pyanatomist 5.x usage

[AlexandreBeaurain]

Hello,

I face a small problem using pyanatomist in a docker container.

The compilation went successfully directly from brainvisa-cmake (on a ubuntu:20.04 container with python3 and branch 5.0), and when launching anatomist directly with

docker run --rm \
    -v /tmp/.X11-unix:/tmp/.X11-unix \
    -v /usr/share/X11/locale:/usr/share/X11/locale:ro \
    --privileged \
    -e DISPLAY=${DISPLAY} \
    -e QT_X11_NO_MITSHM=1 \
    -it ${DOCKER_IMAGE_TAG} anatomist

everything is running like a charm, application window pops correctly, I can load a NII file, and interact with anatomist. You did a really great job as this is an heavy compilation.

Then I have scripts that pilot anatomist with pyanatomist, but fails, for example with this simpliest code

import anatomist.api as anatomist
a = anatomist.Anatomist()
window = a.createWindow('Axial', options={'hidden': True})
t1mri = a.loadObject('/path/to/my/file.nii')
a.addObjects(t1mri, window)
image = window.snapshot('snapshot.jpg')

with backtrace

#0  0x00007fffd8a5265f in QObjectData::dynamicMetaObject() const () from /lib/x86_64-linux-gnu/libQt5Core.so.5
#1  0x00007fffd61d9871 in qpycore_qobject_getattr (qobj=0x1400d60, py_qobj=<AWindow3D(_cpp_rcptr=1) at remote 0x7fffc83b3820>, name=0x7fffc83b5050 "internalRep")
    at ../../qpy/QtCore/qpycore_qobject_getattr.cpp:40
#2  0x00007fffd61a3e7c in meth_QObject___getattr__ (sipSelf=<optimized out>, sipArgs=<optimized out>) at ./sip/QtCore/qobject.sip:449
#3  0x00000000005f5f1a in cfunction_call_varargs (kwargs=<optimized out>, args=<optimized out>, func=<built-in method __getattr__ of AWindow3D object at remote 0x7fffc83b3820>)
    at ../Include/internal/pycore_pyerrors.h:13
#4  PyCFunction_Call (func=<built-in method __getattr__ of AWindow3D object at remote 0x7fffc83b3820>, args=<optimized out>, kwargs=<optimized out>) at ../Objects/call.c:773
#5  0x00000000005f6a46 in _PyObject_MakeTpCall (callable=<built-in method __getattr__ of AWindow3D object at remote 0x7fffc83b3820>, args=<optimized out>, nargs=<optimized out>, keywords=<optimized out>)
    at ../Include/internal/pycore_pyerrors.h:13
#6  0x00000000005f3aed in _PyObject_Vectorcall (kwnames=0x0, nargsf=1, args=0x7fffffffcf10, callable=<built-in method __getattr__ of AWindow3D object at remote 0x7fffc83b3820>)
    at ../Include/cpython/abstract.h:125
#7  _PyObject_Vectorcall (kwnames=0x0, nargsf=1, args=0x7fffffffcf10, callable=<built-in method __getattr__ of AWindow3D object at remote 0x7fffc83b3820>) at ../Include/cpython/abstract.h:115
#8  _PyObject_FastCall (nargs=1, args=0x7fffffffcf10, func=<built-in method __getattr__ of AWindow3D object at remote 0x7fffc83b3820>) at ../Include/cpython/abstract.h:147
#9  object_vacall (base=<optimized out>, callable=<built-in method __getattr__ of AWindow3D object at remote 0x7fffc83b3820>, vargs=<optimized out>) at ../Objects/call.c:1187
#10 0x00000000005f3c75 in PyObject_CallFunctionObjArgs (callable=<optimized out>) at ../Objects/call.c:1260
#11 0x0000000000598bd7 in call_attribute (self=<optimized out>, attr=<built-in method __getattr__ of AWindow3D object at remote 0x7fffc83b3820>, name='internalRep') at ../Objects/typeobject.c:6597
#12 0x000000000059ba67 in slot_tp_getattr_hook (self=<AWindow3D(_cpp_rcptr=1) at remote 0x7fffc83b3820>, name='internalRep') at ../Objects/typeobject.c:6639
#13 0x00000000005c1e02 in PyObject_GetAttr (v=<AWindow3D(_cpp_rcptr=1) at remote 0x7fffc83b3820>, name='internalRep') at ../Include/object.h:470
#14 0x00000000005c21d0 in PyObject_GetAttrString (v=<AWindow3D(_cpp_rcptr=1) at remote 0x7fffc83b3820>, name=<optimized out>) at ../Objects/object.c:846
#15 0x00000000004dc22f in PyObject_HasAttrString (v=<optimized out>, name=<optimized out>) at ../Objects/object.c:854
#16 0x00007fffdaa15e9f in convertTo_anatomist_AObject () from /usr/local/lib/python3.8/dist-packages/anatomist/cpp/anatomistsip.so
#17 0x00007ffff44f35b9 in parsePass1 (parseErrp=parseErrp@entry=0x7fffffffd500, selfp=selfp@entry=0x7fffffffd368, selfargp=selfargp@entry=0x7fffffffd364, sipArgs=sipArgs@entry=
