ProSeg output cannot be opened by spatialdataR

[Bisaloo]

Related to scverse/spatialdata#1137.

• we can read:
  • images
  • points
• we cannot read:
  • shapes

    Error in `ddbs_open_dataset()` at [SpatialData/R/read.R:97:5](vscode-file://vscode-app/usr/share/positron/resources/app/out/vs/code/electron-browser/workbench/workbench.html#):
    ! Failed to open dataset at
      [./spatialdata.zarr/shapes/cell_boundaries/shapes.parquet](vscode-file://vscode-app/usr/share/positron/resources/app/out/vs/code/electron-browser/workbench/workbench.html#)
    ✖ Invalid Input Error: Geoparquet column 'geometry' does not have geometry types
    
    LINE 2: SELECT * FROM read_parquet('./spatialdata.zarr/shapes/cell_boundaries...  ^ ℹ
      Context: rapi_prepare ℹ Error type: INVALID_INPUT
    

  • tables (during the SingleCellExperiment conversion step)

    Error in `purrr::map()`:
    ℹ In index: 1.
    Caused by error in `array()`:
    ! 'data' must be of a vector type, was 'NULL'
    Hide Traceback
    Fix
    Explain
         ▆
      1. ├─SpatialData::readSpatialData("./spatialdata.zarr", shapes = F)
      2. │ └─base::lapply(ls, .readLayer) at [SpatialData/R/read.R:151:5](vscode-file://vscode-app/usr/share/positron/resources/app/out/vs/code/electron-browser/workbench/workbench.html#)
      3. │   └─SpatialData (local) FUN(X[[i]], ...)
      4. │     └─base::lapply(j, function(.) do.call(f, list(.))) at [SpatialData/R/read.R:147:9](vscode-file://vscode-app/usr/share/positron/resources/app/out/vs/code/electron-browser/workbench/workbench.html#)
      5. │       └─SpatialData (local) FUN(X[[i]], ...)
      6. │         ├─base::do.call(f, list(.)) at [SpatialData/R/read.R:147:9](vscode-file://vscode-app/usr/share/positron/resources/app/out/vs/code/electron-browser/workbench/workbench.html#)
      7. │         └─SpatialData (local) `<fn>`("./spatialdata.zarr/tables/table")
      8. │           ├─base::suppressWarnings(...) at [SpatialData/R/read.R:108:5](vscode-file://vscode-app/usr/share/positron/resources/app/out/vs/code/electron-browser/workbench/workbench.html#)
      9. │           │ └─base::withCallingHandlers(...)
     10. │           └─anndataR::read_zarr(x, as = "SingleCellExperiment") at [SpatialData/R/read.R:109:7](vscode-file://vscode-app/usr/share/positron/resources/app/out/vs/code/electron-browser/workbench/workbench.html#)
     11. │             └─zarr_adata$as_SingleCellExperiment(...)
    

[Bisaloo]

I'm not saying this is something that needs changing here. It might also be something that would be better addressed in ProSeg itself. I'm just opening this issue for clearer tracking.