From malonge11 at gmail.com Tue Aug 2 12:50:28 2016 From: malonge11 at gmail.com (Michael Alonge) Date: Tue, 2 Aug 2016 09:50:28 -0700 (PDT) Subject: Cropping Image With Edge Detection Results Message-ID: Hello, I have produced a 2D binary edge map from the canny edge detection tool that identifies circle-like edges in my photo. My question is if my binary edge map has many edges that enclose a space, how can I use this map to crop the original photo to make many smaller photos of those enclosed spaces. In the image above, one can see 6 circle-like objects whose perimeter has been detected. From this, I would like to create 6 arrays that represent the portions of the original image enclosed by these edges. What tools might I use to achieve this? Thank you -------------- next part -------------- An HTML attachment was scrubbed... URL: From malonge11 at gmail.com Tue Aug 2 14:18:21 2016 From: malonge11 at gmail.com (Michael Alonge) Date: Tue, 2 Aug 2016 11:18:21 -0700 (PDT) Subject: Cropping Image With Edge Detection Results In-Reply-To: References: Message-ID: <9c9ded71-52b3-4a03-ba27-b930bd471f92@googlegroups.com> Thank you, this looks like it's going to work great! On Tuesday, August 2, 2016 at 10:10:57 AM UTC-7, Fran?ois Boulogne wrote: > > Hi Michael, > > I think you want to label your features > ( > http://scikit-image.org/docs/dev/auto_examples/segmentation/plot_label.html#sphx-glr-auto-examples-segmentation-plot-label-py) > > and then use their properties > ( > http://scikit-image.org/docs/dev/auto_examples/segmentation/plot_regionprops.html#sphx-glr-auto-examples-segmentation-plot-regionprops-py). > > > With that, you can crop the way you want. You can have a look to this > example: > > https://github.com/scikit-image/skimage-demos/tree/master/digits_recognition > where I separated digits on images like this one: > > https://github.com/scikit-image/skimage-demos/blob/master/digits_recognition/modern_digits_to_detect/small00000000.png > > Best, > > -- > Fran?ois Boulogne. > http://www.sciunto.org > GPG: 32D5F22F > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From fboulogne at sciunto.org Tue Aug 2 13:10:53 2016 From: fboulogne at sciunto.org (=?UTF-8?Q?Fran=c3=a7ois_Boulogne?=) Date: Tue, 2 Aug 2016 19:10:53 +0200 Subject: Cropping Image With Edge Detection Results In-Reply-To: References: Message-ID: Hi Michael, I think you want to label your features (http://scikit-image.org/docs/dev/auto_examples/segmentation/plot_label.html#sphx-glr-auto-examples-segmentation-plot-label-py) and then use their properties (http://scikit-image.org/docs/dev/auto_examples/segmentation/plot_regionprops.html#sphx-glr-auto-examples-segmentation-plot-regionprops-py). With that, you can crop the way you want. You can have a look to this example: https://github.com/scikit-image/skimage-demos/tree/master/digits_recognition where I separated digits on images like this one: https://github.com/scikit-image/skimage-demos/blob/master/digits_recognition/modern_digits_to_detect/small00000000.png Best, -- Fran?ois Boulogne. http://www.sciunto.org GPG: 32D5F22F From dipugee at gmail.com Mon Aug 8 20:09:54 2016 From: dipugee at gmail.com (Dipankar Ganguly) Date: Mon, 8 Aug 2016 17:09:54 -0700 (PDT) Subject: Image edge detection Message-ID: <476b29f9-0e89-495d-aaee-88a9dbc69460@googlegroups.com> I am trying to do an image edge detection project using Python 3.5 under Jupyter on Anaconda's Navigator on my Mac running OS 10.11.6. I have verified that the Envirnoment does have scikit-image installed I have run into this at the very outset. _________________ File "", line 1 import scikit-image as image ^SyntaxError: invalid syntax __________________ How do I solve this? Is there a more recent package I should be using? Thanks. Dipu -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Mon Aug 8 20:24:25 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Mon, 8 Aug 2016 17:24:25 -0700 Subject: Image edge detection In-Reply-To: <476b29f9-0e89-495d-aaee-88a9dbc69460@googlegroups.com> References: <476b29f9-0e89-495d-aaee-88a9dbc69460@googlegroups.com> Message-ID: Hi Dipu Please try one of the examples from the gallery: http://scikit-image.org/docs/dev/auto_examples/ St?fan On 8 August 2016 at 17:09, Dipankar Ganguly wrote: > I am trying to do an image edge detection project using Python 3.5 under Jupyter on Anaconda's Navigator on my Mac running OS 10.11.6. I have verified that the Envirnoment does have scikit-image installed I have run into this at the very outset. > > > _________________ > > File "", line 1 import scikit-image as image > ^SyntaxError: invalid syntax > > __________________ > > > How do I solve this? Is there a more recent package I should be using? > > > Thanks. > > > Dipu > > > > -- > 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/476b29f9-0e89-495d-aaee-88a9dbc69460%40googlegroups.com > > . > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dipugee at gmail.com Tue Aug 9 11:35:37 2016 From: dipugee at gmail.com (=?utf-8?Q?Dipankar_=E2=80=9CDipu=E2=80=9D_Ganguly?=) Date: Tue, 9 Aug 2016 08:35:37 -0700 Subject: Image edge detection In-Reply-To: References: <476b29f9-0e89-495d-aaee-88a9dbc69460@googlegroups.com> Message-ID: <5AB4F386-67B4-4DE3-9E2D-151F23C72F8C@gmail.com> Thank you Stefan. That was very helpful. I now need to convert ?.jpg" and DICOM images into arrays that I can operate on using numpy and other Scikit-image algorithms/tools. What tools/packages could I use for the conversions (Images ?> numpy arrays)? Best. Dipu Dipankar Ganguly Consultant: Strategy/Technology/Commercialization Bothell, WA Cell: 408-203-8814 email: dipugee at gmail.com http://www.linkedin.com/in/dipugee > On Aug 8, 2016, at 5:24 PM, St?fan van der Walt wrote: > > Hi Dipu > > Please try one of the examples from the gallery: > > http://scikit-image.org/docs/dev/auto_examples/ > > St?fan > > On 8 August 2016 at 17:09, Dipankar Ganguly > wrote: > I am trying to do an image edge detection project using Python 3.5 under Jupyter on Anaconda's Navigator on my Mac running OS 10.11.6. I have verified that the Envirnoment does have scikit-image installed I have run into this at the very outset. > > _________________ > File "", line 1 > import scikit-image as image > ^ > SyntaxError: invalid syntax > __________________ > > How do I solve this? Is there a more recent package I should be using? > > Thanks. > > Dipu > > > > -- > 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/476b29f9-0e89-495d-aaee-88a9dbc69460%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/7IskXgM-99E/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/CABDkGQ%3D-HOcA1Xoxxfp8H%2Bohd-ZvV4hK-4oa_J5zkG%3Dqyd09cg%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 Tue Aug 9 14:40:14 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Tue, 9 Aug 2016 11:40:14 -0700 Subject: Image edge detection In-Reply-To: <5AB4F386-67B4-4DE3-9E2D-151F23C72F8C@gmail.com> References: <476b29f9-0e89-495d-aaee-88a9dbc69460@googlegroups.com> <5AB4F386-67B4-4DE3-9E2D-151F23C72F8C@gmail.com> Message-ID: Hi Dipu On 9 August 2016 at 08:35, Dipankar ?Dipu? Ganguly wrote: > I now need to convert ?.jpg" and DICOM images into arrays that I can > operate on using numpy and other Scikit-image algorithms/tools. What > tools/packages could I use for the conversions (Images ?> numpy arrays)? > You can use pydicom to load the DICOM images to numpy arrays: http://pydicom.readthedocs.io/en/stable/working_with_pixel_data.html Thereafter, scikit-image can process them: http://scikit-image.org/docs/stable/user_guide/numpy_images.html If you have more advanced DICOM needs, such as working with multiple slices, or reading meta-data, you may want to look at dcmstack and nibabel as well. Best regards St?fan -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Tue Aug 9 17:23:34 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Tue, 9 Aug 2016 14:23:34 -0700 Subject: Migration to Python 3.x Message-ID: Hi everyone, The previous migration thread stalled, and I would like to revisit the issue. Here is my proposal: 1. All code written for the 0.13 release of scikit-image should still be Python 2.7 and 3.x compatible. 2. 0.13.x will be declared a "Long Term Support" release, with all point releases supporting Python 2.7 until 2020 3. Non-API-breaking features from 0.14 and later *may be backported* to 0.13.x as needed / requested. 4. Any new code written after 0.13 will be Python 3.x only (but see #3 above). My motivations are to: - Remove developer overhead associated with keeping both Python 2 and 3-isms in mind - Reduce testing and maintenance overhead associated with multiple Python versions - Utilize new language features such as the @-operator and required keyword arguments Please let me know if you have any strong feelings to the contrary. Best regards St?fan -------------- next part -------------- An HTML attachment was scrubbed... URL: From dipugee at gmail.com Tue Aug 9 17:30:09 2016 From: dipugee at gmail.com (=?utf-8?Q?Dipankar_=E2=80=9CDipu=E2=80=9D_Ganguly?=) Date: Tue, 9 Aug 2016 14:30:09 -0700 Subject: Image edge detection In-Reply-To: References: <476b29f9-0e89-495d-aaee-88a9dbc69460@googlegroups.com> <5AB4F386-67B4-4DE3-9E2D-151F23C72F8C@gmail.com> Message-ID: <8FEA9192-98EE-4B8C-BC6E-7A1B6EFBFCE9@gmail.com> Thanks again Stefa. Very helpful. I will try using these. I am assuming, I will also find tools to read .jpg images as numpy arrays, my immediate need. Dipu Dipankar ?Dipu? Ganguly dipugee at gmail.com Cell: 408-203-8814 > On Aug 9, 2016, at 11:40 AM, St?fan van der Walt wrote: > > Hi Dipu > > On 9 August 2016 at 08:35, Dipankar ?Dipu? Ganguly > wrote: > I now need to convert ?.jpg" and DICOM images into arrays that I can operate on using numpy and other Scikit-image algorithms/tools. What tools/packages could I use for the conversions (Images ?> numpy arrays)? > > You can use pydicom to load the DICOM images to numpy arrays: > > http://pydicom.readthedocs.io/en/stable/working_with_pixel_data.html > > Thereafter, scikit-image can process them: > > http://scikit-image.org/docs/stable/user_guide/numpy_images.html > > If you have more advanced DICOM needs, such as working with multiple slices, or reading meta-data, you may want to look at dcmstack and nibabel as well. > > Best regards > St?fan > > > -- > You received this message because you are subscribed to a topic in the Google Groups "scikit-image" group. > To unsubscribe from this topic, visit https://groups.google.com/d/topic/scikit-image/7IskXgM-99E/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/CABDkGQm16z6YUJO77MXPeDTsQMR6%3DjktVdikMxCtm4YB7r2fmQ%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 Tue Aug 9 17:34:22 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Tue, 9 Aug 2016 14:34:22 -0700 Subject: Image edge detection In-Reply-To: <8FEA9192-98EE-4B8C-BC6E-7A1B6EFBFCE9@gmail.com> References: <476b29f9-0e89-495d-aaee-88a9dbc69460@googlegroups.com> <5AB4F386-67B4-4DE3-9E2D-151F23C72F8C@gmail.com> <8FEA9192-98EE-4B8C-BC6E-7A1B6EFBFCE9@gmail.com> Message-ID: Hi Dipu On 9 August 2016 at 14:30, Dipankar ?Dipu? Ganguly wrote: > Thanks again Stefa. Very helpful. I will try using these. I am assuming, I > will also find tools to read .jpg images as numpy arrays, my immediate need. > You assume correctly :) If you take a look at the user guide I mentioned earlier, you will find examples of how to do that. from skimage import io image = io.imread('my_image.jpg') Best regards St?fan -------------- next part -------------- An HTML attachment was scrubbed... URL: From dipugee at gmail.com Tue Aug 9 17:40:52 2016 From: dipugee at gmail.com (=?utf-8?Q?Dipankar_=E2=80=9CDipu=E2=80=9D_Ganguly?=) Date: Tue, 9 Aug 2016 14:40:52 -0700 Subject: Image edge detection In-Reply-To: References: <476b29f9-0e89-495d-aaee-88a9dbc69460@googlegroups.com> <5AB4F386-67B4-4DE3-9E2D-151F23C72F8C@gmail.com> <8FEA9192-98EE-4B8C-BC6E-7A1B6EFBFCE9@gmail.com> Message-ID: Hi Stefan: Sorry to bother you again. I am having trouble with "from skimage import xyz? commands. I am using Python 3.5 with Jupyter from Navigator. I am wondering if I am running into version mismatches. Thanks. Dipu Dipankar ?Dipu? Ganguly dipugee at gmail.com Cell: 408-203-8814 > On Aug 9, 2016, at 2:34 PM, St?fan van der Walt wrote: > > Hi Dipu > > On 9 August 2016 at 14:30, Dipankar ?Dipu? Ganguly > wrote: > Thanks again Stefa. Very helpful. I will try using these. I am assuming, I will also find tools to read .jpg images as numpy arrays, my immediate need. > > You assume correctly :) If you take a look at the user guide I mentioned earlier, you will find examples of how to do that. > > from skimage import io > image = io.imread('my_image.jpg') > > Best regards > St?fan > > -- > You received this message because you are subscribed to a topic in the Google Groups "scikit-image" group. > To unsubscribe from this topic, visit https://groups.google.com/d/topic/scikit-image/7IskXgM-99E/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/CABDkGQnfVhr%3DB94rU8EtoMD06OJfc1FJsBFjVozaW7uscTgjvg%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 Tue Aug 9 17:42:55 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Tue, 9 Aug 2016 14:42:55 -0700 Subject: Image edge detection In-Reply-To: References: <476b29f9-0e89-495d-aaee-88a9dbc69460@googlegroups.com> <5AB4F386-67B4-4DE3-9E2D-151F23C72F8C@gmail.com> <8FEA9192-98EE-4B8C-BC6E-7A1B6EFBFCE9@gmail.com> Message-ID: Hi Dipu On 9 August 2016 at 14:40, Dipankar ?Dipu? Ganguly wrote: > Sorry to bother you again. I am having trouble with "from skimage import > xyz? commands. I am using Python 3.5 with Jupyter from Navigator. I am > wondering if I am running into version mismatches. > Yes, I am afraid we don't have an xyz submodule. Perhaps you can share some code with us, along with the error messages you are seeing? St?fan -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Tue Aug 9 17:58:59 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Tue, 9 Aug 2016 14:58:59 -0700 Subject: Migration to Python 3.x In-Reply-To: <20160809214429.GB1817277@phare.normalesup.org> References: <20160809214429.GB1817277@phare.normalesup.org> Message-ID: Hi Emmanuelle On 9 August 2016 at 14:44, Emmanuelle Gouillart < emmanuelle.gouillart at nsup.org> wrote: > about backporting, what kind of backporting mechanism do you have in > mind? Merging commits by hand, or something more elaborate? > Yes, I think backporting bug-fixes from time to time and making a point release should suffice. The ports may sometimes require some 3-to-2'ing. > It may be a silly idea, but can't we do it the other way around, that is > have an experimental branch where developers who wish to write > Python3-only code can work, and in which commits to master are merged if > they are Python 3 compatible? It could give us some time to evaluate > whether most developers want to write code that is not compatible with > Python 2. > I don't think that's a silly idea, but I also don't think that addresses two of the points I raised: - Remove developer overhead associated with keeping both Python 2 and 3-isms in mind I'd like developers to start thinking in Python 