From jni.soma at gmail.com Fri Jul 1 10:35:39 2016 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Fri, 1 Jul 2016 10:35:39 -0400 Subject: Import error when importing from skimage.transform In-Reply-To: <98b2c001-1f06-482f-b800-6e09438e6b86@googlegroups.com> References: <98b2c001-1f06-482f-b800-6e09438e6b86@googlegroups.com> Message-ID: Hi Barbara, Can you look at my response to the original email and post your results? https://groups.google.com/d/msgid/scikit-image/d7a8d058-2202-424e-b6b4-b4cd85c1811e%40googlegroups.com?utm_medium=email&utm_source=footer Sometimes skimage installs to a path that is *not* the path where Python looks for packages. Or sometimes you install the C extensions to the Python path but then try to import the local copy of scikit-image. It's hard to know what's happening without the diagnostics above... On Thu, Jun 30, 2016 at 4:19 PM, Barbara Collignon < barbara.collignon at gmail.com> wrote: > same issue here with python2.7+ > > On Thursday, June 23, 2016 at 8:30:36 PM UTC-4, sja... at nyu.edu wrote: >> >> The environment I'm using is a Jupyter notebook running python 3.5. I can import other packages, but importing anything from skimage.transform results in the following error: >> >> >> ImportError Traceback (most recent call last) in ()----> 1 from skimage.transform import resize >> /home/jupyter/anaconda3/envs/py35/lib/python3.5/site-packages/skimage/transform/__init__.py in ()----> 1 from .hough_transform import (hough_line, hough_line_peaks, 2 probabilistic_hough_line, hough_circle, 3 hough_ellipse) 4 from .radon_transform import radon, iradon, iradon_sart 5 from .finite_radon_transform import frt2, ifrt2 >> /home/jupyter/anaconda3/envs/py35/lib/python3.5/site-packages/skimage/transform/hough_transform.py in () 2 from scipy import ndimage as ndi 3 from .. import measure----> 4 from ._hough_transform import (_hough_circle, 5 hough_ellipse as _hough_ellipse, 6 hough_line as _hough_line, >> ImportError: cannot import name '_hough_circle' >> >> >> We've already tried uninstalling skimage, updating cython and then re-installing. Anyone else encounter this problem? >> >> -- > 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/98b2c001-1f06-482f-b800-6e09438e6b86%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 Fri Jul 1 20:38:01 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Fri, 1 Jul 2016 17:38:01 -0700 Subject: DOI in references? In-Reply-To: References: Message-ID: By all means, add them in! On Jul 1, 2016 16:05, "Fran?ois Boulogne" wrote: > Hi, > > > I have a question about the references. Is it a choice to do not put DOI > pointers when available? For my usage, I have to use a search engine to > find papers referenced in our documentation and it would be more simple > to add and use the DOI. It's also relatively short, the length is not > really a problem. > > Any comment on this? > Thanks. > > -- > Fran?ois Boulogne. > http://www.sciunto.org > GPG: 32D5F22F > > > -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image+unsubscribe at googlegroups.com. > 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/fdbfec75-3e13-adfa-ff6a-ba876ff7ae32%40sciunto.org > . > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From fboulogne at sciunto.org Fri Jul 1 19:05:24 2016 From: fboulogne at sciunto.org (=?UTF-8?Q?Fran=c3=a7ois_Boulogne?=) Date: Sat, 2 Jul 2016 01:05:24 +0200 Subject: DOI in references? Message-ID: Hi, I have a question about the references. Is it a choice to do not put DOI pointers when available? For my usage, I have to use a search engine to find papers referenced in our documentation and it would be more simple to add and use the DOI. It's also relatively short, the length is not really a problem. Any comment on this? Thanks. -- Fran?ois Boulogne. http://www.sciunto.org GPG: 32D5F22F From takowl at gmail.com Mon Jul 4 05:38:50 2016 From: takowl at gmail.com (Thomas Kluyver) Date: Mon, 4 Jul 2016 02:38:50 -0700 (PDT) Subject: Dropping support for 2.7 in 2020 In-Reply-To: References: <20160518064719.GA3031017@phare.normalesup.org> <20160518074002.GC3031017@phare.normalesup.org> <20160518175455.GA4080630@phare.normalesup.org> <20160520105049.GA3583487@phare.normalesup.org> <20160520141800.GD3583487@phare.normalesup.org> Message-ID: I'd like to revive this discussion with a bit of added context. We (principally people from IPython/Jupyter, Matplotlib, Sympy and Scikit-bio) are putting together a statement for Scientific Python community projects to signal that we're not planning to maintain Python 2 support forever. We're saying that we will end Python 2 support in or before 2020, to correspond with the end of support for Python 2.7 itself. http://python3statement.github.io/ The more projects that get on board with this, the better we can make the case that researchers and users need Python 3 to be available. Then we can all benefit from a reduced maintenance burden. So scikit-image wouldn't be making a lone stand on this - there are a number of projects already agreeing to drop Python 2 support by 2020, and we hope there will be more soon. Thanks, Thomas On Monday, 23 May 2016 04:30:21 UTC+1, Juan Nunez-Iglesias wrote: > > I would drop 2.7 sooner. NumPy/SciPy dropping it is the absolute cutoff, > but there?s no reason why we can?t jump the gun (and lead rather than > follow). Py2.7 users can make