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cannot stat ‘parallel-20141022’: No such file or directory #7

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dbaldwin opened this issue Nov 26, 2014 · 14 comments
Closed

cannot stat ‘parallel-20141022’: No such file or directory #7

dbaldwin opened this issue Nov 26, 2014 · 14 comments

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@dbaldwin
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Guys,

I'm excited about this project. Nice vision for what you're doing. Something like this needs to exist in our community. I have a YouTube channel where I cover many different aspects of UAV mapping. You can see it here:

https://www.youtube.com/user/dennisbaldwin

I plan on covering OpenDroneMap as soon as I get more familiar with it. So I just tried installing on a Amazon EC2 instance running Ubuntu 14.04.1 and received the following error:

ubuntu@ip-172-31-8-243:~/OpenDroneMap$ ./install.sh

 created by Daniel Schwarz/daniel.schwarz@topoi.org
 released under Creative Commons/CC-BY
 Attribution

 if the script doesn't finish properly
 (i.e. it doesn't print "script finished" at the end)
 please email me the content of the logs folder
  • script started - Wed Nov 26 20:28:38 UTC 2014

    installing required packages

- updating
- installing

< done - Wed Nov 26 20:31:01 UTC 2014

getting the sources
- already downloaded http://ftp.gnu.org/gnu/parallel/parallel-20141022.tar.bz2
- already downloaded http://www.netlib.org/clapack/clapack-3.2.1-CMAKE.tgz
- already downloaded http://phototour.cs.washington.edu/bundler/distr/bundler-v0.4-source.zip
- already downloaded http://www.cs.jhu.edu/~misha/Code/PoissonRecon/Version2/PoissonRecon.zip
- already downloaded http://www.vlfeat.org/download/vlfeat-0.9.13-bin.tar.gz
- already downloaded http://www.di.ens.fr/cmvs/cmvs-fix2.tar.gz
- already downloaded http://smathermather.github.io/BundlerTools/patched_files/src/graclus/graclus1.2.tar.gz
< done - Wed Nov 26 20:31:01 UTC 2014

  • unzipping sources
    mv: cannot stat ‘parallel-20141022’: No such file or directory

Perhaps I should email Daniel Schwarz but I wanted to open an issue here. I believe the problem is when parallel-20141022.tar.bz2 was unzipped it created the following directory:

parallel-20100922

or at least that's the directory that exists on my system. To get around this I changed the install script from:

mv -f parallel-20141022 "$PARALLEL_PATH"

to:

mv -f parallel-20100922 "$PARALLEL_PATH"

but it looks like that didn't do the trick. After running install.sh again the script stopped here:

parallel
- configuring parallel
- building paralel

With no output like "script finished". I'm continuing to look into the issue and this is my first install so perhaps I'm doing something wrong.

Thanks for getting this project going. I'm hoping to become more familiar with these tools and ultimately help contribute.

All the best,
Dennis Baldwin
db@unmannedairlines.com

@dbaldwin
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As a follow up I tried unzipping using this command as the install script does it:

tar xjf parallel.tar.bz2

and it yielded the directory:

parallel-20100922

I'm off to see if there is a different package at gnu.org.

@smathermather
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Hi @dbaldwin, I think I know what you're running into. I'll take a look and verify tomorrow.

@wildintellect
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I hit this too, it looks like the issue is that parallel.tar.bz2 is in the code checkout. This causes an error when it goes to download a newer version of parallel because it thinks it's already downloaded but the local version is incorrect. Solution is to delete parallel.tar.bz2

@smathermather
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I thought I'd pushed that change... Will do so now.

@smathermather
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Thanks @wildintellect -- @dbaldwin, try pulling and trying again.

@dbaldwin
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I just spun up an Ubuntu 14.04 64 Bit instance on Amazon and the install was flawless. Thanks!

@smathermather
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Awesome.

@smathermather
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@dbaldwin -- any screenshots of output to share? BTW, check out the new branch #13 which includes texturing. It will also create orthophoto for images with GPS coords in EXIF (cc @wildintellect)

@smathermather
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@wildintellect -- can you create an issue for the problems you've seen on 14.04? I want to track that, but don't remember the specifics. Thanks!

