'skeleton_id' to 'skeleton-id'

[habi]

Otherwise, I was not able to get https://skeleton-analysis.org/stable/examples/visualizing_3d_skeletons.html to work...

I found the correct value with

for i in paths_table:
    print(i)

which gave me

skeleton-id
node-id-src
node-id-dst
branch-distance
branch-type
mean-pixel-value
stdev-pixel-value
image-coord-src-0
image-coord-src-1
image-coord-src-2
image-coord-dst-0
image-coord-dst-1
image-coord-dst-2
coord-src-0
coord-src-1
coord-src-2
coord-dst-0
coord-dst-1
coord-dst-2
euclidean-distance
path_id
random_path_id

[jni]

@habi we are in the middle of moving to _ as the separator, that's why there is this line in the example:

paths_table = skan.summarize(skeleton, separator='_')

Perhaps you are using an older version of the example?

Note the separator= kwarg. Please make sure you provide the separator and use a consistent separator throughout your code.

The motivation for the change is discussed in #215 (comment).

I'm going to close this but please let me know if the above doesn't clear up what was going wrong — happy to discuss further!

[habi]

That also explains why paths_table = skan.summarize(skeleton, separator='_'' didn't work when copy-pasting from https://skeleton-analysis.org/stable/examples/visualizing_3d_skeletons.html :)

I got

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[142], line 1
----> 1 paths_table = skan.summarize(skeleton, separator='_')

TypeError: summarize() got an unexpected keyword argument 'separator'

and just removed the separator-option without really understanding the conseqences...

skan.__version__ = '0.11.1' BTW

[jni]

aaah, sorry, the problem is that the docs are skan v0.12 (which is out already) but for some reason that I haven't had time to chase up, the version switcher isn't working correctly (#233). You're after https://skeleton-analysis.org/0.11.x/examples/visualizing_3d_skeletons.html 😅 Sorry about that!

[habi]

No worries, I was still able to get skan working easily, which is a first for any given library I‘ve tried to use.
Now I’m looking at the output of the library on tomographic datasets containing (contrasted) vessels…