3, not the other way around. Barriers for Python 3 implementations should be removed, not raised, given that that's the direction we'll have to move eventually. - Utilize new language features such as the @-operator and required keyword arguments These are not available unless we make Python 3 the default. As for whether most developers *want* to write code that is incompatible with Python 2, my guess is that they won't pay much attention. I've moved to Python 3 more than a year ago already, and quite a few of my personal projects already do not run under Python 2---not because I actively pushed for Python 3, just because I didn't explicitly go back and fix it for the 2.7 case. I also can't think of many reasons to justify that effort. The only people who should be affected by the suggested change are those stuck on Python 2 but need the latest scikit-image features. But perhaps they can also contribute some of the (fairly lightweight) backporting efforts to help out? Best regards St?fan -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Tue Aug 9 18:14:00 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Tue, 9 Aug 2016 15:14:00 -0700 Subject: Migration to Python 3.x In-Reply-To: References: <20160809214429.GB1817277@phare.normalesup.org> Message-ID: Hi Ralf On 9 August 2016 at 15:09, Ralf Gommers wrote: > Hi Stefan, do you propose then to drop Python 3.4 at the same time (@ is > >= 3.5)? > Yes, I guess I am. But if that's too much of a stretch, I will be open to >= 3.4. St?fan -------------- next part -------------- An HTML attachment was scrubbed... URL: From nelle.varoquaux at gmail.com Tue Aug 9 21:55:07 2016 From: nelle.varoquaux at gmail.com (Nelle Varoquaux) Date: Tue, 9 Aug 2016 18:55:07 -0700 Subject: Migration to Python 3.x In-Reply-To: References: <20160809214429.GB1817277@phare.normalesup.org> Message-ID: On 9 August 2016 at 17:28, Juan Nunez-Iglesias wrote: > @Emmanuelle I'm probably among the ones pushing hardest for this, and I can > tell you, I can't wait for this change in policy, and would be sorely > disappointed by having to work in an experimental branch of scikit-image. > Both @-matmul and keyword-only arguments are, imho, compelling reasons to > switch. (Imagine the amount of fiddling with the API that we could do with > keyword-only arguments, without the annoying deprecation cycle!) > > @Ralf I would argue in favour of 3.5, for the above reasons and because > anyone who had the temerity to update to 3.4 is very likely to subsequently > move to 3.5. (Self-selected group of early adopters, plus no backwards > incompatibility issues between the two versions.) That implies that even ubuntu users will have to install python from another source than the package manager. Do you really want this? That means that only fairly advance python users will be able to use the latest scikit-image release. > > Juan. > > On Wed, Aug 10, 2016 at 8:14 AM, St?fan van der Walt > wrote: >> >> Hi Ralf >> >> On 9 August 2016 at 15:09, Ralf Gommers wrote: >>> >>> Hi Stefan, do you propose then to drop Python 3.4 at the same time (@ is >>> >= 3.5)? >> >> >> Yes, I guess I am. But if that's too much of a stretch, I will be open to >> >= 3.4. >> >> 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/CABDkGQmSC7Q7jZJDBuhutj2PXjQTDGDirxafVw-GFuqcN%3DK1_A%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%2BJHcKSM0sERcWwSMXc4dk6uhaAHbBwqtMcK70608b_D3-2H0g%40mail.gmail.com. > > For more options, visit https://groups.google.com/d/optout. From nelle.varoquaux at gmail.com Tue Aug 9 22:46:18 2016 From: nelle.varoquaux at gmail.com (Nelle Varoquaux) Date: Tue, 9 Aug 2016 19:46:18 -0700 Subject: Migration to Python 3.x In-Reply-To: References: <20160809214429.GB1817277@phare.normalesup.org> Message-ID: On 9 August 2016 at 19:17, Ralf Gommers wrote: > > > On Wed, Aug 10, 2016 at 1:55 PM, Nelle Varoquaux > wrote: >> >> On 9 August 2016 at 17:28, Juan Nunez-Iglesias wrote: >> > @Emmanuelle I'm probably among the ones pushing hardest for this, and I >> > can >> > tell you, I can't wait for this change in policy, and would be sorely >> > disappointed by having to work in an experimental branch of >> > scikit-image. >> > Both @-matmul and keyword-only arguments are, imho, compelling reasons >> > to >> > switch. (Imagine the amount of fiddling with the API that we could do >> > with >> > keyword-only arguments, without the annoying deprecation cycle!) >> > >> > @Ralf I would argue in favour of 3.5, for the above reasons and because >> > anyone who had the temerity to update to 3.4 is very likely to >> > subsequently >> > move to 3.5. (Self-selected group of early adopters, plus no backwards >> > incompatibility issues between the two versions.) > > > I agree with this argument, I was just asking to clarify. @ is at least > something interesting that's specifically added for scientific users, so > imho 3.5 is the first 3.x release where in some cases the benefits may start > to be worth the costs. > >> >> That implies that even ubuntu users will have to install python from >> another source than the package manager. Do you really want this? That >> means that only fairly advance python users will be able to use the >> latest scikit-image release. > > > In the grand scheme of things, does Ubuntu matter much for this decision? > There are way more Windows and OS X users, so if it's OK for them (which is > not a given) then it should also be OK for those fewer and on average more > computer-literate Ubuntu users. I don't have a good overview of what OS people are using, but in the different research facilities I've worked or visited, it was always linux based, and users where not really tech-savy. I checked on all of the servers (UW's genome science, the Curie institute, UC Berkeley's stats department, the Mines' machine learning computing facilities.) I have access to, none have python3.5. Some of these servers are "offline", thus conda is useless. All of these research institutes have teams that use in some way image processing. I'll just also mentionned that we had a keynote at scipy this year mentionning she was using python because she just did not have the time anymore to code in C++ and Java. These are the kind of people that may be using scikit-image, that may be interested in the latest version of the package, and yet just not have the time to compile python3.5 from scratch on an outdated server. N > > Ralf > > -- > 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/CABL7CQhEaD0uy0SyrcNO_j%2BDsE%3DX8ALKvsk4XF3v6_bzOocmEw%40mail.gmail.com. > > For more options, visit https://groups.google.com/d/optout. From nelle.varoquaux at gmail.com Tue Aug 9 23:17:00 2016 From: nelle.varoquaux at gmail.com (Nelle Varoquaux) Date: Tue, 9 Aug 2016 20:17:00 -0700 Subject: Migration to Python 3.x In-Reply-To: References: <20160809214429.GB1817277@phare.normalesup.org> Message-ID: On 9 August 2016 at 19:54, Ralf Gommers wrote: > > > On Wed, Aug 10, 2016 at 2:46 PM, Nelle Varoquaux > wrote: >> >> On 9 August 2016 at 19:17, Ralf Gommers wrote: >> > >> > >> > On Wed, Aug 10, 2016 at 1:55 PM, Nelle Varoquaux >> > >> > wrote: >> >> >> >> On 9 August 2016 at 17:28, Juan Nunez-Iglesias >> >> wrote: >> >> > @Emmanuelle I'm probably among the ones pushing hardest for this, and >> >> > I >> >> > can >> >> > tell you, I can't wait for this change in policy, and would be sorely >> >> > disappointed by having to work in an experimental branch of >> >> > scikit-image. >> >> > Both @-matmul and keyword-only arguments are, imho, compelling >> >> > reasons >> >> > to >> >> > switch. (Imagine the amount of fiddling with the API that we could do >> >> > with >> >> > keyword-only arguments, without the annoying deprecation cycle!) >> >> > >> >> > @Ralf I would argue in favour of 3.5, for the above reasons and >> >> > because >> >> > anyone who had the temerity to update to 3.4 is very likely to >> >> > subsequently >> >> > move to 3.5. (Self-selected group of early adopters, plus no >> >> > backwards >> >> > incompatibility issues between the two versions.) >> > >> > >> > I agree with this argument, I was just asking to clarify. @ is at least >> > something interesting that's specifically added for scientific users, so >> > imho 3.5 is the first 3.x release where in some cases the benefits may >> > start >> > to be worth the costs. >> > >> >> >> >> That implies that even ubuntu users will have to install python from >> >> another source than the package manager. Do you really want this? That >> >> means that only fairly advance python users will be able to use the >> >> latest scikit-image release. >> > >> > >> > In the grand scheme of things, does Ubuntu matter much for this >> > decision? >> > There are way more Windows and OS X users, so if it's OK for them (which >> > is >> > not a given) then it should also be OK for those fewer and on average >> > more >> > computer-literate Ubuntu users. >> >> I don't have a good overview of what OS people are using, but in the >> different research facilities I've worked or visited, it was always >> linux based, and users where not really tech-savy. I checked on all of >> the servers (UW's genome science, the Curie institute, UC Berkeley's >> stats department, the Mines' machine learning computing facilities.) I >> have access to, none have python3.5. Some of these servers are >> "offline", thus conda is useless. All of these research institutes >> have teams that use in some way image processing. >> >> I'll just also mentionned that we had a keynote at scipy this year >> mentionning she was using python because she just did not have the >> time anymore to code in C++ and Java. These are the kind of people >> that may be using scikit-image, that may be interested in the latest >> version of the package, and yet just not have the time to compile >> python3.5 from scratch on an outdated server. > > > Fair enough, but there are likely much more outdated servers with Python 2.7 > than with Python 3.4 on them ..... Well? I think it is better to keep python2.7 support :) All the clusters I have access to but 1 has python3. The oldest one is a red hat based cluster with python2.6 (which was python2.3 not so long ago). N > > Ralf > > -- > 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/CABL7CQjye5g5jppRk1hej2g2P3VCKa0mrcHe4Z9u37nSrqBpsg%40mail.gmail.com. > > For more options, visit https://groups.google.com/d/optout. From emmanuelle.gouillart at nsup.org Tue Aug 9 17:44:29 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Tue, 9 Aug 2016 23:44:29 +0200 Subject: Migration to Python 3.x In-Reply-To: References: Message-ID: <20160809214429.GB1817277@phare.normalesup.org> Hi St??fan, about backporting, what kind of backporting mechanism do you have in mind? Merging commits by hand, or something more elaborate? It may be a silly idea, but can't we do it the other way around, that is have an experimental branch where developers who wish to write Python3-only code can work, and in which commits to master are merged if they are Python 3 compatible? It could give us some time to evaluate whether most developers want to write code that is not compatible with Python 2. Best, Emma On Tue, Aug 09, 2016 at 02:23:34PM -0700, St??fan van der Walt wrote: > Hi everyone, > The previous migration thread stalled, and I would like to revisit the issue. > Here is my proposal: > 1. All code written for the 0.13 release of scikit-image should still be Python > 2.7 and 3.x compatible. > 2. 0.13.x will be declared a "Long Term Support" release, with all point > releases supporting Python 2.7 until 2020 > 3. Non-API-breaking features from 0.14 and later *may be backported* to 0.13.x > as needed / requested. > 4. Any new code written after 0.13 will be Python 3.x only (but see #3 above). > My motivations are to: > - Remove developer overhead associated with keeping both Python 2 and 3-isms in > mind > - Reduce testing and maintenance overhead associated with multiple Python > versions > - Utilize new language features such as the @-operator and required keyword > arguments > Please let me know if you have any strong feelings to the contrary. > Best regards > St??fan From jsch at demuc.de Wed Aug 10 00:14:45 2016 From: jsch at demuc.de (=?utf-8?Q?Johannes_Sch=C3=B6nberger?=) Date: Wed, 10 Aug 2016 06:14:45 +0200 Subject: Migration to Python 3.x In-Reply-To: References: <20160809214429.GB1817277@phare.normalesup.org> Message-ID: <3FEC278C-8155-4C85-BB44-0B0F7789D071@demuc.de> As stated earlier, a big -1 from my side on moving to all Python 3.x for 0.14 already. Not because I personally don't think it provides some benefits, but let me explain: I don't see enough of a benefit of replacing a few np.dot's with the @ syntax or pure keyword based arguments for the few functions we add/change in one version jump. It doesn't make the code faster, more correct or more feature complete. The API will look and work the same from a users perspective from 2.7-3.5. Required features (which are usually rare) from newer numpy/scipy versions can be handled easily inside the respective functions with an exception. In my experience, many of the scikit-image users I know are actually less knowledgable about how to setup a new Python environment from scratch. And it seems the latest Ubuntu is still on 3.4 and Mac also doesn't ship with 3.5 - which leaves out the @ syntax anyway. Also, many of the cluster users are still stuck on 2.x for quite a while. I think, we will lose a significant amount of users without a real benefit. I don't see a compelling reason to lock out X% of users at this point. I can only judge by the feedback in this thread, but 3 out of 5 people seem to have problems with the proposed way forward. It would be nice if there was some way of obtaining installation statistics from PyPI or Anaconda to get a better picture here. The real benefit comes with 3.5, hence I propose to follow the current model to support 2.7-3.x and reevaluate the situation for 0.15. Eventually, 3.5 will be more widespread and in the meantime we do not really sacrifice anything on our side. Doing a find/replace on np.dot/__future__ will work in a year just as fine as it does now. Best, Johannes > On 10 Aug 2016, at 05:17, Nelle Varoquaux wrote: > >> On 9 August 2016 at 19:54, Ralf Gommers wrote: >> >> >> On Wed, Aug 10, 2016 at 2:46 PM, Nelle Varoquaux >> wrote: >>> >>>> On 9 August 2016 at 19:17, Ralf Gommers wrote: >>>> >>>> >>>> On Wed, Aug 10, 2016 at 1:55 PM, Nelle Varoquaux >>>> >>>> wrote: >>>>> >>>>> On 9 August 2016 at 17:28, Juan Nunez-Iglesias >>>>> wrote: >>>>>> @Emmanuelle I'm probably among the ones pushing hardest for this, and >>>>>> I >>>>>> can >>>>>> tell you, I can't wait for this change in policy, and would be sorely >>>>>> disappointed by having to work in an experimental branch of >>>>>> scikit-image. >>>>>> Both @-matmul and keyword-only arguments are, imho, compelling >>>>>> reasons >>>>>> to >>>>>> switch. (Imagine the amount of fiddling with the API that we could do >>>>>> with >>>>>> keyword-only arguments, without the annoying deprecation cycle!) >>>>>> >>>>>> @Ralf I would argue in favour of 3.5, for the above reasons and >>>>>> because >>>>>> anyone who had the temerity to update to 3.4 is very likely to >>>>>> subsequently >>>>>> move to 3.5. (Self-selected group of early adopters, plus no >>>>>> backwards >>>>>> incompatibility issues between the two versions.) >>>> >>>> >>>> I agree with this argument, I was just asking to clarify. @ is at least >>>> something interesting that's specifically added for scientific users, so >>>> imho 3.5 is the first 3.x release where in some cases the benefits may >>>> start >>>> to be worth the costs. >>>> >>>>> >>>>> That implies that even ubuntu users will have to install python from >>>>> another source than the package manager. Do you really want this? That >>>>> means that only fairly advance python users will be able to use the >>>>> latest scikit-image release. >>>> >>>> >>>> In the grand scheme of things, does Ubuntu matter much for this >>>> decision? >>>> There are way more Windows and OS X users, so if it's OK for them (which >>>> is >>>> not a given) then it should also be OK for those fewer and on average >>>> more >>>> computer-literate Ubuntu users. >>> >>> I don't have a good overview of what OS people are using, but in the >>> different research facilities I've worked or visited, it was always >>> linux based, and users where not really tech-savy. I checked on all of >>> the servers (UW's genome science, the Curie institute, UC Berkeley's >>> stats department, the Mines' machine learning computing facilities.) I >>> have access to, none have python3.5. Some of these servers are >>> "offline", thus conda is useless. All of these research institutes >>> have teams that use in some way image processing. >>> >>> I'll just also mentionned that we had a keynote at scipy this year >>> mentionning she was using python because she just did not have the >>> time anymore to code in C++ and Java. These are the kind of people >>> that may be using scikit-image, that may be interested in the latest >>> version of the package, and yet just not have the time to compile >>> python3.5 from scratch on an outdated server. >> >> >> Fair enough, but there are likely much more outdated servers with Python 2.7 >> than with Python 3.4 on them ..... > > Well? I think it is better to keep python2.7 support :) > All the clusters I have access to but 1 has python3. The oldest one is > a red hat based cluster with python2.6 (which was python2.3 not so > long ago). > > N > >> >> Ralf >> >> -- >> 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/CABL7CQjye5g5jppRk1hej2g2P3VCKa0mrcHe4Z9u37nSrqBpsg%40mail.gmail.com. >> >> For more options, visit https://groups.google.com/d/optout. > > -- > You received this message because you are subscribed to the Google Groups "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com. > To post to this group, send an email to scikit-image at googlegroups.com. > To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/CAE-UAvT0C5z0jg84oDW0MtTiFkoWJgpdNrMCfGx82ZnwDzLeZg%40mail.gmail.com. > For more options, visit https://groups.google.com/d/optout. From emmanuelle.gouillart at nsup.org Wed Aug 10 04:03:22 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Wed, 10 Aug 2016 10:03:22 +0200 Subject: Migration to Python 3.x In-Reply-To: <3FEC278C-8155-4C85-BB44-0B0F7789D071@demuc.de> References: <3FEC278C-8155-4C85-BB44-0B0F7789D071@demuc.de> Message-ID: <20160810080322.GA2220365@phare.normalesup.org> Regarding an estimation of which OS people are using, let me go back to one of my favorite hobbies :-): looking at the analytics of http://scikit-image.org/. What it says in terms of OSs: - 54% of Windows users - 26% of Linux users - 20% of OSx users These statistics are pretty stable over the period where we have analytics (since last fall). We have 20000 unique visitors on the website every month, enough to make statistics! So, the number of Linux users is certainly smaller than the number of users for which the overwhelming solution will be Anaconda, but it's not ridiculous either. Also, people working on a cluster with no Internet access will not visit the website from the cluster, so it's rather an underestimation of Linux users. And it's likely that a majority of Linux users are running 2.7 (because of https://www.python.org/dev/peps/pep-0394/). I completely agree that it would be great to obtain statistics about who uses Python 2.7 or 3.x but I can't see an easy way to do it. Could we have a button on the website linking to a small form asking whether people are using Python 2.7 or 3.x? Maybe it has already been mentioned on the mailing-list. I think the decision boils down to a developers vs. users dilemma -- let's face it, a very classical problem in open source :-). Personally, I think that scikit-image is far from having reached its potential in terms of number of users, and that multiplying the number of users by a factor of 10 is perfectly feasible. Therefore, my personal goal, as a developer, is rather to focus on the growth of the userbase, meaning better usability, more documentation, more outreach, etc. I find it much more satisfying to see the userbase grow than to be able to use the new features of Python 3.5 -- in an ideal world, we'll have the two, of course. Letting down 1/4 of users who won't benefit from new features is no small decision. That said, 1) if there is an important frustration from at least two of the most active developers of scikit-image, we'll have to make this move soon enough, much earlier than 2020 clearly. 2) so, to estimate when the change should happen (0.14, 0.15?), we need to evaluate the "economics" of such a decision. How many users are going to be impacted? How much development time are we losing by not switching right now? How do we balance these two factors (or others)? All the best, Emma On Wed, Aug 10, 2016 at 06:14:45AM +0200, Johannes Sch??nberger wrote: > In my experience, many of the scikit-image users I know are actually less knowledgable about how to setup a new Python environment from scratch. And it seems the latest Ubuntu is still on 3.4 and Mac also doesn't ship with 3.5 - which leaves out the @ syntax anyway. Also, many of the cluster users are still stuck on 2.x for quite a while. I think, we will lose a significant amount of users without a real benefit. > I don't see a compelling reason to lock out X% of users at this point. I can only judge by the feedback in this thread, but 3 out of 5 people seem to have problems with the proposed way forward. It would be nice if there was some way of obtaining installation statistics from PyPI or Anaconda to get a better picture here. > >> On 9 August 2016 at 19:54, Ralf Gommers wrote: > >>>> In the grand scheme of things, does Ubuntu matter much for this > >>>> decision? There are way more Windows and OS X users, so if it's OK > >>>> for them (which is not a given) then it should also be OK for > >>>> those fewer and on average more computer-literate Ubuntu users. From ralf.gommers at gmail.com Tue Aug 9 18:09:06 2016 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Wed, 10 Aug 2016 10:09:06 +1200 Subject: Migration to Python 3.x In-Reply-To: References: <20160809214429.GB1817277@phare.normalesup.org> Message-ID: On Wed, Aug 10, 2016 at 9:58 AM, St?fan van der Walt wrote: > Hi Emmanuelle > > > On 9 August 2016 at 14:44, Emmanuelle Gouillart < > emmanuelle.gouillart at nsup.org> wrote: > > >> It may be a silly idea, but can't we do it the other way around, that is >> have an experimental branch where developers who wish to write >> Python3-only code can work, and in which commits to master are merged if >> they are Python 3 compatible? It could give us some time to evaluate >> whether most developers want to write code that is not compatible with >> Python 2. >> > > I don't think that's a silly idea, but I also don't think that addresses > two of the points I raised: > > - Remove developer overhead associated with keeping both Python 2 and > 3-isms in mind > > I'd like developers to start thinking in Python 3, not the other way > around. Barriers for Python 3 implementations should be removed, not > raised, given that that's the direction we'll have to move eventually. > > - Utilize new language features such as the @-operator and required > keyword arguments > > These are not available unless we make Python 3 the default. > Hi Stefan, do you propose then to drop Python 3.4 at the same time (@ is >= 3.5)? Ralf -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Tue Aug 9 20:28:03 2016 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Wed, 10 Aug 2016 10:28:03 +1000 Subject: Migration to Python 3.x In-Reply-To: References: <20160809214429.GB1817277@phare.normalesup.org> Message-ID: @Emmanuelle I'm probably among the ones pushing hardest for this, and I can tell you, I can't wait for this change in policy, and would be sorely disappointed by having to work in an experimental branch of scikit-image. Both @-matmul and keyword-only arguments are, imho, compelling reasons to switch. (Imagine the amount of fiddling with the API that we could do with keyword-only arguments, without the annoying deprecation cycle!) @Ralf I would argue in favour of 3.5, for the above reasons and because anyone who had the temerity to update to 3.4 is very likely to subsequently move to 3.5. (Self-selected group of early adopters, plus no backwards incompatibility issues between the two versions.) Juan. On Wed, Aug 10, 2016 at 8:14 AM, St?fan van der Walt wrote: > Hi Ralf > > On 9 August 2016 at 15:09, Ralf Gommers wrote: > >> Hi Stefan, do you propose then to drop Python 3.4 at the same time (@ is >> >= 3.5)? >> > > Yes, I guess I am. But if that's too much of a stretch, I will be open to > >= 3.4. > > 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/CABDkGQmSC7Q7jZJDBuhutj2PXjQTDGDirxafVw-GFuqcN%3DK1_A% > 40mail.gmail.com > > . > > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Tue Aug 9 22:17:55 2016 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Wed, 10 Aug 2016 14:17:55 +1200 Subject: Migration to Python 3.x In-Reply-To: References: <20160809214429.GB1817277@phare.normalesup.org> Message-ID: On Wed, Aug 10, 2016 at 1:55 PM, Nelle Varoquaux wrote: > On 9 August 2016 at 17:28, Juan Nunez-Iglesias wrote: > > @Emmanuelle I'm probably among the ones pushing hardest for this, and I > can > > tell you, I can't wait for this change in policy, and would be sorely > > disappointed by having to work in an experimental branch of scikit-image. > > Both @-matmul and keyword-only arguments are, imho, compelling reasons to > > switch. (Imagine the amount of fiddling with the API that we could do > with > > keyword-only arguments, without the annoying deprecation cycle!) > > > > @Ralf I would argue in favour of 3.5, for the above reasons and because > > anyone who had the temerity to update to 3.4 is very likely to > subsequently > > move to 3.5. (Self-selected group of early adopters, plus no backwards > > incompatibility issues between the two versions.) > I agree with this argument, I was just asking to clarify. @ is at least something interesting that's specifically added for scientific users, so imho 3.5 is the first 3.x release where in some cases the benefits may start to be worth the costs. > That implies that even ubuntu users will have to install python from > another source than the package manager. Do you really want this? That > means that only fairly advance python users will be able to use the > latest scikit-image release. > In the grand scheme of things, does Ubuntu matter much for this decision? There are way more Windows and OS X users, so if it's OK for them (which is not a given) then it should also be OK for those fewer and on average more computer-literate Ubuntu users. Ralf -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Tue Aug 9 22:54:51 2016 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Wed, 10 Aug 2016 14:54:51 +1200 Subject: Migration to Python 3.x In-Reply-To: References: <20160809214429.GB1817277@phare.normalesup.org> Message-ID: On Wed, Aug 10, 2016 at 2:46 PM, Nelle Varoquaux wrote: > On 9 August 2016 at 19:17, Ralf Gommers wrote: > > > > > > On Wed, Aug 10, 2016 at 1:55 PM, Nelle Varoquaux < > nelle.varoquaux at gmail.com> > > wrote: > >> > >> On 9 August 2016 at 17:28, Juan Nunez-Iglesias > wrote: > >> > @Emmanuelle I'm probably among the ones pushing hardest for this, and > I > >> > can > >> > tell you, I can't wait for this change in policy, and would be sorely > >> > disappointed by having to work in an experimental branch of > >> > scikit-image. > >> > Both @-matmul and keyword-only arguments are, imho, compelling reasons > >> > to > >> > switch. (Imagine the amount of fiddling with the API that we could do > >> > with > >> > keyword-only arguments, without the annoying deprecation cycle!) > >> > > >> > @Ralf I would argue in favour of 3.5, for the above reasons and > because > >> > anyone who had the temerity to update to 3.4 is very likely to > >> > subsequently > >> > move to 3.5. (Self-selected group of early adopters, plus no backwards > >> > incompatibility issues between the two versions.) > > > > > > I agree with this argument, I was just asking to clarify. @ is at least > > something interesting that's specifically added for scientific users, so > > imho 3.5 is the first 3.x release where in some cases the benefits may > start > > to be worth the costs. > > > >> > >> That implies that even ubuntu users will have to install python from > >> another source than the package manager. Do you really want this? That > >> means that only fairly advance python users will be able to use the > >> latest scikit-image release. > > > > > > In the grand scheme of things, does Ubuntu matter much for this decision? > > There are way more Windows and OS X users, so if it's OK for them (which > is > > not a given) then it should also be OK for those fewer and on average > more > > computer-literate Ubuntu users. > > I don't have a good overview of what OS people are using, but in the > different research facilities I've worked or visited, it was always > linux based, and users where not really tech-savy. I checked on all of > the servers (UW's genome science, the Curie institute, UC Berkeley's > stats department, the Mines' machine learning computing facilities.) I > have access to, none have python3.5. Some of these servers are > "offline", thus conda is useless. All of these research institutes > have teams that use in some way image processing. > > I'll just also mentionned that we had a keynote at scipy this year > mentionning she was using python because she just did not have the > time anymore to code in C++ and Java. These are the kind of people > that may be using scikit-image, that may be interested in the latest > version of the package, and yet just not have the time to compile > python3.5 from scratch on an outdated server. > Fair enough, but there are likely much more outdated servers with Python 2.7 than with Python 3.4 on them ..... Ralf -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Wed Aug 10 18:13:04 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Wed, 10 Aug 2016 15:13:04 -0700 Subject: Migration to Python 3.x In-Reply-To: References: <20160809214429.GB1817277@phare.normalesup.org> Message-ID: Hi Nelle On 9 August 2016 at 18:55, Nelle Varoquaux wrote: > That implies that even ubuntu users will have to install python from > another source than the package manager. Do you really want this? That > means that only fairly advance python users will be able to use the > latest scikit-image release. > Ubuntu users haven't had the latest scikit-image for quite a while, unfortunately. We are working on fixing that, but not many people have noticed. St?fan -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Wed Aug 10 18:24:29 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Wed, 10 Aug 2016 15:24:29 -0700 Subject: Migration to Python 3.x In-Reply-To: <20160810080322.GA2220365@phare.normalesup.org> References: <3FEC278C-8155-4C85-BB44-0B0F7789D071@demuc.de> <20160810080322.GA2220365@phare.normalesup.org> Message-ID: On 10 August 2016 at 01:03, Emmanuelle Gouillart < emmanuelle.gouillart at nsup.org> wrote: > I completely agree that it would be great to obtain statistics about > who uses Python 2.7 or 3.x but I can't see an easy way to do it. Could we > have a button on the website linking to a small form asking whether > people are using Python 2.7 or 3.x? Maybe it has already been mentioned > on the mailing-list. > I'll work on getting hold of some statistics from PyPA. > 2) so, to estimate when the change should happen (0.14, 0.15?), we need > to evaluate the "economics" of such a decision. How many users are going > to be impacted? How much development time are we losing by not switching > right now? How do we balance these two factors (or others)? > I don't think the developer cost is very high right now. I wanted to test the waters a bit and see how the rest of the team felt, but I think there are enough compelling arguments to stick to 2.7-compatibility for now. We can always revisit the issue again a year or so from now, when the landscape might have changed. Thanks for all the feedback! St?fan -------------- next part -------------- An HTML attachment was scrubbed... URL: From dipugee at gmail.com Thu Aug 11 00:04:23 2016 From: dipugee at gmail.com (=?utf-8?Q?Dipankar_=E2=80=9CDipu=E2=80=9D_Ganguly?