.org/en/latest/releasenotes.html > > > Regards, > Almar > > -- > You received this message because you are subscribed to the Google > Groups "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send > an email to scikit-image+unsubscribe at googlegroups.com > . > For more options, visit https://groups.google.com/d/optout. From georgeshattab at gmail.com Wed Nov 19 02:58:33 2014 From: georgeshattab at gmail.com (Georges H) Date: Tue, 18 Nov 2014 23:58:33 -0800 (PST) Subject: Error with importing canny (filter/feature) In-Reply-To: <1416349013023.e40630db@Nodemailer> References: <9c03555c-197f-4d2e-b015-913088bccea7@googlegroups.com> <1416349013023.e40630db@Nodemailer> Message-ID: <1fb66814-548b-47de-9775-21aba8a2370c@googlegroups.com> Everything is working perfectly i believe i just needed a break, apologies and thanks for the fast replies ! import skimage; print(skimage.__version__) 0.11dev On Tuesday, 18 November 2014 23:16:54 UTC+1, Juan Nunez-Iglesias wrote: > > What do you mean by "*and* 0.10.x"? My guess is you are running everything > from 0.10. On master, from "skimage.feature import canny" should work. Easy > way to check: "import skimage; print(skimage.__version__)". > > You can tell from the URL in that link, which contains "dev", that it is > for the master version. You can find links for the release APIs on the > right hand side. Mind if I ask how you got there? Going to the API > reference from scikit-image.org takes me to 0.10.x. > > > > > On Wed, Nov 19, 2014 at 2:06 AM, Georges H > wrote: > >> Hi Juan, thanks for the fast reply ! >> >> I was mentioning tutorials such as this one : hough_transform >> that >> uses the canny from feature, and many others out there even if canny is >> actually in filter >> >> Got the master and 0.10.x. Canny is not in the feature module unless i >> did something wrong.. >> >> >> >> On Tuesday, 18 November 2014 12:43:31 UTC+1, Juan Nunez-Iglesias wrote: >>> >>> Hi Georges, >>> >>> I believe this is because you are using a tagged version of skimage >>> (probably even the most recent, 0.10.1), but looking at the dev >>> documentation, which reflects a recent move of Canny from filter to feature: >>> https://github.com/scikit-image/scikit-image/pull/1113 >>> >>> Which tutorials are you finding? >>> >>> Anyway, your options are: >>> >>> * Carry on using filter for now, know that this is the expected behaviour >>> * Download the latest `master` branch from github and install that, and >>> use the new feature syntax for Canny. >>> >>> Hope this helps! >>> >>> Juan. >>> >>> >>> >>> >>> On Tue, Nov 18, 2014 at 9:10 PM, Georges H wrote: >>> >>>> Hi everyone, >>>> >>>> So the problem is that canny is not working under feature while i see >>>> all the tutorials online using the feature module >>>> if i look at the directory, it s just not there >>>> >>>> >>> print dir(skimage.feature) >>>> ['BRIEF', 'CENSURE', 'ORB', '__all__', '__builtins__', '__doc__', >>>> '__file__', '__name__', '__package__', '__path__', '_daisy', >>>> '_hessian_det_appx', '_hog', '_texture', 'blob', 'blob_dog', 'blob_doh' >>>> , 'blob_log', 'brief', 'brief_cy', 'censure', 'censure_cy', 'corner', >>>> 'corner_cy', 'corner_fast', 'corner_foerstner', 'corner_harris', >>>> 'corner_kitchen_rosenfeld', 'corner_moravec', 'corner_orientations', >>>> 'corner_peaks', 'corner_shi_tomasi', 'corner_subpix', 'daisy', >>>> 'greycomatrix', 'greycoprops', 'hessian_matrix', 'hessian_matrix_det', >>>> 'hessian_matrix_eigvals', 'hog', 'local_binary_pattern', 'match', >>>> 'match_descriptors', 'match_template', 'orb', 'orb_cy', 'peak', >>>> 'peak_local_max', 'plot_matches', 'structure_tensor', >>>> 'structure_tensor_eigvals', 'template', 'texture', 'util'] >>>> >>>> >>>> looked up a bit on the web this issue, found that it s in feature, >>>> proven by : >>>> >>>> >>> print dir(skimage.filter) >>>> ['LPIFilter2D', '__all__', '__builtins__', '__doc__', '__file__', >>>> '__name__', '__package__', '__path__', '_canny', '_gabor', '_gaussian', >>>> '_rank_order', 'canny', 'denoise_bilateral', 'denoise_tv_bregman', >>>> 'denoise_tv_chambolle', 'deprecated', 'edges', 'gabor_filter', >>>> 'gabor_kernel', 'gaussian_filter', 'hprewitt', 'hscharr', 'hsobel', >>>> 'inverse', 'lpi_filter', 'prewitt', 'rank', 'rank_order', 'restoration' >>>> , 'roberts', 'roberts_negative_diagonal', 'roberts_positive_diagonal', >>>> 'scharr', 'sobel', 'threshold_adaptive', 'threshold_isodata', >>>> 'threshold_otsu', 'threshold_yen', 'thresholding', 'vprewitt', >>>> 'vscharr', 'vsobel', 'wiener'] >>>> >>>> >>>> now the thing is can i fix this and why is it there ? >>>> >>>> Appreciate any help on the matter. >>>> >>>> Note : "from skimage import filter" works perfectly >>>> >>>> >>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "scikit-image" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to scikit-image... at googlegroups.com. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> -- >> You received this message because you are subscribed to the Google Groups >> "scikit-image" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to scikit-image... at googlegroups.com . >> For more options, visit https://groups.google.com/d/optout. >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From steven.silvester at gmail.com Wed Nov 19 07:01:01 2014 From: steven.silvester at gmail.com (Steven Silvester) Date: Wed, 19 Nov 2014 04:01:01 -0800 (PST) Subject: ANN: imageio v1.0 In-Reply-To: <54651C9C.2020108@gmail.com> References: <54651C9C.2020108@gmail.com> Message-ID: Yes, all imports would have to be relative. I've chimed in on #42, but posting my thoughts here: "I'd vote to have a source-only version, and wheels for 64 bit Linux, Windows, and OSX with just the freeimage support. Rather that auto-downloading, it would be nice to present the user with the option of whether to download an external lib, perhaps as a simple Tk dialog. I think partial functionality is fine in this case given the nature of the library." Regards, Steve On Thursday, November 13, 2014 3:03:27 PM UTC-6, Almar Klein wrote: > > Hi all, > > I'm pleased to announce version 1.0 of imageio - a library for reading > and writing images. This library started as a spin-off of the freeimage > plugin in skimage, and is now a fully-fledged library with unit tests > and all. > > Imageio provides an easy interface to read and write a wide range of > image data, including animated images, volumetric data, and scientific > formats. It is cross-platform, runs on Python 2.x and 3.x, and is easy > to install. > > Imageio is plugin-based, making it easy to extend. It could probably use > more scientific formats. I welcome anyone who's interested to contribute! > > install: pip install imageio > website: http://imageio.github.io > release notes: http://imageio.readthedocs.org/en/latest/releasenotes.html > > Regards, > Almar > -------------- next part -------------- An HTML attachment was scrubbed... URL: From witzjean at gmail.com Wed Nov 19 17:34:26 2014 From: witzjean at gmail.com (jeff witz) Date: Wed, 19 Nov 2014 14:34:26 -0800 (PST) Subject: regionprops Very slow on centroid identification