scverse / scverse/spatialdata

Error in aggregate over Image2DModel by Labels2DModel when transform is more complex than translation

Open
#950 3 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

needs: triage priority: medium
Dominant language
Python
Stars
394
Forks
95
Avg merge
4d 3h
Merged PRs (30d)
7

Description

Bug description

I stumbled upon an error when trying to aggregate an Image2DModel by a Labels2DModel in the case one of the two has a transform attached which is more complex than a translation.

Reproducer
import numpy as np
from spatialdata.models import Image2DModel, Labels2DModel
from spatialdata import SpatialData, transform, aggregate
from spatialdata.transformations import Identity, Translation, Scale

sdata = SpatialData()

sdata['image'] = Image2DModel.parse(
    np.ones((1, 10, 10)),
    dims=('c','y', 'x'),
    transformations={
        # 'global': Scale([0.9] * 2, axes=['y', 'x']), # doesn't work with aggregate
        # 'global': Translation([1] * 2, axes=['y', 'x']), # works with aggregate
        'global': Identity(), # works with aggregate
    }
)

labels_array = np.zeros((10, 10)).astype('int')
labels_array[5:8, 5:8] = 1  # Create a

sdata['labels'] = Labels2DModel.parse(
    labels_array,
    dims=('y', 'x'),
    transformations={
        # 'global': Translation([6] * 2, axes=['y', 'x']),
        'global': Identity(),
    }
)

sdata.aggregate(
    values='image',
    by='labels',
    target_coordinate_system='global'
)

ValueError: input arrays must have equal shapes

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by running the provided reproducer for SpatialData.aggregate with Image2DModel and Labels2DModel, comparing Identity, Translation, and Scale transformations. Trace the aggregate path and transformation handling to find why complex transforms produce unequal input shapes; done means the Scale case aggregates successfully without the ValueError while existing Identity and Translation behavior remains intact.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Active
Clarity
Clearly specified
Newbie friendliness
72/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.