CleanCellBoundaries error

[Colin Kern]

I'm getting this error in the CleanCellBoundaries step of the pipeline. Is this a bug in the code, or something I'm doing wrong?

Traceback (most recent call last):
  File "C:\Users\ckern\Anaconda3\lib\runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "C:\Users\ckern\Anaconda3\lib\runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "c:\users\ckern\merlin\merlin\__main__.py", line 3, in <module>
    merlin()
  File "c:\users\ckern\merlin\merlin\merlin.py", line 138, in merlin
    e.run(task, index=args.fragment_index)
  File "c:\users\ckern\merlin\merlin\core\executor.py", line 52, in run
    task.run(index)
  File "c:\users\ckern\merlin\merlin\core\analysistask.py", line 329, in run
    raise e
  File "c:\users\ckern\merlin\merlin\core\analysistask.py", line 320, in run
    self._run_analysis(fragmentIndex)
  File "c:\users\ckern\merlin\merlin\analysis\segment.py", line 168, in _run_analysis
    .read_features(currentFOV)
  File "c:\users\ckern\merlin\merlin\util\spatialfeature.py", line 500, in read_features
    self._load_feature_from_hdf5_group(featureGroup[k]))
  File "c:\users\ckern\merlin\merlin\util\spatialfeature.py", line 456, in _load_feature_from_hdf5_group
    zGroup['p_' + str(p)]))
  File "c:\users\ckern\merlin\merlin\util\spatialfeature.py", line 443, in _load_geometry_from_hdf5_group
    return geometry.shape(geometryDict)
  File "C:\Users\ckern\Anaconda3\lib\site-packages\shapely\geometry\geo.py", line 35, in shape
    if not ob["coordinates"]:
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

I'm attaching my analysis tasks file (renamed from .json to .txt because Github wouldn't let me attach a JSON). Let me know if you need any other information.

with_segmentation.txt

[seichhorn]

Sorry for the delay in getting to this. If you're still having an issue with this, could you tell me what version of Shapely is installed in your environment?

[Colin Kern]

Shapely was version 1.7.0 when I had this error. I just did an update of my conda environment yesterday and shapely is now updated to 1.7.1. Should I try it again?

[seichhorn]

Try downgrading to shapely<1.7a2