Describe the bug
the ORIGINAL_CHANNEL_DIM field currently allows different datatypes
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header[MetaKeys.ORIGINAL_CHANNEL_DIM] = ( |
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"no_channel" if len(data.shape) == len(header[MetaKeys.SPATIAL_SHAPE]) else -1 |
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) |
and this causes errors when collating multiple metatensors:
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collated.meta = default_collate([i.meta or TraceKeys.NONE for i in batch]) |
>>> from monai.data import MetaTensor
>>> a = MetaTensor(1, meta={"original_channel_dim": 1})
>>> b = MetaTensor(1, meta={"original_channel_dim": "no_channel"})
>>> from monai.data import list_data_collate
>>> list_data_collate([a,b])
> collate/stack a list of tensors
Traceback (most recent call last):
File "/usr/local/anaconda3/envs/py38/lib/python3.8/site-packages/torch/utils/data/_utils/collate.py", line 128, in collate
return elem_type({key: collate([d[key] for d in batch], collate_fn_map=collate_fn_map) for key in elem})
File "/usr/local/anaconda3/envs/py38/lib/python3.8/site-packages/torch/utils/data/_utils/collate.py", line 128, in <dictcomp>
return elem_type({key: collate([d[key] for d in batch], collate_fn_map=collate_fn_map) for key in elem})
File "/usr/local/anaconda3/envs/py38/lib/python3.8/site-packages/torch/utils/data/_utils/collate.py", line 120, in collate
return collate_fn_map[elem_type](batch, collate_fn_map=collate_fn_map)
File "/usr/local/anaconda3/envs/py38/lib/python3.8/site-packages/torch/utils/data/_utils/collate.py", line 184, in collate_int_fn
return torch.tensor(batch)
TypeError: new(): invalid data type 'str'
cc @holgerroth
Describe the bug
the
ORIGINAL_CHANNEL_DIMfield currently allows different datatypesMONAI/monai/data/image_reader.py
Lines 307 to 309 in 68074f0
and this causes errors when collating multiple metatensors:
MONAI/monai/data/utils.py
Line 436 in 68074f0
cc @holgerroth