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Hello,
Thank you for creating this great workflow. I am trying to analyze my MERSCOPE data using this tool. After successfully installing the program when I run
import sparrow as sp
it gives the following error
cannot import name 'HybridMappingProxy' from 'xarray.core.utils'
The detail of the error are given below, can you please suggest how I can fix this issue.
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
Cell In[4], line 1
----> 1 from sparrow.datasets.registry import get_registry
File ~/mambaforge/envs/napari-sparrow/lib/python3.10/site-packages/sparrow/__init__.py:9
5 import os
7 os.environ["USE_PYGEOS"] = "0"
----> 9 from . import ( # noqa: E402
10 datasets,
11 io,
12 utils,
13 )
14 from . import image as im # noqa: E402
15 from . import plot as pl # noqa: E402
File ~/mambaforge/envs/napari-sparrow/lib/python3.10/site-packages/sparrow/datasets/__init__.py:1
----> 1 from .cluster_blobs import cluster_blobs, multisample_blobs
2 from .pixie_example import pixie_example
3 from .proteomics import macsima_example, mibi_example, vectra_example
File ~/mambaforge/envs/napari-sparrow/lib/python3.10/site-packages/sparrow/datasets/cluster_blobs.py:16
13 from spatialdata.models import Image2DModel, Labels2DModel, PointsModel, TableModel
14 from spatialdata.transformations import Identity
---> 16 from sparrow.table import add_regionprop_features
17 from sparrow.utils._keys import _CELL_INDEX, _INSTANCE_KEY, _REGION_KEY
18 from sparrow.utils.pylogger import get_pylogger
File ~/mambaforge/envs/napari-sparrow/lib/python3.10/site-packages/sparrow/table/__init__.py:1
----> 1 from ._allocation import allocate, bin_counts
2 from ._allocation_intensity import allocate_intensity
3 from ._annotation import cluster_cleanliness, score_genes, score_genes_iter
File ~/mambaforge/envs/napari-sparrow/lib/python3.10/site-packages/sparrow/table/_allocation.py:20
17 from spatialdata.transformations import Identity
18 from xarray import DataArray
---> 20 from sparrow.image._image import _get_spatial_element, _get_translation
21 from sparrow.shape._shape import filter_shapes_layer
22 from sparrow.table._table import add_table_layer
File ~/mambaforge/envs/napari-sparrow/lib/python3.10/site-packages/sparrow/image/__init__.py:1
----> 1 from sparrow.utils.pylogger import get_pylogger
3 from ._apply import map_channels_zstacks
4 from ._combine import combine
File ~/mambaforge/envs/napari-sparrow/lib/python3.10/site-packages/sparrow/utils/__init__.py:1
----> 1 from sparrow.utils._query import bounding_box_query
2 from sparrow.utils.pylogger import get_pylogger
3 from sparrow.utils.utils import _export_config, _get_polygons_in_napari_format, _get_raster_multiscale
File ~/mambaforge/envs/napari-sparrow/lib/python3.10/site-packages/sparrow/utils/_query.py:10
7 from spatialdata import bounding_box_query as bounding_box_query_spatialdata
8 from spatialdata.transformations import get_transformation
---> 10 from sparrow.image._image import _get_spatial_element, add_labels_layer
11 from sparrow.table._table import add_table_layer
12 from sparrow.utils._keys import _INSTANCE_KEY, _REGION_KEY
File ~/mambaforge/envs/napari-sparrow/lib/python3.10/site-packages/sparrow/image/_image.py:9
7 import xarray as xr
8 from dask.array import Array
----> 9 from datatree import DataTree
10 from spatialdata import SpatialData
11 from spatialdata.models._utils import MappingToCoordinateSystem_t
File ~/mambaforge/envs/napari-sparrow/lib/python3.10/site-packages/datatree/__init__.py:2
1 # import public API
----> 2 from .datatree import DataTree
3 from .extensions import register_datatree_accessor
4 from .io import open_datatree
File ~/mambaforge/envs/napari-sparrow/lib/python3.10/site-packages/datatree/datatree.py:33
31 from xarray.core.merge import dataset_update_method
32 from xarray.core.options import OPTIONS as XR_OPTS
---> 33 from xarray.core.utils import (
34 Default,
35 Frozen,
36 HybridMappingProxy,
37 _default,
38 either_dict_or_kwargs,
39 maybe_wrap_array,
40 )
41 from xarray.core.variable import Variable
43 from . import formatting, formatting_html
ImportError: cannot import name 'HybridMappingProxy' from 'xarray.core.utils'
The text was updated successfully, but these errors were encountered:
Hello,
Thank you for creating this great workflow. I am trying to analyze my MERSCOPE data using this tool. After successfully installing the program when I run
it gives the following error
The detail of the error are given below, can you please suggest how I can fix this issue.
The text was updated successfully, but these errors were encountered: