Re: label_boundaries problem with ndim = label_img.ndim
You don't need to find the boundaries manually before calling mark_boundaries. From the docstring of mark_boundaries:
Parameters ---------- image : (M, N[, 3]) array Grayscale or RGB image. label_img : (M, N) array of int Label array where regions are marked by different integer values.
Currently, you are passing a boolean array to a function that expects an integer array, which is why it's failing.
In general, it's a good idea to try typing "help(function_name)" when things are failing to make sure that you are passing in the right information to the function you're using! (You can then press "q" to exit help.)
I hope that, erm, helps! =)
Juan.
On Wed, Dec 2, 2015 at 6:46 PM, Eyal Saiet ejsaiet@alaska.edu wrote:
thanks Juan, I have tried that too:
- label_image=measure.label(g_median_bin, background=0)
- label_image +=1
- plt.figure()
- plt.imshow(label_image,cmap=plt.cm.gray,interpolation='nearest',
origin='lower') 5. plt.title('label_image') 6. plt.show() 7. props=measure.regionprops(label_image,intensity_image=g_median_bin) 8. label_bound=segmentation.find_boundaries(label_image,connectivity=1, mode='thick',background=0) 9. boundaries=segmentation.mark_boundaries(g_median,label_bound)
Traceback (most recent call last): File attributes_thrash.py", line 127, in <module>
boundaries=segmentation.mark_boundaries(g_median,label_bound)#,color=(1,0,0), outline_color=None, mode='outer', background_label=0) File "/usr/local/lib/python3.4/dist-packages/skimage/segmentation/boundaries.py", line 213, in mark_boundaries background=background_label) File "/usr/local/lib/python3.4/dist-packages/skimage/segmentation/boundaries.py", line 156, in find_boundaries max_label = np.iinfo(label_img.dtype).max File "/usr/local/lib/python3.4/dist-packages/numpy/core/getlimits.py", line 254, in __init__ raise ValueError("Invalid integer data type.") ValueError: Invalid integer data type.
Process finished with exit code 1
On Tue, Dec 1, 2015 at 10:38 PM, Juan Nunez-Iglesias jni.soma@gmail.com wrote:
Hi Eyal,
You are passing a list of regionprops (props, in your code) to "find_boundaries", whereas it expects an array: a single image of labeled objects (label_img, in your code).
Juan.
On Wed, Dec 2, 2015 at 5:33 PM, Eyal Saiet ejsaiet@alaska.edu wrote:
Stefan, I do not understand what is not true about the label_image object. bellow is the code, in addition I added a plot of the label_image object.
- label_image=measure.label(g_median_bin, background=0)
- label_image +=1
- plt.figure()
- plt.imshow(label_image,cmap=plt.cm.gray,interpolation='nearest',
origin='lower') 5. plt.title('label_image') 6. plt.show() 7. props = measure.regionprops(label_image,intensity_image =g_median_bin) 8. label_bound=segmentation.find_boundaries(props,connectivity=1,mode ='thick',background=0) 9. boundaries=segmentation.mark_boundaries(g_median,label_bound)
[image: Inline image 1]
On Tue, Dec 1, 2015 at 8:09 PM, Stefan van der Walt < stefanv@berkeley.edu> wrote:
On 2015-12-01 21:00:16, Arctic_python ejsaiet@alaska.edu wrote:
ndim = label_img.ndimAttributeError: 'list' object has no attribute 'ndim'
- label_image=measure.label(g_median_bin, background=0) #
g_median_bin
is a binary image
That does not seem to be true, given the error message.
Stéfan
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-- Eyal Saiet
Project manager Remote sensing and in-situ measurements
Geophysical Institute University of Alaska Fairbanks Fairbanks, AK 99775 (907) 750 6555 (cell)
ejsaiet@alaska.edu
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-- Eyal Saiet
Project manager Remote sensing and in-situ measurements
Geophysical Institute University of Alaska Fairbanks Fairbanks, AK 99775 (907) 750 6555 (cell)
ejsaiet@alaska.edu
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Juan Nunez-Iglesias