Skip to content

Handling Annotations from QuPath #430

Closed
#513
Closed
Handling Annotations from QuPath#430
#513

Description

@rushin682
rushin682
opened on Mar 18, 2025

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:

Image

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

Activity

  1. quentinblampey commented on Jun 22, 2025

    @quentinblampey
    quentinblampey
    on Jun 22, 2025

    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")

    Image

    @timtreis

  2. quentinblampey commented on Jul 18, 2025

    @quentinblampey
    quentinblampey
    on Jul 18, 2025

    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.

  3. timtreis
    linked a pull request that will close this issuePolygons with holes are now rendered correctly #513on Nov 17, 2025
  4. timtreis
    closed this as completedin #513on Nov 19, 2025
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

      Milestone

      No milestone

      Relationships

      None yet

      Development

      No branches or pull requests

      Issue actions