From ivoflipse at gmail.com Tue Mar 1 09:48:33 2016 From: ivoflipse at gmail.com (Ivo Flipse) Date: Tue, 1 Mar 2016 06:48:33 -0800 (PST) Subject: Livewire segmentation in scikit-image In-Reply-To: References: <53412d16-841c-4269-a1c7-b7a80d099ecd@googlegroups.com> <2d25b2a6-4b6a-44c3-bb2e-3b5dcea48d16@googlegroups.com> Message-ID: Hi Pavlo, I did manage to get your example code working, though I agree with St?fan that the Matplotlib GUI doesn't really enable great interactivity. I also tried loading a different image (a frontal view X-ray of the hips), but since it was really big (4kx4k) your cost calculation became pretty slow, so there's room for improvement there ;-) Also, the choice of filter and threshold didn't work out at all for my image, so that should probably be more configurable. I was rather surprised how well it worked, given that it only calculates a minimal cost path. I reckon that once the edges aren't as strong as they are in this image, it won't perform as well. Then fixing such segmentations suddenly becomes a lot more painful in my experience, because the algorithm won't help you anymore and you don't want to have to draw the entire path by hand. Perhaps Emmanuelle or Juan has any suggestions on how we can make the calculations more robust? Ivo -------------- next part -------------- An HTML attachment was scrubbed... URL: From pdyban at gmail.com Tue Mar 1 15:15:42 2016 From: pdyban at gmail.com (Pavlo Dyban) Date: Tue, 1 Mar 2016 12:15:42 -0800 (PST) Subject: Livewire segmentation in scikit-image In-Reply-To: References: <53412d16-841c-4269-a1c7-b7a80d099ecd@googlegroups.com> <2d25b2a6-4b6a-44c3-bb2e-3b5dcea48d16@googlegroups.com> Message-ID: Hello Ivo, thanks for taking your time for evaluating my code! 1. Matplotlib GUI. What interaction possibilities are missing in your opinion? Click and drag are available already, what else do you think would be helpful for a good illustration of the algorithm? 2. Cost computation. That's a good point. I am not sure if there is a way to effectively compute the shortest path exactly on a large image matrix. A good heuristic that limits search to a local neighbourhood might help here. The bottleneck seems to stem from the dictionary representation of the graph. The conversion takes extremely long for large images. 3. The gradient image. The notebook thresholds a gradient image in order to ignore the minor intensity differences along the boundary. That was chosen as a heuristic and as well as Gaussian smoothing are optional steps inside the algorithm. You can check the API here: https://github.com/pdyban/livewire/blob/master/livewire/livewiresegmentation.py In my next step - until Juan or Emmanuelle reply - I will integrate the shortest path computation from skimage's graph module. Thanks, Pavlo On Tuesday, 1 March 2016 16:12:27 UTC+1, Ivo Flipse wrote: > > > Hi Pavlo, > > I did manage to get your example code working, though I agree with St?fan > that the Matplotlib GUI doesn't really enable great interactivity. > > I also tried loading a different image (a frontal view X-ray of the hips), > but since it was really big (4kx4k) your cost calculation became pretty > slow, so there's room for improvement there ;-) > Also, the choice of filter and threshold didn't work out at all for my > image, so that should probably be more configurable. > I was rather surprised how well it worked, given that it only calculates a > minimal cost path. I reckon that once the edges aren't as strong as they > are in this image, it won't perform as well. > Then fixing such segmentations suddenly becomes a lot more painful in my > experience, because the algorithm won't help you anymore and you don't want > to have to draw the entire path by hand. > Perhaps Emmanuelle or Juan has any suggestions on how we can make the > calculations more robust? > > > > Ivo > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jillc at enthought.com Tue Mar 1 16:17:34 2016 From: jillc at enthought.com (jillc at enthought.com) Date: Tue, 1 Mar 2016 13:17:34 -0800 (PST) Subject: SciPy 2016 Message-ID: **SciPy 2016 Conference (Scientific Computing with Python) Announcement** *Call for Proposals: Submit Your Tutorial and Talk Ideas by March 25, 2015 at http://scipy2016.scipy.org . SciPy 2016 , the 15th annual Scientific Computing with Python conference, will be held July 11-17, 2016 in Austin, Texas. SciPy is a community dedicated to the advancement of scientific computing through open source Python software for mathematics, science, and engineering. The annual SciPy Conference brings together over 650 participants from industry, academia, and government to showcase their latest projects, learn from skilled users and developers, and collaborate on code development. The full program will consist of 2 days of tutorials (July 11-12), 3 days of talks (July 13-15), and 2 days of developer sprints (July 16-17). More info is available on the conference website at http://scipy2016.scipy.org (where you can sign up for the mailing list); or follow @scipyconf on Twitter. We hope you?ll join us - early bird registration is open until May 22, 2016 at http://scipy2016.scipy.org/ehome/146062/332936/?&& We encourage you to submit tutorial or talk proposals in the categories below; please also share with others who you?d like to see participate! Submit via the conference website: http://scipy2016.scipy.org . ------------------------------------------------------------------------------------------------------------------------------ *SUBMIT A SCIPY 2016 TUTORIAL PROPOSAL- DUE MARCH 21, 2016* ------------------------------------------------------------------------------------------------------------------------------ Details and submission here: http://scipy2016.scipy.org/ehome/146062/332967/?&& These sessions provide extremely affordable access to expert training, and consistently receive fantastic feedback from participants. We're looking for submissions on topics from introductory to advanced - we'll have attendees across the gamut looking to learn. Whether you are a major contributor to a scientific Python library or an expert-level user, this is a great opportunity to share your knowledge and stipends are available. ------------------------------------------------------------------------------------------------------------------------------ **SUBMIT A SCIPY 2016 TALK / POSTER PROPOSAL - DUE MARCH 25, 2016* ------------------------------------------------------------------------------------------------------------------------------ Details and submission here: http://scipy2016.scipy.org/ehome/146062/332968/?&& SciPy 2016 will include 2 major topic tracks and 8 mini-symposia tracks. Major topic tracks include: - Python in Data Science (Big data and not so big data) - High Performance Computing Mini-symposia will include the applications of Python in: - Earth and Space Science - Biology and Medicine - Engineering - Social Science - Special Purpose Databases - Case Studies in Industry - Education - Reproducibility If you have any questions or comments, feel free to contact us at: scipy-organizers at scipy.org -------------------------------------------------------------------------- **SCIPY 2016 REGISTRATION IS OPEN** -------------------------------------------------------------------------- Please register early. SciPy early bird registration until May 22, 2016! Register at http://scipy2016.scipy.org. Plus, enter our t-shirt design contest to win a free registration. (Send a vector art file to scipy at enthought.com by March 31 to enter). -------------- next part -------------- An HTML attachment was scrubbed... URL: From pradyumnanpk at gmail.com Tue Mar 1 16:42:19 2016 From: pradyumnanpk at gmail.com (Pradyumna Kumar N) Date: Tue, 1 Mar 2016 13:42:19 -0800 (PST) Subject: 3D skeleton action recognition Message-ID: <226cfd38-d81e-43d0-aaea-67bb7f6b645a@googlegroups.com> Hi all, Does action recognition from 3D skeleton fit into scikit-image? If yes, I would like to implement the functionality. Let me know your thoughts on this. -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Tue Mar 1 16:50:44 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Tue, 1 Mar 2016 13:50:44 -0800 Subject: 3D skeleton action recognition In-Reply-To: <226cfd38-d81e-43d0-aaea-67bb7f6b645a@googlegroups.com> References: <226cfd38-d81e-43d0-aaea-67bb7f6b645a@googlegroups.com> Message-ID: On 1 March 2016 at 13:42, Pradyumna Kumar N wrote: > Does action recognition from 3D skeleton fit into scikit-image? If yes, I > would like to implement the functionality. Let me know your thoughts on > this. I think that is probably out of scope. Perhaps start a scikit, and develop the algorithms there? Once they are mature, there's always the option of merging it into another package. St?fan From ivoflipse at gmail.com Wed Mar 2 05:24:38 2016 From: ivoflipse at gmail.com (Ivo Flipse) Date: Wed, 2 Mar 2016 02:24:38 -0800 (PST) Subject: Livewire segmentation in scikit-image In-Reply-To: References: <53412d16-841c-4269-a1c7-b7a80d099ecd@googlegroups.com> <2d25b2a6-4b6a-44c3-bb2e-3b5dcea48d16@googlegroups.com> Message-ID: <712fe092-fa98-4482-865d-5355c43af1ba@googlegroups.com> Hi Pavlo, Using just Matplotlib GUI, there's not much you can do, since it's rather limited. But I reckon St?fan's problems arose from the fact that updates made to the window are really slow, so you don't see what the algorithm is doing while you're clicking around. Or at least it didn't do that for me. You could make the logic you execute inside the mouse events available as functions, so people can just pass (mouse) coordinates to your functions and get back coordinates to draw (whichever way they like). That way people can easily integrate your code in whatever GUI they use (an Jupyter Notebook widget would be awesome). If you want to improve your own GUI code, you could figure out how to get it to draw a bit more often, so you get more feedback. If you click, perhaps leave a marker and then regularly draw the resulting contour. I'd expect that if I click another time, it would at least draw the line it calculated between those two points. In my experience with livewire tools, such as TurtleSeg, you want to add "checkpoints" where you manually specify points where the contour should pass through. Without regular visual feedback, it's hard to judge whether you need one or not. Still thanks for sharing the code, I hadn't expected such a simple implementation would already work so well Ivo -------------- next part -------------- An HTML attachment was scrubbed... URL: From pdyban at gmail.com Wed Mar 2 08:16:26 2016 From: pdyban at gmail.com (Pavlo Dyban) Date: Wed, 2 Mar 2016 05:16:26 -0800 (PST) Subject: Livewire segmentation in scikit-image In-Reply-To: <712fe092-fa98-4482-865d-5355c43af1ba@googlegroups.com> References: <53412d16-841c-4269-a1c7-b7a80d099ecd@googlegroups.com> <2d25b2a6-4b6a-44c3-bb2e-3b5dcea48d16@googlegroups.com> <712fe092-fa98-4482-865d-5355c43af1ba@googlegroups.com> Message-ID: Hello Ivo, on my machine (Macbook Pro 15) the updates for the example images are interactive. You click in the image once, then the algorithm calculates the shrotest path to every point under mouse while you move the mouse around the image. When you click your mouse for the second time, the last shortest path prediction is saved and displayed over the image. You can then continue moving your mouse and the notebook will keep computing the shortest pathes, until you press Escape key. I am surprised that this has not worked at your machine. Have you tried first with the example image? The code in the notebook is an illustration of the livewire algorithm *principle*. The Python package I propose for inclusion in scikit-image is located under: https://github.com/pdyban/livewire/tree/master/livewire. The test where you can see how the package can be called is here: https://github.com/pdyban/livewire/blob/master/test.py. For example: from livewire import LiveWireSegmentation > > from skimage import dataimage = data.coins() > > algorithm = LiveWireSegmentation(image) > path = algorithm.compute_shortest_path(from_, to_) > More examples can be found in the documentation: http://livewire-segmentation.readthedocs.org/en/latest/ Please let me know if these links answer your questions! I would be happy to contribute my Python package to skimage! Best regards, Pavlo On Wednesday, 2 March 2016 13:15:20 UTC+1, Ivo Flipse wrote: > > Hi Pavlo, > > Using just Matplotlib GUI, there's not much you can do, since it's rather > limited. But I reckon St?fan's problems arose from the fact that updates > made to the window are really slow, so you don't see what the algorithm is > doing while you're clicking around. Or at least it didn't do that for me. > You could make the logic you execute inside the mouse events available as > functions, so people can just pass (mouse) coordinates to your functions > and get back coordinates to draw (whichever way they like). That way people > can easily integrate your code in whatever GUI they use (an Jupyter > Notebook widget would be awesome). > > If you want to improve your own GUI code, you could figure out how to get > it to draw a bit more often, so you get more feedback. If you click, > perhaps leave a marker and then regularly draw the resulting contour. I'd > expect that if I click another time, it would at least draw the line it > calculated between those two points. In my experience with livewire tools, > such as TurtleSeg, you want to add "checkpoints" where you manually specify > points where the contour should pass through. Without regular visual > feedback, it's hard to judge whether you need one or not. > > Still thanks for sharing the code, I hadn't expected such a simple > implementation would already work so well > > Ivo > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Wed Mar 2 16:44:11 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Wed, 2 Mar 2016 13:44:11 -0800 Subject: 0.12 release In-Reply-To: <20160302212445.GA3276684@phare.normalesup.org> References: <20160201185705.GA3207967@phare.normalesup.org> <6F56AC09-BA2B-43F5-A910-37740BEBEC64@demuc.de> <20160203075920.GA2389752@phare.normalesup.org> <20160203172104.GA2977973@phare.normalesup.org> <20160207153232.GA2920916@phare.normalesup.org> <20160223153821.GB1829563@phare.normalesup.org> <20160302212445.GA3276684@phare.normalesup.org> Message-ID: On 2 March 2016 at 13:24, Emmanuelle Gouillart wrote: >> #1937 highlights a bug in our tests (and failing tests, that aren't >> currently showing up), so I would consider that the last blocker. #1937 is a bug fix, so should be merged. The real problem is the bug that it exposes, which is https://github.com/scikit-image/scikit-image/issues/1935 I will work on fixing it this afternoon. St?fan From stefanv at berkeley.edu Wed Mar 2 21:29:33 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Wed, 2 Mar 2016 18:29:33 -0800 Subject: 0.12 release In-Reply-To: References: <6F56AC09-BA2B-43F5-A910-37740BEBEC64@demuc.de> <20160203075920.GA2389752@phare.normalesup.org> <20160203172104.GA2977973@phare.normalesup.org> <20160207153232.GA2920916@phare.normalesup.org> <20160223153821.GB1829563@phare.normalesup.org> <20160302212445.GA3276684@phare.normalesup.org> <20160302215220.GC3276684@phare.normalesup.org> Message-ID: On 2 March 2016 at 16:00, Juan Nunez-Iglesias wrote: > Bug fixes seem precisely inessential to get done ahead of release? Anything > that doesn't break the API can be added in 0.12.1? You can't really release a package with a broken test suite. So you have the option to temporarily disable the tests, but shipping with a known bug feels kind of weird? Either way, I think I've zapped most of the outstanding ones. Waiting for Travis. St?fan From emmanuelle.gouillart at nsup.org Wed Mar 2 16:24:45 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Wed, 2 Mar 2016 22:24:45 +0100 Subject: 0.12 release In-Reply-To: References: <20160201185705.GA3207967@phare.normalesup.org> <6F56AC09-BA2B-43F5-A910-37740BEBEC64@demuc.de> <20160203075920.GA2389752@phare.normalesup.org> <20160203172104.GA2977973@phare.normalesup.org> <20160207153232.GA2920916@phare.normalesup.org> <20160223153821.GB1829563@phare.normalesup.org> Message-ID: <20160302212445.GA3276684@phare.normalesup.org> > #1937 highlights a bug in our tests (and failing tests, that aren't > currently showing up), so I would consider that the last blocker. Well, #1937 has been stalling for a while and I would consider it a minor bug only (differing opinion, anyone?), so how about we postpone #1937 to 0.13? Emma From emmanuelle.gouillart at nsup.org Wed Mar 2 16:52:20 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Wed, 2 Mar 2016 22:52:20 +0100 Subject: 0.12 release In-Reply-To: References: <6F56AC09-BA2B-43F5-A910-37740BEBEC64@demuc.de> <20160203075920.GA2389752@phare.normalesup.org> <20160203172104.GA2977973@phare.normalesup.org> <20160207153232.GA2920916@phare.normalesup.org> <20160223153821.GB1829563@phare.normalesup.org> <20160302212445.GA3276684@phare.normalesup.org> Message-ID: <20160302215220.GC3276684@phare.normalesup.org> On Wed, Mar 02, 2016 at 01:44:11PM -0800, St??fan van der Walt wrote: > On 2 March 2016 at 13:24, Emmanuelle Gouillart > wrote: > >> #1937 highlights a bug in our tests (and failing tests, that aren't > >> currently showing up), so I would consider that the last blocker. > #1937 is a bug fix, so should be merged. The real problem is the bug > that it exposes, which is > https://github.com/scikit-image/scikit-image/issues/1935 > I will work on fixing it this afternoon. Thanks :-D From jni.soma at gmail.com Wed Mar 2 19:00:59 2016 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Thu, 3 Mar 2016 11:00:59 +1100 Subject: 0.12 release In-Reply-To: <20160302215220.GC3276684@phare.normalesup.org> References: <6F56AC09-BA2B-43F5-A910-37740BEBEC64@demuc.de> <20160203075920.GA2389752@phare.normalesup.org> <20160203172104.GA2977973@phare.normalesup.org> <20160207153232.GA2920916@phare.normalesup.org> <20160223153821.GB1829563@phare.normalesup.org> <20160302212445.GA3276684@phare.normalesup.org> <20160302215220.GC3276684@phare.normalesup.org> Message-ID: Bug fixes seem precisely inessential to get done ahead of release? Anything that doesn't break the API can be added in 0.12.1? On Thu, Mar 3, 2016 at 8:52 AM, Emmanuelle Gouillart < emmanuelle.gouillart at nsup.org> wrote: > On Wed, Mar 02, 2016 at 01:44:11PM -0800, St?fan van der Walt wrote: > > On 2 March 2016 at 13:24, Emmanuelle Gouillart > > wrote: > > >> #1937 highlights a bug in our tests (and failing tests, that aren't > > >> currently showing up), so I would consider that the last blocker. > > > #1937 is a bug fix, so should be merged. The real problem is the bug > > that it exposes, which is > > > https://github.com/scikit-image/scikit-image/issues/1935 > > > I will work on fixing it this afternoon. > > Thanks :-D > > -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image+unsubscribe at googlegroups.com. > To post to this group, send an email to scikit-image at googlegroups.com. > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/20160302215220.GC3276684%40phare.normalesup.org > . > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From vimalthilak at gmail.com Thu Mar 3 15:13:23 2016 From: vimalthilak at gmail.com (Vimal Thilak) Date: Thu, 3 Mar 2016 12:13:23 -0800 (PST) Subject: jpeg image being read differently skimage.io.imread Message-ID: Hi, I have two servers on which I have installed skimage. When I do an skimage.io.imread on these two machines with the same image file, I noticed a difference in the shape of the returned image array: Machine 1: image_name = /path/to/JPEG img = skimage.io.imread(image_name) >>> img.shape (3000, 4000, 3) Machine 2: img = skimage.io.imread(image_name) >>> img.shape (2, ) Both machines have skimage version '0.11.3'. I believe that both systems have Pillow installed. I do not know the version of Pillow. I did change the plug-in to matplotlib on Machine 2 and saw that the image was being read correctly. However, I'm curious to know the reason for this difference and what I can do to fix my machine #2 Furthermore, how do I find the version of Pillow installed on my system? A google search didn't come up with anything that was helpful (i.e, copy-pastable solution) :) Thanks, -Vimal -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Wed Mar 2 21:50:26 2016 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Thu, 3 Mar 2016 13:50:26 +1100 Subject: 0.12 release In-Reply-To: References: <6F56AC09-BA2B-43F5-A910-37740BEBEC64@demuc.de> <20160203075920.GA2389752@phare.normalesup.org> <20160203172104.GA2977973@phare.normalesup.org> <20160207153232.GA2920916@phare.normalesup.org> <20160223153821.GB1829563@phare.normalesup.org> <20160302212445.GA3276684@phare.normalesup.org> <20160302215220.GC3276684@phare.normalesup.org> Message-ID: Aren't these pre-existing bugs? At any rate, as you say, might be a moot point, finally. =) On Thu, Mar 3, 2016 at 1:29 PM, St?fan van der Walt wrote: > On 2 March 2016 at 16:00, Juan Nunez-Iglesias wrote: > > Bug fixes seem precisely inessential to get done ahead of release? > Anything > > that doesn't break the API can be added in 0.12.1? > > You can't really release a package with a broken test suite. So you > have the option to temporarily disable the tests, but shipping with a > known bug feels kind of weird? > > Either way, I think I've zapped most of the outstanding ones. Waiting > for Travis. > > St?fan > > -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image+unsubscribe at googlegroups.com. > To post to this group, send an email to scikit-image at googlegroups.com. > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/CABDkGQnz%2BdW7-oC2CpcEpxRYjmotMderNZ2-u84EctjOSOpU-Q%40mail.gmail.com > . > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Fri Mar 4 14:40:18 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Fri, 4 Mar 2016 11:40:18 -0800 Subject: 0.12 release In-Reply-To: References: <6F56AC09-BA2B-43F5-A910-37740BEBEC64@demuc.de> <20160203075920.GA2389752@phare.normalesup.org> <20160203172104.GA2977973@phare.normalesup.org> <20160207153232.GA2920916@phare.normalesup.org> <20160223153821.GB1829563@phare.normalesup.org> <20160302212445.GA3276684@phare.normalesup.org> <20160302215220.GC3276684@phare.normalesup.org> Message-ID: Who wants to merge the last outstanding PR for 0.12! https://github.com/scikit-image/scikit-image/pulls?q=is%3Aopen+is%3Apr+milestone%3A0.12 On 2 March 2016 at 18:50, Juan Nunez-Iglesias wrote: > Aren't these pre-existing bugs? At any rate, as you say, might be a moot > point, finally. =) > > On Thu, Mar 3, 2016 at 1:29 PM, St?fan van der Walt > wrote: >> >> On 2 March 2016 at 16:00, Juan Nunez-Iglesias wrote: >> > Bug fixes seem precisely inessential to get done ahead of release? >> > Anything >> > that doesn't break the API can be added in 0.12.1? >> >> You can't really release a package with a broken test suite. So you >> have the option to temporarily disable the tests, but shipping with a >> known bug feels kind of weird? >> >> Either way, I think I've zapped most of the outstanding ones. Waiting >> for Travis. >> >> St?fan >> >> -- >> You received this message because you are subscribed to the Google Groups >> "scikit-image" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to scikit-image+unsubscribe at googlegroups.com. >> To post to this group, send an email to scikit-image at googlegroups.com. >> To view this discussion on the web, visit >> https://groups.google.com/d/msgid/scikit-image/CABDkGQnz%2BdW7-oC2CpcEpxRYjmotMderNZ2-u84EctjOSOpU-Q%40mail.gmail.com. >> For more options, visit https://groups.google.com/d/optout. > > > -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image+unsubscribe at googlegroups.com. > To post to this group, send email to scikit-image at googlegroups.com. > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/CA%2BJHcKRUYPFNz7n3OARY1rhpZj%3DEvN%3DTPivKOrt0X0izZhbCXw%40mail.gmail.com. > > For more options, visit https://groups.google.com/d/optout. From stefanv at berkeley.edu Fri Mar 4 17:38:09 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Fri, 4 Mar 2016 14:38:09 -0800 Subject: jpeg image being read differently skimage.io.imread In-Reply-To: References: Message-ID: Hi Vimal Can you please try skimage.io.imread(image_name, plugin='matplotlib') ? Thanks! St?fan On 3 March 2016 at 12:13, Vimal Thilak wrote: > Hi, > > I have two servers on which I have installed skimage. When I do an > skimage.io.imread on these two machines with the same image file, I noticed > a difference in the shape of the returned image array: > > Machine 1: > > image_name = /path/to/JPEG > > img = skimage.io.imread(image_name) > >>>> img.shape > > (3000, 4000, 3) > > > Machine 2: > > > img = skimage.io.imread(image_name) > >>>> img.shape > > (2, ) > > > Both machines have skimage version '0.11.3'. I believe that both systems > have Pillow installed. I do not know the version of Pillow. I did change the > plug-in to matplotlib on Machine 2 and saw that the image was being read > correctly. However, I'm curious to know the reason for this difference and > what I can do to fix my machine #2 > > > Furthermore, how do I find the version of Pillow installed on my system? A > google search didn't come up with anything that was helpful (i.e, > copy-pastable solution) :) > > > Thanks, > > > -Vimal > > -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image+unsubscribe at googlegroups.com. > To post to this group, send email to scikit-image at googlegroups.com. > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/ef640963-7d67-4e00-9c2c-d71681104b56%40googlegroups.com. > For more options, visit https://groups.google.com/d/optout. From fboulogne at sciunto.org Sat Mar 5 03:03:06 2016 From: fboulogne at sciunto.org (=?UTF-8?Q?Fran=c3=a7ois_Boulogne?=) Date: Sat, 5 Mar 2016 09:03:06 +0100 Subject: jpeg image being read differently skimage.io.imread In-Reply-To: References: Message-ID: <56DA92BA.6010405@sciunto.org> > Can you please try > > skimage.io.imread(image_name, plugin='matplotlib') ? > I think Vimal said that it works with matplotlib, or misunderstood. To get PIL's version, you can try python -c 'import PIL; print(PIL.VERSION)' Best, -- Fran?ois Boulogne. http://www.sciunto.org GPG: 32D5F22F From emmanuelle.gouillart at nsup.org Sat Mar 5 12:07:14 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Sat, 5 Mar 2016 18:07:14 +0100 Subject: 0.12 release In-Reply-To: References: <20160207153232.GA2920916@phare.normalesup.org> <20160223153821.GB1829563@phare.normalesup.org> <20160302212445.GA3276684@phare.normalesup.org> <20160302215220.GC3276684@phare.normalesup.org> Message-ID: <20160305170714.GA542515@phare.normalesup.org> Awesome!! I'm tagging right now, so please don't merge any PRs!!! On Fri, Mar 04, 2016 at 11:40:18AM -0800, St??fan van der Walt wrote: > Who wants to merge the last outstanding PR for 0.12! > https://github.com/scikit-image/scikit-image/pulls?q=is%3Aopen+is%3Apr+milestone%3A0.12 > On 2 March 2016 at 18:50, Juan Nunez-Iglesias wrote: > > Aren't these pre-existing bugs? At any rate, as you say, might be a moot > > point, finally. =) > > On Thu, Mar 3, 2016 at 1:29 PM, St??fan van der Walt > > wrote: > >> On 2 March 2016 at 16:00, Juan Nunez-Iglesias wrote: > >> > Bug fixes seem precisely inessential to get done ahead of release? > >> > Anything > >> > that doesn't break the API can be added in 0.12.1? > >> You can't really release a package with a broken test suite. So you > >> have the option to temporarily disable the tests, but shipping with a > >> known bug feels kind of weird? > >> Either way, I think I've zapped most of the outstanding ones. Waiting > >> for Travis. > >> St??fan > >> -- > >> You received this message because you are subscribed to the Google Groups > >> "scikit-image" group. > >> To unsubscribe from this group and stop receiving emails from it, send an > >> email to scikit-image+unsubscribe at googlegroups.com. > >> To post to this group, send an email to scikit-image at