@dbaldwin
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I ran a sample of 85 images on a 18 acre tract of land near me. I am impressed with the results so far. The 1st screen shows the dense point cloud and the second shows the texture. Not bad! If it's of any interest I can upload a comparison of what I get from PhotoScan. I plan on doing a YouTube video walking through this process soon. The docs have been helpful, but I feel like a video demonstrating the process will be very useful. Also, I'm excited about the new branch. Since these same photos have been geotagged I'll run it through the new orthophoto process. Glad to see you've been busy!
screen shot 2014-12-24 at 2 38 03 pm
screen shot 2014-12-24 at 2 41 59 pm

@smathermather
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Looks great @dbaldwin! Definitely interested to see the orthophoto.

@smathermather
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Also, I'd love to see how this compares to Photoscan, @dbaldwin.

@dbaldwin
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dbaldwin commented Jan 4, 2015

@smathermather I did an overview video here to introduce the viewers of my channel to this awesome project:

https://www.youtube.com/watch?v=e2qp3o8caPs

Here is a link that contains the source imagery as well as the output of Photoscan Pro:

https://www.dropbox.com/sh/1rt1qdh7tw2mybi/AAAv7zukDC7fszyJMXfc5x8wa?dl=0

@smathermather
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Excellent @dbaldwin! Can you add the video to the readme as a pull request? This will make an excellent addition.

Downloading the data from Dropbox now... .

dakotabenjamin referenced this issue in dakotabenjamin/OpenDroneMap Dec 15, 2015
Add "Script finished" to end
dakotabenjamin pushed a commit that referenced this issue Aug 1, 2016
Improved Docker build and run system with instructions.
mribbons added a commit to mribbons/OpenDroneMap that referenced this issue May 19, 2017
Issue was caused by data in ImageUniqueID tag, even though data
is populated.

By only reading the values we need from metadata we avoid the issue
in pyexiv2.

Should also improve performance.

stacktrace of error:

.#0  strlen () at ../sysdeps/x86_64/strlen.S:106
.OpenDroneMap#1  0x00007fffdb154ce7 in exiv2wrapper::ExifTag::ExifTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, Exiv2::Exifdatum*, Exiv2::ExifData*, Exiv2::ByteOrder) () from /usr/lib/python2.7/dist-packages/libexiv2python.so
.OpenDroneMap#2  0x00007fffdb154eb4 in exiv2wrapper::Image::getExifTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) ()
   from /usr/lib/python2.7/dist-packages/libexiv2python.so
.OpenDroneMap#3  0x00007fffdb15f3e6 in boost::python::objects::caller_py_function_impl<boost::python::detail::caller<exiv2wrapper::ExifTag const (exiv2wrapper::Image::*)(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >), boost::python::default_call_policies, boost::mpl::vector3<exiv2wrapper::ExifTag const, exiv2wrapper::Image&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >::operator()(_object*, _object*) ()
   from /usr/lib/python2.7/dist-packages/libexiv2python.so
.OpenDroneMap#4  0x00007ffff52845cd in boost::python::objects::function::call(_object*, _object*) const () from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
.OpenDroneMap#5  0x00007ffff52847c8 in ?? () from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
.OpenDroneMap#6  0x00007ffff528c823 in boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const ()
   from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
.OpenDroneMap#7  0x00007fffdb15dd63 in boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Exiv2::BasicError<char>, void (*)(Exiv2::BasicError<char> const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Exiv2::BasicError<char> const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) () from /usr/lib/python2.7/dist-packages/libexiv2python.so
.OpenDroneMap#8  0x00007ffff528c7f8 in boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const ()
   from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
.OpenDroneMap#9  0x00007ffff5d01ab8 in boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>::operator()(boost::python::detail::exception_handler const&, boost::function0<void> const&, void (*)(ecto::except::NullTendril const&)) const ()
   from /home/mribbons/OpenDroneMap170517/SuperBuild/install/lib/python2.7/dist-packages/ecto/ecto_main.so
.OpenDroneMap#10 0x00007ffff5d0099f in bool boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ecto::except::NullTendril const&)> >::operator()<bool, boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>, boost::_bi::list2<boost::python::detail::exception_handler const&, boost::function0<void> const&> >(boost::_bi::type<bool>, boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>&, boost::_bi::list2<boost::python::detail::exception_handler const&, boost::function0<void> const&>&, long) ()
   from /home/mribbons/OpenDroneMap170517/SuperBuild/install/lib/python2.7/dist-packages/ecto/ecto_main.so
.OpenDroneMap#11 0x00007ffff5cffbe7 in bool boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ecto::except::NullTendril const&)> > >::operator()<boost::python::detail::exception_handler, boost::function0<void> >(boost::python::detail::exception_handler const&, boost::function0<void> const&) ()
   from /home/mribbons/OpenDroneMap170517/SuperBuild/install/lib/python2.7/dist-packages/ecto/ecto_main.so
.OpenDroneMap#12 0x00007ffff5cfeb54 in boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ecto::except::NullTendril const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) ()
   from /home/mribbons/OpenDroneMap170517/SuperBuild/install/lib/python2.7/dist-packages/ecto/ecto_main.so
.OpenDroneMap#13 0x00007ffff528c7f8 in boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const ()
   from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
...
mribbons added a commit to mribbons/OpenDroneMap that referenced this issue May 19, 2017
Issue was caused by data in ImageUniqueID tag, even though data
is populated.

