Mailman 3 July 2012 - scikit-image

Re: gstreamer
by Otto Fajardo 12 Jul '12

12 Jul '12

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 > > > On 12 July 2012 10:31, Otto Fajardo <otto.fajardob(a)gmail.com> wrote: > >> Hi Tony, >> >> thanks very much for your reply! I solved the problem and found a couple >> of things that can be useful for other users: >> >> 1- I am using Windows XP. >> >> 2- I didn't manage to property install gstreamer. I fail to import >> critical modules. No idea why. >> >> 3- Opencv works! The interesting thing is that it needs pygtk module to >> be installed. >> >> In the past I already tried opencv for this purpose and failed. While >> trying to install gstreamer I install pygtk, and now it works >> fine, both using scikits and opencv itself!!! >> Windows binaries for both opencv and pygtk can be obtained from >> Christoph Gohlke webpage, so it's quite easy to install. >> I think you could mention this in your webpage, could be useful for >> future users. >> >> 4- I found something I think is a but, and I have a suggestion: >> >> * Bug: the method duration is not working well, it gives strange >> results to me. The problem is in video.py line 107. I replace this line by >> return cv.GetCaptureProperty(self.capture, >> cv.CV_CAP_PROP_FRAME_COUNT)/cv.GetCaptureProperty(self.capture, >> cv.CV_CAP_PROP_FPS) >> and now works fine. >> >> * Suggestion: implement a method to directly obtain fps from the video. >> It's quite easy, will be 2 minutes: >> I added two funtions in video.py, one in classs CvVideo: >> def fps(self): >> >> return cv.GetCaptureProperty(self.capture, cv.CV_CAP_PROP_FPS) >> >> and another in class Video: >> >> def fps(self): >> >> return self.video.fps() >> >> >> >> I think this is useful. >> >> >> >> Cheers! >> >> >> >> >> 2012/7/12 Tony Yu <tsyu80(a)gmail.com> >> >>> Hi Otto, >>> >>> See response below. >>> >>> On Wed, Jul 11, 2012 at 5:14 AM, Otto <otto.fajardob(a)gmail.com> wrote: >>> >>>> Hi, >>>> I would like to try the Video function in skimage.io. I installed >>>> gstreamer, toghether with gstreamer sdk providing the python bindings. >>>> So, when I say import pygst from python console, it does not complain. >>>> However, trying to use the Video function like this: >>>> >>>> myvideo = skio.Video(source=source,backend='gstreamer') >>>> >>>> gives this error message: >>>> >>>> >>> <snip> >>> >>> >>>> raise ImportError("GStreamer Python bindings 0.10+ required") >>>> ImportError: GStreamer Python bindings 0.10+ required >>>> >>>> So: how to install properly these python bindings for gstreamer??? >>>> >>> >>> What system are you running and how did you install GStreamer? >>> >>> I don't actually have GStreamer installed, so my usefulness here is >>> limited. Looking at the code though, I'm not sure it's actually failing on >>> the version check (which I think raises an Assertion error, but the caught >>> exception is an ImportError). >>> >>> Could you try running the following imports: >>> >>> import gst >>> import gobject >>> from gst.extend.discoverer import Discoverer >>> >>> >>> >>>> >>>> By the way: Is this module appropiate to open a video file, let's say >>>> an avi file, that is compressed using for example with XViD, and then >>>> retrieve single frames as numpy arrays? >>>> >>>> thanks! >>> >>> >>> If GStreamer can read it, then the video plugin should be able to as >>> well. Yes, you can access a frame with the video's `get` method (which >>> returns a numpy array). >>> >>> You can also use the video functionality by using OpenCV as a backend >>> (but that could be difficult to install, depending on your system). >>> >>> Cheers, >>> -Tony >>> >> >> >

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Re: gstreamer
by Brian Holt 12 Jul '12