In-Reply-To: <8761edpfdk.fsf@sun.ac.za> References: <00059269-0073-45fe-bcf6-9cb7d10abfce@googlegroups.com> <8761edpfdk.fsf@sun.ac.za> Message-ID: <11572cf4-137a-48b8-b01c-e6406a983d59@googlegroups.com> Hello, With the process I've explained before it works at least at 70 FPS, we still have room for a lot of improvement ! For example we will compute each mark on a specific process. Finally we don't use regionprops for the real-time purposes because regionprops can find several zones in a ZOI and we want to considere the choosen zone to be unique. We use numpy.where to find where white pixels are and numpy.min() and numpy.max() to find the bounding box instead of bbox from regionprops. bbox is a little faster than our numpy version but can find several zones. We notice that the a median filter on each ZOI increase stability. Once we get something clean I will send an example. We already use cv2 as we have implemented the camera grabber class in OpenCV (if someone need a complete ximea opencv class mail me), I could test and compare the speed. Regards Le mardi 18 novembre 2014 00:38:35 UTC+1, Stefan van der Walt a ?crit : > > Hi Jeff > > On 2014-11-14 17:27:42, jeff witz > > wrote: > > In order to deal with data in real time I have to be fast (over 100 > fps). > > So I first identify the Zones Of Interests using this example : > > http://scikit-image.org/docs/dev/auto_examples/plot_label.html > > I'm afraid that for a 100 fps applications, you'll currently have to > look at OpenCV. We'd love to get those kinds of execution times, but > it's not easily achievable with our current stack. That said, we are > working on improving regionprops calculations. > > Regards > St?fan > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hughesadam87 at gmail.com Wed Nov 19 19:02:56 2014 From: hughesadam87 at gmail.com (Adam Hughes) Date: Wed, 19 Nov 2014 16:02:56 -0800 (PST) Subject: Easy masking of RGB images In-Reply-To: <87vbmburwk.fsf@sun.ac.za> References: <87vbmburwk.fsf@sun.ac.za> Message-ID: Ah, right you are! Dunno what I was mixed up about... On Wednesday, November 19, 2014 10:33:21 AM UTC-5, Stefan van der Walt wrote: > > Hi Adam > > On 2014-11-19 00:01:06, Adam Hughes > > wrote: > > img1 + img 2 --> adds values > > img1 U img2 --> replaces values > > > > Essentially, overlay all the pixels that are not black. > > > > Is there a library or set of functions somewhere that makes this easy? > I > > remember a while back thinking I would have to write my own > overlay/masking > > utilities to get this behavior, but I hope that's not true. > > It should be fairly straightforward, if I understand correctly: > > mask = (img2 != 0) > img1[mask] = img2[mask] > > Regards > St?fan > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan at sun.ac.za Wed Nov 19 10:33:15 2014 From: stefan at sun.ac.za (Stefan van der Walt) Date: Wed, 19 Nov 2014 17:33:15 +0200 Subject: Easy masking of RGB images In-Reply-To: References: Message-ID: <87vbmburwk.fsf@sun.ac.za> Hi Adam On 2014-11-19 00:01:06, Adam Hughes wrote: > img1 + img 2 --> adds values > img1 U img2 --> replaces values > > Essentially, overlay all the pixels that are not black. > > Is there a library or set of functions somewhere that makes this easy? I > remember a while back thinking I would have to write my own overlay/masking > utilities to get this behavior, but I hope that's not true. It should be fairly straightforward, if I understand correctly: mask = (img2 != 0) img1[mask] = img2[mask] Regards St?fan From jsch at demuc.de Wed Nov 19 17:58:17 2014 From: jsch at demuc.de (Johannes Schoenberger) Date: Wed, 19 Nov 2014 17:58:17 -0500 Subject: regionprops Very slow on centroid identification In-Reply-To: <11572cf4-137a-48b8-b01c-e6406a983d59@googlegroups.com> References: <00059269-0073-45fe-bcf6-9cb7d10abfce@googlegroups.com> <8761edpfdk.fsf@sun.ac.za> <11572cf4-137a-48b8-b01c-e6406a983d59@googlegroups.com> Message-ID: <0A8812E2-4729-4351-A3CD-3A2324AC3FBE@demuc.de> @jeff Look at the skimage.measure.moments_* functions. Using those should be a lot faster than using numpy to compute the moments. From jsch at demuc.de Wed Nov 19 19:25:35 2014 From: jsch at demuc.de (Johannes Schoenberger) Date: Wed, 19 Nov 2014 19:25:35 -0500 Subject: Sobel Message-ID: Hi, Why are we returning the absolute values in the hsobel and vsobel functions? I do not see the benefit. Johannes From jsch at demuc.de Wed Nov 19 22:45:48 2014 From: jsch at demuc.de (Johannes Schoenberger) Date: Wed, 19 Nov 2014 22:45:48 -0500 Subject: Sobel In-Reply-To: References: Message-ID: What is the reference implementation in this case? Scipy? > On Nov 19, 2014, at 10:43 PM, Juan Nunez-Iglesias wrote: > > Is it what the "reference" implementation returns? Either way the sign is valuable info. +1 for returning the actual filter output. > > On Thu, Nov 20, 2014 at 11:25 AM, Johannes Schoenberger wrote: > Hi, > > Why are we returning the absolute values in the hsobel and vsobel functions? > > I do not see the benefit. > > Johannes > > -- > You received this message because you are subscribed to the Google Groups "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. > > > -- > You received this message because you are subscribed to the Google Groups "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. From jsch at demuc.de Wed Nov 19 22:53:03 2014 From: jsch at demuc.de (Johannes Schoenberger) Date: Wed, 19 Nov 2014 22:53:03 -0500 Subject: Sobel In-Reply-To: References: Message-ID: <8E001836-713A-46C1-811B-A729C8B489B9@demuc.de> How do we want to treat this change in behavior? Raise a warning? > On Nov 19, 2014, at 10:45 PM, Johannes Schoenberger wrote: > > What is the reference implementation in this case? Scipy? > >> On Nov 19, 2014, at 10:43 PM, Juan Nunez-Iglesias wrote: >> >> Is it what the "reference" implementation returns? Either way the sign is valuable info. +1 for returning the actual filter output. >> >> On Thu, Nov 20, 2014 at 11:25 AM, Johannes Schoenberger wrote: >> Hi, >> >> Why are we returning the absolute values in the hsobel and vsobel functions? >> >> I do not see the benefit. >> >> Johannes >> >> -- >> You received this message because you are subscribed to the Google Groups "scikit-image" group. >> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com. >> For more options, visit https://groups.google.com/d/optout. >> >> >> -- >> You received this message because you are subscribed to the Google Groups "scikit-image" group. >> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com. >> For more options, visit https://groups.google.com/d/optout. > > -- > You received this message because you are subscribed to the Google Groups "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. From tsyu80 at gmail.com Thu Nov 20 00:07:50 2014 From: tsyu80 at gmail.com (Tony Yu) Date: Wed, 19 Nov 2014 23:07:50 -0600 Subject: Sobel In-Reply-To: <8E001836-713A-46C1-811B-A729C8B489B9@demuc.de> References: <8E001836-713A-46C1-811B-A729C8B489B9@demuc.de> Message-ID: +1 on the change. This caused problems for the SciPy 2014 tutorial and required switching to the scipy implementation. One option