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"nd3 spheres" layer disappears from napari when running Pick job in RELION 5 #1131

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dmichalak opened this issue May 22, 2024 · 0 comments
Open

"nd3 spheres" layer disappears from napari when running Pick job in RELION 5 #1131

dmichalak opened this issue May 22, 2024 · 0 comments

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@dmichalak
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Describe your problem

When picking particles with spheres in napari, if no particles were picked in tomogram 1, then the n3d spheres layer disappears when pressing ']' to view tomogram 2. The layer does not disappear if a sphere was defined in tomogram 1. It seems that it expects the user to define a sphere in every tomogram. The run.out error message is more informative.

Environment:

  • OS: Ubuntu 22.04.4 LTS
  • MPI runtime: OpenMPI 4.1.2
  • RELION version RELION-5.0-beta-3-commit-ad0c1f
  • Memory: 512 GB
  • GPU: RTX 3090

Job options:

  • Full command (see note.txt in the job directory):
`which relion_python_tomo_pick`  spheres --tilt-series-star-file Denoise/job015/tomograms.star --output-directory Picks/job033/  --pipeline_control Picks/job033/ && `which relion_python_tomo_get_particle_poses` spheres --tilt-series-star-file Denoise/job015/tomograms.star --annotations-directory Picks/job033/annotations --output-directory Picks/job033/ --spacing-angstroms 60  --pipeline_control Picks/job033/

Error message:

run.out 
�[0;31m---------------------------------------------------------------------------�[0m
�[0;31mValueError�[0m                                Traceback (most recent call last)
File �[0;32msrc/psygnal/_signal.py:1196�[0m, in �[0;36m_run_emit_loop�[0;34m()�[0m

File �[0;32msrc/psygnal/_signal.py:1225�[0m, in �[0;36m_run_emit_loop_immediate�[0;34m()�[0m

File �[0;32msrc/psygnal/_weak_callback.py:453�[0m, in �[0;36mcb�[0;34m()�[0m

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/pick/spheres.py:69�[0m, in �[0;36mPickSpheresWidget.synchronise_annotator�[0;34m(self=<tomography_python_programs.pick.spheres.PickSpheresWidget object>)�[0m
�[1;32m     68�[0m     �[38;5;28mself�[39m�[38;5;241m.�[39mviewer�[38;5;241m.�[39mlayers�[38;5;241m.�[39mremove(�[38;5;28mself�[39m�[38;5;241m.�[39mpoints_layer)
�[0;32m---> 69�[0m     �[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43mviewer�[49m�[38;5;241;43m.�[39;49m�[43mlayers�[49m�[38;5;241;43m.�[39;49m�[43mremove�[49m�[43m(�[49m�[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43mannotator�[49m�[38;5;241;43m.�[39;49m�[43msurface_layer�[49m�[43m)�[49m
        self.annotator �[0;34m= <napari_threedee.annotators.spheres.annotator.SphereAnnotator object at 0x754b342d3460>�[0m�[0;34m
        �[0mself �[0;34m= <tomography_python_programs.pick.spheres.PickSpheresWidget object at 0x754bc9f0c430>�[0m�[0;34m
        �[0mself.viewer.layers �[0;34m= [<Image layer 'tomogram' at 0x754b844d82e0>]�[0m�[0;34m
        �[0mself.annotator.surface_layer �[0;34m= None�[0m�[0;34m
        �[0mself.viewer �[0;34m= Viewer(camera=Camera(center=(134.25097504957012, 624.4804183213577, 472.5304129756257), zoom=1.6198914971997482, angles=(-19.093573125126735, 15.977671555947397, 137.60177770462866), perspective=0.0, mouse_pan=True, mouse_zoom=True), cursor=Cursor(position=(138.31620318898487, 580.496436869052, 595.5458249047225), scaled=True, size=1, style=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=3, ndisplay=3, last_used=0, range=((0.0, 296.0, 1.0), (0.0, 1270.0, 1.0), (0.0, 952.0, 1.0)), current_step=(147, 634, 475), order=(0, 1, 2), axis_labels=('0', '1', '2')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[<Image layer 'tomogram' at 0x754b844d82e0>], help='use <2> for transform', status={'layer_base': 'tomogram', 'source_type': '', 'plugin': '', 'coordinates': ' [138 580 596]'}, tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=True, mouse_move_callbacks=[], mouse_drag_callbacks=[], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[<function dims_scroll at 0x754bd67603a0>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={'[': <bound method TomogramBrowserWidget.previous_tilt_series of <tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object at 0x754bc9fe28c0>>, ']': <bound method TomogramBrowserWidget.next_tilt_series of <tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object at 0x754bc9fe28c0>>})�[0m
�[1;32m     70�[0m �[38;5;28;01mtry�[39;00m:

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/_collections_abc.py:1163�[0m, in �[0;36mMutableSequence.remove�[0;34m(self=[<Image layer 'tomogram' at 0x754b844d82e0>], value=None)�[0m
�[1;32m   1160�[0m �[38;5;250m�[39m�[38;5;124;03m'''S.remove(value) -- remove first occurrence of value.�[39;00m
�[1;32m   1161�[0m �[38;5;124;03m   Raise ValueError if the value is not present.�[39;00m
�[1;32m   1162�[0m �[38;5;124;03m'''�[39;00m
�[0;32m-> 1163�[0m �[38;5;28;01mdel�[39;00m �[38;5;28mself�[39m[�[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43mindex�[49m�[43m(�[49m�[43mvalue�[49m�[43m)�[49m]
        self �[0;34m= [<Image layer 'tomogram' at 0x754b844d82e0>]�[0m�[0;34m
        �[0mvalue �[0;34m= None�[0m

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/napari/utils/events/containers/_typed.py:230�[0m, in �[0;36mTypedMutableSequence.index�[0;34m(self=[<Image layer 'tomogram' at 0x754b844d82e0>], value=None, start=0, stop=None)�[0m
�[1;32m    228�[0m         �[38;5;28;01mreturn�[39;00m i
�[0;32m--> 230�[0m �[38;5;28;01mraise�[39;00m �[38;5;167;01mValueError�[39;00m(
        trans �[0;34m= <napari.utils.translations.TranslationBundle object at 0x754bddab8c70>�[0m�[0;34m
        �[0mvalue �[0;34m= None�[0m
�[1;32m    231�[0m     trans�[38;5;241m.�[39m_(
�[1;32m    232�[0m         �[38;5;124m"�[39m�[38;5;132;01m{value!r}�[39;00m�[38;5;124m is not in list�[39m�[38;5;124m"�[39m,
�[1;32m    233�[0m         deferred�[38;5;241m=�[39m�[38;5;28;01mTrue�[39;00m,
�[1;32m    234�[0m         value�[38;5;241m=�[39mvalue,
�[1;32m    235�[0m     )
�[1;32m    236�[0m )

