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:
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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.
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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
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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