    (<AWindow3D(_cpp_rcptr=1) at remote 0x7fffc83b3820>,), sipKwdArgs=sipKwdArgs@entry=0x0, kwdlist=kwdlist@entry=0x0, unused=0x0, fmt=0x7fffdaa2d009 "", va=0x7fffffffd370) at ./siplib/siplib.c:4576
#18 0x00007ffff44f5336 in parseKwdArgs (parseErrp=0x7fffffffd500, sipArgs=(<AWindow3D(_cpp_rcptr=1) at remote 0x7fffc83b3820>,), sipKwdArgs=sipKwdArgs@entry=0x0, kwdlist=kwdlist@entry=0x0, 
    unused=unused@entry=0x0, fmt=0x7fffdaa2d006 "BJ0", va_orig=0x7fffffffd3e0) at ./siplib/siplib.c:3740
#19 0x00007ffff44f5635 in sip_api_parse_args (parseErrp=<optimized out>, sipArgs=<optimized out>, fmt=<optimized out>) at ./siplib/siplib.c:3643
#20 0x00007fffda9695bd in meth_anatomist_CommandContext_id () from /usr/local/lib/python3.8/dist-packages/anatomist/cpp/anatomistsip.so
#21 0x00000000005f5f1a in cfunction_call_varargs (kwargs=<optimized out>, args=<optimized out>, func=<built-in method id of CommandContext object at remote 0x7ffff7973e50>)
    at ../Include/internal/pycore_pyerrors.h:13
#22 PyCFunction_Call (func=<built-in method id of CommandContext object at remote 0x7ffff7973e50>, args=<optimized out>, kwargs=<optimized out>) at ../Objects/call.c:773
#23 0x00000000005f6a46 in _PyObject_MakeTpCall (callable=<built-in method id of CommandContext object at remote 0x7ffff7973e50>, args=<optimized out>, nargs=<optimized out>, keywords=<optimized out>)
    at ../Include/internal/pycore_pyerrors.h:13
#24 0x0000000000570a1f in _PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x263d4b0, callable=<built-in method id of CommandContext object at remote 0x7ffff7973e50>)
    at ../Include/cpython/abstract.h:125
#25 _PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x263d4b0, callable=<built-in method id of CommandContext object at remote 0x7ffff7973e50>) at ../Include/cpython/abstract.h:115
#26 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x962aa0) at ../Python/ceval.c:4963
#27 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at ../Python/ceval.c:3469
#28 0x000000000050ac5e in PyEval_EvalFrameEx (throwflag=0, f=
    Frame 0x263d320, for file /usr/local/lib/python3.8/dist-packages/anatomist/direct/api.py, line 1663, in convertSingleObjectParamsToIDs (self=<Anatomist(onLoadNotifier=<ObservableNotifier(_listeners=[], _parameterCount=None, _delayedNotification=None, onAddFirstListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff796a040>], _parameterCount=None, _delayedNotification=None) at remote 0x7ffff796c310>, onRemoveLastListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff79dc270>], _parameterCount=None, _delayedNotification=None) at remote 0x7fffc85c2ca0>) at remote 0x7fffc823fb20>, onDeleteNotifier=<ObservableNotifier(_listeners=[], _parameterCount=None, _delayedNotification=None, onAddFirstListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff76e9ea0>], _parameterCount=None, _delayedNotification=None) at remote 0x7fffc8260a90>, onRemoveLastListener=<Notifier(_listeners=[<functools.partial at remote 0x7fffc825a220>], _parameterCount=None, _delayedNotification=None) at remote 0x...(truncated)) at ../Python/ceval.c:741
#29 function_code_fastcall (globals=<optimized out>, nargs=<optimized out>, args=<optimized out>, co=<optimized out>) at ../Objects/call.c:284
#30 _PyFunction_Vectorcall (kwnames=<optimized out>, nargsf=<optimized out>, stack=0x7fffc8255a98, func=<function at remote 0x7fffd54d93a0>) at ../Objects/call.c:411
#31 _PyObject_Vectorcall (kwnames=<optimized out>, nargsf=<optimized out>, args=0x7fffc8255a98, callable=<function at remote 0x7fffd54d93a0>) at ../Include/cpython/abstract.h:127
#32 method_vectorcall (method=<optimized out>, args=0x7fffc8255aa0, nargsf=<optimized out>, kwnames=<optimized out>) at ../Objects/classobject.c:60
#33 0x00000000005703e6 in _PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x7fffc8255aa0, callable=<method at remote 0x7fffc8269640>) at ../Include/cpython/abstract.h:127
#34 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x962aa0) at ../Python/ceval.c:4963
