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PCL octree, merging a sub tree

Ender1618
So I have a rather large PCL octree, i was hoping to load subtrees of this octree from disk as needed. Is there any way to merge a subtree back into a full octree?

For example i have a tree of depth 16 with a voxel size of 1cm.  Right now I only store occupancy, and get leaf centers to visualize. But with a tree that size i may have ALOT of leaves, more than I could safely fit into system or GPU memory.  I would like to cache the subtrees in as need, and keep them in a LRU queue.
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Re: PCL octree, merging a sub tree

airuno2l
I don't know much about it, but this might get you heading down the right road:  http://pointclouds.org/blog/urcs/ 

On Mon, Jul 30, 2012 at 5:49 PM, Ender1618 <[hidden email]> wrote:
So I have a rather large PCL octree, i was hoping to load subtrees of this
octree from disk as needed. Is there any way to merge a subtree back into a
full octree?

For example i have a tree of depth 16 with a voxel size of 1cm.  Right now I
only store occupancy, and get leaf centers to visualize. But with a tree
that size i may have ALOT of leaves, more than I could safely fit into
system or GPU memory.  I would like to cache the subtrees in as need, and
keep them in a LRU queue.



--
View this message in context: http://www.pcl-users.org/PCL-octree-merging-a-sub-tree-tp4020929.html
Sent from the Point Cloud Library (PCL) Users mailing list archive at Nabble.com.
_______________________________________________
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--
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Re: PCL octree, merging a sub tree

clockwise9
Julius the developer of the PCL octree is doing what you describe in a project that he's involved with.  I don't think the part you're interested in is open sourced and/or available.

Both http://pointclouds.org/blog/trcs/rosen/ and http://pointclouds.org/blog/urcs/ are code sprints to solve the problem you've described.  Unfortunately, I still need to develop the frustum culling and LRU caching aspect to actually make it outofcore.  If you want some more info or help getting started with the outofcore octree code let me know.

Cheers,
Justin

On Mon, Jul 30, 2012 at 6:58 PM, Aaron O'Toole <[hidden email]> <[hidden email]> wrote:
I don't know much about it, but this might get you heading down the right road:  http://pointclouds.org/blog/urcs/ 


On Mon, Jul 30, 2012 at 5:49 PM, Ender1618 <[hidden email]> wrote:
So I have a rather large PCL octree, i was hoping to load subtrees of this
octree from disk as needed. Is there any way to merge a subtree back into a
full octree?

For example i have a tree of depth 16 with a voxel size of 1cm.  Right now I
only store occupancy, and get leaf centers to visualize. But with a tree
that size i may have ALOT of leaves, more than I could safely fit into
system or GPU memory.  I would like to cache the subtrees in as need, and
keep them in a LRU queue.



--
View this message in context: http://www.pcl-users.org/PCL-octree-merging-a-sub-tree-tp4020929.html
Sent from the Point Cloud Library (PCL) Users mailing list archive at Nabble.com.
_______________________________________________
[hidden email] / http://pointclouds.org
http://pointclouds.org/mailman/listinfo/pcl-users



--
- Aaron O'Toole

_______________________________________________
[hidden email] / http://pointclouds.org
http://pointclouds.org/mailman/listinfo/pcl-users



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Re: PCL octree, merging a sub tree

Ender1618
Are any of these out of core implementations near being released? Are there any use examples of the semi-released version available? If not I am afraid I might need to implement a version myself, due to the immediate need I have for something like this.
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Re: PCL octree, merging a sub tree

Ender1618
This post was updated on .
How are people generally approaching this problem? I am not interested in maintaining the original points, but instead the voxel centers of the leaf nodes. Are people generally approaching this as an octree containing other (subtree) cache-able octrees (which can be loaded at different levels of detail via controlling depth)? What exactly is being cached/stored on disk, the voxel centers or the serialized octree occupancy vector (breadth first traversal with each branch described by a one byte bitmask)?
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Re: PCL octree, merging a sub tree

Ender1618
In reply to this post by clockwise9
Do you have an example of your code's usage, where could I a copy of you open sourced code?

clockwise9 wrote
Julius the developer of the PCL octree is doing what you describe in a
project that he's involved with.  I don't think the part you're interested
in is open sourced and/or available.

