Mailman 3 December 2013 - scikit-image

Re: skimage and opencv
by Emmanuelle Gouillart Sept. 22, 2016

Sept. 22, 2016

Hi FranÃ¯Â¿Â½ois, that's an excellent question, and not a troll :-). Opencv is a very powerful library, but it focuses primarily on computer vision (feature detection and extraction, classification, ...), as opposed to image processing in general (with other tasks such as denoising, segmentation, ...). The other big difference is that skimage builds on numpy ndarrays, and uses the full power of the numpy API (including of course the basic facilities for processing arrays as images that come with numpy), as well as some of scipy functions (you could have added scipy.ndimage to your list -- a few functions in skimage are wrappers around scipy.ndimage, that exist for the sake of completeneness). One important consequence is that algorithms working for 3-d or even n-d images can be easily implemented in 3-d/n-d in skimage, whereas opencv is restricted to 2-D images (as far as I know). Thanks to the use of numpy arrays, the API of skimage is also quite pleasant for a numpy user, more than the API of opencv. A related difference is that skimage is written in python and cython, whereas opencv is a C++ library. The two libraries attract a different crowd of developers, and a Python/Cython toolkit based on numpy arrays is easier to develop and maintain inside the Scientific Python ecosystem. I'm sure that other devs/users will have things to add to this discussion! Cheers, Emmanuelle On Thu, Dec 27, 2012 at 02:06:08PM -0800, FranÃ¯Â¿Â½ois wrote: > Hi users and devs, > It came to my knowledge that another python library (based on C++ and C > codes) for image processing exists too : opencv > I understand that numpy intregrates some basic features and we need some > advanced features but I have the feeling that skimages is redoundant with > opencv in some ways. > What's the position of skimage about that? (Don't read this question as a > troll but like a real question). > I mean that similar features exist in both. Would not be possible to > reuse/integrate opencv or merge? what's the reason for keeping them apart? > My observation is there is 4 libraries to manipulate images: > * PIL > * numpy > * skimages > * opencv > That's a lot. > Cheers,

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Re: Contribution: circles and hough transform
by François June 18, 2014

June 18, 2014

Hi, FYI, I plan to work on the detection of ellipses quite soon. Stefan indicated to me a reference which seems fairly simple to implement. Cheers, François.

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What RGB color is this? (quick Q)
by Adam Hughes Dec. 31, 2013

Dec. 31, 2013

I noticed recently that matplotlib.colors limits RGB values to a range (0 - 1), while in scikit image, RGB values can be much larger. For example: *test = np.zeros( (500,500,3) )* *test[:,:,0]=50* *test[:,:,1]=19* *test[:,:,2]=25* *imshow(test); * Produces a teal background. I was curious how the color teal is derived from this? I tried normalizing to 255 and and 50 but neither seemed to produce the same teal color. Thanks.

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Re: Interactive selection of markers/seeds for random walk
by Adam Hughes Dec. 31, 2013

Dec. 31, 2013

Thanks, sorry I had not seen this earlier! On Monday, December 16, 2013 2:08:56 PM UTC-5, Adam Hughes wrote: > > Hi, > > I was wondering if anyone had any examples or tools that would allow one > to interactively select regions for seeds/markers in an image, which we > could subsequently run the randomwalk algorithm over: > > > http://scikit-image.org/docs/dev/auto_examples/plot_random_walker_segmentat… > > I really enjoyed the ilastik tool that scikit image lists under its > related links on the homepage, and wondered if there were any demos for > selection that might be easily adaptable to fit this purpose. > > Thanks! >

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Images and audio
by Juan Nunez-Iglesias Dec. 28, 2013

Dec. 28, 2013

Hi all, I found this article fascinating for its application of image processing techniques, thought you might like it also: http://blog.longnow.org/02013/12/26/reviving-and-restoring-lost-sounds/ I haven't investigated yet whether the raw data are available. If so, a notebook using skimage and some Python audio library to achieve the same thing would be utterly excellent. =) Juan.

