Starting SuRVoS2 from the plugins menu produces error message

[haesleinhuepf]

Hi all,

I installed the SuRVoS2 plugin (from the current main branch here) and tried starting it from the menu Plugins > SuRVoS Workspace. Unfortunately, it doesn't start and outputs the error message posted below instead. Is there anything else I need to do to try it out?

Thanks!

Best,
Robert

INFO - Frontend loading workspace:   - survos2.frontend.frontend:frontend:87
DEBUG - Plugin loaded: superregions, Superregions, <class 'survos2.frontend.plugins.superregions.RegionsPlugin'>  - survos2.frontend.panels:__init__:185
DEBUG - QCSWidget __call__ <survos2.frontend.components.icon_buttons.IconButton object at 0x000001C44281B8B0>  - survos2.frontend.components.base:__call__:72
show_plugin: superregions
DEBUG - Region result None  - survos2.frontend.plugins.superregions:setup:81
DEBUG - Plugin loaded: annotations, Annotations, <class 'survos2.frontend.plugins.annotations.AnnotationPlugin'>  - survos2.frontend.panels:__init__:185
DEBUG - Result of regions existing: None  - survos2.frontend.plugins.superregions:fill:24
WARNING: QLayout: Attempting to add QLayout "" to AnnotationPlugin "annotation_plugin", which already has a layout
22:08:02 WARNING QLayout: Attempting to add QLayout "" to AnnotationPlugin "annotation_plugin", which already has a layout
DEBUG - Result of regions existing: None  - survos2.frontend.plugins.superregions:fill:24
WARNING: QLayout: Attempting to add QLayout "" to AnnotationPlugin "annotation_plugin", which already has a layout
22:08:02 WARNING QLayout: Attempting to add QLayout "" to AnnotationPlugin "annotation_plugin", which already has a layout
show_plugin: annotations
DEBUG - Plugin loaded: features, Features, <class 'survos2.frontend.plugins.features.FeaturesPlugin'>  - survos2.frontend.panels:__init__:185
WARNING: QLayout: Attempting to add QLayout "" to FeaturesPlugin "features_plugin", which already has a layout
22:08:02 WARNING QLayout: Attempting to add QLayout "" to FeaturesPlugin "features_plugin", which already has a layout
show_plugin: features
DEBUG - Feature result None  - survos2.frontend.plugins.features:setup:174
DEBUG - Plugin loaded: server, Server, <class 'survos2.frontend.plugins.server.ServerPlugin'>  - survos2.frontend.panels:__init__:185
---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
~\miniconda3\envs\survos2\lib\site-packages\napari\_qt\menus\plugins_menu.py in _add_toggle_widget(key=('SuRVoS2', 'Workspace'), hook_type='dock')
     84
     85                         if hook_type == 'dock':
---> 86                             self._win.add_plugin_dock_widget(*key)
        global self._win.add_plugin_dock_widget = undefined
        key = ('SuRVoS2', 'Workspace')
     87                         else:
     88                             self._win._add_plugin_function_widget(*key)

~\miniconda3\envs\survos2\lib\site-packages\napari\_qt\qt_main_window.py in add_plugin_dock_widget(self=<napari._qt.qt_main_window.Window object>, plugin_name='SuRVoS2', widget_name='Workspace')
    671
    672         # instantiate the widget
--> 673         wdg = Widget(**kwargs)
        wdg = undefined
        Widget = <class 'survos2._dock_widget.Workspace'>
        kwargs = {'napari_viewer': Viewer(axes=Axes(visible=False, labels=True, colored=True, dashed=False, arrows=True), camera=Camera(center=(0.0, 0.0, 0.0), zoom=1.0, angles=(0.0, 0.0, 90.0), perspective=0.0, interactive=True), cursor=Cursor(position=(1.0, 1.0), scaled=True, size=1, style=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=2, ndisplay=2, last_used=0, range=((0, 2, 1), (0, 2, 1)), current_step=(0, 0), order=(0, 1), axis_labels=('0', '1')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[], scale_bar=ScaleBar(visible=False, colored=False, ticks=True, position=<Position.BOTTOM_RIGHT: 'bottom_right'>, font_size=10.0, unit=None), text_overlay=TextOverlay(visible=False, color=<class 'numpy.ndarray'> (4,) float64, font_size=10.0, position=<TextOverlayPosition.TOP_LEFT: 'top_left'>, text=''), help='', status='Ready', tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_move_callbacks=[], mouse_drag_callbacks=[], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[<function dims_scroll at 0x000001C4241BEB80>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={'Control-Shift-C': <bound method QtViewer.toggle_console_visibility of <napari._qt.qt_viewer.QtViewer object at 0x000001C42442ADC0>>})}
    674
    675         # Add dock widget

