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cellpose-napari crashes when running segmentation on Mac #43

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christinab12 opened this issue Jan 25, 2023 · 2 comments
Open

cellpose-napari crashes when running segmentation on Mac #43

christinab12 opened this issue Jan 25, 2023 · 2 comments

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@christinab12
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christinab12 commented Jan 25, 2023 •
edited

Hi,

I'm trying to run the cellpose-napari on MacOS v.11.7.2 with Intel Graphics and following versions:

cellpose==2.1.1
cellpose-naapri==0.1.5
napari==0.4.16
pyhton==3.9.13

As soon as I hit the "run segmentation" button I get ~/envs/napari/bin/pythonw: line 3: 7607 Segmentation fault: 11 ~/envs/napari/python.app/Contents/MacOS/python "$@"

Is this expected behaviour? Do I need to change my versions? I saw something similar on the closed issues, but that was more than a year ago, not sure what the latest is?

Thanks,
Christina
@jmarkow
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jmarkow commented Jul 7, 2023

Running into the same issue here with an M1 Mac.

cellpose                  2.2.2 
cellpose-napari           0.1.5
napari                    0.4.18 
python                    3.10.0

Not seeing any output in the Terminal, even with verbose turned on via running napari -v . Everything crashes when hitting Run segmentation

@psobolewskiPhD
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Not sure if I'm getting the same thing, but I get a hard crash with PyQt6 (6.5.1 and 6.6.1 from pip) while pyqt5 (conda-forge) is fine. Here's the log:

*** Terminating app due to uncaught exception 'NSRangeException', reason: '*** -[__NSArrayM objectAtIndexedSubscript:]: index 0 beyond bounds for empty array'
*** First throw call stack:
(
	0   CoreFoundation                      0x000000018881a800 __exceptionPreprocess + 176
	1   libobjc.A.dylib                     0x0000000188311eb4 objc_exception_throw + 60
	2   CoreFoundation                      0x0000000188790fc0 -[__NSCFString hasSuffix:] + 0
	3   libqcocoa.dylib                     0x000000016bfaa044 _ZN20QCocoaSystemTrayIcon13emitActivatedEv + 274796
	4   libqcocoa.dylib                     0x000000016bfaa0c8 _ZN20QCocoaSystemTrayIcon13emitActivatedEv + 274928
	5   libqcocoa.dylib                     0x000000016bfa8688 _ZN20QCocoaSystemTrayIcon13emitActivatedEv + 268208
	6   QtWidgets                           0x000000016c7a51a8 _ZN9QListView16selectionChangedERK14QItemSelectionS2_ + 204
	7   QtWidgets.abi3.so                   0x0000000169a0cfa4 _ZN12sipQListView16selectionChangedERK14QItemSelectionS2_ + 272
	8   QtCore                              0x000000016574f48c _ZN11QMetaObject8activateEP7QObjectPKS_iPPv + 3808
	9   QtCore                              0x0000000165915e44 _ZN19QItemSelectionModel20emitSelectionChangedERK14QItemSelectionS2_ + 216
	10  QtCore                              0x0000000165915a2c _ZN19QItemSelectionModel6selectERK14QItemSelection6QFlagsINS_13SelectionFlagEE + 636
	11  QtCore                              0x000000016591570c _ZN19QItemSelectionModel6selectERK11QModelIndex6QFlagsINS_13SelectionFlagEE + 68
	12  QtCore                              0x00000001659168cc _ZN19QItemSelectionModel15setCurrentIndexERK11QModelIndex6QFlagsINS_13SelectionFlagEE + 260
	13  QtWidgets                           0x000000016c603338 _ZNK9QComboBox5countEv + 828
	14  QtWidgets                           0x000000016c6068b4 _ZN9QComboBoxC1ER16QComboBoxPrivateP7QWidget + 2412
	15  QtCore                              0x000000016574f224 _ZN11QMetaObject8activateEP7QObjectPKS_iPPv + 3192
	16  QtCore                              0x00000001658fe944 _ZN18QAbstractItemModel13endInsertRowsEv + 200
	17  QtGui                               0x000000016a3e37a4 _ZN18QStandardItemModel11itemChangedEP13QStandardItem + 2376
	18  QtWidgets                           0x000000016c609910 _ZN9QComboBox10insertItemEiRK5QIconRK7QStringRK8QVariant + 368
	19  QtWidgets.abi3.so                   0x0000000169ba8904 _ZL22meth_QComboBox_addItemP7_objectS0_S0_ + 256
	20  python3.10                          0x00000001041a6b3c cfunction_call + 80
	21  python3.10                          0x000000010415359c _PyObject_MakeTpCall + 612
	22  python3.10                          0x00000001042455d8 call_function + 676
	23  python3.10                          0x0000000104240e60 _PyEval_EvalFrameDefault + 24940
	24  python3.10                          0x000000010423a364 _PyEval_Vector + 2036
	25  python3.10                          0x0000000104156c64 method_vectorcall + 172
	26  python3.10                          0x0000000104245540 call_function + 524
	27  python3.10                          0x0000000104240e60 _PyEval_EvalFrameDefault + 24940
	28  python3.10                          0x000000010423a364 _PyEval_Vector + 2036
	29  python3.10                          0x0000000104153850 _PyObject_FastCallDictTstate + 320
	30  python3.10                          0x0000000104154454 _PyObject_Call_Prepend + 176
	31  python3.10                          0x00000001041cb394 slot_tp_init + 116
	32  python3.10                          0x00000001041c3d64 type_call + 456
	33  python3.10                          0x000000010415359c _PyObject_MakeTpCall + 612
	34  python3.10                          0x00000001042455d8 call_function + 676
	35  python3.10                          0x00000001042413bc _PyEval_EvalFrameDefault + 26312
	36  python3.10                          0x000000010423a364 _PyEval_Vector + 2036
	37  python3.10                          0x0000000104245540 call_function + 524
	38  python3.10                          0x00000001042413bc _PyEval_EvalFrameDefault + 26312
	39  python3.10                          0x000000010423a364 _PyEval_Vector + 2036
	40  python3.10                          0x0000000104156c64 method_vectorcall + 172
	41  python3.10                          0x0000000104245540 call_function + 524
	42  python3.10                          0x00000001042413bc _PyEval_EvalFrameDefault + 26312
	43  python3.10                          0x000000010423a364 _PyEval_Vector + 2036
	44  python3.10                          0x0000000104245540 call_function + 524
	45  python3.10                          0x0000000104240e38 _PyEval_EvalFrameDefault + 24900
	46  python3.10                          0x000000010423a364 _PyEval_Vector + 2036
	47  python3.10                          0x00000001041537ac _PyObject_FastCallDictTstate + 156
	48  python3.10                          0x0000000104154454 _PyObject_Call_Prepend + 176
	49  python3.10                          0x00000001041c9ee0 slot_tp_call + 116
	50  python3.10                          0x000000010415359c _PyObject_MakeTpCall + 612
	51  python3.10                          0x00000001042455d8 call_function + 676
	52  python3.10                          0x0000000104241430 _PyEval_EvalFrameDefault + 26428
	53  python3.10                          0x000000010423a364 _PyEval_Vector + 2036
	54  python3.10                          0x0000000104156c64 method_vectorcall + 172
	55  python3.10                          0x0000000104245540 call_function + 524
	56  python3.10                          0x0000000104240e60 _PyEval_EvalFrameDefault + 24940
	57  python3.10                          0x000000010423a364 _PyEval_Vector + 2036
	58  python3.10                          0x0000000104156c64 method_vectorcall + 172
	59  python3.10                          0x0000000104245540 call_function + 524
	60  python3.10                          0x0000000104240e60 _PyEval_EvalFrameDefault + 24940
	61  python3.10                          0x000000010423a364 _PyEval_Vector + 2036
	62  python3.10                          0x0000000104245540 call_function + 524
	63  python3.10                          0x0000000104240e38 _PyEval_EvalFrameDefault + 24900
	64  python3.10                          0x000000010423a364 _PyEval_Vector + 2036
	65  python3.10                          0x0000000104245540 call_function + 524
	66  python3.10                          0x0000000104240e38 _PyEval_EvalFrameDefault + 24900
	67  python3.10                          0x000000010423a364 _PyEval_Vector + 2036
	68  python3.10                          0x0000000104153de0 PyVectorcall_Call + 156
	69  python3.10                          0x0000000104241658 _PyEval_EvalFrameDefault + 26980
	70  python3.10                          0x000000010423a364 _PyEval_Vector + 2036
	71  python3.10                          0x0000000104156c64 method_vectorcall + 172
	72  python3.10                          0x0000000104153de0 PyVectorcall_Call + 156
	73  python3.10                          0x0000000104241658 _PyEval_EvalFrameDefault + 26980
	74  python3.10                          0x000000010423a364 _PyEval_Vector + 2036
	75  python3.10                          0x00000001041537ac _PyObject_FastCallDictTstate + 156
	76  python3.10                          0x0000000104154454 _PyObject_Call_Prepend + 176
	77  python3.10                          0x00000001041c9ee0 slot_tp_call + 116
	78  python3.10                          0x000000010415359c _PyObject_MakeTpCall + 612
	79  python3.10                          0x00000001042455d8 call_function + 676
	80  python3.10                          0x0000000104241430 _PyEval_EvalFrameDefault + 26428
	81  python3.10                          0x000000010423a364 _PyEval_Vector + 2036
	82  python3.10                          0x0000000104245540 call_function + 524
	83  python3.10                          0x00000001042413bc _PyEval_EvalFrameDefault + 26312
	84  python3.10                          0x000000010423a364 _PyEval_Vector + 2036
	85  QtCore.abi3.so                      0x0000000165443208 _ZNK8PyQtSlot4callEP7_objectS1_ + 68
	86  QtCore.abi3.so                      0x000000016544309
libc++abi: terminating due to uncaught exception of type NSException

arm64 Sonoma
python 3.10
cellpose 2.2.3
torch 2.1.1
napari 0.4.18

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3 participants
@jmarkow @christinab12 @psobolewskiPhD