do with older releases. As St?fan mentioned, > this is not about erasing Py2.7 support, but not releasing new features on > Py2.7. Very different. I envision that we stop producing Py2.7 releases > after 0.13, but we call that an ?LTS? release which will get bugfix > backports until 2020. > > imho, with Py3.4 and especially Py3.5, Py3-only suddenly became very > attractive. My three favourite features are type annotations, keyword-only > arguments (these two together make it much easier to produce correct code > and debug), and the @ matrix multiplication operator. The latter makes > linear algebra code *so* *much* nicer to read and write, and we have our > fair share in scikit-image. For my own projects, I am now Py3.5-only, > always. > > Finally, as others have mentioned, but is worth restating: > - Conda allows user-space installs of Python versions and packages, so you > don?t ever depend on your sysadmin-controlled environment. > - It is *absolutely false* that conda packages are only useful on Windows > ? I have failed to compile scipy both on OSX and Ubuntu boxes. > - It is also *not* a requirement to download the monolithic Anaconda > distro ? with miniconda (which should be the default), you just install > precisely what you need. > - With conda-forge we now have a community-run repository of binary conda > packages. > > So, in short, the switch to Py3 is easier than ever for *all* users, some > might just not realise it yet ;), and switching to a Py3-only programming > environment is a boon to all the scikit-image devs? though again some might > not realise it yet ;). > > Juan. > > On 21 May 2016 at 12:20:38 PM, Nathaniel Smith (n... at vorpus.org > ) wrote: > > On May 20, 2016 07:30, "Michael Sarahan" > > wrote: > > I don't think this is a concern for cython or scikit-image, but many > people at bumping into the language support limit in the C++11 sense with > Python 2.7 on Windows. Since VS 2008 is the de-facto standard compiler for > Python 2.7, people are unable to use C++11 code in modules for Python 2.7. > Some people use newer compilers anyway, which sometimes works, but is > mixing runtimes, and can lead to bugs or crashes. Many people would like > to support Python 2.7 using a different compiler for the whole ecosystem. > One example is Ilastik, by folks at HHMI, using VS 2012 to have a custom > stack: https://github.com/ilastik/ilastik-build-conda > > I think getting mingwpy finished and polished is probably an easier > solution for this problem than forking the entire py27-on-windows ecosystem > :-) > > -n > -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image... at googlegroups.com . > To post to this group, send email to scikit... at googlegroups.com > . > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/CAPJVwB%3DjRQtHn9Xj0xwv3hxtDsjBvKYtJTB38ewBuZ84cNR4xw%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 Mon Jul 4 05:55:04 2016 From: takowl at gmail.com (Thomas Kluyver) Date: Mon, 4 Jul 2016 10:55:04 +0100 Subject: Dropping support for 2.7 in 2020 In-Reply-To: References: <20160518064719.GA3031017@phare.normalesup.org> <20160518074002.GC3031017@phare.normalesup.org> <20160518175455.GA4080630@phare.normalesup.org> <20160520105049.GA3583487@phare.normalesup.org> <20160520141800.GD3583487@phare.normalesup.org> Message-ID: On 4 July 2016 at 10:47, Fran?ois Boulogne wrote: > Does it mean that all new version of those libraries will support > python2.7 until 2020 or just that you can release a bugfix to already > released version supporting 2.7? > > If it's the first option, it means we can't use python3 features before > 2020 and we will be "in late" with these features. > The statement doesn't commit projects to support 2.7 until any specific date - scikit-bio already went Python 3 only with its release last month, for instance. We're agreeing to end Python 2 support by 2020, but projects are welcome to do it earlier than that. For IPython, we're planning for the 6.0 feature release (some time in 2017) to be Python 3 only, while we'll make bugfix releases of the 5.x series for longer than normal to support users on Python 2. -------------- next part -------------- An HTML attachment was scrubbed... URL: From fboulogne at sciunto.org Mon Jul 4 05:47:30 2016 From: fboulogne at sciunto.org (=?UTF-8?Q?Fran=c3=a7ois_Boulogne?=) Date: Mon, 4 Jul 2016 11:47:30 +0200 Subject: Dropping support for 2.7 in 2020 In-Reply-To: References: <20160518064719.GA3031017@phare.normalesup.org> <20160518074002.GC3031017@phare.normalesup.org> <20160518175455.GA4080630@phare.normalesup.org> <20160520105049.GA3583487@phare.normalesup.org> <20160520141800.GD3583487@phare.normalesup.org> Message-ID: Le 04/07/2016 ? 