12 Jul '12

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 On 12 July 2012 10:31, Otto Fajardo <otto.fajardob(a)gmail.com> wrote: > Hi Tony, > > thanks very much for your reply! I solved the problem and found a couple > of things that can be useful for other users: > > 1- I am using Windows XP. > > 2- I didn't manage to property install gstreamer. I fail to import > critical modules. No idea why. > > 3- Opencv works! The interesting thing is that it needs pygtk module to be > installed. > > In the past I already tried opencv for this purpose and failed. While > trying to install gstreamer I install pygtk, and now it works > fine, both using scikits and opencv itself!!! > Windows binaries for both opencv and pygtk can be obtained from > Christoph Gohlke webpage, so it's quite easy to install. > I think you could mention this in your webpage, could be useful for > future users. > > 4- I found something I think is a but, and I have a suggestion: > > * Bug: the method duration is not working well, it gives strange > results to me. The problem is in video.py line 107. I replace this line by > return cv.GetCaptureProperty(self.capture, > cv.CV_CAP_PROP_FRAME_COUNT)/cv.GetCaptureProperty(self.capture, > cv.CV_CAP_PROP_FPS) > and now works fine. > > * Suggestion: implement a method to directly obtain fps from the video. > It's quite easy, will be 2 minutes: > I added two funtions in video.py, one in classs CvVideo: > def fps(self): > > return cv.GetCaptureProperty(self.capture, cv.CV_CAP_PROP_FPS) > > and another in class Video: > > def fps(self): > > return self.video.fps() > > > > I think this is useful. > > > > Cheers! > > > > > 2012/7/12 Tony Yu <tsyu80(a)gmail.com> > >> Hi Otto, >> >> See response below. >> >> On Wed, Jul 11, 2012 at 5:14 AM, Otto <otto.fajardob(a)gmail.com> wrote: >> >>> Hi, >>> I would like to try the Video function in skimage.io. I installed >>> gstreamer, toghether with gstreamer sdk providing the python bindings. >>> So, when I say import pygst from python console, it does not complain. >>> However, trying to use the Video function like this: >>> >>> myvideo = skio.Video(source=source,backend='gstreamer') >>> >>> gives this error message: >>> >>> >> <snip> >> >> >>> raise ImportError("GStreamer Python bindings 0.10+ required") >>> ImportError: GStreamer Python bindings 0.10+ required >>> >>> So: how to install properly these python bindings for gstreamer??? >>> >> >> What system are you running and how did you install GStreamer? >> >> I don't actually have GStreamer installed, so my usefulness here is >> limited. Looking at the code though, I'm not sure it's actually failing on >> the version check (which I think raises an Assertion error, but the caught >> exception is an ImportError). >> >> Could you try running the following imports: >> >> import gst >> import gobject >> from gst.extend.discoverer import Discoverer >> >> >> >>> >>> By the way: Is this module appropiate to open a video file, let's say >>> an avi file, that is compressed using for example with XViD, and then >>> retrieve single frames as numpy arrays? >>> >>> thanks! >> >> >> If GStreamer can read it, then the video plugin should be able to as >> well. Yes, you can access a frame with the video's `get` method (which >> returns a numpy array). >> >> You can also use the video functionality by using OpenCV as a backend >> (but that could be difficult to install, depending on your system). >> >> Cheers, >> -Tony >> > >

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Re: gstreamer
by Otto Fajardo 12 Jul '12