#35 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at ../Python/ceval.c:3469
#36 0x00000000005696da in PyEval_EvalFrameEx (throwflag=0, 
--Type <RET> for more, q to quit, c to continue without paging-- 
    f=Frame 0x7fffc8255900, for file /usr/local/lib/python3.8/dist-packages/anatomist/base.py, line 1401, in <listcomp> (.0=<list_iterator at remote 0x7fffc8270ee0>, i=<AWindow(anatomistinstance=<Anatomist(onLoadNotifier=<ObservableNotifier(_listeners=[], _parameterCount=None, _delayedNotification=None, onAddFirstListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff796a040>], _parameterCount=None, _delayedNotification=None) at remote 0x7ffff796c310>, onRemoveLastListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff79dc270>], _parameterCount=None, _delayedNotification=None) at remote 0x7fffc85c2ca0>) at remote 0x7fffc823fb20>, onDeleteNotifier=<ObservableNotifier(_listeners=[], _parameterCount=None, _delayedNotification=None, onAddFirstListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff76e9ea0>], _parameterCount=None, _delayedNotification=None) at remote 0x7fffc8260a90>, onRemoveLastListener=<Notifier(_listeners=[<functools.partial at remote 0x7fffc825a220>], _parameterCou...(truncated)) at ../Python/ceval.c:741
#37 _PyEval_EvalCodeWithName (_co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=<optimized out>, kwnames=<optimized out>, kwargs=0x7fffc83b66e0, 
    kwcount=<optimized out>, kwstep=1, defs=0x0, defcount=0, kwdefs=0x0, closure=(<cell at remote 0x7fffc82706d0>,), name='<listcomp>', qualname='Anatomist.convertParamsToIDs.<locals>.<listcomp>')
    at ../Python/ceval.c:4298
#38 0x00000000005f6403 in _PyFunction_Vectorcall (func=<optimized out>, stack=0x7fffc83b66d8, nargsf=<optimized out>, kwnames=<optimized out>) at ../Objects/call.c:436
#39 0x000000000056b3fe in _PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x7fffc83b66d8, callable=<function at remote 0x7fffc83b3790>) at ../Include/cpython/abstract.h:127
#40 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x962aa0) at ../Python/ceval.c:4963
#41 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at ../Python/ceval.c:3500
#42 0x00000000005696da in PyEval_EvalFrameEx (throwflag=0, 
    f=Frame 0x7fffc83b6550, for file /usr/local/lib/python3.8/dist-packages/anatomist/base.py, line 1657, in convertParamsToIDs (params=[<AWindow(anatomistinstance=<Anatomist(onLoadNotifier=<ObservableNotifier(_listeners=[], _parameterCount=None, _delayedNotification=None, onAddFirstListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff796a040>], _parameterCount=None, _delayedNotification=None) at remote 0x7ffff796c310>, onRemoveLastListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff79dc270>], _parameterCount=None, _delayedNotification=None) at remote 0x7fffc85c2ca0>) at remote 0x7fffc823fb20>, onDeleteNotifier=<ObservableNotifier(_listeners=[], _parameterCount=None, _delayedNotification=None, onAddFirstListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff76e9ea0>], _parameterCount=None, _delayedNotification=None) at remote 0x7fffc8260a90>, onRemoveLastListener=<Notifier(_listeners=[<functools.partial at remote 0x7fffc825a220>], _parameterCount=None, _delayedNotification=N...(truncated)) at ../Python/ceval.c:741
#43 _PyEval_EvalCodeWithName (_co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=<optimized out>, kwnames=<optimized out>, kwargs=0x7fffc824a598, 
    kwcount=<optimized out>, kwstep=1, defs=0x0, defcount=0, kwdefs=0x0, closure=0x0, name='convertParamsToIDs', qualname='Anatomist.convertParamsToIDs') at ../Python/ceval.c:4298
#44 0x000000000050add0 in _PyFunction_Vectorcall (kwnames=<optimized out>, nargsf=<optimized out>, stack=0x7fffc824a588, func=<function at remote 0x7fffd5337ee0>) at ../Objects/call.c:436
#45 _PyObject_Vectorcall (kwnames=<optimized out>, nargsf=<optimized out>, args=0x7fffc824a588, callable=<function at remote 0x7fffd5337ee0>) at ../Include/cpython/abstract.h:127
