Mailman 3 August 2012 - scikit-image

Re: Geometric transformations
by Johannes Schönberger Aug. 13, 2012

Aug. 13, 2012

Hi Stéfan, I just noticed the documentation on skimage.org is based on one of the old builds of this branch. Maybe you can update this as the API looked different at that point. Johannes Schönberger Am 13.08.2012 um 03:26 schrieb Stéfan van der Walt <stefan(a)sun.ac.za>: > Hi everyone, > > For those of you who work with warping and registration, check out the > freshly merged: > > https://github.com/scikits-image/scikits-image/pull/197 > > This PR went through a long discussion, and I'm very happy with the result! > > Stéfan

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Geometric transformations
by Stéfan van der Walt Aug. 12, 2012

Aug. 12, 2012

Hi everyone, For those of you who work with warping and registration, check out the freshly merged: https://github.com/scikits-image/scikits-image/pull/197 This PR went through a long discussion, and I'm very happy with the result! Stéfan

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Re: EuroSciPy sprint
by Tony Yu Aug. 10, 2012

Aug. 10, 2012

On Thu, Aug 9, 2012 at 1:31 AM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > Hi, everyone > > We'll be sprinting at EuroSciPy, and would like to solicit ideas. > Currently, the sprint description reads as follows. I'd love to hear > other suggestions! > > """ > > scikits-image is a collection of algorithms for image processing. See > http://skimage.org for more detail. > > Ideas for the sprint: > > - Add text, anti-aliasing to the draw module > - Integrate Tony's visualization tools > - Add binary features (BRIEF, BRISK, FREAK) > - Update the user guide > - Better video loading > - Hough transform parameter space explorer > > Outstanding challenges: > > - Blurring kernel estimation: http://bit.ly/Nril3u > - > http://stackoverflow.com/questions/10196198/how-to-remove-convexity-defects… > > And write up this one as an example: > > - > http://stackoverflow.com/questions/8686926/python-image-processing-help-nee… > """ > > Regards > Stéfan > It's depressing to see so many suggestions repeated from our last sprint. That said, we did get a number of great contributions (many weren't on our original list). It sounds like there might be a *3rd* implementation of a an extensible image viewer, so I won't be offended if you punt on the Qt-MPL viewer PR. If you do tackle it, I think a good exercise would be to have someone implement a new plugin for the viewer. (Maybe something as simple as adapting parts of skivi.) In case there are people at the sprint looking for simple problems to tackle, I've also added a number of issues labeled quickfix, that *should* in theory be fairly easy to implement. (Although the decision on the correct implementation may or may not be so easy, but that's why it's nice to have people in one room). To get specific on updating the User Guide: I think a "Getting Started" page would be great. Something that takes the user through a common workflow; e.g.: 1) load an image 2) try using a feature detector or transform. 3) realize that it didn't perform ideally. Now try smoothing or denoising (or something else). 4) successfully find feature. 5) save feature as some sort of data file. One more item to the list: - `imread_collection` should work for any plugin that implements `imread`. (I guess I'll add this as an issue). In regards to the Hough transform parameter space explorer, I have a not-so-elegant implementation here: https://github.com/tonysyu/scikits-image/blob/qtmpl-houghplugin/viewer_exam… Cheers, -Tony

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Re: New core developer: Andreas Mueller
by Stéfan van der Walt Aug. 9, 2012

Aug. 9, 2012

On Thu, Aug 9, 2012 at 8:20 AM, Tony Yu <tsyu80(a)gmail.com> wrote: > It's my pleasure to welcome Andreas Mueller to the scikits-image core > development team. Andreas has made some valuable, high-quality code > contributions to scikits-image, lately. In addition, he's been a great help > in reviewing many of the recent pull requests; now he has the power of the > green button (to merge those PRs). Welcome to the team, Andy! We're excited to have you. Stéfan

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Re: New core developer: Andreas Mueller
by Andreas Müller Aug. 9, 2012

