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. 30, 2013

Dec. 30, 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. 27, 2013

Dec. 27, 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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Close an image window?
by Alasdair McAndrew Dec. 19, 2013

Dec. 19, 2013

This is a trivial question, but I still don't know how to do it. I've started up "ipython --pylab" and then: import skimage.io as io c = io.imread('cameraman.jpg') io.imshow(c,'qt') and this gives me an image in a window labelled "skimage". (I'm using Ubuntu 12.04). But how do I close this window from the console? I've tried: plt.close('skimage') plt.close() plt.close('all') plt.close(1) none of which have any effect. I can of course close them with the mouse, but that seems a little inelegant. Is the method to "close" the window in another package entirely? Thanks!

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slic segmentation
by scott.richardson＠visionsystemsinc.com Dec. 18, 2013

Dec. 18, 2013

I recently upgraded skimage from release 0.8.2.0 to 0.9.3 and noticed that I am getting back a different segmentation than I used to. I see that @jni and @ahojnnes have made quite a few edits to skimage/segmentation/slic_superpixels.py and _slic.pyx, so I suspect that is expected, but I wanted to make sure it wasn't a regression. thanks Scott

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Re: Linking events in skimage.viewer
by Nadav Horesh Dec. 18, 2013

Dec. 18, 2013

Thank you Juan. IIt looks like the event caught by the CanvasToolBase are not whtn I am looking for (mouse click and keyboard events) 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 >> >> -- >> 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 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 Juan Nunez-Iglesias Dec. 18, 2013

Dec. 18, 2013

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 > > -- > 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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Linking events in skimage.viewer
by Nadav Horesh Dec. 18, 2013

Dec. 18, 2013

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: Interactive selection of markers/seeds for random walk
by Kevin Keraudren Dec. 17, 2013

Dec. 17, 2013

Hi, What about skimage.viewer.plugins.labelplugin.LabelPainter, there is an example with the watershed algorithm there: https://github.com/scikit-image/scikit-image/blob/master/viewer_examples/pl… Otherwise, with OpenCV, you could look at the GrabCut example: https://github.com/Itseez/opencv/blob/master/samples/python2/grabcut.py Kind regards, Kevin On Mon, Dec 16, 2013 at 7:08 PM, Adam Hughes <hughesadam87(a)gmail.com> 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! > > -- > 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: New examples
by Stéfan van der Walt Dec. 16, 2013

Dec. 16, 2013

On Sun, Dec 15, 2013 at 10:18 PM, Adam Hughes <hughesadam87(a)gmail.com> wrote: > Actually, it looks like the user guide already has a nice section that might > be the right place for this: > > http://scikit-image.org/docs/0.9.x/user_guide/getting_help.html Another option would be to have a "side scrolling" bar on the top of the gallery. I.e., we take about 300 pixels at the top to show the videos, the rest of the page loads the examples. If that's too complicated, simply linking to the place you mention would be ok. Stéfan

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Re: New examples
by Adam Hughes Dec. 16, 2013

Dec. 16, 2013

Hey Stefan, I would be happy to try :) I'm confident I can gather the videos and stack overflow posts, but do you have a sense of where you'd like this information to fit into the website? In particular, I was thinking it could have either its own category (let's just call it "Outreach" at the moment) at this level: http://scikit-image.org/docs/0.9.x/ Or to lump it into the User Guide section, something like: User Guide: -section 1 -subsection - ... Community: - Video tutorials - Stack overflow posts Of course, it could also be bumped down directly into the User Guide: User Guide: -section1 -subsection -... - Outreach -video tutorials -stack overflow -mailing list discussions -more user examples I'm thinking user examples would be special links to repos or .ipynb files that aren't on the front page, but are often passed around on the mailing list. Any feelings about the organization Stefan? On Friday, December 13, 2013 9:34:38 PM UTC-5, Stefan van der Walt wrote: > > Hey, Adam > > On Sat, Dec 14, 2013 at 2:42 AM, Adam Hughes <hughes...(a)gmail.com<javascript:>> > wrote: > > Perhaps put any videos like this in the gallery as well? > > We could also add links to StackOverflow posts. > > Would you mind being our curator, and send a pull request either on > the website repo or on the docs to make this happen? > > Thank you! > Stéfan >

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Interactive selection of markers/seeds for random walk
by Adam Hughes Dec. 16, 2013

Dec. 16, 2013

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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Re: Restoration module
by Johannes Schönberger Dec. 14, 2013

Dec. 14, 2013

Great contribution! Are there any other "filters" that should go into this new sub-package? Johannes Am 14.12.2013 um 04:07 schrieb Stéfan van der Walt <stefan(a)sun.ac.za>: > Hi everyone, > > Just a heads-up on a new scikit-image submodule: ``skimage.restoration``. > > Thanks to François Orieux, we are fortunate to have the following > deconvolution algorithms implemented: > > [1] `wiener` > [2] `unsupervised_wiener` > [3] `richardson_lucy` > > I'd pay specific attention to Francois' own algorithm [2] -- no more > painful parameter tweaking to get a good Wiener-Hunt deconvolution! > > Thanks also to everyone on the team who worked hard to review and shape this PR. > > Stéfan > > -- > 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: Better results with Canny/Hough for circular particles
by Johannes Schönberger Dec. 14, 2013