Both *http://pointclouds.org/blog/trcs/rosen/* and
http://pointclouds.org/blog/urcs/ are code sprints to solve the problem
you've described.  Unfortunately, I still need to develop the frustum
culling and LRU caching aspect to actually make it outofcore.  If you want
some more info or help getting started with the outofcore octree code let
me know.

Cheers,
Justin

On Mon, Jul 30, 2012 at 6:58 PM, Aaron O'Toole <[hidden email]> <
[hidden email]> wrote:

> I don't know much about it, but this might get you heading down the right
> road:  http://pointclouds.org/blog/urcs/
>
>
> On Mon, Jul 30, 2012 at 5:49 PM, Ender1618 <[hidden email]> wrote:
>
>> So I have a rather large PCL octree, i was hoping to load subtrees of this
>> octree from disk as needed. Is there any way to merge a subtree back into
>> a
>> full octree?
>>
>> For example i have a tree of depth 16 with a voxel size of 1cm.  Right
>> now I
>> only store occupancy, and get leaf centers to visualize. But with a tree
>> that size i may have ALOT of leaves, more than I could safely fit into
>> system or GPU memory.  I would like to cache the subtrees in as need, and
>> keep them in a LRU queue.
>>
>>
>>
>> --
>> View this message in context:
>> http://www.pcl-users.org/PCL-octree-merging-a-sub-tree-tp4020929.html
>> Sent from the Point Cloud Library (PCL) Users mailing list archive at
>> Nabble.com.
>> _______________________________________________
>> [hidden email] / http://pointclouds.org
>> http://pointclouds.org/mailman/listinfo/pcl-users
>>
>
>
>
> --
> - Aaron O'Toole
>
> _______________________________________________
> [hidden email] / http://pointclouds.org
> http://pointclouds.org/mailman/listinfo/pcl-users
>
>

_______________________________________________
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Re: PCL octree, merging a sub tree

Julius Kammerl-2
Hi Ender1618,

like Justin mentioned, it sounds like what you are looking for is the
out-of-core component of PCL.

If you would like to stick to the PCL octree, you can just define a
"top-level" octree with a large voxel size. All points that fall within
these voxels can be stored to disk and loaded when needed.

Best,
Julius

On 08/01/2012 12:38 AM, Ender1618 wrote:

> Do you have an example of your code's usage, where could I a copy of you open
> sourced code?
>
>
> clockwise9 wrote
>>
>> Julius the developer of the PCL octree is doing what you describe in a
>> project that he's involved with.  I don't think the part you're interested
>> in is open sourced and/or available.
>>
>> Both *http://pointclouds.org/blog/trcs/rosen/* and
>> http://pointclouds.org/blog/urcs/ are code sprints to solve the problem
>> you've described.  Unfortunately, I still need to develop the frustum
>> culling and LRU caching aspect to actually make it outofcore.  If you want
>> some more info or help getting started with the outofcore octree code let
>> me know.
>>
>> Cheers,
>> Justin
>>
>> On Mon, Jul 30, 2012 at 6:58 PM, Aaron O'Toole &lt;airuno2L@&gt; <
>> airuno2l@> wrote:
>>
>>> I don't know much about it, but this might get you heading down the right
>>> road:  http://pointclouds.org/blog/urcs/
>>>
>>>
>>> On Mon, Jul 30, 2012 at 5:49 PM, Ender1618 &lt;Ender1618@&gt; wrote:
>>>
>>>> So I have a rather large PCL octree, i was hoping to load subtrees of
>>>> this
>>>> octree from disk as needed. Is there any way to merge a subtree back
>>>> into
>>>> a
>>>> full octree?
>>>>
>>>> For example i have a tree of depth 16 with a voxel size of 1cm.  Right
>>>> now I
>>>> only store occupancy, and get leaf centers to visualize. But with a tree
>>>> that size i may have ALOT of leaves, more than I could safely fit into
>>>> system or GPU memory.  I would like to cache the subtrees in as need,
>>>> and
>>>> keep them in a LRU queue.
>>>>
>>>>
>>>>
>>>> --
>>>> View this message in context:
>>>> http://www.pcl-users.org/PCL-octree-merging-a-sub-tree-tp4020929.html
>>>> Sent from the Point Cloud Library (PCL) Users mailing list archive at
>>>> Nabble.com.
>>>> _______________________________________________
>>>> PCL-users@ / http://pointclouds.org
>>>> http://pointclouds.org/mailman/listinfo/pcl-users
>>>>
>>>
>>>
>>>
>>> --
>>> - Aaron O'Toole
>>>
>>> _______________________________________________
>>> PCL-users@ / http://pointclouds.org
>>> http://pointclouds.org/mailman/listinfo/pcl-users
>>>
>>>
>>
>> _______________________________________________
>> PCL-users@ / http://pointclouds.org
>> http://pointclouds.org/mailman/listinfo/pcl-users
>>
>
>
>
>
> --
> View this message in context: http://www.pcl-users.org/PCL-octree-merging-a-sub-tree-tp4020929p4020959.html
> Sent from the Point Cloud Library (PCL) Users mailing list archive at Nabble.com.
> _______________________________________________
> [hidden email] / http://pointclouds.org
> http://pointclouds.org/mailman/listinfo/pcl-users
>


_______________________________________________
[hidden email] / http://pointclouds.org
http://pointclouds.org/mailman/listinfo/pcl-users

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Re: PCL octree, merging a sub tree

Ender1618
Where can I find the out of core octree implementation for PCL? Is it officially released? The version I have does not seem to contain this.

Julius Kammerl-2 wrote
Hi Ender1618,

like Justin mentioned, it sounds like what you are looking for is the
out-of-core component of PCL.

If you would like to stick to the PCL octree, you can just define a
"top-level" octree with a large voxel size. All points that fall within
these voxels can be stored to disk and loaded when needed.

Best,
Julius

On 08/01/2012 12:38 AM, Ender1618 wrote:
> Do you have an example of your code's usage, where could I a copy of you open
> sourced code?
>
>
> clockwise9 wrote
>>
>> Julius the developer of the PCL octree is doing what you describe in a
>> project that he's involved with.  I don't think the part you're interested
>> in is open sourced and/or available.
>>
>> Both *http://pointclouds.org/blog/trcs/rosen/* and
>> http://pointclouds.org/blog/urcs/ are code sprints to solve the problem
>> you've described.  Unfortunately, I still need to develop the frustum
>> culling and LRU caching aspect to actually make it outofcore.  If you want
>> some more info or help getting started with the outofcore octree code let
>> me know.
>>
>> Cheers,
>> Justin
>>
>> On Mon, Jul 30, 2012 at 6:58 PM, Aaron O'Toole <airuno2L@> <
>> airuno2l@> wrote:
>>
>>> I don't know much about it, but this might get you heading down the right
>>> road:  http://pointclouds.org/blog/urcs/
>>>
>>>
>>> On Mon, Jul 30, 2012 at 5:49 PM, Ender1618 <Ender1618@> wrote:
>>>
>>>> So I have a rather large PCL octree, i was hoping to load subtrees of
>>>> this
>>>> octree from disk as needed. Is there any way to merge a subtree back
>>>> into
>>>> a
>>>> full octree?
>>>>
>>>> For example i have a tree of depth 16 with a voxel size of 1cm.  Right
>>>> now I
>>>> only store occupancy, and get leaf centers to visualize. But with a tree
>>>> that size i may have ALOT of leaves, more than I could safely fit into
>>>> system or GPU memory.  I would like to cache the subtrees in as need,
>>>> and
>>>> keep them in a LRU queue.
>>>>
>>>>
>>>>
>>>> --
>>>> View this message in context:
>>>> http://www.pcl-users.org/PCL-octree-merging-a-sub-tree-tp4020929.html
>>>> Sent from the Point Cloud Library (PCL) Users mailing list archive at
>>>> Nabble.com.
>>>> _______________________________________________
>>>> PCL-users@ / http://pointclouds.org
>>>> http://pointclouds.org/mailman/listinfo/pcl-users
>>>>
>>>
>>>
>>>
>>> --
>>> - Aaron O'Toole
>>>
>>> _______________________________________________
>>> PCL-users@ / http://pointclouds.org
>>> http://pointclouds.org/mailman/listinfo/pcl-users
>>>
>>>
>>
>> _______________________________________________
>> PCL-users@ / http://pointclouds.org
>> http://pointclouds.org/mailman/listinfo/pcl-users
>>
>
>
>
>
> --
> View this message in context: http://www.pcl-users.org/PCL-octree-merging-a-sub-tree-tp4020929p4020959.html
> Sent from the Point Cloud Library (PCL) Users mailing list archive at Nabble.com.
> _______________________________________________
> [hidden email] / http://pointclouds.org
> http://pointclouds.org/mailman/listinfo/pcl-users
>