c:\structure\code\survos2\survos2\_dock_widget.py in __init__(self=<survos2._dock_widget.Workspace object>, napari_viewer=Viewer(axes=Axes(visible=False, labels=True, col..._viewer.QtViewer object at 0x000001C42442ADC0>>}))
     28         from survos2.frontend.frontend import frontend
     29
---> 30         self.dw = frontend(napari_viewer)
        self.dw = undefined
        frontend = <function frontend at 0x000001C442810A60>
        napari_viewer = Viewer(axes=Axes(visible=False, labels=True, colored=True, dashed=False, arrows=True), camera=Camera(center=(0.0, 0.0, 0.0), zoom=1.0, angles=(0.0, 0.0, 90.0), perspective=0.0, interactive=True), cursor=Cursor(position=(1.0, 1.0), scaled=True, size=1, style=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=2, ndisplay=2, last_used=0, range=((0, 2, 1), (0, 2, 1)), current_step=(0, 0), order=(0, 1), axis_labels=('0', '1')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[], scale_bar=ScaleBar(visible=False, colored=False, ticks=True, position=<Position.BOTTOM_RIGHT: 'bottom_right'>, font_size=10.0, unit=None), text_overlay=TextOverlay(visible=False, color=<class 'numpy.ndarray'> (4,) float64, font_size=10.0, position=<TextOverlayPosition.TOP_LEFT: 'top_left'>, text=''), help='', status='Ready', tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_move_callbacks=[], mouse_drag_callbacks=[], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[<function dims_scroll at 0x000001C4241BEB80>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={'Control-Shift-C': <bound method QtViewer.toggle_console_visibility of <napari._qt.qt_viewer.QtViewer object at 0x000001C42442ADC0>>})
     31         self.layout().addWidget(self.dw.ppw)
     32         self.layout().addWidget(self.dw.bpw)

c:\structure\code\survos2\survos2\frontend\frontend.py in frontend(viewer=Viewer(axes=Axes(visible=False, labels=True, col..._viewer.QtViewer object at 0x000001C42442ADC0>>}))
    129     # SuRVoS controls
    130     dw = AttrDict()
--> 131     dw.ppw = PluginPanelWidget()  # Main SuRVoS panel
        global dw.ppw = undefined
        global PluginPanelWidget = <class 'survos2.frontend.panels.PluginPanelWidget'>
    132     dw.bpw = ButtonPanelWidget()  # Additional controls
    133     dw.ppw.setMinimumSize(QSize(450, 750))

c:\structure\code\survos2\survos2\frontend\panels.py in __init__(self=<survos2.frontend.panels.PluginPanelWidget object>, *args=(), **kwargs={})
    184
    185             logger.debug(f"Plugin loaded: {name}, {title}, {plugin_cls}")
--> 186             self.pluginContainer.load_plugin(name, title, plugin_cls)
        self.pluginContainer.load_plugin = <bound method PluginContainer.load_plugin of <survos2.frontend.plugins.base.PluginContainer object at 0x000001C442810AF0>>
        name = 'server'
        title = 'Server'
        plugin_cls = <class 'survos2.frontend.plugins.server.ServerPlugin'>
    187             self.pluginContainer.show_plugin(name, tab)
    188

c:\structure\code\survos2\survos2\frontend\plugins\base.py in load_plugin(self=<survos2.frontend.plugins.base.PluginContainer object>, name='server', title='Server', cls=<class 'survos2.frontend.plugins.server.ServerPlugin'>)
    131         if name in self.plugins:
    132             return
--> 133         widget = cls()
        widget = undefined
        cls = <class 'survos2.frontend.plugins.server.ServerPlugin'>
    134         widget.change_view.connect(self.view_requested)
    135         self.plugins[name] = dict(widget=widget, title=title)

c:\structure\code\survos2\survos2\frontend\plugins\server.py in __init__(self=<survos2.frontend.plugins.server.ServerPlugin object>, parent=None)
    674         self.adv_run_fields.hide()
    675
--> 676         run_fields = self.get_run_fields()
        run_fields = undefined
        self.get_run_fields = <bound method ServerPlugin.get_run_fields of <survos2.frontend.plugins.server.ServerPlugin object at 0x000001C4435A25E0>>
    677         tab1.layout.addWidget(run_fields)
    678         output_config_button = QPushButton("Save config")

c:\structure\code\survos2\survos2\frontend\plugins\server.py in get_run_fields(self=<survos2.frontend.plugins.server.ServerPlugin object>)
    829         run_layout = QGridLayout()
    830
--> 831         workspaces = os.listdir(CHROOT)
        workspaces = undefined
        global os.listdir = <built-in function listdir>
        global CHROOT = '/dls/science/groups/das/SuRVoS/s2/data'
    832         self.workspaces_list = ComboBox()
    833         for s in workspaces:

FileNotFoundError: [WinError 3] The system cannot find the path specified: '/dls/science/groups/das/SuRVoS/s2/data'

[penningavery]

Hi Robert,

Using the INSTALL.txt, steps 8 and 9 ask you to create a directory for the SuRVoS workspaces to be stored in, and then the settings.yaml is edited to point to that directory. The error message you received indicates that those steps weren't followed yet. Hope that helps.

Best,
Avery