mpi-dortmund / napari-boxmanager Goto Github PK

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AssertionError                            Traceback (most recent call last)
File /mnt/data/twagner/Projects/napari/src/napari-boxmanager-github/src/box_manager/_qt/OrganizeLayer.py:521, in OrganizeLayerWidget._new_shapes(self=<box_manager._qt.OrganizeLayer.OrganizeLayerWidget object>)
    510 metadata["is_filament_layer"] = True
    512 kwargs = {
    513     "metadata": metadata,
    514     "face_color": "transparent",
   (...)
    519     "shape_type": "path",
    520 }
--> 521 shape = self.napari_viewer.add_shapes(
        self = <box_manager._qt.OrganizeLayer.OrganizeLayerWidget object at 0x7ff36c1afd00>
        self.napari_viewer = Viewer(axes=Axes(visible=False, labels=True, colored=True, dashed=False, arrows=True), camera=Camera(center=(0.0, 255.5, 255.5), zoom=1.8369140625000002, angles=(0.0, 0.0, 90.0), perspective=0.0, interactive=True), cursor=Cursor(position=(1.0, 100.0, 462.9130781499203, 603.3660287081341), scaled=True, size=1, style=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=4, ndisplay=2, last_used=0, range=((0.0, 2.0, 1.0), (0.0, 200.0, 1.0), (0.0, 512.0, 1.0), (0.0, 512.0, 1.0)), current_step=(1, 100, 256, 256), order=(0, 1, 2, 3), axis_labels=('0', '1', '2', '3')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[<Image layer 'images' at 0x7ff36c1eead0>, <Shapes layer 'filaments (tomo/*.mrc)' at 0x7ff37719e050>], scale_bar=ScaleBar(visible=False, colored=False, color=<class 'numpy.ndarray'> (4,) float32, ticks=True, position=<Position.BOTTOM_RIGHT: 'bottom_right'>, font_size=10.0, box=False, box_color=<class 'numpy.ndarray'> (4,) float32, unit=None), text_overlay=TextOverlay(visible=False, color=<class 'numpy.ndarray'> (4,) float32, font_size=10.0, position=<TextOverlayPosition.TOP_LEFT: 'top_left'>, text=''), overlays=Overlays(interaction_box=InteractionBox(points=None, show=False, show_handle=False, show_vertices=False, selection_box_drag=None, selection_box_final=None, transform_start=<napari.utils.transforms.transforms.Affine object at 0x7ff3771808e0>, transform_drag=<napari.utils.transforms.transforms.Affine object at 0x7ff377180940>, transform_final=<napari.utils.transforms.transforms.Affine object at 0x7ff3771809a0>, transform=<napari.utils.transforms.transforms.Affine object at 0x7ff377180a00>, allow_new_selection=True, selected_vertex=None)), help='', status='', tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=False, mouse_move_callbacks=[<function InteractionBoxMouseBindings.initialize_mouse_events.<locals>.mouse_move at 0x7ff36c2db1c0>], mouse_drag_callbacks=[<function InteractionBoxMouseBindings.initialize_mouse_events.<locals>.mouse_drag at 0x7ff36c444820>], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[<function dims_scroll at 0x7ff37bd29ab0>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={'Shift': <function InteractionBoxMouseBindings.initialize_key_events.<locals>.hold_to_lock_aspect_ratio at 0x7ff36c444700>, 'Control-Shift-R': <function InteractionBoxMouseBindings._reset_active_layer_affine at 0x7ff36c31c790>, 'Control-Shift-A': <function InteractionBoxMouseBindings._transform_active_layer at 0x7ff36c31c670>})
        kwargs = {'metadata': {'do_activate_on_insert': True, 'linked_image_layers': [140683467746000], 'skip_match': None, 'original_path': '/mnt/data/twagner/Projects/TomoTwin/results/202205_GeneralizationTomo/tomo/*.mrc', 'is_2d_stack': True, 0: {'path': '/mnt/data/twagner/Projects/TomoTwin/results/202205_GeneralizationTomo/tomo/tiltseries_rec.box', 'name': 'tiltseries_rec.box', 'image_name': 'tiltseries_rec.mrc', 'real': False, 'write': None}, 1: {'path': '/mnt/data/twagner/Projects/TomoTwin/results/202205_GeneralizationTomo/tomo/tiltseries_rec_lp60.box', 'name': 'tiltseries_rec_lp60.box', 'image_name': 'tiltseries_rec_lp60.mrc', 'real': False, 'write': None}, 'is_filament_layer': True}, 'face_color': 'transparent', 'edge_color': 'red', 'edge_width': 20, 'opacity': 0.4, 'name': 'filaments (tomo/*.mrc)', 'shape_type': 'path'}
    522     ndim=max(self.napari_viewer.dims.ndim, 2),
    523     scale=self.napari_viewer.layers.extent.step,
    524     **kwargs,
    525 )
    526 shape.mode = Mode.ADD_PATH