_______________________________________________
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Re: PCL octree, merging a sub tree

Julius Kammerl-2
Hi Ender1618,

yes, it is still under development. You'll find it in trunk.

Best,
Julius

On 08/01/2012 04:38 PM, Ender1618 wrote:

> Where can I find the out of core octree implementation for PCL? Is it
> officially released? The version I have does not seem to contain this.
>
>
> Julius Kammerl-2 wrote
>>
>> Hi Ender1618,
>>
>> like Justin mentioned, it sounds like what you are looking for is the
>> out-of-core component of PCL.
>>
>> If you would like to stick to the PCL octree, you can just define a
>> "top-level" octree with a large voxel size. All points that fall within
>> these voxels can be stored to disk and loaded when needed.
>>
>> Best,
>> Julius
>>
>> On 08/01/2012 12:38 AM, Ender1618 wrote:
>>> Do you have an example of your code's usage, where could I a copy of you
>>> open
>>> sourced code?
>>>
>>>
>>> clockwise9 wrote
>>>>
>>>> Julius the developer of the PCL octree is doing what you describe in a
>>>> project that he's involved with.  I don't think the part you're
>>>> interested
>>>> in is open sourced and/or available.
>>>>
>>>> Both *http://pointclouds.org/blog/trcs/rosen/* and
>>>> http://pointclouds.org/blog/urcs/ are code sprints to solve the problem
>>>> you've described.  Unfortunately, I still need to develop the frustum
>>>> culling and LRU caching aspect to actually make it outofcore.  If you
>>>> want
>>>> some more info or help getting started with the outofcore octree code
>>>> let
>>>> me know.
>>>>
>>>> Cheers,
>>>> Justin
>>>>
>>>> On Mon, Jul 30, 2012 at 6:58 PM, Aaron O'Toole &lt;airuno2L@&gt; <
>>>> airuno2l@> wrote:
>>>>
>>>>> I don't know much about it, but this might get you heading down the
>>>>> right
>>>>> road:  http://pointclouds.org/blog/urcs/
>>>>>
>>>>>
>>>>> On Mon, Jul 30, 2012 at 5:49 PM, Ender1618 &lt;Ender1618@&gt; wrote:
>>>>>
>>>>>> So I have a rather large PCL octree, i was hoping to load subtrees of
>>>>>> this
>>>>>> octree from disk as needed. Is there any way to merge a subtree back
>>>>>> into
>>>>>> a
>>>>>> full octree?
>>>>>>
>>>>>> For example i have a tree of depth 16 with a voxel size of 1cm.  Right
>>>>>> now I
>>>>>> only store occupancy, and get leaf centers to visualize. But with a
>>>>>> tree
>>>>>> that size i may have ALOT of leaves, more than I could safely fit into
>>>>>> system or GPU memory.  I would like to cache the subtrees in as need,
>>>>>> and
>>>>>> keep them in a LRU queue.
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> View this message in context:
>>>>>> http://www.pcl-users.org/PCL-octree-merging-a-sub-tree-tp4020929.html
>>>>>> Sent from the Point Cloud Library (PCL) Users mailing list archive at
>>>>>> Nabble.com.
>>>>>> _______________________________________________
>>>>>> PCL-users@ / http://pointclouds.org
>>>>>> http://pointclouds.org/mailman/listinfo/pcl-users
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> - Aaron O'Toole
>>>>>
>>>>> _______________________________________________
>>>>> PCL-users@ / http://pointclouds.org
>>>>> http://pointclouds.org/mailman/listinfo/pcl-users
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> PCL-users@ / http://pointclouds.org
>>>> http://pointclouds.org/mailman/listinfo/pcl-users
>>>>
>>>
>>>
>>>
>>>
>>> --
>>> View this message in context:
>>> http://www.pcl-users.org/PCL-octree-merging-a-sub-tree-tp4020929p4020959.html
>>> Sent from the Point Cloud Library (PCL) Users mailing list archive at
>>> Nabble.com.
>>> _______________________________________________
>>> PCL-users@ / http://pointclouds.org
>>> http://pointclouds.org/mailman/listinfo/pcl-users
>>>
>>
>>
>>
>> _______________________________________________
>> PCL-users@ / http://pointclouds.org
>> http://pointclouds.org/mailman/listinfo/pcl-users
>>
>
>
>
>
> --
> View this message in context: http://www.pcl-users.org/PCL-octree-merging-a-sub-tree-tp4020929p4020982.html
> Sent from the Point Cloud Library (PCL) Users mailing list archive at Nabble.com.
> _______________________________________________
> [hidden email] / http://pointclouds.org
> http://pointclouds.org/mailman/listinfo/pcl-users
>


_______________________________________________
[hidden email] / http://pointclouds.org
http://pointclouds.org/mailman/listinfo/pcl-users

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Re: PCL octree, merging a sub tree

Stephen D. Fox
Hi Ender1618-

I am the code sprinter responsible for integrating the Urban Robotics
out of core octree implementation into the PCL code base. The code
base is stable, but it is still under heavy development and there will
likely be an API change in the coming weeks. Currently the code is only
available in trunk, and has not yet been included in an official PCL
release.

For now it is possible to create an out of core tree, build levels of
depth, query the tree for a list of file names, and get occupied voxel
centers. The points at each node are stored in compressed pcd files. In
the pcl_outofcore tools, there is one called pcl_outofcore_process,
which will take one or multiple input point clouds via command line and
build the ooc octree.

If you have any further questions, consult my blog [1] and Justin
Rosen's blog [2] for development notes, and certainly feel free to
contact me off the list.

--
Best regards,

Stephen Fox

[1] http://www.pointclouds.org/blog/urcs/
[2] http://www.pointclouds.org/blog/trcs/rosen/index.php
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Re: PCL octree, merging a sub tree

clockwise9
Ender,

Sorry, I'll try and give a better rundown of how the code works this weekend. 

Ultimately, it'd be great to get your use case, as well as to absorb any additional implementations you might write that are missing, ie LRU caching. Until then, check out our blogs as Stephen has mentioned. 

There's also the pcl_outofcore_viewer that displays the tree at different levels (I still need to add the outofcore part)

On Wednesday, August 1, 2012, Stephen D. Fox wrote:
Hi Ender1618-

I am the code sprinter responsible for integrating the Urban Robotics
out of core octree implementation into the PCL code base. The code
base is stable, but it is still under heavy development and there will
likely be an API change in the coming weeks. Currently the code is only
available in trunk, and has not yet been included in an official PCL
release.

For now it is possible to create an out of core tree, build levels of
depth, query the tree for a list of file names, and get occupied voxel
centers. The points at each node are stored in compressed pcd files. In
the pcl_outofcore tools, there is one called pcl_outofcore_process,
which will take one or multiple input point clouds via command line and
build the ooc octree.

If you have any further questions, consult my blog [1] and Justin
Rosen's blog [2] for development notes, and certainly feel free to
contact me off the list.

--
Best regards,

Stephen Fox

[1] http://www.pointclouds.org/blog/urcs/
[2] http://www.pointclouds.org/blog/trcs/rosen/index.php
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Re: PCL octree, merging a sub tree

Ender1618
This post was updated on .
I have been looking over the code for your out of core octree implementation, I am having some  trouble following how things work. Are you following a methodology similiar to what is described in the paper " Interactive Editing of Large Point Clouds"?
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Re: PCL octree, merging a sub tree

Stephen D. Fox
Ender-

It builds the octree in a similar manner, sorting the points recursively
into octants using 3 bits: (ZYX), where each bit is 1 if the
corresponding coordinate of the point is greater than the coordinate of
the midpoint. If you are not building the level of depth (LOD), then the
points will be in PCD files of the leaf nodes at the maximum depth of
the tree. Interior nodes will simply contain a metadata file (in a
folder on disk named by the sequence of 3-bit octant identifiers,
0,1,2,...7) with the appropriate information to continue walking the tree.

The LOD algorithm currently is not like the paper you cite. In that
paper, the internal nodes are lower resolution ("multi-resolution")
representations of all child leaves, so that walking down the tree bring
an entirely new rendering. This set of points contains all the points
which fall into the bounding box representing that portion or octant
relative to the midpoint of the parent's node, and perhaps subsampled or
downsample.

In contrast, our implementation, using addPointCloud_and_genLOD builds
the LOD by subtracting a uniform random sample of points falling within
the bouding box from the original input cloud. Since the LOD are built
recursively, the remaining points are sorted and passed respectively to
the child nodes. This reduces duplication of data. Each LOD then
contains a portion of the original input cloud, so to render a portion
of the cloud at full resolution, one has to walk the tree in a
depth-first fashion, adding the points from the lower nodes in which you
are interested.

There are benefits to each method, but I am planning to parameterize
this to give more control over how LOD's are computed/generated. In
fact, I will be adding some iterators to the outofcore library soon
which will give some more flexibility in the way you have access to the
individual node data as well.

--
Best regards,

Stephen Fox

On 08/30/2012 07:49 PM, Ender1618 wrote:

> I have been looking over the code for your out of core octree implementation,
> I am some  trouble following how things work. Are you following a
> methodology similiar to what is described in the paper " Interactive Editing
> of Large Point Clouds"?
>
>
>
> --
> View this message in context: http://www.pcl-users.org/PCL-octree-merging-a-sub-tree-tp4020929p4021888.html
> Sent from the Point Cloud Library (PCL) Users mailing list archive at Nabble.com.
> _______________________________________________
> [hidden email] / http://pointclouds.org
> http://pointclouds.org/mailman/listinfo/pcl-users
>
_______________________________________________
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Re: PCL octree, merging a sub tree

Ender1618
Thanks for the info.  Are all your highest LOD leaves at the same depth in the tree, or does a leaf depth vary with the amount of points?

For you LOD system, from your highest level of detail is the next lower level of detail within the same octree cell bounds or is it contained with the parent branches cell bounds? In other words does each successive (lower) level of have a larger spatial bound, or does the bound stay the same with just less points stored within?
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Re: PCL octree, merging a sub tree

Stephen D. Fox
Hi Ender,

> Thanks for the info.  Are all your highest LOD leaves at the same depth in
> the tree, or does a leaf depth vary with the amount of points?
Yes, that is the idea. The tree is of fixed height, and assumed to be
balanced. However, there is a bug in the computation at the moment that
will be fixed when I finish the parameterized LOD construction changes
that I am currently working on. This results when, effectively, there
are too few of points in a given voxel to move all the way down the tree
with a subtractive subsampling as I described in the previous message.

>
> For you LOD system, from your highest level of detail is the next lower
> level of detail within the same octree cell bounds or is it contained with
> the parent branches cell bounds? In other words does each successive (lower)
> level of have a larger spatial bound, or does the bound stay the same with
> just less points stored within?
There is a misunderstanding with the notation here. Some octrees will
call the "root" parent node by the height of the tree. However, we call
the depth of the "root" node as 0, and the depth of the leaves is
related by the maximum depth (height) of the tree -1.

at depth 0: root
depth 1: 8 children, subdividing the bounding box of the root into 8
cubic regions (octants)

The bounding boxes of children of any given node are disjoint subsets of
the space denoted by that node.
--
Best regards,
Stephen Fox
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