Dec. 14, 2013

Am 14.12.2013 um 00:09 schrieb Adam Hughes <hughesadam87(a)gmail.com>: > I'm trying multiple methods for isolating nanoparticles for a paper in which the purpose will be to contextualize a lot of available image processing workflows best suited for sizing, separating and counting nanoparticles. The idea is that imaging nanoparticles is becomes a widely standard necessity, and so I want to present an overview of the availble methods and workflows for best processing images, as well best practices for obtaining high quality images in the lab via SEM/AFM. > > I've already covered approaches via auto thresholding, with optionally applying watersheding to find particle boundaries. OK, segmentation would have been my first suggestion. > IMO, Canny, Hough, Sobel etc... give another approach; whereby, one finds and deals directly with the particle boundaries/outlines. The advantage of this approach is that it lends finer control over the particle boundaries, which are often hazy in SEM images. I think that there are some use cases for this approach. For example, I've observed that canny edge detection gives a great fit to particles that have a halo effect, and so I'm pretty confident that, if we could fill all of the edges, that we'd be sizing the particles very nicely. It's easier to assess the "goodness of fit" looking at just the edges, but obviously it introduces more work. I at least had hoped to present a bit of this edge --> filter ---> fill approach in the paper to complement the threshold approaches to segmentation. > > I tried the morphological operators (open, close, dilation, edge), but they are a bit restrictive. I'd need something that has a variable structure parameter, as Dan mentioned sort of is builtin to canny (ie, it's smart about how it closes the regions). I'll probably just leave it at "the input parameters are crucial for getting closed regions" instead of focusing on how to connect the regions after the fact. > > PS, is anyone familiar with a function in scikit or ndimage to give the perimeter/outline of a filled region? skimage.measure.regionprops, skimage.measure.perimeter

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Restoration module
by Stéfan van der Walt Dec. 13, 2013

Dec. 13, 2013

Hi everyone, Just a heads-up on a new scikit-image submodule: ``skimage.restoration``. Thanks to François Orieux, we are fortunate to have the following deconvolution algorithms implemented: [1] `wiener` [2] `unsupervised_wiener` [3] `richardson_lucy` I'd pay specific attention to Francois' own algorithm [2] -- no more painful parameter tweaking to get a good Wiener-Hunt deconvolution! Thanks also to everyone on the team who worked hard to review and shape this PR. Stéfan

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Re: New examples
by Stéfan van der Walt Dec. 13, 2013

Dec. 13, 2013

Hey, Adam On Sat, Dec 14, 2013 at 2:42 AM, Adam Hughes <hughesadam87(a)gmail.com> wrote: > Perhaps put any videos like this in the gallery as well? We could also add links to StackOverflow posts. Would you mind being our curator, and send a pull request either on the website repo or on the docs to make this happen? Thank you! Stéfan

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New examples
by Adam Hughes Dec. 13, 2013

Dec. 13, 2013

Hey guys, The new examples in the gallery look great, and are quite helpful! I just watched a tutorial from Stefan today (PyData 2012), which was really great: http://vimeo.com/53065496 Perhaps put any videos like this in the gallery as well?

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Re: Better results with Canny/Hough for circular particles
by Adam Hughes Dec. 13, 2013

Dec. 13, 2013

Hi Dan, Thanks for the quick reply. I think that I can get better results if I tweak the parameters. The threshold parameter intuitively makes sense, but I'll have to read a bit to get familiar with sigma and the algorithm in general. Thanks for the explanation; it really helped. I will try out the erosion as well. PS, do you have any feelings towards the applicability of circular hough to my image? On Friday, December 13, 2013 3:03:30 PM UTC-5, Dan Farmer wrote: > > Hi Adam, > > This can be the worst part of image processing, but I'm curious how > much you played with the parameters to Canny? You probably know this, > but canny already tries to close gaps (hysteresis thresholding). What > you want to do is try to lower the low_threshold parameter (values > above the high threshold value get initially labeled as edges, then it > looks for pixels that are connected to edge pixels and whose value is > > low_threshold to link the edges). > > An easy/basic way to get rid of small fragments would be to start with > morphological erosion. > > -Dan > > On Fri, Dec 13, 2013 at 11:47 AM, Adam Hughes <hughes...(a)gmail.com<javascript:>> > wrote: > > Hi, > > > > I have several images of circular particles (see attached for an > example) > > and I've been experimenting with automatic routines to find edges. > > > > I've found that with Canny, I can get really nice edges, but the edges > are > > not always connected. Thus, when I do fill-binary, many of my particles > are > > not painted in due to slight breaks in the border returned by canny. Is > > there an ideal way to fix this, either by connecting "almost" connected > > canny edges? Additionally, what is the best way to filter out small > > fragments and/or non-circular edges? > > > > I've attached an image of the canny outlines; you can see that I > obviously > > want to get rid some of the regions that aren't associated with any > > particles. PS, the coloring of the outlines are based on the brightness > of > > the image at that point underneath it, which has been hidden. (Would be > > happy to share the function if anyone wants it). > > > > Lastly, I tried adapting the circular hough transform example: > > > > > http://scikit-image.org/docs/dev/auto_examples/plot_circular_elliptical_hou… > > > > But struggled with setting it up, due to a naive understanding of the > > algorithm. Given that my image has thousands of particles, but I know > > roughly the size distribution, would the circular hough transform be > useful > > to me? > > > > Thanks > > > > > > -- > > 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...(a)googlegroups.com <javascript:>. > > For more options, visit https://groups.google.com/groups/opt_out. >

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