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Re: Linking events in skimage.viewer
by Nadav Horesh Dec. 26, 2013

Dec. 26, 2013

Thanks Steve. It works also on my system (linux). I'll look over why II had a problem in my original application. Sorry for the late response, Nadav 2013/12/23 Steven Silvester <steven.silvester(a)gmail.com>: > Nadav, > > You want the slider to update the value as it is moving? If so, pass > update_on="move" to Slider(). I tried your example, and my view does update > on key presses. I am using skimage 0.9.3 on Windows 7. > > import matplotlib.pyplot as plt > from skimage import data > from skimage import viewer > from skimage.viewer.plugins.overlayplugin import OverlayPlugin > from skimage.viewer.widgets import Slider > > class Cimage(object): > > def __init__(self): > self.recname = 'howdy' > self.rgb_image = data.camera() > self.gamma = 1 > > def key_press(self, event): > self.view.image = self.view.image[::-1] > > def image_update(self, image, **kwargs): > return image[::-1] - int(kwargs['gamma']) * 5 > > def create_window(self): > self.view = viewer.ImageViewer(self.rgb_image) > > plugin = OverlayPlugin(image_filter=self.image_update) > plugin += Slider('gamma', 1.0, 3.0 > , value=self.gamma, > orientation='vertical', update_on='move') > plugin += Slider('mat mix', 0.0, 1.0, value=0.0, > update_on='move', orientation='vertical') > plugin += Slider('wb mix', 0.0, 1.0, value=0.0, > update_on='move', orientation='horizontal') > > self.view += plugin > self.view.connect_event('key_press_event', self.key_press) > self.view.setWindowTitle(self.recname) > self.view.show() > > def main(): > a = Cimage() > a.create_window() > > if __name__ == '__main__': > main() > > About my earlier example, you would need to call f.canvas.show instead of > plt.show (I ran the code this time). But, if the MPLCanvas methods work, I’d > stick with those. > > Cheers, > Steve > > > > On Mon, Dec 23, 2013 at 8:10 AM, Nadav Horesh <nadavh.horesh(a)gmail.com> > wrote: >> >> Tony, >> I found the .connect_event method of the ImageViewer class just before >> I got the reply from you, and it roughly works. I say roughly because >> in the application there are some sliders that I added (not a part of >> the built-in plugins), and what I see that I see an image update only >> after I touch the sliders. In the linetool, however, the response is >> immediate. >> >> Code snippet: >> >> class Cimage: >> . >> . >> . >> def create_window(self): >> self.view = viewer.ImageViewer(self.rgb_image) >> >> plugin = OverlayPlugin(image_filter=self.image_update) >> plugin += Slider('gamma', 1.0, 3.0, value=self.gamma, >> orientation='vertical') >> plugin += Slider('mat mix', 0.0, 1.0, value=0.0, >> update_on='move', orientation='vertical') >> plugin += Slider('wb mix', 0.0, 1.0, value=0.0, >> update_on='move', orientation='horizontal') >> >> self.view += plugin >> self.view.connect_event('key_press_event', self.key_press) >> self.view.setWindowTitle(self.recname) >> self.view.show() >> . >> . >> . >> in the key_press method execution chain I have >> self.view.image = new_image >> >> so the image is updated, but it does not trigger a display update. >> >> >> >> Steve, >> Here is your code after some typos correction: >> >> #! /usr/bin/python >> >> from __future__ import print_function >> >> from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg >> import matplotlib.pyplot as plt >> from skimage import data >> >> >> class MyCanvas(FigureCanvasQTAgg): >> >> def mousePressEvent(self, event): >> #pass >> print('press') >> self.image = self.image[::-1] >> >> def main(): >> image = data.camera() >> f, ax = plt.subplots() >> f.canvas = MyCanvas(f) >> ax.imshow(image, interpolation='nearest') >> h, w = image.shape >> plt.show() >> >> >> if __name__ == '__main__': >> main() >> >> Running it I see that the method mousePressEvent is not being called >> >> I'll be happy to know if there is something to follow and build an >> application based on the viewer module. >> >> Thank you both very much >> >> Nadav >> >> >> 2013/12/23 Steven Silvester <steven.silvester(a)gmail.com>: >> > Nadav, >> > >> > The canvas itself is a >> > matplotlib.backends.backend_qt4agg.FigureCanvasQTAgg. >> > If you wanted, you could subclass that class and provide your own >> > mousePressEvent and friends. Something like: >> > >> > from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg >> > import matplotlib.pyplot as plt >> > from skimage import data >> > >> > >> > class MyCanvas(FigureCanvasQtAgg): >> > >> > def mousePressEvent(self, event): >> > pass >> > >> > def main(): >> > image = data.camera() >> > f, ax = plt.subplots() >> > f.canvas = MyCanvas() >> > ax.imshow(image, interpolation='nearest') >> > h, w = image.shape >> > plt.show() >> > >> > On Wednesday, December 18, 2013 2:13:02 AM UTC-6, Nadav Horesh wrote: >> >> >> >> I >> >> I started to build an interactive image exploration utility based on >> >> matplotlib. Recently, following a link on this list, I encountered >> >> skimage.viewer, and found that the plugins architecture matches my >> >> needs. >> >> I could not find how to link keyboard and mouse events (and maybe >> >> buttons) >> >> to plugins. Any suggestions? >> >> >> >> I am using version 0.93 on linux (I can install the pre 0.10, if >> >> needed) >> >> >> >> Thanks, >> >> >> >> Nadav >> > >> > -- >> > You received this message because you are subscribed to the Google >> > Groups >> > "scikit-image" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to scikit-image+unsubscribe(a)googlegroups.com. >> > For more options, visit https://groups.google.com/groups/opt_out. >> >> -- >> You received this message because you are subscribed to a topic in the >> Google Groups "scikit-image" group. >> To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/scikit-image/pRZYHjAW78U/unsubscribe. >> To unsubscribe from this group and all of its topics, send an email to >> scikit-image+unsubscribe(a)googlegroups.com. >> >> For more options, visit https://groups.google.com/groups/opt_out. > > > -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image+unsubscribe(a)googlegroups.com. > For more options, visit https://groups.google.com/groups/opt_out.

