KeyError: 'affine' when loadimaged ,on png files

[lg2578]

my transforms are:

train_transforms = Compose(
    [
        LoadImaged(keys=["img", "seg"]),
        AddChanneld(keys=["img", "seg"]),
        Spacingd(keys=["img", "seg"],pixdim=(1.5,1.5),mode=("bilinear", "nearest")),
        CropForegroundd(keys=["img", "seg"],source_key='img'),
        Resized(keys=["img", "seg"],spatial_size=(160,160),mode=("bilinear", "nearest")),
        EnsureTyped(keys=["img", "seg"]),
    ]
)
...
# define dataset, data loader
check_ds = monai.data.Dataset(data=train_files, transform=train_transforms)
# use batch_size=2 to load images and use RandCropByPosNegLabeld to generate 2 x 4 images for network training
check_loader = DataLoader(check_ds, batch_size=2, num_workers=2, collate_fn=list_data_collate)
check_data = monai.utils.misc.first(check_loader)
print(check_data["img"].shape, check_data["seg"].shape)

error occurs when check_data = monai.utils.misc.first(check_loader)
error message:
RuntimeError: Caught RuntimeError in DataLoader worker process 0.
Original Traceback (most recent call last):
File "/opt/conda/lib/python3.7/site-packages/monai/transforms/transform.py", line 89, in apply_transform
return _apply_transform(transform, data, unpack_items)
File "/opt/conda/lib/python3.7/site-packages/monai/transforms/transform.py", line 53, in _apply_transform
return transform(parameters)
File "/opt/conda/lib/python3.7/site-packages/monai/transforms/spatial/dictionary.py", line 245, in call
affine=meta_data["affine"],
KeyError: 'affine'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/opt/conda/lib/python3.7/site-packages/monai/transforms/transform.py", line 89, in apply_transform
return _apply_transform(transform, data, unpack_items)
File "/opt/conda/lib/python3.7/site-packages/monai/transforms/transform.py", line 53, in apply_transform
return transform(parameters)
File "/opt/conda/lib/python3.7/site-packages/monai/transforms/compose.py", line 173, in call
input = apply_transform(transform, input, self.map_items, self.unpack_items, self.log_stats)
File "/opt/conda/lib/python3.7/site-packages/monai/transforms/transform.py", line 113, in apply_transform
raise RuntimeError(f"applying transform {transform}") from e
RuntimeError: applying transform <monai.transforms.spatial.dictionary.Spacingd object at 0x7fa35410a7d0>

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/opt/conda/lib/python3.7/site-packages/torch/utils/data/_utils/worker.py", line 287, in _worker_loop
data = fetcher.fetch(index)
File "/opt/conda/lib/python3.7/site-packages/torch/utils/data/_utils/fetch.py", line 49, in fetch
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/opt/conda/lib/python3.7/site-packages/torch/utils/data/_utils/fetch.py", line 49, in
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/opt/conda/lib/python3.7/site-packages/monai/data/dataset.py", line 97, in getitem
return self._transform(index)
File "/opt/conda/lib/python3.7/site-packages/monai/data/dataset.py", line 83, in _transform
return apply_transform(self.transform, data_i) if self.transform is not None else data_i
File "/opt/conda/lib/python3.7/site-packages/monai/transforms/transform.py", line 113, in apply_transform
raise RuntimeError(f"applying transform {transform}") from e
RuntimeError: applying transform <monai.transforms.compose.Compose object at 0x7fa35410a990>

[Nic-Ma]

Hi @lg2578 ,

I think we don't have affine information so far when loading PNG images.
Maybe you can try again with LoadImaged(keys=["img", "seg"], reader="ITKReader"),?
https://github.com/Project-MONAI/MONAI/blob/dev/monai/transforms/io/dictionary.py#L85

Thanks.