11:38, Thomas Kluyver a ?crit : > I'd like to revive this discussion with a bit of added context. We > (principally people from IPython/Jupyter, Matplotlib, Sympy and > Scikit-bio) are putting together a statement for Scientific Python > community projects to signal that we're not planning to maintain > Python 2 support forever. We're saying that we will end Python 2 > support in or before 2020, to correspond with the end of support for > Python 2.7 itself. > > http://python3statement.github.io/ > > The more projects that get on board with this, the better we can make > the case that researchers and users need Python 3 to be available. > Then we can all benefit from a reduced maintenance burden. So > scikit-image wouldn't be making a lone stand on this - there are a > number of projects already agreeing to drop Python 2 support by 2020, > and we hope there will be more soon. > Thanks for your note. Does it mean that all new version of those libraries will support python2.7 until 2020 or just that you can release a bugfix to already released version supporting 2.7? If it's the first option, it means we can't use python3 features before 2020 and we will be "in late" with these features. From silvertrumpet999 at gmail.com Mon Jul 4 20:12:16 2016 From: silvertrumpet999 at gmail.com (Josh Warner) Date: Mon, 4 Jul 2016 17:12:16 -0700 (PDT) Subject: Dropping support for 2.7 in 2020 In-Reply-To: References: <20160518064719.GA3031017@phare.normalesup.org> <20160518074002.GC3031017@phare.normalesup.org> <20160518175455.GA4080630@phare.normalesup.org> <20160520105049.GA3583487@phare.normalesup.org> <20160520141800.GD3583487@phare.normalesup.org> Message-ID: I think we should support 2.7 through end-of-life. 2020 sounds right. There are a tremendous amount of systems out there still running 2.7. I know more than one lab which standardized on 2.7 years ago, and while we're evaluating the move to 3.x it won't be without major pains. Small, niche packages which work perfectly under 2.7 break in 3.x, and they may or may not be maintained. It only takes a couple of these to render lab equipment with price tags in the 6 figures buggy, problematic, or useless in 3.x. This is problematic when you want a consistent Python experience across a lab or team, but certain pieces just won't work in 3.x. Sounding the trumpets is appropriate, as 2.7 won't be around forever. Quarterly or bi-annually it would be reasonable to send out a reminder. Three years sounds like a long time, but that's about right for this kind of transition. On Monday, July 4, 2016 at 4:55:34 AM UTC-5, Thomas Kluyver wrote: > > On 4 July 2016 at 10:47, Fran?ois Boulogne wrote: > >> Does it mean that all new version of those libraries will support >> python2.7 until 2020 or just that you can release a bugfix to already >> released version supporting 2.7? >> >> If it's the first option, it means we can't use python3 features before >> 2020 and we will be "in late" with these features. >> > > The statement doesn't commit projects to support 2.7 until any specific > date - scikit-bio already went Python 3 only with its release last month, > for instance. We're agreeing to end Python 2 support by 2020, but projects > are welcome to do it earlier than that. > > For IPython, we're planning for the 6.0 feature release (some time in > 2017) to be Python 3 only, while we'll make bugfix releases of the 5.x > series for longer than normal to support users on Python 2. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From parul1sethi at gmail.com Wed Jul 6 08:54:55 2016 From: parul1sethi at gmail.com (parul sethi) Date: Wed, 6 Jul 2016 05:54:55 -0700 (PDT) Subject: Implementing Kadir and Brady's saliency detector in skimage? Message-ID: <7132cb6e-e66f-45be-a71a-327a2e5ff7d9@googlegroups.com> Hi, I required to use Kadir and Brady's saliency detector for feature extraction process, and didn't found it's python implementation. So, i was in process of implementing the same. Will it be of interest to skimage too? I can use some advice from skimage maintainers to build it with specific suitability for skimage module. Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sid.zidane at gmail.com Thu Jul 7 03:37:16 2016 From: sid.zidane at gmail.com (Sid) Date: Thu, 7 Jul 2016 00:37:16 -0700 (PDT) Subject: Warping images using control points Message-ID: Hi I have two images of faces, the source image and the destination image. For each face, I have a set of x and y coordinates stored in two separate numpy arrays. These coordinates correspond to various facial features, as well as the four corners of the image, and points on half the length of the borders. I want to warp the features of the source image onto the destination, such that the corresponding control points in each image are aligned. I used the PiecewiseAffineTransform method, as in the example here . My code is: src_pts = # numpy array of coordinates for the source image dst_pts = # numpy array of coordinates for the destination image image = # image of dimensions (550, 420, 3) tform = skimage.transform.PiecewiseAffineTransform() tform.estimate(src_pts, dst_pts) out = skimage.transform.warp(image, tform) I get an image that is warped but also cropped. To see if I could get the code to work (in case there were errors in my control points), I tried warping the image using the same control points for the source and destination. tform.estimate(src_pts, src_pts) The output is still cropped and is also warped slightly, as can be seen in the attached images. Logically, it doesn't make sense as there should not be any warping since I am using the same points. A big difference between the example and my implementation is that the example has uniformly spaced points, whereas I have 76 points which are much more sparse. Is this the right function to achieve what I want or should I be using something else? Thanks -- Sid -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Sun Jul 10 18:41:08 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Sun, 