Consider adding support for multiscale images (e.g. OME-Zarr)

[uermel]

Hi nninteractive team, thank you for this awesome model and plugin!

I tried using it with an OME-Zarr image (Zarr v2, OME-Zarr v0.4) like this:

napari pda2021-02-12-10.zarr -w napari-nninteractive

You can download it from here: s3://cryoet-data-portal-public/10014/pda2021-02-12-10/Reconstructions/VoxelSpacing13.496/Tomograms/100/pda2021-02-12-10.zarr/ (info on the content here)

When pressing "Initialize" I unfortunately ran into an error related to group vs. array indexing (full trace below).

I think OME-Zarr/Zarr would be great formats to support in the biomedical space!

Full trace

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
File redacted/anaconda/23.1.0-3/x86_64/envs/nninteractive/lib/python3.12/site-packages/napari_nninteractive/widget_main.py:77, in nnInteractiveWidget.on_init(self=, *args=(False,), **kwargs={})
     70     self.session.initialize_from_trained_model_folder(
     71         self.checkpoint_path,
     72         0,
     73         "checkpoint_final.pth",
     74     )
     76 _data = self._viewer.layers[self.session_cfg["name"]].data
---> 77 _data = _data[np.newaxis, ...]
        _data = 
        np.newaxis, ... = (None, Ellipsis)
        np.newaxis = None
        np =      79 if self.session_cfg["ndim_source"] == 2:
     80     _data = _data[np.newaxis, ...]
File redacted/anaconda/23.1.0-3/x86_64/envs/nninteractive/lib/python3.12/site-packages/napari/utils/_proxies.py:150, in PublicOnlyProxy.getitem(self=<MultiScaleData at 0x14ae68d4c7d0. 3 levels, 'fl...(175, 720, 511), (88, 360, 256), (44, 180, 128))>, key=(None, Ellipsis))

149 def getitem(self, key: Any) -> Any:

--> 150     return self.create(super().getitem(key))

self = <MultiScaleData at 0x14ae68d4c7d0. 3 levels, 'float32', shapes: ((175, 720, 511), (88, 360, 256), (44, 180, 128))>

key = (None, Ellipsis)

File redacted/anaconda/23.1.0-3/x86_64/envs/nninteractive/lib/python3.12/site-packages/napari/layers/_multiscale_data.py:76, in MultiScaleData.getitem(self=<MultiScaleData at 0x14ae68d4c7d0. 3 levels, 'fl...(175, 720, 511), (88, 360, 256), (44, 180, 128))>, key=(None, Ellipsis))

72 def getitem(  # type: ignore [override]

73     self, key: Union[int, tuple[slice, ...]]

74 ) -> LayerDataProtocol:

75     """Multiscale indexing."""

---> 76     return self._data[key]

self._data = [dask.array<from-zarr, shape=(175, 720, 511), dtype=float32, chunksize=(175, 256, 256), chunktype=numpy.ndarray>, dask.array<from-zarr, shape=(88, 360, 256), dtype=float32, chunksize=(88, 256, 256), chunktype=numpy.ndarray>, dask.array<from-zarr, shape=(44, 180, 128), dtype=float32, chunksize=(44, 180, 128), chunktype=numpy.ndarray>]

key = (None, Ellipsis)

self = <MultiScaleData at 0x14ae68d4c7d0. 3 levels, 'float32', shapes: ((175, 720, 511), (88, 360, 256), (44, 180, 128))>

TypeError: list indices must be integers or slices, not tuple

[FabianIsensee]

How would you suggest we treat multiscale images? Intuitively I would say we just pick the best resolution as our AutoZoom will perform downscaling at will, but this feature also has its limits (max zoom factor 4, increased resource usage, run time).
Alternatively, in the short term, you can of course convert multiscale images to a series of 3D images and pick the one you prefer

[uermel]

I think being able to choose scale from your dropdown would be great.