12 Jul '12

Hi Tony, thanks very much for your reply! I solved the problem and found a couple of things that can be useful for other users: 1- I am using Windows XP. 2- I didn't manage to property install gstreamer. I fail to import critical modules. No idea why. 3- Opencv works! The interesting thing is that it needs pygtk module to be installed. In the past I already tried opencv for this purpose and failed. While trying to install gstreamer I install pygtk, and now it works fine, both using scikits and opencv itself!!! Windows binaries for both opencv and pygtk can be obtained from Christoph Gohlke webpage, so it's quite easy to install. I think you could mention this in your webpage, could be useful for future users. 4- I found something I think is a but, and I have a suggestion: * Bug: the method duration is not working well, it gives strange results to me. The problem is in video.py line 107. I replace this line by return cv.GetCaptureProperty(self.capture, cv.CV_CAP_PROP_FRAME_COUNT)/cv.GetCaptureProperty(self.capture, cv.CV_CAP_PROP_FPS) and now works fine. * Suggestion: implement a method to directly obtain fps from the video. It's quite easy, will be 2 minutes: I added two funtions in video.py, one in classs CvVideo: def fps(self): return cv.GetCaptureProperty(self.capture, cv.CV_CAP_PROP_FPS) and another in class Video: def fps(self): return self.video.fps() I think this is useful. Cheers! 2012/7/12 Tony Yu <tsyu80(a)gmail.com> > Hi Otto, > > See response below. > > On Wed, Jul 11, 2012 at 5:14 AM, Otto <otto.fajardob(a)gmail.com> wrote: > >> Hi, >> I would like to try the Video function in skimage.io. I installed >> gstreamer, toghether with gstreamer sdk providing the python bindings. >> So, when I say import pygst from python console, it does not complain. >> However, trying to use the Video function like this: >> >> myvideo = skio.Video(source=source,backend='gstreamer') >> >> gives this error message: >> >> > <snip> > > >> raise ImportError("GStreamer Python bindings 0.10+ required") >> ImportError: GStreamer Python bindings 0.10+ required >> >> So: how to install properly these python bindings for gstreamer??? >> > > What system are you running and how did you install GStreamer? > > I don't actually have GStreamer installed, so my usefulness here is > limited. Looking at the code though, I'm not sure it's actually failing on > the version check (which I think raises an Assertion error, but the caught > exception is an ImportError). > > Could you try running the following imports: > > import gst > import gobject > from gst.extend.discoverer import Discoverer > > > >> >> By the way: Is this module appropiate to open a video file, let's say >> an avi file, that is compressed using for example with XViD, and then >> retrieve single frames as numpy arrays? >> >> thanks! > > > If GStreamer can read it, then the video plugin should be able to as well. > Yes, you can access a frame with the video's `get` method (which returns a > numpy array). > > You can also use the video functionality by using OpenCV as a backend (but > that could be difficult to install, depending on your system). > > Cheers, > -Tony >

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gstreamer
by Otto 11 Jul '12

11 Jul '12

Hi, I would like to try the Video function in skimage.io. I installed gstreamer, toghether with gstreamer sdk providing the python bindings. So, when I say import pygst from python console, it does not complain. However, trying to use the Video function like this: myvideo = skio.Video(source=source,backend='gstreamer') gives this error message: Traceback (most recent call last): File "<pyshell#5>", line 1, in <module> cuco = skio.Video(source=source,backend='gstreamer') File "C:\Python26\lib\site-packages\skimage\io\video.py", line 264, in __init__ self.video = GstVideo(source, size, sync) File "C:\Python26\lib\site-packages\skimage\io\video.py", line 124, in __init__ raise ImportError("GStreamer Python bindings 0.10+ required") ImportError: GStreamer Python bindings 0.10+ required So: how to install properly these python bindings for gstreamer??? By the way: Is this module appropiate to open a video file, let's say an avi file, that is compressed using for example with XViD, and then retrieve single frames as numpy arrays? thanks!

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Re: error in skimage.feature.hog
by Brian Holt 11 Jul '12

11 Jul '12

Hi Damian, Here is a link to the pull request I've created to fix the bug https://github.com/scikits-image/scikits-image/pull/213 You make a good point about the form of the resulting vector. I would be quite happy to return a hierarchical (unraveled) ndarray and make it the responsibility of the user to ravel it if they so wish. Comments from others? Brian On 11 July 2012 15:20, Damian Eads <dre25(a)cam.ac.uk> wrote: > Thank you for looking into the bug. On another note, it'd be great if > there was an option to turn off the flattening of the histogram. > > Damian > > On Tue, Jul 10, 2012 at 10:45 PM, Brian Holt <bdholt1(a)gmail.com> wrote: > > I've had a quick look and I can reproduce the bug. It seems to be a > > discrepancy between integer division to compute the number of cells and > then > > subsampling the array which gives a different dimensions. Hopefully I'll > > have a better idea tomorrow. > > > > On Jul 10, 2012 10:38 PM, "Stéfan van der Walt" <stefan(a)sun.ac.za> > wrote: > >> > >> On Tue, Jul 10, 2012 at 6:47 AM, Tony Yu <tsyu80(a)gmail.com> wrote: > >> >> Here is how to reproduce the error: > >> > >> Damian, I'm also tied up until Thursday, but I'll have a look at it > ASAP. > >> > >> > As for the color/grayscale issue, I've been thinking that it would be > >> > good > >> > to have an `@grayscale` function decorator that checks whether an > image > >> > is > >> > rgb/rgba and either raises an error or warns & converts. I haven't > >> > gotten > >> > around to implementing it yet, but it should be fairly simple. > >> > >> Great idea... The easier we can make it to build robust pipelines, the > >> better! The conversion routines have already come a long way, but I > >> am very much in favour of more such enhancements. > >> > >> Stéfan >