#46 method_vectorcall (method=<optimized out>, args=0x7fffc824a590, nargsf=<optimized out>, kwnames=<optimized out>) at ../Objects/classobject.c:60
#47 0x00000000005703e6 in _PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x7fffc824a590, callable=<method at remote 0x7fffc85ad700>) at ../Include/cpython/abstract.h:127
#48 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x962aa0) at ../Python/ceval.c:4963
#49 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at ../Python/ceval.c:3469
#50 0x00000000005009e3 in PyEval_EvalFrameEx (throwflag=0, 
    f=Frame 0x7fffc824a3e0, for file /usr/local/lib/python3.8/dist-packages/anatomist/direct/api.py, line 1380, in <genexpr> (.0=<dict_itemiterator at remote 0x7fffc82679a0>, k='windows', v=[<AWindow(anatomistinstance=<Anatomist(onLoadNotifier=<ObservableNotifier(_listeners=[], _parameterCount=None, _delayedNotification=None, onAddFirstListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff796a040>], _parameterCount=None, _delayedNotification=None) at remote 0x7ffff796c310>, onRemoveLastListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff79dc270>], _parameterCount=None, _delayedNotification=None) at remote 0x7fffc85c2ca0>) at remote 0x7fffc823fb20>, onDeleteNotifier=<ObservableNotifier(_listeners=[], _parameterCount=None, _delayedNotification=None, onAddFirstListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff76e9ea0>], _parameterCount=None, _delayedNotification=None) at remote 0x7fffc8260a90>, onRemoveLastListener=<Notifier(_listeners=[<functools.partial at remote 0x7fffc8...(truncated)) at ../Python/ceval.c:741
#51 gen_send_ex (closing=0, exc=0, arg=0x0, gen=0x7ffff798fcf0) at ../Objects/genobject.c:222
#52 gen_iternext (gen=0x7ffff798fcf0) at ../Objects/genobject.c:543
#53 0x00000000005d6014 in PyIter_Next (iter=<generator at remote 0x7ffff798fcf0>) at ../Objects/abstract.c:2612
#54 PyDict_MergeFromSeq2 (d={}, seq2=<optimized out>, override=1) at ../Objects/dictobject.c:2390
#55 0x00000000005d7606 in dict_update_common (self={}, args=<optimized out>, kwds=0x0, methname=<optimized out>) at ../Objects/dictobject.c:2335
#56 0x00000000005f69af in type_call (kwds=0x0, args=(<generator at remote 0x7ffff798fcf0>,), type=<optimized out>) at ../Objects/typeobject.c:994
#57 _PyObject_MakeTpCall (callable=<type at remote 0x90bf00>, args=<optimized out>, nargs=<optimized out>, keywords=<optimized out>) at ../Objects/call.c:159
#58 0x0000000000570612 in _PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0xa5d7f0, callable=<type at remote 0x90bf00>) at ../Include/cpython/abstract.h:125
#59 _PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0xa5d7f0, callable=<type at remote 0x90bf00>) at ../Include/cpython/abstract.h:115
#60 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x962aa0) at ../Python/ceval.c:4963
#61 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at ../Python/ceval.c:3500
 #62 0x00000000005696da in PyEval_EvalFrameEx (throwflag=0, 
    f=Frame 0xa5d650, for file /usr/local/lib/python3.8/dist-packages/anatomist/direct/api.py, line 1380, in execute (command='WindowConfig', kwargs={'windows': [<AWindow(anatomistinstance=<Anatomist(onLoadNotifier=<ObservableNotifier(_listeners=[], _parameterCount=None, _delayedNotification=None, onAddFirstListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff796a040>], _parameterCount=None, _delayedNotification=None) at remote 0x7ffff796c310>, onRemoveLastListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff79dc270>], _parameterCount=None, _delayedNotification=None) at remote 0x7fffc85c2ca0>) at remote 0x7fffc823fb20>, onDeleteNotifier=<ObservableNotifier(_listeners=[], _parameterCount=None, _delayedNotification=None, onAddFirstListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff76e9ea0>], _parameterCount=None, _delayedNotification=None) at remote 0x7fffc8260a90>, onRemoveLastListener=<Notifier(_listeners=[<functools.partial at remote 0x7fffc825a220>], _paramete--Type <RET> for more, q to quit, c to continue without paging-- 
rCount=Non...(truncated)) at ../Python/ceval.c:741