There is another issue for this to work I found while attempting: It is possible to open a specific scale from an OME-Zarr file like this:

napari pda2021-02-12-10.zarr/0 -w napari-nninteractive

In this case, a simple image layer is added. "Initialize" works. However, the image layer data in this case is stored in a dask array, not a numpy array, causing the trace below when attempting to scribble. Maybe a simple wrap of layer data in np.array would solve this.

Full trace

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
File ~/miniforge3/envs/nninteractive/lib/python3.12/site-packages/vispy/app/backends/_qt.py:506, in QtBaseCanvasBackend.mouseReleaseEvent(self=, ev=)
    504 if self._vispy_canvas is None:
    505     return
--> 506 self._vispy_mouse_release(
        self = 
        ev = 
        BUTTONMAP = {0: 0, 1: 1, 2: 2, 4: 3, 8: 4, 16: 5}    507     native=ev,
    508     pos=_get_event_xy(ev),
    509     button=BUTTONMAP[ev.button()],
    510     modifiers=self._modifiers(ev),
    511 )
File ~/miniforge3/envs/nninteractive/lib/python3.12/site-packages/vispy/app/base.py:224, in BaseCanvasBackend._vispy_mouse_release(self=<vispy.app.backends._qt.CanvasBackendDesktop object>, **kwargs={'button': 1, 'buttons': [1], 'last_event': , 'last_mouse_press': None, 'modifiers': (), 'native': <PyQt5.QtGui.QMouseEvent object>, 'pos': (1390, 576), 'press_event': })

220 def _vispy_mouse_release(self, **kwargs):

221     # default method for delivering mouse release events to the canvas

222     kwargs.update(self._vispy_mouse_data)

--> 224     ev = self._vispy_canvas.events.mouse_release(**kwargs)

self._vispy_canvas.events.mouse_release = <vispy.util.event.EventEmitter object at 0x7bb0383ef0e0>

kwargs = {'native': <PyQt5.QtGui.QMouseEvent object at 0x7bb036f280e0>, 'pos': (1390, 576), 'button': 1, 'modifiers': (), 'buttons': [1], 'press_event': <MouseEvent blocked=False button=1 buttons=[1] delta=[0. 0.] handled=False is_dragging=False last_event=MouseEvent modifiers=() native=<PyQt5.QtGui.QMouseEvent object at 0x7bb036f280e0> pos=[1328  469] press_event=None source=None sources=[] time=1741878794.3510888 type=mouse_press>, 'last_event': <MouseEvent blocked=False button=1 buttons=[1] delta=[0. 0.] handled=False is_dragging=True last_event=MouseEvent modifiers=() native=<PyQt5.QtGui.QMouseEvent object at 0x7bb036f280e0> pos=[1390  576] press_event=MouseEvent source=None sources=[] time=1741878794.5429878 type=mouse_move>, 'last_mouse_press': None}

self = <vispy.app.backends._qt.CanvasBackendDesktop object at 0x7bb036f28830>

self._vispy_canvas.events = <vispy.util.event.EmitterGroup object at 0x7bb038f2e270>

self._vispy_canvas = <NapariSceneCanvas (PyQt5) at 0x7bb0386754c0>    225     if (self._vispy_mouse_data['press_event']

226             and self._vispy_mouse_data['press_event'].button == ev.button):

227         self._vispy_mouse_data['press_event'] = None
File ~/miniforge3/envs/nninteractive/lib/python3.12/site-packages/vispy/util/event.py:453, in EventEmitter.call(self=<vispy.util.event.EventEmitter object>, *args=(), **kwargs={'button': 1, 'buttons': [1], 'last_event': , 'last_mouse_press': None, 'modifiers': (), 'native': <PyQt5.QtGui.QMouseEvent object>, 'pos': (1390, 576), 'press_event': })

450 if self._emitting > 1:

451     raise RuntimeError('EventEmitter loop detected!')

