3D surface modeling of a giant redwood trunk

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mdavie
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Re: 3D surface modeling of a giant redwood trunk

Post by mdavie » Mon Jan 02, 2012 11:28 am

I suppose you could do something like that with ground-based lidar, but I don't know how you could discretely quantify what you were looking at (though I'm sure there's some way).

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M.W.Taylor
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Re: 3D spacial modeling of a giant redwood trunk

Post by M.W.Taylor » Wed Jan 04, 2012 12:36 am

Matt,

You previous posts have been very helpful. Thanks !

MIchael
fooman wrote:Hi Michael,

I can appreciate the issues in data acquisition. Unless your view points are rather small, then it may be possible to capture visible surfaces and interpolate between them. Either that or run a scanner up and down the trunk or along lines next to the trunk.

In terms of software, have you used MeshLab (http://meshlab.sourceforge.net/) - it is free software used for editing point cloud surfaces - I've had a play with it, but not much else. Don't know if there are any useful querying tools for the data.

Out of curiosity, has anyone had a play with submitting tree photos to Photosynth (http://www.photosynth.net/ and querying the resultant point cloud against known data to check accuracy? Lots of tree photo's already coverted to 3d point clouds there (e.g. http://photosynth.net/view.aspx?cid=3d7 ... 2367f10783).

Cheers,
matt
Last edited by M.W.Taylor on Tue Jan 10, 2012 6:10 pm, edited 2 times in total.

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DonCBragg
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Re: 3D spacial modeling of a giant redwood trunk

Post by DonCBragg » Wed Jan 04, 2012 9:54 am

Don and Ed,

I propose we do a special issue of the Bulletin of the Eastern Native Tree Society devoted to Michael and his ascendency to the top of the tree measuring hill. It is time that the whole world understands what he is accomplishing, often single-handedly. Obviously, we'd get stunning images and there would no doubt be some very interesting stories of discovery. If Michael is willing, what do you all think?

Bob[/quote]


Sorry for the delay in responding--I was out for the holidays...

I'd be very interested in material related to this work--the Bulletin of the ENTS can always use new submissions.

Don Bragg

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M.W.Taylor
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Re: 3D surface modeling of a giant redwood trunk

Post by M.W.Taylor » Wed Jan 04, 2012 5:19 pm

mdavie wrote:I suppose you could do something like that with ground-based lidar, but I don't know how you could discretely quantify what you were looking at (though I'm sure there's some way).
Yep. This ground base LIDAR would work well for mapping and volume calculation of Drury Tree. There are a number of programs that will isolate structures from within the cloud to assist.

I with I could afford such a system.

Michael

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M.W.Taylor
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Re: 3D spacial modeling of a giant redwood trunk

Post by M.W.Taylor » Wed Jan 04, 2012 5:23 pm

Bob, Don and Ed,

As Matt pointed out, I am not the first one to model a tree this way. Others are creating much denser cloud sets of tree trunks with LIDAR. However I do not know of any one calculating the precise volumes of trees using a surface of cloud set. This is new as far as I know.

I will do my best to not disappoint.

Michael


DonCBragg wrote:Don and Ed,

I propose we do a special issue of the Bulletin of the Eastern Native Tree Society devoted to Michael and his ascendency to the top of the tree measuring hill. It is time that the whole world understands what he is accomplishing, often single-handedly. Obviously, we'd get stunning images and there would no doubt be some very interesting stories of discovery. If Michael is willing, what do you all think?

Bob

Sorry for the delay in responding--I was out for the holidays...

I'd be very interested in material related to this work--the Bulletin of the ENTS can always use new submissions.

Don Bragg[/quote]

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Re: 3D surface modeling of a giant redwood trunk

Post by M.W.Taylor » Wed Jan 11, 2012 5:00 pm

I have decided to go hi-tech with the majority of the trunk surface modeling. The point by point approach was too slow to practically model a giant redwood tree for precise volume determination.

However there are a handful of widely available technologies including ground LIDAR and optical parallax scanners (Ms Kinect for example) that can quickly and accurately map a trunk. LIDAR has the best range. The problem is in a cluttered forest environment you get a lot of noise and unwanted cloud points. Hundreds of thousands potentially. But these can be filtered out.

See latest map of Drury, Terex and an unnamed giant redwood. ALso attached is a trunk scan of an oak tree using an optical scanner (measures pixel off-set ratio between a digital camera focal center and line laser projection and blends with photo pixel data).
The Impulse200LR and Mapsmart will be useful for hitting tight areas were cloud density is low and/or not reachable by optical scanning technology. I need to create a properly scaled skeleton framework with the MapSmart/Impulse200 combination first. With Drury, this framework is almost complete.

During my point by point mapping of Drury's lower 100ft of trunk, I discovered something interesting about Drury's structure. It was once 3 trees that merged into one. The tree leans a little so the direct over-head view does not show these vestigial side trunk iterations that merged. However I slight nudge on the tilting axis view shows these old trunks fused. I left the graph in the best over-head oblique position to see this. That would explain the flange-like protrusions on the side of Drury's trunk. Despite the old fusions, I still consider Drury to be one tree now.