File /opt/user_software/miniconda3/envs/napari-cryolo/lib/python3.10/site-packages/napari/components/viewer_model.py:5, in add_shapes(self=Viewer(axes=Axes(visible=False, labels=True, col...ings._transform_active_layer at 0x7ff36c31c670>}), data=None, ndim=4, features=None, properties=None, property_choices=None, text=None, shape_type='path', edge_width=20, edge_color='red', edge_color_cycle=None, edge_colormap='viridis', edge_contrast_limits=None, face_color='transparent', face_color_cycle=None, face_colormap='viridis', face_contrast_limits=None, z_index=0, name='filaments (tomo/*.mrc)', metadata={'do_activate_on_insert': True, 'linked_image_layers': [140683467746000], 'skip_match': None, 'original_path': '/mnt/data/twagner/Projects/TomoTwin/results/202205_GeneralizationTomo/tomo/*.mrc', 'is_2d_stack': True, 0: {'image_name': 'tiltseries_rec.mrc', 'name': 'tiltseries_rec.box', 'path': '/mnt/data/twagner/Projects/TomoTwin/results/202205_GeneralizationTomo/tomo/tiltseries_rec.box', 'real': False, 'write': None}, 1: {'image_name': 'tiltseries_rec_lp60.mrc', 'name': 'tiltseries_rec_lp60.box', 'path': '/mnt/data/twagner/Projects/TomoTwin/results/202205_GeneralizationTomo/tomo/tiltseries_rec_lp60.box', 'real': False, 'write': None}, 'is_filament_layer': True}, scale=<class 'numpy.ndarray'> (4,) float64, translate=None, rotate=None, shear=None, affine=None, opacity=0.4, blending='translucent', visible=True, cache=True, experimental_clipping_planes=None)
      3 import inspect
      4 import itertools
----> 5 import os
      6 import warnings
      7 from functools import lru_cache

File /opt/user_software/miniconda3/envs/napari-cryolo/lib/python3.10/_collections_abc.py:1128, in MutableSequence.append(self=[<Image layer 'images' at 0x7ff36c1eead0>, <Shap...ayer 'filaments (tomo/*.mrc)' at 0x7ff37719e050>], value=<Shapes layer 'filaments (tomo/*.mrc)'>)
   1126 def append(self, value):
   1127     'S.append(value) -- append value to the end of the sequence'
-> 1128     self.insert(len(self), value)
        value = <Shapes layer 'filaments (tomo/*.mrc)' at 0x7ff37719e050>
        self = [<Image layer 'images' at 0x7ff36c1eead0>, <Shapes layer 'filaments (tomo/*.mrc)' at 0x7ff37719e050>]