#63 _PyEval_EvalCodeWithName (_co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=<optimized out>, kwnames=<optimized out>, kwargs=0x7fffc83e2598, 
    kwcount=<optimized out>, kwstep=1, defs=0x0, defcount=0, kwdefs=0x0, closure=0x0, name='execute', qualname='Anatomist.execute') at ../Python/ceval.c:4298
#64 0x000000000050add0 in _PyFunction_Vectorcall (kwnames=<optimized out>, nargsf=<optimized out>, stack=0x7fffc83e2588, func=<function at remote 0x7fffd54d9310>) at ../Objects/call.c:436
#65 _PyObject_Vectorcall (kwnames=<optimized out>, nargsf=<optimized out>, args=0x7fffc83e2588, callable=<function at remote 0x7fffd54d9310>) at ../Include/cpython/abstract.h:127
#66 method_vectorcall (method=<optimized out>, args=0x7fffc83e2590, nargsf=<optimized out>, kwnames=<optimized out>) at ../Objects/classobject.c:60
#67 0x000000000056c5d1 in _PyObject_Vectorcall (kwnames=('windows', 'snapshot', 'snapshot_width', 'snapshot_height'), nargsf=<optimized out>, args=<optimized out>, 
    callable=<method at remote 0x7fffc85bb940>) at ../Include/cpython/abstract.h:127
#68 call_function (kwnames=('windows', 'snapshot', 'snapshot_width', 'snapshot_height'), oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=<optimized out>) at ../Python/ceval.c:4963
#69 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at ../Python/ceval.c:3515
#70 0x00000000005696da in PyEval_EvalFrameEx (throwflag=0, 
    f=Frame 0x7fffc83e2400, for file /usr/local/lib/python3.8/dist-packages/anatomist/base.py, line 2603, in snapshot (self=<AWindow(anatomistinstance=<Anatomist(onLoadNotifier=<ObservableNotifier(_listeners=[], _parameterCount=None, _delayedNotification=None, onAddFirstListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff796a040>], _parameterCount=None, _delayedNotification=None) at remote 0x7ffff796c310>, onRemoveLastListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff79dc270>], _parameterCount=None, _delayedNotification=None) at remote 0x7fffc85c2ca0>) at remote 0x7fffc823fb20>, onDeleteNotifier=<ObservableNotifier(_listeners=[], _parameterCount=None, _delayedNotification=None, onAddFirstListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff76e9ea0>], _parameterCount=None, _delayedNotification=None) at remote 0x7fffc8260a90>, onRemoveLastListener=<Notifier(_listeners=[<functools.partial at remote 0x7fffc825a220>], _parameterCount=None, _delayedNotification=None) at remot...(truncated)) at ../Python/ceval.c:741
#71 _PyEval_EvalCodeWithName (_co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=<optimized out>, kwnames=<optimized out>, kwargs=0x7ffff7b43bc0, 
    kwcount=<optimized out>, kwstep=1, defs=0x7fffdac14818, defcount=2, kwdefs=0x0, closure=0x0, name='snapshot', qualname='Anatomist.AWindow.snapshot') at ../Python/ceval.c:4298
#72 0x000000000050add0 in _PyFunction_Vectorcall (kwnames=<optimized out>, nargsf=<optimized out>, stack=0x7ffff7b43bb0, func=<function at remote 0x7fffd53398b0>) at ../Objects/call.c:436
#73 _PyObject_Vectorcall (kwnames=<optimized out>, nargsf=<optimized out>, args=0x7ffff7b43bb0, callable=<function at remote 0x7fffd53398b0>) at ../Include/cpython/abstract.h:127
#74 method_vectorcall (method=<optimized out>, args=0x7ffff7b43bb8, nargsf=<optimized out>, kwnames=<optimized out>) at ../Objects/classobject.c:60
#75 0x00000000005703e6 in _PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x7ffff7b43bb8, callable=<method at remote 0x7ffff7b75980>) at ../Include/cpython/abstract.h:127
#76 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x962aa0) at ../Python/ceval.c:4963
#77 _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>) at ../Python/ceval.c:3469
#78 0x00000000005696da in PyEval_EvalFrameEx (throwflag=0, f=Frame 0x7ffff7b43a40, for file src/sample.py, line 9, in <module> ()) at ../Python/ceval.c:741
#79 _PyEval_EvalCodeWithName (_co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=<optimized out>, kwnames=<optimized out>, kwargs=0x0, 
    kwcount=<optimized out>, kwstep=2, defs=0x0, defcount=0, kwdefs=0x0, closure=0x0, name=0x0, qualname=0x0) at ../Python/ceval.c:4298