would be to create new functions; e.g. `sobel_h`/`sobel_v` (or `sobel_x`/`sobel_y`; in this case, it might make sense to match x/y with the gradient direction rather than the edge direction). Alternatively, we might consider adding a warning and a `deprecation_warning=True` flag to `hsobel`/`vsobel`. That way, users can adapt to the change (if necessary) and turn off the deprecation warning. -Tony On Wed, Nov 19, 2014 at 9:53 PM, Johannes Schoenberger wrote: > How do we want to treat this change in behavior? Raise a warning? > > > On Nov 19, 2014, at 10:45 PM, Johannes Schoenberger > wrote: > > > > What is the reference implementation in this case? Scipy? > > > >> On Nov 19, 2014, at 10:43 PM, Juan Nunez-Iglesias > wrote: > >> > >> Is it what the "reference" implementation returns? Either way the sign > is valuable info. +1 for returning the actual filter output. > >> > >> On Thu, Nov 20, 2014 at 11:25 AM, Johannes Schoenberger > wrote: > >> Hi, > >> > >> Why are we returning the absolute values in the hsobel and vsobel > functions? > >> > >> I do not see the benefit. > >> > >> Johannes > >> > >> -- > >> You received this message because you are subscribed to the Google > Groups "scikit-image" group. > >> To unsubscribe from this group and stop receiving emails from it, send > an email to scikit-image+unsubscribe at googlegroups.com. > >> For more options, visit https://groups.google.com/d/optout. > >> > >> > >> -- > >> You received this message because you are subscribed to the Google > Groups "scikit-image" group. > >> To unsubscribe from this group and stop receiving emails from it, send > an email to scikit-image+unsubscribe at googlegroups.com. > >> For more options, visit https://groups.google.com/d/optout. > > > > -- > > You received this message because you are subscribed to the Google > Groups "scikit-image" group. > > To unsubscribe from this group and stop receiving emails from it, send > an email to scikit-image+unsubscribe at googlegroups.com. > > For more options, visit https://groups.google.com/d/optout. > > -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image+unsubscribe at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan at sun.ac.za Thu Nov 20 05:21:22 2014 From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Thu, 20 Nov 2014 12:21:22 +0200 Subject: Sobel In-Reply-To: References: <8E001836-713A-46C1-811B-A729C8B489B9@demuc.de> Message-ID: Nice suggestion, Tony. -------------- next part -------------- An HTML attachment was scrubbed... URL: From fboulogne at sciunto.org Thu Nov 20 13:05:24 2014 From: fboulogne at sciunto.org (=?UTF-8?B?RnJhbsOnb2lzIEJvdWxvZ25l?=) Date: Thu, 20 Nov 2014 13:05:24 -0500 Subject: Example: Scikit-image and trackpy (bubble tracking in foams) Message-ID: <546E2D64.8030208@sciunto.org> Hi, Just for your information, I wrote an example based on my research to show the use of scikit-image with trackpy for feature detection and tracking. http://nbviewer.ipython.org/github/soft-matter/trackpy-examples/blob/master/notebooks/custom_feature_detection.ipynb Hopefully, this might be helpful for future workshops or presentations. Best, -- Fran?ois Boulogne. http://www.sciunto.org GPG: 32D5F22F From jsch at demuc.de Thu Nov 20 13:37:38 2014 From: jsch at demuc.de (Johannes Schoenberger) Date: Thu, 20 Nov 2014 13:37:38 -0500 Subject: Example: Scikit-image and trackpy (bubble tracking in foams) In-Reply-To: <546E2D64.8030208@sciunto.org> References: <546E2D64.8030208@sciunto.org> Message-ID: Very nice example. Do we want to create a new page on the website with collections of nice iPython notebooks? > On Nov 20, 2014, at 1:05 PM, Fran?ois Boulogne wrote: > > Hi, > > Just for your information, I wrote an example based on my research to > show the use of scikit-image with trackpy for feature detection and > tracking. > http://nbviewer.ipython.org/github/soft-matter/trackpy-examples/blob/master/notebooks/custom_feature_detection.ipynb > > Hopefully, this might be helpful for future workshops or presentations. > > Best, > > -- > Fran?ois Boulogne. > http://www.sciunto.org > GPG: 32D5F22F > > > -- > You received this message because you are subscribed to the Google Groups "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. From jsch at demuc.de Thu Nov 20 13:38:09 2014 From: jsch at demuc.de (Johannes Schoenberger) Date: Thu, 20 Nov 2014 13:38:09 -0500 Subject: Sobel In-Reply-To: References: <8E001836-713A-46C1-811B-A729C8B489B9@demuc.de> Message-ID: <84090922-1CA6-4647-AAB5-D5974CA466DE@demuc.de> I note this and hopefully I will be able to submit a PR over the next days. > On Nov 20, 2014, at 5:21 AM, St?fan van der Walt wrote: > > Nice suggestion, Tony. > > > -- > You received this message because you are subscribed to the Google Groups "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. From jni.soma at gmail.com Wed Nov 19 22:43:00 2014 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Thu, 20 Nov 2014 14:43:00 +1100 Subject: Sobel In-Reply-To: References: Message-ID: Is it what the "reference" implementation returns? Either way the sign is valuable info. +1 for returning the actual filter output. On Thu, Nov 20, 2014 at 11:25 AM, Johannes Schoenberger wrote: > Hi, > > Why are we returning the absolute values in the hsobel and vsobel > functions? > > I do not see the benefit. > > Johannes > > -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image+unsubscribe at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From kmichael.aye at gmail.com Thu Nov 20 18:01:04 2014 From: kmichael.aye at gmail.com (Michael Aye) Date: Thu, 20 Nov 2014 15:01:04 -0800 (PST) Subject: Sobel In-Reply-To: References: Message-ID: <06f04515-947b-4d09-8641-ed0d43b9d945@googlegroups.com> How about establishing a pipeline between a linear ridge detector and alignment of the sobels accordingly to the found ridge? Would be a nice example maybe? Michael On Wednesday, November 19, 2014 4:25:39 PM UTC-8, Johannes Sch?nberger wrote: > > Hi, > > Why are we returning the absolute values in the hsobel and vsobel > functions? > > I do not see the benefit. > > Johannes > -------------- next part -------------- An HTML attachment was scrubbed... URL: From fboulogne at sciunto.org Thu Nov 20 16:05:37 2014 From: fboulogne at sciunto.org (=?UTF-8?B?RnJhbsOnb2lzIEJvdWxvZ25l?