Mailman 3 July 2012 - scikit-image

Cython & memory views
by Stéfan van der Walt July 16, 2012

July 16, 2012

Hi everyone, It would be great if all devs could familiarize themselves with the Cython interface to memoryviews: http://docs.cython.org/src/userguide/memoryviews.html I think we should head in this direction with any new code. If that was too long, here's the gist of it: cdef cnp.ndarray[cnp.double_t, 2] x = ... -> double[:, :] x = ... Stéfan

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Re: SciPy2012 Sprint
by Emmanuelle Gouillart July 16, 2012

July 16, 2012

Hi StÃ¯Â¿Â½fan, on which day will the sprint take place? I could work (from Paris) on some improvements of random walker segmentation (I have a PR almost ready), as well as on incorporating the morphological reconstruction of cellprofiler. Cheers, Emmanuelle On Thu, Jul 12, 2012 at 01:57:11PM -0700, StÃ¯Â¿Â½fan van der Walt wrote: > Hi everyone, > We will have a scikits-image sprint at SciPy2012 next week in Austin. > Since the sprint page has just gone up: > http://conference.scipy.org/scipy2012/sprints/index.php > Let's discuss some additions that we can work on... Suggestions? > StÃ¯Â¿Â½fan

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Re: gstreamer
by Stéfan van der Walt July 14, 2012

July 14, 2012

On Thu, Jul 12, 2012 at 7:18 PM, Tony Yu <tsyu80(a)gmail.com> wrote: > I've only scanned the source for video support. Do you foresee any sticking > points with adding video to the plugin framework? No, I think it would work well if we return a standard Video object, then we implement once class for each video reader (similar to the ImageCollection). Perhaps a specialized ImageCollection? Stéfan

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Re: gstreamer
by Otto Fajardo July 13, 2012

July 13, 2012

Pyffmpeg works well. In windows is very difficult to compile (therefore you have to rely on the binary, and the webpage only provides it for python 2.6), in linux I think it was better, can't recall. Ffms is quite new apparently, looks nice, color space is a bit messy, I have only tested the binary for 2.7, they have also for 3.2. These both support precise frame seeking. Yet another one based on ffmpeg is pymedia. This also works fine, the seeking function is not so good though. Binaries for windows are avaiable from Gohlke's webpage. Compiling with py2exe or cx_freeze: works for pyffmpeg, but not for ffms. I think all these support decoding but not encoding. If you need more details let me know. Otto 2012/7/13 Tony Yu <tsyu80(a)gmail.com> > > > On Thu, Jul 12, 2012 at 4:54 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > >> On Thu, Jul 12, 2012 at 11:37 AM, Tony Yu <tsyu80(a)gmail.com> wrote: >> > Brian: I think a Pyglet plugin would be useful even if it has the >> problems >> >> Any ideas on how this could slot in to the current plugin API? >> >> Stéfan >> > > Good point! If the number of video backends grows we should definitely be > reusing the plugin infrastructure. > > I've only scanned the source for video support. Do you foresee any > sticking points with adding video to the plugin framework? > > -Tony > > > >

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Re: SciPy2012 Sprint
by Tony Yu July 13, 2012