�[0;31mValueError�[0m: None is not in list

The above exception was the direct cause of the following exception:

�[0;31mEmitLoopError�[0m                             Traceback (most recent call last)
File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/_qt/components/tomogram_browser.py:69�[0m, in �[0;36mTomogramBrowserWidget._on_tomogram_selection_change�[0;34m(self=<tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object>)�[0m
�[1;32m     67�[0m �[38;5;28mself�[39m�[38;5;241m.�[39mchanging_tomogram�[38;5;241m.�[39memit()
�[1;32m     68�[0m �[38;5;28mself�[39m�[38;5;241m.�[39mselected_tilt_series �[38;5;241m=�[39m �[38;5;28mself�[39m�[38;5;241m.�[39mtilt_series_list_widget�[38;5;241m.�[39mselected_tilt_series_in_view()
�[0;32m---> 69�[0m �[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43m_load_tomogram�[49m�[43m(�[49m�[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43mselected_tilt_series�[49m�[38;5;241;43m.�[39;49m�[43mname�[49m�[43m,�[49m�[43m �[49m�[43madd_to_viewer�[49m�[38;5;241;43m=�[39;49m�[38;5;28;43;01mTrue�[39;49;00m�[43m)�[49m
        self �[0;34m= <tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object at 0x754bc9fe28c0>�[0m
�[1;32m     70�[0m �[38;5;28mself�[39m�[38;5;241m.�[39m_preload_next_tomograms()

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/_qt/components/tomogram_browser.py:88�[0m, in �[0;36mTomogramBrowserWidget._load_tomogram�[0;34m(self=<tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object>, tilt_series_id='AQB1tomo006', add_to_viewer=True)�[0m
�[1;32m     86�[0m �[38;5;28;01mdef�[39;00m �[38;5;21m_load_tomogram�[39m(�[38;5;28mself�[39m, tilt_series_id: �[38;5;28mstr�[39m, add_to_viewer: �[38;5;28mbool�[39m) �[38;5;241m-�[39m�[38;5;241m>�[39m �[38;5;28;01mNone�[39;00m:
�[1;32m     87�[0m     �[38;5;28;01mif�[39;00m tilt_series_id �[38;5;129;01min�[39;00m �[38;5;28mself�[39m�[38;5;241m.�[39m_cache:
�[0;32m---> 88�[0m         �[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43m_load_tomogram_from_cache�[49m�[43m(�[49m�[43mtilt_series_id�[49m�[43m,�[49m�[43m �[49m�[43madd_to_viewer�[49m�[43m)�[49m
        add_to_viewer �[0;34m= True�[0m�[0;34m
        �[0mtilt_series_id �[0;34m= 'AQB1tomo006'�[0m�[0;34m
        �[0mself �[0;34m= <tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object at 0x754bc9fe28c0>�[0m
�[1;32m     89�[0m         �[38;5;28;01mreturn�[39;00m
�[1;32m     90�[0m     denoised_tomogram_file �[38;5;241m=�[39m �[38;5;28mself�[39m�[38;5;241m.�[39mtilt_series[tilt_series_id]�[38;5;241m.�[39mdenoised_tomogram_file

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/_qt/components/tomogram_browser.py:100�[0m, in �[0;36mTomogramBrowserWidget._load_tomogram_from_cache�[0;34m(self=<tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object>, tilt_series_id='AQB1tomo006', add_to_viewer=True)�[0m
�[1;32m     98�[0m �[38;5;28;01mdef�[39;00m �[38;5;21m_load_tomogram_from_cache�[39m(�[38;5;28mself�[39m, tilt_series_id: �[38;5;28mstr�[39m, add_to_viewer: �[38;5;28mbool�[39m):
�[1;32m     99�[0m     �[38;5;28;01mif�[39;00m add_to_viewer �[38;5;129;01mis�[39;00m �[38;5;28;01mTrue�[39;00m:
�[0;32m--> 100�[0m         �[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43m_update_tomogram_in_viewer�[49m�[43m(�[49m�[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43m_cache�[49m�[43m[�[49m�[43mtilt_series_id�[49m�[43m]�[49m�[43m)�[49m
        self �[0;34m= <tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object at 0x754bc9fe28c0>�[0m�[0;34m
        �[0mself._cache �[0;34m= {'AQB1tomo002': <class 'numpy.ndarray'> (296, 1270, 952) float32, 'AQB1tomo005': <class 'numpy.ndarray'> (296, 1270, 952) float32, 'AQB1tomo006': <class 'numpy.ndarray'> (296, 1270, 952) float32}�[0m�[0;34m
        �[0mtilt_series_id �[0;34m= 'AQB1tomo006'�[0m

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/_qt/components/tomogram_browser.py:84�[0m, in �[0;36mTomogramBrowserWidget._update_tomogram_in_viewer�[0;34m(self=<tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object>, tomogram=<class 'numpy.ndarray'> (296, 1270, 952) float32)�[0m
�[1;32m     75�[0m �[38;5;28;01melse�[39;00m:
�[1;32m     76�[0m     �[38;5;28mself�[39m�[38;5;241m.�[39mviewer�[38;5;241m.�[39madd_image(
�[1;32m     77�[0m         data�[38;5;241m=�[39mtomogram,
�[1;32m     78�[0m         name�[38;5;241m=�[39mIMAGE_LAYER_NAME,
�[0;32m   (...)�[0m
�[1;32m     82�[0m         blending�[38;5;241m=�[39m�[38;5;124m'�[39m�[38;5;124mtranslucent�[39m�[38;5;124m'�[39m,
�[1;32m     83�[0m     )
�[0;32m---> 84�[0m �[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43m_on_tomogram_loaded�[49m�[43m(�[49m�[43m)�[49m
        self �[0;34m= <tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object at 0x754bc9fe28c0>�[0m

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/_qt/components/tomogram_browser.py:108�[0m, in �[0;36mTomogramBrowserWidget._on_tomogram_loaded�[0;34m(self=<tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object>)�[0m
�[1;32m    106�[0m layer�[38;5;241m.�[39mplane�[38;5;241m.�[39mnormal �[38;5;241m=�[39m (�[38;5;241m1�[39m, �[38;5;241m0�[39m, �[38;5;241m0�[39m)
�[1;32m    107�[0m �[38;5;28mself�[39m�[38;5;241m.�[39mviewer�[38;5;241m.�[39mlayers�[38;5;241m.�[39mselection �[38;5;241m=�[39m [layer]
�[0;32m--> 108�[0m �[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43mtomogram_changed�[49m�[38;5;241;43m.�[39;49m�[43memit�[49m�[43m(�[49m�[43m)�[49m
        self.tomogram_changed �[0;34m= <SignalInstance 'tomogram_changed' on <tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object at 0x754bc9fe28c0>>�[0m�[0;34m
        �[0mself �[0;34m= <tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object at 0x754bc9fe28c0>�[0m