=) Date: Thu, 20 Nov 2014 16:05:37 -0500 Subject: Example: Scikit-image and trackpy (bubble tracking in foams) In-Reply-To: <20141120192231.GA28567@phare.normalesup.org> References: <546E2D64.8030208@sciunto.org> <20141120192231.GA28567@phare.normalesup.org> Message-ID: <546E57A1.9090401@sciunto.org> Hi Emmanuelle, Le 20/11/2014 14:22, Emmanuelle Gouillart a ?crit : > Very nice! I just tweeted about it :-). :) > How good is that trackpy library? On Tuesday I was giving a presentation > about scikit-image and someone in the audience asked me if I knew some > good tools for 2D/3D + time image processing, for example for tracking > particles/cells. I didn't know any, and actually I don't know whether > there exist some "classical" and robust algorithms for particle tracking > (like median filter for denoising, otsu thresholding, etc.), or if > everything is very application-dependent. What is your experience about > this? I have a great experience and I warmly recommend the library. It's very easy to use, I'd say an investment of few hours to go through the tutorials and play a bit. The documentation is clear and the two mains steps (feature detection and feature tracking) are well separated. Trackpy provides an algorithm to detect particles, but you can also detect bubbles and probably cells if you write your own detection algorithm. Also, Trackpy smartly uses Pandas. Thus, it's very easy to manipulate the data and store everything in a h5 container. I had the occasion to meet Dan. The authors are very responsive and they are also on this ML afaik. I'm currently using trackpy for another project too. Best, -- Fran?ois Boulogne. http://www.sciunto.org GPG: 32D5F22F From fboulogne at sciunto.org Thu Nov 20 17:33:24 2014 From: fboulogne at sciunto.org (=?UTF-8?B?RnJhbsOnb2lzIEJvdWxvZ25l?=) Date: Thu, 20 Nov 2014 17:33:24 -0500 Subject: Example: Scikit-image and trackpy (bubble tracking in foams) In-Reply-To: <20141120214314.GE28567@phare.normalesup.org> References: <546E2D64.8030208@sciunto.org> <20141120192231.GA28567@phare.normalesup.org> <546E57A1.9090401@sciunto.org> <20141120214314.GE28567@phare.normalesup.org> Message-ID: <546E6C34.9020602@sciunto.org> Le 20/11/2014 16:43, Emmanuelle Gouillart a ?crit : > Great, thanks! It seems that most processing pipelines rely on first > detecting objects of interest (eg with a segmentation step) and then > tracking such objects. Do you know of any (generic-enough) approach that > would perform both steps at the same time, ie if you know that the same > objects must be found in several images this information can be used for > performing the segmentation? > That's a good question. I'm not aware of such algorithm. It reminds me that machine learning could be eventually use also with trackpy. I opened a PR showing how scikit-image and scikit learn could be used together to detect digits: https://github.com/scikit-image/skimage-demos/pull/3 A similar procedure could be used in the situation of several populations of features with different shapes but similar sizes for instance (like a mixture of colloidal spheres and cubes) -- Fran?ois Boulogne. http://www.sciunto.org GPG: 32D5F22F From emmanuelle.gouillart at nsup.org Thu Nov 20 14:22:31 2014 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Thu, 20 Nov 2014 20:22:31 +0100 Subject: Example: Scikit-image and trackpy (bubble tracking in foams) In-Reply-To: <546E2D64.8030208@sciunto.org> References: <546E2D64.8030208@sciunto.org> Message-ID: <20141120192231.GA28567@phare.normalesup.org> Very nice! I just tweeted about it :-). How good is that trackpy library? On Tuesday I was giving a presentation about scikit-image and someone in the audience asked me if I knew some good tools for 2D/3D + time image processing, for example for tracking particles/cells. I didn't know any, and actually I don't know whether there exist some "classical" and robust algorithms for particle tracking (like median filter for denoising, otsu thresholding, etc.), or if everything is very application-dependent. What is your experience about this? Best, Emmanuelle On Thu, Nov 20, 2014 at 01:05:24PM -0500, Fran??ois Boulogne wrote: > Hi, > Just for your information, I wrote an example based on my research to > show the use of scikit-image with trackpy for feature detection and > tracking. > http://nbviewer.ipython.org/github/soft-matter/trackpy-examples/blob/master/notebooks/custom_feature_detection.ipynb > Hopefully, this might be helpful for future workshops or presentations. > Best, From emmanuelle.gouillart at nsup.org Thu Nov 20 14:27:56 2014 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Thu, 20 Nov 2014 20:27:56 +0100 Subject: Example: Scikit-image and trackpy (bubble tracking in foams) In-Reply-To: References: <546E2D64.8030208@sciunto.org> Message-ID: <20141120192756.GB28567@phare.normalesup.org> > Do we want to create a new page on the website with collections of nice iPython notebooks? The problem would be to maintain this notebooks. I would rather advocate to cut the tutorials into shorter examples for the gallery (that can also be downloaded as notebooks), and to integrate the "best" notebooks into the user guide, to be sure that the code is maintained. But we could also have a list of links of nice notebooks hosted elsewhere. Just my 2 cents, Emma From nelle.varoquaux at gmail.com Thu Nov 20 16:38:28 2014 From: nelle.varoquaux at gmail.com (Nelle Varoquaux) Date: Thu, 20 Nov 2014 22:38:28 +0100 Subject: Example: Scikit-image and trackpy (bubble tracking in foams) In-Reply-To: <20141120192231.GA28567@phare.normalesup.org> References: <546E2D64.8030208@sciunto.org> <20141120192231.GA28567@phare.normalesup.org> Message-ID: On 20 November 2014 20:22, Emmanuelle Gouillart wrote: > > Very nice! I just tweeted about it :-). > > How good is that trackpy library? On Tuesday I was giving a presentation > about scikit-image and someone in the audience asked me if I knew some > good tools for 2D/3D + time image processing, for example for tracking > particles/cells. I didn't know any, and actually I don't know whether > there exist some "classical" and robust algorithms for particle tracking > (like median filter for denoising, otsu thresholding, etc.), or if > everything is very application-dependent. What is your experience about > this? There are cell tracking specific softwares such as cell cognition (C++ + python). I think there are a lot of very specific software for cell tracking depending on what the data is. Cheers, N > > Best, > Emmanuelle > > > On Thu, Nov 20, 2014 at 01:05:24PM -0500, Fran?ois Boulogne wrote: >> Hi, > >> Just for your information, I wrote an example based on my research to >> show the use of scikit-image with trackpy for feature detection and >> tracking. >> http://nbviewer.ipython.org/github/soft-matter/trackpy-examples/blob/master/notebooks/custom_feature_detection.ipynb > >> Hopefully, this might be helpful for future workshops or presentations. > >> Best, > > -- > You received this message because you are subscribed to the Google Groups "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. From emmanuelle.gouillart at nsup.org Thu Nov 20 16:43:14 2014 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Thu, 20 Nov 2014 22:43:14 +0100 Subject: Example: Scikit-image and trackpy (bubble tracking in foams) In-Reply-To: <546E57A1.9090401@sciunto.org> References: <546E2D64.8030208@sciunto.org> <20141120192231.GA28567@phare.normalesup.org> <546E57A1.9090401@sciunto.org> Message-ID: <20141120214314.GE28567@phare.normalesup.org> Great, thanks! It seems that most processing pipelines rely on first detecting objects of interest (eg with a segmentation step) and then tracking such objects. Do you know of any (generic-enough) approach that would perform both steps at the same time, ie if you know that the same objects must be found in several images this information can be used for performing the segmentation? On Thu, Nov 