See attached Excel spreadsheet of Drury's cloud map with rotating and tilting graphs. Also see attached screen captures from my 3D graphic software show the optical parallax scans of tree trunks, including Drury. These are HUGE clouds sets that are on average 100k in size. The trunk features are easily captured, with somewhat accurate color, bark texture and features such as burls and holes etc... Note the colorized pixels !

....see attached


Michael Taylor
WNTS VP
http://www.landmarktrees.net
Attachments
this particular view from the latest cloudset shows Drury's structure in a way not possible unless the tree is 3D surface modeled
this particular view from the latest cloudset shows Drury's structure in a way not possible unless the tree is 3D surface modeled
70k point cloud set of same oak tree after filtering out 29k of unwanted noise
70k point cloud set of same oak tree after filtering out 29k of unwanted noise
99k cloud map of oak tree lower bole prior to noise filtering
99k cloud map of oak tree lower bole prior to noise filtering
Optical Scanner easily picks up bark texture and trunk features...note the hole in side of trunk and small burl
Optical Scanner easily picks up bark texture and trunk features...note the hole in side of trunk and small burl
similar view as from photo..note small burl and "key-hole" in trunk at different perspective
similar view as from photo..note small burl and "key-hole" in trunk at different perspective
photoview in real life, not VR like previous two screen captures from 3D modeling software
photoview in real life, not VR like previous two screen captures from 3D modeling software
Last edited by M.W.Taylor on Thu Jan 12, 2012 11:42 pm, edited 1 time in total.

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dbhguru
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Re: 3D surface modeling of a giant redwood trunk

Post by dbhguru » Thu Jan 12, 2012 10:26 am

Michael,

Congratulations. You've created the finest hour for WNTS. Your modeling is exceptional and you keep pushing the technology forward. LTI is appropriately impressed. Please keep up the momentum.

Bob
Robert T. Leverett
Co-founder, Native Native Tree Society
Co-founder and President
Friends of Mohawk Trail State Forest
Co-founder, National Cadre

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edfrank
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Re: 3D surface modeling of a giant redwood trunk

Post by edfrank » Thu Jan 12, 2012 11:34 am

Michael,

The latest stuff is really impressive. All I can do is to encourage you to keep going forward with your work ad keep posting it here on the BBS. I also would encourage you to publish your work more formally in the Bulletin of the Eastern Native Tree Society. Don would welcome the contribution.

Ed
"I love science and it pains me to think that so many are terrified of the subject or feel that choosing science means you cannot also choose compassion, or the arts, or be awe by nature. Science is not meant to cure us of mystery, but to reinvent and revigorate it." by Robert M. Sapolsky

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M.W.Taylor
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Re: 3D surface modeling of a giant redwood trunk

Post by M.W.Taylor » Thu Jan 12, 2012 11:37 pm

Bob & Ed,

Thank you !

I should have more more Iconic Tree cloud sets for you to look at soon. If you download MeshLab, free open source 3D graphics viewer, you can see these models in all their glory. As soon as I get confirmation of people downloading MeshLab on this blog, I will post the PLY(X,Y,Z position + R,G,B color code for each cloud point) graphics files on ENTS.

Link to download MeshLab: http://meshlab.sourceforge.net/

I was planning to give specific details on how I did this in the Dendromorphometry book. The equipment costs =$500.

Ground Base LIDAR may have just been rendered obsolete for tree trunk mapping in terms of cost and equipment weight. We'll see soon.

The attached pictures are screen captures from MeshLab for another big redwood trunk I scanned with my exploring partner Mike Hanuschick. You can see his bald head, eyes, nose, chin, silver camera, maroon shirt and blue jeans. If you have the MeshLab software you can soom around to the other side of the tree and see Mike's backside...or go up and look down and see the top of Mike's head and shoulders.. The optical scanner was sensitive enough to pick up the human form from 30 feet away.

I hope have more big tree trunk scans to post in a few days.


Michael Taylor

WNTS VP
http://www.landmarktrees.net
Attachments
Mike under a redwood tree. Note bark color and texture and image of Mike under tree
Mike under a redwood tree. Note bark color and texture and image of Mike under tree
Mike under a redwood tree. Slightly different angle
Mike under a redwood tree. Slightly different angle

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edfrank
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Re: 3D surface modeling of a giant redwood trunk

Post by edfrank » Fri Jan 13, 2012 12:29 am

Mike,

I have downloaded and installed MeshLab, so at least one person as done it so far.

Ed
"I love science and it pains me to think that so many are terrified of the subject or feel that choosing science means you cannot also choose compassion, or the arts, or be awe by nature. Science is not meant to cure us of mystery, but to reinvent and revigorate it." by Robert M. Sapolsky

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