Open3d: Segmentation fault when estimate normals

[hongyuli]

Hi, I'm trying to explore the open3D with my own data, but always got Segmentation fault (core dumped) when using estimate_normals(search_param=o3d.geometry.KDTreeSearchParamHybrid(radius=, max_nn= ))

My data is attached. I also tried examples/Python/Basic/pointcloud.py, which does run successfully.

Thanks.

data.zip

[syncle]

Could you specify radius or max_nn= and run the example again?

[hongyuli]

Thanks for following up.

I understand the radius value is used to specify the search range to compute normals, so I tried a variety of values from centimeter to meter order (with and without voxel downsample in relative smaller value as well). Also tried different max_nn values which should specify the maximum neighbors for normal estimation. Still get the same error.

[TobiasFischerP4D]

Same here. Sadly I cannot share the data :(

gdb trace:

0x00007fffd68999f0 in flann::flann_algorithm_t flann::get_param<flann::flann_algorithm_t>(std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, flann::any, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, flann::any> > > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) ()
   from /home/[readacted]/lib/python3.6/site-packages/open3d/open3d.cpython-36m-x86_64-linux-gnu.so

[TobiasFischerP4D]

Here's the actual backtrace, not just the SIGSEGV message:

Thread 1 "python3" received signal SIGSEGV, Segmentation fault.
0x00007fffd68999f0 in flann::flann_algorithm_t flann::get_param<flann::flann_algorithm_t>(std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, flann::any, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, flann::any> > > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) ()
   from /home/[...]/venv/lib/python3.6/site-packages/open3d/open3d.cpython-36m-x86_64-linux-gnu.so

(gdb) backtrace
#0  0x00007fffd68999f0 in flann::flann_algorithm_t flann::get_param<flann::flann_algorithm_t>(std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, flann::any, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, flann::any> > > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) ()
   from /home/[...]/venv/lib/python3.6/site-packages/open3d/open3d.cpython-36m-x86_64-linux-gnu.so



md5-2b5dbce8ac808b7b5faf99d8d7fd0c9b



#1  0x00007fffd689e9f8 in flann::Index<flann::L2<double> >::Index(flann::Matrix<double> const&, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, flann::any, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, flann::any> > > const&, flann::L2<double>) ()
   from /home/[...]/venv/lib/python3.6/site-packages/open3d/open3d.cpython-36m-x86_64-linux-gnu.so



md5-2b5dbce8ac808b7b5faf99d8d7fd0c9b



#2  0x00007fffd6894085 in open3d::geometry::KDTreeFlann::SetRawData(Eigen::Map<Eigen::Matrix<double, -1, -1, 0, -1, -1> const, 0, Eigen::Stride<0, 0> > const&) ()
   from /home/[...]/venv/lib/python3.6/site-packages/open3d/open3d.cpython-36m-x86_64-linux-gnu.so



md5-2b5dbce8ac808b7b5faf99d8d7fd0c9b



#3  0x00007fffd689445d in open3d::geometry::KDTreeFlann::SetGeometry(open3d::geometry::Geometry const&) ()
   from /home/[...]/venv/lib/python3.6/site-packages/open3d/open3d.cpython-36m-x86_64-linux-gnu.so



md5-2b5dbce8ac808b7b5faf99d8d7fd0c9b



#4  0x00007fffd6888628 in open3d::geometry::PointCloud::EstimateNormals(open3d::geometry::KDTreeSearchParam const&, bool) ()
   from /home/[...]/venv/lib/python3.6/site-packages/open3d/open3d.cpython-36m-x86_64-linux-gnu.so

And then comes Python stuff.

[TobiasFischerP4D]

Ok so apparently Open3D and PCL are incompatible at some level in our setup (maybe both using FLANN leads to a collision..?). We are using some custom pybind11 stuff to interface PCL, and not including that module gets rid of the segfault. Go figure...

[oafolabi]

I ran into a similar issue with Open3D and PCL as well.

[SeungBack]

Same issue here. importing both 'open3d' and 'pcl' at the same time occurs the segmentation error.
Removing "import pcl" and leaving only "import open3d" resolved the error as @TobiasFischerP4D mentioned.

[femust]

Same here

[manhha1402]

I have the same problem using KDTRee in PCL: pcl::KdTreeFLANN. It leads to segmentation fault with Open3D