[vmtk-users] vmtksurfacereader for ascii STL

[Elaine T. <ela...@ga...>]

Hi,

I am wondering why the vmtk that I have (I think it's version 1.0.1) cannot
read stl in ascii format. It works for binary format.I know the fix for
surface writing is like that:

 vmtksurfacewriter -i @.o -mode ascii -ofile foo.vtk

But for vmtksurfacereader/ surfaceviewer, I got the following error when I
am trying to read an ascii STL:

[etang@desktop Elaine_practice]$ vmtksurfacereader -ifile foo.stl



Creating vmtkSurfaceReader instance.

Automatic piping vmtksurfacereader

Parsing options vmtksurfacereader

    InputFileName = foo.stl

Explicit piping vmtksurfacereader

Input vmtksurfacereader members:

    Id = 0

    Disabled = 0

    Format =

    GuessFormat = 1

    Surface = 0

    InputFileName = foo.stl

    SurfaceOutputFileName =

Executing vmtksurfacereader ...

Reading STL surface file.

ERROR: In /home/etang/vmtk/vmtk-build/VTK/IO/vtkSTLReader.cxx, line 446

vtkSTLReader (0x18b281c0): STLReader error reading file: foo.stl Premature
EOF while reading end solid.



*** glibc detected *** python: double free or corruption (!prev):
0x0000000018b30710 ***

======= Backtrace: =========

/lib64/libc.so.6[0x352bc7166f]

/lib64/libc.so.6(cfree+0x4b)[0x352bc7589b]

/lib64/libc.so.6(fclose+0x14b)[0x352bc6001b]

/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkIO.so.5.10(_ZN12vtkSTLReader11RequestDataEP14vtkInformationPP20vtkInformationVectorS3_+0x24c)[0x2b8c67cbbe4c]

/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkFiltering.so.5.10(_ZN12vtkExecutive13CallAlgorithmEP14vtkInformationiPP20vtkInformationVectorS3_+0x54)[0x2b8c66f386d4]

/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkFiltering.so.5.10(_ZN23vtkDemandDrivenPipeline11ExecuteDataEP14vtkInformationPP20vtkInformationVectorS3_+0x4c)[0x2b8c66f2c8bc]

/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkFiltering.so.5.10(_ZN23vtkDemandDrivenPipeline14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3_+0x293)[0x2b8c66f2f653]

/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkFiltering.so.5.10(_ZN32vtkStreamingDemandDrivenPipeline14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3_+0x2a9)[0x2b8c6709ee69]

/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkFiltering.so.5.10(_ZN23vtkDemandDrivenPipeline10UpdateDataEi+0x9e)[0x2b8c66f2eb9e]

/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkFiltering.so.5.10(_ZN32vtkStreamingDemandDrivenPipeline6UpdateEi+0x7b)[0x2b8c67099fdb]

/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkFilteringPythonD.so.5.10[0x2b8c6691efff]

python(PyEval_EvalFrameEx+0x68e2)[0x49c862]

python(PyEval_EvalFrameEx+0x6b2f)[0x49caaf]

python(PyEval_EvalFrameEx+0x6b2f)[0x49caaf]

python(PyEval_EvalCodeEx+0x89b)[0x49dd1b]

python(PyEval_EvalFrameEx+0x5712)[0x49b692]

python(PyEval_EvalCodeEx+0x89b)[0x49dd1b]

python(PyEval_EvalFrameEx+0x5712)[0x49b692]

python(PyEval_EvalCodeEx+0x89b)[0x49dd1b]

python[0x4fc9ff]

python(PyObject_Call+0x5d)[0x4189cd]

python(PyEval_EvalFrameEx+0x399d)[0x49991d]

python(PyEval_EvalFrameEx+0x6b2f)[0x49caaf]

python(PyEval_EvalFrameEx+0x6b2f)[0x49caaf]

python(PyEval_EvalCodeEx+0x89b)[0x49dd1b]

python[0x4fc9ff]

python(PyObject_Call+0x5d)[0x4189cd]

python[0x41fedf]

python(PyObject_Call+0x5d)[0x4189cd]

python[0x46cf78]

python[0x466292]

python(PyObject_Call+0x5d)[0x4189cd]

python(PyEval_EvalFrameEx+0x111a)[0x49709a]

python(PyEval_EvalFrameEx+0x6b2f)[0x49caaf]

python(PyEval_EvalCodeEx+0x89b)[0x49dd1b]

python(PyEval_EvalCode+0x32)[0x49dd92]

python(PyRun_FileExFlags+0xc1)[0x4bfe31]

python(PyRun_SimpleFileExFlags+0x1d8)[0x4c00e8]

python(Py_Main+0xa7d)[0x414bbd]

