reg cleanup - Githubissues

thewtex commented 2 months ago

DOC: A first pass at a logo
ENH: Optionally return the Inverse transform also
ENH: Support an initial transform from a MRML Transform Node

thewtex commented 2 months ago

HDF5 segfault backtrace:

Thread 1 "SlicerApp-real" received signal SIGSEGV, Segmentation fault.
0x00007f34d7a3d58f in H5::Exception::~Exception() ()
   from /home/matt/bin/Slicer-5.7.0-2024-06-04-linux-amd64/bin/../lib/Slicer-5.7/libitkhdf5_cpp-shared-5.4.so.1
(gdb) where
#0  0x00007f34d7a3d58f in H5::Exception::~Exception() ()
   from /home/matt/bin/Slicer-5.7.0-2024-06-04-linux-amd64/bin/../lib/Slicer-5.7/libitkhdf5_cpp-shared-5.4.so.1
#1  0x00007f34fc8fdaff in ?? ()
   from /home/matt/bin/Slicer-5.7.0-2024-06-04-linux-amd64/bin/../lib/Slicer-5.7/libITKCommon-5.4.so.1
#2  0x00007f30deed443c in itk::HDF5TransformIOTemplate<double>::Read() ()
   from /home/matt/bin/Slicer-5.7.0-2024-06-04-linux-amd64/lib/Python/lib/python3.9/site-packages/itk/_ITKIOTransformHDF5Python.so
#3  0x00007f30e50787a3 in itk::TransformFileReaderTemplate<double>::Update() ()
   from /home/matt/bin/Slicer-5.7.0-2024-06-04-linux-amd64/lib/Python/lib/python3.9/site-packages/itk/_ITKIOTransformBasePython.so
#4  0x00007f30e504c7cc in ?? ()
   from /home/matt/bin/Slicer-5.7.0-2024-06-04-linux-amd64/lib/Python/lib/python3.9/site-packages/itk/_ITKIOTransformBasePython.so
#5  0x00007f34ecb02cf3 in ?? () from /home/matt/bin/Slicer-5.7.0-2024-06-04-linux-amd64/bin/../lib/Python/lib/libpython3.9.so
#6  0x00007f34eca76597 in ?? () from /home/matt/bin/Slicer-5.7.0-2024-06-04-linux-amd64/bin/../lib/Python/lib/libpython3.9.so
#7  0x00007f34eca7d070 in _PyEval_EvalFrameDefault ()

thewtex commented 2 months ago

I built Slicer from scratch, both Debug and Release builds, and I do not observe the crash.

Symbols are updated here: https://github.com/InsightSoftwareConsortium/ITK/pull/4736 but I have not been able to test if it actually addresses the issue.

thewtex commented 2 months ago

With Slicer-5.7.0-2024-07-03-linux-amd64:

HDF5-DIAG: Error detected in HDF5 (1.12.1) thread 0:
  #000: /work/ITK-source/ITK/Modules/ThirdParty/HDF5/src/itkhdf5/src/H5T.c line 2271 in itk_H5Tis_variable_str(): not a datatype
error: [/home/matt/bin/Slicer-5.7.0-2024-07-03-linux-amd64/bin/SlicerApp-real] exit abnormally - Report the problem.

thewtex commented 2 months ago

Backtrace:

#0  0x00007fbeff03d58f in H5::Exception::~Exception() () from /home/matt/bin/Slicer-5.7.0-2024-07-03-linux-amd64/bin/../lib/Slicer-5.7/libitkhdf5_cpp-shared-5.4.so.1
[Current thread is 1 (Thread 0x7fbf4ee84940 (LWP 3709604))]
(gdb)
(gdb) where
#0  0x00007fbeff03d58f in H5::Exception::~Exception() () from /home/matt/bin/Slicer-5.7.0-2024-07-03-linux-amd64/bin/../lib/Slicer-5.7/libitkhdf5_cpp-shared-5.4.so.1
#1  0x00007fbf23efdaff in ?? () from /home/matt/bin/Slicer-5.7.0-2024-07-03-linux-amd64/bin/../lib/Slicer-5.7/libITKCommon-5.4.so.1
#2  0x00007fbad28d443c in itk::HDF5TransformIOTemplate<double>::Read() ()
   from /home/matt/bin/Slicer-5.7.0-2024-07-03-linux-amd64/lib/Python/lib/python3.9/site-packages/itk/_ITKIOTransformHDF5Python.so
#3  0x00007fbad3e787a3 in itk::TransformFileReaderTemplate<double>::Update() ()
   from /home/matt/bin/Slicer-5.7.0-2024-07-03-linux-amd64/lib/Python/lib/python3.9/site-packages/itk/_ITKIOTransformBasePython.so

SlicerMorph / SlicerANTs

reg cleanup #8