Aug. 9, 2012

Hey everyone. Thanks Tony. I'm happy to be on board :) Looking forward to help out in this awesome project! Cheers, Andy ----- Ursprüngliche Mail ----- Von: "Tony Yu" <tsyu80(a)gmail.com> An: scikits-image(a)googlegroups.com Gesendet: Donnerstag, 9. August 2012 16:20:46 Betreff: New core developer: Andreas Mueller Hi everyone, It's my pleasure to welcome Andreas Mueller to the scikits-image core development team. Andreas has made some valuable, high-quality code contributions to scikits-image, lately. In addition, he's been a great help in reviewing many of the recent pull requests; now he has the power of the green button (to merge those PRs). Andreas: I know you already have a pretty full plate, but I look forward to many more contributions from you in the near future ;) Cheers, -Tony

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New core developer: Andreas Mueller
by Tony Yu Aug. 9, 2012

Aug. 9, 2012

Hi everyone, It's my pleasure to welcome Andreas Mueller to the scikits-image core development team. Andreas has made some valuable, high-quality code contributions to scikits-image, lately. In addition, he's been a great help in reviewing many of the recent pull requests; now he has the power of the green button (to merge those PRs). Andreas: I know you already have a pretty full plate, but I look forward to many more contributions from you in the near future ;) Cheers, -Tony

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EuroSciPy sprint
by Stéfan van der Walt Aug. 9, 2012

Aug. 9, 2012

Hi, everyone We'll be sprinting at EuroSciPy, and would like to solicit ideas. Currently, the sprint description reads as follows. I'd love to hear other suggestions! """ scikits-image is a collection of algorithms for image processing. See http://skimage.org for more detail. Ideas for the sprint: - Add text, anti-aliasing to the draw module - Integrate Tony's visualization tools - Add binary features (BRIEF, BRISK, FREAK) - Update the user guide - Better video loading - Hough transform parameter space explorer Outstanding challenges: - Blurring kernel estimation: http://bit.ly/Nril3u - http://stackoverflow.com/questions/10196198/how-to-remove-convexity-defects… And write up this one as an example: - http://stackoverflow.com/questions/8686926/python-image-processing-help-nee… """ Regards Stéfan

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Re: Bug in regionprops
by Tony Yu Aug. 4, 2012

Aug. 4, 2012

On Thu, Aug 2, 2012 at 9:28 PM, Tony Yu <tsyu80(a)gmail.com> wrote: > > > On Tue, Jul 31, 2012 at 4:42 AM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > >> Hi Jeff >> >> On Jul 31, 2012 9:07 AM, "jeff witz" <witzjean(a)gmail.com> wrote: >> > >> > I must use regionprops in order to identify a lot of el >> >>> Hello, >>> >>> I must use regionprops in order to identify a lot of ellipse in a >>> picture. I have constated a mistake in the implementation of the >>> 'Orientation' identification. >>> in skimage/measure/_regionprops.py at line 298 the function atan is used >>> to recover the angle. In my case I constate that a lot of the ellipse are >>> correctly identified using atan, but in some cases the 'MinorAxisLength' >>> and the 'MajorAxisLength' are swapped. You can solve this issue using the >>> atan2 function that take into account the trigonometric quadrant. >>> >>> Best Regards, >>> >>> >>> >>> Hi Jeff, > > Thanks for the bug report. Johannes just added a PR to fix this issue: > > https://github.com/scikits-image/scikits-image/pull/238 > > Do you have a short, self-contained example that you could submit as a > test. If you're comfortable with git, you can submit a PR to his branch > with the test. If not, maybe you could just post the example to this list, > and one of us can add it to the PR? > > Thanks, > -Tony > For some reason, Johannes's emails aren't showing up on the list, so I'll follow up to prevent duplicate work: Johannes added a test, and PR 238 has been merged. Cheers, -Tony

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Re: Bug in regionprops
by Tony Yu Aug. 2, 2012