#80 0x000000000068db17 in PyEval_EvalCodeEx (closure=0x0, kwdefs=0x0, defcount=0, defs=0x0, kwcount=0, kws=0x0, argcount=0, args=0x0, locals=<optimized out>, globals=<optimized out>, _co=<optimized out>)
    at ../Python/ceval.c:4327
#81 PyEval_EvalCode (co=<optimized out>, globals=<optimized out>, locals=<optimized out>) at ../Python/ceval.c:718
#82 0x000000000067eeb1 in run_eval_code_obj (co=0x7ffff7a5c190, 
    globals={'__name__': '__main__', '__doc__': None, '__package__': None, '__loader__': <SourceFileLoader(name='__main__', path='src/sample.py') at remote 0x7ffff7b33fa0>, '__spec__': None, '__annotations__': {}, '__builtins__': <module at remote 0x7ffff7b570e0>, '__file__': 'src/sample.py', '__cached__': None, 'anatomist': <module at remote 0x7ffff79c1b80>, 'sys': <module at remote 0x7ffff7b4be00>, 'sip': <module at remote 0x7ffff1fe1ae0>, 'name': 'QUrl', 'a': <Anatomist(onLoadNotifier=<ObservableNotifier(_listeners=[], _parameterCount=None, _delayedNotification=None, onAddFirstListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff796a040>], _parameterCount=None, _delayedNotification=None) at remote 0x7ffff796c310>, onRemoveLastListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff79dc270>], _parameterCount=None, _delayedNotification=None) at remote 0x7fffc85c2ca0>) at remote 0x7fffc823fb20>, onDeleteNotifier=<ObservableNotifier(_listeners=[], _parameterCount=None, _dela
yedNotification=None, o...(truncated), 
    locals={'__name__': '__main__', '__doc__': None, '__package__': None, '__loader__': <SourceFileLoader(name='__main__', path='src/sample.py') at remote 0x7ffff7b33fa0>, '__spec__': None, '__annotations__': {}, '__builtins__': <module at remote 0x7ffff7b570e0>, '__file__': 'src/sample.py', '__cached__': None, 'anatomist': <module at remote 0x7ffff79c1b80>, 'sys': <module at remote 0x7ffff7b4be00>, 'sip': <module at remote 0x7ffff1fe1ae0>, 'name': 'QUrl', 'a': <Anatomist(onLoadNotifier=<ObservableNotifier(_listeners=[], _parameterCount=None, _delayedNotification=None, onAddFirstListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff796a040>], _parameterCount=None, _delayedNotification=None) at remote 0x7ffff796c310>, onRemoveLastListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff79dc270>], _parameterCount=None, _delayedNotification=None) at remote 0x7fffc85c2ca0>) at remote 0x7fffc823fb20>, onDeleteNotifier=<ObservableNotifier(_listeners=[], _parameterCount=None, _delayedNotification=None, o...(truncated)) at ../Python/pythonrun.c:1166
#83 0x000000000067ef2f in run_mod (mod=<optimized out>, filename=<optimized out>, 
    globals={'__name__': '__main__', '__doc__': None, '__package__': None, '__loader__': <SourceFileLoader(name='__main__', path='src/sample.py') at remote 0x7ffff7b33fa0>, '__spec__': None, '__annotations__': {}, '__builtins__': <module at remote 0x7ffff7b570e0>, '__file__': 'src/sample.py', '__cached__': None, 'anatomist': <module at remote 0x7ffff79c1b80>, 'sys': <module at remote 0x7ffff7b4be00>, 'sip': <module at remote 0x7ffff1fe1ae0>, 'name': 'QUrl', 'a': <Anatomist(onLoadNotifier=<ObservableNotifier(_listeners=[], _parameterCount=None, _delayedNotification=None, onAddFirstListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff796a040>], _parameterCount=None, _delayedNotification=None) at remote 0x7ffff796c310>, onRemoveLastListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff79dc270>], _parameterCount=None, _delayedNotification=None) at remote 0x7fffc85c2ca0>) at remote 0x7fffc823fb20>, onDeleteNotifier=<ObservableNotifier(_listeners=[], _parameterCount=None, _delayedNotification=None, o...(truncated), 
    locals={'__name__': '__main__', '__doc__': None, '__package__': None, '__loader__': <SourceFileLoader(name='__main__', path='src/sample.py') at remote 0x7ffff7b33fa0>, '__spec__': None, '__annotations--Type <RET> for more, q to quit, c to continue without paging--
