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InsightSoftwareConsortium / itkwidgets

An elegant Python interface for visualization on the web platform to interactively generate insights into multidimensional images, point sets, and geometry.
https://itkwidgets.readthedocs.io/
Apache License 2.0
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`TypeError` when attempting to view a buffered subimage with `itkwidgets==1.0a35` #678

Open tbirdso opened 1 year ago

tbirdso commented 1 year ago

Overview

Observed an error when attempting to view an itk.Image with itkwidgets==1.0a35.

I am not 100% certain that the error lies in itkwidgets. The stack trace includes ngff_zarr, dask_image, and scipy.

Full Exception Message

> itkwidgets.view(subimage)
Traceback (most recent call last):
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\IPython\core\interactiveshell.py", line 3508, in run_code
    exec(code_obj, self.user_global_ns, self.user_ns)
  File "C:\Users\tom.birdsong\AppData\Local\Temp\ipykernel_9092\2030550360.py", line 2, in <module>
    itkwidgets.view(subimage)
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\itkwidgets\viewer.py", line 465, in view
    viewer = Viewer(data=data, **kwargs)
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\itkwidgets\viewer.py", line 136, in __init__
    data = build_init_data(input_data)
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\itkwidgets\_initialization_params.py", line 88, in build_init_data
    result = _get_viewer_image(data, label=False)
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\itkwidgets\integrations\__init__.py", line 78, in _get_viewer_image
    multiscales = to_multiscales(ngff_image, method=method)
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\ngff_zarr\to_multiscales.py", line 317, in to_multiscales
    images = _downsample_dask_image(
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\ngff_zarr\methods\_dask_image.py", line 396, in _downsample_dask_image
    downscaled_array = dask_image.ndinterp.affine_transform(
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\dask_image\ndinterp\__init__.py", line 93, in affine_transform
    ndimage_affine_transform(np.zeros([0] * image.ndim),
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\scipy\ndimage\_interpolation.py", line 599, in affine_transform
    offset = _ni_support._normalize_sequence(offset, input.ndim)
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\scipy\ndimage\_ni_support.py", line 63, in _normalize_sequence
    if not is_str and isinstance(input, Iterable):
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\abc.py", line 98, in __instancecheck__
    return _abc_instancecheck(cls, instance)
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\abc.py", line 102, in __subclasscheck__
    return _abc_subclasscheck(cls, subclass)
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\abc.py", line 102, in __subclasscheck__
    return _abc_subclasscheck(cls, subclass)
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\typing_extensions.py", line 583, in __subclasscheck__
    return super().__subclasscheck__(other)
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\abc.py", line 102, in __subclasscheck__
    return _abc_subclasscheck(cls, subclass)
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\typing_extensions.py", line 639, in _proto_hook
    raise TypeError("Instance and class checks can only be used with"
TypeError: Instance and class checks can only be used with @runtime_checkable protocols

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\IPython\core\interactiveshell.py", line 2105, in showtraceback
    stb = self.InteractiveTB.structured_traceback(
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\IPython\core\ultratb.py", line 1396, in structured_traceback
    return FormattedTB.structured_traceback(
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\IPython\core\ultratb.py", line 1287, in structured_traceback
    return VerboseTB.structured_traceback(
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\IPython\core\ultratb.py", line 1140, in structured_traceback
    formatted_exception = self.format_exception_as_a_whole(etype, evalue, etb, number_of_lines_of_context,
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\IPython\core\ultratb.py", line 1055, in format_exception_as_a_whole
    frames.append(self.format_record(record))
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\IPython\core\ultratb.py", line 955, in format_record
    frame_info.lines, Colors, self.has_colors, lvals
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\IPython\core\ultratb.py", line 778, in lines
    return self._sd.lines
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\stack_data\utils.py", line 144, in cached_property_wrapper
    value = obj.__dict__[self.func.__name__] = self.func(obj)
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\stack_data\core.py", line 734, in lines
    pieces = self.included_pieces
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\stack_data\utils.py", line 144, in cached_property_wrapper
    value = obj.__dict__[self.func.__name__] = self.func(obj)
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\stack_data\core.py", line 681, in included_pieces
    pos = scope_pieces.index(self.executing_piece)
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\stack_data\utils.py", line 144, in cached_property_wrapper
    value = obj.__dict__[self.func.__name__] = self.func(obj)
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\stack_data\core.py", line 660, in executing_piece
    return only(
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\executing\executing.py", line 182, in only
    if isinstance(it, Sized):
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\typing.py", line 769, in __instancecheck__
    return self.__subclasscheck__(type(obj))
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\typing.py", line 774, in __subclasscheck__
    return issubclass(cls, self.__origin__)
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\abc.py", line 102, in __subclasscheck__
    return _abc_subclasscheck(cls, subclass)
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\abc.py", line 102, in __subclasscheck__
    return _abc_subclasscheck(cls, subclass)
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\typing_extensions.py", line 583, in __subclasscheck__
    return super().__subclasscheck__(other)
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\abc.py", line 102, in __subclasscheck__
    return _abc_subclasscheck(cls, subclass)
  File "C:\Users\tom.birdsong\Anaconda3\envs\venv-itk\lib\site-packages\typing_extensions.py", line 639, in _proto_hook
    raise TypeError("Instance and class checks can only be used with"
TypeError: Instance and class checks can only be used with @runtime_checkable protocols

Platform Information

Windows 10 Python 3.8.5 itk == 5.4rc1 itkwidgets == 1.0a35 dask == 2023.5.0 ~2022.8.0~ dask-image == 2023.3.0 ~2021.12.0~ ngff-zarr == 0.4.6 scipy == 1.10.1

Additional Details

The subimage was extracted from a requested/buffered region in a larger image using itk.extract_image_filter.

> print(subimage)
Image (00000247B1238600)
  RTTI typeinfo:   class itk::Image<float,3>
  Reference Count: 1
  Modified Time: 4416
  Debug: Off
  Object Name: 
  Observers: 
    none
  Source: (none)
  Source output name: (none)
  Release Data: Off
  Data Released: False
  Global Release Data: Off
  PipelineMTime: 4404
  UpdateMTime: 4415
  RealTimeStamp: 0 seconds 
  LargestPossibleRegion: 
    Dimension: 3
    Index: [6321, 9160, 2699]
    Size: [556, 556, 501]
  BufferedRegion: 
    Dimension: 3
    Index: [6321, 9160, 2699]
    Size: [556, 556, 501]
  RequestedRegion: 
    Dimension: 3
    Index: [6321, 9160, 2699]
    Size: [556, 556, 501]
  Spacing: [0.0018, 0.0018, 0.002]
  Origin: [13.3776, 18.4878, 7.398]
  Direction: 
-1 0 0
0 -1 0
0 0 -1

  IndexToPointMatrix: 
-0.0018 0 0
0 -0.0018 0
0 0 -0.002

  PointToIndexMatrix: 
-555.556 0 0
0 -555.556 0
0 0 -500

  Inverse Direction: 
-1 0 0
0 -1 0
0 0 -1

  PixelContainer: 
    ImportImageContainer (00000247B5450870)
      RTTI typeinfo:   class itk::ImportImageContainer<unsigned __int64,float>
      Reference Count: 1
      Modified Time: 4413
      Debug: Off
      Object Name: 
      Observers: 
        none
      Pointer: 0000024805EDE040
      Container manages memory: true
      Size: 154877136
      Capacity: 154877136

EDIT: Updated platform information.

thewtex commented 1 year ago

@tbirdso thanks for the report!

Looks likely to be a dask-image / scipy issue. For reference, could you please add:

?

tbirdso commented 1 year ago

Looks likely to be a dask-image / scipy issue. For reference, could you please add:

Sure thing, I've added this information to the issue summary. My dask-image version looks old, will attempt to reproduce with the most recent version.

EDIT: I am able to reproduce with the latest version of dask-image. I have updated the issue summary accordingly.