--> 453 self._invoke_callback(cb, event)

event = <MouseEvent blocked=False button=1 buttons=[1] delta=[0. 0.] handled=False is_dragging=True last_event=MouseEvent modifiers=() native=<PyQt5.QtGui.QMouseEvent object at 0x7bb036f280e0> pos=[1390  576] press_event=MouseEvent source=None sources=[] time=1741878794.5762613 type=mouse_release>

self = <vispy.util.event.EventEmitter object at 0x7bb0383ef0e0>

cb = <bound method VispyCanvas._on_mouse_release of <napari._vispy.canvas.VispyCanvas object at 0x7bb0383b3c50>>    454 if event.blocked:

455     break
File ~/miniforge3/envs/nninteractive/lib/python3.12/site-packages/vispy/util/event.py:471, in EventEmitter._invoke_callback(self=<vispy.util.event.EventEmitter object>, cb=<bound method VispyCanvas._on_mouse_release of <napari._vispy.canvas.VispyCanvas object>>, event=)

469     cb(event)

470 except Exception:

--> 471     _handle_exception(self.ignore_callback_errors,

self = <vispy.util.event.EventEmitter object at 0x7bb0383ef0e0>

cb = <bound method VispyCanvas._on_mouse_release of <napari._vispy.canvas.VispyCanvas object at 0x7bb0383b3c50>>

event = <MouseEvent blocked=False button=1 buttons=[1] delta=[0. 0.] handled=False is_dragging=True last_event=MouseEvent modifiers=() native=<PyQt5.QtGui.QMouseEvent object at 0x7bb036f280e0> pos=[1390  576] press_event=MouseEvent source=None sources=[] time=1741878794.5762613 type=mouse_release>

(cb, event) = (<bound method VispyCanvas._on_mouse_release of <napari._vispy.canvas.VispyCanvas object at 0x7bb0383b3c50>>, <MouseEvent blocked=False button=1 buttons=[1] delta=[0. 0.] handled=False is_dragging=True last_event=MouseEvent modifiers=() native=<PyQt5.QtGui.QMouseEvent object at 0x7bb036f280e0> pos=[1390  576] press_event=MouseEvent source=None sources=[] time=1741878794.5762613 type=mouse_release>)    472                       self.print_callback_errors,

473                       self, cb_event=(cb, event))
File ~/miniforge3/envs/nninteractive/lib/python3.12/site-packages/vispy/util/event.py:469, in EventEmitter._invoke_callback(self=<vispy.util.event.EventEmitter object>, cb=<bound method VispyCanvas._on_mouse_release of <napari._vispy.canvas.VispyCanvas object>>, event=)

467 def _invoke_callback(self, cb, event):

468     try:

--> 469         cb(event)

cb = <bound method VispyCanvas._on_mouse_release of <napari._vispy.canvas.VispyCanvas object at 0x7bb0383b3c50>>

event = <MouseEvent blocked=False button=1 buttons=[1] delta=[0. 0.] handled=False is_dragging=True last_event=MouseEvent modifiers=() native=<PyQt5.QtGui.QMouseEvent object at 0x7bb036f280e0> pos=[1390  576] press_event=MouseEvent source=None sources=[] time=1741878794.5762613 type=mouse_release>    470     except Exception:

471         _handle_exception(self.ignore_callback_errors,

472                           self.print_callback_errors,

473                           self, cb_event=(cb, event))
File ~/miniforge3/envs/nninteractive/lib/python3.12/site-packages/napari/_vispy/canvas.py:484, in VispyCanvas._on_mouse_release(self=<napari._vispy.canvas.VispyCanvas object>, event=)

472 def _on_mouse_release(self, event: MouseEvent) -> None:

473     """Called whenever mouse released in canvas.

