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<p class="MsoNormal"><a name="_MailEndCompose"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Nick and Peter,<o:p></o:p></span></a></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">It will take me a while to get back into C++ to figure out what is happening with the flex.int() constructor! However, I like your suggestion of using dxtbx
– I didn’t know it had methods to do something like this, so I’ll see what I can find. I will definitely send you the image off-board anyways, just so you have an idea what I am seeing.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">By the way, Aaron had answered me, and by then I had managed to reproduce the problem entirely using phenix.python and only numpy to create an empty array,
and then attempting to convert that into flex:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">import numpy<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">from scitbx.array_family import flex<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">a=numpy.ndarray(shape=[3072,3072],dtype=numpy.uint16)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">flex.int(a)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Jun<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;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>
</span><a href="mailto:jun.aishima@synchrotron.org.au"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#7F7F7F;text-decoration:none">jun.aishima@synchrotron.org.au</span></a><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#7F7F7F">
| </span><a href="www.synchrotron.org.au"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#7F7F7F;text-decoration:none">www.synchrotron.org.au</span></a><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#7F7F7F"><br>
800 Blackburn Road, Clayton, Victoria 3168</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> cctbxbb-bounces@phenix-online.org [mailto:cctbxbb-bounces@phenix-online.org]
<b>On Behalf Of </b>Nicholas Sauter<br>
<b>Sent:</b> Tuesday, 3 May 2016 3:04 PM<br>
<b>To:</b> cctbx mailing list<br>
<b>Subject:</b> Re: [cctbxbb] problem when using Python to convert from numpy array to flex.int array<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Jun,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">You'll have to drill down a bit further to assess what exactly is the argument being passed (<span style="font-size:11.5pt;font-family:"Calibri","sans-serif"">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><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:11.5pt;font-family:"Calibri","sans-serif"">Nick</span><o:p></o:p></p>
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<o:p></o:p></p>
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<p class="MsoNormal">Nicholas K. Sauter, Ph. D.<br>
Computer Staff Scientist, Molecular Biophysics and Integrated Bioimaging Division<o:p></o:p></p>
<div>
<p class="MsoNormal">Lawrence Berkeley National Laboratory<br>
1 Cyclotron Rd., Bldg. 33R0345<br>
Berkeley, CA 94720<br>
(510) 486-5713<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Mon, May 2, 2016 at 8:34 PM, Jun Aishima <<a href="mailto:jun.aishima@synchrotron.org.au" target="_blank">jun.aishima@synchrotron.org.au</a>> wrote:<o:p></o:p></p>
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<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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).<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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:<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">**********<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">import fabio<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">file=fabio.open('testcrystal_1_001.img') # adsc detector image<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">file.data[0]<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">from scitbx.array_family import flex<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><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.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">**********<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">At the end of this email is the stack trace I get.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Jun Aishima<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">**********<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">show_stack(1): <stdin>(1) <module><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">libc backtrace (23 frames, most recent call last):<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> /home/aishimaj/spotter/bin/python() [0x414199]<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> /lib64/libc.so.6(__libc_start_main+0xfd) [0x366d21ed5d]<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> /home/aishimaj/spotter/bin/python(Py_Main+0xb22) [0x4150b2]<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> /home/aishimaj/spotter/bin/python(PyRun_AnyFileExFlags+0x6b) [0x4ce82b]<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> /home/aishimaj/spotter/bin/python(PyRun_InteractiveLoopFlags+0x4e) [0x4ce01e]<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> /home/aishimaj/spotter/bin/python(PyRun_InteractiveOneFlags+0x1ff) [0x4cdd9f]<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> /home/aishimaj/spotter/bin/python(PyEval_EvalCode+0x32) [0x4ad362]<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> /home/aishimaj/spotter/bin/python(PyEval_EvalCodeEx+0x877) [0x4ad257]<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> /home/aishimaj/spotter/bin/python(PyEval_EvalFrameEx+0x6a0b) [0x4aa8bb]<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> /home/aishimaj/spotter/bin/python(PyObject_Call+0x47) [0x419ba7]<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> /home/aishimaj/spotter/bin/python() [0x46df9f]<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> /home/aishimaj/spotter/bin/python() [0x47623f]<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> /home/aishimaj/spotter/bin/python(PyObject_Call+0x47) [0x419ba7]<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> /home/aishimaj/spotter/bin/python() [0x42296f]<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> /home/aishimaj/spotter/bin/python(PyObject_Call+0x47) [0x419ba7]<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> /beamline/phenix/bootstrap/build/lib/libboost_python.so(+0x2d088) [0x7f5561101088]<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> /beamline/phenix/bootstrap/build/lib/libboost_python.so(boost::python::handle_exception_impl(boost::function0<void>)+0x43) [0x7f5561112013]<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> /beamline/phenix/bootstrap/build/lib/libboost_python.so(+0x2fe08) [0x7f5561103e08]<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> /beamline/phenix/bootstrap/build/lib/libboost_python.so(boost::python::objects::function::call(_object*, _object*) const+0xef) [0x7f55611031ff]<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> /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]<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> /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]<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> /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]<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> /lib64/libc.so.6() [0x366d2326a0]<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Segmentation fault (Python and libc call stacks above)<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> This crash may be due to a problem in any imported<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> Python module, including modules which are not part<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> of the cctbx project. To disable the traps leading<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> to this message, define these environment variables<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> (e.g. assign the value 1):<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> BOOST_ADAPTBX_FPE_DEFAULT<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> BOOST_ADAPTBX_SIGNALS_DEFAULT<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> This will NOT solve the problem, just mask it, but<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> may allow you to proceed in case it is not critical.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#888888"> <o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><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 style="color:#888888"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#888888"> <o:p></o:p></span></p>
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<a href="http://phenix-online.org/mailman/listinfo/cctbxbb" target="_blank">http://phenix-online.org/mailman/listinfo/cctbxbb</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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