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juno_ui Runtime Error: ValueError: shape mismatch #60

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stevenlovegrove opened this issue Sep 24, 2024 · 0 comments
Open

juno_ui Runtime Error: ValueError: shape mismatch #60

stevenlovegrove opened this issue Sep 24, 2024 · 0 comments

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@stevenlovegrove
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After following the directions in the readme, I launch juno_ui which opens correctly. When I open a sample (such as astronaut), I see only a white line on the left side of the display area. As soon as I move my mouse over the area, juno_ui crashes with:

WARNING:root:openblas_set_num_threads not found
WARNING: QMainWindowLayout::count: ?
WARNING:vispy:QMainWindowLayout::count: ?
WARNING: Back buffer dpr of 2 doesn't match <NSViewBackingLayer: 0x600000ec7000> contents scale of 1 - updating layer to match.
WARNING:vispy:Back buffer dpr of 2 doesn't match <NSViewBackingLayer: 0x600000ec7000> contents scale of 1 - updating layer to match.
2024-09-24 13:30:51.308 Python[13979:15403776] WARNING: Secure coding is not enabled for restorable state! Enable secure coding by implementing NSApplicationDelegate.applicationSupportsSecureRestorableState: and returning YES.
WARNING: Traceback (most recent call last):
  File "/opt/homebrew/lib/python3.10/site-packages/superqt/utils/_throttler.py", line 286, in _set_future_result
    result = self._func(*self._args[: self._max_args], **self._kwargs)
  File "/opt/homebrew/lib/python3.10/site-packages/superqt/utils/_throttler.py", line 226, in weak_func
    return method(*args, **kwargs)
  File "/opt/homebrew/lib/python3.10/site-packages/napari/_vispy/canvas.py", line 456, in _on_mouse_move
    self._process_mouse_event(mouse_move_callbacks, event)
  File "/opt/homebrew/lib/python3.10/site-packages/napari/_vispy/canvas.py", line 390, in _process_mouse_event
    event.view_direction = self._calculate_view_direction(event.pos)
  File "/opt/homebrew/lib/python3.10/site-packages/napari/_vispy/canvas.py", line 671, in _calculate_view_direction
    view_direction_nd[list(self.viewer.dims.displayed)] = d
ValueError: shape mismatch: value array of shape (3,) could not be broadcast to indexing result of shape (2,)
WARNING:vispy:Traceback (most recent call last):
  File "/opt/homebrew/lib/python3.10/site-packages/superqt/utils/_throttler.py", line 286, in _set_future_result
    result = self._func(*self._args[: self._max_args], **self._kwargs)
  File "/opt/homebrew/lib/python3.10/site-packages/superqt/utils/_throttler.py", line 226, in weak_func
    return method(*args, **kwargs)
  File "/opt/homebrew/lib/python3.10/site-packages/napari/_vispy/canvas.py", line 456, in _on_mouse_move
    self._process_mouse_event(mouse_move_callbacks, event)
  File "/opt/homebrew/lib/python3.10/site-packages/napari/_vispy/canvas.py", line 390, in _process_mouse_event
    event.view_direction = self._calculate_view_direction(event.pos)
  File "/opt/homebrew/lib/python3.10/site-packages/napari/_vispy/canvas.py", line 671, in _calculate_view_direction
    view_direction_nd[list(self.viewer.dims.displayed)] = d
ValueError: shape mismatch: value array of shape (3,) could not be broadcast to indexing result of shape (2,)
fish: Job 1, 'juno_ui' terminated by signal SIGABRT (Abort)
/opt/homebrew/Cellar/[email protected]/3.10.13_2/Frameworks/Python.framework/Versions/3.10/lib/python3.10/multiprocessing/resource_tracker.py:224: UserWarning: resource_tracker: There appear to be 1 leaked semaphore objects to clean up at shutdown
  warnings.warn('resource_tracker: There appear to be %d '

My platform is MacOS in case it is relevant.

Possible solution:
Since the environments.yml file doesn't include pinned versions, I figured this was a dependency incompatibility. I wrote a small script to take the most recent versions of the unpinned deps at the time of 2023-09-01 which appears like a time when this repo may have been more active. This generated a modified environment.yml:

name: juno
channels:
- conda-forge
dependencies:
- python=3.11
- numpy=1.25.2
- scipy=1.11.2
- pandas=2.1.0
- petname=2.6
- matplotlib=3.7.2
- tqdm
- pyyaml=6.0.1
- imageio=2.31.1
- zarr
- dask
- napari=0.4.18
- pytest=7.4.0
- pyqt>=5.12,<6.0

which no longer crashes for me. I'm not sure if it is functionally correct, since I don't know how to use the software, but I thought I'd post in case this is useful for anyone.

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