/lib64/libc.so.6(__libc_start_main+0xf4)[0x352bc1d9c4]

python[0x413d69]

======= Memory map: ========

00400000-0055d000 r-xp 00000000 fd:03 49283158
/usr/local/bin/python2.7

0075d000-00799000 rw-p 0015d000 fd:03 49283158
/usr/local/bin/python2.7

00799000-007a8000 rw-p 00799000 00:00 0

1847f000-18b51000 rw-p 1847f000 00:00 0
[heap]

352b800000-352b81c000 r-xp 00000000 fd:03 141230281
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352bf52000-352bf53000 rw-p 00152000 fd:03 141230442
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352bf53000-352bf58000 rw-p 352bf53000 00:00 0

352c000000-352c082000 r-xp 00000000 fd:03 141230452
/lib64/libm-2.5.so

352c082000-352c281000 ---p 00082000 fd:03 141230452
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352c281000-352c282000 r--p 00081000 fd:03 141230452
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352c282000-352c283000 rw-p 00082000 fd:03 141230452
          /lib64/libm-2.5.so

352c400000-352c402000 r-xp 00000000 fd:03 141230450
/lib64/libdl-2.5.so

352c402000-352c602000 ---p 00002000 fd:03 141230450
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352c602000-352c603000 r--p 00002000 fd:03 141230450
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352c603000-352c604000 rw-p 00003000 fd:03 141230450
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352c800000-352c816000 r-xp 00000000 fd:03 141230445
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352c816000-352ca16000 ---p 00016000 fd:03 141230445
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352ca16000-352ca17000 r--p 00016000 fd:03 141230445
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352ca17000-352ca18000 rw-p 00017000 fd:03 141230445
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352ca18000-352ca1c000 rw-p 352ca18000 00:00 0

352cc00000-352cc14000 r-xp 00000000 fd:03 146729449
/usr/lib64/libz.so.1.2.3

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352d601000-352d602000 rw-p 00001000 fd:03 146709883
/usr/lib64/libXau.so.6.0.0

352d800000-352d805000 r-xp 00000000 fd:03 146729413
/usr/lib64/libXdmcp.so.6.0.0

352d805000-352da04000 ---p 00005000 fd:03 146729413
/usr/lib64/libXdmcp.so.6.0.0

352da04000-352da05000 rw-p 00004000 fd:03 146729413
     /usr/lib64/libXdmcp.so.6.0.0

352dc00000-352dd05000 r-xp 00000000 fd:03 146729418
/usr/lib64/libX11.so.6.2.0

352dd05000-352df05000 ---p 00105000 fd:03 146729418
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352e400000-352e410000 r-xp 00000000 fd:03 146729536
/usr/lib64/libXext.so.6.4.0

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/usr/lib64/libXext.so.6.4.0

3531400000-3531415000 r-xp 00000000 fd:03 141230456
/lib64/libselinux.so.1

3531415000-3531615000 ---p 00015000 fd:03 141230456
/lib64/libselinux.so.1

3531615000-3531617000 rw-p 00015000 fd:03 141230456
/lib64/libselinux.so.1

3531617000-3531618000 rw-p 3531617000 00:00 0

3531800000-353183b000 r-xp 00000000 fd:03 141230455
                     /lib64/libsepol.so.1

353183b000-3531a3b000 ---p 0003b000 fd:03 141230455
/lib64/libsepol.so.1

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/lib64/libsepol.so.1

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/lib64/libgcc_s-4.1.2-20080825.so.1

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/lib64/libgcc_s-4.1.2-20080825.so.1

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/usr/lib64/libSM.so.6.0.0

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3535a00000-3535a02000 r-xp 00000000 fd:03 141230457
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/usr/local/lib/python2.7/lib-dynload/operator.so

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/usr/local/lib/python2.7/lib-dynload/_bisect.so