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Re: error in skimage.feature.hog
by Damian Eads 11 Jul '12

11 Jul '12

Thank you for looking into the bug. On another note, it'd be great if there was an option to turn off the flattening of the histogram. Damian On Tue, Jul 10, 2012 at 10:45 PM, Brian Holt <bdholt1(a)gmail.com> wrote: > I've had a quick look and I can reproduce the bug. It seems to be a > discrepancy between integer division to compute the number of cells and then > subsampling the array which gives a different dimensions. Hopefully I'll > have a better idea tomorrow. > > On Jul 10, 2012 10:38 PM, "Stéfan van der Walt" <stefan(a)sun.ac.za> wrote: >> >> On Tue, Jul 10, 2012 at 6:47 AM, Tony Yu <tsyu80(a)gmail.com> wrote: >> >> Here is how to reproduce the error: >> >> Damian, I'm also tied up until Thursday, but I'll have a look at it ASAP. >> >> > As for the color/grayscale issue, I've been thinking that it would be >> > good >> > to have an `@grayscale` function decorator that checks whether an image >> > is >> > rgb/rgba and either raises an error or warns & converts. I haven't >> > gotten >> > around to implementing it yet, but it should be fairly simple. >> >> Great idea... The easier we can make it to build robust pipelines, the >> better! The conversion routines have already come a long way, but I >> am very much in favour of more such enhancements. >> >> Stéfan

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Re: error in skimage.feature.hog
by Brian Holt 10 Jul '12

10 Jul '12

I've had a quick look and I can reproduce the bug. It seems to be a discrepancy between integer division to compute the number of cells and then subsampling the array which gives a different dimensions. Hopefully I'll have a better idea tomorrow. On Jul 10, 2012 10:38 PM, "Stéfan van der Walt" <stefan(a)sun.ac.za> wrote: > > On Tue, Jul 10, 2012 at 6:47 AM, Tony Yu <tsyu80(a)gmail.com> wrote: > >> Here is how to reproduce the error: > > Damian, I'm also tied up until Thursday, but I'll have a look at it ASAP. > > > As for the color/grayscale issue, I've been thinking that it would be good > > to have an `@grayscale` function decorator that checks whether an image is > > rgb/rgba and either raises an error or warns & converts. I haven't gotten > > around to implementing it yet, but it should be fairly simple. > > Great idea... The easier we can make it to build robust pipelines, the > better! The conversion routines have already come a long way, but I > am very much in favour of more such enhancements. > > Stéfan

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Re: error in skimage.feature.hog
by Stéfan van der Walt 10 Jul '12

10 Jul '12

On Tue, Jul 10, 2012 at 6:47 AM, Tony Yu <tsyu80(a)gmail.com> wrote: >> Here is how to reproduce the error: Damian, I'm also tied up until Thursday, but I'll have a look at it ASAP. > As for the color/grayscale issue, I've been thinking that it would be good > to have an `@grayscale` function decorator that checks whether an image is > rgb/rgba and either raises an error or warns & converts. I haven't gotten > around to implementing it yet, but it should be fairly simple. Great idea... The easier we can make it to build robust pipelines, the better! The conversion routines have already come a long way, but I am very much in favour of more such enhancements. Stéfan

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Re: error in skimage.feature.hog
by Tony Yu 10 Jul '12