__': {}, '__builtins__': <module at remote 0x7ffff7b570e0>, '__file__': 'src/sample.py', '__cached__': None, 'anatomist': <module at remote 0x7ffff79c1b80>, 'sys': <module at remote 0x7ffff7b4be00>, 'sip': <module at remote 0x7ffff1fe1ae0>, 'name': 'QUrl', 'a': <Anatomist(onLoadNotifier=<ObservableNotifier(_listeners=[], _parameterCount=None, _delayedNotification=None, onAddFirstListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff796a040>], _parameterCount=None, _delayedNotification=None) at remote 0x7ffff796c310>, onRemoveLastListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff79dc270>], _parameterCount=None, _delayedNotification=None) at remote 0x7fffc85c2ca0>) at remote 0x7fffc823fb20>, onDeleteNotifier=<ObservableNotifier(_listeners=[], _parameterCount=None, _delayedNotification=None, o...(truncated), flags=<optimized out>, arena=<optimized out>) at ../Python/pythonrun.c:1188
#84 0x000000000067efd1 in pyrun_file (fp=fp@entry=0x960410, filename=filename@entry='src/sample.py', start=start@entry=257, 
    globals=globals@entry={'__name__': '__main__', '__doc__': None, '__package__': None, '__loader__': <SourceFileLoader(name='__main__', path='src/sample.py') at remote 0x7ffff7b33fa0>, '__spec__': None, '__annotations__': {}, '__builtins__': <module at remote 0x7ffff7b570e0>, '__file__': 'src/sample.py', '__cached__': None, 'anatomist': <module at remote 0x7ffff79c1b80>, 'sys': <module at remote 0x7ffff7b4be00>, 'sip': <module at remote 0x7ffff1fe1ae0>, 'name': 'QUrl', 'a': <Anatomist(onLoadNotifier=<ObservableNotifier(_listeners=[], _parameterCount=None, _delayedNotification=None, onAddFirstListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff796a040>], _parameterCount=None, _delayedNotification=None) at remote 0x7ffff796c310>, onRemoveLastListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff79dc270>], _parameterCount=None, _delayedNotification=None) at remote 0x7fffc85c2ca0>) at remote 0x7fffc823fb20>, onDeleteNotifier=<ObservableNotifier(_listeners=[], _parameterCount=None, _delayedNotification=None, o...(truncated), 
    locals=locals@entry={'__name__': '__main__', '__doc__': None, '__package__': None, '__loader__': <SourceFileLoader(name='__main__', path='src/sample.py') at remote 0x7ffff7b33fa0>, '__spec__': None, '__annotations__': {}, '__builtins__': <module at remote 0x7ffff7b570e0>, '__file__': 'src/sample.py', '__cached__': None, 'anatomist': <module at remote 0x7ffff79c1b80>, 'sys': <module at remote 0x7ffff7b4be00>, 'sip': <module at remote 0x7ffff1fe1ae0>, 'name': 'QUrl', 'a': <Anatomist(onLoadNotifier=<ObservableNotifier(_listeners=[], _parameterCount=None, _delayedNotification=None, onAddFirstListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff796a040>], _parameterCount=None, _delayedNotification=None) at remote 0x7ffff796c310>, onRemoveLastListener=<Notifier(_listeners=[<functools.partial at remote 0x7ffff79dc270>], _parameterCount=None, _delayedNotification=None) at remote 0x7fffc85c2ca0>) at remote 0x7fffc823fb20>, onDeleteNotifier=<ObservableNotifier(_listeners=[], _parameterCount=None, _delayedNotification=None, o...(truncated), closeit=closeit@entry=1, flags=0x7fffffffe938) at ../Python/pythonrun.c:1085
#85 0x000000000067f377 in pyrun_simple_file (flags=0x7fffffffe938, closeit=1, filename='src/sample.py', fp=0x960410) at ../Python/pythonrun.c:439
#86 PyRun_SimpleFileExFlags (fp=0x960410, filename=<optimized out>, closeit=1, flags=0x7fffffffe938) at ../Python/pythonrun.c:472
#87 0x00000000006b7902 in pymain_run_file (cf=0x7fffffffe938, config=0x961ea0) at ../Modules/main.c:385
#88 pymain_run_python (exitcode=0x7fffffffe930) at ../Modules/main.c:610
#89 Py_RunMain () at ../Modules/main.c:689
#90 0x00000000006b7c8d in Py_BytesMain (argc=<optimized out>, argv=<optimized out>) at ../Modules/main.c:743
#91 0x00007ffff7ded0b3 in __libc_start_main (main=0x4eed30 <main>, argc=2, argv=0x7fffffffeb18, init=<optimized out>, fini=<optimized out>, rtld_fini=<optimized out>, stack_end=0x7fffffffeb08)
    at ../csu/libc-start.c:308
#92 0x00000000005fb12e in _start () at ../Objects/obmalloc.c:1233