10 Jul 2016 15:41:08 -0700 Subject: Implementing Kadir and Brady's saliency detector in skimage? In-Reply-To: <7132cb6e-e66f-45be-a71a-327a2e5ff7d9@googlegroups.com> References: <7132cb6e-e66f-45be-a71a-327a2e5ff7d9@googlegroups.com> Message-ID: Hi Parul We are happy to evaluate any PR for inclusion. Saliency detection is within scope. Best regards St?fan On Jul 6, 2016 05:54, "parul sethi" wrote: > Hi, > > I required to use Kadir and Brady's saliency detector for feature > extraction process, and didn't found it's python implementation. So, i was > in process of implementing the same. > Will it be of interest to skimage too? I can use some advice from skimage > maintainers to build it with specific suitability for skimage module. > > Thank you. > > -- > 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/7132cb6e-e66f-45be-a71a-327a2e5ff7d9%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 Mon Jul 11 15:35:14 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Mon, 11 Jul 2016 12:35:14 -0700 Subject: Warping images using control points In-Reply-To: References: Message-ID: Hi Sid Sorry, I think you've been a victim of a known inconsistency---unfortunately, one I'm not sure how to address. The transforms module uses a (x, y) coordinate convention to be consistent with most of the warping literature out there. But the rest of scikit-image uses a (row, column) convention. The following code works for me: from skimage import io, transform import numpy as np image = io.imread('image.jpg') h, w = image.shape[:2] rng = np.random.RandomState(0) xs = rng.randint(0, w - 1, 76) ys = rng.randint(0, h - 1, 76) src_pts = np.column_stack([xs, ys]) dst_pts = src_pts tform = transform.PiecewiseAffineTransform() tform.estimate(src_pts, dst_pts) out = transform.warp(image, tform) import matplotlib.pyplot as plt plt.imshow(out) plt.show() Best regards St?fan On 7 July 2016 at 00:37, Sid wrote: > Hi > > I have two images of faces, the source image and the destination image. > For each face, I have a set of x and y coordinates stored in two separate > numpy arrays. These coordinates correspond to various facial features, as > well as the four corners of the image, and points on half the length of the > borders. > > I want to warp the features of the source image onto the destination, such > that the corresponding control points in each image are aligned. I used the > PiecewiseAffineTransform method, as in the example here > > . > > My code is: > > src_pts = # numpy array of coordinates for the source image > dst_pts = # numpy array of coordinates for the destination image > > image = # image of dimensions (550, 420, 3) > > tform = skimage.transform.PiecewiseAffineTransform() > tform.estimate(src_pts, dst_pts) > > out = skimage.transform.warp(image, tform) > > > I get an image that is warped but also cropped. To see if I could get the > code to work (in case there were errors in my control points), I tried > warping the image using the same control points for the source and > destination. > > tform.estimate(src_pts, src_pts) > > The output is still cropped and is also warped slightly, as can be seen in > the attached images. Logically, it doesn't make sense as there should not > be any warping since I am using the same points. A big difference between > the example and my implementation is that the example has uniformly spaced > points, whereas I have 76 points which are much more sparse. Is this the > right function to achieve what I want or should I be using something else? > > > Thanks > > -- > Sid > > > > > > > > > > > > > > > -- > 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/e51ad552-af63-49e0-afbc-2d4b5597d5e4%40googlegroups.com > > . > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Mon Jul 11 15:09:16 2016 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Mon, 11 Jul 2016 14:09:16 -0500 Subject: Dropping support for 2.7 in 2020 In-Reply-To: References: <20160518064719.GA3031017@phare.normalesup.org> <20160518074002.GC3031017@phare.normalesup.org> <20160518175455.GA4080630@phare.normalesup.org> <20160520105049.GA3583487@phare.normalesup.org> <20160520141800.GD3583487@phare.normalesup.org> Message-ID: For what it's worth, I strongly support the statement, and would prefer to drop 2.7 support much earlier. This does *not* mean ignoring people submitting 2.7 bug reports. It means that, like Python itself, *new* versions would not support Py2.7. Bug fixes would be ported to e.g. the 0.13.x branch. This in no way interferes people with systems that "just work" and who understandably don't want to risk breaking them. Juan. On Mon, Jul 4, 2016 at 7:12 PM, Josh Warner wrote: > I think we should support 2.7 through end-of-life. 2020 sounds right. > > There are a tremendous amount of systems out there still running 2.7. I > know more than one lab which standardized on 2.7 years ago, and while we're > evaluating the move to 3.x it won't be without major pains. Small, niche > packages which work perfectly under 2.7 break in 3.x, and they may or may > not be maintained. It only takes a couple of these to render lab equipment > with price tags in the 6 figures buggy, problematic, or useless in 3.x. > This is problematic when you want a consistent Python experience across a > lab or team, but certain pieces just won't work in 3.x. > > Sounding