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Re: Linking events in skimage.viewer
by Steven Silvester Dec. 23, 2013

Dec. 23, 2013

Nadav, You want the slider to update the value as it is moving? If so, pass update_on="move" to Slider(). I tried your example, and my view does update on key presses. I am using skimage 0.9.3 on Windows 7. import matplotlib.pyplot as pltfrom skimage import datafrom skimage import viewerfrom skimage.viewer.plugins.overlayplugin import OverlayPluginfrom skimage.viewer.widgets import Slider class Cimage(object): def __init__(self): self.recname = 'howdy' self.rgb_image = data.camera() self.gamma = 1 def key_press(self, event): self.view.image = self.view.image[::-1] def image_update(self, image, **kwargs): return image[::-1] - int(kwargs['gamma']) * 5 def create_window(self): self.view = viewer.ImageViewer(self.rgb_image) plugin = OverlayPlugin(image_filter=self.image_update) plugin += Slider('gamma', 1.0, 3.0, value=self.gamma, orientation='vertical', update_on='move') plugin += Slider('mat mix', 0.0, 1.0, value=0.0, update_on='move', orientation='vertical') plugin += Slider('wb mix', 0.0, 1.0, value=0.0, update_on='move', orientation='horizontal') self.view += plugin self.view.connect_event('key_press_event', self.key_press) self.view.setWindowTitle(self.recname) self.view.show() def main(): a = Cimage() a.create_window() if __name__ == '__main__': main() About my earlier example, you would need to call f.canvas.show instead of plt.show (I ran the code this time). But, if the MPLCanvas methods work, I’d stick with those. Cheers, Steve On Mon, Dec 23, 2013 at 8:10 AM, Nadav Horesh <nadavh.horesh(a)gmail.com>wrote: > Tony, > I found the .connect_event method of the ImageViewer class just before > I got the reply from you, and it roughly works. I say roughly because > in the application there are some sliders that I added (not a part of > the built-in plugins), and what I see that I see an image update only > after I touch the sliders. In the linetool, however, the response is > immediate. > > Code snippet: > > class Cimage: > . > . > . > def create_window(self): > self.view = viewer.ImageViewer(self.rgb_image) > > plugin = OverlayPlugin(image_filter=self.image_update) > plugin += Slider('gamma', 1.0, 3.0, value=self.gamma, > orientation='vertical') > plugin += Slider('mat mix', 0.0, 1.0, value=0.0, > update_on='move', orientation='vertical') > plugin += Slider('wb mix', 0.0, 1.0, value=0.0, > update_on='move', orientation='horizontal') > > self.view += plugin > self.view.connect_event('key_press_event', self.key_press) > self.view.setWindowTitle(self.recname) > self.view.show() > . > . > . > in the key_press method execution chain I have > self.view.image = new_image > > so the image is updated, but it does not trigger a display update. > > > > Steve, > Here is your code after some typos correction: > > #! /usr/bin/python > > from __future__ import print_function > > from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg > import matplotlib.pyplot as plt > from skimage import data > > > class MyCanvas(FigureCanvasQTAgg): > > def mousePressEvent(self, event): > #pass > print('press') > self.image = self.image[::-1] > > def main(): > image = data.camera() > f, ax = plt.subplots() > f.canvas = MyCanvas(f) > ax.imshow(image, interpolation='nearest') > h, w = image.shape > plt.show() > > > if __name__ == '__main__': > main() > > Running it I see that the method mousePressEvent is not being called > > I'll be happy to know if there is something to follow and build an > application based on the viewer module. > > Thank you both very much > > Nadav > > > 2013/12/23 Steven Silvester <steven.silvester(a)gmail.com>: > > Nadav, > > > > The canvas itself is a > matplotlib.backends.backend_qt4agg.FigureCanvasQTAgg. > > If you wanted, you could subclass that class and provide your own > > mousePressEvent and friends. Something like: > > > > from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg > > import matplotlib.pyplot as plt > > from skimage import data > > > > > > class MyCanvas(FigureCanvasQtAgg): > > > > def mousePressEvent(self, event): > > pass > > > > def main(): > > image = data.camera() > > f, ax = plt.subplots() > > f.canvas = MyCanvas() > > ax.imshow(image, interpolation='nearest') > > h, w = image.shape > > plt.show() > > > > On Wednesday, December 18, 2013 2:13:02 AM UTC-6, Nadav Horesh wrote: > >> > >> I > >> I started to build an interactive image exploration utility based on > >> matplotlib. Recently, following a link on this list, I encountered > >> skimage.viewer, and found that the plugins architecture matches my > needs. > >> I could not find how to link keyboard and mouse events (and maybe > buttons) > >> to plugins. Any suggestions? > >> > >> I am using version 0.93 on linux (I can install the pre 0.10, if needed) > >> > >> Thanks, > >> > >> Nadav > > > > -- > > You received this message because you are subscribed to the Google Groups > > "scikit-image" group. > > To unsubscribe from this group and stop receiving emails from it, send an > > email to scikit-image+unsubscribe(a)googlegroups.com. > > For more options, visit https://groups.google.com/groups/opt_out. > > -- > You received this message because you are subscribed to a topic in the > Google Groups "scikit-image" group. > To unsubscribe from this topic, visit > https://groups.google.com/d/topic/scikit-image/pRZYHjAW78U/unsubscribe. > To unsubscribe from this group and all of its topics, send an email to > scikit-image+unsubscribe(a)googlegroups.com. > For more options, visit https://groups.google.com/groups/opt_out. >

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Re: Linking events in skimage.viewer
by Steven Silvester Dec. 23, 2013

