polygon_query() throws AttributeError: 'NoneType' object has no attribute 'intersects' error

[olivermccallion]

Hi,

I'm trying to perform a polygon_query() on a Xenium object:

SpatialData object with:
├── Images
│     ├── 'he_image': MultiscaleSpatialImage[cyx] (3, 33558, 57706), (3, 16779, 28853), (3, 8389, 14426), (3, 4194, 7213), (3, 2097, 3606)
│     └── 'morphology_focus': MultiscaleSpatialImage[cyx] (5, 44236, 25670), (5, 22118, 12835), (5, 11059, 6417), (5, 5529, 3208), (5, 2764, 1604)
├── Labels
│     ├── 'cell_labels': MultiscaleSpatialImage[yx] (44236, 25670), (22118, 12835), (11059, 6417), (5529, 3208), (2764, 1604)
│     └── 'nucleus_labels': MultiscaleSpatialImage[yx] (44236, 25670), (22118, 12835), (11059, 6417), (5529, 3208), (2764, 1604)
├── Points
│     └── 'transcripts': DataFrame with shape: (3153129, 11) (3D points)
├── Shapes
│     ├── 'cell_boundaries': GeoDataFrame shape: (21922, 1) (2D shapes)
│     ├── 'cell_circles': GeoDataFrame shape: (21922, 2) (2D shapes)
│     ├── 'glomeruli': GeoDataFrame shape: (5, 1) (2D shapes)
│     ├── 'infiltrate_1': GeoDataFrame shape: (1, 1) (2D shapes)
│     ├── 'nucleus_boundaries': GeoDataFrame shape: (21669, 1) (2D shapes)
│     ├── 'peri-infiltrate_boundary-hi': GeoDataFrame shape: (9, 1) (2D shapes)
└── Tables
      └── 'table': AnnData (21922, 477)
with coordinate systems:
▸ 'global', with elements:
        he_image (Images), morphology_focus (Images), cell_labels (Labels), nucleus_labels (Labels), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), decent_tissue (Shapes), glomeruli (Shapes), infiltrate_1 (Shapes),  nucleus_boundaries (Shapes), peri-infiltrate_boundary-hi (Shapes)

However, whilst I'm able to perform a bounding box query, a polygon query using a region annotated in napari throws the following error:
Code:

polygon = sdata.shapes['infiltrate_1'].geometry.iloc[0]
query_sdata = polygon_query(sdata, polygon, target_coordinate_system="global")
query_sdata

Error:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[10], line 1
----> 1 query_sdata = sdata.query.polygon(polygon, target_coordinate_system="global")

File /opt/anaconda3/envs/spatialdata_py3.10/lib/python3.10/site-packages/spatialdata/_core/spatialdata.py:1761, in QueryManager.polygon(self, polygon, target_coordinate_system, filter_table)
   1753 """
   1754 Perform a polygon query on the SpatialData object.
   1755 
   1756 Please see
   1757 :func:`spatialdata.polygon_query` for the complete docstring.
   1758 """
   1759 from spatialdata._core.query.spatial_query import polygon_query
-> 1761 return polygon_query(  # type: ignore[return-value]
   1762     self._sdata,
   1763     polygon=polygon,
   1764     target_coordinate_system=target_coordinate_system,
   1765     filter_table=filter_table,
   1766 )

File /opt/anaconda3/envs/spatialdata_py3.10/lib/python3.10/functools.py:878, in singledispatch.<locals>.wrapper(*args, **kw)
    874 if not args:
    875     raise TypeError(f'{funcname} requires at least '
    876                     '1 positional argument')
--> 878 return dispatch(args[0].__class__)(*args, **kw)

File /opt/anaconda3/envs/spatialdata_py3.10/lib/python3.10/site-packages/spatialdata/_core/query/spatial_query.py:828, in _(sdata, polygon, target_coordinate_system, filter_table, shapes, points, images, labels)
    826 for element_type in ["points", "images", "labels", "shapes"]:
    827     elements = getattr(sdata, element_type)
--> 828     queried_elements = _dict_query_dispatcher(
    829         elements,
    830         polygon_query,
    831         polygon=polygon,
    832         target_coordinate_system=target_coordinate_system,
    833     )
    834     new_elements[element_type] = queried_elements
    836 tables = _get_filtered_or_unfiltered_tables(filter_table, new_elements, sdata)

File /opt/anaconda3/envs/spatialdata_py3.10/lib/python3.10/site-packages/spatialdata/_core/query/spatial_query.py:398, in _dict_query_dispatcher(elements, query_function, **kwargs)
    396 assert isinstance(d, dict)
    397 if target_coordinate_system in d:
--> 398     result = query_function(element, **kwargs)
    399     if result is not None:
    400         # query returns None if it is empty
    401         queried_elements[key] = result

File /opt/anaconda3/envs/spatialdata_py3.10/lib/python3.10/functools.py:878, in singledispatch.<locals>.wrapper(*args, **kw)
    874 if not args:
    875     raise TypeError(f'{funcname} requires at least '
    876                     '1 positional argument')
--> 878 return dispatch(args[0].__class__)(*args, **kw)