File �[0;32msrc/psygnal/_signal.py:1176�[0m, in �[0;36memit�[0;34m()�[0m

File �[0;32msrc/psygnal/_signal.py:1213�[0m, in �[0;36m_run_emit_loop�[0;34m()�[0m

File �[0;32msrc/psygnal/_signal.py:1196�[0m, in �[0;36m_run_emit_loop�[0;34m()�[0m

File �[0;32msrc/psygnal/_signal.py:1225�[0m, in �[0;36m_run_emit_loop_immediate�[0;34m()�[0m

File �[0;32msrc/psygnal/_weak_callback.py:453�[0m, in �[0;36mcb�[0;34m()�[0m

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/pick/spheres.py:69�[0m, in �[0;36mPickSpheresWidget.synchronise_annotator�[0;34m(self=<tomography_python_programs.pick.spheres.PickSpheresWidget object>)�[0m
�[1;32m     67�[0m �[38;5;28;01mif�[39;00m �[38;5;28mself�[39m�[38;5;241m.�[39mpoints_layer �[38;5;129;01mis�[39;00m �[38;5;129;01mnot�[39;00m �[38;5;28;01mNone�[39;00m:
�[1;32m     68�[0m     �[38;5;28mself�[39m�[38;5;241m.�[39mviewer�[38;5;241m.�[39mlayers�[38;5;241m.�[39mremove(�[38;5;28mself�[39m�[38;5;241m.�[39mpoints_layer)
�[0;32m---> 69�[0m     �[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43mviewer�[49m�[38;5;241;43m.�[39;49m�[43mlayers�[49m�[38;5;241;43m.�[39;49m�[43mremove�[49m�[43m(�[49m�[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43mannotator�[49m�[38;5;241;43m.�[39;49m�[43msurface_layer�[49m�[43m)�[49m
        self.annotator �[0;34m= <napari_threedee.annotators.spheres.annotator.SphereAnnotator object at 0x754b342d3460>�[0m�[0;34m
        �[0mself �[0;34m= <tomography_python_programs.pick.spheres.PickSpheresWidget object at 0x754bc9f0c430>�[0m�[0;34m
        �[0mself.viewer.layers �[0;34m= [<Image layer 'tomogram' at 0x754b844d82e0>]�[0m�[0;34m
        �[0mself.annotator.surface_layer �[0;34m= None�[0m�[0;34m
        �[0mself.viewer �[0;34m= Viewer(camera=Camera(center=(134.25097504957012, 624.4804183213577, 472.5304129756257), zoom=1.6198914971997482, angles=(-19.093573125126735, 15.977671555947397, 137.60177770462866), perspective=0.0, mouse_pan=True, mouse_zoom=True), cursor=Cursor(position=(138.31620318898487, 580.496436869052, 595.5458249047225), scaled=True, size=1, style=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=3, ndisplay=3, last_used=0, range=((0.0, 296.0, 1.0), (0.0, 1270.0, 1.0), (0.0, 952.0, 1.0)), current_step=(147, 634, 475), order=(0, 1, 2), axis_labels=('0', '1', '2')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[<Image layer 'tomogram' at 0x754b844d82e0>], help='use <2> for transform', status={'layer_base': 'tomogram', 'source_type': '', 'plugin': '', 'coordinates': ' [138 580 596]'}, tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=True, mouse_move_callbacks=[], mouse_drag_callbacks=[], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[<function dims_scroll at 0x754bd67603a0>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={'[': <bound method TomogramBrowserWidget.previous_tilt_series of <tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object at 0x754bc9fe28c0>>, ']': <bound method TomogramBrowserWidget.next_tilt_series of <tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object at 0x754bc9fe28c0>>})�[0m
�[1;32m     70�[0m �[38;5;28;01mtry�[39;00m:
�[1;32m     71�[0m     n3d_spheres �[38;5;241m=�[39m �[38;5;28mself�[39m�[38;5;241m.�[39mload_particles()

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/_collections_abc.py:1163�[0m, in �[0;36mMutableSequence.remove�[0;34m(self=[<Image layer 'tomogram' at 0x754b844d82e0>], value=None)�[0m
�[1;32m   1159�[0m �[38;5;28;01mdef�[39;00m �[38;5;21mremove�[39m(�[38;5;28mself�[39m, value):
�[1;32m   1160�[0m �[38;5;250m    �[39m�[38;5;124;03m'''S.remove(value) -- remove first occurrence of value.�[39;00m
�[1;32m   1161�[0m �[38;5;124;03m       Raise ValueError if the value is not present.�[39;00m
�[1;32m   1162�[0m �[38;5;124;03m    '''�[39;00m
�[0;32m-> 1163�[0m     �[38;5;28;01mdel�[39;00m �[38;5;28mself�[39m[�[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43mindex�[49m�[43m(�[49m�[43mvalue�[49m�[43m)�[49m]
        self �[0;34m= [<Image layer 'tomogram' at 0x754b844d82e0>]�[0m�[0;34m
        �[0mvalue �[0;34m= None�[0m

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/napari/utils/events/containers/_typed.py:230�[0m, in �[0;36mTypedMutableSequence.index�[0;34m(self=[<Image layer 'tomogram' at 0x754b844d82e0>], value=None, start=0, stop=None)�[0m
�[1;32m    227�[0m     �[38;5;28;01mif�[39;00m v �[38;5;129;01mis�[39;00m value �[38;5;129;01mor�[39;00m v �[38;5;241m==�[39m value:
�[1;32m    228�[0m         �[38;5;28;01mreturn�[39;00m i
�[0;32m--> 230�[0m �[38;5;28;01mraise�[39;00m �[38;5;167;01mValueError�[39;00m(
        trans �[0;34m= <napari.utils.translations.TranslationBundle object at 0x754bddab8c70>�[0m�[0;34m
        �[0mvalue �[0;34m= None�[0m
�[1;32m    231�[0m     trans�[38;5;241m.�[39m_(
�[1;32m    232�[0m         �[38;5;124m"�[39m�[38;5;132;01m{value!r}�[39;00m�[38;5;124m is not in list�[39m�[38;5;124m"�[39m,
�[1;32m    233�[0m         deferred�[38;5;241m=�[39m�[38;5;28;01mTrue�[39;00m,
�[1;32m    234�[0m         value�[38;5;241m=�[39mvalue,
�[1;32m    235�[0m     )
�[1;32m    236�[0m )

