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:
  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 <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.


  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)



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.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

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Remote sensing and in-situ measurements

Geophysical Institute 
University of Alaska Fairbanks
Fairbanks, AK 99775

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Eyal Saiet

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Remote sensing and in-situ measurements

Geophysical Institute 
University of Alaska Fairbanks
Fairbanks, AK 99775

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