Handling Annotations from QuPath

[rushin682]

Certain issues noticed:

• Geometry type not validated from QuPath (i.e Polygons are sometimes just multi polygons. So analysis only considered first array of coords)
• MultiPolygons are not being plotted (Possibly intersecting points issue.)

Attached test geojson file : test_geojson.txt

Fix possibilities:

• Coordinate based Validator for geometry type
• Recompute polygons in Multipolygon setting

All Polygons plot:

Single Multipolygon plot error:

ValueError                                Traceback (most recent call last)
Cell In[116], [line 1](vscode-notebook-cell:?execution_count=116&line=1)
----> [1](vscode-notebook-cell:?execution_count=116&line=1) sdata.pl.render_images("he_image").pl.render_shapes(f"multipolygon_single", fill_alpha=0, outline_alpha=1.0, outlide_width=0.5).pl.show()

File ~/miniforge3/envs/spatialdata/lib/python3.10/site-packages/spatialdata_plot/pl/basic.py:918, 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)
    [913](https://file+.vscode-resource.vscode-cdn.net/Users/rushin.gindra/Documents/scverse_x_owkin/notebooks/~/miniforge3/envs/spatialdata/lib/python3.10/site-packages/spatialdata_plot/pl/basic.py:913)     wanted_elements, wanted_shapes_on_this_cs, wants_shapes = _get_wanted_render_elements(
    [914](https://file+.vscode-resource.vscode-cdn.net/Users/rushin.gindra/Documents/scverse_x_owkin/notebooks/~/miniforge3/envs/spatialdata/lib/python3.10/site-packages/spatialdata_plot/pl/basic.py:914)         sdata, wanted_elements, params_copy, cs, "shapes"
    [915](https://file+.vscode-resource.vscode-cdn.net/Users/rushin.gindra/Documents/scverse_x_owkin/notebooks/~/miniforge3/envs/spatialdata/lib/python3.10/site-packages/spatialdata_plot/pl/basic.py:915)     )
    [917](https://file+.vscode-resource.vscode-cdn.net/Users/rushin.gindra/Documents/scverse_x_owkin/notebooks/~/miniforge3/envs/spatialdata/lib/python3.10/site-packages/spatialdata_plot/pl/basic.py:917)     if wanted_shapes_on_this_cs:
--> [918](https://file+.vscode-resource.vscode-cdn.net/Users/rushin.gindra/Documents/scverse_x_owkin/notebooks/~/miniforge3/envs/spatialdata/lib/python3.10/site-packages/spatialdata_plot/pl/basic.py:918)         _render_shapes(
    [919](https://file+.vscode-resource.vscode-cdn.net/Users/rushin.gindra/Documents/scverse_x_owkin/notebooks/~/miniforge3/envs/spatialdata/lib/python3.10/site-packages/spatialdata_plot/pl/basic.py:919)             sdata=sdata,
    [920](https://file+.vscode-resource.vscode-cdn.net/Users/rushin.gindra/Documents/scverse_x_owkin/notebooks/~/miniforge3/envs/spatialdata/lib/python3.10/site-packages/spatialdata_plot/pl/basic.py:920)             render_params=params_copy,
    [921](https://file+.vscode-resource.vscode-cdn.net/Users/rushin.gindra/Documents/scverse_x_owkin/notebooks/~/miniforge3/envs/spatialdata/lib/python3.10/site-packages/spatialdata_plot/pl/basic.py:921)             coordinate_system=cs,
    [922](https://file+.vscode-resource.vscode-cdn.net/Users/rushin.gindra/Documents/scverse_x_owkin/notebooks/~/miniforge3/envs/spatialdata/lib/python3.10/site-packages/spatialdata_plot/pl/basic.py:922)             ax=ax,
    [923](https://file+.vscode-resource.vscode-cdn.net/Users/rushin.gindra/Documents/scverse_x_owkin/notebooks/~/miniforge3/envs/spatialdata/lib/python3.10/site-packages/spatialdata_plot/pl/basic.py:923)             fig_params=fig_params,
    [924](https://file+.vscode-resource.vscode-cdn.net/Users/rushin.gindra/Documents/scverse_x_owkin/notebooks/~/miniforge3/envs/spatialdata/lib/python3.10/site-packages/spatialdata_plot/pl/basic.py:924)             scalebar_params=scalebar_params,
    [925](https://file+.vscode-resource.vscode-cdn.net/Users/rushin.gindra/Documents/scverse_x_owkin/notebooks/~/miniforge3/envs/spatialdata/lib/python3.10/site-packages/spatialdata_plot/pl/basic.py:925)             legend_params=legend_params,
    [926](https://file+.vscode-resource.vscode-cdn.net/Users/rushin.gindra/Documents/scverse_x_owkin/notebooks/~/miniforge3/envs/spatialdata/lib/python3.10/site-packages/spatialdata_plot/pl/basic.py:926)         )
    [928](https://file+.vscode-resource.vscode-cdn.net/Users/rushin.gindra/Documents/scverse_x_owkin/notebooks/~/miniforge3/envs/spatialdata/lib/python3.10/site-packages/spatialdata_plot/pl/basic.py:928) elif cmd == "render_points" and has_points:
    [929](https://file+.vscode-resource.vscode-cdn.net/Users/rushin.gindra/Documents/scverse_x_owkin/notebooks/~/miniforge3/envs/spatialdata/lib/python3.10/site-packages/spatialdata_plot/pl/basic.py:929)     wanted_elements, wanted_points_on_this_cs, wants_points = _get_wanted_render_elements(
    [930](https://file+.vscode-resource.vscode-cdn.net/Users/rushin.gindra/Documents/scverse_x_owkin/notebooks/~/miniforge3/envs/spatialdata/lib/python3.10/site-packages/spatialdata_plot/pl/basic.py:930)         sdata, wanted_elements, params_copy, cs, "points"
    [931](https://file+.vscode-resource.vscode-cdn.net/Users/rushin.gindra/Documents/scverse_x_owkin/notebooks/~/miniforge3/envs/spatialdata/lib/python3.10/site-packages/spatialdata_plot/pl/basic.py:931)     )

