Multiscale image visualization #352
Description
Hi! I was testing with visualization of multiscale images. However, I cannot make this simple example work. Any tips?
I'm using the latest 0.5.5 release version.
Example code:
import numpy as np from spatialdata import SpatialData from spatialdata.models import Image2DModel # A sample multiscale image img = np.random.randint(0, 255, size=(3,2000, 2000), dtype=np.uint8) multiscale_image = Image2DModel.parse(img, dims=("c","y","x"), c_coords=("r", "g", "b"), scale_factors=[2,4], chunks=(3,256,256)) sdata = SpatialData(images={"img": multiscale_image}) from napari_spatialdata import Interactive interactive = Interactive(sdata) interactive.run()The error will occur once I select the 'img' element in napari.
Traceback (most recent call last): File "/.venv/lib/python3.12/site-packages/napari_spatialdata/_sdata_widgets.py", line 145, in run layer = self.sdata_widget.viewer_model.get_sdata_image( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/.venv/lib/python3.12/site-packages/napari_spatialdata/_viewer.py", line 468, in get_sdata_image rgb_image, rgb = _adjust_channels_order(element=sdata.images[original_name]) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/.venv/lib/python3.12/site-packages/napari_spatialdata/utils/_utils.py", line 262, in _adjust_channels_order new_raster = new_raster.msi.reindex_data_arrays({"c": ["r", "g", "b", "a"][: len(c_coords)]}) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/.venv/lib/python3.12/site-packages/multiscale_spatial_image/multiscale_spatial_image.py", line 188, in reindex_data_arrays return self._dt.map_over_datasets( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/.venv/lib/python3.12/site-packages/xarray/core/datatree.py", line 1462, in map_over_datasets return map_over_datasets(func, self, *args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/.venv/lib/python3.12/site-packages/xarray/core/datatree_mapping.py", line 103, in map_over_datasets results = func_with_error_context(*node_dataset_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/.venv/lib/python3.12/site-packages/xarray/core/datatree_mapping.py", line 133, in wrapper return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/.venv/lib/python3.12/site-packages/multiscale_spatial_image/utils.py", line 22, in _func return func(ds, *args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^ File "/.venv/lib/python3.12/site-packages/multiscale_spatial_image/operations/operations.py", line 18, in reindex_data_arrays return ds["image"].reindex(*args, **kwargs).to_dataset() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ TypeError: DataArray.reindex() takes from 1 to 2 positional arguments but 6 were given Raised whilst mapping function over node with path 'scale0'