label_boundaries problem with ndim = label_img.ndim

[Eyal Saiet]

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 at 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 at 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)
>>
>>
>>
>>
>> [image: Inline image 1]
>>
>> On Tue, Dec 1, 2015 at 8:09 PM, Stefan van der Walt <stefanv at berkeley.edu
>> > wrote:
>>
>>> On 2015-12-01 21:00:16, Arctic_python <ejsaiet at 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
>>>
>>> --
>>> 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/PwmizxFahYE/unsubscribe.
>>> To unsubscribe from this group and all its topics, send an email to
>>> scikit-image+unsubscribe at googlegroups.com.
>>> To post to this group, send an email to scikit-image at googlegroups.com.
>>> To view this discussion on the web, visit
>>> https://groups.google.com/d/msgid/scikit-image/87zixt8mie.fsf%40berkeley.edu
>>> .
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
>>
>>
>> --
>> Eyal Saiet
>>
>> Project manager
>> Remote sensing and in-situ measurements
>>
>> Geophysical Institute
>> University of Alaska Fairbanks
>> Fairbanks, AK 99775
>> (907) 750 6555 (cell)
>>
>> ejsaiet at alaska.edu
>>
>> --
>> 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 at googlegroups.com.
>> To post to this group, send email to scikit-image at googlegroups.com.
>> To view this discussion on the web, visit
>> https://groups.google.com/d/msgid/scikit-image/CA%2BysReAKgzF%3DJXEjz7hti8sz0EBS_Hr%3DPaFWTxN6FV-GtROB0w%40mail.gmail.com
>> <https://groups.google.com/d/msgid/scikit-image/CA%2BysReAKgzF%3DJXEjz7hti8sz0EBS_Hr%3DPaFWTxN6FV-GtROB0w%40mail.gmail.com?utm_medium=email&utm_source=footer>
>> .
>>
>> For more options, visit https://groups.google.com/d/optout.
>>
>
> --
> 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/PwmizxFahYE/unsubscribe.
> To unsubscribe from this group and all its topics, send an email to
> scikit-image+unsubscribe at googlegroups.com.
> To post to this group, send email to scikit-image at googlegroups.com.
> To view this discussion on the web, visit
> https://groups.google.com/d/msgid/scikit-image/CA%2BJHcKT5TijcW_Xa%3DEJt%2Bdi-o_3Hn5PmuHJzXc0YyM44vFr%2BDA%40mail.gmail.com
> <https://groups.google.com/d/msgid/scikit-image/CA%2BJHcKT5TijcW_Xa%3DEJt%2Bdi-o_3Hn5PmuHJzXc0YyM44vFr%2BDA%40mail.gmail.com?utm_medium=email&utm_source=footer>
> .
>
> For more options, visit https://groups.google.com/d/optout.
>



-- 
Eyal Saiet

Project manager
Remote sensing and in-situ measurements

Geophysical Institute
University of Alaska Fairbanks
Fairbanks, AK 99775
(907) 750 6555 (cell)

ejsaiet at alaska.edu
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20151201/0de5884a/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 20790 bytes
Desc: not available
URL: <http://mail.python.org/pipermail/scikit-image/attachments/20151201/0de5884a/attachment.png>