Dec. 23, 2013

Nadav, The canvas itself is a matplotlib.backends.backend_qt4agg.FigureCanvasQTAgg. If you wanted, you could subclass that class and provide your own mousePressEvent and friends. Something like: from matplotlib.backends.backend_qt4agg import FigureCanvasQTAggimport matplotlib.pyplot as pltfrom skimage import data class MyCanvas(FigureCanvasQtAgg): def mousePressEvent(self, event): pass def main(): image = data.camera() f, ax = plt.subplots() f.canvas = MyCanvas() ax.imshow(image, interpolation='nearest') h, w = image.shape plt.show() On Wednesday, December 18, 2013 2:13:02 AM UTC-6, Nadav Horesh wrote: I > I started to build an interactive image exploration utility based on > matplotlib. Recently, following a link on this list, I encountered > skimage.viewer, and found that the plugins architecture matches my needs. > I could not find how to link keyboard and mouse events (and maybe buttons) > to plugins. Any suggestions? > > I am using version 0.93 on linux (I can install the pre 0.10, if needed) > > Thanks, > > Nadav >

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Re: Linking events in skimage.viewer
by Tony Yu Dec. 22, 2013

Dec. 22, 2013

On Wed, Dec 18, 2013 at 5:36 AM, Nadav Horesh <nadavh.horesh(a)gmail.com>wrote: > Thank you Juan. IIt looks like the event caught by the CanvasToolBase > are not whtn I am looking for (mouse click and keyboard events) > Hi Nadav, I'm not sure I follow. The canvas tools use matplotlib events because the image canvas is drawn with matplotlib. The `CanvasToolBase` class shows an example of using the tool's `connect_event` to connect to "key_press_event" (keyboard events). The `LineTool` class shows an example connecting to keyboard events through "button_press_event". Note that this event system is only for the image canvas. If another widget (e.g. a slider) has focus, then the events are handled by Qt's infrastructure. Cheers, -Tony > > Thank you again, > > Nadav > > 2013/12/18 Juan Nunez-Iglesias <jni.soma(a)gmail.com>: > > Hi Nadav, > > > > I don't have much experience with interactive tools, but I think this is > the > > right place to start for examples: > > > https://github.com/scikit-image/scikit-image/blob/master/skimage/viewer/can… > > > > You'll see that the LineProfile plugin uses the LineTool canvas tool: > > > https://github.com/scikit-image/scikit-image/blob/master/skimage/viewer/plu… > > > > Hopefully this helps, otherwise @tonysyu might be able to step in and > offer > > a bit more guidance. > > > > Juan. > > > > > > > > > > On Wed, Dec 18, 2013 at 7:13 PM, Nadav Horesh <nadavh.horesh(a)gmail.com> > > wrote: > >> > >> I > >> I started to build an interactive image exploration utility based on > >> matplotlib. Recently, following a link on this list, I encountered > >> skimage.viewer, and found that the plugins architecture matches my > needs. > >> I could not find how to link keyboard and mouse events (and maybe > buttons) > >> to plugins. Any suggestions? > >> > >> I am using version 0.93 on linux (I can install the pre 0.10, if needed) > >> > >> Thanks, > >> > >> Nadav > >

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Enforce SLIC connectivity
by Guillem Palou Dec. 20, 2013

Dec. 20, 2013

Hello all, I have implemented the post-processing step of the SLIc superpixels to enforce superpixel connectivity. The algorithm is essentially the same of the original paper: "R.Achanta et al. SLIC Superpixels Compared to State-of-the-art Superpixel Methods, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 34, num. 11, p. 2274 - 2282, May 2012.": 1. Loop through all the image 2. Get the size of a connected component (adjacent pixels with same label) 3. If the size is less than a threshold, merge it to an adjacent cluster At the end, the generated superpixels are 4-connected (or 6 in 3 dimensions), so each label corresponds to a single connected component. This differs from the actual implementation, where a label may have multiple disconnected components. To be said, the processing time does not suffer. See the corresponding pull request

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