value_key is ignored in aggregate() for images #274

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1. LucaMarconato

   added

   method: aggregation 🔢

   on May 22, 2023
2. LucaMarconato commented on Sep 13, 2026

   

   LucaMarconato

   on Sep 13, 2026

   MemberAuthor

   More actions

   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",
   # ]
   # ///
   """Issue #274: `value_key` is ignored in `aggregate()` when aggregating images by labels
   (all channels are used)."""
   import numpy as np
   
   from spatialdata import aggregate
   from spatialdata.models import Image2DModel, Labels2DModel
   
   img = Image2DModel.parse(np.random.default_rng(0).random((3, 20, 20)), c_coords=["ch0", "ch1", "ch2"])
   lab = np.zeros((20, 20), dtype=np.int32)  # uint8 labels crash aggregate(), see #1229
   lab[2:8, 2:8] = 1
   lab[10:18, 10:18] = 2
   labels = Labels2DModel.parse(lab)
   
   res_all = aggregate(values=img, by=labels, agg_func="mean")
   print("no value_key      -> var:", res_all["table"].var_names.tolist())
   try:
       res = aggregate(values=img, by=labels, value_key=["ch1"], agg_func="mean")
       var = res["table"].var_names.tolist()
       print("value_key=['ch1'] -> var:", var)
       honoured = var == ["ch1"]
   except Exception as e:  # noqa: BLE001
       print("value_key=['ch1'] ->", type(e).__name__, str(e)[:150])
       honoured = None
   if honoured:
       print("VERDICT: NOT REPRODUCED (value_key selects the channels)")
   elif honoured is False:
       print("VERDICT: REPRODUCED (value_key silently ignored for images)")
   else:
       print("VERDICT: REPRODUCED (value_key not supported for images: raises instead of selecting channels)")

   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):

   no value_key      -> var: ['channel_ch0_mean', 'channel_ch1_mean', 'channel_ch2_mean']
   value_key=['ch1'] -> var: ['channel_ch0_mean', 'channel_ch1_mean', 'channel_ch2_mean']
   VERDICT: REPRODUCED (value_key silently ignored for images)
   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.
3. LucaMarconato

   added

   priority: medium

   needs: triage

   on Sep 13, 2026