10 Jul '12

On Tue, Jul 10, 2012 at 9:31 AM, Damian Eads <dre25(a)cam.ac.uk> wrote: > Hi, > > I'm very impressed with the progress made on scikits since its > inception in 2009. I checked out the latest skimage from Git and tried > running the HoG code on a non-square image, but it returns an error. > Moreover, if I don't convert from RGB to gray, I get a shape mismatch > error. In the latter case, a more user-friendly error message would > be more informative. Alternatively, you can either convert it to > grayscale or compute a gradient image for each channel and for each > pixel use the largest. > > Here is how to reproduce the error: > > In [1]: import skimage.color > > In [2]: import skimage.data > ** Message: pygobject_register_sinkfunc is deprecated (GstObject) > > In [3]: import skimage.feature > > In [4]: I=skimage.data.imread("motorbikes041.png") # see attached > > In [5]: I2=skimage.color.rgb2gray(I) > > In [6]: print I2.shape, I2.dtype > (150, 200) float64 > > In [7]: skimage.feature.hog(I2) > --------------------------------------------------------------------------- > ValueError Traceback (most recent call last) > > /data/repo/scikits-image/skimage/<ipython console> in <module>() > > > /usr/local/lib/python2.6/dist-packages/scikits_image-0.7dev-py2.6-linux-i686.egg/skimage/feature/hog.pyc > in hog(image, orientations, pixels_per_cell, cells_per_block, > visualise, normalise) > 121 > 122 orientation_histogram[:, :, i] = uniform_filter(temp_mag, > --> 123 size=(cy, cx))[cy / 2::cy, cx / 2::cx] > 124 > 125 # now for each cell, compute the histogram > > > ValueError: shape mismatch: objects cannot be broadcast to a single shape > > -------------- > > However, if I select a square subarray, it works fine. > > In [8]: x=skimage.feature.hog(I2[:128,:128]) > > Thanks, > > Damian > > Actually, I get a different error: ValueError: could not broadcast input array from shape (19,25) into shape (18,25) In this case, it's not a problem with non-square images, but something to do with how images are sampled. Your 150 x 200 image gives the error above, but a 148 x 200 image works fine. I won't have time to look at this right now, but this behavior might be a clue for someone else who does have time. As for the color/grayscale issue, I've been thinking that it would be good to have an `@grayscale` function decorator that checks whether an image is rgb/rgba and either raises an error or warns & converts. I haven't gotten around to implementing it yet, but it should be fairly simple. Cheers, -Tony

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error in skimage.feature.hog
by Damian Eads 10 Jul '12

10 Jul '12

Hi, I'm very impressed with the progress made on scikits since its inception in 2009. I checked out the latest skimage from Git and tried running the HoG code on a non-square image, but it returns an error. Moreover, if I don't convert from RGB to gray, I get a shape mismatch error. In the latter case, a more user-friendly error message would be more informative. Alternatively, you can either convert it to grayscale or compute a gradient image for each channel and for each pixel use the largest. Here is how to reproduce the error: In [1]: import skimage.color In [2]: import skimage.data ** Message: pygobject_register_sinkfunc is deprecated (GstObject) In [3]: import skimage.feature In [4]: I=skimage.data.imread("motorbikes041.png") # see attached In [5]: I2=skimage.color.rgb2gray(I) In [6]: print I2.shape, I2.dtype (150, 200) float64 In [7]: skimage.feature.hog(I2) --------------------------------------------------------------------------- ValueError Traceback (most recent call last) /data/repo/scikits-image/skimage/<ipython console> in <module>() /usr/local/lib/python2.6/dist-packages/scikits_image-0.7dev-py2.6-linux-i686.egg/skimage/feature/hog.pyc in hog(image, orientations, pixels_per_cell, cells_per_block, visualise, normalise) 121 122 orientation_histogram[:, :, i] = uniform_filter(temp_mag, --> 123 size=(cy, cx))[cy / 2::cy, cx / 2::cx] 124 125 # now for each cell, compute the histogram ValueError: shape mismatch: objects cannot be broadcast to a single shape -------------- However, if I select a square subarray, it works fine. In [8]: x=skimage.feature.hog(I2[:128,:128]) Thanks, Damian -- Damian Eads, PhD Research Associate, Machine Intelligence Laboratory Engineering Department, University of Cambridge Trumpington Street, Cambridge, CB2 1PZ, ENGLAND Web: http://mi.eng.cam.ac.uk/~dre25

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