=) Date: Wed, 10 Aug 2016 21:04:23 -0700 Subject: Image edge detection In-Reply-To: References: <476b29f9-0e89-495d-aaee-88a9dbc69460@googlegroups.com> <5AB4F386-67B4-4DE3-9E2D-151F23C72F8C@gmail.com> <8FEA9192-98EE-4B8C-BC6E-7A1B6EFBFCE9@gmail.com> Message-ID: <1C25E464-0A0D-4920-8D1C-4EC6F52E2355@gmail.com> Your suggestions have been very helpful and allowed me to make good progress. Do you know where I can find the Python source code for the edge filters in MatPlotlib? Thanks. Dipu Dipankar Ganguly Consultant: Strategy/Technology/Commercialization Bothell, WA Cell: 408-203-8814 email: dipugee at gmail.com http://www.linkedin.com/in/dipugee > On Aug 9, 2016, at 2:42 PM, St?fan van der Walt wrote: > > Hi Dipu > > On 9 August 2016 at 14:40, Dipankar ?Dipu? Ganguly > wrote: > Sorry to bother you again. I am having trouble with "from skimage import xyz? commands. I am using Python 3.5 with Jupyter from Navigator. I am wondering if I am running into version mismatches. > > Yes, I am afraid we don't have an xyz submodule. > > Perhaps you can share some code with us, along with the error messages you are seeing? > > St?fan > > -- > You received this message because you are subscribed to a topic in the Google Groups "scikit-image" group. > To unsubscribe from this topic, visit https://groups.google.com/d/topic/scikit-image/7IskXgM-99E/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/CABDkGQnhpOQemWLzN5G2ACwwXgLca1cON1aCsmkBy283ZtHY2g%40mail.gmail.com . > For more options, visit https://groups.google.com/d/optout . -------------- next part -------------- An HTML attachment was scrubbed... URL: From siqueiraaf at gmail.com Thu Aug 11 09:22:22 2016 From: siqueiraaf at gmail.com (Alexandre Fioravante de Siqueira) Date: Thu, 11 Aug 2016 06:22:22 -0700 (PDT) Subject: Translating Multi-Otsu Threshold from java In-Reply-To: <182f6557-808f-4603-9860-35fe40cf0558@googlegroups.com> References: <26620e4c-ba27-46b8-a8e4-8d9daada6d90@googlegroups.com> <4ce0276b-b208-45e4-a8a4-b925639e6b30@googlegroups.com> <0027471f-101e-49cf-a5b5-a8ecdfe7216f@googlegroups.com> <182f6557-808f-4603-9860-35fe40cf0558@googlegroups.com> Message-ID: <0b64a75a-c486-4036-a795-a9bfd81d820d@googlegroups.com> Hi all, I am having a bad time trying to correct the first version of this code. The values from my function and Tosa's does not match. In my tests, my maxSigma is higher than his; I believe I am having a problem with the values returned from the histogram. Could you give me a hand on that? This is the code so far: https://github.com/alexandrejaguar/software/blob/master/threshold_multiotsu.py Thanks for your time! Kind regards, Alex Em segunda-feira, 9 de maio de 2016 19:06:46 UTC+2, Alexandre Fioravante de Siqueira escreveu: > > Done (for now): https://github.com/scikit-image/scikit-image/pull/2076. > > Em segunda-feira, 9 de maio de 2016 12:14:59 UTC+2, Alexandre Fioravante > de Siqueira escreveu: >> >> Hi all, >> the preliminary code is ready, but it could be improved a lot. For >> instance, there's a function named maxsigma() which has a lot of nested for >> loops. >> Here is the code: >> https://gist.github.com/alexandrejaguar/fd767149b3a667f8be125734893f020d >> Could you give me a hand to improve that? >> Thank you very much! >> Kind regards, >> >> Alex >> >> Em domingo, 8 de maio de 2016 17:20:31 UTC+2, Alexandre Fioravante de >> Siqueira escreveu: >>> >>> Hi Josh, >>> OK, I'm on it. I'll try to implement from the paper. >>> >>> Alex >>> >>> Em quarta-feira, 4 de maio de 2016 01:34:38 UTC+2, Josh Warner escreveu: >>>> >>>> We do have Otsu, and I think it would be within the scope of >>>> scikit-image. >>>> >>>> I think I'd find use for this, personally, and depending on the >>>> implementation you may be able to reuse code from simple binary Otsu >>>> internally. >>>> >>>> Seems reasonable - PR would be welcome! >>>> >>>> Josh >>>> >>>> On Tuesday, May 3, 2016 at 10:47:00 AM UTC-5, Alexandre Fioravante de >>>> Siqueira wrote: >>>>> >>>>> Hi everyone, >>>>> I was thinking about using multi-Otsu thresholding for some research. >>>>> I am used to use the ImageJ available plugin, >>>>> http://imagej.net/Multi_Otsu_Threshold. >>>>> Could you give me a hand on writing such a function which could do >>>>> this for python? Maybe putting it into scikit-image. Or else, could you >>>>> point me a better alternative? >>>>> Thank you very much! >>>>> >>>>> Alex >>>>> >>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Thu Aug 11 00:25:29 2016 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Thu, 11 Aug 2016 14:25:29 +1000 Subject: Migration to Python 3.x In-Reply-To: References: <3FEC278C-8155-4C85-BB44-0B0F7789D071@demuc.de> <20160810080322.GA2220365@phare.normalesup.org> Message-ID: Hi everyone, First of all, I excitedly jumped on the bandwagon because Stefan mentioned 0.13, but I actually even I considered that a bit early for dropping Py2 when I read it. =) I would say that the right time to drop Py2 is either 0.15 or 1.0, and that we should follow a standard deprecation cycle. What this means is some warning (on the home page, or on installation, for example) that as of version ., scikit-image will be Python 3-only, with the previous release being an LTS release with Python 2 support. An important corollary to this thread is signing the Python 3 statement , which pledges dropping Python 2 support by **2020**. We can commit to a longer timeline than envisioned by St?fan's initial proposal, but I would like to commit to a timeline, because I think having the scikit-image logo on that page would definitely add momentum to the transition. Which it (cough) clearly needs. As St?fan has noted, Ubuntu users haven't had 0.12 in the package manager in ages and the sky hasn't fallen. A long-term support release is *not* the same as abandoning our users. I would find it much less burdensome to backport certain bug fixes and critical features to 0.13.25 (or whatever) than to keep supporting 2.7 ad infinitum. The deprecation cycle in particular just bugs the hell out of me. About the benefits of switching, Johannes, although you argue that Python3 doesn't make the code "more correct", this is not strictly the case: keyword-only arguments, better readability (with @), and typing, *all* make it easier to avoid bugs. You can hardly claim that skimage is bug-free. I'll note that in my own project, gala, a user discovered a monster bug that will result in me issuing a correction to the paper: https://github.com/janelia-flyem/gala/issues/63 Both typing and keyword-only arguments would have prevented this bug. Emma, thank you so much for those statistics. They are so valuable. =) I agree *a lot* about outreach + docs, and growing our user base. But I think all those efforts should focus on Python 3 anyway. So anyway, I hope I've added some fuel to the fire with my bug disaster, above. =) And I hope we can agree on a timeline, even if the timeline is not quite as aggressive as Jupyter's or St?fan's original proposal. Thanks all! Juan. On Thu, Aug 11, 2016 at 8:24 AM, St?fan van der Walt wrote: > On 10 August 2016 at 01:03, Emmanuelle Gouillart < > emmanuelle.gouillart at nsup.org> wrote: > >> I completely agree that it would be great to obtain statistics about >> who uses Python 2.7 or 3.x but I can't see an easy way to do it. Could we >> have a button on the website linking to a small form asking whether >> people are using Python 2.7 or 3.x? Maybe it has already been mentioned >> on the mailing-list. >> > > I'll work on getting hold of some statistics from PyPA. > > >> 2) so, to estimate when the change should happen (0.14, 0.15?), we need >> to evaluate the "economics" of such a decision. How many users are going >> to be impacted? How much development time are we losing by not switching >> right now? How do we balance these two factors (or others)? >> > > I don't think the developer cost is very high right now. I wanted to test > the waters a bit and see how the rest of the team felt, but I think there > are enough compelling arguments to stick to 2.7-compatibility for now. We > can always revisit the issue again a year or so from now, when the > landscape might have changed. > > Thanks for all the feedback! > > 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/CABDkGQ%3DEzzSY1j9qy%2BD3VkzVP4zeHknBrqkBZ%3D9m7Q_ > H4qSvCA%40mail.gmail.com > > . > > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From takowl at gmail.com Fri Aug 12 11:29:23 2016 From: takowl at gmail.com (Thomas Kluyver) Date: Fri, 12 Aug 2016 08:29:23 -0700 (PDT) Subject: Migration to Python 3.x In-Reply-To: <3FEC278C-8155-4C85-BB44-0B0F7789D071@demuc.de> References: <20160809214429.GB1817277@phare.normalesup.org> <3FEC278C-8155-4C85-BB44-0B0F7789D071@demuc.de> Message-ID: A small factual correction: On Wednesday, 10 August 2016 05:14:49 UTC+1, Johannes Sch?nberger wrote: > > And it seems the latest Ubuntu is still on 3.4... > This is not accurate - Ubuntu 16.04 (the LTS release that came out in April this year), has Python 3.5: http://packages.ubuntu.com/xenial/python3 Ubuntu 15.10 is no longer supported (non-LTS releases get 9 months support). Of course there will still be users on 14.04, and even 12.04, for some time. I don't want to push an aggressive policy on the project, but I would encourage you to make plans for dropping Python 2 support at some time in the next few years, and sign http://python3statement.github.io/ . I know this may feel like 'users vs developers' at the moment, but I don't think it's that simple. The split between Python 3 and 2 has been causing users headaches for several years now. The only realistic way to end this is to complete the transition, so that Python 3 becomes the standard answer for everything but large legacy codebases. There's little impetus to make Python 3 available in institutional environments so long as people assume that all important Python projects will always support Python 2. So when we make this decision as a community, rather than individual projects, I think it ultimately helps both users and developers. These groups also have common interests - developers who spend less effort on compatibility work can pay more attention to more interesting improvements. With the Python 3 statement, we believe we're setting a relaxed timetable: projects only commit to dropping Python 2 support by 2020, which is still four years away. We expect to be on Python 3.7 by that time. The aim is not to leave Python 2 users in the lurch, but to give everyone plenty of notice that support for Python 2 will come to an end, so that they can plan a transition in good time. Thanks, Thomas -------------- next part -------------- An HTML attachment was scrubbed... URL: From pkmkicha at gmail.com Wed Aug 17 06:16:07 2016 From: pkmkicha at gmail.com (KRISHNAMOOORTHY P) Date: Wed, 17 Aug 2016 03:16:07 -0700 (PDT) Subject: Matlab Equlilavent Functions Message-ID: <393defef-f5b2-41ee-a2ac-701a3674190a@googlegroups.com> Is there a Python Equivalent Functions for following matlab functions - strel - imdilate - imclose - bwmorph - bwareaopen -------------- next part -------------- An HTML attachment was scrubbed... URL: From silvertrumpet999 at gmail.com Wed Aug 17 22:11:59 2016 From: silvertrumpet999 at gmail.com (Josh Warner) Date: Wed, 17 Aug 2016 19:11:59 -0700 (PDT) Subject: Matlab Equlilavent Functions In-Reply-To: <393defef-f5b2-41ee-a2ac-701a3674190a@googlegroups.com> References: <393defef-f5b2-41ee-a2ac-701a3674190a@googlegroups.com> Message-ID: <442a6617-f537-479c-9074-2b04b23d9c52@googlegroups.com> This functionality is mostly available in `skimage.morphology`. Matlab's strel is instead some utility functions, most notably `disk`. Morphological operations of dilation and erosion, as well as closing/opening, are available there as well. The names are slightly different but their use is straightforward. Use binary_* prefix for binary and no prefix for grayscale, e.g. binary_dilation vs dilation. On Wednesday, August 17, 2016 at 5:16:07 AM UTC-5, KRISHNAMOOORTHY P wrote: > > Is there a Python Equivalent Functions for following matlab functions > > > - strel > - imdilate > - imclose > - bwmorph > - bwareaopen > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pkmkicha at gmail.com Thu Aug 18 05:09:48 2016 From: pkmkicha at gmail.com (KRISHNAMOOORTHY P) Date: Thu, 18 Aug 2016 02:09:48 -0700 (PDT) Subject: Matlab Equlilavent Functions In-Reply-To: <442a6617-f537-479c-9074-2b04b23d9c52@googlegroups.com> References: <393defef-f5b2-41ee-a2ac-701a3674190a@googlegroups.com> <442a6617-f537-479c-9074-2b04b23d9c52@googlegroups.com> Message-ID: <9012e0ab-6e7e-4c61-822a-dcdce7fb800f@googlegroups.com> Thank you very much for your help From fboulogne at sciunto.org Fri Aug 19 11:54:54 2016 From: fboulogne at sciunto.org (=?UTF-8?Q?Fran=c3=a7ois_Boulogne?