File /opt/user_software/miniconda3/envs/napari-cryolo/lib/python3.10/site-packages/napari/components/layerlist.py:166, in LayerList.insert(self=[<Image layer 'images' at 0x7ff36c1eead0>, <Shap...ayer 'filaments (tomo/*.mrc)' at 0x7ff37719e050>], index=1, value=<Shapes layer 'filaments (tomo/*.mrc)'>)
    164 self._clean_cache()
    165 new_layer.events.set_data.connect(self._clean_cache)
--> 166 super().insert(index, new_layer)
        new_layer = <Shapes layer 'filaments (tomo/*.mrc)' at 0x7ff37719e050>
        index = 1

File /opt/user_software/miniconda3/envs/napari-cryolo/lib/python3.10/site-packages/napari/utils/events/containers/_selectable_list.py:66, in SelectableEventedList.insert(self=[<Image layer 'images' at 0x7ff36c1eead0>, <Shap...ayer 'filaments (tomo/*.mrc)' at 0x7ff37719e050>], index=1, value=<Shapes layer 'filaments (tomo/*.mrc)'>)
     65 def insert(self, index: int, value: _T):
---> 66     super().insert(index, value)
        index = 1
        value = <Shapes layer 'filaments (tomo/*.mrc)' at 0x7ff37719e050>
     67     if self._activate_on_insert:
     68         # Make layer selected and unselect all others
     69         self.selection.active = value

File /opt/user_software/miniconda3/envs/napari-cryolo/lib/python3.10/site-packages/napari/utils/events/containers/_evented_list.py:188, in EventedList.insert(self=[<Image layer 'images' at 0x7ff36c1eead0>, <Shap...ayer 'filaments (tomo/*.mrc)' at 0x7ff37719e050>], index=1, value=<Shapes layer 'filaments (tomo/*.mrc)'>)
    186 self.events.inserting(index=index)
    187 super().insert(index, value)
--> 188 self.events.inserted(index=index, value=value)
        index = 1
        value = <Shapes layer 'filaments (tomo/*.mrc)' at 0x7ff37719e050>
        self.events.inserted = <napari.utils.events.event.EventEmitter object at 0x7ff377162a10>
        self.events = <napari.utils.events.event.EmitterGroup object at 0x7ff377162800>
        self = [<Image layer 'images' at 0x7ff36c1eead0>, <Shapes layer 'filaments (tomo/*.mrc)' at 0x7ff37719e050>]
    189 self._connect_child_emitters(value)

File /opt/user_software/miniconda3/envs/napari-cryolo/lib/python3.10/site-packages/napari/utils/events/event.py:757, in EventEmitter.__call__(self=<napari.utils.events.event.EventEmitter object>, *args=(), **kwargs={'index': 1, 'value': <Shapes layer 'filaments (tomo/*.mrc)'>})
    754     self._block_counter.update([cb])
    755     continue
--> 757 self._invoke_callback(cb, event if pass_event else None)
        event = <Event blocked=False handled=False native=None source=None sources=[] type='inserted'>
        self = <napari.utils.events.event.EventEmitter object at 0x7ff377162a10>
        cb = <bound method SelectMetricWidget._handle_insert of <box_manager._qt.SelectMetric.SelectMetricWidget object at 0x7ff36c1af370>>
        pass_event = True
    758 if event.blocked:
    759     break

File /opt/user_software/miniconda3/envs/napari-cryolo/lib/python3.10/site-packages/napari/utils/events/event.py:794, in EventEmitter._invoke_callback(self=<napari.utils.events.event.EventEmitter object>, cb=<bound method SelectMetricWidget._handle_insert ...ager._qt.SelectMetric.SelectMetricWidget object>>, event=<Event blocked=False handled=False native=None source=None sources=[] type='inserted'>)
    792     self.disconnect(cb)
    793     return
--> 794 _handle_exception(
        self = <napari.utils.events.event.EventEmitter object at 0x7ff377162a10>
        event = <Event blocked=False handled=False native=None source=None sources=[] type='inserted'>
        cb = <bound method SelectMetricWidget._handle_insert of <box_manager._qt.SelectMetric.SelectMetricWidget object at 0x7ff36c1af370>>
        (cb, event) = (<bound method SelectMetricWidget._handle_insert of <box_manager._qt.SelectMetric.SelectMetricWidget object at 0x7ff36c1af370>>, <Event blocked=False handled=False native=None source=None sources=[] type='inserted'>)
    795     self.ignore_callback_errors,
    796     self.print_callback_errors,
    797     self,
    798     cb_event=(cb, event),
    799 )