�[0;31mEmitLoopError�[0m: 

While emitting signal 'tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget.tomogram_changed', a ValueError occurred in a callback:

  Signal emitted at: /home/michalakdj/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/_qt/components/tomogram_browser.py:108, in _on_tomogram_loaded
    >  self.tomogram_changed.emit()

  Callback error at: /home/michalakdj/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/napari/utils/events/containers/_typed.py:230, in index
    >  raise ValueError(

    Local variables:
       value = None
       start = 0
       stop = None
       convert = <function _noop at 0x754bddb0a5f0>
       i = 0
       v = <Image layer 'tomogram' at 0x754b844d82e0>

See ValueError above for original traceback.
�[0;31m---------------------------------------------------------------------------�[0m
�[0;31mValueError�[0m                                Traceback (most recent call last)
File �[0;32msrc/psygnal/_signal.py:1196�[0m, in �[0;36m_run_emit_loop�[0;34m()�[0m

File �[0;32msrc/psygnal/_signal.py:1225�[0m, in �[0;36m_run_emit_loop_immediate�[0;34m()�[0m

File �[0;32msrc/psygnal/_weak_callback.py:453�[0m, in �[0;36mcb�[0;34m()�[0m

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/pick/spheres.py:68�[0m, in �[0;36mPickSpheresWidget.synchronise_annotator�[0;34m(self=<tomography_python_programs.pick.spheres.PickSpheresWidget object>)�[0m
�[1;32m     67�[0m �[38;5;28;01mif�[39;00m �[38;5;28mself�[39m�[38;5;241m.�[39mpoints_layer �[38;5;129;01mis�[39;00m �[38;5;129;01mnot�[39;00m �[38;5;28;01mNone�[39;00m:
�[0;32m---> 68�[0m     �[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43mviewer�[49m�[38;5;241;43m.�[39;49m�[43mlayers�[49m�[38;5;241;43m.�[39;49m�[43mremove�[49m�[43m(�[49m�[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43mpoints_layer�[49m�[43m)�[49m
        self.points_layer �[0;34m= <Points layer 'n3d spheres' at 0x754b7846c400>�[0m�[0;34m
        �[0mself �[0;34m= <tomography_python_programs.pick.spheres.PickSpheresWidget object at 0x754bc9f0c430>�[0m�[0;34m
        �[0mself.viewer.layers �[0;34m= [<Image layer 'tomogram' at 0x754b844d82e0>]�[0m�[0;34m
        �[0mself.viewer �[0;34m= Viewer(camera=Camera(center=(134.25097504957012, 624.4804183213577, 472.5304129756257), zoom=1.6198914971997482, angles=(-19.093573125126735, 15.977671555947397, 137.60177770462866), perspective=0.0, mouse_pan=True, mouse_zoom=True), cursor=Cursor(position=(168.02505784420777, 609.1196656123706, 591.684795982022), scaled=True, size=1, style=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=3, ndisplay=3, last_used=0, range=((0.0, 296.0, 1.0), (0.0, 1270.0, 1.0), (0.0, 952.0, 1.0)), current_step=(147, 634, 475), order=(0, 1, 2), axis_labels=('0', '1', '2')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[<Image layer 'tomogram' at 0x754b844d82e0>], help='use <2> for transform', status={'layer_base': 'tomogram', 'source_type': '', 'plugin': '', 'coordinates': ' [168 609 592]'}, tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=True, mouse_move_callbacks=[], mouse_drag_callbacks=[], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[<function dims_scroll at 0x754bd67603a0>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={'[': <bound method TomogramBrowserWidget.previous_tilt_series of <tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object at 0x754bc9fe28c0>>, ']': <bound method TomogramBrowserWidget.next_tilt_series of <tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object at 0x754bc9fe28c0>>})�[0m
�[1;32m     69�[0m     �[38;5;28mself�[39m�[38;5;241m.�[39mviewer�[38;5;241m.�[39mlayers�[38;5;241m.�[39mremove(�[38;5;28mself�[39m�[38;5;241m.�[39mannotator�[38;5;241m.�[39msurface_layer)

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/_collections_abc.py:1163�[0m, in �[0;36mMutableSequence.remove�[0;34m(self=[<Image layer 'tomogram' at 0x754b844d82e0>], value=<Points layer 'n3d spheres'>)�[0m
�[1;32m   1160�[0m �[38;5;250m�[39m�[38;5;124;03m'''S.remove(value) -- remove first occurrence of value.�[39;00m
�[1;32m   1161�[0m �[38;5;124;03m   Raise ValueError if the value is not present.�[39;00m
�[1;32m   1162�[0m �[38;5;124;03m'''�[39;00m
�[0;32m-> 1163�[0m �[38;5;28;01mdel�[39;00m �[38;5;28mself�[39m[�[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43mindex�[49m�[43m(�[49m�[43mvalue�[49m�[43m)�[49m]
        self �[0;34m= [<Image layer 'tomogram' at 0x754b844d82e0>]�[0m�[0;34m
        �[0mvalue �[0;34m= <Points layer 'n3d spheres' at 0x754b7846c400>�[0m

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/napari/utils/events/containers/_typed.py:230�[0m, in �[0;36mTypedMutableSequence.index�[0;34m(self=[<Image layer 'tomogram' at 0x754b844d82e0>], value=<Points layer 'n3d spheres'>, start=0, stop=None)�[0m
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�[0;32m--> 230�[0m �[38;5;28;01mraise�[39;00m �[38;5;167;01mValueError�[39;00m(
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        �[0mvalue �[0;34m= <Points layer 'n3d spheres' at 0x754b7846c400>�[0m
�[1;32m    231�[0m     trans�[38;5;241m.�[39m_(
�[1;32m    232�[0m         �[38;5;124m"�[39m�[38;5;132;01m{value!r}�[39;00m�[38;5;124m is not in list�[39m�[38;5;124m"�[39m,
�[1;32m    233�[0m         deferred�[38;5;241m=�[39m�[38;5;28;01mTrue�[39;00m,
�[1;32m    234�[0m         value�[38;5;241m=�[39mvalue,
�[1;32m    235�[0m     )
�[1;32m    236�[0m )

�[0;31mValueError�[0m: <Points layer 'n3d spheres' at 0x754b7846c400> is not in list

The above exception was the direct cause of the following exception:

�[0;31mEmitLoopError�[0m                             Traceback (most recent call last)
File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/_qt/components/tomogram_browser.py:69�[0m, in �[0;36mTomogramBrowserWidget._on_tomogram_selection_change�[0;34m(self=<tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object>)�[0m
�[1;32m     67�[0m �[38;5;28mself�[39m�[38;5;241m.�[39mchanging_tomogram�[38;5;241m.�[39memit()
�[1;32m     68�[0m �[38;5;28mself�[39m�[38;5;241m.�[39mselected_tilt_series �[38;5;241m=�[39m �[38;5;28mself�[39m�[38;5;241m.�[39mtilt_series_list_widget�[38;5;241m.�[39mselected_tilt_series_in_view()
�[0;32m---> 69�[0m �[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43m_load_tomogram�[49m�[43m(�[49m�[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43mselected_tilt_series�[49m�[38;5;241;43m.�[39;49m�[43mname�[49m�[43m,�[49m�[43m �[49m�[43madd_to_viewer�[49m�[38;5;241;43m=�[39;49m�[38;5;28;43;01mTrue�[39;49;00m�[43m)�[49m
        self �[0;34m= <tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object at 0x754bc9fe28c0>�[0m
�[1;32m     70�[0m �[38;5;28mself�[39m�[38;5;241m.�[39m_preload_next_tomograms()

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/_qt/components/tomogram_browser.py:96�[0m, in �[0;36mTomogramBrowserWidget._load_tomogram�[0;34m(self=<tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object>, tilt_series_id='AQB1tomo008', add_to_viewer=True)�[0m
�[1;32m     94�[0m �[38;5;28mself�[39m�[38;5;241m.�[39m_cache[tilt_series_id] �[38;5;241m=�[39m tomogram
�[1;32m     95�[0m �[38;5;28;01mif�[39;00m add_to_viewer:
�[0;32m---> 96�[0m     �[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43m_update_tomogram_in_viewer�[49m�[43m(�[49m�[43mtomogram�[49m�[43m)�[49m
        tomogram �[0;34m= <class 'numpy.ndarray'> (296, 1270, 952) float32�[0m�[0;34m
        �[0mself �[0;34m= <tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object at 0x754bc9fe28c0>�[0m

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/_qt/components/tomogram_browser.py:84�[0m, in �[0;36mTomogramBrowserWidget._update_tomogram_in_viewer�[0;34m(self=<tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object>, tomogram=<class 'numpy.ndarray'> (296, 1270, 952) float32)�[0m
�[1;32m     75�[0m �[38;5;28;01melse�[39;00m:
�[1;32m     76�[0m     �[38;5;28mself�[39m�[38;5;241m.�[39mviewer�[38;5;241m.�[39madd_image(
�[1;32m     77�[0m         data�[38;5;241m=�[39mtomogram,
�[1;32m     78�[0m         name�[38;5;241m=�[39mIMAGE_LAYER_NAME,
�[0;32m   (...)�[0m
�[1;32m     82�[0m         blending�[38;5;241m=�[39m�[38;5;124m'�[39m�[38;5;124mtranslucent�[39m�[38;5;124m'�[39m,
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�[0;32m---> 84�[0m �[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43m_on_tomogram_loaded�[49m�[43m(�[49m�[43m)�[49m
        self �[0;34m= <tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object at 0x754bc9fe28c0>�[0m

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/_qt/components/tomogram_browser.py:108�[0m, in �[0;36mTomogramBrowserWidget._on_tomogram_loaded�[0;34m(self=<tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object>)�[0m
�[1;32m    106�[0m layer�[38;5;241m.�[39mplane�[38;5;241m.�[39mnormal �[38;5;241m=�[39m (�[38;5;241m1�[39m, �[38;5;241m0�[39m, �[38;5;241m0�[39m)
�[1;32m    107�[0m �[38;5;28mself�[39m�[38;5;241m.�[39mviewer�[38;5;241m.�[39mlayers�[38;5;241m.�[39mselection �[38;5;241m=�[39m [layer]
�[0;32m--> 108�[0m �[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43mtomogram_changed�[49m�[38;5;241;43m.�[39;49m�[43memit�[49m�[43m(�[49m�[43m)�[49m
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        �[0mself �[0;34m= <tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object at 0x754bc9fe28c0>�[0m

File �[0;32msrc/psygnal/_signal.py:1176�[0m, in �[0;36memit�[0;34m()�[0m

File �[0;32msrc/psygnal/_signal.py:1213�[0m, in �[0;36m_run_emit_loop�[0;34m()�[0m

File �[0;32msrc/psygnal/_signal.py:1196�[0m, in �[0;36m_run_emit_loop�[0;34m()�[0m

File �[0;32msrc/psygnal/_signal.py:1225�[0m, in �[0;36m_run_emit_loop_immediate�[0;34m()�[0m

File �[0;32msrc/psygnal/_weak_callback.py:453�[0m, in �[0;36mcb�[0;34m()�[0m

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/pick/spheres.py:68�[0m, in �[0;36mPickSpheresWidget.synchronise_annotator�[0;34m(self=<tomography_python_programs.pick.spheres.PickSpheresWidget object>)�[0m
�[1;32m     66�[0m �[38;5;28mself�[39m�[38;5;241m.�[39mannotator�[38;5;241m.�[39menabled �[38;5;241m=�[39m �[38;5;28;01mFalse�[39;00m
�[1;32m     67�[0m �[38;5;28;01mif�[39;00m �[38;5;28mself�[39m�[38;5;241m.�[39mpoints_layer �[38;5;129;01mis�[39;00m �[38;5;129;01mnot�[39;00m �[38;5;28;01mNone�[39;00m:
�[0;32m---> 68�[0m     �[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43mviewer�[49m�[38;5;241;43m.�[39;49m�[43mlayers�[49m�[38;5;241;43m.�[39;49m�[43mremove�[49m�[43m(�[49m�[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43mpoints_layer�[49m�[43m)�[49m
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        �[0mself �[0;34m= <tomography_python_programs.pick.spheres.PickSpheresWidget object at 0x754bc9f0c430>�[0m�[0;34m
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�[1;32m     69�[0m     �[38;5;28mself�[39m�[38;5;241m.�[39mviewer�[38;5;241m.�[39mlayers�[38;5;241m.�[39mremove(�[38;5;28mself�[39m�[38;5;241m.�[39mannotator�[38;5;241m.�[39msurface_layer)
�[1;32m     70�[0m �[38;5;28;01mtry�[39;00m:

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/_collections_abc.py:1163�[0m, in �[0;36mMutableSequence.remove�[0;34m(self=[<Image layer 'tomogram' at 0x754b844d82e0>], value=<Points layer 'n3d spheres'>)�[0m
�[1;32m   1159�[0m �[38;5;28;01mdef�[39;00m �[38;5;21mremove�[39m(�[38;5;28mself�[39m, value):
�[1;32m   1160�[0m �[38;5;250m    �[39m�[38;5;124;03m'''S.remove(value) -- remove first occurrence of value.�[39;00m
�[1;32m   1161�[0m �[38;5;124;03m       Raise ValueError if the value is not present.�[39;00m
�[1;32m   1162�[0m �[38;5;124;03m    '''�[39;00m
�[0;32m-> 1163�[0m     �[38;5;28;01mdel�[39;00m �[38;5;28mself�[39m[�[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43mindex�[49m�[43m(�[49m�[43mvalue�[49m�[43m)�[49m]
        self �[0;34m= [<Image layer 'tomogram' at 0x754b844d82e0>]�[0m�[0;34m
        �[0mvalue �[0;34m= <Points layer 'n3d spheres' at 0x754b7846c400>�[0m

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/napari/utils/events/containers/_typed.py:230�[0m, in �[0;36mTypedMutableSequence.index�[0;34m(self=[<Image layer 'tomogram' at 0x754b844d82e0>], value=<Points layer 'n3d spheres'>, start=0, stop=None)�[0m
�[1;32m    227�[0m     �[38;5;28;01mif�[39;00m v �[38;5;129;01mis�[39;00m value �[38;5;129;01mor�[39;00m v �[38;5;241m==�[39m value:
�[1;32m    228�[0m         �[38;5;28;01mreturn�[39;00m i
�[0;32m--> 230�[0m �[38;5;28;01mraise�[39;00m �[38;5;167;01mValueError�[39;00m(
        trans �[0;34m= <napari.utils.translations.TranslationBundle object at 0x754bddab8c70>�[0m�[0;34m
        �[0mvalue �[0;34m= <Points layer 'n3d spheres' at 0x754b7846c400>�[0m
�[1;32m    231�[0m     trans�[38;5;241m.�[39m_(
�[1;32m    232�[0m         �[38;5;124m"�[39m�[38;5;132;01m{value!r}�[39;00m�[38;5;124m is not in list�[39m�[38;5;124m"�[39m,
�[1;32m    233�[0m         deferred�[38;5;241m=�[39m�[38;5;28;01mTrue�[39;00m,
�[1;32m    234�[0m         value�[38;5;241m=�[39mvalue,
�[1;32m    235�[0m     )
�[1;32m    236�[0m )

�[0;31mEmitLoopError�[0m: 

While emitting signal 'tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget.tomogram_changed', a ValueError occurred in a callback:

  Signal emitted at: /home/michalakdj/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/_qt/components/tomogram_browser.py:108, in _on_tomogram_loaded
    >  self.tomogram_changed.emit()

  Callback error at: /home/michalakdj/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/napari/utils/events/containers/_typed.py:230, in index
    >  raise ValueError(

    Local variables:
       value = <Points layer 'n3d spheres' at 0x754b7846c400>
       start = 0
       stop = None
       convert = <function _noop at 0x754bddb0a5f0>
       i = 0
       v = <Image layer 'tomogram' at 0x754b844d82e0>

See ValueError above for original traceback.
�[0;31m---------------------------------------------------------------------------�[0m
�[0;31mValueError�[0m                                Traceback (most recent call last)
File �[0;32msrc/psygnal/_signal.py:1196�[0m, in �[0;36m_run_emit_loop�[0;34m()�[0m

File �[0;32msrc/psygnal/_signal.py:1225�[0m, in �[0;36m_run_emit_loop_immediate�[0;34m()�[0m

File �[0;32msrc/psygnal/_weak_callback.py:453�[0m, in �[0;36mcb�[0;34m()�[0m

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/pick/spheres.py:68�[0m, in �[0;36mPickSpheresWidget.synchronise_annotator�[0;34m(self=<tomography_python_programs.pick.spheres.PickSpheresWidget object>)�[0m
�[1;32m     67�[0m �[38;5;28;01mif�[39;00m �[38;5;28mself�[39m�[38;5;241m.�[39mpoints_layer �[38;5;129;01mis�[39;00m �[38;5;129;01mnot�[39;00m �[38;5;28;01mNone�[39;00m:
�[0;32m---> 68�[0m     �[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43mviewer�[49m�[38;5;241;43m.�[39;49m�[43mlayers�[49m�[38;5;241;43m.�[39;49m�[43mremove�[49m�[43m(�[49m�[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43mpoints_layer�[49m�[43m)�[49m
        self.points_layer �[0;34m= <Points layer 'n3d spheres' at 0x754b7846c400>�[0m�[0;34m
        �[0mself �[0;34m= <tomography_python_programs.pick.spheres.PickSpheresWidget object at 0x754bc9f0c430>�[0m�[0;34m
        �[0mself.viewer.layers �[0;34m= [<Image layer 'tomogram' at 0x754b844d82e0>]�[0m�[0;34m
        �[0mself.viewer �[0;34m= Viewer(camera=Camera(center=(134.25097504957012, 624.4804183213577, 472.5304129756257), zoom=1.6198914971997482, angles=(-19.093573125126735, 15.977671555947397, 137.60177770462866), perspective=0.0, mouse_pan=True, mouse_zoom=True), cursor=Cursor(position=(168.65673457295958, 610.490941355705, 589.6356189088904), scaled=True, size=1, style=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=3, ndisplay=3, last_used=0, range=((0.0, 296.0, 1.0), (0.0, 1270.0, 1.0), (0.0, 952.0, 1.0)), current_step=(147, 634, 475), order=(0, 1, 2), axis_labels=('0', '1', '2')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[<Image layer 'tomogram' at 0x754b844d82e0>], help='use <2> for transform', status={'layer_base': 'tomogram', 'source_type': '', 'plugin': '', 'coordinates': ' [169 610 590]'}, tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=True, mouse_move_callbacks=[], mouse_drag_callbacks=[], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[<function dims_scroll at 0x754bd67603a0>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={'[': <bound method TomogramBrowserWidget.previous_tilt_series of <tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object at 0x754bc9fe28c0>>, ']': <bound method TomogramBrowserWidget.next_tilt_series of <tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object at 0x754bc9fe28c0>>})�[0m
�[1;32m     69�[0m     �[38;5;28mself�[39m�[38;5;241m.�[39mviewer�[38;5;241m.�[39mlayers�[38;5;241m.�[39mremove(�[38;5;28mself�[39m�[38;5;241m.�[39mannotator�[38;5;241m.�[39msurface_layer)