=) Date: Fri, 19 Aug 2016 17:54:54 +0200 Subject: Next sprint? Message-ID: <8bd209d5-3e4e-7e23-0811-8a82b3e14a77@sciunto.org> Hi, I'm wondering if there is a sprint schedule during euroscipy. It seems that it didn't really happen last time in the US. I think it would be a good occasion to review PR. We have several PR waiting for reviews and bugs waiting for decisions... it tends to grow :) Best. -- Fran?ois Boulogne. http://www.sciunto.org GPG: 32D5F22F From emmanuelle.gouillart at nsup.org Fri Aug 19 12:08:55 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Fri, 19 Aug 2016 18:08:55 +0200 Subject: Next sprint? In-Reply-To: <8bd209d5-3e4e-7e23-0811-8a82b3e14a77@sciunto.org> References: <8bd209d5-3e4e-7e23-0811-8a82b3e14a77@sciunto.org> Message-ID: <20160819160855.GE3478821@phare.normalesup.org> Hi Fran??ois, if you're going to Euroscipy you should definitely propose a sprint (you can do this on the Euroscipy website I think). Sprints are going to take place on Saturday 27th during the whole day (and usually it's possible to organize smaller sprints on evenings as well). I'd be glad to take part to the sprint but remotely, since being 8-month pregnant is incompatible with travelling too far :-). I don't know if other devs are going to be at Euroscipy, but sprints are usually a great opportunity for new contributors to get started. Best Emma On Fri, Aug 19, 2016 at 05:54:54PM +0200, Fran??ois Boulogne wrote: > Hi, > I'm wondering if there is a sprint schedule during euroscipy. It seems > that it didn't really happen last time in the US. I think it would be a > good occasion to review PR. We have several PR waiting for reviews and > bugs waiting for decisions... it tends to grow :) > Best. From fboulogne at sciunto.org Sat Aug 20 03:22:50 2016 From: fboulogne at sciunto.org (=?UTF-8?Q?Fran=c3=a7ois_Boulogne?=) Date: Sat, 20 Aug 2016 09:22:50 +0200 Subject: Next sprint? In-Reply-To: <20160819160855.GE3478821@phare.normalesup.org> References: <8bd209d5-3e4e-7e23-0811-8a82b3e14a77@sciunto.org> <20160819160855.GE3478821@phare.normalesup.org> Message-ID: <3876776c-59fb-8d1c-08dd-bb83f0f4c835@sciunto.org> Hi Emma, > if you're going to Euroscipy you should definitely propose a sprint (you > can do this on the Euroscipy website I think). Sprints are going to take > place on Saturday 27th during the whole day (and usually it's possible to > organize smaller sprints on evenings as well). Unfortunately, I won't be at euroscipy this year but I'm ready to be online if something happens there. Otherwise, I'll start a poll to see if part of the team would be available; I know that timezones do not help. > I'd be glad to take part to the sprint but remotely, since being 8-month > pregnant is incompatible with travelling too far :-). :) Take care! Best, -- Fran?ois Boulogne. http://www.sciunto.org GPG: 32D5F22F From jni.soma at gmail.com Mon Aug 22 00:47:16 2016 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Mon, 22 Aug 2016 14:47:16 +1000 Subject: Management of PRs, issues, and threads Message-ID: Hi everyone, We've had a couple of community fails on GitHub recently: https://github.com/scikit-image/scikit-image/pull/1474#issuecomment-241283056 https://github.com/scikit-image/scikit-image/issues/2080 (The last one is missing a presumably-deleted comment where someone outside the project recommended to a potential contributor to just fork the project!). That's just the couple I've noticed, I'm sure there are lots more. We definitely have many, many abandoned PRs from >1y, >2y ago. Obviously, something in our process isn't working. I don't have immediate solutions, but here's a couple of suggestions: - we need a system to assign core devs to PRs/issues. Currently, it's too easy for all of us to go, "someone else on the team will handle this". We need a fair way to assign a manager to each issue/PR. The assigned dev wouldn't necessarily be responsible for review, but they would be responsible for chasing up other reviewers. - NEVER close a PR without the explicit consent of the contributor, OR after the contributor has been non-responsive for e.g. 1mo and two pings. In this last situation I would even suggest that we need two core devs to sign off. Other suggestions welcome in this thread. We should try to get a new process hammered out very soon. I also want to acknowledge @soupault for his triage/labelling work, which is a massive step in the right direction. But we need to follow up his triage with some actual process. Juan. -------------- next part -------------- An HTML attachment was scrubbed... URL: From drkoundinyadesiraju at gmail.com Tue Aug 23 01:40:05 2016 From: drkoundinyadesiraju at gmail.com (Koundinya Desiraju) Date: Mon, 22 Aug 2016 22:40:05 -0700 (PDT) Subject: IHC Image color deconvolution Message-ID: <74882dde-6af5-4cb8-a02d-debd5e2e1678@googlegroups.com> In this tutorial, http://scikit-image.org/docs/dev/auto_examples/color_exposure/plot_ihc_color_separation.html#sphx-glr-auto-examples-color-exposure-plot-ihc-color-separation-py After color deconvolution the haematoxylin and DAB channels were plotted in grayscale but I want to show them in respective colors. For example, I want to show DAB channel in brown. Can anyone kindly post How to do that? Thanks, Koundinya -------------- next part -------------- An HTML attachment was scrubbed... URL: From emmanuelle.gouillart at nsup.org Mon Aug 22 17:26:51 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Mon, 22 Aug 2016 23:26:51 +0200 Subject: Management of PRs, issues, and threads In-Reply-To: References: Message-ID: <20160822212651.GC1708463@phare.normalesup.org> Hi Juan, thanks for bringing these issues to light. How about we tackle the queue of open PRs from its two ends? That is, for the new PRs we have this manager system (we still need to decide how to assign them), and at the same time we go through old PRs to try to unblock or (worst case) close them? Best, Emma On Mon, Aug 22, 2016 at 02:47:16PM +1000, Juan Nunez-Iglesias wrote: > Hi everyone, > We've had a couple of community fails on GitHub recently: > https://github.com/scikit-image/scikit-image/pull/1474#issuecomment-241283056 > https://github.com/scikit-image/scikit-image/issues/2080 > (The last one is missing a presumably-deleted comment where someone outside the > project recommended to a potential contributor to just fork the project!). > That's just the couple I've noticed, I'm sure there are lots more. We > definitely have many, many abandoned PRs from >1y, >2y ago. > Obviously, something in our process isn't working. I don't have immediate > solutions, but here's a couple of suggestions: > - we need a system to assign core devs to PRs/issues. Currently, it's too easy > for all of us to go, "someone else on the team will handle this". We need a > fair way to assign a manager to each issue/PR. The assigned dev wouldn't > necessarily be responsible for review, but they would be responsible for > chasing up other reviewers. > - NEVER close a PR without the explicit consent of the contributor, OR after > the contributor has been non-responsive for e.g. 1mo and two pings. In this > last situation I would even suggest that we need two core devs to sign off. > Other suggestions welcome in this thread. We should try to get a new process > hammered out very soon. > I also want to acknowledge @soupault for his triage/labelling work, which is a > massive step in the right direction. But we need to follow up his triage with > some actual process. > Juan. From jni.soma at gmail.com Tue Aug 23 22:08:00 2016 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Tue, 23 Aug 2016 22:08:00 -0400 Subject: IHC Image color deconvolution In-Reply-To: <74882dde-6af5-4cb8-a02d-debd5e2e1678@googlegroups.com> References: <74882dde-6af5-4cb8-a02d-debd5e2e1678@googlegroups.com> Message-ID: Hi Koundinya, It looks like this is not a trivial question, because the conversion between the two spaces is nonlinear. See the code here: https://github.com/scikit-image/scikit-image/blob/master/skimage/color/colorconv.py#L1437 I originally thought that it would be possible to convert each channel separately, but the `exp` call makes this either difficult or impossible (I haven't yet decided which, but I wasn't able to get it to work in a short amount of time). Here's my initial attempt, which was a complete failure, for the record: In [1]: from skimage import data In [2]: from skimage.color import rgb2hed In [3]: from skimage.color import hed2rgb In [4]: import matplotlib.pyplot as plt In [5]: ihc_rgb = data.immunohistochemistry() In [6]: ihc_hed = rgb2hed(ihc_rgb) In [8]: import numpy as np In [9]: h, e, d = np.transpose(ihc_hed, (2, 0, 1)) In [10]: empty = np.zeros_like(h) In [11]: h_rgb = hed2rgb(np.dstack((h, empty, empty))) In [12]: e_rgb = hed2rgb(np.dstack((empty, e, empty))) In [13]: d_rgb = hed2rgb(np.dstack((empty, empty, d))) In [14]: fig, axes = plt.subplots(2, 2, figsize=(6, 7), sharex=True, ...: sharey=True, ...: subplot_kw={'adjustable': 'box-forced'}) In [15]: axes[0, 0].imshow(ihc_rgb); axes[0, 0].set_title('Original image') Out[15]: In [16]: axes[0, 1].imshow(h_rgb); axes[0, 1].set_title('Hematoxylin') Out[16]: In [17]: axes[1, 0].imshow(e_rgb); axes[1, 0].set_title('Eosin') Out[17]: In [18]: axes[1, 1].imshow(d_rgb); axes[1, 1].set_title('DAB') Out[18]: In [19]: for ax in axes.ravel(): ...: ax.axis('off') Result: Maybe someone else in the list has some ideas? Juan. From: Koundinya Desiraju Reply: scikit-image at googlegroups.com Date: 23 August 2016 at 3:40:09 PM To: scikit-image Subject: IHC Image color deconvolution In this tutorial, http://scikit-image.org/docs/dev/auto_examples/color_exposure/plot_ihc_color_separation.html#sphx-glr-auto-examples-color-exposure-plot-ihc-color-separation-py After color deconvolution the haematoxylin and DAB channels were plotted in grayscale but I want to show them in respective colors. For example, I want to show DAB channel in brown. Can anyone kindly post How to do that? Thanks, Koundinya -- 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/74882dde-6af5-4cb8-a02d-debd5e2e1678%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: deconv.png Type: image/png Size: 302111 bytes Desc: not available URL: From cedric.espenel at gmail.com Fri Aug 26 00:17:42 2016 From: cedric.espenel at gmail.com (Cedric Espenel) Date: Thu, 25 Aug 2016 21:17:42 -0700 (PDT) Subject: IHC Image color deconvolution In-Reply-To: <74882dde-6af5-4cb8-a02d-debd5e2e1678@googlegroups.com> References: <74882dde-6af5-4cb8-a02d-debd5e2e1678@googlegroups.com> Message-ID: <5394a2f0-98a1-4254-ac14-851e9c956bb7@googlegroups.com> Hi Koundinya, I'm not sure if that will answer your question but if you try: from matplotlib.colors import LinearSegmentedColormap cmap_Hema = LinearSegmentedColormap.from_list('mycmap', ['white', 'navy']) cmap_DAB = LinearSegmentedColormap.from_list('mycmap', ['white', 'saddlebrown']) cmap_Eosin = LinearSegmentedColormap.from_list('mycmap', ['darkviolet', 'white']) You won't be able to get back to the original color but it will do a descent job: Sincerely, Cedric On Monday, August 22, 2016 at 10:40:06 PM UTC-7, Koundinya Desiraju wrote: > > In this tutorial, > http://scikit-image.org/docs/dev/auto_examples/color_exposure/plot_ihc_color_separation.html#sphx-glr-auto-examples-color-exposure-plot-ihc-color-separation-py > > After color deconvolution the haematoxylin and DAB channels were plotted > in grayscale but I want to show them in respective colors. For example, I > want to show DAB channel in brown. Can anyone kindly post How to do that? > > Thanks, > Koundinya > -------------- next part -------------- An HTML attachment was scrubbed... URL: From chrisspen at gmail.com Sun Aug 28 20:31:28 2016 From: chrisspen at gmail.com (Chris Spencer) Date: Sun, 28 Aug 2016 17:31:28 -0700 (PDT) Subject: Distance Estimation Message-ID: Hi, Can scikit-image be used for supervised learning? I have training data, where each sample is composed of a raw RGB image, a black-and-white image mask showing the laser projection onto the image, and the laser range finder distance measurements in millimetres. Is there any algorithm in scikit-image that I could use to train a predictor that could estimate the distance at each pixel in an image? I've gone through all the examples, and none of them seemed to directly apply. The image segmentation example seemed to be the closest, but that didn't use supervised learning, so I wasn't sure how I could adapt it's code. Can this goal be accomplished with sckit-image? If not, is there another library and algorithm you could recommend? Regards, Chris -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Mon Aug 29 16:13:33 2016 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Mon, 29 Aug 2016 13:13:33 -0700 Subject: Fwd: PyData Community Cookbook - August Update Message-ID: <1472501613.509939.709586801.1704EAF6@webmail.messagingengine.com> Hi everyone Is anyone interested in writing a scikit-image chapter for the following book? St?fan ----- Original message ----- From: Andy Ray Terrel Subject: PyData Community Cookbook - August Update Date: Sat, 20 Aug 2016 07:14:58 -0500 Hello everyone, You are receiving this email because you were either invited and committed to join our project. Please feel free to forward this message to a more appropriate list or person. For questions please email pydata- cookbook at numfocus.org. Katy Huff and myself are starting a project to build a cookbook of advanced material for the PyData community. The cookbook will be published by Addison-Wesley. We have invited a number of contributors to see if such a project would have some interest and received overwhelmingly positive feedback. The book will cover several major topics, organized as such, with some sample packages: - IDE: IPython/Jupyter - Data Structures / Numerics: NumPy, Pandas, Xray, PyTables - Viz: Matplotlib, Bokeh, Seaborn, yt - Algorithms / Science: SciPy, Scikit-learn, Scikit-image, statsmodels, sympy, gensim - Performance / Scale: Cython, Numexpr, Numba, Dask, pyspark We expect each submission to be about 15 - 20 pages describing an example of the power of each library. While we have reached out to the projects about putting each submission together we are happy to accept chapters for libraries we did not initially identify. To facilitate the book we have put together a repository for collecting and reviewing submissions at https://github.com/pydata/pydata-cookbook . We are asking for submissions in rst but would appreciate any other files, such as jupyter notebooks or code, for a digital appendix as well. If you read this far and are interested in contributing. The proposed schedule is the following: Sept 1: Submit a pull request with a title, abstract and author list for the submission. Nov 15: Submit a completed chapter. Dec 31: Reviews for chapters finished. Jan 31: All chapter revisions due. Thanks for you time! -- Andy R. Terrel, PhD President, NumFOCUS andy at numfocus.