<div dir="ltr">Jun,<div><br></div><div>You'll have to drill down a bit further to assess what exactly is the argument being passed (<font face="Calibri, sans-serif"><span style="font-size:15px">file.data[3071]) to the constructor of <a href="http://flex.int">flex.int</a>. 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?</span></font></div><div><font face="Calibri, sans-serif"><span style="font-size:15px"><br></span></font></div><div><font face="Calibri, sans-serif"><span style="font-size:15px">Nick</span></font></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr"><div>Nicholas K. Sauter, Ph. D.<br>Computer Staff Scientist, Molecular Biophysics and Integrated Bioimaging Division<div>Lawrence Berkeley National Laboratory<br>1 Cyclotron Rd., Bldg. 33R0345<br>Berkeley, CA 94720<br>(510) 486-5713<br></div></div></div></div></div>
<br><div class="gmail_quote">On Mon, May 2, 2016 at 8:34 PM, Jun Aishima <span dir="ltr"><<a href="mailto:jun.aishima@synchrotron.org.au" target="_blank">jun.aishima@synchrotron.org.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div lang="EN-AU" link="blue" vlink="purple">
<div>
<p class="MsoNormal">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).<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">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:<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">**********<u></u><u></u></p>
<p class="MsoNormal">import fabio<u></u><u></u></p>
<p class="MsoNormal">file=fabio.open('testcrystal_1_001.img') # adsc detector image<u></u><u></u></p>
<p class="MsoNormal">file.data[0]<u></u><u></u></p>
<p class="MsoNormal">from scitbx.array_family import flex<u></u><u></u></p>
<p class="MsoNormal"><a href="http://flex.int" target="_blank">flex.int</a>(file.data[3071]) # this is a 3072x3072 image. For some reason, row 0 causes no problems.<u></u><u></u></p>
<p class="MsoNormal">**********<u></u><u></u></p>
<p class="MsoNormal">At the end of this email is the stack trace I get.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">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.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Jun Aishima<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">**********<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">show_stack(1): <stdin>(1) <module><u></u><u></u></p>
<p class="MsoNormal">libc backtrace (23 frames, most recent call last):<u></u><u></u></p>
<p class="MsoNormal"> /home/aishimaj/spotter/bin/python() [0x414199]<u></u><u></u></p>
<p class="MsoNormal"> /lib64/libc.so.6(__libc_start_main+0xfd) [0x366d21ed5d]<u></u><u></u></p>
<p class="MsoNormal"> /home/aishimaj/spotter/bin/python(Py_Main+0xb22) [0x4150b2]<u></u><u></u></p>
<p class="MsoNormal"> /home/aishimaj/spotter/bin/python(PyRun_AnyFileExFlags+0x6b) [0x4ce82b]<u></u><u></u></p>
<p class="MsoNormal"> /home/aishimaj/spotter/bin/python(PyRun_InteractiveLoopFlags+0x4e) [0x4ce01e]<u></u><u></u></p>
<p class="MsoNormal"> /home/aishimaj/spotter/bin/python(PyRun_InteractiveOneFlags+0x1ff) [0x4cdd9f]<u></u><u></u></p>
<p class="MsoNormal"> /home/aishimaj/spotter/bin/python(PyEval_EvalCode+0x32) [0x4ad362]<u></u><u></u></p>
<p class="MsoNormal"> /home/aishimaj/spotter/bin/python(PyEval_EvalCodeEx+0x877) [0x4ad257]<u></u><u></u></p>
<p class="MsoNormal"> /home/aishimaj/spotter/bin/python(PyEval_EvalFrameEx+0x6a0b) [0x4aa8bb]<u></u><u></u></p>
<p class="MsoNormal"> /home/aishimaj/spotter/bin/python(PyObject_Call+0x47) [0x419ba7]<u></u><u></u></p>