File ~/miniforge3/envs/spatialdata/lib/python3.10/site-packages/spatialdata_plot/pl/render.py:312, in _render_shapes(sdata, render_params, coordinate_system, ax, fig_params, scalebar_params, legend_params)
...
    [140](https://file+.vscode-resource.vscode-cdn.net/Users/rushin.gindra/Documents/scverse_x_owkin/notebooks/~/miniforge3/envs/spatialdata/lib/python3.10/site-packages/matplotlib/path.py:140)     raise ValueError("The first element of 'code' must be equal "
    [141](https://file+.vscode-resource.vscode-cdn.net/Users/rushin.gindra/Documents/scverse_x_owkin/notebooks/~/miniforge3/envs/spatialdata/lib/python3.10/site-packages/matplotlib/path.py:141)                      f"to 'MOVETO' ({self.MOVETO}).  "
    [142](https://file+.vscode-resource.vscode-cdn.net/Users/rushin.gindra/Documents/scverse_x_owkin/notebooks/~/miniforge3/envs/spatialdata/lib/python3.10/site-packages/matplotlib/path.py:142)                      f"Your first code is {codes[0]}")

ValueError: 'codes' must be a 1D list or array with the same length of 'vertices'. Your vertices have shape (168, 2) but your codes have shape (44,)

@LucaMarconato @timtreis

[quentinblampey]

I have the same error, but with a shape generated from Sopa. To make it easier to reproduce, I share the shapes:
https://drive.google.com/file/d/1dVAuPHGeiBKnb6MfFxAHirZtK48h8fP6/view?usp=sharing

It's a valid shape, and GeoPandas has no issue plotting it:

import geopandas as gpd
import matplotlib.pyplot as plt
from spatialdata import SpatialData
from spatialdata.models import ShapesModel
import spatialdata_plot

# get only the first shape for simplicity
gdf = gpd.read_parquet("shapes_reproduce.parquet").loc[:1]

gdf.plot() # nicely plots the shape

But spatialdata-plot throws an error:

sdata = SpatialData(shapes={"tissue": ShapesModel.parse(gdf)})
sdata.pl.render_shapes("tissue").pl.show()

ValueError: 'codes' must be a 1D list or array with the same length of 'vertices'. Your vertices have shape (36981, 2) but your codes have shape (41748,)

Note 1: It works if I do gdf.geometry = gdf.buffer(1), which indicates the issue must be related to the polygon holes.

Note 2: I wonder why, more generally, the internal functions of GeoPandas are not used directly for plotting the polygons? It would also solve the issue related to plotting polygons with holes #333. Since it also use matplotlib internally, it seems natural to re-use them.

from geopandas.plotting import _plot_polygon_collection

fig, ax = plt.subplots(figsize=(2, 5))
_plot_polygon_collection(ax, gdf)
plt.axis("equal")

@timtreis

[quentinblampey]

Hi @timtreis, do you have any updates on this? Do you want me to have a look, or are you already working on this?

I guess the fix is just to use _plot_polygon_collection from geopandas.plotting to replace the shapes rendering, but I'm not super familiar with the codebase of spatialdata-plot, so I don't know how easy it is to make this change.