from ngio.experimental.iterators import FeatureExtractorIterator
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
Cell In[14], [line 8](vscode-notebook-cell:?execution_count=14&line=8)
6 import pandas as pd
7 import dask.array as da
----> [8](vscode-notebook-cell:?execution_count=14&line=8) import ngio
9 from ome_zarr.image import NgffMultiscales
10 from ome_zarr.scene import NgffScene
File c:\Users\johan\miniforge3\envs\autoscape\Lib\site-packages\ngio\__init__.py:13
10 __email__ = "lorenzo.cerrone@uzh.ch"
12 from ngio.common import Dimensions, Roi, RoiSlice
---> [13](file:///C:/Users/johan/miniforge3/envs/autoscape/Lib/site-packages/ngio/__init__.py:13) from ngio.hcs import (
14 OmeZarrPlate,
15 OmeZarrWell,
16 create_empty_plate,
17 create_empty_well,
18 open_ome_zarr_plate,
19 open_ome_zarr_well,
20 )
21 from ngio.images import (
22 ChannelSelectionModel,
23 Image,
(...)
31 open_ome_zarr_container,
32 )
33 from ngio.ome_zarr_meta.ngio_specs import (
34 AxesSetup,
35 DefaultNgffVersion,
(...)
[3](file:///C:/Users/johan/miniforge3/envs/autoscape/Lib/site-packages/ngio/hcs/__init__.py:3)8 PixelSize,
39 )
File c:\Users\johan\miniforge3\envs\autoscape\Lib\site-packages\ngio\hcs\__init__.py:3
1 """OME-Zarr HCS objects models."""
----> 3 from ngio.hcs._plate import (
4 OmeZarrPlate,
5 OmeZarrWell,
6 create_empty_plate,
7 create_empty_well,
8 open_ome_zarr_plate,
9 open_ome_zarr_well,
10 )
12 __all__ = [
13 "OmeZarrPlate",
14 "OmeZarrWell",
(...)
18 "open_ome_zarr_well",
1[9](file:///C:/Users/johan/miniforge3/envs/autoscape/Lib/site-packages/ngio/hcs/_plate.py:9) ]
File c:\Users\johan\miniforge3\envs\autoscape\Lib\site-packages\ngio\hcs\_plate.py:9
6 from collections.abc import Sequence
7 from typing import Literal
----> 9 from ngio.images import (
10 OmeZarrContainer,
11 concatenate_image_tables,
12 concatenate_image_tables_as,
13 concatenate_image_tables_as_async,
14 concatenate_image_tables_async,
15 list_image_tables,
16 list_image_tables_async,
17 )
18 from ngio.ome_zarr_meta import (
19 DefaultNgffVersion,
20 ImageInWellPath,
(...)
28 update_ngio_well_meta,
29 )
[3](file:///C:/Users/johan/miniforge3/envs/autoscape/Lib/site-packages/ngio/images/__init__.py:3)0 from ngio.tables import (
31 ConditionTable,
32 DefaultTableBackend,
(...)
41 TypedTable,
42 )
File c:\Users\johan\miniforge3\envs\autoscape\Lib\site-packages\ngio\images\__init__.py:3
1 """OME-Zarr object models."""
----> 3 from ngio.images._create_synt_container import create_synthetic_ome_zarr
4 from ngio.images._image import ChannelSelectionModel, Image, ImagesContainer
5 from ngio.images._label import Label, LabelsContainer
File c:\Users\johan\miniforge3\envs\autoscape\Lib\site-packages\ngio\images\_create_synt_container.py:[12](file:///C:/Users/johan/miniforge3/envs/autoscape/Lib/site-packages/ngio/images/_create_synt_container.py:12)
10 from ngio.common._pyramid import ChunksLike, ShardsLike
11 from ngio.common._synt_images_utils import fit_to_shape
---> 12 from ngio.images._ome_zarr_container import OmeZarrContainer, create_ome_zarr_from_array
13 from ngio.ome_zarr_meta.ngio_specs import (
14 Channel,
15 DefaultNgffVersion,
16 NgffVersions,
17 )
18 from ngio.resources import AVAILABLE_SAMPLES, SampleInfo, get_sample_info
File c:\Users\johan\miniforge3\envs\autoscape\Lib\site-packages\ngio\images\_ome_zarr_container.py:[13](file:///C:/Users/johan/miniforge3/envs/autoscape/Lib/site-packages/ngio/images/_ome_zarr_container.py:13)
11 from ngio.common._pyramid import ChunksLike, ShardsLike
12 from ngio.images._create_utils import init_image_like
---> 13 from ngio.images._image import Image, ImagesContainer
14 from ngio.images._label import Label, LabelsContainer
15 from ngio.images._masked_image import MaskedImage, MaskedLabel
File c:\Users\johan\miniforge3\envs\autoscape\Lib\site-packages\ngio\images\_image.py:[19](file:///C:/Users/johan/miniforge3/envs/autoscape/Lib/site-packages/ngio/images/_image.py:19)
13 from ngio.common import (
14 Dimensions,
15 InterpolationOrder,
16 Roi,
17 )
18 from ngio.common._pyramid import ChunksLike, ShardsLike
---> 19 from ngio.images._abstract_image import AbstractImage, abstract_derive
20 from ngio.io_pipes import (
21 SlicingInputType,
22 TransformProtocol,
23 )
24 from ngio.ome_zarr_meta import (
25 ImageMetaHandler,
26 NgioImageMeta,
27 PixelSize,
28 )
File c:\Users\johan\miniforge3\envs\autoscape\Lib\site-packages\ngio\images\_abstract_image.py:[63](file:///C:/Users/johan/miniforge3/envs/autoscape/Lib/site-packages/ngio/images/_abstract_image.py:63)
51 from ngio.ome_zarr_meta.ngio_specs import (
52 Channel,
53 NgffVersions,
54 NgioLabelMeta,
55 )
56 from ngio.ome_zarr_meta.ngio_specs._axes import (
57 AxesSetup,
58 DefaultSpaceUnit,
(...)