474

475     Parameters---------------------------------------------------------------------------

TypeError                                 Traceback (most recent call last)

File redacted/anaconda/23.1.0-3/x86_64/envs/nninteractive/lib/python3.12/site-packages/napari_nninteractive/widget_main.py:77, in nnInteractiveWidget.on_init(self=<napari_nninteractive.widget_main.nnInteractiveWidget object>, *args=(False,), **kwargs={})

70     self.session.initialize_from_trained_model_folder(

71         self.checkpoint_path,

72         0,

73         "checkpoint_final.pth",

74     )

76 _data = self._viewer.layers[self.session_cfg["name"]].data

---> 77 _data = _data[np.newaxis, ...]

_data = <MultiScaleData at 0x14ae68d4c7d0. 3 levels, 'float32', shapes: ((175, 720, 511), (88, 360, 256), (44, 180, 128))>

np.newaxis, ... = (None, Ellipsis)

np.newaxis = None

np = <module 'numpy' from 'redacted/anaconda/23.1.0-3/x86_64/envs/nninteractive/lib/python3.12/site-packages/numpy/init.py'>     79 if self.session_cfg["ndim_source"] == 2:

80     _data = _data[np.newaxis, ...]
File redacted/anaconda/23.1.0-3/x86_64/envs/nninteractive/lib/python3.12/site-packages/napari/utils/_proxies.py:150, in PublicOnlyProxy.getitem(self=<MultiScaleData at 0x14ae68d4c7d0. 3 levels, 'fl...(175, 720, 511), (88, 360, 256), (44, 180, 128))>, key=(None, Ellipsis))

149 def getitem(self, key: Any) -> Any:

--> 150     return self.create(super().getitem(key))

self = <MultiScaleData at 0x14ae68d4c7d0. 3 levels, 'float32', shapes: ((175, 720, 511), (88, 360, 256), (44, 180, 128))>

key = (None, Ellipsis)

File redacted/anaconda/23.1.0-3/x86_64/envs/nninteractive/lib/python3.12/site-packages/napari/layers/_multiscale_data.py:76, in MultiScaleData.getitem(self=<MultiScaleData at 0x14ae68d4c7d0. 3 levels, 'fl...(175, 720, 511), (88, 360, 256), (44, 180, 128))>, key=(None, Ellipsis))

72 def getitem(  # type: ignore [override]

73     self, key: Union[int, tuple[slice, ...]]

74 ) -> LayerDataProtocol:

75     """Multiscale indexing."""

---> 76     return self._data[key]

self._data = [dask.array<from-zarr, shape=(175, 720, 511), dtype=float32, chunksize=(175, 256, 256), chunktype=numpy.ndarray>, dask.array<from-zarr, shape=(88, 360, 256), dtype=float32, chunksize=(88, 256, 256), chunktype=numpy.ndarray>, dask.array<from-zarr, shape=(44, 180, 128), dtype=float32, chunksize=(44, 180, 128), chunktype=numpy.ndarray>]

key = (None, Ellipsis)

self = <MultiScaleData at 0x14ae68d4c7d0. 3 levels, 'float32', shapes: ((175, 720, 511), (88, 360, 256), (44, 180, 128))>

TypeError: list indices must be integers or slices, not tuple

(...)    482     None

483     """

--> 484     self._process_mouse_event(mouse_release_callbacks, event)

event = <MouseEvent blocked=False button=1 buttons=[1] delta=[0. 0.] handled=False is_dragging=True last_event=MouseEvent modifiers=() native=<PyQt5.QtGui.QMouseEvent object at 0x7bb036f280e0> pos=[1390  576] press_event=MouseEvent source=None sources=[] time=1741878794.5762613 type=mouse_release>

self = <napari._vispy.canvas.VispyCanvas object at 0x7bb0383b3c50>

File ~/miniforge3/envs/nninteractive/lib/python3.12/site-packages/napari/_vispy/canvas.py:417, in VispyCanvas._process_mouse_event(self=<napari._vispy.canvas.VispyCanvas object>, mouse_callbacks=, event=<ReadOnlyWrapper at 0x7bb02e681e00 for MouseEvent>)

415 layer = self.viewer.layers.selection.active

416 if layer is not None:

