Mailman 3 May 2012 - scikit-image

Re: Release 0.6
by Tony Yu 09 May '12

09 May '12

On Wed, May 9, 2012 at 8:21 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > On Wed, May 9, 2012 at 4:36 PM, Tony Yu <tsyu80(a)gmail.com> wrote: > > I updated the docs to clarify this. I considered renaming the attribute > > `image_viewer` but I thought it too verbose for a commonly-used > attribute. > > Personally, I'd probably prefer "view" or "image_view" or any of those > more explicit spellings. > > Stéfan > What do think about "viewer"? -Tony

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Re: filter_iter on github
by Stéfan van der Walt 09 May '12

09 May '12

Hi Nadav On Tue, May 8, 2012 at 8:18 AM, Nadav Horesh <nadavh.horesh(a)gmail.com> wrote: > Just made my first github commit on > https://github.com/Nadav-Horesh/filter_iter Excellent! This is going to make it much easier to review your code. Could you remove the .so files? An easy way to always ignore them is to add a ".gitignore" file to the repo with *.so on a single line. Stéfan

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Re: Release 0.6
by Stéfan van der Walt 09 May '12

09 May '12

On Wed, May 9, 2012 at 4:36 PM, Tony Yu <tsyu80(a)gmail.com> wrote: > I updated the docs to clarify this. I considered renaming the attribute > `image_viewer` but I thought it too verbose for a commonly-used attribute. Personally, I'd probably prefer "view" or "image_view" or any of those more explicit spellings. Stéfan

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Re: Release 0.6
by Tony Yu 09 May '12

09 May '12

On Wed, May 9, 2012 at 3:43 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > Hi Tony > > On Tue, May 8, 2012 at 8:21 PM, Tony Yu <tsyu80(a)gmail.com> wrote: > > I just uploaded a draft of a user-guide entry for the viewer. This is > > probably the best entry point for understanding the design of the viewer > and > > its use. > > That's very handy! The only part that is still opaque to me is the > "imgview" property. Where does that come from? > > Stéfan > I updated the docs to clarify this. I considered renaming the attribute `image_viewer` but I thought it too verbose for a commonly-used attribute. -Tony

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Re: Release 0.6
by Stéfan van der Walt 09 May '12

09 May '12

Hi Tony On Tue, May 8, 2012 at 8:21 PM, Tony Yu <tsyu80(a)gmail.com> wrote: > I just uploaded a draft of a user-guide entry for the viewer. This is > probably the best entry point for understanding the design of the viewer and > its use. That's very handy! The only part that is still opaque to me is the "imgview" property. Where does that come from? Stéfan

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Re: Error building docs
by Stéfan van der Walt 09 May '12

09 May '12

On Wed, May 9, 2012 at 7:25 AM, Tony Yu <tsyu80(a)gmail.com> wrote: > I don't know, @stefanv: why are inheritance trees generated? ;) > > The build runs fine if 'sphinx.ext.inheritance_diagram' is removed from the > list of sphinx extensions. Well, let's do that then :) Stéfan

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Re: Error building docs
by Tony Yu 09 May '12

09 May '12

On Wed, May 9, 2012 at 1:03 AM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > On May 8, 2012 8:53 PM, "Tony Yu" <tsyu80(a)gmail.com> wrote: > > > > I'm getting an IOError when rebuilding the docs and I can't figure out > the cause. The error is raised during the build of the api docs and appears > to be in `source/api/skimage.filter.lpi_filter.txt`: > > > > writing output... [ 22%] api/skimage.filter.lpi_filter > > > Exception occurred: > > File "/Library/Python/2.6/site-packages/sphinx/ext/graphviz.py", line > 219, in render_dot_html > > mapfile = open(outfn + '.map', 'rb') > > IOError: [Errno 2] No such file or directory: > '/Users/Tony/python/devel/skimage/doc/build/html/_images/inheritance-f7d294ea888e27c920fbf193effa642a3152b1be.png.map' > > Why are inheritance trees generated? I didn't think we enabled those? > > Stéfan > I don't know, @stefanv: why are inheritance trees generated?<https://github.com/scikits-image/scikits-image/commit/35a94b760e627ed44b858…> ;) The build runs fine if 'sphinx.ext.inheritance_diagram' is removed from the list of sphinx extensions. -Tony

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Re: Error building docs
by Stéfan van der Walt 09 May '12

09 May '12

On May 8, 2012 8:53 PM, "Tony Yu" <tsyu80(a)gmail.com> wrote: > > I'm getting an IOError when rebuilding the docs and I can't figure out the cause. The error is raised during the build of the api docs and appears to be in `source/api/skimage.filter.lpi_filter.txt`: > > writing output... [ 22%] api/skimage.filter.lpi_filter > Exception occurred: > File "/Library/Python/2.6/site-packages/sphinx/ext/graphviz.py", line 219, in render_dot_html > mapfile = open(outfn + '.map', 'rb') > IOError: [Errno 2] No such file or directory: '/Users/Tony/python/devel/skimage/doc/build/html/_images/inheritance-f7d294ea888e27c920fbf193effa642a3152b1be.png.map' Why are inheritance trees generated? I didn't think we enabled those? Stéfan