61 TimeUnits,
62 )
---> 63 from ngio.tables import RoiTable
64 from ngio.utils import (
65 NgioDeprecationWarning,
66 NgioFileExistsError,
(...)
69 ZarrGroupHandler,
70 )
71 from ngio.utils._zarr_utils import find_dimension_separator
File c:\Users\johan\miniforge[3](file:///C:/Users/johan/miniforge3/envs/autoscape/Lib/site-packages/ngio/tables/__init__.py:3)\envs\autoscape\Lib\site-packages\ngio\tables\__init__.py:3
1 """Ngio Tables implementations."""
----> 3 from ngio.tables._tables_container import (
4 ConditionTable,
5 FeatureTable,
6 GenericRoiTable,
7 MaskingRoiTable,
8 RoiTable,
9 Table,
10 TablesContainer,
11 TableType,
12 TypedTable,
13 open_table,
14 open_table_as,
15 open_tables_container,
16 )
17 from ngio.tables.backends import (
18 DefaultTableBackend,
19 ImplementedTableBackends,
20 TableBackend,
21 TableBackendProtocol,
22 )
23 from ngio.tables.v1._generic_table import GenericTable
File c:\Users\johan\miniforge3\envs\autoscape\Lib\site-packages\ngio\tables\_tables_container.py:[5](file:///C:/Users/johan/miniforge3/envs/autoscape/Lib/site-packages/ngio/tables/_tables_container.py:5)
1 """Module for handling the /tables group in an OME-NGFF file."""
3 from typing import Literal, Protocol, TypeVar
----> 5 import anndata as ad
6 import pandas as pd
7 import polars as pl
File c:\Users\johan\miniforge3\envs\autoscape\Lib\site-packages\anndata\__init__.py:[29](file:///C:/Users/johan/miniforge3/envs/autoscape/Lib/site-packages/anndata/__init__.py:29)
25 if sys.version_info < (3, 11):
26 # Backport package for exception groups
27 import exceptiongroup # noqa: F401
---> 29 from ._core.anndata import AnnData
30 from ._core.merge import concat
31 from ._core.raw import Raw
File c:\Users\johan\miniforge3\envs\autoscape\Lib\site-packages\anndata\_core\anndata.py:[25](file:///C:/Users/johan/miniforge3/envs/autoscape/Lib/site-packages/anndata/_core/anndata.py:25)
22 from scipy import sparse
23 from scipy.sparse import issparse
---> 25 from .. import utils
26 from .._settings import settings
27 from ..compat import DaskArray, SpArray, ZarrArray, _move_adj_mtx
File c:\Users\johan\miniforge3\envs\autoscape\Lib\site-packages\anndata\utils.py:[15](file:///C:/Users/johan/miniforge3/envs/autoscape/Lib/site-packages/anndata/utils.py:15)
11 from scipy import sparse
13 import anndata
---> 15 from ._core.sparse_dataset import BaseCompressedSparseDataset
16 from .compat import CupyArray, CupySparseMatrix, DaskArray, SpArray
17 from .logging import get_logger
File c:\Users\johan\miniforge3\envs\autoscape\Lib\site-packages\anndata\_core\sparse_dataset.py:[32](file:///C:/Users/johan/miniforge3/envs/autoscape/Lib/site-packages/anndata/_core/sparse_dataset.py:32)
29 from scipy.sparse import _sparsetools
31 from .. import abc
---> 32 from .._settings import settings
33 from ..compat import H5Group, SpArray, ZarrArray, ZarrGroup, _read_attr
34 from .index import _fix_slice_bounds, _subset, unpack_index
File c:\Users\johan\miniforge3\envs\autoscape\Lib\site-packages\anndata\_settings.py:[17](file:///C:/Users/johan/miniforge3/envs/autoscape/Lib/site-packages/anndata/_settings.py:17)
14 from types import GenericAlias
15 from typing import TYPE_CHECKING, Generic, NamedTuple, TypeVar, cast
---> 17 from anndata.compat import CAN_USE_SPARSE_ARRAY
18 from anndata.compat.exceptiongroups import add_note
20 if TYPE_CHECKING:
File c:\Users\johan\miniforge3\envs\autoscape\Lib\site-packages\anndata\compat\__init__.py:[97](file:///C:/Users/johan/miniforge3/envs/autoscape/Lib/site-packages/anndata/compat/__init__.py:97)
94 import zarr
96 if Version(zarr.__version__).major > 2:
---> 97 raise ImportError("zarr-python major version > 2 is not supported")
99 from zarr.core import Array as ZarrArray
100 from zarr.hierarchy import Group as ZarrGroup
ImportError: zarr-python major version > 2 is not supportedI am not familiar with anndata enough to make a good judgement here but it seems that anndata is pinned to zarr-python<3 whereas ngfio (at least the latest version) is pinned to zarr>3?
Hi @lorenzocerrone , I just tried the object detection workflow we discussed over at #111 and I am getting an import error when trying to load the FeatureIterator class:
I am not familiar with anndata enough to make a good judgement here but it seems that anndata is pinned to zarr-python<3 whereas ngfio (at least the latest version) is pinned to zarr>3?