<p class="MsoNormal"> /home/aishimaj/spotter/bin/python() [0x46df9f]<u></u><u></u></p>
<p class="MsoNormal"> /home/aishimaj/spotter/bin/python() [0x47623f]<u></u><u></u></p>
<p class="MsoNormal"> /home/aishimaj/spotter/bin/python(PyObject_Call+0x47) [0x419ba7]<u></u><u></u></p>
<p class="MsoNormal"> /home/aishimaj/spotter/bin/python() [0x42296f]<u></u><u></u></p>
<p class="MsoNormal"> /home/aishimaj/spotter/bin/python(PyObject_Call+0x47) [0x419ba7]<u></u><u></u></p>
<p class="MsoNormal"> /beamline/phenix/bootstrap/build/lib/libboost_python.so(+0x2d088) [0x7f5561101088]<u></u><u></u></p>
<p class="MsoNormal"> /beamline/phenix/bootstrap/build/lib/libboost_python.so(boost::python::handle_exception_impl(boost::function0<void>)+0x43) [0x7f5561112013]<u></u><u></u></p>
<p class="MsoNormal"> /beamline/phenix/bootstrap/build/lib/libboost_python.so(+0x2fe08) [0x7f5561103e08]<u></u><u></u></p>
<p class="MsoNormal"> /beamline/phenix/bootstrap/build/lib/libboost_python.so(boost::python::objects::function::call(_object*, _object*) const+0xef) [0x7f55611031ff]<u></u><u></u></p>
<p class="MsoNormal"> /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]<u></u><u></u></p>
<p class="MsoNormal"> /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]<u></u><u></u></p>
<p class="MsoNormal"> /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]<u></u><u></u></p>
<p class="MsoNormal"> /lib64/libc.so.6() [0x366d2326a0]<u></u><u></u></p>
<p class="MsoNormal">Segmentation fault (Python and libc call stacks above)<u></u><u></u></p>
<p class="MsoNormal"> This crash may be due to a problem in any imported<u></u><u></u></p>
<p class="MsoNormal"> Python module, including modules which are not part<u></u><u></u></p>
<p class="MsoNormal"> of the cctbx project. To disable the traps leading<u></u><u></u></p>
<p class="MsoNormal"> to this message, define these environment variables<u></u><u></u></p>
<p class="MsoNormal"> (e.g. assign the value 1):<u></u><u></u></p>
<p class="MsoNormal"> BOOST_ADAPTBX_FPE_DEFAULT<u></u><u></u></p>
<p class="MsoNormal"> BOOST_ADAPTBX_SIGNALS_DEFAULT<u></u><u></u></p>
<p class="MsoNormal"> This will NOT solve the problem, just mask it, but<u></u><u></u></p>
<p class="MsoNormal"> may allow you to proceed in case it is not critical.<span class="HOEnZb"><font color="#888888"><u></u><u></u></font></span></p><span class="HOEnZb"><font color="#888888">
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><b><span style="font-family:"Arial","sans-serif";color:#7f7f7f">Jun Aishima | Post Doc - MX | Australian Synchrotron
<br>
</span></b><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#7f7f7f">p: (03) 8540 4114 | f: (03) 8540 4200
<br>
<a href="mailto:jun.aishima@synchrotron.org.au" target="_blank"><span style="color:#7f7f7f;text-decoration:none">jun.aishima@synchrotron.org.au</span></a> |
<a href="http://www.synchrotron.org.au" target="_blank"><span style="color:#7f7f7f;text-decoration:none">www.synchrotron.org.au</span></a><br>
800 Blackburn Road, Clayton, Victoria 3168</span><span><u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
</font></span></div>
</div>
<br>_______________________________________________<br>
cctbxbb mailing list<br>
<a href="mailto:cctbxbb@phenix-online.org">cctbxbb@phenix-online.org</a><br>
<a href="http://phenix-online.org/mailman/listinfo/cctbxbb" rel="noreferrer" target="_blank">http://phenix-online.org/mailman/listinfo/cctbxbb</a><br>
<br></blockquote></div><br></div>