Mailman 3 February 2012 - scikit-image

StackOverflow fun
by Stéfan van der Walt 07 Feb '12

07 Feb '12

Hi all, https://plus.google.com/104831275312843762750/posts/Ai9Bd5DQfAv What can I say...you guys collectively kick ass :) Cheers Stéfan

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Re: skimage module not found by iPython's completion?
by Tony Yu 06 Feb '12

06 Feb '12

2012/2/6 Stéfan van der Walt <stefan(a)sun.ac.za> > On Mon, Feb 6, 2012 at 11:12 AM, Tony Yu <tsyu80(a)gmail.com> wrote: > > As for the second issue: We don't automatically import any subpackages > > (other than `util`). This was a design decision since automatic imports > of > > all subpackages would increase load times (there may be other reasons > too). > > On the other hand, if you just want to see which submodules are available > > for import, you can write `import skimage.<tab>` (note the dot before > <tab>) > > or `from skimage import<tab>` in ipython. > > Besides, Tony is busy updating all the module level docstrings, so > that "skimage?" should soon deliver useful results :) > > Cheers > Stéfan > Wait a minute... Let me quote what I wrote in the original email: "One thing I'd like to see is a package docstring listing all subpackages..." Note: I didn't say that I would implement it ;) -Tony

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Re: skimage module not found by iPython's completion?
by Stéfan van der Walt 06 Feb '12

06 Feb '12

On Mon, Feb 6, 2012 at 11:12 AM, Tony Yu <tsyu80(a)gmail.com> wrote: > As for the second issue: We don't automatically import any subpackages > (other than `util`). This was a design decision since automatic imports of > all subpackages would increase load times (there may be other reasons too). > On the other hand, if you just want to see which submodules are available > for import, you can write `import skimage.<tab>` (note the dot before <tab>) > or `from skimage import<tab>` in ipython. Besides, Tony is busy updating all the module level docstrings, so that "skimage?" should soon deliver useful results :) Cheers Stéfan

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Re: Documentation sprint over the weekend
by Stéfan van der Walt 06 Feb '12

06 Feb '12

On Mon, Feb 6, 2012 at 3:28 AM, Michael Aye <kmichael.aye(a)gmail.com> wrote: > I think it would be helpful, if the gallery would mention from which > version on a feature/method is available. Currently, for example, it > seems not clear from the website that exposure and harris are only > available from github only, or did I miss something? Thanks, Michael, that's a good point. Tony's suggestions sound like the way to go; in the mean time, here's a PR to add the version number to each example: https://github.com/scikits-image/scikits-image/pull/124 Stéfan

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Re: skimage module not found by iPython's completion?
by Michael Aye 06 Feb '12

06 Feb '12

Thanks, works fine! Michael On Feb 6, 8:12 pm, Tony Yu <tsy...(a)gmail.com> wrote: > On Mon, Feb 6, 2012 at 12:43 PM, Michael Aye <kmichael....(a)gmail.com> wrote: > > Hi all, > > > I noticed some weirds things with iPython's completion regarding > > skimage v0.12. > > When typing 'import sk' and then pressing <tab> to complete the import > > line, iPython cannot find skimage. > > But if I type 'import skimage' on my own, it works. > > Then, I type 'skimage.' and press <tab> to inspect the module, and I > > get: > > > skimage.data_dir skimage.img_as_int skimage.pkg_dir > > skimage.util > > skimage.get_log skimage.img_as_ubyte skimage.test > > skimage.version > > skimage.img_as_float skimage.img_as_uint skimage.test_verbose > > > (= half missing). > > > Anybody knows what's going on here? I'm puzzled... > > > Best regards, > > Michael > > Huh, I guess I didn't notice this first issue until you mentioned it. Turns > out<http://stackoverflow.com/questions/1552961/ipython-tab-completes-only...>there's > an easy fix: Run `%rehashx` in ipython to rebuild the database of > known modules. > > As for the second issue: We don't automatically import any subpackages > (other than `util`). This was a design decision since automatic imports of > all subpackages would increase load times (there may be other reasons too). > On the other hand, if you just want to see which submodules are available > for import, you can write `import skimage.<tab>` (note the dot before > <tab>) or `from skimage import<tab>` in ipython. > > Hope that helps, > -Tony

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Re: skimage module not found by iPython's completion?
by Tony Yu 06 Feb '12