20, 2014 at 04:05:37PM -0500, Fran??ois Boulogne wrote: > Hi Emmanuelle, > Le 20/11/2014 14:22, Emmanuelle Gouillart a ??crit : > > Very nice! I just tweeted about it :-). > :) > > How good is that trackpy library? On Tuesday I was giving a presentation > > about scikit-image and someone in the audience asked me if I knew some > > good tools for 2D/3D + time image processing, for example for tracking > > particles/cells. I didn't know any, and actually I don't know whether > > there exist some "classical" and robust algorithms for particle tracking > > (like median filter for denoising, otsu thresholding, etc.), or if > > everything is very application-dependent. What is your experience about > > this? > I have a great experience and I warmly recommend the library. It's very > easy to use, I'd say an investment of few hours to go through the > tutorials and play a bit. > The documentation is clear and the two mains steps (feature detection > and feature tracking) are well separated. Trackpy provides an algorithm > to detect particles, but you can also detect bubbles and probably cells > if you write your own detection algorithm. > Also, Trackpy smartly uses Pandas. Thus, it's very easy to manipulate > the data and store everything in a h5 container. > I had the occasion to meet Dan. The authors are very responsive and they > are also on this ML afaik. > I'm currently using trackpy for another project too. > Best, From stefan at sun.ac.za Thu Nov 20 21:03:52 2014 From: stefan at sun.ac.za (Stefan van der Walt) Date: Fri, 21 Nov 2014 04:03:52 +0200 Subject: Example: Scikit-image and trackpy (bubble tracking in foams) In-Reply-To: <20141120192756.GB28567@phare.normalesup.org> References: <546E2D64.8030208@sciunto.org> <20141120192756.GB28567@phare.normalesup.org> Message-ID: <87y4r52ttj.fsf@sun.ac.za> Thanks for sharing, Fran?ois--this is a great example of how well packages across the Python ecosystem function together. On 2014-11-20 21:27:56, Emmanuelle Gouillart wrote: >> Do we want to create a new page on the website with collections of nice iPython notebooks? > > The problem would be to maintain this notebooks. I would rather advocate > to cut the tutorials into shorter examples for the gallery (that can also > be downloaded as notebooks), and to integrate the "best" notebooks into > the user guide, to be sure that the code is maintained. Also, we have the scikit-image-demos and skimage-tutorials repositories--it would fit in either, as long as it gets reworked to include the data. St?fan From stefan at sun.ac.za Thu Nov 20 21:10:13 2014 From: stefan at sun.ac.za (Stefan van der Walt) Date: Fri, 21 Nov 2014 04:10:13 +0200 Subject: Sobel In-Reply-To: <84090922-1CA6-4647-AAB5-D5974CA466DE@demuc.de> References: <8E001836-713A-46C1-811B-A729C8B489B9@demuc.de> <84090922-1CA6-4647-AAB5-D5974CA466DE@demuc.de> Message-ID: <87vbm92tiy.fsf@sun.ac.za> Thanks very much, @ahojnnes From hughesadam87 at gmail.com Fri Nov 21 13:36:01 2014 From: hughesadam87 at gmail.com (Adam Hughes) Date: Fri, 21 Nov 2014 10:36:01 -0800 (PST) Subject: Example: Scikit-image and trackpy (bubble tracking in foams) In-Reply-To: <546E2D64.8030208@sciunto.org> References: <546E2D64.8030208@sciunto.org> Message-ID: I like this example very much! Someone mentioned should you guys host a place to ipython notebooks of image processing? I think this would be a great idea. I posted a set of notebooks in the "Gallery of Interesting IPynbs" page, which does not have an image processing section. I had considered making one, but didn't want to step on any toes. There are so many notebooks on there now, that it probably would be better to have your own collection on scikit image. FYI here is the entry I put in the ipython notebook gallery of interesting notebooks: pyparty: Intuitive Particle Processing in Python , Adam Hughes Notebook to Generate the Published Figures | Also, check out the pyparty tutorial notebooks . On Thursday, November 20, 2014 1:06:49 PM UTC-5, Fran?ois Boulogne wrote: > > Hi, > > Just for your information, I wrote an example based on my research to > show the use of scikit-image with trackpy for feature detection and > tracking. > > http://nbviewer.ipython.org/github/soft-matter/trackpy-examples/blob/master/notebooks/custom_feature_detection.ipynb > > Hopefully, this might be helpful for future workshops or presentations. > > Best, > > -- > Fran?ois Boulogne. > http://www.sciunto.org > GPG: 32D5F22F > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Sun Nov 23 08:01:55 2014 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Sun, 23 Nov 2014 05:01:55 -0800 (PST) Subject: Example: Scikit-image and trackpy (bubble tracking in foams) In-Reply-To: References: Message-ID: <1416747715312.62550709@Nodemailer> Thanks Fran?ois for an awesome tutorial! It was a very interesting read. And :+1: Adam's idea of hosting the skimage IPynbs somewhere. St?fan, does skimage-demos live on the web anywhere? On Sat, Nov 22, 2014 at 5:36 AM, Adam Hughes wrote: > I like this example very much! > Someone mentioned should you guys host a place to ipython notebooks of > image processing? > I think this would be a great idea. I posted a set of notebooks in the > "Gallery of Interesting IPynbs" page, which does not have an image > processing section. I had considered making one, but didn't want to step > on any toes. There are so many notebooks on there now, that it probably > would be better to have your own collection on scikit image. > FYI here is the entry I put in the ipython notebook gallery of interesting > notebooks: > pyparty: Intuitive Particle Processing in Python > , Adam Hughes Notebook > to Generate the Published Figures > | > Also, check out the pyparty tutorial notebooks > . > On Thursday, November 20, 2014 1:06:49 PM UTC-5, Fran?ois Boulogne wrote: >> >> Hi, >> >> Just for your information, I wrote an example based on my research to >> show the use of scikit-image with trackpy for feature detection and >> tracking. >> >> http://nbviewer.ipython.org/github/soft-matter/trackpy-examples/blob/master/notebooks/custom_feature_detection.ipynb >> >> Hopefully, this might be helpful for future workshops or presentations. >> >> Best, >> >> -- >> Fran?ois Boulogne. >> http://www.sciunto.org >> GPG: 32D5F22F >> >> >> > -- > You received this message because you are subscribed to the Google Groups "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -------------- next part -------------- An HTML attachment was scrubbed... URL: From witzjean at gmail.com Wed Nov 26 09:28:24 2014 From: witzjean at gmail.com (jeff witz) Date: Wed, 26 Nov 2014 06:28:24 -0800 (PST) Subject: regionprops Very slow on centroid identification In-Reply-To: <0A8812E2-4729-4351-A3CD-3A2324AC3FBE@demuc.de> References: <00059269-0073-45fe-bcf6-9cb7d10abfce@googlegroups.com> <8761edpfdk.fsf@sun.ac.za> <11572cf4-137a-48b8-b01c-e6406a983d59@googlegroups.com> <0A8812E2-4729-4351-A3CD-3A2324AC3FBE@demuc.de> Message-ID: <1c8f0fd4-74b9-4bf5-b815-231be054e7f9@googlegroups.com> Hi, Thank you all for your answers. finally I use OpenCV to perform the real-time computation and still use