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              /usr/local/lib/python2.7/lib-dynload/_heapq.so

2b8c64408000-2b8c64413000 r-xp 00000000 fd:03 160366729
/usr/local/lib/python2.7/lib-dynload/_socket.so

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/usr/local/lib/python2.7/lib-dynload/_socket.so

2b8c64617000-2b8c64619000 r-xp 00000000 fd:03 160366702
/usr/local/lib/python2.7/lib-dynload/_functools.so

2b8c64619000-2b8c64819000 ---p 00002000 fd:03 160366702
/usr/local/lib/python2.7/lib-dynload/_functools.so

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/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/vtkGenericFilteringPython.so

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/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/vtkGenericFilteringPython.so

2b8c6c004000-2b8c6c030000 r-xp 00000000 00:19 199503476
/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkGenericFilteringPythonD.so.5.10.0

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/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkGenericFilteringPythonD.so.5.10.0

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2b8c6c233000-2b8c6c25b000 r-xp 00000000 00:19 199503480
/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkGenericFiltering.so.5.10.0

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2b8c6c45d000-2b8c6c464000 r-xp 00000000 00:19 199503698
/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/vtkRenderingPython.so

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/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/vtkRenderingPython.so

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/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/vtkRenderingPython.so

2b8c6c665000-2b8c6c942000 r-xp 00000000 00:19 199503695
/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkRenderingPythonD.so.5.10.0

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/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkRenderingPythonD.so.5.10.0

2b8c6cb71000-2b8c6cf3e000 r-xp 00000000 00:19 199503699
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/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkftgl.so.5.10.0

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/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkftgl.so.5.10.0

2b8c6d419000-2b8c6d498000 r-xp 00000000 00:19 199502256
/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkfreetype.so.5.10.0

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/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkfreetype.so.5.10.0

2b8c6d6b9000-2b8c6d763000 r-xp 00000000 fd:03 146729910
/usr/lib64/libGL.so.195.36.15

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/usr/lib64/libGL.so.195.36.15

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/usr/lib64/libGL.so.195.36.15

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/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkVolumeRendering.so.5.10.0

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2b8c6eec3000-2b8c6eec5000 rw-p 2b8c6eec3000 00:00 0

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/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkexoIIc.so.5.10.0

2b8c6ef09000-2b8c6f109000 ---p 00044000 00:19 199502497
/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkexoIIc.so.5.10.0

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/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkexoIIc.so.5.10.0

2b8c6f10a000-2b8c6f10f000 r-xp 00000000 00:19 199504151
/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/vtkWidgetsPython.so

2b8c6f10f000-2b8c6f30e000 ---p 00005000 00:19 199504151
    /home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/vtkWidgetsPython.so

2b8c6f30e000-2b8c6f30f000 rw-p 00004000 00:19 199504151
/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/vtkWidgetsPython.so

2b8c6f30f000-2b8c6f4fb000 r-xp 00000000 00:19 199504148
/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkWidgetsPythonD.so.5.10.0

2b8c6f4fb000-2b8c6f6fa000 ---p 001ec000 00:19 199504148
/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkWidgetsPythonD.so.5.10.0

2b8c6f6fa000-2b8c6f719000 rw-p 001eb000 00:19 199504148
/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkWidgetsPythonD.so.5.10.0

2b8c6f719000-2b8c6f8ec000 r-xp 00000000 00:19 199504152
/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkWidgets.so.5.10.0

2b8c6f8ec000-2b8c6faeb000 ---p 001d3000 00:19 199504152
/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkWidgets.so.5.10.0

2b8c6faeb000-2b8c6fb08000 rw-p 001d2000 00:19 199504152
/home/etang/vmtk/vmtk-build/Install/lib/vtk-5.10/libvtkWidgets.so.5.10.0

2b8c6fe8f000-2b8c70064000 rw-p 2b8c6fb58000 00:00 0

2b8c70064000-2b8c702d6000 rw-p 2b8c6fb09000 00:00 0

7fff7e116000-7fff7e132000 rw-p 7ffffffe2000 00:00 0
[stack]

ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0
[vdso]




And there is no 'mode' option for surfacereader. Was this because of my
installation? Is there any fix without re-installing?


Thanks a lot!
-- 
Elaine Tang