--> 417     mouse_callbacks(layer, event)

event = <ReadOnlyWrapper at 0x7bb02e681e00 for MouseEvent at 0x7bafc360d550>

layer = <ScribbleLayer layer 'nnInteractive - Scribble Layer' at 0x7bafa7386c90>

mouse_callbacks = <function mouse_release_callbacks at 0x7bb03beaafc0>

File ~/miniforge3/envs/nninteractive/lib/python3.12/site-packages/napari/utils/interactions.py:216, in mouse_release_callbacks(obj=<ScribbleLayer layer 'nnInteractive - Scribble Layer'>, event=<ReadOnlyWrapper at 0x7bb02e681e00 for MouseEvent>)

213 obj._persisted_mouse_event[gen].wrapped = event

214 with contextlib.suppress(StopIteration):

215     # Run last part of the function to trigger release event

--> 216     next(gen)

gen = <generator object draw at 0x7baf50596c40>    217 # Finally delete the generator and stored event

218 del obj._mouse_drag_gen[func]
File ~/miniforge3/envs/nninteractive/lib/python3.12/site-packages/napari/layers/labels/_labels_mouse_bindings.py:37, in draw(layer=<ScribbleLayer layer 'nnInteractive - Scribble Layer'>, event=<ReadOnlyWrapper at 0x7bb02e60b500 for ReadOnlyWrapper>)

34     new_label = layer.selected_label

36 # on press

---> 37 with layer.block_history():

layer = <ScribbleLayer layer 'nnInteractive - Scribble Layer' at 0x7bafa7386c90>     38     layer._draw(new_label, coordinates, coordinates)

39     yield
File ~/miniforge3/envs/nninteractive/lib/python3.12/contextlib.py:144, in _GeneratorContextManager.exit(self=<contextlib._GeneratorContextManager object>, typ=None, value=None, traceback=None)

142 if typ is None:

143     try:

--> 144         next(self.gen)

self.gen = <generator object Labels.block_history at 0x7baf5051b5e0>

self = <contextlib._GeneratorContextManager object at 0x7bafc3652e40>    145     except StopIteration:

146         return False
File ~/miniforge3/envs/nninteractive/lib/python3.12/site-packages/napari/layers/labels/labels.py:1008, in Labels.block_history(self=<ScribbleLayer layer 'nnInteractive - Scribble Layer'>)

1006 try:

1007     yield

-> 1008     self._commit_staged_history()

self = <ScribbleLayer layer 'nnInteractive - Scribble Layer' at 0x7bafa7386c90>   1009 finally:

1010     self._block_history = prev
File ~/miniforge3/envs/nninteractive/lib/python3.12/site-packages/napari_nninteractive/layers/scribble_layer.py:65, in ScribbleLayer._commit_staged_history(self=<ScribbleLayer layer 'nnInteractive - Scribble Layer'>)

63 super()._commit_staged_history()

64 self._is_free = False

---> 65 self.events.finished(action=ActionType.ADDED, value="ADD")

self = <ScribbleLayer layer 'nnInteractive - Scribble Layer' at 0x7bafa7386c90>

self.events.finished = <napari.utils.events.event.EventEmitter object at 0x7baf501b7f50>

self.events = <napari.utils.events.event.EmitterGroup object at 0x7baf501ee480>

ActionType.ADDED = <ActionType.ADDED: 'added'>

ActionType = <enum 'ActionType'>

File ~/miniforge3/envs/nninteractive/lib/python3.12/site-packages/napari/utils/events/event.py:764, in EventEmitter.call(self=<napari.utils.events.event.EventEmitter object>, *args=(), **kwargs={'action': <ActionType.ADDED: 'added'>, 'value': 'ADD'})

761     self._block_counter.update([cb])

