Napari missing a plugin

[sun647]

Hello,

I am running the tomo tutorial dataset EMPIAR-10164 with relion 5 --tomo. I was able to pick the spheres in napari and save the spheres. However, after I closed napari window, it didn't write out any particle star files. It gave me the error message that a plugin is missing to write the layers. I can manually save the n3d sphere layer but not the sphere meshes layer. I noticed that the napari-meshio plugin is already installed when the napari window opened.

Have anyone experienced the same? How should I work around it? It seems there is also a problem between napari and numpy.

Thanks,
Chen

/data/csun/Projects/EMPIAR-10164/myrelion5tomo/Picks/job014/spheremeshes save failed.
No data written! A plugin could not be found to write these 1 layers to /data/csun/Projects/EMPIAR-10164/myrelion5tomo/Picks/job014/spheremeshes

TypeError Traceback (most recent call last)
File ~/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/napari/qt/menus/file_menu.py:81, in FileMenu.init..()
26 super().init(trans.('&File'), window.qt_window)
27 self.open_sample_menu = NapariMenu(trans.('Open Sample'), self)
28 ACTIONS = [
29 {
30 'text': trans._('Open File(s)...'),
31 'slot': window._qt_viewer.open_files_dialog,
32 'shortcut': 'Ctrl+O',
33 },
34 {
35 'text': trans.('Open Files as Stack...'),
36 'slot': window._qt_viewer.open_files_dialog_as_stack_dialog,
37 'shortcut': 'Ctrl+Alt+O',
38 },
39 {
40 'text': trans.('Open Folder...'),
41 'slot': window._qt_viewer.open_folder_dialog,
42 'shortcut': 'Ctrl+Shift+O',
43 },
44 {
45 'menu': trans.('Open with Plugin'),
46 'items': [
47 {
48 'text': 'Open File(s)...',
49 'slot': self._open_files_w_plugin,
50 },
51 {
52 'text': 'Open Files as Stack...',
53 'slot': self.open_files_as_stack_w_plugin,
54 },
55 {
56 'text': 'Open Folder...',
57 'slot': self.open_folder_w_plugin,
58 },
59 ],
60 },
61 {'menu': self.open_sample_menu},
62 {},
63 {
64 'text': trans.('Preferences'),
65 'slot': self.open_preferences,
66 'shortcut': 'Ctrl+Shift+P',
67 'statusTip': trans.('Open preferences dialog'),
68 'menuRole': QAction.PreferencesRole,
69 },
70 {},
71 {
72 'text': trans.('Save Selected Layer(s)...'),
73 'slot': lambda: window._qt_viewer._save_layers_dialog(
74 selected=True
75 ),
76 'shortcut': 'Ctrl+S',
77 'enabled': self.layer_count,
78 },
79 {
80 'text': trans.('Save All Layers...'),
---> 81 'slot': lambda: window._qt_viewer._save_layers_dialog(
trans = <napari.utils.translations.TranslationBundle object at 0x7f89a3d5dba0>
window = <napari.qt.qt_main_window.Window object at 0x7f8999ba4cd0>
QAction.PreferencesRole = 5
QAction = <class 'PyQt5.QtWidgets.QAction'>
window.qt_window = <napari.qt.qt_main_window.QtMainWindow object at 0x7f8999729630>
QAction.QuitRole = 6
82 selected=False
83 ),
84 'shortcut': 'Ctrl+Shift+S',
85 'enabled': self.layer_count,
86 },
87 {
88 'text': trans.('Save Screenshot...'),
89 'slot': window.qt_viewer.screenshot_dialog,
90 'shortcut': 'Alt+S',
91 'statusTip': trans.(
92 'Save screenshot of current display, default .png'
93 ),
94 },
95 {
96 'text': trans.('Save Screenshot with Viewer...'),
97 'slot': self.screenshot_dialog,
98 'shortcut': 'Alt+Shift+S',
99 'statusTip': trans.(
100 'Save screenshot of current display with the viewer, default .png'
101 ),
102 },
103 {
104 'text': trans.('Copy Screenshot to Clipboard'),
105 'slot': window.qt_viewer.clipboard,
106 'shortcut': 'Alt+C',
107 'statusTip': trans.(
108 'Copy screenshot of current display to the clipboard'
109 ),
110 },
111 {
112 'text': trans.('Copy Screenshot with Viewer to Clipboard'),
113 'slot': window.clipboard,
114 'shortcut': 'Alt+Shift+C',
115 'statusTip': trans.(
116 'Copy screenshot of current display with the viewer to the clipboard'
117 ),
118 },
119 {},
120 {
121 'text': trans.('Close Window'),
122 'slot': self.close_window,
123 'shortcut': 'Ctrl+W',
124 },
125 {
126 'when': running_as_constructor_app(),
127 'text': trans.('Restart'),
128 'slot': window.qt_window.restart,
129 },
130 # OS X will rename this to Quit and put it in the app menu.
131 # This quits the entire QApplication and closes all windows.
132 {
133 'text': trans.('Exit'),
134 'slot': self._close_app,
135 'shortcut': 'Ctrl+Q',
136 'menuRole': QAction.QuitRole,
137 },
138 ]
139 populate_menu(self, ACTIONS)
141 self._pref_dialog = None