By only reading the values we need from metadata we avoid the issue
in pyexiv2.

Should also improve performance.

stacktrace of error:

.#0  strlen () at ../sysdeps/x86_64/strlen.S:106
.OpenDroneMap#1  0x00007fffdb154ce7 in exiv2wrapper::ExifTag::ExifTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, Exiv2::Exifdatum*, Exiv2::ExifData*, Exiv2::ByteOrder) () from /usr/lib/python2.7/dist-packages/libexiv2python.so
.OpenDroneMap#2  0x00007fffdb154eb4 in exiv2wrapper::Image::getExifTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) ()
   from /usr/lib/python2.7/dist-packages/libexiv2python.so
.OpenDroneMap#3  0x00007fffdb15f3e6 in boost::python::objects::caller_py_function_impl<boost::python::detail::caller<exiv2wrapper::ExifTag const (exiv2wrapper::Image::*)(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >), boost::python::default_call_policies, boost::mpl::vector3<exiv2wrapper::ExifTag const, exiv2wrapper::Image&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >::operator()(_object*, _object*) ()
   from /usr/lib/python2.7/dist-packages/libexiv2python.so
.OpenDroneMap#4  0x00007ffff52845cd in boost::python::objects::function::call(_object*, _object*) const () from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
.OpenDroneMap#5  0x00007ffff52847c8 in ?? () from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
.OpenDroneMap#6  0x00007ffff528c823 in boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const ()
   from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
.OpenDroneMap#7  0x00007fffdb15dd63 in boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Exiv2::BasicError<char>, void (*)(Exiv2::BasicError<char> const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Exiv2::BasicError<char> const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) () from /usr/lib/python2.7/dist-packages/libexiv2python.so
.OpenDroneMap#8  0x00007ffff528c7f8 in boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const ()
   from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
.OpenDroneMap#9  0x00007ffff5d01ab8 in boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>::operator()(boost::python::detail::exception_handler const&, boost::function0<void> const&, void (*)(ecto::except::NullTendril const&)) const ()
   from /home/mribbons/OpenDroneMap170517/SuperBuild/install/lib/python2.7/dist-packages/ecto/ecto_main.so
.OpenDroneMap#10 0x00007ffff5d0099f in bool boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ecto::except::NullTendril const&)> >::operator()<bool, boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>, boost::_bi::list2<boost::python::detail::exception_handler const&, boost::function0<void> const&> >(boost::_bi::type<bool>, boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>&, boost::_bi::list2<boost::python::detail::exception_handler const&, boost::function0<void> const&>&, long) ()
   from /home/mribbons/OpenDroneMap170517/SuperBuild/install/lib/python2.7/dist-packages/ecto/ecto_main.so
.OpenDroneMap#11 0x00007ffff5cffbe7 in bool boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ecto::except::NullTendril const&)> > >::operator()<boost::python::detail::exception_handler, boost::function0<void> >(boost::python::detail::exception_handler const&, boost::function0<void> const&) ()
   from /home/mribbons/OpenDroneMap170517/SuperBuild/install/lib/python2.7/dist-packages/ecto/ecto_main.so
.OpenDroneMap#12 0x00007ffff5cfeb54 in boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ecto::except::NullTendril const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) ()
   from /home/mribbons/OpenDroneMap170517/SuperBuild/install/lib/python2.7/dist-packages/ecto/ecto_main.so
.OpenDroneMap#13 0x00007ffff528c7f8 in boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const ()
   from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
...
mribbons added a commit to mribbons/OpenDroneMap that referenced this issue May 19, 2017
Resolves OpenDroneMap#580

Issue was caused by attempting to read data in ImageUniqueID tag,
even though data is populated.