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Mon Aug 29 16:17:48 2016 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Mon, 29 Aug 2016 13:17:48 -0700 Subject: Task board Message-ID: <1472501868.510757.709588497.3AE0E834@webmail.messagingengine.com> Hi, everyone As Juan mentioned recently, it's becoming harder to keep track of the motion of the project as a whole. Sometimes, tickets lounge unattended for an unacceptable long time. I can think of two main routes for improving the situation: 1) Improve our team structure, so that individuals take responsibility for moving certain aspects of the project forward. 2) Processes / systems to help us get a grasp on the current state of things I have some ideas around (1) that need fleshing out, but in the mean time I was looking at http://zube.io to address part of (2). Do you have any experience with this system? Zube can be compared against HuBoard, gh-board, and ZenHub. A test scikit-image board is here: https://zube.io/projects/4670/kanban (it's vanilla, I haven't done anything with it yet) Let me hear your thoughts. St?fan From stefanv at berkeley.edu Mon Aug 29 20:47:45 2016 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Mon, 29 Aug 2016 17:47:45 -0700 Subject: Inclusive community statement Message-ID: <1472518065.560834.709801233.3F5E5296@webmail.messagingengine.com> Dear contributors and users You may know that I am not very fond of Codes of Conduct in general. I think they are well intentioned, but they are also often aggressive, use words more commonly associated with law enforcement, and may leave one feeling a tad scared and unenthusiastic. At the same time, I do think it is important to be inviting to newcomers of all groups, and to make that clear on our website. What would you say to a "Community Guidelines" or "How We Work (together)" statement on the scikit-image front page? Something along the lines of: "We welcome each and every contributor to scikit-image. Our aim is enthusiastic and productive collaboration, to build an excellent software library, and to have a ton of fun doing it. We encourage one another to be gentle in criticism of others' work, humble in acknowledging our own mistakes, and generous in our praise. If you ever feel like you are not being treated as well as you should, please get in touch with one of the project leads. We are committed to making this community a safe and welcome space." Best regards St?fan From dipugee at gmail.com Mon Aug 29 20:53:45 2016 From: dipugee at gmail.com (=?utf-8?Q?Dipankar_=E2=80=9CDipu=E2=80=9D_Ganguly?=) Date: Mon, 29 Aug 2016 17:53:45 -0700 Subject: Image edge detection In-Reply-To: References: <476b29f9-0e89-495d-aaee-88a9dbc69460@googlegroups.com> Message-ID: Hi: I have ImageJ installed on the same Mac that I am using to develop IPython Image Processing algorithms under Anaconda Navigator?s Jupyter. Can I load ImageJ as a package in my Image Processing environment and call its functions as I do with Scikit-image? Thanks Dipu Dipankar ?Dipu? Ganguly dipugee at gmail.com Cell: 408-203-8814 > On Aug 8, 2016, at 5:24 PM, St?fan van der Walt wrote: > > Hi Dipu > > Please try one of the examples from the gallery: > > http://scikit-image.org/docs/dev/auto_examples/ > > St?fan > > On 8 August 2016 at 17:09, Dipankar Ganguly > wrote: > I am trying to do an image edge detection project using Python 3.5 under Jupyter on Anaconda's Navigator on my Mac running OS 10.11.6. I have verified that the Envirnoment does have scikit-image installed I have run into this at the very outset. > > _________________ > File "", line 1 > import scikit-image as image > ^ > SyntaxError: invalid syntax > __________________ > > How do I solve this? Is there a more recent package I should be using? > > Thanks. > > Dipu > > > > -- > 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/476b29f9-0e89-495d-aaee-88a9dbc69460%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/7IskXgM-99E/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/CABDkGQ%3D-HOcA1Xoxxfp8H%2Bohd-ZvV4hK-4oa_J5zkG%3Dqyd09cg%40mail.gmail.com . > For more options, visit https://groups.google.com/d/optout . -------------- next part -------------- An HTML attachment was scrubbed... URL: From emmanuelle.gouillart at nsup.org Mon Aug 29 16:44:35 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Mon, 29 Aug 2016 22:44:35 +0200 Subject: Fwd: PyData Community Cookbook - August Update In-Reply-To: <1472501613.509939.709586801.1704EAF6@webmail.messagingengine.com> References: <1472501613.509939.709586801.1704EAF6@webmail.messagingengine.com> Message-ID: <20160829204435.GC1302378@phare.normalesup.org> Hi St??fan, is it something that we could re-use for the documentation of scikit-image, in the user guide for example? Best Emma On Mon, Aug 29, 2016 at 01:13:33PM -0700, Stefan van der Walt wrote: > Hi everyone > Is anyone interested in writing a scikit-image chapter for the following book? > St??fan > ----- Original message ----- > From: Andy Ray Terrel > Subject: PyData Community Cookbook - August Update > Date: Sat, 20 Aug 2016 07:14:58 -0500 > Hello everyone, > You are receiving this email because you were either invited and committed to > join our project. Please feel free to forward this message to a more > appropriate list or person. For questions please email > pydata-cookbook at numfocus.org. > Katy Huff and myself are starting a project to build a cookbook of advanced > material for the PyData community. The cookbook will be published by > Addison-Wesley. We have invited a number of contributors to see if such a > project would have some interest and received overwhelmingly positive > feedback. > The book will cover several major topics, organized as such, with some sample > packages: > - IDE: IPython/Jupyter > - Data Structures / Numerics: NumPy, Pandas, Xray, PyTables > - Viz: Matplotlib, Bokeh, Seaborn, yt > - Algorithms / Science: SciPy, Scikit-learn, Scikit-image, statsmodels, sympy, > gensim > - Performance / Scale: Cython, Numexpr, Numba, Dask, pyspark > We expect each submission to be about 15 - 20 pages describing an example of > the power of each library. While we have reached out to the projects about > putting each submission together we are happy to accept chapters for libraries > we did not initially identify. > To facilitate the book we have put together a repository for collecting and > reviewing submissions at https://github.com/pydata/pydata-cookbook . We are > asking for submissions in rst but would appreciate any other files, such as > jupyter notebooks or code, for a digital appendix as well. > If you read this far and are interested in contributing. The proposed schedule > is the following: > Sept 1: Submit a pull request with a title, abstract and author list for the > submission. > Nov 15: Submit a completed chapter. > Dec 31: Reviews for chapters finished. > Jan 31: All chapter revisions due. > Thanks for you time! From emmanuelle.gouillart at nsup.org Mon Aug 29 17:38:18 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Mon, 29 Aug 2016 23:38:18 +0200 Subject: Task board In-Reply-To: <1472501868.510757.709588497.3AE0E834@webmail.messagingengine.com> References: <1472501868.510757.709588497.3AE0E834@webmail.messagingengine.com> Message-ID: <20160829213818.GE1302378@phare.normalesup.org> Hi St??fan, thanks for continuing the discussion on this important subject. I would reformulate your two points as 1) social aspects/community management and 2) technical tools and processes. In my opinion, we need a little bit of both. Dashboards can be useful if they save time and provide meaningful information that would be painful to retrieve otherwise. One should nevertheless be wary of too many metrics and quantitative indices (a problem that cripples the creativity of scientific research!): it is sometimes very tempting to merge two small PRs instead of spending time on a single difficult one. I don't have much to say about the 2nd point since I don't know the tool. For the 1st point, here are some ideas and suggestions from the top of my head - assigning / self-assigning PRs might be a good idea, as Juan suggested - when a PR is stalling and the contributor is not responding, we should either take over if possible, or close it after some warnings. - keeping a good balance between the number of active contributors and active reviewers is hard. Recently several people have contributed several PRs, demonstrating an expertise in some domain of image processing. Maybe we should ask them whether they would be willing to review PRs and be more active in including these persons. - in the core team, maybe we should say more explicitely when we are or are not available (announce it somewhere? have a google calendar?). I know that there are periods of time where I can't spend any time on scikit-image, it can be weeks or even months. If the rest of the team had such information for every core member, it would save time because someone else could try to take over. We could also have pairs of people with similar expertise (segmentation, computer vision, architecture, etc.), who could work in pairs and replace the other person when one is not available. - we could take turns to be in charge of checking the global advance of PRs. It's a pain of a job, but if it's one week every two months it's not so bad. Here are my 2 cents. I think it's a question of focussing our resources better, and maybe empowering new people, because I'm not sure we can spend much more time on the reviewing process. Cheers, Emma On Mon, Aug 29, 2016 at 01:17:48PM -0700, Stefan van der Walt wrote: > Hi, everyone > As Juan mentioned recently, it's becoming harder to keep track of the > motion of the project as a whole. Sometimes, tickets lounge unattended > for an unacceptable long time. > I can think of two main routes for improving the situation: > 1) Improve our team structure, so that individuals take responsibility > for moving certain aspects of the project forward. > 2) Processes / systems to help us get a grasp on the current state of > things > I have some ideas around (1) that need fleshing out, but in the mean > time I was looking at http://zube.io to address part of (2). > Do you have any experience with this system? Zube can be compared > against HuBoard, gh-board, and ZenHub. A test scikit-image board is > here: https://zube.io/projects/4670/kanban (it's vanilla, I haven't > done anything with it yet) > Let me hear your thoughts. > St??fan From siqueiraaf at gmail.com Tue Aug 30 09:29:09 2016 From: siqueiraaf at gmail.com (Alexandre Fioravante de Siqueira) Date: Tue, 30 Aug 2016 06:29:09 -0700 (PDT) Subject: PyData Community Cookbook - August Update In-Reply-To: <1472501613.509939.709586801.1704EAF6@webmail.messagingengine.com> References: <1472501613.509939.709586801.1704EAF6@webmail.messagingengine.com> Message-ID: <88f1b8ed-4b37-4de4-af09-4cbb2ea7e7d5@googlegroups.com> Hi all, I'd be glad to contribute, if you're still searching. I could use some previous written material I have here. If it is ok, please tell me what I need to do. Kind regards, Alex Em segunda-feira, 29 de agosto de 2016 22:13:56 UTC+2, stefanv escreveu: > > Hi everyone > > Is anyone interested in writing a scikit-image chapter for the following > book? > > St?fan > > ----- Original message ----- > From: Andy Ray Terrel > > Subject: PyData Community Cookbook - August Update > Date: Sat, 20 Aug 2016 07:14:58 -0500 > > Hello everyone, > > You are receiving this email because you were either invited and committed > to join our project. Please feel free to forward this message to a more > appropriate list or person. For questions please email > pydata-... at numfocus.org . > > Katy Huff and myself are starting a project to build a cookbook of > advanced material for the PyData community. The cookbook will be published > by Addison-Wesley. We have invited a number of contributors to see if such > a project would have some interest and received overwhelmingly positive > feedback. > > The book will cover several major topics, organized as such, with some > sample packages: > > - IDE: IPython/Jupyter > - Data Structures / Numerics: NumPy, Pandas, Xray, PyTables > - Viz: Matplotlib, Bokeh, Seaborn, yt > - Algorithms / Science: SciPy, Scikit-learn, Scikit-image, statsmodels, > sympy, gensim > - Performance / Scale: Cython, Numexpr, Numba, Dask, pyspark > > > We expect each submission to be about 15 - 20 pages describing an example > of the power of each library. While we have reached out to the projects > about putting each submission together we are happy to accept chapters for > libraries we did not initially identify. > > To facilitate the book we have put together a repository for collecting > and reviewing submissions at https://github.com/pydata/pydata-cookbook . > We are asking for submissions in rst but would appreciate any other files, > such as jupyter notebooks or code, for a digital appendix as well. > > If you read this far and are interested in contributing. The proposed > schedule is the following: > > Sept 1: Submit a pull request with a title, abstract and author list for > the submission. > Nov 15: Submit a completed chapter. > Dec 31: Reviews for chapters finished. > Jan 31: All chapter revisions due. > > Thanks for you time! > > > -- > Andy R. Terrel, PhD > President, NumFOCUS > an... at numfocus.