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/_collections_abc.py:1163�[0m, in �[0;36mMutableSequence.remove�[0;34m(self=[<Image layer 'tomogram' at 0x754b844d82e0>], value=<Points layer 'n3d spheres'>)�[0m
�[1;32m   1160�[0m �[38;5;250m�[39m�[38;5;124;03m'''S.remove(value) -- remove first occurrence of value.�[39;00m
�[1;32m   1161�[0m �[38;5;124;03m   Raise ValueError if the value is not present.�[39;00m
�[1;32m   1162�[0m �[38;5;124;03m'''�[39;00m
�[0;32m-> 1163�[0m �[38;5;28;01mdel�[39;00m �[38;5;28mself�[39m[�[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43mindex�[49m�[43m(�[49m�[43mvalue�[49m�[43m)�[49m]
        self �[0;34m= [<Image layer 'tomogram' at 0x754b844d82e0>]�[0m�[0;34m
        �[0mvalue �[0;34m= <Points layer 'n3d spheres' at 0x754b7846c400>�[0m

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/napari/utils/events/containers/_typed.py:230�[0m, in �[0;36mTypedMutableSequence.index�[0;34m(self=[<Image layer 'tomogram' at 0x754b844d82e0>], value=<Points layer 'n3d spheres'>, start=0, stop=None)�[0m
�[1;32m    228�[0m         �[38;5;28;01mreturn�[39;00m i
�[0;32m--> 230�[0m �[38;5;28;01mraise�[39;00m �[38;5;167;01mValueError�[39;00m(
        trans �[0;34m= <napari.utils.translations.TranslationBundle object at 0x754bddab8c70>�[0m�[0;34m
        �[0mvalue �[0;34m= <Points layer 'n3d spheres' at 0x754b7846c400>�[0m
�[1;32m    231�[0m     trans�[38;5;241m.�[39m_(
�[1;32m    232�[0m         �[38;5;124m"�[39m�[38;5;132;01m{value!r}�[39;00m�[38;5;124m is not in list�[39m�[38;5;124m"�[39m,
�[1;32m    233�[0m         deferred�[38;5;241m=�[39m�[38;5;28;01mTrue�[39;00m,
�[1;32m    234�[0m         value�[38;5;241m=�[39mvalue,
�[1;32m    235�[0m     )
�[1;32m    236�[0m )

�[0;31mValueError�[0m: <Points layer 'n3d spheres' at 0x754b7846c400> is not in list

The above exception was the direct cause of the following exception:

�[0;31mEmitLoopError�[0m                             Traceback (most recent call last)
File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/_qt/components/tomogram_browser.py:69�[0m, in �[0;36mTomogramBrowserWidget._on_tomogram_selection_change�[0;34m(self=<tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object>)�[0m
�[1;32m     67�[0m �[38;5;28mself�[39m�[38;5;241m.�[39mchanging_tomogram�[38;5;241m.�[39memit()
�[1;32m     68�[0m �[38;5;28mself�[39m�[38;5;241m.�[39mselected_tilt_series �[38;5;241m=�[39m �[38;5;28mself�[39m�[38;5;241m.�[39mtilt_series_list_widget�[38;5;241m.�[39mselected_tilt_series_in_view()
�[0;32m---> 69�[0m �[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43m_load_tomogram�[49m�[43m(�[49m�[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43mselected_tilt_series�[49m�[38;5;241;43m.�[39;49m�[43mname�[49m�[43m,�[49m�[43m �[49m�[43madd_to_viewer�[49m�[38;5;241;43m=�[39;49m�[38;5;28;43;01mTrue�[39;49;00m�[43m)�[49m
        self �[0;34m= <tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object at 0x754bc9fe28c0>�[0m
�[1;32m     70�[0m �[38;5;28mself�[39m�[38;5;241m.�[39m_preload_next_tomograms()

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/_qt/components/tomogram_browser.py:96�[0m, in �[0;36mTomogramBrowserWidget._load_tomogram�[0;34m(self=<tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object>, tilt_series_id='AQB1tomo012', add_to_viewer=True)�[0m
�[1;32m     94�[0m �[38;5;28mself�[39m�[38;5;241m.�[39m_cache[tilt_series_id] �[38;5;241m=�[39m tomogram
�[1;32m     95�[0m �[38;5;28;01mif�[39;00m add_to_viewer:
�[0;32m---> 96�[0m     �[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43m_update_tomogram_in_viewer�[49m�[43m(�[49m�[43mtomogram�[49m�[43m)�[49m
        tomogram �[0;34m= <class 'numpy.ndarray'> (296, 1270, 952) float32�[0m�[0;34m
        �[0mself �[0;34m= <tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object at 0x754bc9fe28c0>�[0m

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/_qt/components/tomogram_browser.py:84�[0m, in �[0;36mTomogramBrowserWidget._update_tomogram_in_viewer�[0;34m(self=<tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object>, tomogram=<class 'numpy.ndarray'> (296, 1270, 952) float32)�[0m
�[1;32m     75�[0m �[38;5;28;01melse�[39;00m:
�[1;32m     76�[0m     �[38;5;28mself�[39m�[38;5;241m.�[39mviewer�[38;5;241m.�[39madd_image(
�[1;32m     77�[0m         data�[38;5;241m=�[39mtomogram,
�[1;32m     78�[0m         name�[38;5;241m=�[39mIMAGE_LAYER_NAME,
�[0;32m   (...)�[0m
�[1;32m     82�[0m         blending�[38;5;241m=�[39m�[38;5;124m'�[39m�[38;5;124mtranslucent�[39m�[38;5;124m'�[39m,
�[1;32m     83�[0m     )
�[0;32m---> 84�[0m �[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43m_on_tomogram_loaded�[49m�[43m(�[49m�[43m)�[49m
        self �[0;34m= <tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object at 0x754bc9fe28c0>�[0m

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/_qt/components/tomogram_browser.py:108�[0m, in �[0;36mTomogramBrowserWidget._on_tomogram_loaded�[0;34m(self=<tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object>)�[0m
�[1;32m    106�[0m layer�[38;5;241m.�[39mplane�[38;5;241m.�[39mnormal �[38;5;241m=�[39m (�[38;5;241m1�[39m, �[38;5;241m0�[39m, �[38;5;241m0�[39m)
�[1;32m    107�[0m �[38;5;28mself�[39m�[38;5;241m.�[39mviewer�[38;5;241m.�[39mlayers�[38;5;241m.�[39mselection �[38;5;241m=�[39m [layer]
�[0;32m--> 108�[0m �[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43mtomogram_changed�[49m�[38;5;241;43m.�[39;49m�[43memit�[49m�[43m(�[49m�[43m)�[49m
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        �[0mself �[0;34m= <tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object at 0x754bc9fe28c0>�[0m

