Question about soma_tree (influence in tree.D(1)) about treestoolbox HOT 9 CLOSED

Hi @natsrm ,
thank you for appreciation!
Generally my advice would be not overwriting functions with a variable (what you did in the case of soma_tree), otherwise the function cannot be called anymore in that script.
Concerning your issue, one possibility I can think of is that you used the '-b' options of soma_tree and have a multifurcation at your root node. In that case the diameter is decreased at each branch point to account for overlapping surfaces. --> If you have a trifurcation at your root: 18.8 / sqrt(2) / sqrt(2) = 9.4

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Hi @MarcelBeining ,
Thank you for your fast reply!
For me the only option that appears as "available" to use with soma_tree is '-s', and I use the default which is none. But yes you're right, I have multifurcations!!! So how can I fix this? Is there a way to not use option '-b' in soma_tree? Or is the best thing to just apply elimt_tree?
Thanks,
Nats

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@MarcelBeining An update:
I used elimt_tree to remove all multifurcations, and later applied soma_tree just as before. My outputs are still the same, even without having trifurcations...

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Hi @natsrm ,
hm it's hard to say what the problem is without debugging it with your tree. Can you provide the tree as a download link so I can have a look? If you don't want to have it public, you can also send it to me via [email protected]

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Hi @MarcelBeining ,
It's actually from Neuromorpho so no problem! The difference between this tree and the original from the repository, is I have aligned all of them with Vaa3D (Blastneuron). As a sample I am just sending you one:
https://wetransfer.com/downloads/0e0685c9901f23cf9f1e505e9207a8f220190402133039/b25b3ab59b2db9edd34255c661cae69120190402133039/565588

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Hm, when I am using your providing tree and execute your code:

tree = load_tree('traced-WT-Female-hippo-122-1.CNG.swc_preprocessed.swc');

q_tree = quaddiameter_tree(tree, 0.01, [], []);
s_tree = soma_tree(q_tree, tree.D(1), [], []);

tree.D(1)
s_tree.D(1)

I get

ans =

   18.8000


ans =

   18.8000

Can you confirm, using the same code and file?
By the way, what version of TREES do you use? How did you download and install?

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Hi @MarcelBeining ,

Using the same file and the same code I still get the problem...

tree.D(1)
ans = 18.8000
s_tree.D(1)
ans = 9.4000

My version is 1.15, and I downloaded the zipped version from the website.

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Oh no, 1.15 is a legacy version!
Please download from the newest master branch:
https://github.com/cuntzlab/treestoolbox/archive/master.zip
Overwrite your version and try again!
Sorry for the confusion!

I will tell @hermanncuntz to better mark on his webpage what the newest version is!

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Oh no! That's very unfortunate... Yes, then the webpage could use some changes! Ahaha because it talks about 1.15 as the "stable version", and even on the "how to get started", it specificly says to download v1.15, which is why I used that...

With the newest master branch it works fine!!! The values are the same!
Now this explains why I didn't understand when you talked about option '-b' in soma_tree, because in fact in v1.15 this option does not exist!

Thank you for all your help @MarcelBeining 👍

How to solve: Make sure you are not using v1.15, but the newest master branch! :)

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