762     continue

--> 764 self._invoke_callback(cb, event if pass_event else None)

event = 

self = <napari.utils.events.event.EventEmitter object at 0x7baf501b7f50>

cb = <bound method LayerControls.on_interaction of <napari_nninteractive.widget_main.nnInteractiveWidget object at 0x7baf9caa1be0>>

pass_event = True    765 if event.blocked:

766     break
File ~/miniforge3/envs/nninteractive/lib/python3.12/site-packages/napari/utils/events/event.py:802, in EventEmitter._invoke_callback(self=<napari.utils.events.event.EventEmitter object>, cb=<bound method LayerControls.on_interaction of <n...eractive.widget_main.nnInteractiveWidget object>>, event=)

800     self.disconnect(cb)

801     return

--> 802 _handle_exception(

self = <napari.utils.events.event.EventEmitter object at 0x7baf501b7f50>

event = 

cb = <bound method LayerControls.on_interaction of <napari_nninteractive.widget_main.nnInteractiveWidget object at 0x7baf9caa1be0>>

(cb, event) = (<bound method LayerControls.on_interaction of <napari_nninteractive.widget_main.nnInteractiveWidget object at 0x7baf9caa1be0>>, )    803     self.ignore_callback_errors,

804     self.print_callback_errors,

805     self,

806     cb_event=(cb, event),

807 )
File ~/miniforge3/envs/nninteractive/lib/python3.12/site-packages/napari/utils/events/event.py:789, in EventEmitter._invoke_callback(self=<napari.utils.events.event.EventEmitter object>, cb=<bound method LayerControls.on_interaction of <n...eractive.widget_main.nnInteractiveWidget object>>, event=)

787 try:

788     if event is not None:

--> 789         cb(event)

event = 

cb = <bound method LayerControls.on_interaction of <napari_nninteractive.widget_main.nnInteractiveWidget object at 0x7baf9caa1be0>>    790     else:

791         cb()
File ~/miniforge3/envs/nninteractive/lib/python3.12/site-packages/napari_nninteractive/widget_controls.py:378, in LayerControls.on_interaction(self=<napari_nninteractive.widget_main.nnInteractiveWidget object>, event=)

371 if (

372     self.add_ckbx.isChecked()

373     and event.action == ActionType.ADDED

374     and not self._viewer.layers[event.source.name].is_free()

375 ):

376     self._viewer.layers[event.source.name].refresh()

--> 378     self.add_interaction()

self = <napari_nninteractive.widget_main.nnInteractiveWidget object at 0x7baf9caa1be0>

File ~/miniforge3/envs/nninteractive/lib/python3.12/site-packages/napari_nninteractive/widget_main.py:178, in nnInteractiveWidget.add_interaction(self=<napari_nninteractive.widget_main.nnInteractiveWidget object>)

176     self.session.add_bbox_interaction(bbox, _prompt, _auto_run)

177 elif _index == 2:

--> 178     self.session.add_scribble_interaction(data, _prompt, _auto_run)

data = array([[[0, 0, ..., 0, 0],

[0, 0, ..., 0, 0],

...,

[0, 0, ..., 0, 0],

[0, 0, ..., 0, 0]],
   [[0, 0, ..., 0, 0],
    [0, 0, ..., 0, 0],
    ...,
    [0, 0, ..., 0, 0],
    [0, 0, ..., 0, 0]],

   ...,

   [[0, 0, ..., 0, 0],
    [0, 0, ..., 0, 0],
    ...,
    [0, 0, ..., 0, 0],
    [0, 0, ..., 0, 0]],

   [[0, 0, ..., 0, 0],
    [0, 0, ..., 0, 0],
    ...,
    [0, 0, ..., 0, 0],
    [0, 0, ..., 0, 0]]], dtype=uint8)
    self = <napari_nninteractive.widget_main.nnInteractiveWidget object at 0x7baf9caa1be0>
    _prompt = True
    _auto_run = True
    self.session = <nnInteractive.inference.inference_session.nnInteractiveInferenceSession object at 0x7baf9c830650>    179 elif _index == 3:
180     self.session.add_lasso_interaction(data, _prompt, _auto_run)