googlegroups.com. > >> To view this discussion on the web, visit > >> https://groups.google.com/d/msgid/scikit-image/CABDkGQnz%2BdW7-oC2CpcEpxRYjmotMderNZ2-u84EctjOSOpU-Q%40mail.gmail.com. > >> For more options, visit https://groups.google.com/d/optout. > > -- > > You received this message because you are subscribed to the Google Groups > > "scikit-image" group. > > To unsubscribe from this group and stop receiving emails from it, send an > > email to scikit-image+unsubscribe at googlegroups.com. > > To post to this group, send email to scikit-image at googlegroups.com. > > To view this discussion on the web, visit > > https://groups.google.com/d/msgid/scikit-image/CA%2BJHcKRUYPFNz7n3OARY1rhpZj%3DEvN%3DTPivKOrt0X0izZhbCXw%40mail.gmail.com. > > For more options, visit https://groups.google.com/d/optout. From emmanuelle.gouillart at nsup.org Sun Mar 6 17:30:00 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Sun, 6 Mar 2016 23:30:00 +0100 Subject: 0.12 release In-Reply-To: <20160305170714.GA542515@phare.normalesup.org> References: <20160223153821.GB1829563@phare.normalesup.org> <20160302212445.GA3276684@phare.normalesup.org> <20160302215220.GC3276684@phare.normalesup.org> <20160305170714.GA542515@phare.normalesup.org> Message-ID: <20160306223000.GA3358700@phare.normalesup.org> So, I tagged v0.12.0 and pushed a 0.12.x branch to scikit-image/scikit-image Now the release can be published on PyPi, I think :-) Emma On Sat, Mar 05, 2016 at 06:07:14PM +0100, Emmanuelle Gouillart wrote: > Awesome!! I'm tagging right now, so please don't merge any PRs!!! > On Fri, Mar 04, 2016 at 11:40:18AM -0800, St??fan van der Walt wrote: > > Who wants to merge the last outstanding PR for 0.12! > > https://github.com/scikit-image/scikit-image/pulls?q=is%3Aopen+is%3Apr+milestone%3A0.12 > > On 2 March 2016 at 18:50, Juan Nunez-Iglesias wrote: > > > Aren't these pre-existing bugs? At any rate, as you say, might be a moot > > > point, finally. =) > > > On Thu, Mar 3, 2016 at 1:29 PM, St??fan van der Walt > > > wrote: > > >> On 2 March 2016 at 16:00, Juan Nunez-Iglesias wrote: > > >> > Bug fixes seem precisely inessential to get done ahead of release? > > >> > Anything > > >> > that doesn't break the API can be added in 0.12.1? > > >> You can't really release a package with a broken test suite. So you > > >> have the option to temporarily disable the tests, but shipping with a > > >> known bug feels kind of weird? > > >> Either way, I think I've zapped most of the outstanding ones. Waiting > > >> for Travis. > > >> St??fan > > >> -- > > >> You received this message because you are subscribed to the Google Groups > > >> "scikit-image" group. > > >> To unsubscribe from this group and stop receiving emails from it, send an > > >> email to scikit-image+unsubscribe at googlegroups.com. > > >> To post to this group, send an email to scikit-image at googlegroups.com. > > >> To view this discussion on the web, visit > > >> https://groups.google.com/d/msgid/scikit-image/CABDkGQnz%2BdW7-oC2CpcEpxRYjmotMderNZ2-u84EctjOSOpU-Q%40mail.gmail.com. > > >> For more options, visit https://groups.google.com/d/optout. > > > -- > > > You received this message because you are subscribed to the Google Groups > > > "scikit-image" group. > > > To unsubscribe from this group and stop receiving emails from it, send an > > > email to scikit-image+unsubscribe at googlegroups.com. > > > To post to this group, send email to scikit-image at googlegroups.com. > > > To view this discussion on the web, visit > > > https://groups.google.com/d/msgid/scikit-image/CA%2BJHcKRUYPFNz7n3OARY1rhpZj%3DEvN%3DTPivKOrt0X0izZhbCXw%40mail.gmail.com. > > > For more options, visit https://groups.google.com/d/optout. From jeanpatrick.pommier at gmail.com Mon Mar 7 03:06:38 2016 From: jeanpatrick.pommier at gmail.com (Jean-Patrick Pommier) Date: Mon, 7 Mar 2016 00:06:38 -0800 (PST) Subject: failed to build version 0.12 Message-ID: Hello, Thank you for this new version of scikit-image. I met the following message when i try to upgrade scikit-image (linux): $ pip install --upgrade scikit-image Collecting scikit-image Using cached scikit-image-0.12.0.tar.gz Complete output from command python setup.py egg_info: Partial import of skimage during the build process. Traceback (most recent call last): File "", line 1, in File "/tmp/pip-build-rR00uc/scikit-image/setup.py", line 146, in **extra File "/usr/lib/python2.7/site-packages/numpy/distutils/core.py", line 135, in setup config = configuration() File "/tmp/pip-build-rR00uc/scikit-image/setup.py", line 69, in configuration config.add_subpackage('skimage') File "/usr/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage caller_level = 2) File "/usr/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage caller_level = caller_level + 1) File "/usr/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "skimage/setup.py", line 21, in configuration config.add_subpackage('morphology') File "/usr/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage caller_level = 2) File "/usr/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage caller_level = caller_level + 1) File "/usr/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "skimage/morphology/setup.py", line 19, in configuration cython(['_skeletonize_3d_cy.pyx.in'], working_path=base_path) File "skimage/_build.py", line 39, in cython if not _changed(pyxfile): File "skimage/_build.py", line 70, in _changed with open(filename, 'rb') as f: IOError: [Errno 2] No such file or directory: '/tmp/pip-build-rR00uc/scikit-image/skimage/morphology/_skeletonize_3d_cy.pyx.in' I got the same message working with sudo or from a virtual env. Best regards jean-patrick -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Mon Mar 7 03:43:04 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Mon, 7 Mar 2016 00:43:04 -0800 Subject: failed to build version 0.12 In-Reply-To: References: Message-ID: Hi Jean-Patrick On 7 March 2016 at 00:06, Jean-Patrick Pommier wrote: > '/tmp/pip-build-rR00uc/scikit-image/skimage/morphology/_skeletonize_3d_cy.pyx.in' scikit-image now requires a newer version of Cython to build. See: https://github.com/scikit-image/scikit-image/blob/master/DEPENDS.txt#L5 Best regards St?fan From jenshnielsen at gmail.com Mon Mar 7 04:35:35 2016 From: jenshnielsen at gmail.com (Jens Nielsen) Date: Mon, 7 Mar 2016 01:35:35 -0800 (PST) Subject: failed to build version 0.12 In-Reply-To: References: Message-ID: <1b8fa5cd-7eaf-4d70-bb24-70e440a7b13a@googlegroups.com> Sorry but I am also seeing this happening with Cython 0.23.4 so I doubt that the Cython version is the problem. (test) ? ~ pip list cycler (0.10.0) Cython (0.23.4) dask (0.8.0) decorator (4.0.9) matplotlib (1.5.1) networkx (1.11) numpy (1.10.4) Pillow (3.1.1) pip (8.1.0) pyparsing (2.1.0) python-dateutil (2.5.0) pytz (2015.7) scipy (0.17.0) setuptools (20.2.2) six (1.10.0) toolz (0.7.4) wheel (0.29.0) (test) ? ~ pip install scikit-image Collecting scikit-image Using cached scikit-image-0.12.0.tar.gz Complete output from command python setup.py egg_info: Partial import of skimage during the build process. Traceback (most recent call last): File "", line 1, in File "/private/var/folders/zz/yg37r3x91_d5kkj0k8x8g0cm0000gn/T/pip-build-rqta5vux/scikit-image/setup.py", line 146, in **extra File "/Users/jhn/Envs/test/lib/python3.5/site-packages/numpy/distutils/core.py", line 135, in setup config = configuration() File "/private/var/folders/zz/yg37r3x91_d5kkj0k8x8g0cm0000gn/T/pip-build-rqta5vux/scikit-image/setup.py", line 69, in configuration config.add_subpackage('skimage') File "/Users/jhn/Envs/test/lib/python3.5/site-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage caller_level = 2) File "/Users/jhn/Envs/test/lib/python3.5/site-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage caller_level = caller_level + 1) File "/Users/jhn/Envs/test/lib/python3.5/site-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "skimage/setup.py", line 21, in configuration config.add_subpackage('morphology') File "/Users/jhn/Envs/test/lib/python3.5/site-packages/numpy/distutils/misc_util.py", line 1002, in add_subpackage caller_level = 2) File "/Users/jhn/Envs/test/lib/python3.5/site-packages/numpy/distutils/misc_util.py", line 971, in get_subpackage caller_level = caller_level + 1) File "/Users/jhn/Envs/test/lib/python3.5/site-packages/numpy/distutils/misc_util.py", line 908, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "skimage/morphology/setup.py", line 19, in configuration cython(['_skeletonize_3d_cy.pyx.in'], working_path=base_path) File "/private/var/folders/zz/yg37r3x91_d5kkj0k8x8g0cm0000gn/T/pip-build-rqta5vux/scikit-image/skimage/_build.py", line 39, in cython if not _changed(pyxfile): File "/private/var/folders/zz/yg37r3x91_d5kkj0k8x8g0cm0000gn/T/pip-build-rqta5vux/scikit-image/skimage/_build.py", line 70, in _changed with open(filename, 'rb') as f: FileNotFoundError: [Errno 2] No such file or directory: '/private/var/folders/zz/yg37r3x91_d5kkj0k8x8g0cm0000gn/T/pip-build-rqta5vux/scikit-image/skimage/morphology/_skeletonize_3d_cy.pyx.in' ---------------------------------------- Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/zz/yg37r3x91_d5kkj0k8x8g0cm0000gn/T/pip-build-rqta5vux/scikit-image/ The problem is that skimage/morphology/setup.py contains: cython(['_skeletonize_3d_cy.pyx.in'], working_path=base_path) but that file is not in the pypi tar ball. It should presumably try to process the template processed file _skeletonize_3d_cy.pyx? Best Jens On Monday, 7 March 2016 08:43:25 UTC, stefanv wrote: > > Hi Jean-Patrick > > On 7 March 2016 at 00:06, Jean-Patrick Pommier > > wrote: > > '/tmp/pip-build-rR00uc/scikit-image/skimage/morphology/_ > skeletonize_3d_cy.pyx.in' > > scikit-image now requires a newer version of Cython to build. See: > > https://github.com/scikit-image/scikit-image/blob/master/DEPENDS.txt#L5 > > Best regards > St?fan > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Mon Mar 7 04:37:59 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Mon, 7 Mar 2016 01:37:59 -0800 Subject: failed to build version 0.12 In-Reply-To: <1b8fa5cd-7eaf-4d70-bb24-70e440a7b13a@googlegroups.com> References: <1b8fa5cd-7eaf-4d70-bb24-70e440a7b13a@googlegroups.com> Message-ID: On 7 March 2016 at 01:35, Jens Nielsen wrote: > cython(['_skeletonize_3d_cy.pyx.in'], working_path=base_path) That's a bug, thanks. St?fan From stefanv at berkeley.edu Mon Mar 7 04:39:52 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Mon, 7 Mar 2016 01:39:52 -0800 Subject: failed to build version 0.12 In-Reply-To: References: Message-ID: On 7 March 2016 at 01:15, Johannes Sch?nberger wrote: > For the 0.12.1 release, maybe we can fail more in a more informative error message in this case? > > Maybe I am wrong, but I think someone else had the same problem very recently? Please see: https://github.com/scikit-image/scikit-image/pull/1986 St?fan From stefanv at berkeley.edu Mon Mar 7 04:47:01 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Mon, 7 Mar 2016 01:47:01 -0800 Subject: failed to build version 0.12 In-Reply-To: <1b8fa5cd-7eaf-4d70-bb24-70e440a7b13a@googlegroups.com> References: <1b8fa5cd-7eaf-4d70-bb24-70e440a7b13a@googlegroups.com> Message-ID: On 7 March 2016 at 01:35, Jens Nielsen wrote: > The problem is that skimage/morphology/setup.py contains: > > cython(['_skeletonize_3d_cy.pyx.in'], working_path=base_path) > > but that file is not in the pypi tar ball. It should presumably try to > process the template processed file _skeletonize_3d_cy.pyx? I've pushed 0.12.1 to pypi to fix the problem; please let me know if that works for you. Thanks St?fan From jenshnielsen at gmail.com Mon Mar 7 04:51:27 2016 From: jenshnielsen at gmail.com (Jens Nielsen) Date: Mon, 7 Mar 2016 01:51:27 -0800 (PST) Subject: failed to build version 0.12 In-Reply-To: References: <1b8fa5cd-7eaf-4d70-bb24-70e440a7b13a@googlegroups.com> Message-ID: <203cd744-c575-483a-bddd-4ba97dd84447@googlegroups.com> It does indeed. ? ~ pip3 install --upgrade scikit-image Collecting scikit-image Downloading scikit-image-0.12.1.tar.gz (22.5MB) 100% |????????????????????????????????