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From drkoundinyadesiraju at gmail.com Tue Aug 30 03:56:06 2016 From: drkoundinyadesiraju at gmail.com (Koundinya Desiraju) Date: Tue, 30 Aug 2016 07:56:06 +0000 Subject: IHC Image color deconvolution In-Reply-To: <5394a2f0-98a1-4254-ac14-851e9c956bb7@googlegroups.com> References: <74882dde-6af5-4cb8-a02d-debd5e2e1678@googlegroups.com> <5394a2f0-98a1-4254-ac14-851e9c956bb7@googlegroups.com> Message-ID: Thank you Cedric. That helped a lot. Regards, Koundinya On Fri, Aug 26, 2016 at 9:47 AM Cedric Espenel wrote: > Hi Koundinya, > > I'm not sure if that will answer your question but if you try: > > from matplotlib.colors import LinearSegmentedColormap > cmap_Hema = LinearSegmentedColormap.from_list('mycmap', ['white', 'navy']) > cmap_DAB = LinearSegmentedColormap.from_list('mycmap', ['white', > 'saddlebrown']) > cmap_Eosin = LinearSegmentedColormap.from_ > > list('mycmap', ['darkviolet', > 'white']) > > You won't be able to get back to the original color but it will do a descent job: > > > > > > > > > > > > > Sincerely, > > Cedric > > > On Monday, August 22, 2016 at 10:40:06 PM UTC-7, Koundinya Desiraju wrote: > >> In this tutorial, >> http://scikit-image.org/docs/dev/auto_examples/color_exposure/plot_ihc_color_separation.html#sphx-glr-auto-examples-color-exposure-plot-ihc-color-separation-py >> >> After color deconvolution the haematoxylin and DAB channels were plotted >> in grayscale but I want to show them in respective colors. For example, I >> want to show DAB channel in brown. Can anyone kindly post How to do that? >> >> Thanks, >> Koundinya >> > -- > 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/yumvSsa7irc/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/5394a2f0-98a1-4254-ac14-851e9c956bb7%40googlegroups.com > > . > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Tue Aug 30 13:06:42 2016 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Tue, 30 Aug 2016 10:06:42 -0700 Subject: Fwd: PyData Community Cookbook - August Update In-Reply-To: <20160829204435.GC1302378@phare.normalesup.org> References: <1472501613.509939.709586801.1704EAF6@webmail.messagingengine.com> <20160829204435.GC1302378@phare.normalesup.org> Message-ID: <1472576802.757608.710583985.061974DE@webmail.messagingengine.com> On Mon, Aug 29, 2016, at 13:44, Emmanuelle Gouillart wrote: > is it something that we could re-use for the documentation of > scikit-image, in the user guide for example? Good question! Let's ask Andy (on CC). St?fan From stefanv at berkeley.edu Tue Aug 30 13:26:28 2016 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Tue, 30 Aug 2016 10:26:28 -0700 Subject: Task board In-Reply-To: <20160829213818.GE1302378@phare.normalesup.org> References: <1472501868.510757.709588497.3AE0E834@webmail.messagingengine.com> <20160829213818.GE1302378@phare.normalesup.org> Message-ID: <1472577988.761451.710591665.5D8E3C44@webmail.messagingengine.com> Hi Emmanuelle On Mon, Aug 29, 2016, at 14:38, Emmanuelle Gouillart wrote: > In my opinion, we need a little bit of both. Dashboards can be useful if > they save time and provide meaningful information that would be painful > to retrieve otherwise. One should nevertheless be wary of too many > metrics and quantitative indices (a problem that cripples the > creativity of scientific research!): it is sometimes very tempting to > merge two small PRs instead of spending time on a single difficult one. What I liked about Zube is that it has the potential to give you a good "bird's eye view" of PRs. We could probably achieve the same using (tags + some script), or (tags + gh-board). But it's good to know what's being worked on, what's on the back-burner, etc. in one glance. I don't care too much about metrics and burndown charts etc., which I think are less applicable to a community driven project. > - when a PR is stalling and the contributor is not responding, we should > either take over if possible, or close it after some warnings. We should feel confident to triage more aggressively. Open tickets that hang around also sap resources, in making it harder to find the right things to work on when you only have a little bit of time. > - in the core team, maybe we should say more explicitely when we are or > are not available (announce it somewhere? have a google calendar?). I think this ties in with your next point. It's hard to track calendars; perhaps more practical is to track commitment? There is already a (dangerous) notion of "first person to comment essentially owns the review for the PR", but we should make it more explicit: both so that folks don't feel afraid to review PRs ("oh no, I'm becoming responsible for this thing!") and so that there is someone actively watching over its progress. That way, we can also easily find PRs that have no "owners". > - we could take turns to be in charge of checking the global advance of > PRs. It's a pain of a job, but if it's one week every two months it's > not so bad. I like this idea; I've been wondering how we could move "ownership" of the project around to create better focus and more autonomy, and this may be a good, gentle start to that. I'd be curious how others felt about this idea? > Here are my 2 cents. I think it's a question of focussing our resources > better, and maybe empowering new people, because I'm not sure we can > spend much more time on the reviewing process. Growing the core team is crucial. Our user base is growing nicely, but that is not helpful unless we convert a certain percentage of those users to contributors. And it should be clear to contributors that reviewing is a priority and a good way to become involved (everyone wants to code, though :). We have a document (http://scikit-image.org/docs/stable/contribute.html) that invites users to contribute, but we can simplify those instructions for newcomers, and also add a "Please help us review some code" button on the front page? St?fan From stefanv at berkeley.edu Tue Aug 30 13:31:05 2016 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Tue, 30 Aug 2016 10:31:05 -0700 Subject: IHC Image color deconvolution In-Reply-To: References: <74882dde-6af5-4cb8-a02d-debd5e2e1678@googlegroups.com> <5394a2f0-98a1-4254-ac14-851e9c956bb7@googlegroups.com> Message-ID: <1472578265.762202.710608801.7D46FF12@webmail.messagingengine.com> On Tue, Aug 30, 2016, at 00:56, Koundinya Desiraju wrote: > Thank you Cedric. That helped a lot. Would you like to add this to the gallery example, so that other users can do the same? St?fan -------------- next part -------------- An HTML attachment was scrubbed... URL: From nadavh.horesh at gmail.com Tue Aug 30 05:08:38 2016 From: nadavh.horesh at gmail.com (Nadav Horesh) Date: Tue, 30 Aug 2016 12:08:38 +0300 Subject: Interactive image processing in jupyter notebook In-Reply-To: References: Message-ID: I am trying to find a *working* notebook showing interactive image processing using ipywidget "interact" function. I found only an outdated notebook "Image Processing with skimage". Is there an example I can really use? Nadav -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Tue Aug 30 19:54:09 2016 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Tue, 30 Aug 2016 16:54:09 -0700 Subject: Task board In-Reply-To: References: <1472501868.510757.709588497.3AE0E834@webmail.messagingengine.com> <20160829213818.GE1302378@phare.normalesup.org> <1472577988.761451.710591665.5D8E3C44@webmail.messagingengine.com> Message-ID: <1472601249.1617176.710940585.4C1ED035@webmail.messagingengine.com> Hi Johannes On Tue, Aug 30, 2016, at 12:58, Johannes Sch?nberger wrote: > I agree that Github does not provide a good overview of active/passive > issues. I am overwhelmed by the amount of issues and, usually, after a > week of scikit-image "abstinence" :-), I have to start from scratch to > find the relevant issues. Tags don't really help me in this regard > either... Did you look at the proposed Zube (or the alternatives)? I'd be curious to hear what you think. > > We have a document (http://scikit-image.org/docs/stable/contribute.html) > > that invites users to contribute, but we can simplify those instructions > > for newcomers, and also add a "Please help us review some code" button > > on the front page? > > +1, In my opinion, reviewing is almost more important than writing the > code. With the current system, Github only "rewards" people who > contribute code and, I think, this is part of the problem. With every > commit, people get credit in the form of # commits or # lines of code and > Github shows the stats nicely in the profile or the project graphs. Maybe > there is a way to create an equivalent for the reviewing process, e.g., # > comments and # merged PRs. > > What do people think about this idea? We can extend our release script to pull that information from GitHub. Would it be helpful to credit with new releases, or should this come as more continuous feedback, e.g. a weekly mail to the list with statistics? St?fan From nadavh.horesh at gmail.com Tue Aug 30 14:08:35 2016 From: nadavh.horesh at gmail.com (Nadav Horesh) Date: Tue, 30 Aug 2016 21:08:35 +0300 Subject: Interactive image processing in jupyter notebook In-Reply-To: <08237d17-b9f3-4168-a6c8-bf8b287a20e6@Spark> References: <08237d17-b9f3-4168-a6c8-bf8b287a20e6@Spark> Message-ID: Thanks, it is what I am looking for. Nadav On Aug 30, 2016 4:34 PM, "Juan Nunez-Iglesias" wrote: > Hi Nadav, > > Have a look at the filters lesson in github.com/scikit-image/ > skimage-tutorials. It's not a "real" image processing application, but > rather an illustration, but it should be enough of a template for you to > modify it. > > Juan. > > > On 30 Aug 2016, 7:08 PM +1000, Nadav Horesh , > wrote: > > I am trying to find a *working* notebook showing interactive image > processing using ipywidget "interact" function. I found only an outdated > notebook "Image Processing with skimage". > Is there an example I can really use? > > Nadav > > -- > 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%2BoBP_vBxk4HgbgWLdq_RxXu35%2BqU8UD- > DY0AyutivxL%3DQqwUQ%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/08237d17-b9f3-4168-a6c8-bf8b287a20e6%40Spark > > . > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From emmanuelle.gouillart at nsup.org Tue Aug 30 15:22:54 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Tue, 30 Aug 2016 21:22:54 +0200 Subject: Fwd: PyData Community Cookbook - August Update In-Reply-To: <1472576802.757608.710583985.061974DE@webmail.messagingengine.com> References: <1472501613.509939.709586801.1704EAF6@webmail.messagingengine.com> <20160829204435.GC1302378@phare.normalesup.org> <1472576802.757608.710583985.061974DE@webmail.messagingengine.com> Message-ID: <20160830192254.GA1722536@phare.normalesup.org> Probably we would not include the chapter as published on the website, the idea would be more to take some of the materials for the user guide. On Tue, Aug 30, 2016 at 10:06:42AM -0700, Stefan van der Walt wrote: > On Mon, Aug 29, 2016, at 13:44, Emmanuelle Gouillart wrote: > > is it something that we could re-use for the documentation of > > scikit-image, in the user guide for example? > Good question! Let's ask Andy (on CC). > St??fan From jsch at demuc.de Tue Aug 30 15:58:43 2016 From: jsch at demuc.de (=?utf-8?Q?Johannes_Sch=C3=B6nberger?=) Date: Tue, 30 Aug 2016 21:58:43 +0200 Subject: Task board In-Reply-To: <1472577988.761451.710591665.5D8E3C44@webmail.messagingengine.com> References: <1472501868.510757.709588497.3AE0E834@webmail.messagingengine.com> <20160829213818.GE1302378@phare.normalesup.org> <1472577988.761451.710591665.5D8E3C44@webmail.messagingengine.com> Message-ID: Hi, Please, find my comments inline. >> In my opinion, we need a little bit of both. Dashboards can be useful if >> they save time and provide meaningful information that would be painful >> to retrieve otherwise. One should nevertheless be wary of too many >> metrics and quantitative indices (a problem that cripples the >> creativity of scientific research!): it is sometimes very tempting to >> merge two small PRs instead of spending time on a single difficult one. > > What I liked about Zube is that it has the potential to give you a good > "bird's eye view" of PRs. We could probably achieve the same using > (tags + some script), or (tags + gh-board). But it's good to know > what's being worked on, what's on the back-burner, etc. in one glance. > I don't care too much about metrics and burndown charts etc., which I > think are less applicable to a community driven project. I agree that Github does not provide a good overview of active/passive issues. I am overwhelmed by the amount of issues and, usually, after a week of scikit-image "abstinence" :-), I have to start from scratch to find the relevant issues. Tags don't really help me in this regard either... >> - when a PR is stalling and the contributor is not responding, we should >> either take over if possible, or close it after some warnings. > > We should feel confident to triage more aggressively. Open tickets that > hang around also sap resources, in making it harder to find the right > things to work on when you only have a little bit of time. +1, there should be a cleanup of old issues that are stale for months if not years. >> - in the core team, maybe we should say more explicitely when we are or >> are not available (announce it somewhere? have a google calendar?). > > I think this ties in with your next point. It's hard to track > calendars; perhaps more practical is to track commitment? There is > already a (dangerous) notion of "first person to comment essentially > owns the review for the PR", but we should make it more explicit: both > so that folks don't feel afraid to review PRs ("oh no, I'm becoming > responsible for this thing!") and so that there is someone actively > watching over its progress. That way, we can also easily find PRs that > have no "owners". > >> - we could take turns to be in charge of checking the global advance of >> PRs. It's a pain of a job, but if it's one week every two months it's >> not so bad. > > I like this idea; I've been wondering how we could move "ownership" of > the project around to create better focus and more autonomy, and this > may be a good, gentle start to that. > > I'd be curious how others felt about this idea? > >> Here are my 2 cents. I think it's a question of focussing our resources >> better, and maybe empowering new people, because I'm not sure we can >> spend much more time on the reviewing process. > > Growing the core team is crucial. Our user base is growing nicely, but > that is not helpful unless we convert a certain percentage of those > users to contributors. And it should be clear to contributors that > reviewing is a priority and a good way to become involved (everyone > wants to code, though :). > > We have a document (http://scikit-image.org/docs/stable/contribute.html) > that invites users to contribute, but we can simplify those instructions > for newcomers, and also add a "Please help us review some code" button > on the front page? +1, In my opinion, reviewing is almost more important than writing the code. With the current system, Github only "rewards" people who contribute code and, I think, this is part of the problem. With every commit, people get credit in the form of # commits or # lines of code and Github shows the stats nicely in the profile or the project graphs. Maybe there is a way to create an equivalent for the reviewing process, e.g., # comments and # merged PRs. What do people think about this idea? Best, Johannes From emmanuelle.gouillart at nsup.org Tue Aug 30 16:42:38 2016 From: emmanuelle.gouillart at nsup.org (Emmanuelle Gouillart) Date: Tue, 30 Aug 2016 22:42:38 +0200 Subject: Inclusive community statement In-Reply-To: <1472518065.560834.709801233.3F5E5296@webmail.messagingengine.com> References: <1472518065.560834.709801233.3F5E5296@webmail.messagingengine.com> Message-ID: <20160830204238.GC1722536@phare.normalesup.org> Hi St??fan, I also think that this document would be more appropriate than a generic code of conduct. Maybe we could also add a link to http://scikit-image.org/docs/stable/contribute.html so that people can get started? Best Emma On Mon, Aug 29, 2016 at 05:47:45PM -0700, Stefan van der Walt wrote: > Dear contributors and users > You may know that I am not very fond of Codes of Conduct in general. I > think they are well intentioned, but they are also often aggressive, use > words more commonly associated with law enforcement, and may leave one > feeling a tad scared and unenthusiastic. > At the same time, I do think it is important to be inviting to newcomers > of all groups, and to make that clear on our website. > What would you say to a "Community Guidelines" or "How We Work > (together)" statement on the scikit-image front page? > Something along the lines of: > "We welcome each and every contributor to scikit-image. Our aim is > enthusiastic and productive collaboration, to build an excellent > software library, and to have a ton of fun doing it. We encourage one > another to be gentle in criticism of others' work, humble in > acknowledging our own mistakes, and generous in our praise. > If you ever feel like you are not being treated as well as you should, > please get in touch with one of the project leads. We are committed to > making this community a safe and welcome space." > Best regards > St??fan From jni.soma at gmail.com Tue Aug 30 09:34:07 2016 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Tue, 30 Aug 2016 23:34:07 +1000 Subject: Interactive image processing in jupyter notebook In-Reply-To: References: Message-ID: <08237d17-b9f3-4168-a6c8-bf8b287a20e6@Spark> Hi Nadav, Have a look at the filters lesson in github.com/scikit-image/skimage-tutorials. It's not a "real" image processing application, but rather an illustration, but it should be enough of a template for you to modify it. Juan. On 30 Aug 2016, 7:08 PM +1000, Nadav Horesh , wrote: > > I am trying to find a *working* notebook showing interactive image processing using ipywidget "interact" function. I found only an outdated notebook "Image Processing with skimage". > Is there an example I can really use? > > > Nadav > > > > > -- > 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 (mailto:scikit-image+unsubscribe at googlegroups.com). > To post to this group, send email to scikit-image at googlegroups.com (mailto:scikit-image at googlegroups.com). > To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/CA%2BoBP_vBxk4HgbgWLdq_RxXu35%2BqU8UD-DY0AyutivxL%3DQqwUQ%40mail.gmail.com (https://groups.google.com/d/msgid/scikit-image/CA%2BoBP_vBxk4HgbgWLdq_RxXu35%2BqU8UD-DY0AyutivxL%3DQqwUQ%40mail.gmail.com?utm_medium=email&utm_source=footer). > For more options, visit https://groups.google.com/d/optout. -------------- next part -------------- An HTML attachment was scrubbed... URL: From siqueiraaf at gmail.com Wed Aug 31 13:41:50 2016 From: siqueiraaf at gmail.com (Alexandre Fioravante de Siqueira) Date: Wed, 31 Aug 2016 10:41:50 -0700 (PDT) Subject: Fwd: PyData Community Cookbook - August Update In-Reply-To: References: <1472501613.509939.709586801.1704EAF6@webmail.messagingengine.com> <20160829204435.GC1302378@phare.normalesup.org> <1472576802.757608.710583985.061974DE@webmail.messagingengine.com> <20160830192254.GA1722536@phare.normalesup.org> Message-ID: Dear all, have you figured it out? The deadline is tomorrow, and I would really like to participate. Thanks! Alex Em quarta-feira, 31 de agosto de 2016 15:37:06 UTC+2, Egor Panfilov escreveu: > > Sounds interesting, and I'd be glad to contribute. Although, it is not > clear what kind of content do authors expect. I believe that the vast > majority of `skimage` functionality is already well-described in the > documentation and conference notebooks. > If someone of `skimage` original authors could prepare a draft of the > planned chapter (i.e. table of contents), I think it would be quite easy to > make it happen soon and in the best possible way. > > Regards, > Egor > > 2016-08-30 22:22 GMT+03:00 Emmanuelle Gouillart: > >> Probably we would not include the chapter as published on the website, >> the idea would be more to take some of the materials for the user guide. >> >> On Tue, Aug 30, 2016 at 10:06:42AM -0700, Stefan van der Walt wrote: >> > On Mon, Aug 29, 2016, at 13:44, Emmanuelle Gouillart wrote: >> > > is it something that we could re-use for the documentation of >> > > scikit-image, in the user guide for example? >> >> > Good question! Let's ask Andy (on CC). >> >> > St?fan >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Wed Aug 31 16:05:11 2016 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Wed, 31 Aug 2016 13:05:11 -0700 Subject: Inclusive community statement In-Reply-To: <20160830204238.GC1722536@phare.normalesup.org> References: <1472518065.560834.709801233.3F5E5296@webmail.messagingengine.com> <20160830204238.GC1722536@phare.normalesup.org> Message-ID: <1472673911.2661144.711957689.05E255E9@webmail.messagingengine.com> On Tue, Aug 30, 2016, at 13:42, Emmanuelle Gouillart wrote: > I also think that this document would be more appropriate than a generic > code of conduct. Maybe we could also add a link to > http://scikit-image.org/docs/stable/contribute.html so that people can > get started? I've made an initial PR here: https://github.com/scikit-image/scikit-image-web/pull/36 Comments welcome! St?fan From jalopcar at gmail.com Wed Aug 31 17:02:04 2016 From: jalopcar at gmail.com (Jaime Lopez Carvajal) Date: Wed, 31 Aug 2016 14:02:04 -0700 (PDT) Subject: Migration of mailing list to @python.org In-Reply-To: References: Message-ID: <43ed7fcb-3e2e-4867-abe0-d27b83cc8d9b@googlegroups.com> Hi Stefan, Do you have a possible date when you are going to activate the scikit-image version on mailman python? Because I check it and it is currently empty. BTW, I dont have any rush, I just want to know. Thank in advance, Jaime On Wednesday, May 18, 2016 at 6:36:07 PM UTC-5, stefanv wrote: > > Hi, everyone > > I would like to migrate the mailing list over to mailman on Python.org. > We're currently on Google Groups, but we don't have good archives or > predictable permalinks based on message-id, and message export is a pain > (I've scraped the entire list content, but needless to say that is less > than ideal). > > I will port the content and automatically subscribe existing members. > > Let me know if you have any objections. > > Best regards > St?fan > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Wed Aug 31 17:52:29 2016 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Wed, 31 Aug 2016 14:52:29 -0700 Subject: Migration of mailing list to @python.org In-Reply-To: <43ed7fcb-3e2e-4867-abe0-d27b83cc8d9b@googlegroups.com> References: <43ed7fcb-3e2e-4867-abe0-d27b83cc8d9b@googlegroups.com> Message-ID: <1472680349.2684017.712060281.1B51B7D3@webmail.messagingengine.com> Hi Jaime On Wed, Aug 31, 2016, at 14:02, Jaime Lopez Carvajal wrote: > Do you have a possible date when you are going to activate the scikit- image version on mailman python? > Because I check it and it is currently empty. > BTW, I dont have any rush, I just want to know. Thanks for the reminder---I'll proceed to back up the Google Groups to that archive, and then switch everyone over. St?fan From stefanv at berkeley.edu Wed Aug 31 17:54:04 2016 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Wed, 31 Aug 2016 14:54:04 -0700 Subject: Fwd: PyData Community Cookbook - August Update In-Reply-To: References: <1472501613.509939.709586801.1704EAF6@webmail.messagingengine.com> <20160829204435.GC1302378@phare.normalesup.org> <1472576802.757608.710583985.061974DE@webmail.messagingengine.com> <20160830192254.GA1722536@phare.normalesup.org> Message-ID: <1472680444.2684150.712061369.2AC87F0C@webmail.messagingengine.com> Hi Alex On Wed, Aug 31, 2016, at 10:41, Alexandre Fioravante de Siqueira wrote: > have you figured it out? The deadline is tomorrow, and I would really > like to participate. Would you please submit an initial pull request on the team's behalf? You can add me, Egor, Emmanuelle, and anyone else who expresses interest here as co-authors. Emmanuelle, I will double check that the chapter is fully open when it is done so that we can remix parts for the user guide. Thanks St?fan From jalopcar at gmail.com Wed Aug 31 18:30:50 2016 From: jalopcar at gmail.com (Jaime Lopez Carvajal) Date: Wed, 31 Aug 2016 15:30:50 -0700 (PDT) Subject: Migration of mailing list to @python.org In-Reply-To: <1472680349.2684017.712060281.1B51B7D3@webmail.messagingengine.com> References: <43ed7fcb-3e2e-4867-abe0-d27b83cc8d9b@googlegroups.com> <1472680349.2684017.712060281.1B51B7D3@webmail.messagingengine.com> Message-ID: <6c918d86-af2c-4d5f-8821-301695879ce1@googlegroups.com> Hi Stefan, I know you must be working on several topics at same time, I wish to have your commitment. Best wishes, Jaime On Wednesday, August 31, 2016 at 4:52:31 PM UTC-5, stefanv wrote: > > Hi Jaime > > On Wed, Aug 31, 2016, at 14:02, Jaime Lopez Carvajal wrote: > > Do you have a possible date when you are going to activate the scikit- > image version on mailman python? > > Because I check it and it is currently empty. > > BTW, I dont have any rush, I just want to know. > > Thanks for the reminder---I'll proceed to back up the Google Groups to > that archive, and then switch everyone over. > > St?fan > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Wed Aug 31 19:12:24 2016 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Wed, 31 Aug 2016 16:12:24 -0700 Subject: Distance Estimation In-Reply-To: References: Message-ID: <1472685144.113590.712117217.1B48040B@webmail.messagingengine.com> Hi Chris On Sun, Aug 28, 2016, at 17:31, Chris Spencer wrote: > Is there any algorithm in scikit-image that I could use to train a predictor that could estimate the distance at each pixel in an image? > I've gone through all the examples, and none of them seemed to directly apply. The image segmentation example seemed to be the closest, but that didn't use supervised learning, so I wasn't sure how I could adapt it's code. Could you explain what you mean by "estimate the distance"? St?fan From stefanv at berkeley.edu Wed Aug 31 19:35:52 2016 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Wed, 31 Aug 2016 16:35:52 -0700 Subject: IHC Image color deconvolution In-Reply-To: <74882dde-6af5-4cb8-a02d-debd5e2e1678@googlegroups.com> References: <74882dde-6af5-4cb8-a02d-debd5e2e1678@googlegroups.com> Message-ID: <1472686552.117268.712132521.3AE3410E@webmail.messagingengine.com> On Mon, Aug 22, 2016, at 22:40, Koundinya Desiraju wrote: > In this tutorial, > http://scikit-image.org/docs/dev/auto_examples/color_exposure/plot_ihc_color_separation.html#sphx-glr-auto-examples-color-exposure-plot-ihc-color-separation-py > > After color deconvolution the haematoxylin and DAB channels were > plotted in grayscale but I want to show them in respective colors. For > example, I want to show DAB channel in brown. Can anyone kindly post > How to do that? Cedric submitted a PR to add this to the examples gallery: https://github.com/scikit-image/scikit-image/pull/2279 Please review! Thanks St?fan -------------- next part -------------- An HTML attachment was scrubbed... URL: From multicolor.mood at gmail.com Wed Aug 31 09:37:01 2016 From: multicolor.mood at gmail.com (Egor Panfilov) Date: Wed, 31 Aug 2016 16:37:01 +0300 Subject: Fwd: PyData Community Cookbook - August Update In-Reply-To: <20160830192254.GA1722536@phare.normalesup.org> References: <1472501613.509939.709586801.1704EAF6@webmail.messagingengine.com> <20160829204435.GC1302378@phare.normalesup.org> <1472576802.757608.710583985.061974DE@webmail.messagingengine.com> <20160830192254.GA1722536@phare.normalesup.org> Message-ID: Sounds interesting, and I'd be glad to contribute. Although, it is not clear what kind of content do authors expect. I believe that the vast majority of `skimage` functionality is already well-described in the documentation and conference notebooks. If someone of `skimage` original authors could prepare a draft of the planned chapter (i.e. table of contents), I think it would be quite easy to make it happen soon and in the best possible way. Regards, Egor 2016-08-30 22:22 GMT+03:00 Emmanuelle Gouillart < emmanuelle.gouillart at nsup.org>: > Probably we would not include the chapter as published on the website, > the idea would be more to take some of the materials for the user guide. > > On Tue, Aug 30, 2016 at 10:06:42AM -0700, Stefan van der Walt wrote: > > On Mon, Aug 29, 2016, at 13:44, Emmanuelle Gouillart wrote: > > > is it something that we could re-use for the documentation of > > > scikit-image, in the user guide for example? > > > Good question! Let's ask Andy (on CC). > > > 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/20160830192254.GA1722536%40phare.normalesup.org. > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From chrisspen at gmail.com Wed Aug 31 21:29:38 2016 From: chrisspen at gmail.com (Chris Spencer) Date: Wed, 31 Aug 2016 21:29:38 -0400 Subject: Distance Estimation In-Reply-To: <1472685144.113590.712117217.1B48040B@webmail.messagingengine.com> References: <1472685144.113590.712117217.1B48040B@webmail.messagingengine.com> Message-ID: Given a JPG image of a scene, convert that into a depth map, where each pixel is associated with a discrete distance estimate. On Wed, Aug 31, 2016 at 7:12 PM, Stefan van der Walt wrote: > Hi Chris > > On Sun, Aug 28, 2016, at 17:31, Chris Spencer wrote: > > Is there any algorithm in scikit-image that I could use to train a > predictor that could estimate the distance at each pixel in an image? > > > I've gone through all the examples, and none of them seemed to directly > apply. The image segmentation example seemed to be the closest, but that > didn't use supervised learning, so I wasn't sure how I could adapt it's > code. > > Could you explain what you mean by "estimate the distance"? > > St?fan > > -- > You received this message because you are subscribed to a topic in the > Google Groups "scikit-image" group. > To unsubscribe from this topic, visit https://groups.google.com/d/ > topic/scikit-image/qvGm0zOv2rc/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 an email to scikit-image at googlegroups.com. > To view this discussion on the web, visit https://groups.google.com/d/ > msgid/scikit-image/1472685144.113590.712117217.1B48040B% > 40webmail.messagingengine.com. > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From chrisspen at gmail.com Wed Aug 31 21:30:20 2016 From: chrisspen at gmail.com (Chris Spencer) Date: Wed, 31 Aug 2016 21:30:20 -0400 Subject: Distance Estimation In-Reply-To: References: <1472685144.113590.712117217.1B48040B@webmail.messagingengine.com> Message-ID: Essentially, what's described here: http://www.cs.cornell.edu/~asaxena/learningdepth/ On Wed, Aug 31, 2016 at 9:29 PM, Chris Spencer wrote: > Given a JPG image of a scene, convert that into a depth map, where each > pixel is associated with a discrete distance estimate. > > On Wed, Aug 31, 2016 at 7:12 PM, Stefan van der Walt > wrote: > >> Hi Chris >> >> On Sun, Aug 28, 2016, at 17:31, Chris Spencer wrote: >> > Is there any algorithm in scikit-image that I could use to train a >> predictor that could estimate the distance at each pixel in an image? >> >> > I've gone through all the examples, and none of them seemed to directly >> apply. The image segmentation example seemed to be the closest, but that >> didn't use supervised learning, so I wasn't sure how I could adapt it's >> code. >> >> Could you explain what you mean by "estimate the distance"? >> >> St?fan >> >> -- >> You received this message because you are subscribed to a topic in the >> Google Groups "scikit-image" group. >> To unsubscribe from this topic, visit https://groups.google.com/d/to >> pic/scikit-image/qvGm0zOv2rc/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 an email to scikit-image at googlegroups.com. >> To view this discussion on the web, visit https://groups.google.com/d/ms >> gid/scikit-image/1472685144.113590.712117217.1B48040B%40webm >> ail.messagingengine.com. >> For more options, visit https://groups.google.com/d/optout. >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: