Error is raised if no cells are detected.

[adamltyson]

Full traceback

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
File ~/miniconda3/envs/image-analysis3/lib/python3.10/site-packages/cellfinder_napari/detect/detect.py:190, in detect_widget.<locals>.widget.<locals>.<lambda>(points=[])
    179 misc_inputs = MiscInputs(
    180     start_plane, end_plane, n_free_cpus, analyse_local, debug
    181 )
    183 worker = Worker(
    184     data_inputs,
    185     detection_inputs,
    186     classification_inputs,
    187     misc_inputs,
    188 )
    189 worker.returned.connect(
--> 190     lambda points: add_layers(points, viewer=viewer)
        points = []
        viewer = Viewer(axes=Axes(visible=False, labels=True, colored=True, dashed=False, arrows=True), camera=Camera(center=(0.0, 1933.5, 2707.5), zoom=0.20065020022629942, angles=(0.0, 0.0, 90.0), perspective=0.0, interactive=True), cursor=Cursor(position=(15.0, 3802.424157249758, -659.055301633289), scaled=True, size=1, style=<CursorStyle.STANDARD: 'standard'>), dims=Dims(ndim=3, ndisplay=2, last_used=0, range=((0.0, 30.0, 1.0), (0.0, 3868.0, 1.0), (0.0, 5416.0, 1.0)), current_step=(15, 1934, 2708), order=(0, 1, 2), axis_labels=('0', '1', '2')), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False), layers=[<Image layer 'ch02' at 0x7f707f2507f0>, <Image layer 'ch00' at 0x7f707dd48ac0>], 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 0x7f7035072800>, transform_drag=<napari.utils.transforms.transforms.Affine object at 0x7f7035072860>, transform_final=<napari.utils.transforms.transforms.Affine object at 0x7f70350728c0>, transform=<napari.utils.transforms.transforms.Affine object at 0x7f7035072920>, 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 0x7f70bbe441f0>], mouse_drag_callbacks=[<function InteractionBoxMouseBindings.initialize_mouse_events.<locals>.mouse_drag at 0x7f70bbe45090>], mouse_double_click_callbacks=[], mouse_wheel_callbacks=[<function dims_scroll at 0x7f7037d33880>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, keymap={'Shift': <function InteractionBoxMouseBindings.initialize_key_events.<locals>.hold_to_lock_aspect_ratio at 0x7f70bbe87910>, 'Control-Shift-R': <function InteractionBoxMouseBindings._reset_active_layer_affine at 0x7f70bbf1d630>, 'Control-Shift-A': <function InteractionBoxMouseBindings._transform_active_layer at 0x7f70bbf1d5a0>})
    191 )
    193 # Make sure if the worker emits an error, it is propagated to this thread
    194 def reraise(e):

File ~/miniconda3/envs/image-analysis3/lib/python3.10/site-packages/cellfinder_napari/utils.py:55, in add_layers(points=[], viewer=Viewer(axes=Axes(visible=False, labels=True, col...ings._transform_active_layer at 0x7f70bbf1d5a0>}))
     51 def add_layers(points: List[Cell], viewer: napari.Viewer) -> None:
     52     """
     53     Adds classified cell candidates as two separate point layers to the napari viewer.
     54     """
---> 55     detected, rejected = cells_to_array(points)
        points = []
     57     viewer.add_points(
     58         rejected,
     59         name="Rejected",
   (...)
     66         metadata=dict(point_type=Cell.UNKNOWN),
     67     )
     68     viewer.add_points(
     69         detected,
     70         name="Detected",
   (...)
     76         metadata=dict(point_type=Cell.CELL),
     77     )

File ~/miniconda3/envs/image-analysis3/lib/python3.10/site-packages/cellfinder_napari/utils.py:97, in cells_to_array(cells=[])
     95 def cells_to_array(cells: List[Cell]) -> Tuple[np.ndarray, np.ndarray]:
     96     df = pd.DataFrame([c.to_dict() for c in cells])
---> 97     points = cells_df_as_np(df[df["type"] == Cell.CELL])
        df = Empty DataFrame
Columns: []
Index: []
        Cell.CELL = 2
     98     rejected = cells_df_as_np(df[df["type"] == Cell.UNKNOWN])
     99     return points, rejected

File ~/miniconda3/envs/image-analysis3/lib/python3.10/site-packages/pandas/core/frame.py:3761, in DataFrame.__getitem__(self=Empty DataFrame
Columns: []
Index: [], key='type')
   3759 if self.columns.nlevels > 1:
   3760     return self._getitem_multilevel(key)
-> 3761 indexer = self.columns.get_loc(key)
        key = 'type'
        self = Empty DataFrame
Columns: []
Index: []
   3762 if is_integer(indexer):
   3763     indexer = [indexer]

File ~/miniconda3/envs/image-analysis3/lib/python3.10/site-packages/pandas/core/indexes/range.py:349, in RangeIndex.get_loc(self=RangeIndex(start=0, stop=0, step=1), key='type')
    347         raise KeyError(key) from err
    348 if isinstance(key, Hashable):
--> 349     raise KeyError(key)
        key = 'type'
    350 self._check_indexing_error(key)
    351 raise KeyError(key)

KeyError: 'type'