File /opt/anaconda3/envs/spatialdata_py3.10/lib/python3.10/site-packages/spatialdata/_core/query/spatial_query.py:912, in _(element, polygon, target_coordinate_system, **kwargs)
    910 else:
    911     buffered[OLD_INDEX] = buffered.index
--> 912 indices = buffered.geometry.apply(lambda x: x.intersects(polygon))
    913 if np.sum(indices) == 0:
    914     return None

File /opt/anaconda3/envs/spatialdata_py3.10/lib/python3.10/site-packages/geopandas/geoseries.py:673, in GeoSeries.apply(self, func, convert_dtype, args, **kwargs)
    670         kwargs["convert_dtype"] = True
    672 # to avoid warning
--> 673 result = super().apply(func, args=args, **kwargs)
    674 if isinstance(result, GeoSeries):
    675     if self.crs is not None:

File /opt/anaconda3/envs/spatialdata_py3.10/lib/python3.10/site-packages/pandas/core/series.py:4924, in Series.apply(self, func, convert_dtype, args, by_row, **kwargs)
   4789 def apply(
   4790     self,
   4791     func: AggFuncType,
   (...)
   4796     **kwargs,
   4797 ) -> DataFrame | Series:
   4798     """
   4799     Invoke function on values of Series.
   4800 
   (...)
   4915     dtype: float64
   4916     """
   4917     return SeriesApply(
   4918         self,
   4919         func,
   4920         convert_dtype=convert_dtype,
   4921         by_row=by_row,
   4922         args=args,
   4923         kwargs=kwargs,
-> 4924     ).apply()

File /opt/anaconda3/envs/spatialdata_py3.10/lib/python3.10/site-packages/pandas/core/apply.py:1427, in SeriesApply.apply(self)
   1424     return self.apply_compat()
   1426 # self.func is Callable
-> 1427 return self.apply_standard()

File /opt/anaconda3/envs/spatialdata_py3.10/lib/python3.10/site-packages/pandas/core/apply.py:1507, in SeriesApply.apply_standard(self)
   1501 # row-wise access
   1502 # apply doesn't have a `na_action` keyword and for backward compat reasons
   1503 # we need to give `na_action="ignore"` for categorical data.
   1504 # TODO: remove the `na_action="ignore"` when that default has been changed in
   1505 #  Categorical (GH51645).
   1506 action = "ignore" if isinstance(obj.dtype, CategoricalDtype) else None
-> 1507 mapped = obj._map_values(
   1508     mapper=curried, na_action=action, convert=self.convert_dtype
   1509 )
   1511 if len(mapped) and isinstance(mapped[0], ABCSeries):
   1512     # GH#43986 Need to do list(mapped) in order to get treated as nested
   1513     #  See also GH#25959 regarding EA support
   1514     return obj._constructor_expanddim(list(mapped), index=obj.index)

File /opt/anaconda3/envs/spatialdata_py3.10/lib/python3.10/site-packages/pandas/core/base.py:919, in IndexOpsMixin._map_values(self, mapper, na_action, convert)
    916 arr = self._values
    918 if isinstance(arr, ExtensionArray):
--> 919     return arr.map(mapper, na_action=na_action)
    921 return algorithms.map_array(arr, mapper, na_action=na_action, convert=convert)

File /opt/anaconda3/envs/spatialdata_py3.10/lib/python3.10/site-packages/pandas/core/arrays/base.py:2322, in ExtensionArray.map(self, mapper, na_action)
   2302 def map(self, mapper, na_action=None):
   2303     """
   2304     Map values using an input mapping or function.
   2305 
   (...)
   2320         a MultiIndex will be returned.
   2321     """
-> 2322     return map_array(self, mapper, na_action=na_action)

File /opt/anaconda3/envs/spatialdata_py3.10/lib/python3.10/site-packages/pandas/core/algorithms.py:1743, in map_array(arr, mapper, na_action, convert)
   1741 values = arr.astype(object, copy=False)
   1742 if na_action is None:
-> 1743     return lib.map_infer(values, mapper, convert=convert)
   1744 else:
   1745     return lib.map_infer_mask(
   1746         values, mapper, mask=isna(values).view(np.uint8), convert=convert
   1747     )

File lib.pyx:2972, in pandas._libs.lib.map_infer()

File /opt/anaconda3/envs/spatialdata_py3.10/lib/python3.10/site-packages/spatialdata/_core/query/spatial_query.py:912, in _.<locals>.<lambda>(x)
    910 else:
    911     buffered[OLD_INDEX] = buffered.index
--> 912 indices = buffered.geometry.apply(lambda x: x.intersects(polygon))
    913 if np.sum(indices) == 0:
    914     return None

AttributeError: 'NoneType' object has no attribute 'intersects'

Plotting both the query polygon and transcripts confirms that the coordinate systems are congruent, and using 10X Xenium Explorer exported coordinates as used in this notebook (https://github.com/quentinblampey/spatialdata_xenium_explorer/blob/master/docs/10x_tutorials/xenium/xenium_tuto.ipynb) also throws the same error.

Could you point me in the right direction for what's going wrong?

My environment is:
Uploading env.txt…

[easlinger]

I have had the same issue -- Based on where it fails in the loop across elements, I think it might have something to do with if a nucleus isn't detected in a particular segment?

I will note that everything seems to work alright if line 913 in spatial_query.py is changed to:

    indices = buffered.geometry.apply(
        lambda x: False if x is None else x.intersects(polygon))