Mailman 3 September 2013 - scikit-image

Any plans for 0.9 release?
by Pierre Villeneuve 14 Sep '13

14 Sep '13

I am eagerly awaiting the new RANSAC model fitting tools in the current dev version. I am working on Windows 8 x64 and it turns into a total mess when I try to compile skimage myself. I normally rely on the binaries at Chris Gohlke's site, but he only has the current stable version 0.8.2. I am just curious to know if there is a planned timeframe for releasing 0.9? Thanks!

2 1

Re: Intensity plot of along the line
by Guillaume Gay 14 Sep '13

14 Sep '13

There's a line profile tool in the Tony Yu's ImageViewer.. On 12/09/2013 18:29, Thomas A Caswell wrote: > scipy.ndimage.interpolation.map_coordinates > (http://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.interpola…) > + matplotlib will do what you want. > > Tom > > > On Thu, Sep 12, 2013 at 11:19 AM, Dan <dkin(a)walla.co.il > <mailto:dkin@walla.co.il>> wrote: > > Hi, > > Is there a way to generate an intensity plot of along the line > using scikit-image (like Plot Profile option in imageJ) (example: > http://imagej.1557.x6.nabble.com/file/n3682337/cracks.png). > > 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 > <mailto:scikit-image%2Bunsubscribe@googlegroups.com>. > For more options, visit https://groups.google.com/groups/opt_out. > > > > > -- > Thomas A Caswell > PhD Candidate University of Chicago > Nagel and Gardel labs > tcaswell(a)uchicago.edu <mailto:tcaswell@uchicago.edu> > jfi.uchicago.edu/~tcaswell <http://jfi.uchicago.edu/%7Etcaswell> > o: 773.702.7204 > -- > 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.

3 3

Re: Intensity plot of along the line
by Stéfan van der Walt 14 Sep '13

14 Sep '13

On Thu, Sep 12, 2013 at 6:29 PM, Thomas A Caswell <tcaswell(a)uchicago.edu> wrote: > scipy.ndimage.interpolation.map_coordinates > (http://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.interpola…) > + matplotlib will do what you want. For the record, map_coordinates is quite hard to use--have a look at skimage.transform.warp as well. Stéfan

1 0

Re: Get border pixels of labelled region
by Juan Nunez-Iglesias 13 Sep '13

13 Sep '13

The input is a grayscale image, not a binary image. It finds contours of a given intensity threshold. The output is a list of arrays. Each array has shape (Q, 2), and it is a set of x, y coordinates of the points in the contour. If you want to look at the contours, you need to convert this to an image somehow. This example uses matplotlib's `plot` function to draw the contours on the image: http://scikit-image.org/docs/dev/auto_examples/plot_contours.html#example-p… Alternately, you can round the contour coordinates to int and use those to make a new image: conts = find_contours(image, threshold) contour_image = zeros_like(image) for c in conts: c = np.round(c).astype(int) coords = (c[:, 0], c[:, 1]) contour_image[coords] = 1 imshow(contour_image) On Fri, Sep 13, 2013 at 5:26 PM, Payal Gupta <erpayal2010(a)gmail.com> wrote: > hi juan.... > > i can't understand array after using find_contour which return a ndarray. > it is main prob i wanna find out contour array. > > > On Fri, Sep 13, 2013 at 6:07 AM, Juan Nunez-Iglesias <jni.soma(a)gmail.com>wrote: > >> Hi Payal, >> >> I think we're getting somewhere. =) Thanks for the image. >> >> Questions: >> 1) Are you looking to segment out different cars? That is, do you want >> each car to have its own contour? With your current thresholding, you can >> see that the four cars on the right are all connected, so you would get a >> single contour of the whole blob, rather than a contour of each car. >> 2) I just saw the doc<http://www.mathworks.com.au/help/images/ref/bwboundaries.html>for bwboundaries. Do you want the interior holes of the objects to have its >> own contour, or do you want just a contour *around* each object and don't >> care about the interior? Also, do you care about parent/child object >> relationships? My guess is no to both these questions. For example, do you >> want a contour around the windshield of each car? >> >> Comments: >> >> Note that when you do rgb2gray on a thresholded RGB image, you no longer >> have a binary image, but a grayscale image with levels 0, 0.333, 0.667, and >> 1.0. I think you probably mean to do rgb2gray followed by threshold. >> >> Either way, my suspicion is that you want to segment the cars first (get >> one binary blob object per car), then find their contours. Am I right? >> >> Juan. >> >> >> On Thu, Sep 12, 2013 at 8:24 PM, Payal Gupta <erpayal2010(a)gmail.com>wrote: >> >>> hi Juan... >>> i have done it.... :) :) >>> plz solve the contour problem. :( :( >>> reply me >>> >>> On Thursday, September 12, 2013 9:19:36 AM UTC+5:30, Juan Nunez-Iglesias >>> wrote: >>> >>>> On Thu, Sep 12, 2013 at 2:58 AM, Payal Gupta <erpay...(a)gmail.com>wrote: >>>> >>>>> hello... >>>>> i m also use this prog to count white pixel and black pixel bt i cant >>>>> save an image and cant count the pixel. >>>>> can you help me. >>>>> >>>> >>>> "white pixels" and "black pixels" will mean different things with >>>> different images. Can you send us a sample image? >>>> >>> -- >>> 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/rXRS0KT2PdU/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. >

1 0

Re: Get border pixels of labelled region
by Payal Gupta 13 Sep '13

13 Sep '13

hi juan.... i can't understand array after using find_contour which return a ndarray. it is main prob i wanna find out contour array. On Fri, Sep 13, 2013 at 6:07 AM, Juan Nunez-Iglesias <jni.soma(a)gmail.com>wrote: > Hi Payal, > > I think we're getting somewhere. =) Thanks for the image. > > Questions: > 1) Are you looking to segment out different cars? That is, do you want > each car to have its own contour? With your current thresholding, you can > see that the four cars on the right are all connected, so you would get a > single contour of the whole blob, rather than a contour of each car. > 2) I just saw the doc<http://www.mathworks.com.au/help/images/ref/bwboundaries.html>for bwboundaries. Do you want the interior holes of the objects to have its > own contour, or do you want just a contour *around* each object and don't > care about the interior? Also, do you care about parent/child object > relationships? My guess is no to both these questions. For example, do you > want a contour around the windshield of each car? > > Comments: > > Note that when you do rgb2gray on a thresholded RGB image, you no longer > have a binary image, but a grayscale image with levels 0, 0.333, 0.667, and > 1.0. I think you probably mean to do rgb2gray followed by threshold. > > Either way, my suspicion is that you want to segment the cars first (get > one binary blob object per car), then find their contours. Am I right? > > Juan. > > > On Thu, Sep 12, 2013 at 8:24 PM, Payal Gupta <erpayal2010(a)gmail.com>wrote: > >> hi Juan... >> i have done it.... :) :) >> plz solve the contour problem. :( :( >> reply me >> >> On Thursday, September 12, 2013 9:19:36 AM UTC+5:30, Juan Nunez-Iglesias >> wrote: >> >>> On Thu, Sep 12, 2013 at 2:58 AM, Payal Gupta <erpay...(a)gmail.com> wrote: >>> >>>> hello... >>>> i m also use this prog to count white pixel and black pixel bt i cant >>>> save an image and cant count the pixel. >>>> can you help me. >>>> >>> >>> "white pixels" and "black pixels" will mean different things with >>> different images. Can you send us a sample image? >>> >> -- >> 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/rXRS0KT2PdU/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. >

1 0

Re: Get border pixels of labelled region
by Payal Gupta 13 Sep '13

13 Sep '13

hi Juan... i have done it.... :) :) plz solve the contour problem. :( :( reply me On Thursday, September 12, 2013 9:19:36 AM UTC+5:30, Juan Nunez-Iglesias wrote: > > On Thu, Sep 12, 2013 at 2:58 AM, Payal Gupta <erpay...(a)gmail.com<javascript:> > > wrote: > >> hello... >> i m also use this prog to count white pixel and black pixel bt i cant >> save an image and cant count the pixel. >> can you help me. >> > > "white pixels" and "black pixels" will mean different things with > different images. Can you send us a sample image? >

2 1

Intensity plot of along the line
by Dan 12 Sep '13

12 Sep '13

Hi, Is there a way to generate an intensity plot of along the line using scikit-image (like Plot Profile option in imageJ) (example: http://imagej.1557.x6.nabble.com/file/n3682337/cracks.png). Thanks.

2 1

Get border pixels of labelled region
by Robin Wilson 12 Sep '13

12 Sep '13

Hi all, Is there a way to get the pixels on the border of a labelled region in an image using skimage? I've done edge detection, and then filled the resulting shapes (after some edge linking), and would now like to be able to get the pixels on the border of each of these shapes. I would have thought that getting borders would be an option in regionprops, but it doesn't seem to be. Any ideas? Cheers, Robin

3 4

Re: Get border pixels of labelled region
by Juan Nunez-Iglesias 12 Sep '13

12 Sep '13

On Thu, Sep 12, 2013 at 2:58 AM, Payal Gupta <erpayal2010(a)gmail.com> wrote: > hello... > i m also use this prog to count white pixel and black pixel bt i cant save > an image and cant count the pixel. > can you help me. > "white pixels" and "black pixels" will mean different things with different images. Can you send us a sample image?

1 0

Re: Get border pixels of labelled region
by Payal Gupta 11 Sep '13

11 Sep '13

hello... i m also use this prog to count white pixel and black pixel bt i cant save an image and cant count the pixel. can you help me. from skimage import measure from numpy import array import skimage.io as io from skimage import data_dir from skimage.data import coins,camera import matplotlib.pyplot as plt import skimage.color as color from skimage.data import camera from skimage.filter import canny, sobel import Image from skimage import data,filter image = io.imread("IMG_1.jpg") thresh = filter.threshold_otsu(image) binary = image > thresh imag= color.colorconv.rgb2grey(binary) img = array(imag) print img x = np.array((255, 255)) x = np.array((255, 255), dtype=np.uint8) #x[:] = np.arange(255) io.imsave('imag.png', x) #im = Image.open() white_points = 0 black_points=0 for row in range(0,244): for col in range(0, 461): if(img(row,col)==1): white_points = white_points+1 else: black_points = black_points+1 print white_points On Wed, Sep 11, 2013 at 1:49 PM, Payal Gupta <erpayal2010(a)gmail.com> wrote: > hello everyone... > i used find_contour function which returns a 2D ndarray . i can't > understand the return array so any body help me. > *program :* > > image = io.imread("IMG_2.jpg") > > thresh = filter.threshold_otsu(image) > > binary = image > thresh > > imag= color.colorconv.rgb2grey(binary) > > img = array(imag) > > edge_canny = canny(img) > > edge_sobel = sobel(img) > > contours = measure.find_contours(imag,0.9,'high') > > print contours > > fig, (ax0, ax1) = plt.subplots(ncols=2) > > ax0.imshow(imag ,cmap=plt.cm.gray) > > ax0.set_title('Roberts Edge Detection') > > ax0.axis('off') > > ax1.imshow(edge_canny, cmap=plt.cm.gray) > > ax1.set_title('Sobel Edge Detection') > > ax1.axis('off') > > > *returns array:* > > > [array([[ 135. , 72.9 ], > [ 134. , 72.9 ], > [ 133. , 72.9 ], > ..., > [ 1. , 21.52941176], > [ 0.47058824, 21. ], > [ 0. , 20.9 ]]), array([[ 0. , > 104.35137034], > [ 1. , 104.35137034], > [ 1.64862966, 105. ], > [ 2. , 105.1 ], 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[ 135. , 50.1 ]])] > >>> > Click here to Reply or Forward > Why this ad?Ads – > Best CTET Coaching Delhi<http://www.googleadservices.com/pagead/aclk?sa=L&ai=CXWpUwCYwUq__JrOoiga6x4…> > Classroom Coaching by Experts with Study Material & Mock Tests. 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Free Shipping, COD, Shop Now! > jabong.com/Sandals/Fastest_Delivery<http://www.googleadservices.com/pagead/aclk?sa=L&ai=CsfKtwCYwUq__JrOoiga6x4…> > ICICI™ Car Insurance<http://www.googleadservices.com/pagead/aclk?sa=L&ai=CenrHwCYwUq__JrOoiga6x4…> > Free Quick Quotes In 30 secs .Now, Also Use Fb to login & Insure > ICICILombard.com/Car_Insurance<http://www.googleadservices.com/pagead/aclk?sa=L&ai=CenrHwCYwUq__JrOoiga6x4…> > Jobs In TCS<http://www.googleadservices.com/pagead/aclk?sa=L&ai=CqOzuwCYwUq__JrOoiga6x4…> > Apply today - Upload your profile A Unique 4th Generation Job Portal > www.wisdomjobs.com<http://www.googleadservices.com/pagead/aclk?sa=L&ai=CqOzuwCYwUq__JrOoiga6x4…> > > <http://www.googleadservices.com/pagead/aclk?sa=L&ai=CXWpUwCYwUq__JrOoiga6x4…> > > > On Thu, Sep 5, 2013 at 12:19 PM, Juan Nunez-Iglesias <jni.soma(a)gmail.com>wrote: > >> Hi Payal, >> >> I think you're misunderstanding the purpose of "find_boundaries"... Not >> quite your fault since the documentation is pretty sparse there. >> >> I'll use my favourite fuzzball as an example: >> >> [image: Inline image 1] >> >> "find_boundaries" is meant to take in a segmentation, which is an image >> in which each region has a different integer label, like this one: >> >> [image: Inline image 2] >> >> Then, find_boundaries merely looks for pixels where the neighbouring >> labels are different: >> >> [image: Inline image 3] >> >> It's not doing any edge detection per se, it's just a tool for displaying >> segmentations when it is easier to look at edges than at regions (above). I >> think what you are after is edge detection? Maybe an image like this one: >> >> [image: Inline image 4] >> ? >> >> For that, you should directly use the edge detection algorithms, such as >> Sobel or Canny, without previously thresholding your image. Have a close >> look at the examples gallery to figure out if any are close to what you are >> after, and try to apply the code there to your own image: >> >> http://scikit-image.org/docs/dev/auto_examples/ >> >> Some of the more pertinent ones, I think: >> http://scikit-image.org/docs/dev/auto_examples/plot_canny.html >> http://scikit-image.org/docs/dev/auto_examples/plot_edge_filter.html >> >> http://scikit-image.org/docs/dev/auto_examples/plot_join_segmentations.html >> http://scikit-image.org/docs/dev/auto_examples/plot_label.html >> http://scikit-image.org/docs/dev/auto_examples/plot_marked_watershed.html >> >> http://scikit-image.org/docs/dev/auto_examples/plot_random_walker_segmentat… >> http://scikit-image.org/docs/dev/auto_examples/plot_watershed.html >> >> http://scikit-image.org/docs/dev/auto_examples/applications/plot_coins_segm… >> >> Note that in the edge detection examples, Canny/Sobel is applied to the >> image *before* any thresholding — unlike the example code you provided. >> >> Juan. >> >> >> On Wed, Sep 4, 2013 at 5:31 PM, Payal Gupta <erpayal2010(a)gmail.com>wrote: >> >>> hello everyone... >>> i will try this code,in this i want to do read a image then do edge >>> detection after that find the boundaries of image object. but >>> find_boundaries return me a bool array but i need a integer array. is it >>> any solution of this. >>> >>> >>> code:: >>> >>> import Image >>> >>> from skimage import segmentation as seg,io,filter >>> >>> imge = io.imread("IMG_1.jpg") >>> >>> thresh = filter.threshold_otsu(imge) >>> >>> binary = imge> thresh >>> >>> edge_canny = filter.canny(binary) >>> >>> bimg =seg.find_boundaries(binary) >>> >>> print(bimg) >>> >>> fig, (ax0, ax1) = plt.subplots(ncols=2) >>> >>> ax0.imshow(bimg,cmap=plt.cm.gray) >>> ax1.imshow(binary,cmap=plt.cm.gray) >>> >>> >>> On Tue, Sep 3, 2013 at 7:42 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: >>> >>>> >>>> On 3 Sep 2013 11:45, "Payal Gupta" <erpayal2010(a)gmail.com> wrote: >>>> > >>>> > thanks it working but i confused when i use function of skimage >>>> library. i want to change rgb image to a graylevel image but inbuilt >>>> function rgb2gray not convert gray level image. >>>> > reply. >>>> >>>> If you want help on this list, please provide code examples of what you >>>> are attempting. >>>> >>>> Stéfan >>>> >>>> -- >>>> 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/rXRS0KT2PdU/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. >>> >> >> -- >> 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/rXRS0KT2PdU/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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scikit-image September 2013