exceeding rasterize's maximum label index #987

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1. LouisK92 commented on Sep 22, 2025

   

   LouisK92

   on Sep 22, 2025

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   A quick workaround (assuming that cell labels don't overlap) would be the following. Note that I used circles instead of points for the example, which is closer to what I actually wanted. In case of points the .iloc fails since we'd deal with a dask dataframe in that case.

   import numpy as np
   import spatialdata as sd
   from spatialdata.models import ShapesModel
   
   def get_n_coords(n):
       coords = np.random.rand(n, 2)
       return coords
       
   sdata = sd.SpatialData(shapes={"shapes": ShapesModel.parse(get_n_coords(65536), geometry=0, radius=np.ones(65536))})
   
   img_extent = sd.get_extent(sdata['shapes']) # NOTE: Here I actually use sd.get_extent(sdata['image'])
   
   N = 65535 # number of shapes that are rasterised per step
   n_cells = len(sdata['shapes'])
   n_iter = n_cells // N + bool(n_cells % N)
   
   rasterize_args = {
       "min_coordinate": [int(img_extent["x"][0]), int(img_extent["y"][0])],
       "max_coordinate": [int(img_extent["x"][1]), int(img_extent["y"][1])],
       "target_coordinate_system": "global",
       "target_unit_to_pixels": 1,
       "return_regions_as_labels": True,
   }
   
   for i in range(n_iter):
       labels_image_ = sd.rasterize(sdata['shapes'].iloc[i*N:min((i+1)*N, n_cells)], ["x", "y"], **rasterize_args)
       if i == 0:
           labels_image = labels_image_
       else:
           labels_image.values[labels_image_.values > 0] = labels_image_.values[labels_image_.values > 0]
   
   sdata['labels'] = labels_image
2. LucaMarconato commented on May 21, 2026

   

   LucaMarconato

   on May 21, 2026

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   Related discussion: #187
3. LucaMarconato commented on Sep 13, 2026

   

   LucaMarconato

   on Sep 13, 2026

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   This whole message is AI-generated. The issue was automatically discovered and reported by an AI agent (Claude) during an autonomous bug hunt on the spatialdata code base. It has not been verified or triaged by a human yet; the needs: triage label is set so that a maintainer can confirm it. The reproduction script below was executed by the agent in an isolated environment (see Environment) and its output is pasted verbatim.

   I re-attempted to reproduce this issue on the current main branch (commit ccf1ea048d054b6624214bf618008a9f9ae223e0) as part of a triage pass over open issues, and confirmed it reproduces.

   Reproduction script (PEP 723 inline metadata; run with uv run repro.py, no other setup needed):

   # /// script
   # requires-python = ">=3.12"
   # dependencies = [
   #     "spatialdata @ git+https://github.com/scverse/spatialdata.git@ccf1ea048d054b6624214bf618008a9f9ae223e0",
   # ]
   # ///
   """#987: rasterize(..., return_regions_as_labels=True) refuses more than 65535 shapes (uint16 output)."""
   import warnings
   import numpy as np
   from spatialdata import get_extent, rasterize
   from spatialdata.models import ShapesModel
   
   warnings.simplefilter("ignore")
   rng = np.random.default_rng(0)
   bug = False
   for n in [65_534, 70_000]:
       shapes = ShapesModel.parse(rng.uniform(0, 1000, (n, 2)), geometry=0, radius=np.full(n, 0.5))
       ext = get_extent(shapes)
       try:
           lab = rasterize(shapes, ["x", "y"], min_coordinate=[ext["x"][0], ext["y"][0]], max_coordinate=[ext["x"][1], ext["y"][1]],
                           target_coordinate_system="global", target_unit_to_pixels=1, return_regions_as_labels=True)
           print(f"{n} circles: OK, labels dtype {lab.dtype}")
       except Exception as e:  # noqa: BLE001
           print(f"{n} circles: {type(e).__name__}: {str(e)[:100]}")
           bug = True
   print("VERDICT:", "REPRODUCED (hard uint16 limit; rasterize_bins already uses _get_uint_dtype to pick uint32/uint64)" if bug else "NOT REPRODUCED")

   Environment: uv run --no-project --python 3.13, which resolves spatialdata from git+https://github.com/scverse/spatialdata.git@ccf1ea048d054b6624214bf618008a9f9ae223e0 (extra dependencies, if any, are pinned in the script's inline metadata above).

   Output (verbatim, only uv package-resolution/install log lines removed):

   65534 circles: OK, labels dtype uint16
   70000 circles: ValueError: Maximum label index is 70000. Values higher than 65535 are not supported.
   VERDICT: REPRODUCED (hard uint16 limit; rasterize_bins already uses _get_uint_dtype to pick uint32/uint64)
   exit=0
   

   Agent's severity assessment: medium (see the priority: * label added to this issue).

   ---

   Automatically generated; discovered by an AI agent (Claude) and not yet reviewed by a human.
4. LucaMarconato

   added

   priority: medium

   needs: triage

   on Sep 13, 2026
5. timtreis

   added a commit that references this issue on Oct 9, 2026

   fix(xenium): address review on CSV-only reader

   ...

   59d3c4c