06 Feb '12

On Mon, Feb 6, 2012 at 12:43 PM, Michael Aye <kmichael.aye(a)gmail.com> wrote: > Hi all, > > I noticed some weirds things with iPython's completion regarding > skimage v0.12. > When typing 'import sk' and then pressing <tab> to complete the import > line, iPython cannot find skimage. > But if I type 'import skimage' on my own, it works. > Then, I type 'skimage.' and press <tab> to inspect the module, and I > get: > > skimage.data_dir skimage.img_as_int skimage.pkg_dir > skimage.util > skimage.get_log skimage.img_as_ubyte skimage.test > skimage.version > skimage.img_as_float skimage.img_as_uint skimage.test_verbose > > (= half missing). > > Anybody knows what's going on here? I'm puzzled... > > Best regards, > Michael Huh, I guess I didn't notice this first issue until you mentioned it. Turns out<http://stackoverflow.com/questions/1552961/ipython-tab-completes-only-some-…>there's an easy fix: Run `%rehashx` in ipython to rebuild the database of known modules. As for the second issue: We don't automatically import any subpackages (other than `util`). This was a design decision since automatic imports of all subpackages would increase load times (there may be other reasons too). On the other hand, if you just want to see which submodules are available for import, you can write `import skimage.<tab>` (note the dot before <tab>) or `from skimage import<tab>` in ipython. Hope that helps, -Tony

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skimage module not found by iPython's completion?
by Michael Aye 06 Feb '12

06 Feb '12

Hi all, I noticed some weirds things with iPython's completion regarding skimage v0.12. When typing 'import sk' and then pressing <tab> to complete the import line, iPython cannot find skimage. But if I type 'import skimage' on my own, it works. Then, I type 'skimage.' and press <tab> to inspect the module, and I get: skimage.data_dir skimage.img_as_int skimage.pkg_dir skimage.util skimage.get_log skimage.img_as_ubyte skimage.test skimage.version skimage.img_as_float skimage.img_as_uint skimage.test_verbose (= half missing). Anybody knows what's going on here? I'm puzzled... Best regards, Michael

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Re: Documentation sprint over the weekend
by Tony Yu 06 Feb '12

06 Feb '12

On Mon, Feb 6, 2012 at 6:28 AM, Michael Aye <kmichael.aye(a)gmail.com> wrote: > I think it would be helpful, if the gallery would mention from which > version on a feature/method is available. Currently, for example, it > seems not clear from the website that exposure and harris are only > available from github only, or did I miss something? > > Best regards, > Michael > Hi Michael, You're correct: exposure and harris are only available in the development version of scikits-image. Currently we just have different versions of the docs for each release (and for the dev version). For example, there's are a separate gallery for skimage v0.4<http://scikits-image.org/docs/0.4/auto_examples/index.html> . It might be a bit much to add labels to each example in the gallery, but I do think it should be clearer that you're looking at the development version of the documentation. (I think the only indication is on the homepage and the url.) Maybe we should specify the version in the sidebar and add links to older versions. We could also add version notes (e.g. "New in skimage v0.5") in the examples themselves and/or in the function docstrings---could this be automated some how? -Tony > > On Feb 4, 8:47 pm, Tony Yu <tsy...(a)gmail.com> wrote: > > On Sat, Feb 4, 2012 at 7:28 AM, Emmanuelle Gouillart < > > > > emmanuelle.gouill...(a)nsup.org> wrote: > > > Hi, > > > > > I'll try to work on the "getting help" part of the user guide, then. > > > > > Cheers, > > > Emmanuelle > > > > I'll get to work on the data-types and processing pipeline. I may not > have > > as much time as expected, though, since I got sidetracked by other PRs. > > > > Cheers, > > -Tony > > > > > > > > > > > > > > > > > > > > > > - Introduction > > > > (installation -- link to existing docs, overview and how we fit in > > > > on top of scipy, our goals, what we provide) > > > > - Reading and displaying image > > > > (io module, display, fancy=True, using matplotlib, etc.) > > > > - Data-types and the pipeline > > > > (dtype conversion, how to ensure your output is in the right > > > > format, all functions accept any input but returns preferred dtype > > > > output--user should call img_as_*) > > > > - Getting help > > > > (reference guide, examples gallery, maybe image processing > specific > > > > websites similar to metaoptimize.com/qa ) > > > > > > And some tutorials are always welcome--although I think the gallery > > > > now largely fulfills that role. > > > > > > Did I miss anything important? > > > > > > We also need a man-page for skivi (the image viewer). I've uploaded > a > > > template: > > > > >https://github.com/scikits-image/scikits-image/blob/debian/debian/ski. > .. > > > > > > > One thing I'd like to see is a package docstring listing all > > > subpackages (+ > > > > > 1-sentence descriptions of those subpackages; e.g. type `np?` in > > > ipython); > > > > > and then each subpackage would have it's own docstring listing of > > > functions > > > > > (e.g. type `numpy.linalg?` in ipython). I guess this is separate > from > > > the > > > > > user guide, but it's still really valuable for learning the > package. > > > > > > Yes, good point! > > > > > > > While we're talking about release 0.5, I think we should try to > clean > > > out a > > > > > number of pull requests. Some of them should be quick: > > > > > > > PR 99: Rewrite dtype._convert function > > > > > > Merged (by me). > > > > > > > PR 105: ENH: Allow choice between 4 and 8 neighbor mode. > > > > > > Merged (by Tony). > > > > > > > PR 95: debian/control updates to reflect name space transition > > > > > > Rejected (mainly adding the author's name, but very few changes). I > > > > updated the control file to be up to date in the meantime. > > > > > > > PR 107: Add rescale_intensity function with test and example. > > > > > > I'm keen to merge this; we're just waiting for the rest of the list > to > > > > comment on the matplotlib 1.0 dependency. > > > > > > Cheers > > > > Stéfan >

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Re: Documentation sprint over the weekend
by Michael Aye 06 Feb '12

06 Feb '12

I think it would be helpful, if the gallery would mention from which version on a feature/method is available. Currently, for example, it seems not clear from the website that exposure and harris are only available from github only, or did I miss something? Best regards, Michael On Feb 4, 8:47 pm, Tony Yu <tsy...(a)gmail.com> wrote: > On Sat, Feb 4, 2012 at 7:28 AM, Emmanuelle Gouillart < > > emmanuelle.gouill...(a)nsup.org> wrote: > > Hi, > > > I'll try to work on the "getting help" part of the user guide, then. > > > Cheers, > > Emmanuelle > > I'll get to work on the data-types and processing pipeline. I may not have > as much time as expected, though, since I got sidetracked by other PRs. > > Cheers, > -Tony > > > > > > > > > > > > - Introduction > > > (installation -- link to existing docs, overview and how we fit in > > > on top of scipy, our goals, what we provide) > > > - Reading and displaying image > > > (io module, display, fancy=True, using matplotlib, etc.) > > > - Data-types and the pipeline > > > (dtype conversion, how to ensure your output is in the right > > > format, all functions accept any input but returns preferred dtype > > > output--user should call img_as_*) > > > - Getting help > > > (reference guide, examples gallery, maybe image processing specific > > > websites similar to metaoptimize.com/qa ) > > > > And some tutorials are always welcome--although I think the gallery > > > now largely fulfills that role. > > > > Did I miss anything important? > > > > We also need a man-page for skivi (the image viewer). I've uploaded a > > template: > > >https://github.com/scikits-image/scikits-image/blob/debian/debian/ski... > > > > > One thing I'd like to see is a package docstring listing all > > subpackages (+ > > > > 1-sentence descriptions of those subpackages; e.g. type `np?` in > > ipython); > > > > and then each subpackage would have it's own docstring listing of > > functions > > > > (e.g. type `numpy.linalg?` in ipython). I guess this is separate from > > the > > > > user guide, but it's still really valuable for learning the package. > > > > Yes, good point! > > > > > While we're talking about release 0.5, I think we should try to clean > > out a > > > > number of pull requests. Some of them should be quick: > > > > > PR 99: Rewrite dtype._convert function > > > > Merged (by me). > > > > > PR 105: ENH: Allow choice between 4 and 8 neighbor mode. > > > > Merged (by Tony). > > > > > PR 95: debian/control updates to reflect name space transition > > > > Rejected (mainly adding the author's name, but very few changes). I > > > updated the control file to be up to date in the meantime. > > > > > PR 107: Add rescale_intensity function with test and example. > > > > I'm keen to merge this; we're just waiting for the rest of the list to > > > comment on the matplotlib 1.0 dependency. > > > > Cheers > > > Stéfan

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Re: Documentation sprint over the weekend
by Emmanuelle Gouillart 04 Feb '12

04 Feb '12

Hi, I'll try to work on the "getting help" part of the user guide, then. Cheers, Emmanuelle > - Introduction > (installation -- link to existing docs, overview and how we fit in > on top of scipy, our goals, what we provide) > - Reading and displaying image > (io module, display, fancy=True, using matplotlib, etc.) > - Data-types and the pipeline > (dtype conversion, how to ensure your output is in the right > format, all functions accept any input but returns preferred dtype > output--user should call img_as_*) > - Getting help > (reference guide, examples gallery, maybe image processing specific > websites similar to metaoptimize.com/qa ) > And some tutorials are always welcome--although I think the gallery > now largely fulfills that role. > Did I miss anything important? > We also need a man-page for skivi (the image viewer). I've uploaded a template: > https://github.com/scikits-image/scikits-image/blob/debian/debian/skivi.1 > > One thing I'd like to see is a package docstring listing all subpackages (+ > > 1-sentence descriptions of those subpackages; e.g. type `np?` in ipython); > > and then each subpackage would have it's own docstring listing of functions > > (e.g. type `numpy.linalg?` in ipython). I guess this is separate from the > > user guide, but it's still really valuable for learning the package. > Yes, good point! > > While we're talking about release 0.5, I think we should try to clean out a > > number of pull requests. Some of them should be quick: > > PR 99: Rewrite dtype._convert function > Merged (by me). > > PR 105: ENH: Allow choice between 4 and 8 neighbor mode. > Merged (by Tony). > > PR 95: debian/control updates to reflect name space transition > Rejected (mainly adding the author's name, but very few changes). I > updated the control file to be up to date in the meantime. > > PR 107: Add rescale_intensity function with test and example. > I'm keen to merge this; we're just waiting for the rest of the list to > comment on the matplotlib 1.0 dependency. > Cheers > StÃ¯Â¿Â½fan

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