File /opt/user_software/miniconda3/envs/napari-cryolo/lib/python3.10/site-packages/napari/utils/events/event.py:781, in EventEmitter._invoke_callback(self=<napari.utils.events.event.EventEmitter object>, cb=<bound method SelectMetricWidget._handle_insert ...ager._qt.SelectMetric.SelectMetricWidget object>>, event=<Event blocked=False handled=False native=None source=None sources=[] type='inserted'>)
    779 try:
    780     if event is not None:
--> 781         cb(event)
        event = <Event blocked=False handled=False native=None source=None sources=[] type='inserted'>
        cb = <bound method SelectMetricWidget._handle_insert of <box_manager._qt.SelectMetric.SelectMetricWidget object at 0x7ff36c1af370>>
    782     else:
    783         cb()

File /mnt/data/twagner/Projects/napari/src/napari-boxmanager-github/src/box_manager/_qt/SelectMetric.py:723, in SelectMetricWidget._handle_insert(self=<box_manager._qt.SelectMetric.SelectMetricWidget object>, event=<Event blocked=False handled=False native=None source=None sources=[] type='inserted'>)
    720     pass
    722 prev_expansion = self.table_widget.get_expansion_state()
--> 723 self._add_remove_table(layer, ButtonActions.ADD)
        layer = <Shapes layer 'filaments (tomo/*.mrc)' at 0x7ff37719e050>
        ButtonActions.ADD = <ButtonActions.ADD: 0>
        self = <box_manager._qt.SelectMetric.SelectMetricWidget object at 0x7ff36c1af370>
    724 if "set_lock" in layer.metadata and layer.metadata["set_lock"]:
    725     layer.editable = False

File /mnt/data/twagner/Projects/napari/src/napari-boxmanager-github/src/box_manager/_qt/SelectMetric.py:1318, in SelectMetricWidget._add_remove_table(self=<box_manager._qt.SelectMetric.SelectMetricWidget object>, layer=<Shapes layer 'filaments (tomo/*.mrc)'>, action=<ButtonActions.ADD: 0>)
   1314 layer_name = layer.name
   1316 if action == ButtonActions.ADD:
   1317     if self.table_model.add_group(
-> 1318         layer_name, self._prepare_entries(layer, name=layer_name)[0]
        self.table_model = <box_manager._qt.SelectMetric.GroupModel object at 0x7ff36c1af2e0>
        self = <box_manager._qt.SelectMetric.SelectMetricWidget object at 0x7ff36c1af370>
        layer_name = 'filaments (tomo/*.mrc)'
        layer = <Shapes layer 'filaments (tomo/*.mrc)' at 0x7ff37719e050>
   1319     ):
   1320         entries = self._prepare_entries(layer)
   1321         for entry in entries:

File /mnt/data/twagner/Projects/napari/src/napari-boxmanager-github/src/box_manager/_qt/SelectMetric.py:1129, in SelectMetricWidget._prepare_entries(self=<box_manager._qt.SelectMetric.SelectMetricWidget object>, layer=<Shapes layer 'filaments (tomo/*.mrc)'>, name='filaments (tomo/*.mrc)')
   1127     features_copy["identifier"] = "" if name is not None else 0
   1128 else:
-> 1129     assert False, layer.data
        layer = <Shapes layer 'filaments (tomo/*.mrc)' at 0x7ff37719e050>
   1131 range_list = [
   1132     entry for entry in layer.metadata if isinstance(entry, int)
   1133 ]
   1134 full_range = np.arange(
   1135     *self.napari_viewer.dims.range[0], dtype=int
   1136 ).tolist()

AssertionError: []