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QSM- Output csv file

Added by ARSENIOU GEORGIOS over 1 year ago

Hi all,

I would like to ask you a couple of questions about the QSM output csv file named “detailed”. The file is consisted from thousands of rows, that are probably associated with the fitted cylinders. I would like to know for each branch, how many cylinders are fitted, what is the length, the diameter, the volume and the order of the corresponding branch. The same I would like to know about the trunk i.e. what are the fitted cylinders, volume, DBH. Furthermore, I would like to know what is the main stem and the total height of the tree. Could you please explain me how I can derive this information from the resulted csv file? The current form of the csv file does not help me to get what I need to know. I am attaching a screenshot of the csv column names.

Finally, I used the algorithm to create QSM for an Austrian Pine but the resulted model was not good, because most of the laser hits come from the needles and the point cloud density in the interior part of the tree (i.e. stem and branches) is less dense. Do you have any suggestions for a set of filters or a pipeline process specifically for conifers that eliminate most of the needle hits but retain the branches and the stem? I am attaching a screenshot of the resulted QSM.

I use the Computree 4.0

Thanks,
Georgios Arseniou


Replies (6)

RE: QSM- Output csv file - Added by Hackenberg Jan over 1 year ago

Hi

second question first:
Yes I have two options for coniferous trees. The first one is full automatic, you find the pipeline here:
http://rdinnovation.onf.fr/projects/computree-simpletree-beta-version/files
The CT script file is named SimpleTree_Beta_4.33.06_Plot_Coniferous.xsct2, but you need to stick with the last version I uploaded on the same page (4.33.06) most likely or reprogram it with a newer/older version. The script is also bit described in this video (https://www.youtube.com/watch?v=8zHqHAk6Iek) and (https://www.youtube.com/watch?v=VCXuIF9J2sQ). You can see that you will loose the majority of branches though.
The second option is to use my supervised machine learning filter, if I remember correctly I named it something like advanced belton et al - which is the closest publication I found for my own filter. In fact I replaced the feature space by a more advanced one, but that is deep computational geometry stuff. You find a video here:https://www.youtube.com/watch?v=ZYdmWVxtPDE. The procedure is slow, but you can remain branches.

The stem can be extracted by extracting all branch cylinders with rbanch order 0. There is also a branch ID. You can iterate over all branch id’s and extract single branches. Lets say you have extracted the branch number 1. It might have something like 100 cylinders. The diameter is obviously two times the radius of the first of the 50 cylinders. For the volume you can either directly take the Growthvolume or sum up the volume of all 50 cylinders. The length up to the tip is a bit more demanding. Take the start x,y,z of the first cylinder. Compute the distance to all 50 end points and choose the largest distance.

For the extracting branch parts: during my phd a uploaded a bunch of R-tutorials on youtube. Unfortunately I forgot the old youtube channel name, but maybe another user can help you here out.

I hope this helps
Jan

RE: QSM- Output csv file - Added by Hackenberg Jan over 1 year ago

PS I saw you use CT version 4. I think this one is pretty old? You should stick to a newer version if possible. Test out:Diabolo_Release_SimpleTree_Beta_4.33.06_Computree 5.0.054b.zip from the dl page I posted above or one of Alexandres newer 5.xx.xx CT releases which he might uploaded from September on. The SimpleTree in CT4 still contains a lot of bugs which I fixed later on and the above confierous solutions might even not exist there.

RE: QSM- Output csv file - Added by ARSENIOU GEORGIOS over 1 year ago

Hello Dr. Hackenberg,

Thank you very much for your detailed answer. I have some more questions. So, branch cylinders of order 0 belong to the main stem or just trunk? How can we detect the main stem that goes also inside the crown? Also, what about branch ID=-1, does it belong to the stem? Furthermore, what is the difference between segment ID and parent segment ID? If we want to calculate the volume of a branch we can add together the growth volume of each cylinder that belongs to this certain branch. If we want to calculate the branch length, can we simply add the growth length of the cylinders in this branch? Could you also explain me the difference between the columns growth length and length? and the difference between the columns length to leave and length to segment? How can we extract DBH and total tree height, and what are the Units for all these measurement values?