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Re: Release 0.6
by Tony Yu 08 May '12

08 May '12

On Tue, May 8, 2012 at 9:25 PM, Tony Yu <tsyu80(a)gmail.com> wrote: > > > On Tue, May 8, 2012 at 3:48 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > >> Hi everyone, >> >> It's time for another release of scikits-image! I would very much >> appreciate your help in reviewing the following outstanding >> pull-requests: >> >> >> - Tony Yu's neat visualization tools, previously packaged as skloupe: >> >> https://github.com/scikits-image/scikits-image/pull/165 >> >> - Fast image warping: >> >> https://github.com/scikits-image/scikits-image/pull/184 >> >> - RegionProps (still awaiting tests, but review the rest so long) >> >> https://github.com/scikits-image/scikits-image/pull/183 >> >> >> This release is due in about 10 days. I'm also happy to report that >> our Debian package has been submitted for approval; thanks go to >> Yaroslav Halchenko! >> >> Stéfan >> > > I went ahead and merged the fast image-warping PR. I've read through the > code a couple of times already, and I think it looks pretty good. (Sorry if > anyone else was planning to review it before merging.) > > -Tony > I just uploaded a draft of a user-guide entry for the viewer<https://github.com/tonysyu/scikits-image/blob/mpl-viewer/doc/source/user_gu…>. This is probably the best entry point for understanding the design of the viewer and its use. Also, I want apologize for the size of the PR: When I went to add the user-guide entry, I was shocked at the number of files added in the commit. As I mentioned in previous emails, the main parts are the viewer base classes<https://github.com/tonysyu/scikits-image/blob/mpl-viewer/skimage/viewer/vie…> and the plugin base class<https://github.com/tonysyu/scikits-image/blob/mpl-viewer/skimage/viewer/plu…>. The rest are more-or-less example uses of these classes. Best, -Tony

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Error building docs
by Tony Yu 08 May '12

08 May '12

I'm getting an IOError when rebuilding the docs and I can't figure out the cause. The error is raised during the build of the api docs and appears to be in `source/api/skimage.filter.lpi_filter.txt`: writing output... [ 22%] api/skimage.filter.lpi_filter Exception occurred: File "/Library/Python/2.6/site-packages/sphinx/ext/graphviz.py", line 219, in render_dot_html mapfile = open(outfn + '.map', 'rb') IOError: [Errno 2] No such file or directory: '/Users/Tony/python/devel/skimage/doc/build/html/_images/inheritance-f7d294ea888e27c920fbf193effa642a3152b1be.png.map' The full sphinx traceback is at the end of this email. NOTE: this error only occurs when *RE*building. Running `make clean` and then `make html` in the doc directory works fine, but re-running `make html` will raise this error. Any ideas what's going on here? -Tony # Sphinx version: 1.1.3 # Python version: 2.6.1 # Docutils version: 0.9 release # Jinja2 version: 2.6 Traceback (most recent call last): File "/Library/Python/2.6/site-packages/sphinx/cmdline.py", line 189, in main app.build(force_all, filenames) File "/Library/Python/2.6/site-packages/sphinx/application.py", line 204, in build self.builder.build_update() File "/Library/Python/2.6/site-packages/sphinx/builders/__init__.py", line 196, in build_update 'out of date' % len(to_build)) File "/Library/Python/2.6/site-packages/sphinx/builders/__init__.py", line 252, in build self.write(docnames, list(updated_docnames), method) File "/Library/Python/2.6/site-packages/sphinx/builders/__init__.py", line 292, in write self.write_doc(docname, doctree) File "/Library/Python/2.6/site-packages/sphinx/builders/html.py", line 419, in write_doc self.docwriter.write(doctree, destination) File "/Library/Python/2.6/site-packages/docutils/writers/__init__.py", line 77, in write self.translate() File "/Library/Python/2.6/site-packages/sphinx/writers/html.py", line 38, in translate self.document.walkabout(visitor) File "/Library/Python/2.6/site-packages/docutils/nodes.py", line 173, in walkabout if child.walkabout(visitor): File "/Library/Python/2.6/site-packages/docutils/nodes.py", line 173, in walkabout if child.walkabout(visitor): File "/Library/Python/2.6/site-packages/docutils/nodes.py", line 165, in walkabout visitor.dispatch_visit(self) File "/Library/Python/2.6/site-packages/docutils/nodes.py", line 1611, in dispatch_visit return method(node) File "/Library/Python/2.6/site-packages/sphinx/ext/inheritance_diagram.py", line 340, in html_visit_inheritance_diagram alt='Inheritance diagram of ' + node['content']) File "/Library/Python/2.6/site-packages/sphinx/ext/graphviz.py", line 219, in render_dot_html mapfile = open(outfn + '.map', 'rb') IOError: [Errno 2] No such file or directory: '/Users/Tony/python/devel/skimage/doc/build/html/_images/inheritance-f7d294ea888e27c920fbf193effa642a3152b1be.png.map'

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