Re: label_boundaries problem with ndim = label_img.ndim

thanks Juan, I have tried that too: 1. label_image=measure.label(g_median_bin, background=0) 2. label_image +=1 3. plt.figure() 4. 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 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 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.

1. label_image=measure.label(g_median_bin, background=0) 2. label_image +=1 3. plt.figure() 4. 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

...

wrote:

...

On 2015-12-01 21:00:16, Arctic_python wrote:

...

ndim = label_img.ndim AttributeError: 'list' object has no attribute 'ndim'

1. 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