the trumpets is appropriate, as 2.7 won't be around forever. > Quarterly or bi-annually it would be reasonable to send out a reminder. > Three years sounds like a long time, but that's about right for this kind > of transition. > > On Monday, July 4, 2016 at 4:55:34 AM UTC-5, Thomas Kluyver wrote: >> >> On 4 July 2016 at 10:47, Fran?ois Boulogne wrote: >> >>> Does it mean that all new version of those libraries will support >>> python2.7 until 2020 or just that you can release a bugfix to already >>> released version supporting 2.7? >>> >>> If it's the first option, it means we can't use python3 features before >>> 2020 and we will be "in late" with these features. >>> >> >> The statement doesn't commit projects to support 2.7 until any specific >> date - scikit-bio already went Python 3 only with its release last month, >> for instance. We're agreeing to end Python 2 support by 2020, but projects >> are welcome to do it earlier than that. >> >> For IPython, we're planning for the 6.0 feature release (some time in >> 2017) to be Python 3 only, while we'll make bugfix releases of the 5.x >> series for longer than normal to support users on Python 2. >> > -- > 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/dc739979-e63f-4ce0-849b-66f8a659c8fc%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 Wed Jul 13 02:25:38 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Tue, 12 Jul 2016 23:25:38 -0700 Subject: Licensing tutorial material Message-ID: Hi, everyone Currently, our tutorial repo has no license. Everyone who has contributed, is it OK if I license it under CC-BY 4.0? Thanks! St?fan -------------- next part -------------- An HTML attachment was scrubbed... URL: From silvertrumpet999 at gmail.com Wed Jul 13 19:10:03 2016 From: silvertrumpet999 at gmail.com (Josh Warner) Date: Wed, 13 Jul 2016 16:10:03 -0700 (PDT) Subject: Licensing tutorial material In-Reply-To: References: Message-ID: <9534f453-5d9b-4558-96d7-81be919bae2c@googlegroups.com> Yes from me. (The panorama images are/were already under that exact license ). On Wednesday, July 13, 2016 at 5:21:02 PM UTC-5, Johannes Sch?nberger wrote: > > If there is any content from me in the tutorial, feel free to use CC-BY > 4.0. > > > On Jul 13, 2016, at 3:11 PM, Juan Nunez-Iglesias > wrote: > > > > Yes from me. > > > > On Wed, Jul 13, 2016 at 1:25 AM, St?fan van der Walt < > stefanv at berkeley.edu> wrote: > > Hi, everyone > > > > Currently, our tutorial repo has no license. Everyone who has > contributed, is it OK if I license it under CC-BY 4.0? > > > > Thanks! > > St?fan > > > > -- > > You received this message because you are subscribed to the Google > Groups "scikit-image" group. > > To unsubscribe from this group and stop receiving emails from it, send > an email to scikit-image+unsubscribe at googlegroups.com. > > To post to this group, send email to scikit-image at googlegroups.com. > > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/CABDkGQmrcXpEExNu7vXQL-czpDpTeMqTMj2Y56iMNoWHkR8HEA%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%2BJHcKQ%2Bjk3Fcv5A8QEBjW_Nf%2Br6d_yRAk-dy0JOfPDfez-CqA%40mail.gmail.com. > > > For more options, visit https://groups.google.com/d/optout. > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jni.soma at gmail.com Wed Jul 13 17:11:50 2016 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Wed, 13 Jul 2016 16:11:50 -0500 Subject: Licensing tutorial material In-Reply-To: References: Message-ID: Yes from me. On Wed, Jul 13, 2016 at 1:25 AM, St?fan van der Walt wrote: > Hi, everyone > > Currently, our tutorial repo has no license. Everyone who has > contributed, is it OK if I license it under CC-BY 4.0? > > Thanks! > St?fan > > -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image+unsubscribe at googlegroups.com. > To post to this group, send email to scikit-image at googlegroups.com. > To view this discussion on the web, visit > https://groups.google.com/d/msgid/scikit-image/CABDkGQmrcXpEExNu7vXQL-czpDpTeMqTMj2Y56iMNoWHkR8HEA%40mail.gmail.com > > . > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jsch at demuc.de Wed Jul 13 18:20:59 2016 From: jsch at demuc.de (=?utf-8?Q?Johannes_Sch=C3=B6nberger?=) Date: Wed, 13 Jul 2016 16:20:59 -0600 Subject: Licensing tutorial material In-Reply-To: References: Message-ID: If there is any content from me in the tutorial, feel free to use CC-BY 4.0. > On Jul 13, 2016, at 3:11 PM, Juan Nunez-Iglesias wrote: > > Yes from me. > > On Wed, Jul 13, 2016 at 1:25 AM, St?fan van der Walt wrote: > Hi, everyone > > Currently, our tutorial repo has no license. Everyone who has contributed, is it OK if I license it under CC-BY 4.0? > > Thanks! > St?fan > > -- > You received this message because you are subscribed to the Google Groups "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe at googlegroups.com. > To post to this group, send email to scikit-image at googlegroups.com. > To view this discussion on the web, visit https://groups.google.com/d/msgid/scikit-image/CABDkGQmrcXpEExNu7vXQL-czpDpTeMqTMj2Y56iMNoWHkR8HEA%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%2BJHcKQ%2Bjk3Fcv5A8QEBjW_Nf%2Br6d_yRAk-dy0JOfPDfez-CqA%40mail.gmail.com. > For more options, visit https://groups.google.com/d/optout. From remi.cura at gmail.com Thu Jul 21 09:26:34 2016 From: remi.cura at gmail.com (=?UTF-8?Q?R=C3=A9mi_Cura?