Finally, on the website that you previously mentioned, there is a pipeline named “SimpleTree_Beta_###_Plot_Leave_off”, is it a pipeline that you suggest for modeling trees without leaves? Thank you in advance and please excuse me for bombardizing you with questions.

Georgios

RE: QSM- Output csv file - Added by Hackenberg Jan over 1 year ago

Hi Georgios

So, branch cylinders of order 0 belong to the main stem or just trunk?
stem

How can we detect the main stem that goes also inside the crown?
with branch order 0, but your version contains more errors that the newer version I posted previously in the other answer
Also, what about branch ID=-1, does it belong to the stem?
yes you could simply have checked it out. I highly recommend R software for all what you are doing.
Furthermore, what is the difference between segment ID and parent segment ID?
read about trees in informatician on wiki. or my papers. the simpletree paper or my thesis on researchgate.
If we want to calculate the volume of a branch we can add together the growth volume of each cylinder that belongs to this certain branch.
no not the growth volume. you need to add the volume, i should give it also in your version. Or compute it from cylinder formula, but dont mess up units.
If we want to calculate the branch length, can we simply add the growth length of the cylinders in this branch?
no similar to before. compute length from startx,y,z and endx,y,z - you can also use this result to compute the volume from above answer.
Could you also explain me the difference between the columns growth length and length?
Read the simpletree paper. Growth length does not show up, but its the pendant to the volume. The Growthvolume is the volume you would measure from a branchpart if you would cut the tree there at the according cylinder position. the growthlength is the cumlative length of all branch parts including side branches. gives nice plots vs the radius both of those parameters. you should read enquist et al for the volume part. well its something similar what i do when building my growthvolume power function in the simpletree paper.
and the difference between the columns length to leave and length to segment? 
length to leave is the length to the leave of the same branch and same branch order. Length to segment i dont know anymore if it is not the length of the segment...

cheers
Jan

RE: QSM- Output csv file - Added by Hackenberg Jan over 1 year ago

Hi Georgios

So, branch cylinders of order 0 belong to the main stem or just trunk?
stem

How can we detect the main stem that goes also inside the crown?
with branch order 0, but your version contains more errors that the newer version I posted previously in the other answer
Also, what about branch ID=-1, does it belong to the stem?
yes you could simply have checked it out. I highly recommend R software for all what you are doing.
Furthermore, what is the difference between segment ID and parent segment ID?
read about trees in informatician on wiki. or my papers. the simpletree paper or my thesis on researchgate.
If we want to calculate the volume of a branch we can add together the growth volume of each cylinder that belongs to this certain branch.
no not the growth volume. you need to add the volume, i should give it also in your version. Or compute it from cylinder formula, but dont mess up units.
If we want to calculate the branch length, can we simply add the growth length of the cylinders in this branch?
no similar to before. compute length from startx,y,z and endx,y,z - you can also use this result to compute the volume from above answer.
Could you also explain me the difference between the columns growth length and length?
Read the simpletree paper. Growth length does not show up, but its the pendant to the volume. The Growthvolume is the volume you would measure from a branchpart if you would cut the tree there at the according cylinder position. the growthlength is the cumlative length of all branch parts including side branches. gives nice plots vs the radius both of those parameters. you should read enquist et al for the volume part. well its something similar what i do when building my growthvolume power function in the simpletree paper.
and the difference between the columns length to leave and length to segment? 
length to leave is the length to the leave of the same branch and same branch order. Length to segment i dont know anymore if it is not the length of the segment...

cheers
Jan

RE: QSM- Output csv file - Added by Hackenberg Jan over 1 year ago

Finally, on the website that you previously mentioned, there is a pipeline named “SimpleTree_Beta_###_Plot_Leave_off”, is it a pipeline that you suggest for modeling trees without leaves?
yes but feel free to use the coniferous script if you are only interested in stem. also for broadleaves, but the the bending of stem might be an issue. analyse yourself.

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