vukoz-oel / 3d-forest-classic Goto Github PK

Need some sort of CI setup for Mac OS, linux and Windows for automatic deploy.
I just start configure Travis CI yaml for linux.

implement command line for using text interface

Hi,

I am unable to open previous projects. when i try to open and .3df file I get this message:

"the actual path differs from the path savedin the project.Do you want to use the actaul path and look up the project files in the directory?"

if i press yes, it says the selected file does not exist and says to "check the path to the project file or try to import the whole project." even though im already trying to import the whole project. gives me the option of "yes or abort" both cause the app to crash.

When i try to open the open the PCD or txt file of the individual trees segemntent and exported from the project through Project>Import>Vegetation Cloud Import the program crashes too.

the project file is on my hard drive so i tried setting it up on my computer drive but i get the same message.

Hi guys,

thanks for developing and providing this great application!

I used 3D forest for ground classification, tree segmentation and some tree attribute calculations.
I just want to know how I should cite your work.
Should I refer to this paper: Trochta, J., Krůček, M., Vrška, T., & Král, K. (2017). 3D Forest: An application for descriptions of three-dimensional forest structures using terrestrial LiDAR. PloS one, 12(5), e0176871. Or is there a more recent one?

Also, the contact form on 3dforest.eu does not seem to work at the moment.

Cheers

Hi,

thanks a lot for your great work.

I found that if I use the default parameters for automatic tree segmentation of the sample data you provided (https://github.com/VUKOZ-OEL/3d-forest-classic-data). The results were poor. I tried to adjust the parameters by myself, but have no idea how to select them well. It would be great if you could provide the best setting of them.

Thank you in advance.

Best regards,
Binbin

Hi, I am a master's student at Nottingham Trent University and I am using 3D Forest for my thesis. I am trying to use the tree measuring feature but the application keeps on crashing and I'm really confused as to what is going wrong. I've imported the base cloud and separated the terrain and vegetation as the wiki says, but the options for measuring and volume are still greyed out. The only options I can click are 'Tree Cloud Edit', 'Position Lowest Points', and 'Position RHT', all of which I have tried to do but nothing happens and the options are still greyed. Anything else I try to do results in the application crashing. Any help on this would be much appreciated as I only have until tomorrow to get it sorted as it is the last aspect of my project. Cheers.

Hi, after several problems solved previously and during 3D Forest compiling, i managed to compile it on Ubuntu 22.04. But when i start the executable, sometimes it crashes with the message "Segmentation fault (core dump)" and sometimes starts normally.
I used gdb and the backtrace output of segmentation fault is this:

gdb 3DForest
GNU gdb (Ubuntu 12.1-0ubuntu1~22.04) 12.1
Copyright (C) 2022 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Type "show copying" and "show warranty" for details.
This GDB was configured as "x86_64-linux-gnu".
Type "show configuration" for configuration details.
For bug reporting instructions, please see:
<https://www.gnu.org/software/gdb/bugs/>.
Find the GDB manual and other documentation resources online at:
    <http://www.gnu.org/software/gdb/documentation/>.

For help, type "help".
Type "apropos word" to search for commands related to "word"...
Reading symbols from 3DForest...
(No debugging symbols found in 3DForest)
(gdb) r
Starting program: /home/loris/Scaricati/3d-forest-classic-052/build/3DForest 
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
[New Thread 0x7fffe5804640 (LWP 549918)]
[New Thread 0x7fffdfcb5640 (LWP 549919)]
[New Thread 0x7fffdf4b4640 (LWP 549920)]
[New Thread 0x7fffdeb3e640 (LWP 549921)]

Thread 1 "3DForest" received signal SIGSEGV, Segmentation fault.
XDisplayKeycodes (dpy=dpy@entry=0x820, min_keycode_return=min_keycode_return@entry=0x555555a73e64, max_keycode_return=max_keycode_return@entry=0x555555a73e68) at ../../src/Misc.c:53
53	../../src/Misc.c: File o directory non esistente.
(gdb) bt
#0  XDisplayKeycodes (dpy=dpy@entry=0x820, 
    min_keycode_return=min_keycode_return@entry=0x555555a73e64, 
    max_keycode_return=max_keycode_return@entry=0x555555a73e68)
    at ../../src/Misc.c:53
#1  0x00007fffefbc5ebc in InitPerDisplay (dpy=dpy@entry=0x820, 
    app=app@entry=0x555555a13a80, name=name@entry=0x7ffff5e14f6f "VTK", 
    classname=0x7ffff5e14f6b "vtk") at ../../src/Display.c:201
#2  0x00007fffefbc63fb in XtDisplayInitialize (app=0x555555a13a80, dpy=0x820, 
    name=0x7ffff5e14f6f "VTK", classname=<optimized out>, urlist=0x0, 
    num_urs=0, argc=0x7fffffffc34c, argv=0x0) at ../../src/Display.c:394
#3  0x00007ffff5dea5dc in vtkXRenderWindowInteractor::Initialize (
    this=0x5555559e7130)
    at /home/loris/Scaricati/vtk-v8.1.0/Rendering/OpenGL2/vtkXRenderWindowInteractor.cxx:329
#4  0x00007ffff2f024c4 in pcl::visualization::PCLVisualizer::createInteractor (
    this=0x555555b2a050) at /usr/local/include/vtk-8.1/vtkSmartPointer.h:128
#5  0x00007ffff2f02f78 in pcl::visualization::PCLVisualizer::PCLVisualizer (
    this=0x555555b2a050, ren=..., wind=..., name="data viewer", 
    create_interactor=<optimized out>)
    at /home/loris/Scaricati/pcl-pointpicking/visualization/src/pcl_visualizer.cpp:202
#6  0x000055555567fd45 in MainWindow::MainWindow() ()
#7  0x00005555555c8240 in main ()
(gdb) frame 5
#5  0x00007ffff2f02f78 in pcl::visualization::PCLVisualizer::PCLVisualizer (
    this=0x555555b2a050, ren=..., wind=..., name="data viewer", 
    create_interactor=<optimized out>)
    at /home/loris/Scaricati/pcl-pointpicking/visualization/src/pcl_visualizer.cpp:202
202	    createInteractor ();
(gdb) frame 4
#4  0x00007ffff2f024c4 in pcl::visualization::PCLVisualizer::createInteractor (
    this=0x555555b2a050) at /usr/local/include/vtk-8.1/vtkSmartPointer.h:128
128	  T* operator->() const
(gdb) frame 3
#3  0x00007ffff5dea5dc in vtkXRenderWindowInteractor::Initialize (
    this=0x5555559e7130)
    at /home/loris/Scaricati/vtk-v8.1.0/Rendering/OpenGL2/vtkXRenderWindowInteractor.cxx:329
329	      XtDisplayInitialize(vtkXRenderWindowInteractor::App,this->DisplayId,

I'm not sure if the problem that causes the segmentation fault is generated whether by pcl visualizer or by vtkXRenderWindowInteractor.

EDIT
Solved this issue, see #35.

Hi,
it seems to me that DBH cloud edit is not working as expected. after i exit the tool, and re-run DBH estimation, there's no change to estimated DBH.

Not sure if I was using the tool in a wrong way. but when checking the source code, I reckon the function void MainWindow::dbhCloudStopEdit() is supposed to be called when exiting DBH Cloud Edit tool. But the function seems not to be connected to any toolbar event.

cheers,

change project file for better saving of state of layers and estiamted parameters

Good day. I am writing about your program. I have a few questions:
1 You can explain the parameters of automatic tree segmentation in a simple way.
2. How does the cloud affect the automatic segmentation of trees? When processing a cloud of the terrain program, it captures some tree crowns, while with a separate loaded terrain cloud and vegetation clouds, the processing process improves.
3 Is it possible to make quality software so that the new layers of the vision are repainted in a certain color. Because black on black was hard to understand. It was not written on the githab in the guide, or I did not see it.
I hope for your answer.

Hello

I've installed 3D forest on a Virtual Machine with over 128 GB of RAM
The programme seems to run properly, nevertheless there are several crashes happening during the work in process, which make the workflow almost impossible to manage.

For example:

• When I try to import directlly a basecloud, the window disappears and the entire software crashes
• After I've imported las format cloud point , and did the voxel terrain segmentation , the automatic tree segmentation crashes all of a sudden
• the exported .txt file formats can't be loaded back to the workspace

Althought I found this bugs challenging , I do believe this software is an amazing tool!
I hope I'll be able to find a solution to these issues.