=) Date: Thu, 21 Jul 2016 06:26:34 -0700 (PDT) Subject: Active contour : snake balloon? Message-ID: Hello everybody. I'm a real fan of skimage, and use it for numerous image processing stuf. I'm stuck in a segmentation problem: I have an old Paris map, and I try to separate the streets and the buildings. I have rough street axis. This looks like a watershed problem, but sme of the building footprints are not closed, so the watershed starting in streets is bleeding in the buildings. To avoid that, I was thinking of snake, starting conservatively in the streets, then make them balloon . I can't find the parameters so the snake balloons. Is this possible, would you have any advice? Cheers R?mi-C -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Auto Generated Inline Image 1 Type: image/png Size: 223209 bytes Desc: not available URL: From jni.soma at gmail.com Sat Jul 23 03:13:49 2016 From: jni.soma at gmail.com (Juan Nunez-Iglesias) Date: Sat, 23 Jul 2016 17:13:49 +1000 Subject: Active contour : snake balloon? In-Reply-To: References: Message-ID: Hi R?mi! This is a cool problem but I'm afraid I don't have a solution for you. I'm not familiar with snakes so I can't help you with the parameters. One thing I will say is that all methods will benefit from a ground truth dataset, where you have manually painted the result you're looking for. Once you have that you can really expand your parameter and method search dramatically because you don't have to look at each answer. Do you have such a dataset? Good luck! Juan. On Thu, Jul 21, 2016 at 11:26 PM, R?mi Cura wrote: > Hello everybody. > I'm a real fan of skimage, > and use it for numerous image processing stuf. > > I'm stuck in a segmentation problem: I have an old Paris map, and I try to > separate the streets and the buildings. > I have rough street axis. > This looks like a watershed problem, but sme of the building footprints > are not closed, so the watershed starting in streets is bleeding in the > buildings. > > To avoid that, I was thinking of snake, starting conservatively in the > streets, then make them balloon . > > I can't find the parameters so the snake balloons. > Is this possible, > would you have any advice? > > Cheers > R?mi-C > > > > > > -- > 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/fb202508-b0af-4af6-a2fc-15d7db6317a1%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: Auto Generated Inline Image 1 Type: image/png Size: 223209 bytes Desc: not available URL: From mob.irl at gmail.com Sun Jul 24 09:59:04 2016 From: mob.irl at gmail.com (Michael O'Brien) Date: Sun, 24 Jul 2016 06:59:04 -0700 (PDT) Subject: HoG Descriptors and Bag of Words Message-ID: Hi all, I'm new to computer vision/machine learning and I was hoping I could ask the community for some advise. I've calculated HoG descriptors for frames in a video but I'm not sure how best to group/join/??? them so I can then run Kmeans clustering on them. I'm hoping to use the (Visual) Bag of Words method to classify using random forrests but I'm a novice when it comes to ndarrays and not sure of the correct terminology. I know the HoG descriptors are flattened arrays but in order to cluster the frames/image descriptors I would need to group all the descriptors together. What is the best way to create a data structure suitable for kmeans when you have 100,000's of individual descriptors and do I need to pre-process the ndarrays ? Michael -------------- next part -------------- An HTML attachment was scrubbed... URL: From mob.irl at gmail.com Sun Jul 24 11:13:30 2016 From: mob.irl at gmail.com (Michael O'Brien) Date: Sun, 24 Jul 2016 08:13:30 -0700 (PDT) Subject: HoG Descriptors and Bag of Words In-Reply-To: References: Message-ID: <0481fceb-29d9-4ffe-975c-1a6a2b2193ee@googlegroups.com> Some properties of the individual ndarray (aka HoG descriptor) ('NDarry Size', 251328) ('NDarray Number of Dimensions', 1) ('NDarray length of 1 array element in Bytes', 8) ('NDarray Total byes consumed by elements', 2010624) ('NDarray DataType', dtype('float64')) On Sunday, 24 July 2016 14:59:04 UTC+1, Michael O'Brien wrote: > > Hi all, > > I'm new to computer vision/machine learning and I was hoping I could ask > the community for some advise. I've calculated HoG descriptors for frames > in a video but I'm not sure how best to group/join/??? them so I can then > run Kmeans clustering on them. I'm hoping to use the (Visual) Bag of Words > method to classify using random forrests but I'm a novice when it comes to > ndarrays and not sure of the correct terminology. > > I know the HoG descriptors are flattened arrays but in order to cluster > the frames/image descriptors I would need to group all the descriptors > together. What is the best way to create a data structure suitable for > kmeans when you have 100,000's of individual descriptors and do I need to > pre-process the ndarrays ? > > Michael > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mob.irl at gmail.com Tue Jul 26 15:06:41 2016 From: mob.irl at gmail.com (Michael O'Brien) Date: Tue, 26 Jul 2016 12:06:41 -0700 (PDT) Subject: HoG Descriptors and Bag of Words In-Reply-To: References: Message-ID: And is there a way to select the top N HoG Descriptors from the flattened array? On Sunday, 24 July 2016 14:59:04 UTC+1, Michael O'Brien wrote: > > Hi all, > > I'm new to computer vision/machine learning