skimage for the initialisation on my real code. I've joined a file that allows one to compare the computation we need to make. There is a basic numpy method, the OpenCV one and the Skimage regionprops one. I don't find relevant to include a naive python implementation. Please note that the values computed for visualization are for illustration only and doesn't represent a real experiment. I Hope it can help to benchmark the future improvement of regionprops. Best regards -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: UnitTestExtenso.py Type: text/x-python Size: 7208 bytes Desc: not available URL: From joel.bernier at gmail.com Wed Nov 26 13:23:00 2014 From: joel.bernier at gmail.com (Joel Bernier) Date: Wed, 26 Nov 2014 10:23:00 -0800 (PST) Subject: 3d blob detection Message-ID: Any hope of modifying some of the tools in skimage.feature (say blob_log() ) to handle 3d images? I have a good application in the really of processing X-rya diffraction data? -J -------------- next part -------------- An HTML attachment was scrubbed... URL: From jsch at demuc.de Wed Nov 26 10:52:29 2014 From: jsch at demuc.de (Johannes Schoenberger) Date: Wed, 26 Nov 2014 10:52:29 -0500 Subject: regionprops Very slow on centroid identification In-Reply-To: <1c8f0fd4-74b9-4bf5-b815-231be054e7f9@googlegroups.com> References: <00059269-0073-45fe-bcf6-9cb7d10abfce@googlegroups.com> <8761edpfdk.fsf@sun.ac.za> <11572cf4-137a-48b8-b01c-e6406a983d59@googlegroups.com> <0A8812E2-4729-4351-A3CD-3A2324AC3FBE@demuc.de> <1c8f0fd4-74b9-4bf5-b815-231be054e7f9@googlegroups.com> Message-ID: Hi Jeff, I mentioned this before, but since you do not care about individual regions, there is no reason to burden yourself with the overhead of the regionprops function. Try this modified function: ``` def barycenter_skimage2(image,minx,miny,maxx,maxy,thresh,border,White_Mark): """ skimage computation of the barycenter (moment 1 of image) on ZOI using regionprops """ bw=image[minx:maxx+1,miny:maxy+1]>thresh if(White_Mark==False): bw=1-bw Onex,Oney=np.where(bw==1) minx_=Onex.min() maxx_=Onex.max() miny_=Oney.min() maxy_=Oney.max() M = measure.moments(bw.astype(np.double), order=1) Px=M[0, 1]/M[0, 0] Py=M[1, 0]/M[0, 0] Px+=minx Py+=miny # Determination of the new bounding box using global coordinates and the margin minx=minx-border+minx_ miny=miny-border+miny_ maxx=minx+border+maxx_ maxy=miny+border+maxy_ return Px,Py,minx,miny,maxx,maxy ``` We could add a templated version of the moments functions for uint8 to make this a fairer comparison. The regionprops function would also gain from this, since the `double` version is only used for the weighted moments. Best, Johannes > On Nov 26, 2014, at 9:28 AM, jeff witz wrote: > > Hi, > > Thank you all for your answers. finally I use OpenCV to perform the real-time computation and still use skimage for the initialisation on my real code. > > I've joined a file that allows one to compare the computation we need to make. > > There is a basic numpy method, the OpenCV one and the Skimage regionprops one. I don't find relevant to include a naive python implementation. > > Please note that the values computed for visualization are for illustration only and doesn't represent a real experiment. > > I Hope it can help to benchmark the future improvement of regionprops. > > Best regards > > -- > You received this message because you are subscribed to the Google Groups "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. > From matthew.brett at gmail.com Wed Nov 26 19:41:09 2014 From: matthew.brett at gmail.com (Matthew Brett) Date: Wed, 26 Nov 2014 16:41:09 -0800 Subject: OK to upload OSX wheels for 10.10? Message-ID: Hi, OSX is now at 10.10, and the current wheels won't get installed by system python, homebrew or macports on 10.10, because they lack the relevant bits to their filenames. Specifically the wheel files need to have the text "macosx_10_10_intel.macosx_10_10_x86_64" in their filename. I'd like to upload new wheeels to pypi (which are just rebuilt copies of the old one) with the longer filenames, as in: scikit_image-0.10.1-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl etc. I propose to leave the old ones there in case anyone is depending on them. Is that OK with y'all? Cheers, Matthew From jsch at demuc.de Wed Nov 26 17:11:57 2014 From: jsch at demuc.de (Johannes Schoenberger) Date: Wed, 26 Nov 2014 17:11:57 -0500 Subject: regionprops Very slow on centroid identification In-Reply-To: References: <00059269-0073-45fe-bcf6-9cb7d10abfce@googlegroups.com> <8761edpfdk.fsf@sun.ac.za> <11572cf4-137a-48b8-b01c-e6406a983d59@googlegroups.com> <0A8812E2-4729-4351-A3CD-3A2324AC3FBE@demuc.de> <1c8f0fd4-74b9-4bf5-b815-231be054e7f9@googlegroups.com> Message-ID: @Jeff, See https://github.com/scikit-image/scikit-image/pull/1239 > On Nov 26, 2014, at 10:52 AM, Johannes Schoenberger wrote: > > Hi Jeff, > > I mentioned this before, but since you do not care about individual regions, there is no reason to burden yourself with the overhead of the regionprops function. > > Try this modified function: > > > ``` > def barycenter_skimage2(image,minx,miny,maxx,maxy,thresh,border,White_Mark): > """ > skimage computation of the barycenter (moment 1 of image) on ZOI using regionprops > """ > bw=image[minx:maxx+1,miny:maxy+1]>thresh > if(White_Mark==False): > bw=1-bw > Onex,Oney=np.where(bw==1) > minx_=Onex.min() > maxx_=Onex.max() > miny_=Oney.min() > maxy_=Oney.max() > M = measure.moments(bw.astype(np.double), order=1) > Px=M[0, 1]/M[0, 0] > Py=M[1, 0]/M[0, 0] > Px+=minx > Py+=miny > # Determination of the new bounding box using global coordinates and the margin > minx=minx-border+minx_ > miny=miny-border+miny_ > maxx=minx+border+maxx_ > maxy=miny+border+maxy_ > return Px,Py,minx,miny,maxx,maxy > ``` > > > We could add a templated version of the moments functions for uint8 to make this a fairer comparison. The regionprops function would also gain from this, since the `double` version is only used for the weighted moments. > > Best, Johannes > >> On Nov 26, 2014, at 9:28 AM, jeff witz wrote: >> >> Hi, >> >> Thank you all for your answers. finally I use OpenCV to perform the real-time computation and still use skimage for the initialisation on my real code. >> >> I've joined a file that allows one to compare the computation we need to make. >> >> There is a basic numpy method, the OpenCV one and the Skimage regionprops one. I don't find relevant to include a naive python implementation. >> >> Please note that the values computed for visualization are for illustration only and doesn't represent a real experiment. >> >> I Hope it can help to benchmark the future improvement of regionprops. >> >> Best regards >> >> -- >> You received this message because you are subscribed to the Google Groups "scikit-image" group. >> To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com. >> For more options, visit https://groups.google.com/d/optout. >> > > -- > You received this message because you are subscribed to the Google Groups "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. From stefan at sun.ac.za Wed Nov 26 10:17:28 2014 