Re: image segmentation error (tuple index out of range)
Done! https://github.com/scikit-image/scikit-image/issues/1867 On Thu, Jan 07, 2016 at 11:47:14PM -0800, Stéfan van der Walt wrote:
Hi, Emmanuelle
Please file a ticket so that we don't forget about this missing feature.
Thanks! Stéfan
On Jan 8, 2016 09:44, "Emmanuelle Gouillart" <emmanuelle.gouillart@nsup.org> wrote:
Hello Anurag,
my guess is that your image is an RGB image, so that its shape is (n_rows, n_cols, 3). I could reproduce your problem using the RGB astronaut image from scikit-image (data.astronaut()). ``threshold_otsu`` is not very well adapted to RGB images because it mixes together the color channels by first raveling all pixels. [Note for dev team: this should be better documented, and we should look for a thresholding algorithm compatible with RGB images]
Therefore ``image > thresh`` is a 3-D array (or 2-D color, you can try imshow on this array). You can try determining the threshold value on a grayscale image if it's possible for you, using the as_grey keyword argument in io.imread. Or you can determine a threshold for each color channel.
Cheers, Emma
On Thu, Jan 07, 2016 at 09:04:48PM -0800, Anurag Phadke wrote: > Hello, > I am trying to run "image segmentation" on the attached image. Code at: > https://gist.github.com/anuragphadke/7eb0e4398ef005632c6d
> However, on running the above script, i get the following error:
> Traceback (most recent call last): > Â File "a.py", line 21, in <module> > Â Â Â bw = closing(image > thresh, square(3)) > Â File "/Library/Python/2.7/site-packages/skimage/morphology/misc.py", line 37, > in func_out > Â Â Â return func(image, selem=selem, *args, **kwargs) > Â File "/Library/Python/2.7/site-packages/skimage/morphology/grey.py", line > 122, in func_out > Â Â Â out_temp = func(image, selem, out=out_temp, *args, **kwargs) > Â File "/Library/Python/2.7/site-packages/skimage/morphology/grey.py", line > 349, in closing > Â Â Â dilated = dilation(image, selem) > Â File "/Library/Python/2.7/site-packages/skimage/morphology/misc.py", line 37, > in func_out > Â Â Â return func(image, selem=selem, *args, **kwargs) > Â File "/Library/Python/2.7/site-packages/skimage/morphology/grey.py", line > 251, in dilation > Â Â Â nd.grey_dilation(image, footprint=selem, output=out) > Â File "/usr/local/lib/python2.7/site-packages/scipy/ndimage/ morphology.py", > line 1295, in grey_dilation > Â Â Â sz = footprint.shape[ii] > IndexError: tuple index out of range
> Any idea what might be wrong here? I tried multiple images and multiple file > formats (jpg / png etc.)
> -anurag
thx emma + Stefan. Here's my temporary work-around: Convert to Grayscale, save as JPG, run the code. -anurag On Thu, Jan 7, 2016 at 11:59 PM, Emmanuelle Gouillart < emmanuelle.gouillart@nsup.org> wrote:
Done! https://github.com/scikit-image/scikit-image/issues/1867
On Thu, Jan 07, 2016 at 11:47:14PM -0800, Stéfan van der Walt wrote:
Hi, Emmanuelle
Please file a ticket so that we don't forget about this missing feature.
Thanks! Stéfan
On Jan 8, 2016 09:44, "Emmanuelle Gouillart" < emmanuelle.gouillart@nsup.org> wrote:
Hello Anurag,
my guess is that your image is an RGB image, so that its shape is (n_rows, n_cols, 3). I could reproduce your problem using the RGB astronaut image from scikit-image (data.astronaut()).
``threshold_otsu``
is not very well adapted to RGB images because it mixes together the color channels by first raveling all pixels. [Note for dev team: this should be better documented, and we should look for a thresholding algorithm compatible with RGB images]
Therefore ``image > thresh`` is a 3-D array (or 2-D color, you can
try
imshow on this array). You can try determining the threshold value
on a
grayscale image if it's possible for you, using the as_grey keyword argument in io.imread. Or you can determine a threshold for each
color
channel.
Cheers, Emma
On Thu, Jan 07, 2016 at 09:04:48PM -0800, Anurag Phadke wrote: > Hello, > I am trying to run "image segmentation" on the attached image.
Code at:
> However, on running the above script, i get the following error:
> Traceback (most recent call last): > File "a.py", line 21, in <module> > bw = closing(image > thresh, square(3)) > File
"/Library/Python/2.7/site-packages/skimage/morphology/misc.py",
line 37, > in func_out > return func(image, selem=selem, *args, **kwargs) > File
"/Library/Python/2.7/site-packages/skimage/morphology/grey.py",
line > 122, in func_out > out_temp = func(image, selem, out=out_temp, *args, **kwargs) > File
"/Library/Python/2.7/site-packages/skimage/morphology/grey.py",
line > 349, in closing > dilated = dilation(image, selem) > File
"/Library/Python/2.7/site-packages/skimage/morphology/misc.py",
line 37, > in func_out > return func(image, selem=selem, *args, **kwargs) > File
"/Library/Python/2.7/site-packages/skimage/morphology/grey.py",
line > 251, in dilation > nd.grey_dilation(image, footprint=selem, output=out) > File "/usr/local/lib/python2.7/site-packages/scipy/ndimage/ morphology.py", > line 1295, in grey_dilation > sz = footprint.shape[ii] > IndexError: tuple index out of range
> Any idea what might be wrong here? I tried multiple images and
multiple
file > formats (jpg / png etc.)
> -anurag
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participants (2)
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Anurag -
Emmanuelle Gouillart