By only reading the values we need from metadata we avoid the issue
in pyexiv2.

Should also improve performance.

stacktrace of error:

.#0  strlen () at ../sysdeps/x86_64/strlen.S:106
.OpenDroneMap#1  0x00007fffdb154ce7 in exiv2wrapper::ExifTag::ExifTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, Exiv2::Exifdatum*, Exiv2::ExifData*, Exiv2::ByteOrder) () from /usr/lib/python2.7/dist-packages/libexiv2python.so
.OpenDroneMap#2  0x00007fffdb154eb4 in exiv2wrapper::Image::getExifTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) ()
   from /usr/lib/python2.7/dist-packages/libexiv2python.so
.OpenDroneMap#3  0x00007fffdb15f3e6 in boost::python::objects::caller_py_function_impl<boost::python::detail::caller<exiv2wrapper::ExifTag const (exiv2wrapper::Image::*)(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >), boost::python::default_call_policies, boost::mpl::vector3<exiv2wrapper::ExifTag const, exiv2wrapper::Image&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >::operator()(_object*, _object*) ()
   from /usr/lib/python2.7/dist-packages/libexiv2python.so
.OpenDroneMap#4  0x00007ffff52845cd in boost::python::objects::function::call(_object*, _object*) const () from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
.OpenDroneMap#5  0x00007ffff52847c8 in ?? () from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
.OpenDroneMap#6  0x00007ffff528c823 in boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const ()
   from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
.OpenDroneMap#7  0x00007fffdb15dd63 in boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Exiv2::BasicError<char>, void (*)(Exiv2::BasicError<char> const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Exiv2::BasicError<char> const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) () from /usr/lib/python2.7/dist-packages/libexiv2python.so
.OpenDroneMap#8  0x00007ffff528c7f8 in boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const ()
   from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
.OpenDroneMap#9  0x00007ffff5d01ab8 in boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>::operator()(boost::python::detail::exception_handler const&, boost::function0<void> const&, void (*)(ecto::except::NullTendril const&)) const ()
   from /home/mribbons/OpenDroneMap170517/SuperBuild/install/lib/python2.7/dist-packages/ecto/ecto_main.so
.OpenDroneMap#10 0x00007ffff5d0099f in bool boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ecto::except::NullTendril const&)> >::operator()<bool, boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>, boost::_bi::list2<boost::python::detail::exception_handler const&, boost::function0<void> const&> >(boost::_bi::type<bool>, boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>&, boost::_bi::list2<boost::python::detail::exception_handler const&, boost::function0<void> const&>&, long) ()
   from /home/mribbons/OpenDroneMap170517/SuperBuild/install/lib/python2.7/dist-packages/ecto/ecto_main.so
.OpenDroneMap#11 0x00007ffff5cffbe7 in bool boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ecto::except::NullTendril const&)> > >::operator()<boost::python::detail::exception_handler, boost::function0<void> >(boost::python::detail::exception_handler const&, boost::function0<void> const&) ()
   from /home/mribbons/OpenDroneMap170517/SuperBuild/install/lib/python2.7/dist-packages/ecto/ecto_main.so
.OpenDroneMap#12 0x00007ffff5cfeb54 in boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ecto::except::NullTendril const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) ()
   from /home/mribbons/OpenDroneMap170517/SuperBuild/install/lib/python2.7/dist-packages/ecto/ecto_main.so
.OpenDroneMap#13 0x00007ffff528c7f8 in boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const ()
   from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
...
mgctech-gk pushed a commit to mgctech-gk/OpenDroneMap that referenced this issue Jul 15, 2017
* Partial restart of opensfm

* Added Odm25dMeshing module, CGAL read Ply file example

* Proof of concept 2.5D colored mesh working. Still need to do smoothing / filtering