| 22.5MB 75kB/s Requirement already up-to-date: six>=1.7.3 in /usr/local/lib/python3.5/site-packages (from scikit-image) Requirement already up-to-date: networkx>=1.8 in /usr/local/lib/python3.5/site-packages (from scikit-image) Requirement already up-to-date: pillow>=2.1.0 in /usr/local/lib/python3.5/site-packages (from scikit-image) Collecting dask[array]>=0.5.0 (from scikit-image) Requirement already up-to-date: decorator>=3.4.0 in /usr/local/lib/python3.5/site-packages (from networkx>=1.8->scikit-image) Collecting toolz>=0.7.2 (from dask[array]>=0.5.0->scikit-image) Requirement already up-to-date: numpy in /usr/local/lib/python3.5/site-packages (from dask[array]>=0.5.0->scikit-image) Building wheels for collected packages: scikit-image Running setup.py bdist_wheel for scikit-image ... done Stored in directory: /Users/jhn/Library/Caches/pip/wheels/41/88/c2/e86fe4aa654d61f49c7b95776a15f605081851ef3b08c01d2f Successfully built scikit-image Installing collected packages: toolz, dask, scikit-image Found existing installation: scikit-image 0.11.3 Uninstalling scikit-image-0.11.3: Successfully uninstalled scikit-image-0.11.3 Successfully installed dask-0.8.0 scikit-image-0.12.1 toolz-0.7.4 Thanks for the ultra quick turn around Jens On Monday, 7 March 2016 09:47:23 UTC, stefanv wrote: > > On 7 March 2016 at 01:35, Jens Nielsen > > wrote: > > The problem is that skimage/morphology/setup.py contains: > > > > cython(['_skeletonize_3d_cy.pyx.in'], working_path=base_path) > > > > but that file is not in the pypi tar ball. It should presumably try to > > process the template processed file _skeletonize_3d_cy.pyx? > > I've pushed 0.12.1 to pypi to fix the problem; please let me know if > that works for you. > > Thanks > St?fan > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Mon Mar 7 04:54:01 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Mon, 7 Mar 2016 01:54:01 -0800 Subject: failed to build version 0.12 In-Reply-To: <203cd744-c575-483a-bddd-4ba97dd84447@googlegroups.com> References: <1b8fa5cd-7eaf-4d70-bb24-70e440a7b13a@googlegroups.com> <203cd744-c575-483a-bddd-4ba97dd84447@googlegroups.com> Message-ID: On 7 March 2016 at 01:51, Jens Nielsen wrote: > Successfully installed dask-0.8.0 scikit-image-0.12.1 toolz-0.7.4 > Thanks for the ultra quick turn around Excellent, thanks for testing! With the next release cycle, I will probably do release candidates first like all the adults do ;) St?fan From matteo.niccoli at gmail.com Mon Mar 7 11:06:06 2016 From: matteo.niccoli at gmail.com (Matteo) Date: Mon, 7 Mar 2016 08:06:06 -0800 (PST) Subject: Problem with using sp.ndimage.label to get largest object in a binary image Message-ID: Hello there I'm putting together some code to grab an image with a map, colorbar, and possibly text and other elements, guess what the largest object in the image is -assuming it is the map - crop the image to the map extent, then reduce the number of colors in the map. My Jupiter notebook is at this location on GitHub: https://github.com/mycarta/rainbowbot/blob/master/crop_image_reduce_colors.ipynb The issue I have with this code is that: If I run it with the current test image (https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_notebooks/test1.png) or even a nimage with map touching the border(https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_notebooks/test2.png) the code seems to work. However, in the case of an image with larger blocks of text (https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_notebooks/test_with_text.png) the output of [9] is an array that is all zeroes, although as far as I know it should not. Can anyone suggest why this is happening? I am sure it is something I am overlooking in my code/understanding of image processing. Thanks Matteo -------------- next part -------------- An HTML attachment was scrubbed... URL: From jeanpatrick.pommier at gmail.com Mon Mar 7 12:20:39 2016 From: jeanpatrick.pommier at gmail.com (Jean-Patrick Pommier) Date: Mon, 7 Mar 2016 09:20:39 -0800 (PST) Subject: failed to build version 0.12 In-Reply-To: References: Message-ID: Thank you! Successfully built scikit-image dask toolz Installing collected packages: toolz, dask, scikit-image Found existing installation: scikit-image 0.11.3 Not uninstalling scikit-image at /usr/lib/python2.7/site-packages, outside environment /home/jeanpat/Developpements/DIP4FISH Successfully installed dask-0.8.0 scikit-image-0.12.1 toolz-0.7.4 (DIP4FISH)[jeanpat at dip4fish ~]$ python2 Python 2.7.11 (default, Dec 6 2015, 15:43:46) [GCC 5.2.0] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import skimage >>> print skimage.__version__ 0.12.1 >>> Le lundi 7 mars 2016 09:06:38 UTC+1, Jean-Patrick Pommier a ?crit : > > Hello, > > Thank you for this new version of scikit-image. > > I met the following message when i try to upgrade scikit-image (linux): > > $ pip install --upgrade scikit-image > Collecting scikit-image > Using cached scikit-image-0.12.0.tar.gz > Complete output from command python setup.py egg_info: > Partial import of skimage during the build process. > Traceback (most recent call last): > File "", line 1, in > File "/tmp/pip-build-rR00uc/scikit-image/setup.py", line 146, in > > **extra > File "/usr/lib/python2.7/site-packages/numpy/distutils/core.py", > line 135, in setup > config = configuration() > File "/tmp/pip-build-rR00uc/scikit-image/setup.py", line 69, in > configuration > config.add_subpackage('skimage') > File "/usr/lib/python2.7/site-packages/numpy/distutils/misc_util.py" > , line 1002, in add_subpackage > caller_level = 2) > File "/usr/lib/python2.7/site-packages/numpy/distutils/misc_util.py" > , line 971, in get_subpackage > caller_level = caller_level + 1) > File "/usr/lib/python2.7/site-packages/numpy/distutils/misc_util.py" > , line 908, in _get_configuration_from_setup_py > config = setup_module.configuration(*args) > File "skimage/setup.py", line 21, in configuration > config.add_subpackage('morphology') > File "/usr/lib/python2.7/site-packages/numpy/distutils/misc_util.py" > , line 1002, in add_subpackage > caller_level = 2) > File "/usr/lib/python2.7/site-packages/numpy/distutils/misc_util.py" > , line 971, in get_subpackage > caller_level = caller_level + 1) > File "/usr/lib/python2.7/site-packages/numpy/distutils/misc_util.py" > , line 908, in _get_configuration_from_setup_py > config = setup_module.configuration(*args) > File "skimage/morphology/setup.py", line 19, in configuration > cython(['_skeletonize_3d_cy.pyx.in'], working_path=base_path) > File "skimage/_build.py", line 39, in cython > if not _changed(pyxfile): > File "skimage/_build.py", line 70, in _changed > with open(filename, 'rb') as f: > IOError: [Errno 2] No such file or directory: > '/tmp/pip-build-rR00uc/scikit-image/skimage/morphology/_ > skeletonize_3d_cy.pyx.in' > > I got the same message working with sudo or from a virtual env. > > Best regards > jean-patrick > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jsch at demuc.de Mon Mar 7 04:15:42 2016 From: jsch at demuc.de (=?utf-8?Q?Johannes_Sch=C3=B6nberger?=) Date: Mon, 7 Mar 2016 10:15:42 +0100 Subject: failed to build version 0.12 In-Reply-To: References: Message-ID: For the 0.12.1 release, maybe we can fail more in a more informative error message in this case? Maybe I am wrong, but I think someone else had the same problem very recently? > On Mar 7, 2016, at 9:43 AM, St?fan van der Walt wrote: > > Hi Jean-Patrick > > On 7 March 2016 at 00:06, Jean-Patrick Pommier > wrote: >> '/tmp/pip-build-rR00uc/scikit-image/skimage/morphology/_skeletonize_3d_cy.pyx.in' > > scikit-image now requires a newer version of Cython to build. See: > > https://github.com/scikit-image/scikit-image/blob/master/DEPENDS.txt#L5 > > Best regards > St?fan > > -- > You received this message because you are subscribed to the Google Groups "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com. > To post to this group, send an email to scikit-image at googlegroups.com. > To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/CABDkGQnVf5_J0nEL2P-Q7%3DoarfnsdDDxkTpK-x6wkhMOcKnkUw%40mail.gmail.com. > For more options, visit https://groups.google.com/d/optout. From stefanv at berkeley.edu Mon Mar 7 15:22:06 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Mon, 7 Mar 2016 12:22:06 -0800 Subject: failed to build version 0.12 In-Reply-To: <20160307201500.GB1028544@phare.normalesup.org> References: <20160307193103.GA1028544@phare.normalesup.org> <20160307201500.GB1028544@phare.normalesup.org> Message-ID: On 7 March 2016 at 12:15, Emmanuelle Gouillart wrote: > On Mon, Mar 07, 2016 at 08:52:20PM +0100, Johannes Sch?nberger wrote: >> @Emma, that sounds right. So, maybe there is something else wrong? > > yes, that was something else that was solved by St?fan in 0.12.1. I was > just replying to this e-mail since it was the one that mentioned cython Right, so what was happening is that the .in file was missing, so the build process could not check whether the generated .pyx file was outdated or not. St?fan From himanshu2014iit at gmail.com Mon Mar 7 04:56:01 2016 From: himanshu2014iit at gmail.com (Himanshu Mishra) Date: Mon, 7 Mar 2016 15:26:01 +0530 Subject: failed to build version 0.12 In-Reply-To: References: <1b8fa5cd-7eaf-4d70-bb24-70e440a7b13a@googlegroups.com> <203cd744-c575-483a-bddd-4ba97dd84447@googlegroups.com> Message-ID: > With the next release cycle, I will probably do release candidates > first like all the adults do ;) > > Release candidates, yay ! :) Himanshu Mishra -------------- next part -------------- An HTML attachment was scrubbed... URL: From emmanuelle.gouillart at nsup.org Mon Mar 7 14:31:03 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Mon, 7 Mar 2016 20:31:03 +0100 Subject: failed to build version 0.12 In-Reply-To: References: Message-ID: <20160307193103.GA1028544@phare.normalesup.org> Just to be sure: when doing "pip install scikit-image", there's no need for cython to be installed (any version of cython), right? The .c are shipped with the .tar.gz on PyPi, so I guess it should be fine without Cython... Emma On Mon, Mar 07, 2016 at 12:43:04AM -0800, St??fan van der Walt wrote: > Hi Jean-Patrick > On 7 March 2016 at 00:06, Jean-Patrick Pommier > wrote: > > '/tmp/pip-build-rR00uc/scikit-image/skimage/morphology/_skeletonize_3d_cy.pyx.in' > scikit-image now requires a newer version of Cython to build. See: > https://github.com/scikit-image/scikit-image/blob/master/DEPENDS.txt#L5 > Best regards > St??fan From jsch at demuc.de Mon Mar 7 14:52:20 2016 From: jsch at demuc.de (=?utf-8?Q?Johannes_Sch=C3=B6nberger?=) Date: Mon, 7 Mar 2016 20:52:20 +0100 Subject: failed to build version 0.12 In-Reply-To: <20160307193103.GA1028544@phare.normalesup.org> References: <20160307193103.GA1028544@phare.normalesup.org> Message-ID: @Emma, that sounds right. So, maybe there is something else wrong? > On Mar 7, 2016, at 8:31 PM, Emmanuelle Gouillart wrote: > > Just to be sure: when doing "pip install scikit-image", there's no need > for cython to be installed (any version of cython), right? The .c are > shipped with the .tar.gz on PyPi, so I guess it should be fine without > Cython... > > Emma > > > > On Mon, Mar 07, 2016 at 12:43:04AM -0800, St?fan van der Walt wrote: >> Hi Jean-Patrick > >> On 7 March 2016 at 00:06, Jean-Patrick Pommier >> wrote: >>> '/tmp/pip-build-rR00uc/scikit-image/skimage/morphology/_skeletonize_3d_cy.pyx.in' > >> scikit-image now requires a newer version of Cython to build. See: > >> https://github.com/scikit-image/scikit-image/blob/master/DEPENDS.txt#L5 > >> Best regards >> St?fan > > -- > You received this message because you are subscribed to the Google Groups "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com. > To post to this group, send an email to scikit-image at googlegroups.com. > To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/20160307193103.GA1028544%40phare.normalesup.org. > For more options, visit https://groups.google.com/d/optout. From emmanuelle.gouillart at nsup.org Mon Mar 7 15:15:00 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Mon, 7 Mar 2016 21:15:00 +0100 Subject: failed to build version 0.12 In-Reply-To: References: <20160307193103.GA1028544@phare.normalesup.org> Message-ID: <20160307201500.GB1028544@phare.normalesup.org> On Mon, Mar 07, 2016 at 08:52:20PM +0100, Johannes Sch??nberger wrote: > @Emma, that sounds right. So, maybe there is something else wrong? yes, that was something else that was solved by St??fan in 0.12.1. I was just replying to this e-mail since it was the one that mentioned cython From emmanuelle.gouillart at nsup.org Mon Mar 7 16:50:09 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Mon, 7 Mar 2016 22:50:09 +0100 Subject: release: scikit-image 0.12 is out! Message-ID: <20160307215009.GA1343452@phare.normalesup.org> Announcement: scikit-image 0.12 =============================== The scikit-image team is very pleased to announce the release of version 0.12 of scikit-image. scikit-image is an image processing toolbox for Python and SciPy, that includes algorithms for segmentation, geometric transformations, color space manipulation, analysis, filtering, morphology, feature detection, and more, for 2-D and 3-D (sometimes n-D) images. For more information, examples, and documentation, please visit our website: http://scikit-image.org and our example gallery http://scikit-image.org/docs/dev/auto_examples/ This release includes new features such as image inpainting, seam carving, image comparison metrics, and a parallelization framework based on dask. The release has also improved the support of 3-D images, with 3-D skeletonization, 3-D phantom data. and partial support of measure.regionprops for 3-D images. Also note that the handling of background pixels by measure.label, a function labeling connected components, has changed to be consistent with scipy.ndimage.label. For this release, we merged over 200 pull requests from 64 contributors, with bug fixes, cleanups, improved documentation and new features. Release notes are available on http://scikit-image.org/docs/0.12.x/release_notes_and_installation.html#release-notes and include a more detailed list of changes, and the complete list of contributors to this release. The release can be downloaded on PyPi https://pypi.python.org/pypi/scikit-image or directly installed using pip pip install --upgrade scikit-image Please let us know any issues you might have on the issue tracker https://github.com/scikit-image/scikit-image/issues Many thanks to all the developers who made this release possible, and a warm welcome to our new contributors. Happy image processing! The scikit-image team From matteo.niccoli at gmail.com Tue Mar 8 09:59:36 2016 From: matteo.niccoli at gmail.com (Matteo) Date: Tue, 8 Mar 2016 06:59:36 -0800 (PST) Subject: Problem with using sp.ndimage.label to get largest object in a binary image In-Reply-To: References: Message-ID: <057d7338-f94a-4151-8200-0bf3edeb50dc@googlegroups.com> Hello Juan Thanks for your reply. Here is a second notebook with the problem image to look at. https://github.com/mycarta/rainbowbot/blob/master/crop_image_reduce_colors_text_test.ipynb I have not had time to change anything except for running it, and won't be able until tonight. When I do, I will look into your suggestions, and recommendations, and any other comments you may have from seeing the notebook. But, so, the background counts when it comes to labeling/size? I had assumed the operations would only apply to bright elements, that's the misunderstanding. Also, being here, the way, is there a better way, or a dedicated operation, to get the largest object/blob in a binary image? Cheers, Matteo On Monday, March 7, 2016 at 11:18:25 PM UTC-7, Juan Nunez-Iglesias wrote: > > Hi Matteo, > > It would be useful if you showed us the notebook being run with the > problematic image, as well as the original. > > Having said that, it looks like perhaps you should replace this line: > mask_sizes[0] = 0 > > with > > sizes[0] = 0 > > higher up. Perhaps your background is bigger than your foreground in the > problem image. =) > > Juan. > > PS: Incidentally, have a look at skimage.morphology.remove_small_objects > and skimage.morphology.remove_small_holes (this last one is in the > just-released 0.12 version). > > PPS: Also incidentally, for ndimage we often use the convention "from > scipy import ndimage as ndi" > > PPPS: Also, skimage.io.imread can directly load images from URLs. =) > > On Tue, Mar 8, 2016 at 3:06 AM, Matteo > > wrote: > >> Hello there >> >> I'm putting together some code to grab an image with a map, colorbar, and >> possibly text and other elements, guess what the largest object in the >> image is -assuming it is the map - crop the image to the map extent, then >> reduce the number of colors in the map. >> My Jupiter notebook is at this location on GitHub: >> >> https://github.com/mycarta/rainbowbot/blob/master/crop_image_reduce_colors.ipynb >> >> The issue I have with this code is that: >> If I run it with the current test image ( >> https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_notebooks/test1.png) >> or even a nimage with map touching the border( >> https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_notebooks/test2.png) >> the code seems to work. >> >> However, in the case of an image with larger blocks of text ( >> https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_notebooks/test_with_text.png >> ) >> the output of [9] is an array that is all zeroes, although as far as I >> know it should not. Can anyone suggest why this is happening? >> >> I am sure it is something I am overlooking in my code/understanding of >> image processing. >> >> Thanks >> Matteo >> >> -- >> You received this message because you are subscribed to the Google Groups >> "scikit-image" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to scikit-image... at googlegroups.com . >> To post to this group, send email to scikit... at googlegroups.com >> . >> To view this discussion on the web, visit >> https://groups.google.com/d/msgid/scikit-image/b5e56392-b181-4f70-a090-115a14ffe05c%40googlegroups.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 Mar 8 01:18:04 2016 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Tue, 8 Mar 2016 17:18:04 +1100 Subject: Problem with using sp.ndimage.label to get largest object in a binary image In-Reply-To: References: Message-ID: Hi Matteo, It would be useful if you showed us the notebook being run with the problematic image, as well as the original. Having said that, it looks like perhaps you should replace this line: mask_sizes[0] = 0 with sizes[0] = 0 higher up. Perhaps your background is bigger than your foreground in the problem image. =) Juan. PS: Incidentally, have a look at skimage.morphology.remove_small_objects and skimage.morphology.remove_small_holes (this last one is in the just-released 0.12 version). PPS: Also incidentally, for ndimage we often use the convention "from scipy import ndimage as ndi" PPPS: Also, skimage.io.imread can directly load images from URLs. =) On Tue, Mar 8, 2016 at 3:06 AM, Matteo wrote: > Hello there > > I'm putting together some code to grab an image with a map, colorbar, and > possibly text and other elements, guess what the largest object in the > image is -assuming it is the map - crop the image to the map extent, then > reduce the number of colors in the map. > My Jupiter notebook is at this location on GitHub: > > https://github.com/mycarta/rainbowbot/blob/master/crop_image_reduce_colors.ipynb > > The issue I have with this code is that: > If I run it with the current test image ( > https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_notebooks/test1.png) > or even a nimage with map touching the border( > https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_notebooks/test2.png) > the code seems to work. > > However, in the case of an image with larger blocks of text ( > https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_notebooks/test_with_text.png > ) > the output of [9] is an array that is all zeroes, although as far as I > know it should not. Can anyone suggest why this is happening? > > I am sure it is something I am overlooking in my code/understanding of > image processing. > > Thanks > Matteo > > -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image+unsubscribe at googlegroups.com. > To post to this group, send email to scikit-image at googlegroups.com. > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/b5e56392-b181-4f70-a090-115a14ffe05c%40googlegroups.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 Mar 8 17:44:56 2016 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Wed, 9 Mar 2016 09:44:56 +1100 Subject: Problem with using sp.ndimage.label to get largest object in a binary image In-Reply-To: <057d7338-f94a-4151-8200-0bf3edeb50dc@googlegroups.com> References: <057d7338-f94a-4151-8200-0bf3edeb50dc@googlegroups.com> Message-ID: Hi Matteo, ndimage.label keeps 0 as 0 (background) and then labels every nonzero blob as 1, 2, ... n. Then, numpy.bincount is completely agnostic as to whether you are looking at images or any other kind of array, and is just going to count the values, including 0. As I mentioned, remove_small_objects does what you want but you need to find out the size of the largest blob and pass that in as the min_size parameter. Juan. On Wed, Mar 9, 2016 at 1:59 AM, Matteo wrote: > Hello Juan > > Thanks for your reply. > Here is a second notebook with the problem image to look at. > https://github.com/mycarta/rainbowbot/blob/master/crop_image_reduce_colors_text_test.ipynb > > I have not had time to change anything except for running it, and won't be > able until tonight. When I do, I will look into your suggestions, and > recommendations, and any other comments you may have from seeing the > notebook. > But, so, the background counts when it comes to labeling/size? I had > assumed the operations would only apply to bright elements, that's the > misunderstanding. > > Also, being here, the way, is there a better way, or a dedicated > operation, to get the largest object/blob in a binary image? > > Cheers, > Matteo > > On Monday, March 7, 2016 at 11:18:25 PM UTC-7, Juan Nunez-Iglesias wrote: >> >> Hi Matteo, >> >> It would be useful if you showed us the notebook being run with the >> problematic image, as well as the original. >> >> Having said that, it looks like perhaps you should replace this line: >> mask_sizes[0] = 0 >> >> with >> >> sizes[0] = 0 >> >> higher up. Perhaps your background is bigger than your foreground in the >> problem image. =) >> >> Juan. >> >> PS: Incidentally, have a look at skimage.morphology.remove_small_objects >> and skimage.morphology.remove_small_holes (this last one is in the >> just-released 0.12 version). >> >> PPS: Also incidentally, for ndimage we often use the convention "from >> scipy import ndimage as ndi" >> >> PPPS: Also, skimage.io.imread can directly load images from URLs. =) >> >> On Tue, Mar 8, 2016 at 3:06 AM, Matteo wrote: >> >>> Hello there >>> >>> I'm putting together some code to grab an image with a map, colorbar, >>> and possibly text and other elements, guess what the largest object in the >>> image is -assuming it is the map - crop the image to the map extent, then >>> reduce the number of colors in the map. >>> My Jupiter notebook is at this location on GitHub: >>> >>> https://github.com/mycarta/rainbowbot/blob/master/crop_image_reduce_colors.ipynb >>> >>> The issue I have with this code is that: >>> If I run it with the current test image ( >>> https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_notebooks/test1.png) >>> or even a nimage with map touching the border( >>> https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_notebooks/test2.png) >>> the code seems to work. >>> >>> However, in the case of an image with larger blocks of text ( >>> https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_notebooks/test_with_text.png >>> ) >>> the output of [9] is an array that is all zeroes, although as far as I >>> know it should not. Can anyone suggest why this is happening? >>> >>> I am sure it is something I am overlooking in my code/understanding of >>> image processing. >>> >>> Thanks >>> Matteo >>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "scikit-image" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to scikit-image... at googlegroups.com. >>> To post to this group, send email to scikit... at googlegroups.com. >>> To view this discussion on the web, visit >>> https://groups.google.com/d/msgid/scikit-image/b5e56392-b181-4f70-a090-115a14ffe05c%40googlegroups.com >>> >>> . >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image+unsubscribe at googlegroups.com. > To post to this group, send email to scikit-image at googlegroups.com. > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/057d7338-f94a-4151-8200-0bf3edeb50dc%40googlegroups.com > > . > > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matteo.niccoli at gmail.com Wed Mar 9 12:50:18 2016 From: matteo.niccoli at gmail.com (Matteo Niccoli) Date: Wed, 9 Mar 2016 10:50:18 -0700 Subject: Problem with using sp.ndimage.label to get largest object in a binary image In-Reply-To: References: <057d7338-f94a-4151-8200-0bf3edeb50dc@googlegroups.com> Message-ID: Thanks again Juan Once I've had a chance to experiment with these options and get a polished, working notebook running, I will re-post it. Matteo On Tue, Mar 8, 2016 at 3:44 PM, Juan Nunez-Iglesias wrote: > Hi Matteo, > > ndimage.label keeps 0 as 0 (background) and then labels every nonzero blob > as 1, 2, ... n. Then, numpy.bincount is completely agnostic as to whether > you are looking at images or any other kind of array, and is just going to > count the values, including 0. > > As I mentioned, remove_small_objects does what you want but you need to > find out the size of the largest blob and pass that in as the min_size > parameter. > > Juan. > > On Wed, Mar 9, 2016 at 1:59 AM, Matteo wrote: > >> Hello Juan >> >> Thanks for your reply. >> Here is a second notebook with the problem image to look at. >> https://github.com/mycarta/rainbowbot/blob/master/crop_image_reduce_colors_text_test.ipynb >> >> I have not had time to change anything except for running it, and won't >> be able until tonight. When I do, I will look into your suggestions, and >> recommendations, and any other comments you may have from seeing the >> notebook. >> But, so, the background counts when it comes to labeling/size? I had >> assumed the operations would only apply to bright elements, that's the >> misunderstanding. >> >> Also, being here, the way, is there a better way, or a dedicated >> operation, to get the largest object/blob in a binary image? >> >> Cheers, >> Matteo >> >> On Monday, March 7, 2016 at 11:18:25 PM UTC-7, Juan Nunez-Iglesias wrote: >>> >>> Hi Matteo, >>> >>> It would be useful if you showed us the notebook being run with the >>> problematic image, as well as the original. >>> >>> Having said that, it looks like perhaps you should replace this line: >>> mask_sizes[0] = 0 >>> >>> with >>> >>> sizes[0] = 0 >>> >>> higher up. Perhaps your background is bigger than your foreground in the >>> problem image. =) >>> >>> Juan. >>> >>> PS: Incidentally, have a look at skimage.morphology.remove_small_objects >>> and skimage.morphology.remove_small_holes (this last one is in the >>> just-released 0.12 version). >>> >>> PPS: Also incidentally, for ndimage we often use the convention "from >>> scipy import ndimage as ndi" >>> >>> PPPS: Also, skimage.io.imread can directly load images from URLs. =) >>> >>> On Tue, Mar 8, 2016 at 3:06 AM, Matteo wrote: >>> >>>> Hello there >>>> >>>> I'm putting together some code to grab an image with a map, colorbar, >>>> and possibly text and other elements, guess what the largest object in the >>>> image is -assuming it is the map - crop the image to the map extent, then >>>> reduce the number of colors in the map. >>>> My Jupiter notebook is at this location on GitHub: >>>> >>>> https://github.com/mycarta/rainbowbot/blob/master/crop_image_reduce_colors.ipynb >>>> >>>> The issue I have with this code is that: >>>> If I run it with the current test image ( >>>> https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_notebooks/test1.png) >>>> or even a nimage with map touching the border( >>>> https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_notebooks/test2.png) >>>> the code seems to work. >>>> >>>> However, in the case of an image with larger blocks of text ( >>>> https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_notebooks/test_with_text.png >>>> ) >>>> the output of [9] is an array that is all zeroes, although as far as I >>>> know it should not. Can anyone suggest why this is happening? >>>> >>>> I am sure it is something I am overlooking in my code/understanding of >>>> image processing. >>>> >>>> Thanks >>>> Matteo >>>> >>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "scikit-image" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to scikit-image... at googlegroups.com. >>>> To post to this group, send email to scikit... at googlegroups.com. >>>> To view this discussion on the web, visit >>>> https://groups.google.com/d/msgid/scikit-image/b5e56392-b181-4f70-a090-115a14ffe05c%40googlegroups.com >>>> >>>> . >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> -- >> You received this message because you are subscribed to the Google Groups >> "scikit-image" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to scikit-image+unsubscribe at googlegroups.com. >> To post to this group, send email to scikit-image at googlegroups.com. >> To view this discussion on the web, visit >> https://groups.google.com/d/msgid/scikit-image/057d7338-f94a-4151-8200-0bf3edeb50dc%40googlegroups.com >> >> . >> >> For more options, visit https://groups.google.com/d/optout. >> > > -- > You received this message because you are subscribed to a topic in the > Google Groups "scikit-image" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/scikit-image/2_OZaXf2xEs/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > scikit-image+unsubscribe