and I was hoping I could ask > the community for some advise. I've calculated HoG descriptors for frames > in a video but I'm not sure how best to group/join/??? them so I can then > run Kmeans clustering on them. I'm hoping to use the (Visual) Bag of Words > method to classify using random forrests but I'm a novice when it comes to > ndarrays and not sure of the correct terminology. > > I know the HoG descriptors are flattened arrays but in order to cluster > the frames/image descriptors I would need to group all the descriptors > together. What is the best way to create a data structure suitable for > kmeans when you have 100,000's of individual descriptors and do I need to > pre-process the ndarrays ? > > Michael > -------------- next part -------------- An HTML attachment was scrubbed... URL: From winecoding at gmail.com Wed Jul 27 22:59:58 2016 From: winecoding at gmail.com (wine lover) Date: Wed, 27 Jul 2016 19:59:58 -0700 (PDT) Subject: the underlying cause of getting the error message of Reason: "broken data stream when reading image file" Message-ID: Hi, I am trying to test the skimage by running the following python script from skimage import io data = io.imread("./test_data/tiger.jpeg")print(data.shape) It gives the following error messages. What can be the reason? Thank you very much for the help. bash-4.1$ python test.py Traceback (most recent call last): File "/test/tfw/lib/python3.4/site-packages/scikit_image-0.12.3-py3.4-linux-x86_64.egg/skimage/io/_plugins/pil_plugin.py", line 53, in pil_to_ndarray im.getdata()[0] File "/test/tfw/lib/python3.4/site-packages/Pillow-3.2.0-py3.4-linux-x86_64.egg/PIL/Image.py", line 1151, in getdata File "/test/tfw/lib/python3.4/site-packages/Pillow-3.2.0-py3.4-linux-x86_64.egg/PIL/ImageFile.py", line 235, in load File "/test/tfw/lib/python3.4/site-packages/Pillow-3.2.0-py3.4-linux-x86_64.egg/PIL/ImageFile.py", line 59, in raise_ioerror OSError: broken data stream when reading image file During handling of the above exception, another exception occurred: Traceback (most recent call last): File "test.py", line 2, in data = io.imread("./test_data/tiger.jpeg") File "/test/tfw/lib/python3.4/site-packages/scikit_image-0.12.3-py3.4-linux-x86_64.egg/skimage/io/_io.py", line 61, in imread img = call_plugin('imread', fname, plugin=plugin, **plugin_args) File "/test/tfw/lib/python3.4/site-packages/scikit_image-0.12.3-py3.4-linux-x86_64.egg/skimage/io/manage_plugins.py", line 211, in call_plugin return func(*args, **kwargs) File "/test/tfw/lib/python3.4/site-packages/scikit_image-0.12.3-py3.4-linux-x86_64.egg/skimage/io/_plugins/pil_plugin.py", line 37, in imread return pil_to_ndarray(im, dtype=dtype, img_num=img_num) File "/test/tfw/lib/python3.4/site-packages/scikit_image-0.12.3-py3.4-linux-x86_64.egg/skimage/io/_plugins/pil_plugin.py", line 61, in pil_to_ndarray raise ValueError(error_message) ValueError: Could not load "" Reason: "broken data stream when reading image file" Please see documentation at: http://pillow.readthedocs.org/en/latest/installation.html#external-libraries -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Thu Jul 28 04:27:01 2016 From: stefanv at berkeley.edu (=?UTF-8?Q?St=C3=A9fan_van_der_Walt?=) Date: Thu, 28 Jul 2016 01:27:01 -0700 Subject: the underlying cause of getting the error message of Reason: "broken data stream when reading image file" In-Reply-To: References: Message-ID: Hi, It sounds like the image might be corrupt. Can you load it using other image viewers? Also, did you try different plugins? St?fan On Jul 27, 2016 20:00, "wine lover" wrote: > Hi, > > I am trying to test the skimage by running the following python script > > from skimage import io > data = io.imread("./test_data/tiger.jpeg")print(data.shape) > > > It gives the following error messages. What can be the reason? Thank you > very much for the help. > > > bash-4.1$ python test.py > > Traceback (most recent call last): File > "/test/tfw/lib/python3.4/site-packages/scikit_image-0.12.3-py3.4-linux-x86_64.egg/skimage/io/_plugins/pil_plugin.py", > line 53, in pil_to_ndarray im.getdata()[0] File > "/test/tfw/lib/python3.4/site-packages/Pillow-3.2.0-py3.4-linux-x86_64.egg/PIL/Image.py", > line 1151, in getdata File > "/test/tfw/lib/python3.4/site-packages/Pillow-3.2.0-py3.4-linux-x86_64.egg/PIL/ImageFile.py", > line 235, in load File > "/test/tfw/lib/python3.4/site-packages/Pillow-3.2.0-py3.4-linux-x86_64.egg/PIL/ImageFile.py", > line 59, in raise_ioerror OSError: broken data stream when reading image > file > > During handling of the above exception, another exception occurred: > > Traceback (most recent call last): File "test.py", line 2, in data = > io.imread("./test_data/tiger.jpeg") File > "/test/tfw/lib/python3.4/site-packages/scikit_image-0.12.3-py3.4-linux-x86_64.egg/skimage/io/_io.py", > line 61, in imread img = call_plugin('imread', fname, plugin=plugin, > **plugin_args) File > "/test/tfw/lib/python3.4/site-packages/scikit_image-0.12.3-py3.4-linux-x86_64.egg/skimage/io/manage_plugins.py", > line 211, in call_plugin return func(*args, **kwargs) File > "/test/tfw/lib/python3.4/site-packages/scikit_image-0.12.3-py3.4-linux-x86_64.egg/skimage/io/_plugins/pil_plugin.py", > line 37, in imread return pil_to_ndarray(im, dtype=dtype, img_num=img_num) > File > "/test/tfw/lib/python3.4/site-packages/scikit_image-0.12.3-py3.4-linux-x86_64.egg/skimage/io/_plugins/pil_plugin.py", > line 61, in pil_to_ndarray raise ValueError(error_message) ValueError: > Could not load "" Reason: "broken data stream when reading image file" > Please see documentation at: > http://pillow.readthedocs.org/en/latest/installation.html#external-libraries > > -- > 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/fe62dc05-e818-4352-a236-3fb10593bc1a%40googlegroups.com > > . > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From winecoding at gmail.com Thu Jul 28 10:08:40 2016 From: winecoding at gmail.com (wine lover) Date: Thu, 28 Jul 2016 07:08:40 -0700 (PDT) Subject: the underlying cause of getting the error message of Reason: "broken data stream when reading image file" In-Reply-To: References: Message-ID: Hi St?fan, The image itself could me opened and viewed using other viewers. Would you like to let me know what are the plugins you were referring to? I am new to skimage. Thanks. On Thursday, July 28, 2016 at 3:27:04 AM UTC-5, stefanv wrote: > > Hi, > > It sounds like the image might be corrupt. Can you load it using other > image viewers? Also, did you try different plugins? > > St?fan > > On Jul 27, 2016 20:00, "wine lover" > > wrote: > >> Hi, >> >> I am trying to test the skimage by running the following python script >> >> from skimage import io >> data = io.imread("./test_data/tiger.jpeg")print(data.shape) >> >> >> It gives the following error messages. What can be the reason? Thank you >> very much for the help. >> >> >> bash-4.1$ python test.py >> >> Traceback (most recent call last): File >> "/test/tfw/lib/python3.4/site-packages/scikit_image-0.12.3-py3.4-linux-x86_64.egg/skimage/io/_plugins/pil_plugin.py", >> line 53, in pil_to_ndarray im.getdata()[0] File >> "/test/tfw/lib/python3.4/site-packages/Pillow-3.2.0-py3.4-linux-x86_64.egg/PIL/Image.py", >> line 1151, in getdata File >> "/test/tfw/lib/python3.4/site-packages/Pillow-3.2.0-py3.4-linux-x86_64.egg/PIL/ImageFile.py", >> line 235, in load File >> "/test/tfw/lib/python3.4/site-packages/Pillow-3.2.0-py3.4-linux-x86_64.egg/PIL/ImageFile.py", >> line 59, in raise_ioerror OSError: broken data stream when reading image >> file >> >> During handling of the above exception, another exception occurred: >> >> Traceback (most recent call last): File "test.py", line 2, in data = >> io.imread("./test_data/tiger.jpeg") File >> "/test/tfw/lib/python3.4/site-packages/scikit_image-0.12.3-py3.4-linux-x86_64.egg/skimage/io/_io.py", >> line 61, in imread img = call_plugin('imread', fname, plugin=plugin, >> **plugin_args) File >> "/test/tfw/lib/python3.4/site-packages/scikit_image-0.12.3-py3.4-linux-x86_64.egg/skimage/io/manage_plugins.py", >> line 211, in call_plugin return func(*args, **kwargs) File >> "/test/tfw/lib/python3.4/site-packages/scikit_image-0.12.3-py3.4-linux-x86_64.egg/skimage/io/_plugins/pil_plugin.py", >> line 37, in imread return pil_to_ndarray(im, dtype=dtype, img_num=img_num) >> File >> "/test/tfw/lib/python3.4/site-packages/scikit_image-0.12.3-py3.4-linux-x86_64.egg/skimage/io/_plugins/pil_plugin.py", >> line 61, in pil_to_ndarray raise ValueError(error_message) ValueError: >> Could not load "" Reason: "broken data stream when reading image file" >> Please see documentation at: >> http://pillow.readthedocs.org/en/latest/installation.html#external-libraries >> >> -- >> You received this message because you are subscribed to the Google Groups >> "scikit-image" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to scikit-image... at googlegroups.com . >> To post to this group, send email to scikit... at googlegroups.com >> . >> To view this discussion on the web, visit >> https://groups.google.com/d/msgid/scikit-image/fe62dc05-e818-4352-a236-3fb10593bc1a%40googlegroups.com >> >> . >> For more options, visit https://groups.google.com/d/optout. >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From parul1sethi at gmail.com Thu Jul 28 02:03:46 2016 From: parul1sethi at gmail.com (Parul Sethi) Date: Thu, 28 Jul 2016 11:33:46 +0530 Subject: Implementing Kadir and Brady's saliency detector in skimage? In-Reply-To: References: <7132cb6e-e66f-45be-a71a-327a2e5ff7d9@googlegroups.com> Message-ID: So sorry for the long pause. Thankyou for the response! I'll soon be done with it. On 11 Jul 2016 4:11 am, "St?fan van der Walt" wrote: > Hi Parul > > We are happy to evaluate any PR for inclusion. Saliency detection is > within scope. > > Best regards > St?fan > On Jul 6, 2016 05:54, "parul sethi" wrote: > >> Hi, >> >> I required to use Kadir and Brady's saliency detector for feature >> extraction process, and didn't found it's python implementation. So, i was >> in process of implementing the same. >> Will it be of interest to skimage too? I can use some advice from skimage >> maintainers to build it with specific suitability for skimage module. >> >> Thank you. >> >> -- >> 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/7132cb6e-e66f-45be-a71a-327a2e5ff7d9%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/FzZ1VkJt-Ks/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%2BcAy%3DLzc5MOR-CzummOuWiyDWrvoN_mXNX%2BNBh868Ew%40mail.gmail.com > > . > For more options, visit https://groups.google.com/d/optout. > -------------- next part -------------- An HTML attachment was scrubbed... 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