Aug. 2, 2012

On Tue, Jul 31, 2012 at 4:42 AM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > Hi Jeff > > On Jul 31, 2012 9:07 AM, "jeff witz" <witzjean(a)gmail.com> wrote: > > > > I must use regionprops in order to identify a lot of el > >> Hello, >> >> I must use regionprops in order to identify a lot of ellipse in a >> picture. I have constated a mistake in the implementation of the >> 'Orientation' identification. >> in skimage/measure/_regionprops.py at line 298 the function atan is used >> to recover the angle. In my case I constate that a lot of the ellipse are >> correctly identified using atan, but in some cases the 'MinorAxisLength' >> and the 'MajorAxisLength' are swapped. You can solve this issue using the >> atan2 function that take into account the trigonometric quadrant. >> >> Best Regards, >> >> >> >> Hi Jeff, Thanks for the bug report. Johannes just added a PR to fix this issue: https://github.com/scikits-image/scikits-image/pull/238 Do you have a short, self-contained example that you could submit as a test. If you're comfortable with git, you can submit a PR to his branch with the test. If not, maybe you could just post the example to this list, and one of us can add it to the PR? Thanks, -Tony

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Re: Qt-MPL image viewer
by Tony Yu Aug. 1, 2012

Aug. 1, 2012

On Sat, Jul 28, 2012 at 10:08 AM, Tony Yu <tsyu80(a)gmail.com> wrote: > So I've been hacking on a new implementation of an > image-viewer/interactive-image-processor. See PR 229: > > https://github.com/scikits-image/scikits-image/pull/229 > > The previous implementation was written purely in Matplotlib, partly for > portability. Unfortunately, I found this implementation a bit limiting > because Matplotlib doesn't provide quite-enough widget support. In > addition, there was no way to add custom toolbars or menus without getting > toolkit-specific. > > So, I've added a new implementation that requires PyQt but also uses > Matplotlib because of the wealth of plotting functionality that it provides. > > There's a lot that I added in my original implementation that needs to be > updated for this implementation (an image collection viewer, and Guillaume > Gay's contrast setter and line-profile plugins). I'm of the opinion, > however, that these should be implemented later in order to reduce the work > to review this PR (that's actually why I moved the line profile plugin<https://github.com/tonysyu/scikits-image/blob/qtmpl-lineprofile/skimage/vie…>to a separate branch). > > Overall, I'm pretty happy with the current implementation. The basic idea > is that there's a viewer class (to view images, of course). You can then > connect plugins to the viewer, which typically calls some sort of filter > function, but that's in no way a requirement (for example, the line-profile > plugin measures values in the image). Also, there are widgets that get > attached to these plugins (currently, just a slider and a combo box) to > adjust filtering or plugin parameters. > > There are two ways to implement a plugin: The first is by subclassing the > base `Plugin` class<https://github.com/tonysyu/scikits-image/blob/qtmpl-viewer/skimage/viewer/p…>. > The second (which I shamelessly stole from Bokeh) instantiates a plugin > and just adds widgets<https://github.com/tonysyu/scikits-image/blob/qtmpl-viewer/viewer_examples/…>(using the addition operator) to control filter parameters. The first is > probably more flexible, while the second is convenient for people who may > not be as comfortable with object-oriented programming (plus I think it > reads really well). > > It's a big PR, but I'd really appreciate comments and suggestions. > > Cheers, > -Tony > > P.S. Stefan: In a separate branch, I've added the Hough Transform plugin > you so desired. Right now it's a little hacky, partly because I haven't yet > built the infrastructure to support this type of plot (not only does it > plot an overlay but also Matplotlib lines; in addition, parameters have to > be delegated to two different functions). Nevertheless, the implementation > is surprisingly short<https://github.com/tonysyu/scikits-image/blob/qtmpl-houghplugin/viewer_exam…>, > despite not adding anything else to support this use case. > Update: I just added a CollectionViewer class (to view image collections) to a separate branch that reimplements the CollectionViewer from the original (pure-MPL) PR: https://github.com/tonysyu/scikits-image/commit/c942db45ee0c663a5a70f8346a8… Cheers, -Tony

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