at googlegroups.com. > To post to this group, send email to scikit-image at googlegroups.com. > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/CA%2BJHcKSGywM5%2BLKA-fniCebFs3arTy4_y48Oq0JTh7hqc5r%3DBg%40mail.gmail.com > > . > > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Wed Mar 9 19:28:58 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Wed, 9 Mar 2016 16:28:58 -0800 Subject: Fused data types Message-ID: Hi everyone There is a PR asking for comments on how we wish to proceed with Fused Datatypes: https://github.com/scikit-image/scikit-image/pull/1977 What input & output types should be supported in which combinations? St?fan From matteo.niccoli at gmail.com Thu Mar 10 23:19:51 2016 From: matteo.niccoli at gmail.com (Matteo Niccoli) Date: Thu, 10 Mar 2016 21:19:51 -0700 Subject: Problem with using sp.ndimage.label to get largest object in a binary image In-Reply-To: References: <057d7338-f94a-4151-8200-0bf3edeb50dc@googlegroups.com> Message-ID: Hello Juan I've cleaned up the notebook and moved things around a bit. But mainly, I modified the *ndimaged.label* part (thanks to you for my better understanding of how it works), and also replaced the masking with *remove_small_objects*. here's my new notebook: https://github.com/mycarta/rainbowbot/blob/master/crop_image_reduce_colors_text_test.ipynb The one part that puzzled me for a bit is that things did not work when I used skimage.io.imread to import the image, but then I figured out it was because of the alpha channel... :-) [image: Inline image 1] Cheers, Matteo On Tue, Mar 8, 2016 at 3:44 PM, Juan Nunez-Iglesias wrote: > Hi Matteo, > > ndimage.label keeps 0 as 0 (background) and then labels every nonzero blob > as 1, 2, ... n. Then, numpy.bincount is completely agnostic as to whether > you are looking at images or any other kind of array, and is just going to > count the values, including 0. > > As I mentioned, remove_small_objects does what you want but you need to > find out the size of the largest blob and pass that in as the min_size > parameter. > > Juan. > > On Wed, Mar 9, 2016 at 1:59 AM, Matteo wrote: > >> Hello Juan >> >> Thanks for your reply. >> Here is a second notebook with the problem image to look at. >> https://github.com/mycarta/rainbowbot/blob/master/crop_image_reduce_colors_text_test.ipynb >> >> I have not had time to change anything except for running it, and won't >> be able until tonight. When I do, I will look into your suggestions, and >> recommendations, and any other comments you may have from seeing the >> notebook. >> But, so, the background counts when it comes to labeling/size? I had >> assumed the operations would only apply to bright elements, that's the >> misunderstanding. >> >> Also, being here, the way, is there a better way, or a dedicated >> operation, to get the largest object/blob in a binary image? >> >> Cheers, >> Matteo >> >> On Monday, March 7, 2016 at 11:18:25 PM UTC-7, Juan Nunez-Iglesias wrote: >>> >>> Hi Matteo, >>> >>> It would be useful if you showed us the notebook being run with the >>> problematic image, as well as the original. >>> >>> Having said that, it looks like perhaps you should replace this line: >>> mask_sizes[0] = 0 >>> >>> with >>> >>> sizes[0] = 0 >>> >>> higher up. Perhaps your background is bigger than your foreground in the >>> problem image. =) >>> >>> Juan. >>> >>> PS: Incidentally, have a look at skimage.morphology.remove_small_objects >>> and skimage.morphology.remove_small_holes (this last one is in the >>> just-released 0.12 version). >>> >>> PPS: Also incidentally, for ndimage we often use the convention "from >>> scipy import ndimage as ndi" >>> >>> PPPS: Also, skimage.io.imread can directly load images from URLs. =) >>> >>> On Tue, Mar 8, 2016 at 3:06 AM, Matteo wrote: >>> >>>> Hello there >>>> >>>> I'm putting together some code to grab an image with a map, colorbar, >>>> and possibly text and other elements, guess what the largest object in the >>>> image is -assuming it is the map - crop the image to the map extent, then >>>> reduce the number of colors in the map. >>>> My Jupiter notebook is at this location on GitHub: >>>> >>>> https://github.com/mycarta/rainbowbot/blob/master/crop_image_reduce_colors.ipynb >>>> >>>> The issue I have with this code is that: >>>> If I run it with the current test image ( >>>> https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_notebooks/test1.png) >>>> or even a nimage with map touching the border( >>>> https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_notebooks/test2.png) >>>> the code seems to work. >>>> >>>> However, in the case of an image with larger blocks of text ( >>>> https://github.com/mycarta/rainbowbot/blob/master/stuff4matching_cmap_notebooks/test_with_text.png >>>> ) >>>> the output of [9] is an array that is all zeroes, although as far as I >>>> know it should not. Can anyone suggest why this is happening? >>>> >>>> I am sure it is something I am overlooking in my code/understanding of >>>> image processing. >>>> >>>> Thanks >>>> Matteo >>>> >>>> -- >>>> You received this message because you are subscribed to the Google >>>> Groups "scikit-image" group. >>>> To unsubscribe from this group and stop receiving emails from it, send >>>> an email to scikit-image... at googlegroups.com. >>>> To post to this group, send email to scikit... at googlegroups.com. >>>> To view this discussion on the web, visit >>>> https://groups.google.com/d/msgid/scikit-image/b5e56392-b181-4f70-a090-115a14ffe05c%40googlegroups.com >>>> >>>> . >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> -- >> You received this message because you are subscribed to the Google Groups >> "scikit-image" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to scikit-image+unsubscribe at googlegroups.com. >> To post to this group, send email to scikit-image at googlegroups.com. >> To view this discussion on the web, visit >> https://groups.google.com/d/msgid/scikit-image/057d7338-f94a-4151-8200-0bf3edeb50dc%40googlegroups.com >> >> . >> >> For more options, visit https://groups.google.com/d/optout. >> > > -- > You received this message because you are subscribed to a topic in the > Google Groups "scikit-image" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/scikit-image/2_OZaXf2xEs/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > scikit-image+unsubscribe at googlegroups.com. > To post to this group, send email to scikit-image at googlegroups.com. > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/CA%2BJHcKSGywM5%2BLKA-fniCebFs3arTy4_y48Oq0JTh7hqc5r%3DBg%40mail.gmail.com > > . > > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2016-03-10 at 9.10.51 PM.png Type: image/png Size: 81391 bytes Desc: not available URL: From dassouki at gmail.com Fri Mar 11 08:17:02 2016 From: dassouki at gmail.com (Ahmed Dassouki) Date: Fri, 11 Mar 2016 05:17:02 -0800 (PST) Subject: Extracting attributes from images using Scikit-image Message-ID: Hi folks, I posted this question on stackoverflow on how to extract images using scikit-image. I am using the following code to generate the images: plt.rcParams['image.cmap'] = 'spectral' labels = seg.slic(color_image, n_segments=6, compactness=4). The end goal is to build an attribute table of the images dataset. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jatinkatyal96 at gmail.com Sun Mar 13 10:17:00 2016 From: jatinkatyal96 at gmail.com (Jatin Katyal) Date: Sun, 13 Mar 2016 07:17:00 -0700 (PDT) Subject: Saving an image Message-ID: <5e40f6a8-1bfc-40f4-bef1-53cb5e5432f4@googlegroups.com> Hi guys, this is Jatin. I was using scikit-image module and was going through examples, after some time I realised that in all examples images are being opened as numpy.ndarray but nowhere these images were saved as .jpg or .png(or any other format). Can you tell me how to save these images which I modified? -------------- next part -------------- An HTML attachment was scrubbed... URL: From jatinkatyal96 at gmail.com Sun Mar 13 10:28:10 2016 From: jatinkatyal96 at gmail.com (Jatin Katyal) Date: Sun, 13 Mar 2016 07:28:10 -0700 (PDT) Subject: Saving an image In-Reply-To: References: <5e40f6a8-1bfc-40f4-bef1-53cb5e5432f4@googlegroups.com> Message-ID: Thank you Himanshu, I don't know why I did not see documentation. BTW, it is "imsave". On Sunday, March 13, 2016 at 7:52:03 PM UTC+5:30, Himanshu Mishra wrote: > Hi Jatin, > > Did you try the `io` module of `skimage` ? I believe we can save the > images (numpy ndarray) using `io.save()`. > > Regards, > Himanshu Mishra > > On Sun, Mar 13, 2016 at 7:47 PM, Jatin Katyal > wrote: > >> Hi guys, this is Jatin. I was using scikit-image module and was going >> through examples, after some time I realised that in all examples images >> are being opened as numpy.ndarray but nowhere these images were saved as >> .jpg or .png(or any other format). Can you tell me how to save these images >> which I modified? >> >> -- >> You received this message because you are subscribed to the Google Groups >> "scikit-image" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to scikit-image... at googlegroups.com . >> To post to this group, send email to scikit... at googlegroups.com >> . >> To view this discussion on the web, visit >> https://groups.google.com/d/msgid/scikit-image/5e40f6a8-1bfc-40f4-bef1-53cb5e5432f4%40googlegroups.com >> >> . >> For more options, visit https://groups.google.com/d/optout. >> > > > > -- > Himanshu Mishra > -------------- next part -------------- An HTML attachment was scrubbed... URL: From fboulogne at sciunto.org Sun Mar 13 10:51:13 2016 From: fboulogne at sciunto.org (=?UTF-8?Q?Fran=c3=a7ois_Boulogne?=) Date: Sun, 13 Mar 2016 15:51:13 +0100 Subject: Saving an image In-Reply-To: References: <5e40f6a8-1bfc-40f4-bef1-53cb5e5432f4@googlegroups.com> Message-ID: <56E57E61.5040608@sciunto.org> Le 13/03/2016 15:28, Jatin Katyal a ?crit : > > Thank you Himanshu, I don't know why I did not see documentation. > It is. Right here: http://scikit-image.org/docs/stable/user_guide.html It's probably a matter of visibility/location. Best, -- Fran?ois Boulogne. http://www.sciunto.org GPG: 32D5F22F From himanshu2014iit at gmail.com Sun Mar 13 10:21:23 2016 From: himanshu2014iit at gmail.com (Himanshu Mishra) Date: Sun, 13 Mar 2016 19:51:23 +0530 Subject: Saving an image In-Reply-To: <5e40f6a8-1bfc-40f4-bef1-53cb5e5432f4@googlegroups.com> References: <5e40f6a8-1bfc-40f4-bef1-53cb5e5432f4@googlegroups.com> Message-ID: Hi Jatin, Did you try the `io` module of `skimage` ? I believe we can save the images (numpy ndarray) using `io.save()`. Regards, Himanshu Mishra On Sun, Mar 13, 2016 at 7:47 PM, Jatin Katyal wrote: > Hi guys, this is Jatin. I was using scikit-image module and was going > through examples, after some time I realised that in all examples images > are being opened as numpy.ndarray but nowhere these images were saved as > .jpg or .png(or any other format). Can you tell me how to save these images > which I modified? > > -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image+unsubscribe at googlegroups.com. > To post to this group, send email to scikit-image at googlegroups.com. > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/5e40f6a8-1bfc-40f4-bef1-53cb5e5432f4%40googlegroups.com > > . > For more options, visit https://groups.google.com/d/optout. > -- Himanshu Mishra -------------- next part -------------- An HTML attachment was scrubbed... URL: From fboulogne at sciunto.org Mon Mar 14 08:05:49 2016 From: fboulogne at sciunto.org (=?UTF-8?Q?Fran=c3=a7ois_Boulogne?=) Date: Mon, 14 Mar 2016 13:05:49 +0100 Subject: Saving an image In-Reply-To: <56E57E61.5040608@sciunto.org> References: <5e40f6a8-1bfc-40f4-bef1-53cb5e5432f4@googlegroups.com> <56E57E61.5040608@sciunto.org> Message-ID: <56E6A91D.3010305@sciunto.org> Le 13/03/2016 15:51, Fran?ois Boulogne a ?crit : > Le 13/03/2016 15:28, Jatin Katyal a ?crit : >> Thank you Himanshu, I don't know why I did not see documentation. >> > > It is. Right here: http://scikit-image.org/docs/stable/user_guide.html > > It's probably a matter of visibility/location. > FYI, an additional link has been added at the top of the gallery: https://github.com/scikit-image/scikit-image/pull/2001 I hope it will gain visibility. Best, -- Fran?ois Boulogne. http://www.sciunto.org GPG: 32D5F22F From stefanv at berkeley.edu Fri Mar 18 01:05:39 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Thu, 17 Mar 2016 22:05:39 -0700 Subject: Cython + numpy 1.11 -- can you make it work? Message-ID: Hi all, I'm trying to make skimage work with the latest numpy pre-release, but to no avail. I see failures in the test suite when running this branch: stefanv/int_fixes_np1.11 If you can crack this one, I would be much obliged! Best regards St?fan From pauloj.raposo at gmail.com Fri Mar 18 01:32:25 2016 From: pauloj.raposo at gmail.com (Paulo Raposo) Date: Thu, 17 Mar 2016 22:32:25 -0700 (PDT) Subject: filters.entropy Message-ID: Hi All, I'm using scikit to run entropy filters on spatial images. I get a message pretty frequently: Bitdepth of 15 may result in bad rank filter performance due to large number of bins. Does this just mean it's slow? Or that there could be errors in the output? Thanks!! Paulo -------------- next part -------------- An HTML attachment was scrubbed... URL: From pauloj.raposo at gmail.com Fri Mar 18 06:03:57 2016 From: pauloj.raposo at gmail.com (Paulo Raposo) Date: Fri, 18 Mar 2016 03:03:57 -0700 (PDT) Subject: filters.entropy In-Reply-To: <-3012192180848849656@unknownmsgid> References: <-3012192180848849656@unknownmsgid> Message-ID: <62ffbc1b-8d01-4b12-97ff-df49067f5a2d@googlegroups.com> Many thanks! P On Friday, March 18, 2016 at 4:29:56 AM UTC-4, Johannes Sch?nberger wrote: > > Just means that it will be slow. We should probably reformulate. > > Cheers, Johannes > > On Mar 18, 2016, at 06:32, Paulo Raposo > > wrote: > > Hi All, > > I'm using scikit to run entropy filters on spatial images. I get a message > pretty frequently: > > Bitdepth of 15 may result in bad rank filter performance due to large > number of bins. > > Does this just mean it's slow? Or that there could be errors in the output? > > Thanks!! > Paulo > > -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image... at googlegroups.com . > To post to this group, send email to scikit... at googlegroups.com > . > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/b6d891d1-eed3-4909-adf6-9f5f0a01f4f6%40googlegroups.com > > . > For more options, visit https://groups.google.com/d/optout. > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jsch at demuc.de Fri Mar 18 04:29:54 2016 From: jsch at demuc.de (=?UTF-8?Q?Johannes_Sch=C3=B6nberger?