File ~/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/napari/_qt/qt_viewer.py:767, in QtViewer._save_layers_dialog(self=<napari._qt.qt_viewer.QtViewer object>, selected=False)
763 writer = _npe2_decode_selected_filter(
764 ext_str, selected_filter, writers
765 )
766 with warnings.catch_warnings(record=True) as wa:
--> 767 saved = self.viewer.layers.save(
self = <napari._qt.qt_viewer.QtViewer object at 0x7f89997296c0>
self.viewer.layers = [<Image layer 'tomogram' at 0x7f897c170b50>, <Points layer 'n3d spheres' at 0x7f89581878b0>, <Surface layer 'sphere meshes' at 0x7f895875d0c0>]
self.viewer = Viewer(camera=Camera(center=(135.3438649875377, 260.5870937773653, 270.0601484860371), zoom=1.114589259259259, angles=(1.6221426385038984, -8.724935607783912, 89.13874617226506), perspective=0.0, mouse_pan=True, mouse_zoom=True), cursor=Cursor(position=(141.72788964110683, 502.972477849981, 204.7259809784764), scaled=True, size=1, style=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=3, ndisplay=3, last_used=0, range=((0.0, 270.0, 1.0), (-15.363716125488281, 540.0, 1.0), (0.0, 540.0, 1.0)), current_step=(134, 269, 269), order=(0, 1, 2), axis_labels=('0', '1', '2')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[<Image layer 'tomogram' at 0x7f897c170b50>, <Points layer 'n3d spheres' at 0x7f89581878b0>, <Surface layer 'sphere meshes' at 0x7f895875d0c0>], help='use <2> for transform', status={'layer_base': 'tomogram', 'source_type': '', 'plugin': '', 'coordinates': ' [142 503 205]'}, tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=True, mouse_move_callbacks=[], mouse_drag_callbacks=[<bound method SphereAnnotator._add_point_on_mouse_alt_click of <napari_threedee.annotators.spheres.annotator.SphereAnnotator object at 0x7f895805d600>>], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[<function dims_scroll at 0x7f899b26a560>], _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 0x7f89a31ea560>>, ']': <bound method TomogramBrowserWidget.next_tilt_series of <tomography_python_programs._qt.components.tomogram_browser.TomogramBrowserWidget object at 0x7f89a31ea560>>, 'R': <bound method SphereAnnotator._set_radius_from_mouse_event of <napari_threedee.annotators.spheres.annotator.SphereAnnotator object at 0x7f895805d600>>, 'N': <bound method SphereAnnotator._enable_add_mode of <napari_threedee.annotators.spheres.annotator.SphereAnnotator object at 0x7f895805d600>>})
filename = '/data/csun/Projects/CART/EMPIAR-10164/myrelion5tomo/myrelion/Picks/job014/20250206alllayers'
selected = False
writer = None
768 filename, selected=selected, _writer=writer
769 )
770 logging.debug('Saved %s', saved)
771 error_messages = "\n".join(str(x.message.args[0]) for x in wa)

File ~/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/napari/components/layerlist.py:476, in LayerList.save(self=[<Image layer 'tomogram' at 0x7f897c170b50>, <Po...Surface layer 'sphere meshes' at 0x7f895875d0c0>], path='/data/csun/Projects/CART/EMPIAR-10164/myrelion5tomo/myrelion/Picks/job014/20250206alllayers', selected=False, plugin=None, _writer=None)
473 warnings.warn(msg)
474 return []
--> 476 return save_layers(path, layers, plugin=plugin, _writer=_writer)
layers = [<Image layer 'tomogram' at 0x7f897c170b50>, <Points layer 'n3d spheres' at 0x7f89581878b0>, <Surface layer 'sphere meshes' at 0x7f895875d0c0>]
path = '/data/csun/Projects/CART/EMPIAR-10164/myrelion5tomo/myrelion/Picks/job014/20250206alllayers'
plugin = None
_writer = None

File ~/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/napari/plugins/io.py:225, in save_layers(path='/data/csun/Projects/CART/EMPIAR-10164/myrelion5tomo/myrelion/Picks/job014/20250206alllayers', layers=[<Image layer 'tomogram'>, <Points layer 'n3d spheres'>, <Surface layer 'sphere meshes'>], plugin=None, _writer=None)
223 writer_name = ''
224 if len(layers) > 1:
--> 225 written, writer_name = _write_multiple_layers_with_plugins(
writer_name = ''
layers = [<Image layer 'tomogram' at 0x7f897c170b50>, <Points layer 'n3d spheres' at 0x7f89581878b0>, <Surface layer 'sphere meshes' at 0x7f895875d0c0>]
path = '/data/csun/Projects/EMPIAR-10164/myrelion5tomo/myrelion/Picks/job014/20250206alllayers'
plugin = None
_writer = None
226 path, layers, plugin_name=plugin, _writer=_writer
227 )
228 elif len(layers) == 1:
229 _written, writer_name = _write_single_layer_with_plugins(
230 path, layers[0], plugin_name=plugin, _writer=_writer
231 )

File ~/miniconda3/envs/relion-5.0/lib/python3.10/site-packages/napari/plugins/io.py:387, in _write_multiple_layers_with_plugins(path='/data/csun/Projects/CART/EMPIAR-10164/myrelion5tomo/myrelion/Picks/job014/20250206alllayers', layers=[<Image layer 'tomogram'>, <Points layer 'n3d spheres'>, <Surface layer 'sphere meshes'>], plugin_name=None, writer=None)
380 else:
381 msg = trans.(
382 'Unable to find plugin capable of writing this combination of layer types: {layer_types}',
383 deferred=True,
384 layer_types=layer_types,
385 )
--> 387 raise TypeError(msg)
msg = "Unable to find plugin capable of writing this combination of layer types: ['image', 'points', 'surface']"
389 try:
390 return (
391 writer_function(abspath_or_url(path), layer_data),
392 implementation.plugin_name,
393 )

TypeError: Unable to find plugin capable of writing this combination of layer types: ['image', 'points', 'surface']