* Add BigTIFF creation option to odm_orthophoto

* Smoothing improvements (work in progress)

* Tweaked a few parameters

* Docker packages.Dockerfile Updates

Moved to phusion/baseimage
Removed .git folder in docker image
Also removed .git from the COPY in Dockerfile
Dropped Test files and git info from Dockerfile

* Ignore updates

* Add baseline code for DEM gen

* Add all options to BIGTIFF param

* Add gdaladdo to build overviews

* Docker updates

* Docker Improvements

* jet_smooth_points working

* bilateral smoothing working

* Dockerfile updates

* Last tweaks, ready for testing

* Added support for resume from opensfm reconstruction stages.

* Added support for resume from opensfm reconstruction stages.

* Started modifying cmake build rules to build 25dmesh module

* Got odm_25dmeshing to compile under OpenDroneMap env

* Integrated 2.5D mesh into pipeline. Still needs testing

* Fixed path bug

* Fixed incorrect filename.

* Cleaned up dockerfile, updated core2.dockerfile, removed unused packages.dockerfile (OpenDroneMap#536)

* Add DEM generator to control script

* Add reinstall and uninstall options to configuration script

* Add reinstall instructions to README

* Update LAS conversion to JSON

* Expose DEM gen options to command line

* Removed odm_texturing, cleaned up 2.5d generation algorithm, added params in ODM pipeline

* Added max_vertex_25d parameter, added TBB library support for parallel execution, cleanup

* Added --skip-25dmesh parameter

* Increased lower limit for wlop

* Added overflow check in normalsDirectionCount

* Changed default wlop iterations value

* Add LAS writer forward option

* Added libgmp-dev libmpfr-dev dependencies

* Started improving 2.5d mesh generation to fix seg faults in mvs texturing

* z-occlusion filtering, removed outlier removal, still need testing

* Removed max-vertex-25d parameter

* Grid upsampling, much faster processing

* Re-added outlier removal code

* Polyhedron construction, refining, simplification

* Readded outlier removal parameter, removed tinyply dependency, mesh refinement, edge collapse

* Update Version

* Remove ref to packages.Dockerfile in README

* Parameter tweaks

* Re-add OpenSfM to benchmarking

* Added details for installing Grass version

Clarified that code works only with Grass 7 or higher version

* Linked contour map generation with ODM DEM model

This update links the grass contour code to the ODM project DEM model generated with PDAL, which is located in the project folder /odm_georeferencing/odm_georeferencing_model_dem.tif. 
It also enables contour and relief maps to be created across regions as it ignores the Location PROJ_INFO with the -o flag.

* Clarifies GRASS version

More detail for GRASS compile and install and links code to ODM project DEM file.

* Give proper warning when resize is equal to image size.

* Remove outdated instructions from readme

* Updated pdal matrix transform pipeline, updated PDAL version

* Use custom MVS repo

* Update MVS Texturing

* Update to version 0.3.1

* Removed extract true from filters.pmf

* added skip-resize flag to possible arguments and added its implementation

* added copy method to io.py

* replaced shutil.copyfile with io.copy

* Temporarily changed opensfm-processes to 1

* Link to "Viewing results" wiki page from README.md

* Added warning when an orthophoto cannot be generated due to excessive resolution

* Avoid crash in pyexiv2 with some image files.
Resolves OpenDroneMap#580

Issue was caused by attempting to read data in ImageUniqueID tag,
even though data is populated.

By only reading the values we need from metadata we avoid the issue
in pyexiv2.

Should also improve performance.

stacktrace of error:

.#0  strlen () at ../sysdeps/x86_64/strlen.S:106
.#1  0x00007fffdb154ce7 in exiv2wrapper::ExifTag::ExifTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, Exiv2::Exifdatum*, Exiv2::ExifData*, Exiv2::ByteOrder) () from /usr/lib/python2.7/dist-packages/libexiv2python.so
.#2  0x00007fffdb154eb4 in exiv2wrapper::Image::getExifTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) ()
   from /usr/lib/python2.7/dist-packages/libexiv2python.so
.#3  0x00007fffdb15f3e6 in boost::python::objects::caller_py_function_impl<boost::python::detail::caller<exiv2wrapper::ExifTag const (exiv2wrapper::Image::*)(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >), boost::python::default_call_policies, boost::mpl::vector3<exiv2wrapper::ExifTag const, exiv2wrapper::Image&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >::operator()(_object*, _object*) ()
   from /usr/lib/python2.7/dist-packages/libexiv2python.so
.OpenDroneMap#4  0x00007ffff52845cd in boost::python::objects::function::call(_object*, _object*) const () from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
.OpenDroneMap#5  0x00007ffff52847c8 in ?? () from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
.OpenDroneMap#6  0x00007ffff528c823 in boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const ()
   from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
.OpenDroneMap#7  0x00007fffdb15dd63 in boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Exiv2::BasicError<char>, void (*)(Exiv2::BasicError<char> const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Exiv2::BasicError<char> const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) () from /usr/lib/python2.7/dist-packages/libexiv2python.so
.OpenDroneMap#8  0x00007ffff528c7f8 in boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const ()
   from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
.OpenDroneMap#9  0x00007ffff5d01ab8 in boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>::operator()(boost::python::detail::exception_handler const&, boost::function0<void> const&, void (*)(ecto::except::NullTendril const&)) const ()
   from /home/mribbons/OpenDroneMap170517/SuperBuild/install/lib/python2.7/dist-packages/ecto/ecto_main.so
.OpenDroneMap#10 0x00007ffff5d0099f in bool boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ecto::except::NullTendril const&)> >::operator()<bool, boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>, boost::_bi::list2<boost::python::detail::exception_handler const&, boost::function0<void> const&> >(boost::_bi::type<bool>, boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>&, boost::_bi::list2<boost::python::detail::exception_handler const&, boost::function0<void> const&>&, long) ()
   from /home/mribbons/OpenDroneMap170517/SuperBuild/install/lib/python2.7/dist-packages/ecto/ecto_main.so
.OpenDroneMap#11 0x00007ffff5cffbe7 in bool boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ecto::except::NullTendril const&)> > >::operator()<boost::python::detail::exception_handler, boost::function0<void> >(boost::python::detail::exception_handler const&, boost::function0<void> const&) ()
   from /home/mribbons/OpenDroneMap170517/SuperBuild/install/lib/python2.7/dist-packages/ecto/ecto_main.so
.OpenDroneMap#12 0x00007ffff5cfeb54 in boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ecto::except::NullTendril const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) ()
   from /home/mribbons/OpenDroneMap170517/SuperBuild/install/lib/python2.7/dist-packages/ecto/ecto_main.so
.OpenDroneMap#13 0x00007ffff528c7f8 in boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const ()
   from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
...

* Revert incorrect permission change from 992935e

* added output of the final transform to text file (also fixed a small typo)

* forgot a self.

* Improved GPS Altitude tag detection and parsing

* added argument for setting transform file path

* added usage of outputTransformFile in python code. also updated readme to contain the file

* forgot _file suffix

* also have to set transform file here

* Fix x,y dimensions in exif after resize.

In numpy arrays, shape[0] corresponds to y and shape[1] corresponds to x.

* Modified dockerfile, configure.sh script to install lidar2dems module

* Added lidar2dems superbuild module, modified dockerfile, configure.sh to install lidar2dems deps

* Started adding odm_dem module

* Wrote ODM_DEM cell

* Syntax fix, decimation parameter fix, tweaks

* Updated checksum

* Removed convert_to_dem

* Typo

* Labeled units

* configure.sh: Yes to GAL deps

Change-Id: If31faf28039f771238173490152d039a39e682ee

* Upgraded PDAL to include ground kernel patch commit

* Updated l2d md5

* Added automated DEM clipping

* Skip classification if only DSM is requested, decimation parameter passing

* Updated repo URLs, modified core2.dockerfile

* Added env_paths option in system.run, added path to superbuild install directory for odm_dem module, fixed lidar2dems install

* Fixed path error

* Added dependency on opensfm

* Removed MD5 check for lidar2dems

* Added dem-initial-distance parameter

* Parameter order fix

* Changed dem-initial-distance default value

* Update settings.yaml

* Add new dem settings
dakotabenjamin pushed a commit that referenced this issue Feb 16, 2019
peddyhh pushed a commit to peddyhh/ODM that referenced this issue Jun 7, 2020
Add "Script finished" to end

Former-commit-id: 1ae18ba
peddyhh pushed a commit to peddyhh/ODM that referenced this issue Jun 7, 2020
…cker

Improved Docker build and run system with instructions.

Former-commit-id: 6ec59ab
peddyhh pushed a commit to peddyhh/ODM that referenced this issue Jun 7, 2020
Resolves OpenDroneMap#580

Issue was caused by attempting to read data in ImageUniqueID tag,
even though data is populated.

By only reading the values we need from metadata we avoid the issue
in pyexiv2.

Should also improve performance.

stacktrace of error:

.#0  strlen () at ../sysdeps/x86_64/strlen.S:106
.OpenDroneMap#1  0x00007fffdb154ce7 in exiv2wrapper::ExifTag::ExifTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, Exiv2::Exifdatum*, Exiv2::ExifData*, Exiv2::ByteOrder) () from /usr/lib/python2.7/dist-packages/libexiv2python.so
.OpenDroneMap#2  0x00007fffdb154eb4 in exiv2wrapper::Image::getExifTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) ()
   from /usr/lib/python2.7/dist-packages/libexiv2python.so
.OpenDroneMap#3  0x00007fffdb15f3e6 in boost::python::objects::caller_py_function_impl<boost::python::detail::caller<exiv2wrapper::ExifTag const (exiv2wrapper::Image::*)(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >), boost::python::default_call_policies, boost::mpl::vector3<exiv2wrapper::ExifTag const, exiv2wrapper::Image&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >::operator()(_object*, _object*) ()
   from /usr/lib/python2.7/dist-packages/libexiv2python.so
.OpenDroneMap#4  0x00007ffff52845cd in boost::python::objects::function::call(_object*, _object*) const () from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
.OpenDroneMap#5  0x00007ffff52847c8 in ?? () from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
.OpenDroneMap#6  0x00007ffff528c823 in boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const ()
   from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
.OpenDroneMap#7  0x00007fffdb15dd63 in boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Exiv2::BasicError<char>, void (*)(Exiv2::BasicError<char> const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Exiv2::BasicError<char> const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) () from /usr/lib/python2.7/dist-packages/libexiv2python.so
.OpenDroneMap#8  0x00007ffff528c7f8 in boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const ()
   from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
.OpenDroneMap#9  0x00007ffff5d01ab8 in boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>::operator()(boost::python::detail::exception_handler const&, boost::function0<void> const&, void (*)(ecto::except::NullTendril const&)) const ()
   from /home/mribbons/OpenDroneMap170517/SuperBuild/install/lib/python2.7/dist-packages/ecto/ecto_main.so
.OpenDroneMap#10 0x00007ffff5d0099f in bool boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ecto::except::NullTendril const&)> >::operator()<bool, boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>, boost::_bi::list2<boost::python::detail::exception_handler const&, boost::function0<void> const&> >(boost::_bi::type<bool>, boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>&, boost::_bi::list2<boost::python::detail::exception_handler const&, boost::function0<void> const&>&, long) ()
   from /home/mribbons/OpenDroneMap170517/SuperBuild/install/lib/python2.7/dist-packages/ecto/ecto_main.so
.OpenDroneMap#11 0x00007ffff5cffbe7 in bool boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ecto::except::NullTendril const&)> > >::operator()<boost::python::detail::exception_handler, boost::function0<void> >(boost::python::detail::exception_handler const&, boost::function0<void> const&) ()
   from /home/mribbons/OpenDroneMap170517/SuperBuild/install/lib/python2.7/dist-packages/ecto/ecto_main.so
.OpenDroneMap#12 0x00007ffff5cfeb54 in boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ecto::except::NullTendril const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) ()
   from /home/mribbons/OpenDroneMap170517/SuperBuild/install/lib/python2.7/dist-packages/ecto/ecto_main.so
.OpenDroneMap#13 0x00007ffff528c7f8 in boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const ()
   from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
...


Former-commit-id: 992935e
peddyhh pushed a commit to peddyhh/ODM that referenced this issue Jun 7, 2020
Bring in latest master

Former-commit-id: 6ce8435
pierotofy pushed a commit that referenced this issue Sep 21, 2020
Add "Script finished" to end

Former-commit-id: 1ae18ba
pierotofy pushed a commit that referenced this issue Sep 21, 2020
Improved Docker build and run system with instructions.

Former-commit-id: 6ec59ab
pierotofy pushed a commit that referenced this issue Sep 21, 2020
Resolves #580

Issue was caused by attempting to read data in ImageUniqueID tag,
even though data is populated.

By only reading the values we need from metadata we avoid the issue
in pyexiv2.

Should also improve performance.

stacktrace of error:

.#0  strlen () at ../sysdeps/x86_64/strlen.S:106
.#1  0x00007fffdb154ce7 in exiv2wrapper::ExifTag::ExifTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, Exiv2::Exifdatum*, Exiv2::ExifData*, Exiv2::ByteOrder) () from /usr/lib/python2.7/dist-packages/libexiv2python.so
.#2  0x00007fffdb154eb4 in exiv2wrapper::Image::getExifTag(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >) ()
   from /usr/lib/python2.7/dist-packages/libexiv2python.so
.#3  0x00007fffdb15f3e6 in boost::python::objects::caller_py_function_impl<boost::python::detail::caller<exiv2wrapper::ExifTag const (exiv2wrapper::Image::*)(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >), boost::python::default_call_policies, boost::mpl::vector3<exiv2wrapper::ExifTag const, exiv2wrapper::Image&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >::operator()(_object*, _object*) ()
   from /usr/lib/python2.7/dist-packages/libexiv2python.so
.#4  0x00007ffff52845cd in boost::python::objects::function::call(_object*, _object*) const () from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
.#5  0x00007ffff52847c8 in ?? () from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
.#6  0x00007ffff528c823 in boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const ()
   from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
.#7  0x00007fffdb15dd63 in boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<Exiv2::BasicError<char>, void (*)(Exiv2::BasicError<char> const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(Exiv2::BasicError<char> const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) () from /usr/lib/python2.7/dist-packages/libexiv2python.so
.#8  0x00007ffff528c7f8 in boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const ()
   from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
.#9  0x00007ffff5d01ab8 in boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>::operator()(boost::python::detail::exception_handler const&, boost::function0<void> const&, void (*)(ecto::except::NullTendril const&)) const ()
   from /home/mribbons/OpenDroneMap170517/SuperBuild/install/lib/python2.7/dist-packages/ecto/ecto_main.so
.#10 0x00007ffff5d0099f in bool boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ecto::except::NullTendril const&)> >::operator()<bool, boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>, boost::_bi::list2<boost::python::detail::exception_handler const&, boost::function0<void> const&> >(boost::_bi::type<bool>, boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>&, boost::_bi::list2<boost::python::detail::exception_handler const&, boost::function0<void> const&>&, long) ()
   from /home/mribbons/OpenDroneMap170517/SuperBuild/install/lib/python2.7/dist-packages/ecto/ecto_main.so
.#11 0x00007ffff5cffbe7 in bool boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ecto::except::NullTendril const&)> > >::operator()<boost::python::detail::exception_handler, boost::function0<void> >(boost::python::detail::exception_handler const&, boost::function0<void> const&) ()
   from /home/mribbons/OpenDroneMap170517/SuperBuild/install/lib/python2.7/dist-packages/ecto/ecto_main.so
.#12 0x00007ffff5cfeb54 in boost::detail::function::function_obj_invoker2<boost::_bi::bind_t<bool, boost::python::detail::translate_exception<ecto::except::NullTendril, void (*)(ecto::except::NullTendril const&)>, boost::_bi::list3<boost::arg<1>, boost::arg<2>, boost::_bi::value<void (*)(ecto::except::NullTendril const&)> > >, bool, boost::python::detail::exception_handler const&, boost::function0<void> const&>::invoke(boost::detail::function::function_buffer&, boost::python::detail::exception_handler const&, boost::function0<void> const&) ()
   from /home/mribbons/OpenDroneMap170517/SuperBuild/install/lib/python2.7/dist-packages/ecto/ecto_main.so
.#13 0x00007ffff528c7f8 in boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const ()
   from /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.58.0
...


Former-commit-id: 992935e
pierotofy pushed a commit that referenced this issue Sep 21, 2020
Bring in latest master

Former-commit-id: 6ce8435
pierotofy pushed a commit to pierotofy/ODM that referenced this issue Jul 7, 2022
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