File ~/miniforge3/envs/nninteractive/lib/python3.12/site-packages/nnInteractive/inference/inference_session.py:277, in nnInteractiveInferenceSession.add_scribble_interaction(self=<nnInteractive.inference.inference_session.nnInteractiveInferenceSession object>, scribble_image=array([[[0, 0, ..., 0, 0],

[0, 0, ..., 0... 0, 0],

[0, 0, ..., 0, 0]]], dtype=uint8), include_interaction=True, run_prediction=True)

275 def add_scribble_interaction(self, scribble_image: np.ndarray,  include_interaction: bool, run_prediction: bool = True):

276     assert all([i == j for i, j in zip(self.original_image_shape[1:], scribble_image.shape)]), f'Given scribble image must match input image shape. Input image was: {self.original_image_shape[1:]}, given: {scribble_image.shape}'

--> 277     self._finish_preprocessing_and_initialize_interactions()

self = <nnInteractive.inference.inference_session.nnInteractiveInferenceSession object at 0x7baf9c830650>    279     scribble_image = torch.from_numpy(scribble_image)

281     # crop (as in preprocessing)
File ~/miniforge3/envs/nninteractive/lib/python3.12/site-packages/nnInteractive/inference/inference_session.py:107, in nnInteractiveInferenceSession._finish_preprocessing_and_initialize_interactions(self=<nnInteractive.inference.inference_session.nnInteractiveInferenceSession object>)

101 """

102 Block until both the image preprocessing and the interactions tensor initialization

103 are finished.

104 """

105 if self.preprocess_future is not None:

106     # Wait for image preprocessing to complete.

--> 107     self.preprocess_future.result()

self.preprocess_future = <Future at 0x7bb0f057c830 state=finished raised TypeError>

self = <nnInteractive.inference.inference_session.nnInteractiveInferenceSession object at 0x7baf9c830650>    108     del self.preprocess_future

109     self.preprocess_future = None
File ~/miniforge3/envs/nninteractive/lib/python3.12/concurrent/futures/_base.py:449, in Future.result(self=None, timeout=None)

447     raise CancelledError()

448 elif self._state == FINISHED:

--> 449     return self.__get_result()

self = None    451 self._condition.wait(timeout)

453 if self._state in [CANCELLED, CANCELLED_AND_NOTIFIED]:
File ~/miniforge3/envs/nninteractive/lib/python3.12/concurrent/futures/_base.py:401, in Future.__get_result(self=None)

399 if self._exception:

400     try:

--> 401         raise self._exception

self = None    402     finally:

403         # Break a reference cycle with the exception in self._exception

404         self = None
File ~/miniforge3/envs/nninteractive/lib/python3.12/concurrent/futures/thread.py:59, in _WorkItem.run(self=None)

56     return

58 try:

---> 59     result = self.fn(*self.args, **self.kwargs)

self = None     60 except BaseException as exc:

61     self.future.set_exception(exc)
File ~/miniforge3/envs/nninteractive/lib/python3.12/site-packages/nnInteractive/inference/inference_session.py:149, in nnInteractiveInferenceSession._background_set_image(self=<nnInteractive.inference.inference_session.nnInteractiveInferenceSession object>, image=dask.array<getitem, shape=(1, 175, 720, 511), dt...size=(1, 175, 256, 256), chunktype=numpy.ndarray>, image_properties={'spacing': array([1., 1., 1.])})

147 def _background_set_image(self, image: np.ndarray, image_properties: dict):

148     # Convert and clone the image tensor.

--> 149     image_torch = torch.clone(torch.from_numpy(image))

image = dask.array<getitem, shape=(1, 175, 720, 511), dtype=float32, chunksize=(1, 175, 256, 256), chunktype=numpy.ndarray>    151     # Crop to nonzero region.

152     if self.verbose:
TypeError: expected np.ndarray (got Array)