Jun,
You'll have to drill down a bit further to assess what exactly is the
argument being passed (file.data[3071]) to the constructor of flex.int.
Otherwise you can send the raw image file & I'll have a look. Why aren't
you using dxtbx to read the raw data directly to a scitbx flex type?
Nick
Nicholas K. Sauter, Ph. D.
Computer Staff Scientist, Molecular Biophysics and Integrated Bioimaging
Division
Lawrence Berkeley National Laboratory
1 Cyclotron Rd., Bldg. 33R0345
Berkeley, CA 94720
(510) 486-5713
On Mon, May 2, 2016 at 8:34 PM, Jun Aishima <jun.aishima at synchrotron.org.au>
wrote:
> I have used the bootstrap method to build cctbx with my own Python (in a
> virtual environment). I setup my virtual environment, then source
> $CCTBX/build/setpaths.sh (bash).
>
>
>
> I am currently trying to turn a detector image (uint16) read in with
> fabio, which results in a numpy ndarray, and then turn that into a scitbx
> flex array. Since I’ve had problems doing this in my system, I’ve written a
> little script that reproduces the problem:
>
>
>
> **********
>
> import fabio
>
> file=fabio.open('testcrystal_1_001.img') # adsc detector image
>
> file.data[0]
>
> from scitbx.array_family import flex
>
> flex.int(file.data[3071]) # this is a 3072x3072 image. For some reason,
> row 0 causes no problems.
>
> **********
>
> At the end of this email is the stack trace I get.
>
>
>
> Has anybody had similar issues? I first saw this when I was trying to
> convert the entire image into a flex array, but now I’ve seen it with only
> one row [3071], while still working for [0:1500], so it doesn’t seem like a
> simple memory issue. Any help would be appreciated.
>
>
>
> Jun Aishima
>
>
>
> **********
>
>
>
> show_stack(1): <stdin>(1) <module>
>
> libc backtrace (23 frames, most recent call last):
>
> /home/aishimaj/spotter/bin/python() [0x414199]
>
> /lib64/libc.so.6(__libc_start_main+0xfd) [0x366d21ed5d]
>
> /home/aishimaj/spotter/bin/python(Py_Main+0xb22) [0x4150b2]
>
> /home/aishimaj/spotter/bin/python(PyRun_AnyFileExFlags+0x6b) [0x4ce82b]
>
> /home/aishimaj/spotter/bin/python(PyRun_InteractiveLoopFlags+0x4e)
> [0x4ce01e]
>
> /home/aishimaj/spotter/bin/python(PyRun_InteractiveOneFlags+0x1ff)
> [0x4cdd9f]
>
> /home/aishimaj/spotter/bin/python(PyEval_EvalCode+0x32) [0x4ad362]
>
> /home/aishimaj/spotter/bin/python(PyEval_EvalCodeEx+0x877) [0x4ad257]
>
> /home/aishimaj/spotter/bin/python(PyEval_EvalFrameEx+0x6a0b) [0x4aa8bb]
>
> /home/aishimaj/spotter/bin/python(PyObject_Call+0x47) [0x419ba7]
>
> /home/aishimaj/spotter/bin/python() [0x46df9f]
>
> /home/aishimaj/spotter/bin/python() [0x47623f]
>
> /home/aishimaj/spotter/bin/python(PyObject_Call+0x47) [0x419ba7]
>
> /home/aishimaj/spotter/bin/python() [0x42296f]
>
> /home/aishimaj/spotter/bin/python(PyObject_Call+0x47) [0x419ba7]
>
> /beamline/phenix/bootstrap/build/lib/libboost_python.so(+0x2d088)
> [0x7f5561101088]
>
>
> /beamline/phenix/bootstrap/build/lib/libboost_python.so(boost::python::handle_exception_impl(boost::function0<void>)+0x43)
> [0x7f5561112013]
>
> /beamline/phenix/bootstrap/build/lib/libboost_python.so(+0x2fe08)
> [0x7f5561103e08]
>
>
> /beamline/phenix/bootstrap/build/lib/libboost_python.so(boost::python::objects::function::call(_object*,
> _object*) const+0xef) [0x7f55611031ff]
>
>
> /beamline/phenix/bootstrap/build/lib/scitbx_array_family_flex_ext.so(boost::python::objects::signature_py_function_impl<boost::python::detail::caller<scitbx::af::versa<int,
> scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > >*
> (*)(boost::python::numeric::array const&),
> boost::python::detail::constructor_policy<boost::python::default_call_policies>,
> boost::mpl::vector2<scitbx::af::versa<int,
> scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > >*,
> boost::python::numeric::array const&> >, boost::mpl::v_item<void,
> boost::mpl::v_item<boost::python::api::object,
> boost::mpl::v_mask<boost::mpl::vector2<scitbx::af::versa<int,
> scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > >*,
> boost::python::numeric::array const&>, 1>, 1>, 1> >::operator()(_object*,
> _object*)+0x52) [0x7f555ed68452]
>
>
> /beamline/phenix/bootstrap/build/lib/scitbx_array_family_flex_ext.so(scitbx::af::boost_python::flex_int_from_numpy_array(boost::python::numeric::array
> const&)+0x29) [0x7f555f039f79]
>
>
> /beamline/phenix/bootstrap/build/lib/scitbx_array_family_flex_ext.so(scitbx::af::versa<int,
> scitbx::af::flex_grid<scitbx::af::small<long, 10ul> > >
> scitbx::af::boost_python::versa_flex_from_numpy_array<int>(boost::python::numeric::array
> const&)+0x1c87) [0x7f555f0415c7]
>
> /lib64/libc.so.6() [0x366d2326a0]
>
> Segmentation fault (Python and libc call stacks above)
>
> This crash may be due to a problem in any imported
>
> Python module, including modules which are not part
>
> of the cctbx project. To disable the traps leading
>
> to this message, define these environment variables
>
> (e.g. assign the value 1):
>
> BOOST_ADAPTBX_FPE_DEFAULT
>
> BOOST_ADAPTBX_SIGNALS_DEFAULT
>
> This will NOT solve the problem, just mask it, but
>
> may allow you to proceed in case it is not critical.
>
>
>
>
> *Jun Aishima | Post Doc - MX | Australian Synchrotron *p: (03) 8540
> 4114 | f: (03) 8540 4200
> jun.aishima at synchrotron.org.au | www.synchrotron.org.au
> 800 Blackburn Road, Clayton, Victoria 3168
>
>
>
> _______________________________________________
> cctbxbb mailing list
> cctbxbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/cctbxbb
>
>
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