July 13, 2012

On Thu, Jul 12, 2012 at 10:47 PM, Tony Yu <tsyu80(a)gmail.com> wrote: > > > On Thu, Jul 12, 2012 at 5:49 PM, Emmanuelle Gouillart < > emmanuelle.gouillart(a)nsup.org> wrote: > >> Hi Stéfan, >> >> on which day will the sprint take place? >> >> I could work (from Paris) on some improvements of random walker >> segmentation (I have a PR almost ready), as well as on incorporating the >> morphological reconstruction of cellprofiler. >> >> Cheers, >> Emmanuelle >> >> >> On Thu, Jul 12, 2012 at 01:57:11PM -0700, Stéfan van der Walt wrote: >> > Hi everyone, >> >> > We will have a scikits-image sprint at SciPy2012 next week in Austin. >> > Since the sprint page has just gone up: >> >> > http://conference.scipy.org/scipy2012/sprints/index.php >> >> > Let's discuss some additions that we can work on... Suggestions? >> >> > Stéfan >> > > > Emmanuelle: I have an *old* PR for morphological reconstruction (based on > cellprofiler) if you want it. This is from before the scikits-image -> > skimage rename, so it might not be that useful. > > As for ideas (some of these might not be feasible): > > * Updating the PR to add backends for different toolkits (OpenCL, OpenCV, > etc) > PR: https://github.com/scikits-image/scikits-image/pull/14 > discussion: > https://groups.google.com/forum/?fromgroups#!topic/scikits-image/DapafiVCJoU > > * Integrate video support into plugin framework (related: I think Stefan > mentioned cleaning up the plugin framework as we were closing some bugs for > the 0.6 release). > > * Additions to the User Guide (ideas for topics?) > > * Finally, I'd really like to see some tutorial-style examples, similar to > the segmentation example: > > http://scikits-image.org/docs/dev/auto_examples/applications/plot_coins_seg… > > Cheers! > -Tony > > Emmanuelle: I realized that the old PR was not that hard to adapt, so I updated it and submitted it as a new PR. I hope you don't mind. https://github.com/scikits-image/scikits-image/pull/215 As I note in the PR, I doubt I spent much time reviewing the CellProfiler code, so it probably needs a good read through. -Tony

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Re: gstreamer
by Tony Yu July 13, 2012

July 13, 2012

On Thu, Jul 12, 2012 at 4:54 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > On Thu, Jul 12, 2012 at 11:37 AM, Tony Yu <tsyu80(a)gmail.com> wrote: > > Brian: I think a Pyglet plugin would be useful even if it has the > problems > > Any ideas on how this could slot in to the current plugin API? > > Stéfan > Good point! If the number of video backends grows we should definitely be reusing the plugin infrastructure. I've only scanned the source for video support. Do you foresee any sticking points with adding video to the plugin framework? -Tony

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SciPy2012 Sprint
by Stéfan van der Walt July 12, 2012

July 12, 2012

Hi everyone, We will have a scikits-image sprint at SciPy2012 next week in Austin. Since the sprint page has just gone up: http://conference.scipy.org/scipy2012/sprints/index.php Let's discuss some additions that we can work on... Suggestions? Stéfan

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Re: gstreamer
by Stéfan van der Walt July 12, 2012

July 12, 2012

On Thu, Jul 12, 2012 at 11:37 AM, Tony Yu <tsyu80(a)gmail.com> wrote: > Brian: I think a Pyglet plugin would be useful even if it has the problems Any ideas on how this could slot in to the current plugin API? Stéfan

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Re: gstreamer
by Tony Yu July 12, 2012

July 12, 2012

On Thu, Jul 12, 2012 at 6:38 AM, Otto Fajardo <otto.fajardob(a)gmail.com>wrote: > I don't remember very well, but I think that one disadvantage of pyglet > could be that it does not allow to seek precisely to a frame number, but it > does seeking with time or something like this, that happens to be not very > precise. For my application I need to retrieve a frame in the sequence with > precision ... > > By the way, there is also ffms, based in ffmpegsource, and also does the > job. This for python 2.7, for 2.6 there is pyffmpeg. > > > > > > 2012/7/12 Brian Holt <bdholt1(a)gmail.com> > >> I've been using Pyglet to do the same job... Here is a gist: >> gist.github.com/3097115 >> >> If its useful, I could put in a PR. >> >> Brian >> > I think it would be great to have enhanced support for videos. Otto: I would definitely like to see ffmpeg support. Do you have any comments about the two wrappers in addition to version support? Brian: I think a Pyglet plugin would be useful even if it has the problems that Otto mentions. These video backends tend to be pretty difficult to install on certain systems, so anything to lower the barrier for entry would be good. -Tony

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io.imsave() problems with passing arguments to plugin "freeimage"
by Sigmund July 12, 2012

July 12, 2012

Hallo! To read uncompressed TIFF files I use the freeimage plugin. The reading works great but since last week I need to save a summed Image. I used the io.imsave() with the freeimage plugin but by default it writs a compressed TIFF file. The freeimage documentation provides Flags to use for different compressions or for a non compressed type (TIFF_NONE). Can someone tell me how to pass theses Flags to the plugin? I saw that Christophs 'tifffile' plugin does the job but still I would like to know how to use the freeimage plug-n for it. Thanks! Siggi

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