File �[0;32msrc/psygnal/_signal.py:1176�[0m, in �[0;36memit�[0;34m()�[0m

File �[0;32msrc/psygnal/_signal.py:1213�[0m, in �[0;36m_run_emit_loop�[0;34m()�[0m

File �[0;32msrc/psygnal/_signal.py:1196�[0m, in �[0;36m_run_emit_loop�[0;34m()�[0m

File �[0;32msrc/psygnal/_signal.py:1225�[0m, in �[0;36m_run_emit_loop_immediate�[0;34m()�[0m

File �[0;32msrc/psygnal/_weak_callback.py:453�[0m, in �[0;36mcb�[0;34m()�[0m

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/pick/spheres.py:68�[0m, in �[0;36mPickSpheresWidget.synchronise_annotator�[0;34m(self=<tomography_python_programs.pick.spheres.PickSpheresWidget object>)�[0m
�[1;32m     66�[0m �[38;5;28mself�[39m�[38;5;241m.�[39mannotator�[38;5;241m.�[39menabled �[38;5;241m=�[39m �[38;5;28;01mFalse�[39;00m
�[1;32m     67�[0m �[38;5;28;01mif�[39;00m �[38;5;28mself�[39m�[38;5;241m.�[39mpoints_layer �[38;5;129;01mis�[39;00m �[38;5;129;01mnot�[39;00m �[38;5;28;01mNone�[39;00m:
�[0;32m---> 68�[0m     �[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43mviewer�[49m�[38;5;241;43m.�[39;49m�[43mlayers�[49m�[38;5;241;43m.�[39;49m�[43mremove�[49m�[43m(�[49m�[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43mpoints_layer�[49m�[43m)�[49m
        self.points_layer �[0;34m= <Points layer 'n3d spheres' at 0x754b7846c400>�[0m�[0;34m
        �[0mself �[0;34m= <tomography_python_programs.pick.spheres.PickSpheresWidget object at 0x754bc9f0c430>�[0m�[0;34m
        �[0mself.viewer.layers �[0;34m= [<Image layer 'tomogram' at 0x754b844d82e0>]�[0m�[0;34m
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�[1;32m     69�[0m     �[38;5;28mself�[39m�[38;5;241m.�[39mviewer�[38;5;241m.�[39mlayers�[38;5;241m.�[39mremove(�[38;5;28mself�[39m�[38;5;241m.�[39mannotator�[38;5;241m.�[39msurface_layer)
�[1;32m     70�[0m �[38;5;28;01mtry�[39;00m:

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/_collections_abc.py:1163�[0m, in �[0;36mMutableSequence.remove�[0;34m(self=[<Image layer 'tomogram' at 0x754b844d82e0>], value=<Points layer 'n3d spheres'>)�[0m
�[1;32m   1159�[0m �[38;5;28;01mdef�[39;00m �[38;5;21mremove�[39m(�[38;5;28mself�[39m, value):
�[1;32m   1160�[0m �[38;5;250m    �[39m�[38;5;124;03m'''S.remove(value) -- remove first occurrence of value.�[39;00m
�[1;32m   1161�[0m �[38;5;124;03m       Raise ValueError if the value is not present.�[39;00m
�[1;32m   1162�[0m �[38;5;124;03m    '''�[39;00m
�[0;32m-> 1163�[0m     �[38;5;28;01mdel�[39;00m �[38;5;28mself�[39m[�[38;5;28;43mself�[39;49m�[38;5;241;43m.�[39;49m�[43mindex�[49m�[43m(�[49m�[43mvalue�[49m�[43m)�[49m]
        self �[0;34m= [<Image layer 'tomogram' at 0x754b844d82e0>]�[0m�[0;34m
        �[0mvalue �[0;34m= <Points layer 'n3d spheres' at 0x754b7846c400>�[0m

File �[0;32m~/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/napari/utils/events/containers/_typed.py:230�[0m, in �[0;36mTypedMutableSequence.index�[0;34m(self=[<Image layer 'tomogram' at 0x754b844d82e0>], value=<Points layer 'n3d spheres'>, start=0, stop=None)�[0m
�[1;32m    227�[0m     �[38;5;28;01mif�[39;00m v �[38;5;129;01mis�[39;00m value �[38;5;129;01mor�[39;00m v �[38;5;241m==�[39m value:
�[1;32m    228�[0m         �[38;5;28;01mreturn�[39;00m i
�[0;32m--> 230�[0m �[38;5;28;01mraise�[39;00m �[38;5;167;01mValueError�[39;00m(
        trans �[0;34m= <napari.utils.translations.TranslationBundle object at 0x754bddab8c70>�[0m�[0;34m
        �[0mvalue �[0;34m= <Points layer 'n3d spheres' at 0x754b7846c400>�[0m
�[1;32m    231�[0m     trans�[38;5;241m.�[39m_(
�[1;32m    232�[0m         �[38;5;124m"�[39m�[38;5;132;01m{value!r}�[39;00m�[38;5;124m is not in list�[39m�[38;5;124m"�[39m,
�[1;32m    233�[0m         deferred�[38;5;241m=�[39m�[38;5;28;01mTrue�[39;00m,
�[1;32m    234�[0m         value�[38;5;241m=�[39mvalue,
�[1;32m    235�[0m     )
�[1;32m    236�[0m )

�[0;31mEmitLoopError�[0m: 

While emitting signal 'tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget.tomogram_changed', a ValueError occurred in a callback:

  Signal emitted at: /home/michalakdj/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/_qt/components/tomogram_browser.py:108, in _on_tomogram_loaded
    >  self.tomogram_changed.emit()

  Callback error at: /home/michalakdj/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/napari/utils/events/containers/_typed.py:230, in index
    >  raise ValueError(

    Local variables:
       value = <Points layer 'n3d spheres' at 0x754b7846c400>
       start = 0
       stop = None
       convert = <function _noop at 0x754bddb0a5f0>
       i = 0
       v = <Image layer 'tomogram' at 0x754b844d82e0>

See ValueError above for original traceback.
run.err 
/home/michalakdj/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/starfile/parser.py:177: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use ``sep='\s+'`` instead
  df = pd.read_csv(
/home/michalakdj/mambaforge/envs/relion-5.0/lib/python3.10/site-packages/starfile/parser.py:194: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing `errors` and catch exceptions explicitly instead
  self.dataframes[key] = df.apply(pd.to_numeric, errors='ignore')
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