CleanCellBoundaries error #67
Description
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.