LucaMarconato
commented
1 year ago My mistake, I had to use the parameter color, not key. This leads to another bug: AttributeError: 'SpatialImage' object has no attribute 'index'
sdata.pl.render_labels('blobs_labels', color='channel_0_sum').pl.show()/Users/macbook/embl/projects/basel/spatialdata/src/spatialdata/_core/operations/aggregate.py:244: UserWarning: Converting `region_key: region` to categorical dtype.
table = TableModel.parse(table, region=shapes_name, region_key=region_key, instance_key=instance_key)
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
Cell In[26], line 8
4 from napari_spatialdata import Interactive
6 sdata = blobs()
----> 8 sdata.pl.render_labels('blobs_labels', color='channel_0_sum').pl.show()
10 # Interactive(sdata)
File ~/embl/projects/basel/spatialdata-plot/src/spatialdata_plot/pl/basic.py:696, in PlotAccessor.show(self, coordinate_systems, legend_fontsize, legend_fontweight, legend_loc, legend_fontoutline, na_in_legend, colorbar, wspace, hspace, ncols, frameon, figsize, dpi, fig, title, share_extent, pad_extent, ax, return_ax, save)
689 if is_categorical_dtype(colors):
690 _maybe_set_colors(
691 source=sdata.table,
692 target=sdata.table,
693 key=params.color,
694 palette=params.palette,
695 )
--> 696 _render_labels(
697 sdata=sdata,
698 render_params=params,
699 coordinate_system=cs,
700 ax=ax,
701 fig_params=fig_params,
702 scalebar_params=scalebar_params,
703 legend_params=legend_params,
704 )
706 if title is not None:
707 if len(title) == 1:
File ~/embl/projects/basel/spatialdata-plot/src/spatialdata_plot/pl/render.py:448, in _render_labels(sdata, render_params, coordinate_system, ax, fig_params, scalebar_params, legend_params)
445 instance_id = table.obs[instance_key].values
447 # get color vector (categorical or continuous)
--> 448 color_source_vector, color_vector, categorical = _set_color_source_vec(
449 sdata=sdata_filt,
450 element=sdata_filt.labels[label_key],
451 element_name=label_key,
452 value_to_plot=render_params.color,
453 layer=render_params.layer,
454 groups=render_params.groups,
455 palette=render_params.palette,
456 na_color=render_params.cmap_params.na_color,
457 alpha=render_params.fill_alpha,
458 )
460 if (render_params.fill_alpha != render_params.outline_alpha) and render_params.contour_px is not None:
461 # First get the labels infill and plot them
462 labels_infill = _map_color_seg(
463 seg=label.values,
464 cell_id=instance_id,
(...)
470 na_color=render_params.cmap_params.na_color,
471 )
File ~/embl/projects/basel/spatialdata-plot/src/spatialdata_plot/pl/utils.py:831, in _set_color_source_vec(sdata, element, value_to_plot, element_name, layer, groups, palette, na_color, alpha)
826 raise ValueError(
827 f"Color key '{value_to_plot}' for element '{element_name}' been found in multiple locations: {origins}."
828 )
830 if len(origins) == 1:
--> 831 vals = get_values(value_key=value_to_plot, sdata=sdata, element_name=element_name)
832 color_source_vector = vals[value_to_plot]
834 # if all([isinstance(x, str) for x in color_source_vector]):
835 # raise TypeError(
836 # f"Color key '{value_to_plot}' for element '{element_name}' has string values, "
(...)
839
840 # numerical case, return early
File ~/embl/projects/basel/spatialdata/src/spatialdata/_core/query/relational_query.py:268, in get_values(value_key, element, sdata, element_name)
266 if sdata is not None:
267 assert element_name is not None
--> 268 matched_table = match_table_to_element(sdata=sdata, element_name=element_name)
269 if origin == "obs":
270 return matched_table.obs[value_key_values]
File ~/embl/projects/basel/spatialdata/src/spatialdata/_core/query/relational_query.py:151, in match_table_to_element(sdata, element_name)
149 assert element_type in ["labels", "shapes"], f"Element {element_name} ({element_type}) is not supported"
150 elements_dict = {element_type: {element_name: element}}
--> 151 return _filter_table_by_elements(sdata.table, elements_dict, match_rows=True)
File ~/embl/projects/basel/spatialdata/src/spatialdata/_core/query/relational_query.py:114, in _filter_table_by_elements(table, elements_dict, match_rows)
112 assert "element" in locals()
113 assert "name" in locals()
--> 114 n0 = np.setdiff1d(element.index.to_numpy(), table.obs[instance_key].to_numpy())
115 n1 = np.setdiff1d(table.obs[instance_key].to_numpy(), element.index.to_numpy())
116 raise ValueError(
117 f"Instances in the table and in the element don't correspond: found {len(n0)} indices in the "
118 f"element {name} but not in the table and found {len(n1)} indices in the table but not in the "
119 "element"
120 )
File ~/miniconda3/envs/ome/lib/python3.10/site-packages/xarray/core/common.py:278, in AttrAccessMixin.__getattr__(self, name)
276 with suppress(KeyError):
277 return source[name]
--> 278 raise AttributeError(
279 f"{type(self).__name__!r} object has no attribute {name!r}"
280 )
AttributeError: 'SpatialImage' object has no attribute 'index'
timtreis
This code tries to plots the
varpresent in the table in theblobsdataset, which is mapped to thelabels.This is the output produced (tried for all the
var_names:'channel_0_sum','channel_1_sum','channel_2_sum', but all lead to the same plot)This is the output produced by
napari_spatialdata).