[cctbxbb] problem when using Python to convert from numpy array to flex.int array
Jun Aishima
jun.aishima at synchrotron.org.au
Mon May 2 22:11:39 PDT 2016
Nick and Peter,
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.
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:
import numpy
from scitbx.array_family import flex
a=numpy.ndarray(shape=[3072,3072],dtype=numpy.uint16)
flex.int(a)
Jun
Jun Aishima | Post Doc - MX | Australian Synchrotron
p: (03) 8540 4114 | f: (03) 8540 4200
jun.aishima at synchrotron.org.au<mailto:jun.aishima at synchrotron.org.au> | www.synchrotron.org.au
800 Blackburn Road, Clayton, Victoria 3168
From: cctbxbb-bounces at phenix-online.org [mailto:cctbxbb-bounces at phenix-online.org] On Behalf Of Nicholas Sauter
Sent: Tuesday, 3 May 2016 3:04 PM
To: cctbx mailing list
Subject: Re: [cctbxbb] problem when using Python to convert from numpy array to flex.int array
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<http://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<mailto: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<http://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<mailto:jun.aishima at synchrotron.org.au> | www.synchrotron.org.au<http://www.synchrotron.org.au>
800 Blackburn Road, Clayton, Victoria 3168
_______________________________________________
cctbxbb mailing list
cctbxbb at phenix-online.org<mailto:cctbxbb at phenix-online.org>
http://phenix-online.org/mailman/listinfo/cctbxbb
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/cctbxbb/attachments/20160503/0325ac3a/attachment-0001.htm>
More information about the cctbxbb
mailing list