From: stefan at sun.ac.za (Stefan van der Walt) Date: Wed, 26 Nov 2014 17:17:28 +0200 Subject: regionprops Very slow on centroid identification In-Reply-To: <1c8f0fd4-74b9-4bf5-b815-231be054e7f9@googlegroups.com> References: <00059269-0073-45fe-bcf6-9cb7d10abfce@googlegroups.com> <8761edpfdk.fsf@sun.ac.za> <11572cf4-137a-48b8-b01c-e6406a983d59@googlegroups.com> <0A8812E2-4729-4351-A3CD-3A2324AC3FBE@demuc.de> <1c8f0fd4-74b9-4bf5-b815-231be054e7f9@googlegroups.com> Message-ID: <87wq6iyos7.fsf@sun.ac.za> Hi Jeff On 2014-11-26 16:28:24, jeff witz wrote: > Please note that the values computed for visualization are for illustration > only and doesn't represent a real experiment. Thank you very much for the script--it will come in handy. When I run it on my system, I see the following lovely error message: Traceback (most recent call last): File "/tmp/UnitTestExtenso.py", line 192, in barycenter_opencv(image,int(minx[0]),int(miny[0]),int(maxx[0]),int(maxy[0]),thresh,border,True) File "/tmp/UnitTestExtenso.py", line 110, in barycenter_opencv miny_, minx_, h, w= cv2.boundingRect(bw) cv2.error: /build/buildd/opencv-2.4.9+dfsg/modules/imgproc/src/contours.cpp:1895: error: (-215) points.checkVector(2) >= 0 && (points.depth() == CV_32F || points.depth() == CV_32S) in function boundingRect St?fan From tcaswell at gmail.com Wed Nov 26 13:42:13 2014 From: tcaswell at gmail.com (Thomas Caswell) Date: Wed, 26 Nov 2014 18:42:13 +0000 Subject: 3d blob detection References: Message-ID: It might be worth having a look at https://github.com/soft-matter/trackpy/pull/162 On Wed Nov 26 2014 at 1:34:54 PM Joel Bernier wrote: > Any hope of modifying some of the tools in skimage.feature (say blob_log() > ) > to handle 3d images? I have a good application in the really of > processing X-rya diffraction data? > > -J > > -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image+unsubscribe at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan at sun.ac.za Wed Nov 26 19:49:40 2014 From: stefan at sun.ac.za (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Thu, 27 Nov 2014 02:49:40 +0200 Subject: OK to upload OSX wheels for 10.10? In-Reply-To: References: Message-ID: Hi Matthew On Nov 27, 2014 2:41 AM, "Matthew Brett" wrote: > > I'd like to upload new wheeels to pypi (which are just rebuilt copies > of the old one) with the longer filenames, as in: > > scikit_image-0.10.1-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl > > etc. I propose to leave the old ones there in case anyone is > depending on them. Is that OK with y'all? Thanks very much! Please go ahead. St?fan -------------- next part -------------- An HTML attachment was scrubbed... URL: From julien.derr at gmail.com Thu Nov 27 10:27:15 2014 From: julien.derr at gmail.com (Julien Derr) Date: Thu, 27 Nov 2014 07:27:15 -0800 (PST) Subject: Rotation with scpecification of the center ? Message-ID: Hi everyone, this is my first post here, so I am really a newbie... I haev seen on the doc that it is possible to specify the center of rotation (http://scikit-image.org/docs/dev/api/skimage.transform.html#skimage.transform.rotate) with rotate(image2,90 , resize=False, order=1, mode='constant', cval=0.0, center=(1140,1383)) but my computer doesn't seem very happy with this parameter center : rotate() got an unexpected keyword argument 'center' how can I specify the center of rotation ? thanks a lot, Julien -------------- next part -------------- An HTML attachment was scrubbed... URL: From jsch at demuc.de Thu Nov 27 08:41:27 2014 From: jsch at demuc.de (Johannes Schoenberger) Date: Thu, 27 Nov 2014 08:41:27 -0500 Subject: Sobel In-Reply-To: <87vbm92tiy.fsf@sun.ac.za> References: <8E001836-713A-46C1-811B-A729C8B489B9@demuc.de> <84090922-1CA6-4647-AAB5-D5974CA466DE@demuc.de> <87vbm92tiy.fsf@sun.ac.za> Message-ID: <51B216DF-57F7-4B37-AE3D-1CB8B5E45DC1@demuc.de> What?s the desired path here? 1) `sobel_h`/`sobel_v` (or `sobel_x`/`sobel_y`; in this case, it might make sense to match x/y with the gradient direction rather than the edge direction) 2) deprecation warning kwarg? I am voting for option 1. > On Nov 20, 2014, at 9:10 PM, Stefan van der Walt wrote: > > Thanks very much, @ahojnnes > > -- > You received this message because you are subscribed to the Google Groups "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. From jni.soma at gmail.com Wed Nov 26 18:56:44 2014 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Thu, 27 Nov 2014 10:56:44 +1100 Subject: 3d blob detection In-Reply-To: References: Message-ID: Hi Joel, I'm the self-appointed Guardian of the of the Dimensions here at scikit-image. =) This is a good idea and I will pop it near the top of the list for conversion to 3D. Of course, pull requests are very welcome! If you would like to try your hand at it, I'm happy to help you through any hairy bits. =) Juan. On Thu, Nov 27, 2014 at 5:42 AM, Thomas Caswell wrote: > It might be worth having a look at > https://github.com/soft-matter/trackpy/pull/162 > > > On Wed Nov 26 2014 at 1:34:54 PM Joel Bernier > wrote: > >> Any hope of modifying some of the tools in skimage.feature (say >> blob_log() >> ) >> to handle 3d images? I have a good application in the really of >> processing X-rya diffraction data... >> >> -J >> >> -- >> You received this message because you are subscribed to the Google Groups >> "scikit-image" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to scikit-image+unsubscribe at googlegroups.com. >> For more options, visit https://groups.google.com/d/optout. >> > -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image+unsubscribe at googlegroups.com. > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jsch at demuc.de Thu Nov 27 10:08:38 2014 From: jsch at demuc.de (=?utf-8?Q?Johannes_Sch=C3=B6nberger?=) Date: Thu, 27 Nov 2014 16:08:38 +0100 (CET) Subject: Sobel In-Reply-To: <87h9xkae5f.fsf@sun.ac.za> References: <8E001836-713A-46C1-811B-A729C8B489B9@demuc.de> <84090922-1CA6-4647-AAB5-D5974CA466DE@demuc.de> <87vbm92tiy.fsf@sun.ac.za> <51B216DF-57F7-4B37-AE3D-1CB8B5E45DC1@demuc.de> <87h9xkae5f.fsf@sun.ac.za> Message-ID: <8FCE96DD-5453-410D-8835-DAE38070174B@demuc.de> Ok. Then option 1) but with h and v. > On Nov 27, 2014, at 9:53 AM, Stefan van der Walt wrote: > > Apologies for my curt previous reply--I thought I was responding to a > ticket on GitHub! > >> On 2014-11-27 15:41:27, Johannes Schoenberger wrote: >> What?s the desired path here? >> >> 1) `sobel_h`/`sobel_v` (or `sobel_x`/`sobel_y`; in this case, it might >> make sense to match x/y with the gradient direction rather than the >> edge direction) > > I'd be careful of using `x` and `y`, given that we're trying to > standardize on a different convention. I would expect `sobel_h` to > highlight horizontal edges (since `sobel` is known as an edge detector). > > 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/d/optout. From stefan at sun.ac.za Thu Nov 27 09:53:16 2014 From: stefan at sun.ac.za (Stefan van der Walt) Date: Thu, 27 Nov 2014 16:53:16 +0200 Subject: Sobel In-Reply-To: <51B216DF-57F7-4B37-AE3D-1CB8B5E45DC1@demuc.de> References: <8E001836-713A-46C1-811B-A729C8B489B9@demuc.de> <84090922-1CA6-4647-AAB5-D5974CA466DE@demuc.de> <87vbm92tiy.fsf@sun.ac.za> <51B216DF-57F7-4B37-AE3D-1CB8B5E45DC1@demuc.de> Message-ID: <87h9xkae5f.fsf@sun.ac.za> Apologies for my curt previous reply--I thought I was responding to a ticket on GitHub! On 2014-11-27 15:41:27, Johannes Schoenberger wrote: > What?s the desired path here? > > 1) `sobel_h`/`sobel_v` (or `sobel_x`/`sobel_y`; in this case, it might > make sense to match x/y with the gradient direction rather than the > edge direction) I'd be careful of using `x` and `y`, given that we're trying to standardize on a different convention. I would expect `sobel_h` to highlight horizontal edges (since `sobel` is known as an edge detector). St?fan From stefan at sun.ac.za Thu Nov 27 11:06:22 2014 From: stefan at sun.ac.za (Stefan van der Walt) Date: Thu, 27 Nov 2014 18:06:22 +0200 Subject: Rotation with scpecification of the center ? In-Reply-To: References: Message-ID: <87k32gk4qp.fsf@sun.ac.za> Hi Julien On 2014-11-27 17:27:15, Julien Derr wrote: > Hi everyone, this is my first post here, so I am really a newbie... Welcome! > rotate() got an unexpected keyword argument 'center' > > how can I specify the center of rotation ? This only got introduced recently, so your version may not have it yet (check your version by printing skimage.__version__) You can either compile the latest version yourself, or wait for the release of 0.11, which should happen within the next month or so. Regards St?fan From julien.derr at gmail.com Fri Nov 28 05:57:58 2014 From: julien.derr at gmail.com (Julien Derr) Date: Fri, 28 Nov 2014 02:57:58 -0800 (PST) Subject: Rotation with scpecification of the center ? In-Reply-To: <87k32gk4qp.fsf@sun.ac.za> References: <87k32gk4qp.fsf@sun.ac.za> Message-ID: <13cebb0e-a6c9-45d3-9e4e-777c1a4dfead@googlegroups.com> thanks! is there an easy tutorial for how to compile the latest version on ubuntu ? On Thursday, November 27, 2014 5:06:27 PM UTC+1, Stefan van der Walt wrote: > > Hi Julien > > On 2014-11-27 17:27:15, Julien Derr > > wrote: > > Hi everyone, this is my first post here, so I am really a newbie... > > Welcome! > > > rotate() got an unexpected keyword argument 'center' > > > > how can I specify the center of rotation ? > > This only got introduced recently, so your version may not have it yet > (check your version by printing skimage.__version__) > > You can either compile the latest version yourself, or wait for the > release of 0.11, which should happen within the next month or so. > > Regards > St?fan > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hannesschoenberger at gmail.com Fri Nov 28 10:15:47 2014 From: hannesschoenberger at gmail.com (=?UTF-8?Q?Johannes_Sch=C3=B6nberger?=) Date: Fri, 28 Nov 2014 07:15:47 -0800 (PST) Subject: Sobel In-Reply-To: <06f04515-947b-4d09-8641-ed0d43b9d945@googlegroups.com> References: <06f04515-947b-4d09-8641-ed0d43b9d945@googlegroups.com> Message-ID: <81c98a94-931c-4e3c-8d54-e1eb7adac845@googlegroups.com> @Michael That sounds like a cool example. Would you be willing to code that? On Thursday, November 20, 2014 6:01:04 PM UTC-5, Michael Aye wrote: > > How about establishing a pipeline between a linear ridge detector and > alignment of the sobels accordingly to the found ridge? Would be a nice > example maybe? > > Michael > > On Wednesday, November 19, 2014 4:25:39 PM UTC-8, Johannes Sch?nberger > wrote: >> >> Hi, >> >> Why are we returning the absolute values in the hsobel and vsobel >> functions? >> >> I do not see the benefit. >> >> Johannes >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From fboulogne at sciunto.org Fri Nov 28 08:06:04 2014 From: fboulogne at sciunto.org (=?UTF-8?B?RnJhbsOnb2lzIEJvdWxvZ25l?=) Date: Fri, 28 Nov 2014 08:06:04 -0500 Subject: Example: Scikit-image and trackpy (bubble tracking in foams) In-Reply-To: <871tona3bo.fsf@sun.ac.za> References: <546E2D64.8030208@sciunto.org> <20141120192756.GB28567@phare.normalesup.org> <871tona3bo.fsf@sun.ac.za> Message-ID: <5478733C.9040703@sciunto.org> > Francois, it'd be fantastic to have this one in there as well. > Sure ! :) -- Fran?ois Boulogne. http://www.sciunto.org GPG: 32D5F22F From fboulogne at sciunto.org Fri Nov 28 08:07:40 2014 From: fboulogne at sciunto.org (=?UTF-8?B?RnJhbsOnb2lzIEJvdWxvZ25l?=) Date: Fri, 28 Nov 2014 08:07:40 -0500 Subject: Rotation with scpecification of the center ? In-Reply-To: <13cebb0e-a6c9-45d3-9e4e-777c1a4dfead@googlegroups.com> References: <87k32gk4qp.fsf@sun.ac.za> <13cebb0e-a6c9-45d3-9e4e-777c1a4dfead@googlegroups.com> Message-ID: <5478739C.7040505@sciunto.org> Hi Julien, Le 28/11/2014 05:57, Julien Derr a ?crit : > > thanks! is there an easy tutorial for how to compile the latest > version on ubuntu ? I think you can follow the compilation from source presented on this page: http://scikit-image.org/docs/0.10.x/install.html Best -- Fran?ois Boulogne. http://www.sciunto.org GPG: 32D5F22F From stefan at sun.ac.za Fri Nov 28 07:59:23 2014 From: stefan at sun.ac.za (Stefan van der Walt) Date: Fri, 28 Nov 2014 14:59:23 +0200 Subject: Example: Scikit-image and trackpy (bubble tracking in foams) In-Reply-To: <20141120192756.GB28567@phare.normalesup.org> References: <546E2D64.8030208@sciunto.org> <20141120192756.GB28567@phare.normalesup.org> Message-ID: <871tona3bo.fsf@sun.ac.za> On 2014-11-20 21:27:56, Emmanuelle Gouillart wrote: >> Do we want to create a new page on the website with collections of nice iPython notebooks? > > The problem would be to maintain this notebooks. I would rather advocate > to cut the tutorials into shorter examples for the gallery (that can also > be downloaded as notebooks), and to integrate the "best" notebooks into > the user guide, to be sure that the code is maintained. I think the guideline for now is to put examples with no additional dependencies in the gallery, and the rest in skimage-demos. Francois, it'd be fantastic to have this one in there as well. St?fan From kmichael.aye at gmail.com Sat Nov 29 02:52:53 2014 From: kmichael.aye at gmail.com (Michael Aye) Date: Fri, 28 Nov 2014 23:52:53 -0800 (PST) Subject: Sobel In-Reply-To: <81c98a94-931c-4e3c-8d54-e1eb7adac845@googlegroups.com> References: <06f04515-947b-4d09-8641-ed0d43b9d945@googlegroups.com> <81c98a94-931c-4e3c-8d54-e1eb7adac845@googlegroups.com> Message-ID: <158a7a57-a4ec-4a51-be9e-2db10d91992e@googlegroups.com> I will give it a try. That might come in handy for me anyway! ;) On Friday, November 28, 2014 8:15:48 AM UTC-7, Johannes Sch?nberger wrote: > > @Michael That sounds like a cool example. Would you be willing to code > that? > > On Thursday, November 20, 2014 6:01:04 PM UTC-5, Michael Aye wrote: >> >> How about establishing a pipeline between a linear ridge detector and >> alignment of the sobels accordingly to the found ridge? Would be a nice >> example maybe? >> >> Michael >> >> On Wednesday, November 19, 2014 4:25:39 PM UTC-8, Johannes Sch?nberger >> wrote: >>> >>> Hi, >>> >>> Why are we returning the absolute values in the hsobel and vsobel >>> functions? >>> >>> I do not see the benefit. >>> >>> Johannes >>> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: