Closed davodogster closed 1 year ago
Hi Sam,
Yes could work ! I suggest you use model= "simpletree" with _readQSM function. Your input has to be like this :
startX; startY ; startZ ; endX ; endY ; radius ; axis_ID; branching_order
Be consistent with the colum order. _axisID and _branchingorder can be 0 and will be recalculated when using build_archi function.
Best
Olivier
I notice no 'endZ' so is that not required? @oliviermartin7 My second Q is we also have the skeleton in MTG format. https://mtg.readthedocs.io/en/latest/user/intro.html#mtg-file Do you think it's possible to do the same with MTG to aRchi?
I will plan to try this.
Thank you! Sam
@davodogster. oups ! You're right I forgot the z. So it is:
startX; startY ; startZ ; endX ; endY ; endZ; radius ; axis_ID; branching_order
For MTG, it is something we have to do for a while but we did not yet... If you are keen to code it would be awesome to add it to aRchi !!
Best,
Olivier
@VEZY
Yes I didn't have time to get into this yet. @davodogster you can look into this repo for the MTG format: https://github.com/VEZY/XploRer/
You can read an MTG, and then extract its content as a data.frame with data.tree::ToDataFrameTree. An example is given here.
The full doc is here: https://vezy.github.io/XploRer/index.html
Keep in mind this package is currently in a stale state because R is too slow for heavy computations, so I rapidly switched to Julia and developed this package instead. So XploRer lacks a lot of features compared to MultiScaleTreeGraph.jl.
Thanks a lot Rémi for the information @VEZY !!
Hi @oliviermartin7
I have a tree skeleton with edges and vertices like this in SWC Skeletor (github) format:![image](https://user-images.githubusercontent.com/46079516/227090369-5724f581-d941-464e-932e-03118d973948.png)
Do you think it's easy to convert it to the aRchi skeleton format so we can derive tree params/architecture metrics from it? Please let me know if you can assist or have suggestions.
Cheers, Sam