Eagerly waiting for the response!

Thank you

Hi,

I'm trying to use the software on a windows system but after creating a project the software crashes after trying to import a point cloud. The clouds are relatively small so I'm not sure where the problem lies. In the command line it says 'importing las file', 'importing las finished' then just dies.

Hi, I installed the program from the .exe in windows 10 and it did not generate any errors.

I try to load my point cloud, but it doesn't show up on the screen, I don't know if it's a matrix problem or what's going on.

This is my point cloud information

How can I put the right matrix on the program?

Thanks

Hello,

Importing PDAL (https://pdal.io/stages/writers.pcd.html) created .pcd gives error:

Failed to find match for field 'x'.
Failed to find match for field 'y'.
Failed to find match for field 'z'.
Failed to find match for field 'intensity'.

in 3D Forest's console.

Can you point out, what I did wrong? Do the fields have to be specified somehow specifically?

The .pcd file that I'm trying to import starts like:

VERSION 0.7
FIELDS x y z intensity
SIZE 8 8 8 8
TYPE F F F F
COUNT 1 1 1 1
...

So it seems like it has the right fields.

OTOH, I'm converting from a .las, where the convention is X, Y, Z (capitalized).

First of all, thank you of this great open source application.

I'm trying to use the 3D Forest application for Windows (version 0.52) to segment a large point cloud obtained from a TLS of a trees parcel.
The point cloud is in a binary PCD format containing the 3D points with their intensity (X, Y, Z, I).
Importation and separation of the terrain from the vegetation by octree went well, but the automatic tree segmentation crashes.
I have try different parameter values, and point cloud sizes (from 47 million to 24 million of points), but the application keep crashing in most of the cases and I'm not able to test adequate parameter values.
The application seems to crash in SegmentationOctree::setTreeElements(), but it's not easy to confirm, because the console disappears immediately.

To try to identify the problem, I have download (cloned) the code, but I was not able to resolve all the compilation problems. (I will open an issue for this compilation problem too).

Hi,
3D Forest is an amazing tool that is very convenient and fast. However, it seems that only 2D hull exports are supported?

After obtaining corwn convex/concave hull, canopy volume and other canopy parameters can be obtained.
Now I want to export the hull for each of the resulting crowns, but there doesn't seem to be any support in 3D Forest for turning the 3D hull everywhere into a triangular network sheet format (such as.obj,.stl, etc.) and exporting.

It's also possible that I didn't discover this feature of 3D Forest.

I hope I can hear from you.

Running on windows 11, V052

Hi,

Please i am getting an error whenever i try to compute the 3D convex hull crown volume.

Generic warning: In D:\sourceCodes\VTK\Common\Core\vtkMath.cxx, line 564
Unable to factor linear system.

Please how can i solve this?

Problem with 0.51. None of the trees are colored or shown anymore. All pcd files vanish from the screen after Automatic tree segmentation. They are still in the list on the left and I have to change color then zoom in or out to get it to show on the screen. Any change made on the left will not show in the main window until I zoom in or out. This seems to cause the screen to refresh and the changes are then update. Previous version did not have this problem.
After I deleted two of the pcd files on the left I no longer have mouse control of the point cloud. I can no longer pan or rotate etc. All I can do is draw a box which does nothing.
I have yet to be able to save a project. There is no save button period. If I click file/ close project then try to reopen later it fails with empty job files or it just crashes and closes. Had the same problem with previous version. Looking at the 3df file it seems sometimes it gets corrupted.
This time I tried to open a project I was working on for a couple hours and it could not find the terrain and veg files which are in the folder.
If I hit abort it loaded all files but the terrain and veg. The rotate and pan etc are working again and now bounding boxes show up around some trees. Thats new.
This was first time I was able to load a previous project. It only lost two of the files terrain and Veg. It also did not save tree position or any of the info to attribute table like DBH height etc.

Windows 10

Hello,
is there any way to export canopy outside points?

Hi,

I know others have asked the same question, but I still haven't managed to resolve the issue. When I try to import a point cloud with .las extension the application crashes immediately. For the transformation matrix I have imported the values that Cloud Compare software chooses, so I think this can't be the issue. Additionally, I've tried to drastically reduce the point cloud size to match the size of the test data you provide. Do you have any other suggestions for me to try?

Kind regards,

Niamh

Hi,
I am windows .NET user, I would really like to use your software, but I can only see the source code.
Is there any possibility to load pointcloud via command line and retrieve a result in a file?

I also tried to build the source code from cmake, but since I am not good with C++ I do not know how to resolve the errors:

Hi!

I'm having substantial difficulty getting the plot to be visible once uploaded and then once it is, it disappears very quickly and cannot be visualized using the different points of view feature. Any thoughts on why this might be occurring?

Thanks in advance,
Maddie

Dear author, could you please provide the tree species information and collection area of this data source?

Hi,

if trees are standing too close to each other, the system is not able to seperate the vegetation cloud into single trees automatically...so are some tips how i can improve the tree seperation?

Greets
Josi

Hi there,

I am aware that this issue has been raised many times but unfortunately I am not finding any solution in the previous answers.

3DForest is crashing on import, after creating a project, no matter what I do. I have tried using small files (8mb) through to large (>5GB) because I first thought this was the main issue. I then checked the .las version and I am using .las version 1.2, so it is not that. I have tried removing spaces from file and folder names with no luck. I have also tried using version 0.5 rather than 0.52.

Thanks, any advice would be much appreciated.

I am trying to import a file as either las or pcd and the program crashes with no message. I think it may be too large. Is there a work around for files ~5GB?

Hi,

First of all, big thanks for the open-source program. I am going to use this program for extracting the parameters of trees, including DBH, tree height, and tree crown spread, from the point cloud data acquired by the UAV LiDAR. As the point density is normally lower than that acquired by the Terrestrial Laser Scanner, the performance of the segmentation of the tree is not as good as the result from the TLS point cloud. So, is there any tips for me to enhance the performance of the tree segmentation, such as the settings of the built-in functions and the workflow of the point cloud processing apart from the modification of the flight planning and the site selection for the tree (i.e. a site with less structural complexity)?

Best regards
Michael

Hi,

I'm trying to compile 3D Forest in Window with Visual Studio.

I have been able to install libraries and to generate the project with CMake after some minor modifications in the CMakeLists.txt file.
But the Visual Studio solution doesn't compiles. It seem that the PCL library you're using is very different that the one I'm using and I did not find any version of PCL having the methods you're calling.

For instance:

1. In the file sourceCode/segmentation.cpp, I had to make the following modification at line 604 to correct an error at line 607 (extract.setIndices (indicesptr);):

-    boost::shared_ptr<std::vector<int> > indicesptr (new std::vector<int> (indices));
+    pcl::IndicesPtr indicesptr (new pcl::Indices(indices));

2. In the file sourceCode/mainwindow.cpp at line 1739: std::vector<std::string> clouds = event.getCloudNames();, the method getCloudNames() is called in object const pcl::visualization::AreaPickingEvent& event, but there is no method of this name in the pcl:visualization::AreaPickingEvent class.

Do you have any explanations or solutions for my problems?

Thank's

Quite often I get this error pop up when I attempt to Crowns > set automatic

Warning: In C:\pcldep\VTK-7.0.0\Filters\Core\vtkMassProperties.cxx, line 120
vtkMassProperties (0x41ab3700): Input data type must be VTK_TRIANGLE not 1

The program crashes after I close the warning. What causes this to happen?

Add a text to all dialog windows in the Trees menu:
Select a tree you want to measure. Ctrl+A to select All trees.

Hello,
I just test only one tree and noticed that it takes more than 30 mins to perform crown segmentation. my cpu i9 with 64g memory.
I wonder there is installation issue or not. is that normal to take that long?

Getting following errors:
/home/tan/project/pcl_work/3DForest/sourceCode/mainwindow.cpp:6496:12: error: ‘const class pcl::visualization::AreaPickingEvent’_ has no member named ‘getActors’ if(event.getActors (actors) == false) ^ /home/tan/project/pcl_work/3DForest/sourceCode/mainwindow.cpp:6509:11: error: ‘const class pcl::visualization::AreaPickingEvent’ has no member named ‘getActorsIndices’ event.getActorsIndices(cam_it->second.actor, indices); ^ /home/tan/project/pcl_work/3DForest/sourceCode/mainwindow.cpp: In member function ‘void MainWindow::pointEvent(const pcl::visualization::PointPickingEvent&, void*)’: /home/tan/project/pcl_work/3DForest/sourceCode/mainwindow.cpp:6593:27: error: ‘const class pcl::visualization::PointPickingEvent’ has no member named ‘getProp’ vtkProp3D* prop = event.getProp();
The errors are self explanatory. Please update working code

Hi
3d Forest Team Thank you for the Awesome software! I love it! In the beginning i had some Problems with crash of the Software but after a while i could handle it! During working with it, i had some thoughts which could improve the Software
Layers:
-It would be nice if i could see the color of the Layer in the Layerlist behind the name.
-It could be nice to reaname layers or Tree numbers especially in the Layerlist.
-If i select a treecloud it would be nice it the cloud would be highlighted in the Preview!
-Could be good to Shift+Select and Delete all selected Layers. For exampte if the Autotree-Segmentation was wrong and i have to delete 80 Layers, before retry it with other Factors.
Attribut-Table:
Its sad that the Values of the Table are not saved in the Project. If 3d Forest crashes all is gone and some, like the 3D Convex-Hull Calculation, take a lot time and CPU-Power. Or mb just the Option to reimport the Attributs from csv or txt.
Faktors:
-i miss the hight of the CrownCenter Position

• it would be nice to calculate FLat crown Projektionareas for Windload analysis, you need the Area and the Center of the Area, maybe for different azimut degrees. Like North , North-West....; alternatively biggest and smallest.
• For the QSM it would be nice to have the Position Values of the "Center of Mass" to evaluate the
  Export:
  I think it could be nice To Export all Attributes in one Table as a .csv
• After Calculate the Convex Volume it would be nice to Export the Convex-Hull as a 3d Data of all Tree's, best with the Stem.
  Final-wish: A Tool to calculate directly the Windload on the Crown like :https://www.arboa.com/de/sia-berechnung: but with the real Crownshape from the Lidar for Treestatic based on Pointclouds.
  Thank you for reading!
  Greets

Hi! I have a TLS point cloud in WGS84 but this CRS is not compatible with the 3D Forest software. Does anybody know what is de CRS compatible with 3D Forest and/or how to transform my point cloud CRS to work in 3D Forest?

Good day! just asking me, Is in your pipeline to create a python version of your software? Would be great!

Hi! I am new to 3D Forest and I'm attempting to use it on single, isolated trees in their "leaf-on" state.

I was able to separate terrain and vegetation and then was able to select the tree points from the vegetation. However, after separating the tree from the vegetation and terrain, I ran into issues. I used the Tree Reconstruction tool before attempting Tree Volume QSM. The volume QSM is giving a value of 0 in the attribute table (there are no values under any other attributes aside from length). I tried the QSM Data Export tool but that also didn't export a file. I used the default values for everything just to see if it would run but that may have been the issue?

I've read through the Wiki a few times but I'm having some issues learning where I may have gone down a wrong path. If anyone would be able to assist me in starting out or direct me to some useful resources, I would greatly appreciate it!

All the best,
Jillian

EDIT: I am now also experiencing issues with 3D Forest crashing during automatic tree segmentation.

Hi,

I am writing to understand the cause that 3D Forest crashes when importing las data.
The point clouds are small so I'm not sure where the problem lies.
Is the cause of crash setting transformation matrix?

Also, I try to load point cloud, but this doesn't show up on the screen.
What is the problem?

I hope I can hear from you.

create hillshade computation for terrain

Hi !
Is there a possibility to export QSM as mesh model ? Do you plan to add this feature in next versions ?
Best regards

Hi there! I am really interested in the 3dForest project, and I am hoping for some help.

Firstly, can you help me understand the transformation matrix, is it just in the projection that the LAS file it using? in my case NAD83, zone 8N.

This issue may be related to my problems with the first, but when I import an las file, the command prompt says the import is complete, but no point cloud appears. Do you have any ideas what I may be doing wrong? The las file is quite large.

Cheers, and thanks for your hard work on this.
Jeff