This is like SIP / C++ objects doesn't handle methods for adding objects or for doing a snapshot.

Is anyone have a clue on what's going on, or what I'm doing wrong?

Thanks in advance.

[denisri]

I see. You have compiled anatomist in a Ubuntu 20.04 system. Well, unfortunately it doesn't work well, as you have seen.
The sip tool in Ubuntu 20.04 has a bug (https://www.riverbankcomputing.com/pipermail/pyqt/2021-December/044423.html) which makes pyanatomist crash frequently. Moreover we have observed crashes in Qt when closing brainvisa windows on this system, which we have no clues about. Thus we have decided to skip ubuntu 20 and wait for 22.04. We have a working singularity container based on a prerelease, which works (casa-dev-5.3.sif), and which contains a different version of sip and PyQt (rebuilt for this system), to avoid the above bug. It has not been thoroughly tested yet, but seems to work for now.

[AlexandreBeaurain]

Thank you for your quick response.

May I ask which version of PyQT and SIP you successfully used ?

[denisri]

For now we have used sip 4.19.15 and PyQt 5.12.1. When a fixed version of sip is released we might switch to a newer one, but developers would have to rebuild everything since binary compatibility would be lost. Let's say we can do it while the image is still a prerelease, until we declare it an "official" image (the official one is 5.0 running ubuntu 18.04 for now).

[AlexandreBeaurain]

We successfully ran pyanatomist in an ubuntu 18.04 container. Thanks a lot.