=) Date: Fri, 18 Mar 2016 09:29:54 +0100 Subject: filters.entropy In-Reply-To: References: Message-ID: <-3012192180848849656@unknownmsgid> Just means that it will be slow. We should probably reformulate. Cheers, Johannes On Mar 18, 2016, at 06:32, Paulo Raposo wrote: Hi All, I'm using scikit to run entropy filters on spatial images. I get a message pretty frequently: Bitdepth of 15 may result in bad rank filter performance due to large number of bins. Does this just mean it's slow? Or that there could be errors in the output? Thanks!! Paulo -- You received this message because you are subscribed to the Google Groups "scikit-image" group. To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com. To post to this group, send email to scikit-image at googlegroups.com. To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/b6d891d1-eed3-4909-adf6-9f5f0a01f4f6%40googlegroups.com . For more options, visit https://groups.google.com/d/optout. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jalopcar at gmail.com Mon Mar 21 16:44:37 2016 From: jalopcar at gmail.com (Jaime Lopez Carvajal) Date: Mon, 21 Mar 2016 13:44:37 -0700 (PDT) Subject: RGB and CIR visualization Message-ID: <1129f1f2-b6a9-450c-9b30-61dc14957154@googlegroups.com> Hi, I am loading a 4-band image using* io.imread*, but I am having problems to visualize the true color *(R,G,B)* and Composite Infrared *(IR,R,G)* images. I have try different band combinations, but I couldnt view the right visualization (see attached image) Any suggestion? Thanks in advance, Jaime -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: RGB & CIR.png Type: image/png Size: 612365 bytes Desc: not available URL: From stefanv at berkeley.edu Mon Mar 21 18:22:58 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Mon, 21 Mar 2016 15:22:58 -0700 Subject: RGB and CIR visualization In-Reply-To: <1129f1f2-b6a9-450c-9b30-61dc14957154@googlegroups.com> References: <1129f1f2-b6a9-450c-9b30-61dc14957154@googlegroups.com> Message-ID: Hi Jaime On 21 March 2016 at 13:44, Jaime Lopez Carvajal wrote: > I am loading a 4-band image using io.imread, but I am having problems to > visualize the true color (R,G,B) and Composite Infrared (IR,R,G) images. > I have try different band combinations, but I couldnt view the right > visualization (see attached image) > Any suggestion? Can you tell us what you expect to see? Can you also share an example image? Thanks St?fan From nelle.varoquaux at gmail.com Mon Mar 21 10:32:16 2016 From: nelle.varoquaux at gmail.com (Nelle Varoquaux) Date: Mon, 21 Mar 2016 15:32:16 +0100 Subject: Scipy2016: call for proposals In-Reply-To: References: Message-ID: Dear all, This is a quick reminder that the deadline for submitting talks and posters proposal is next friday. Thanks, Nelle On 22 February 2016 at 10:15, Nelle Varoquaux wrote: > > Dear all, > > SciPy 2016, the Fifteenth Annual Conference on Python in Science, takes > place in Austin, TX on July, 11th to 17th. The conference features two days > of tutorials by followed by three days of presentations, and concludes with > two days of developer sprints on projects of interest to attendees. . > > The topics presented at SciPy are very diverse, with a focus on advanced > software engineering and original uses of Python and its scientific > libraries, either in theoretical or experimental research, from both > academia and the industry. This year we are happy to announce two > specialized tracks that run in parallel to the general conference (Data > Science , High Performance Computing) and 8 mini-symposia (Earth and Space > Science, Biology and Medicine, Engineering, Social Sciences, Special > Purpose Databases, Case Studies in Industry, Education, Reproducibility) > > Submissions for talks and posters are welcome on our website ( > http://scipy2016.scipy.org). In your abstract, please provide details on > what Python tools are being employed, and how. The talk and poster > submission deadline is March 25th, 2016, while the tutorial submission > deadline is March, 21st, 2016. > > > Important dates: > > Mar 21: Tutorial Proposals Due > Mar 25: Talk and Poster Proposals Due > May 11: Plotting Contest Submissions Due > Apr 22: Tutorials Announced > Apr 22: Financial Aid Submissions Due > May 4: Talk and Posters Announced > May 11: Financial Aid Recipients Notified > May 22: Early Bird Registration Deadline > Jul 11-12: SciPy 2016 Tutorials > Jul 13-15: SciPy 2016 General Conference > Jul 16-17: SciPy 2016 Sprints > > We look forward to an exciting conference and hope to see you in Austin in > July! > > > The Scipy 2016 > http://scipy2016.scipy.org/ > > Conference Chairs: Aric Hagberg, Prabhu Ramachandran > Tutorial Chairs: Justin Vincent, Ben Root > Program Chair: Serge Rey, Nelle Varoquaux > Proceeding Chairs: Sebastian Benthall > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jalopcar at gmail.com Mon Mar 21 19:02:38 2016 From: jalopcar at gmail.com (Jaime Lopez Carvajal) Date: Mon, 21 Mar 2016 16:02:38 -0700 (PDT) Subject: RGB and CIR visualization In-Reply-To: References: <1129f1f2-b6a9-450c-9b30-61dc14957154@googlegroups.com> Message-ID: <1aea0d79-d55c-474a-a526-e3009d6aad17@googlegroups.com> Hi Stefan, Of course, I would like to visualize the image like this (attached image), that was obtained using ArcMap software, with the usual band order for True Color (RGB) and Composite Infrared (CIR) in remote sensing applications. The tiff image that I loaded has 4 bands, so I would think that the order would be: band0(Red), band1(Green), band2(Blue), band3(Infrarred), so if I want to visualize the true color image, I would need to use this instruction: TrueColor_img = img11[:,:,(0,1,2)] but as you can see, the obtained visualization is very different from natural color. I hope this helps, Jaime On Monday, March 21, 2016 at 6:23:20 PM UTC-4, stefanv wrote: > > Hi Jaime > > On 21 March 2016 at 13:44, Jaime Lopez Carvajal > wrote: > > I am loading a 4-band image using io.imread, but I am having problems to > > visualize the true color (R,G,B) and Composite Infrared (IR,R,G) images. > > I have try different band combinations, but I couldnt view the right > > visualization (see attached image) > > Any suggestion? > > Can you tell us what you expect to see? Can you also share an example > image? > > Thanks > St?fan > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: RGB & CIR b.png Type: image/png Size: 1241084 bytes Desc: not available URL: From stefanv at berkeley.edu Mon Mar 21 19:23:30 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Mon, 21 Mar 2016 16:23:30 -0700 Subject: RGB and CIR visualization In-Reply-To: <1aea0d79-d55c-474a-a526-e3009d6aad17@googlegroups.com> References: <1129f1f2-b6a9-450c-9b30-61dc14957154@googlegroups.com> <1aea0d79-d55c-474a-a526-e3009d6aad17@googlegroups.com> Message-ID: Hi Jaime On 21 March 2016 at 16:02, Jaime Lopez Carvajal wrote: > Of course, I would like to visualize the image like this (attached image), > that was obtained using ArcMap software, with the usual band order for True > Color (RGB) and Composite Infrared (CIR) in remote sensing applications. > The tiff image that I loaded has 4 bands, so I would think that the order > would be: band0(Red), band1(Green), band2(Blue), band3(Infrarred), > so if I want to visualize the true color image, I would need to use this > instruction: > TrueColor_img = img11[:,:,(0,1,2)] I'll take a look. Can you please upload an example tiff? Thanks St?fan From jalopcar at gmail.com Mon Mar 21 19:36:06 2016 From: jalopcar at gmail.com (Jaime Lopez Carvajal) Date: Mon, 21 Mar 2016 16:36:06 -0700 (PDT) Subject: RGB and CIR visualization In-Reply-To: References: <1129f1f2-b6a9-450c-9b30-61dc14957154@googlegroups.com> <1aea0d79-d55c-474a-a526-e3009d6aad17@googlegroups.com> Message-ID: Hi Stefan, Sure, I attached a small fraction of original image, because Remote Sensing images are very big. The TIFF image has 4 bands. Hope this helps, Jaime On Monday, March 21, 2016 at 7:23:53 PM UTC-4, stefanv wrote: > > Hi Jaime > > On 21 March 2016 at 16:02, Jaime Lopez Carvajal > wrote: > > Of course, I would like to visualize the image like this (attached > image), > > that was obtained using ArcMap software, with the usual band order for > True > > Color (RGB) and Composite Infrared (CIR) in remote sensing applications. > > The tiff image that I loaded has 4 bands, so I would think that the > order > > would be: band0(Red), band1(Green), band2(Blue), band3(Infrarred), > > so if I want to visualize the true color image, I would need to use this > > instruction: > > TrueColor_img = img11[:,:,(0,1,2)] > > I'll take a look. Can you please upload an example tiff? > > Thanks > St?fan > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: stadium.tif Type: image/tiff Size: 94289 bytes Desc: not available URL: From stefanv at berkeley.edu Mon Mar 21 20:17:44 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Mon, 21 Mar 2016 17:17:44 -0700 Subject: RGB and CIR visualization In-Reply-To: References: <1129f1f2-b6a9-450c-9b30-61dc14957154@googlegroups.com> <1aea0d79-d55c-474a-a526-e3009d6aad17@googlegroups.com> Message-ID: Hi Jaime These are the layers coming out of the TIFF reader: https://gist.github.com/6881c3527b3099c49891 Can you recognize which ones are which? Do they look correct? Maybe you can compare them against the ones you see in ArcMap. Thanks! St?fan On 21 March 2016 at 16:36, Jaime Lopez Carvajal wrote: > Hi Stefan, > > Sure, I attached a small fraction of original image, because Remote Sensing > images are very big. > The TIFF image has 4 bands. > > Hope this helps, Jaime > > On Monday, March 21, 2016 at 7:23:53 PM UTC-4, stefanv wrote: >> >> Hi Jaime >> >> On 21 March 2016 at 16:02, Jaime Lopez Carvajal wrote: >> > Of course, I would like to visualize the image like this (attached >> > image), >> > that was obtained using ArcMap software, with the usual band order for >> > True >> > Color (RGB) and Composite Infrared (CIR) in remote sensing applications. >> > The tiff image that I loaded has 4 bands, so I would think that the >> > order >> > would be: band0(Red), band1(Green), band2(Blue), band3(Infrarred), >> > so if I want to visualize the true color image, I would need to use this >> > instruction: >> > TrueColor_img = img11[:,:,(0,1,2)] >> >> I'll take a look. Can you please upload an example tiff? >> >> Thanks >> St?fan > > -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image+unsubscribe at googlegroups.com. > To post to this group, send email to scikit-image at googlegroups.com. > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/eb050d76-64f7-4f24-a67f-aa2a4795d1c5%40googlegroups.com. > > For more options, visit https://groups.google.com/d/optout. From nelle.varoquaux at gmail.com Mon Mar 21 13:32:29 2016 From: nelle.varoquaux at gmail.com (Nelle Varoquaux) Date: Mon, 21 Mar 2016 18:32:29 +0100 Subject: Scipy2016: call for proposals In-Reply-To: References: Message-ID: I'm terribly sorry about this second email. The deadline for submitting talks and posters for scipy 2016 is this friday (friday 25th), and not next friday (april fools day). Thanks, Nelle On 21 March 2016 at 15:32, Nelle Varoquaux wrote: > Dear all, > > This is a quick reminder that the deadline for submitting talks and > posters proposal is next friday. > > Thanks, > Nelle > > On 22 February 2016 at 10:15, Nelle Varoquaux > wrote: > >> >> Dear all, >> >> SciPy 2016, the Fifteenth Annual Conference on Python in Science, takes >> place in Austin, TX on July, 11th to 17th. The conference features two days >> of tutorials by followed by three days of presentations, and concludes with >> two days of developer sprints on projects of interest to attendees. . >> >> The topics presented at SciPy are very diverse, with a focus on advanced >> software engineering and original uses of Python and its scientific >> libraries, either in theoretical or experimental research, from both >> academia and the industry. This year we are happy to announce two >> specialized tracks that run in parallel to the general conference (Data >> Science , High Performance Computing) and 8 mini-symposia (Earth and Space >> Science, Biology and Medicine, Engineering, Social Sciences, Special >> Purpose Databases, Case Studies in Industry, Education, Reproducibility) >> >> Submissions for talks and posters are welcome on our website ( >> http://scipy2016.scipy.org). In your abstract, please provide details on >> what Python tools are being employed, and how. The talk and poster >> submission deadline is March 25th, 2016, while the tutorial submission >> deadline is March, 21st, 2016. >> >> >> Important dates: >> >> Mar 21: Tutorial Proposals Due >> Mar 25: Talk and Poster Proposals Due >> May 11: Plotting Contest Submissions Due >> Apr 22: Tutorials Announced >> Apr 22: Financial Aid Submissions Due >> May 4: Talk and Posters Announced >> May 11: Financial Aid Recipients Notified >> May 22: Early Bird Registration Deadline >> Jul 11-12: SciPy 2016 Tutorials >> Jul 13-15: SciPy 2016 General Conference >> Jul 16-17: SciPy 2016 Sprints >> >> We look forward to an exciting conference and hope to see you in Austin >> in July! >> >> >> The Scipy 2016 >> http://scipy2016.scipy.org/ >> >> Conference Chairs: Aric Hagberg, Prabhu Ramachandran >> Tutorial Chairs: Justin Vincent, Ben Root >> Program Chair: Serge Rey, Nelle Varoquaux >> Proceeding Chairs: Sebastian Benthall >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjgohlke at gmail.com Mon Mar 21 22:35:23 2016 From: cjgohlke at gmail.com (Christoph Gohlke) Date: Mon, 21 Mar 2016 19:35:23 -0700 Subject: RGB and CIR visualization In-Reply-To: References: <1129f1f2-b6a9-450c-9b30-61dc14957154@googlegroups.com> <1aea0d79-d55c-474a-a526-e3009d6aad17@googlegroups.com> Message-ID: <56F0AF6B.8010505@gmail.com> I think the issue might be that the bands contain uint8 data stored as uint16 (one extra bit seems used for GDAL's nodata) and the display function `show_img` does not handle this. In this case casting the RGB array to uint8 before display might work: show_img(img11a.astype('uint8')) Christoph On 3/21/2016 5:17 PM, St?fan van der Walt wrote: > Hi Jaime > > These are the layers coming out of the TIFF reader: > > https://gist.github.com/6881c3527b3099c49891 > > Can you recognize which ones are which? Do they look correct? Maybe > you can compare them against the ones you see in ArcMap. > > Thanks! > St?fan > > On 21 March 2016 at 16:36, Jaime Lopez Carvajal wrote: >> Hi Stefan, >> >> Sure, I attached a small fraction of original image, because Remote Sensing >> images are very big. >> The TIFF image has 4 bands. >> >> Hope this helps, Jaime >> >> On Monday, March 21, 2016 at 7:23:53 PM UTC-4, stefanv wrote: >>> >>> Hi Jaime >>> >>> On 21 March 2016 at 16:02, Jaime Lopez Carvajal wrote: >>>> Of course, I would like to visualize the image like this (attached >>>> image), >>>> that was obtained using ArcMap software, with the usual band order for >>>> True >>>> Color (RGB) and Composite Infrared (CIR) in remote sensing applications. >>>> The tiff image that I loaded has 4 bands, so I would think that the >>>> order >>>> would be: band0(Red), band1(Green), band2(Blue), band3(Infrarred), >>>> so if I want to visualize the true color image, I would need to use this >>>> instruction: >>>> TrueColor_img = img11[:,:,(0,1,2)] >>> >>> I'll take a look. Can you please upload an example tiff? >>> >>> Thanks >>> St?fan >> >> -- >> You received this message because you are subscribed to the Google Groups >> "scikit-image" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to scikit-image+unsubscribe at googlegroups.com. >> To post to this group, send email to scikit-image at googlegroups.com. >> To view this discussion on the web, visit >> https://groups.google.com/d/msgid/scikit-image/eb050d76-64f7-4f24-a67f-aa2a4795d1c5%40googlegroups.com. >> >> For more options, visit https://groups.google.com/d/optout. > From jalopcar at gmail.com Tue Mar 22 09:16:21 2016 From: jalopcar at gmail.com (Jaime Lopez Carvajal) Date: Tue, 22 Mar 2016 06:16:21 -0700 (PDT) Subject: RGB and CIR visualization In-Reply-To: References: <1129f1f2-b6a9-450c-9b30-61dc14957154@googlegroups.com> <1aea0d79-d55c-474a-a526-e3009d6aad17@googlegroups.com> Message-ID: <9ab16b08-40b5-4107-be47-5b685da89f3c@googlegroups.com> Hi Stefan, Accord to ArcMAp, the order of layers is 0,1,2,3 correspond to Red, Green, Blue, Infrared. This way, if I want to visualize a true color image, I just use layers [0,1,2], in that order, and for CIR image the order would be [4,1,2]. So the order you ask me is: layers [0,1,2,3] = layers [Red, Green, Blue, Infrared] Thanks, Jaime On Monday, March 21, 2016 at 8:23:53 PM UTC-4, stefanv wrote: > > Hi Jaime > > These are the layers coming out of the TIFF reader: > > https://gist.github.com/6881c3527b3099c49891 > > Can you recognize which ones are which? Do they look correct? Maybe > you can compare them against the ones you see in ArcMap. > > Thanks! > St?fan > > On 21 March 2016 at 16:36, Jaime Lopez Carvajal > wrote: > > Hi Stefan, > > > > Sure, I attached a small fraction of original image, because Remote > Sensing > > images are very big. > > The TIFF image has 4 bands. > > > > Hope this helps, Jaime > > > > On Monday, March 21, 2016 at 7:23:53 PM UTC-4, stefanv wrote: > >> > >> Hi Jaime > >> > >> On 21 March 2016 at 16:02, Jaime Lopez Carvajal > wrote: > >> > Of course, I would like to visualize the image like this (attached > >> > image), > >> > that was obtained using ArcMap software, with the usual band order > for > >> > True > >> > Color (RGB) and Composite Infrared (CIR) in remote sensing > applications. > >> > The tiff image that I loaded has 4 bands, so I would think that the > >> > order > >> > would be: band0(Red), band1(Green), band2(Blue), band3(Infrarred), > >> > so if I want to visualize the true color image, I would need to use > this > >> > instruction: > >> > TrueColor_img = img11[:,:,(0,1,2)] > >> > >> I'll take a look. Can you please upload an example tiff? > >> > >> Thanks > >> 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... at googlegroups.com . > > To post to this group, send email to scikit... at googlegroups.com > . > > To view this discussion on the web, visit > > > https://groups.google.com/d/msgid/scikit-image/eb050d76-64f7-4f24-a67f-aa2a4795d1c5%40googlegroups.com. > > > > > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jalopcar at gmail.com Tue Mar 22 09:19:17 2016 From: jalopcar at gmail.com (Jaime Lopez Carvajal) Date: Tue, 22 Mar 2016 06:19:17 -0700 (PDT) Subject: RGB and CIR visualization In-Reply-To: <56F0AF6B.8010505@gmail.com> References: <1129f1f2-b6a9-450c-9b30-61dc14957154@googlegroups.com> <1aea0d79-d55c-474a-a526-e3009d6aad17@googlegroups.com> <56F0AF6B.8010505@gmail.com> Message-ID: <8ba59034-3246-48e5-9b32-019c8140145e@googlegroups.com> Hi Christoph, Thanks for your suggestion, I will try that, and will tell you if it works. Jaime On Monday, March 21, 2016 at 10:35:21 PM UTC-4, Christoph Gohlke wrote: > > I think the issue might be that the bands contain uint8 data stored as > uint16 (one extra bit seems used for GDAL's nodata) and the display > function `show_img` does not handle this. In this case casting the RGB > array to uint8 before display might work: show_img(img11a.astype('uint8')) > > Christoph > > > On 3/21/2016 5:17 PM, St?fan van der Walt wrote: > > Hi Jaime > > > > These are the layers coming out of the TIFF reader: > > > > https://gist.github.com/6881c3527b3099c49891 > > > > Can you recognize which ones are which? Do they look correct? Maybe > > you can compare them against the ones you see in ArcMap. > > > > Thanks! > > St?fan > > > > On 21 March 2016 at 16:36, Jaime Lopez Carvajal > wrote: > >> Hi Stefan, > >> > >> Sure, I attached a small fraction of original image, because Remote > Sensing > >> images are very big. > >> The TIFF image has 4 bands. > >> > >> Hope this helps, Jaime > >> > >> On Monday, March 21, 2016 at 7:23:53 PM UTC-4, stefanv wrote: > >>> > >>> Hi Jaime > >>> > >>> On 21 March 2016 at 16:02, Jaime Lopez Carvajal > wrote: > >>>> Of course, I would like to visualize the image like this (attached > >>>> image), > >>>> that was obtained using ArcMap software, with the usual band order > for > >>>> True > >>>> Color (RGB) and Composite Infrared (CIR) in remote sensing > applications. > >>>> The tiff image that I loaded has 4 bands, so I would think that the > >>>> order > >>>> would be: band0(Red), band1(Green), band2(Blue), band3(Infrarred), > >>>> so if I want to visualize the true color image, I would need to use > this > >>>> instruction: > >>>> TrueColor_img = img11[:,:,(0,1,2)] > >>> > >>> I'll take a look. Can you please upload an example tiff? > >>> > >>> Thanks > >>> 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... at googlegroups.com . > >> To post to this group, send email to scikit... at googlegroups.com > . > >> To view this discussion on the web, visit > >> > https://groups.google.com/d/msgid/scikit-image/eb050d76-64f7-4f24-a67f-aa2a4795d1c5%40googlegroups.com. > > >> > >> For more options, visit https://groups.google.com/d/optout. > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jalopcar at gmail.com Tue Mar 22 09:42:02 2016 From: jalopcar at gmail.com (Jaime Lopez Carvajal) Date: Tue, 22 Mar 2016 06:42:02 -0700 (PDT) Subject: RGB and CIR visualization In-Reply-To: <8ba59034-3246-48e5-9b32-019c8140145e@googlegroups.com> References: <1129f1f2-b6a9-450c-9b30-61dc14957154@googlegroups.com> <1aea0d79-d55c-474a-a526-e3009d6aad17@googlegroups.com> <56F0AF6B.8010505@gmail.com> <8ba59034-3246-48e5-9b32-019c8140145e@googlegroups.com> Message-ID: <1aac1e9f-d2db-4ae1-b3e5-14ea05075ab8@googlegroups.com> Hi Christoph, You was right, that was the problem, and I can see the visualizations that I want. See the attached image with results. Thanks, Jaime On Tuesday, March 22, 2016 at 9:19:17 AM UTC-4, Jaime Lopez Carvajal wrote: > > Hi Christoph, > > Thanks for your suggestion, I will try that, and will tell you if it works. > > Jaime > > On Monday, March 21, 2016 at 10:35:21 PM UTC-4, Christoph Gohlke wrote: >> >> I think the issue might be that the bands contain uint8 data stored as >> uint16 (one extra bit seems used for GDAL's nodata) and the display >> function `show_img` does not handle this. In this case casting the RGB >> array to uint8 before display might work: >> show_img(img11a.astype('uint8')) >> >> Christoph >> >> >> On 3/21/2016 5:17 PM, St?fan van der Walt wrote: >> > Hi Jaime >> > >> > These are the layers coming out of the TIFF reader: >> > >> > https://gist.github.com/6881c3527b3099c49891 >> > >> > Can you recognize which ones are which? Do they look correct? Maybe >> > you can compare them against the ones you see in ArcMap. >> > >> > Thanks! >> > St?fan >> > >> > On 21 March 2016 at 16:36, Jaime Lopez Carvajal >> wrote: >> >> Hi Stefan, >> >> >> >> Sure, I attached a small fraction of original image, because Remote >> Sensing >> >> images are very big. >> >> The TIFF image has 4 bands. >> >> >> >> Hope this helps, Jaime >> >> >> >> On Monday, March 21, 2016 at 7:23:53 PM UTC-4, stefanv wrote: >> >>> >> >>> Hi Jaime >> >>> >> >>> On 21 March 2016 at 16:02, Jaime Lopez Carvajal >> wrote: >> >>>> Of course, I would like to visualize the image like this (attached >> >>>> image), >> >>>> that was obtained using ArcMap software, with the usual band order >> for >> >>>> True >> >>>> Color (RGB) and Composite Infrared (CIR) in remote sensing >> applications. >> >>>> The tiff image that I loaded has 4 bands, so I would think that the >> >>>> order >> >>>> would be: band0(Red), band1(Green), band2(Blue), band3(Infrarred), >> >>>> so if I want to visualize the true color image, I would need to use >> this >> >>>> instruction: >> >>>> TrueColor_img = img11[:,:,(0,1,2)] >> >>> >> >>> I'll take a look. Can you please upload an example tiff? >> >>> >> >>> Thanks >> >>> 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... at googlegroups.com. >> >> To post to this group, send email to scikit... at googlegroups.com. >> >> To view this discussion on the web, visit >> >> >> https://groups.google.com/d/msgid/scikit-image/eb050d76-64f7-4f24-a67f-aa2a4795d1c5%40googlegroups.com. >> >> >> >> >> For more options, visit https://groups.google.com/d/optout. >> > >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: RGB & CIR c.png Type: image/png Size: 224994 bytes Desc: not available URL: From jalopcar at gmail.com Tue Mar 22 10:02:43 2016 From: jalopcar at gmail.com (Jaime Lopez Carvajal) Date: Tue, 22 Mar 2016 07:02:43 -0700 (PDT) Subject: RGB and CIR visualization In-Reply-To: <9ab16b08-40b5-4107-be47-5b685da89f3c@googlegroups.com> References: <1129f1f2-b6a9-450c-9b30-61dc14957154@googlegroups.com> <1aea0d79-d55c-474a-a526-e3009d6aad17@googlegroups.com> <9ab16b08-40b5-4107-be47-5b685da89f3c@googlegroups.com> Message-ID: Hi Stefan, The problem was about radiometric resolution, because the original image is 16-bit, so I have to convert to 8-bit to visualize correctly. Keep doing skimage great, I am using it on my research project about object based image classification. Thanks for your time, Jaime On Tuesday, March 22, 2016 at 9:16:21 AM UTC-4, Jaime Lopez Carvajal wrote: > > Hi Stefan, > > Accord to ArcMAp, the order of layers is 0,1,2,3 correspond to Red, Green, > Blue, Infrared. > This way, if I want to visualize a true color image, I just use layers > [0,1,2], in that order, and for CIR image the order would be [4,1,2]. > So the order you ask me is: layers [0,1,2,3] = layers [Red, Green, Blue, > Infrared] > > Thanks, Jaime > > On Monday, March 21, 2016 at 8:23:53 PM UTC-4, stefanv wrote: >> >> Hi Jaime >> >> These are the layers coming out of the TIFF reader: >> >> https://gist.github.com/6881c3527b3099c49891 >> >> Can you recognize which ones are which? Do they look correct? Maybe >> you can compare them against the ones you see in ArcMap. >> >> Thanks! >> St?fan >> >> On 21 March 2016 at 16:36, Jaime Lopez Carvajal >> wrote: >> > Hi Stefan, >> > >> > Sure, I attached a small fraction of original image, because Remote >> Sensing >> > images are very big. >> > The TIFF image has 4 bands. >> > >> > Hope this helps, Jaime >> > >> > On Monday, March 21, 2016 at 7:23:53 PM UTC-4, stefanv wrote: >> >> >> >> Hi Jaime >> >> >> >> On 21 March 2016 at 16:02, Jaime Lopez Carvajal >> wrote: >> >> > Of course, I would like to visualize the image like this (attached >> >> > image), >> >> > that was obtained using ArcMap software, with the usual band order >> for >> >> > True >> >> > Color (RGB) and Composite Infrared (CIR) in remote sensing >> applications. >> >> > The tiff image that I loaded has 4 bands, so I would think that the >> >> > order >> >> > would be: band0(Red), band1(Green), band2(Blue), band3(Infrarred), >> >> > so if I want to visualize the true color image, I would need to use >> this >> >> > instruction: >> >> > TrueColor_img = img11[:,:,(0,1,2)] >> >> >> >> I'll take a look. Can you please upload an example tiff? >> >> >> >> Thanks >> >> 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... at googlegroups.com. >> > To post to this group, send email to scikit... at googlegroups.com. >> > To view this discussion on the web, visit >> > >> https://groups.google.com/d/msgid/scikit-image/eb050d76-64f7-4f24-a67f-aa2a4795d1c5%40googlegroups.com. >> >> > >> > For more options, visit https://groups.google.com/d/optout. >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: