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Hello, I am having a very similar issue as #1616, i.e. I can use Error: Potentially useful info: Furthermore, if I do use ...
Am stumped. Any advice / direction would be greatly appreciated, thank you! |
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Answered by
rijobro
Mar 18, 2021
Replies: 1 comment 2 replies
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Do you think you could create a minimum example that demonstrates your problem? You can use one of the freely available datasets, something like this: from glob import glob
import os
from monai.apps import download_and_extract
from monai.transforms import <transforms>
from monai.data import CacheDataset, DataLoader, Dataset
# get data
directory = os.environ.get("MONAI_DATA_DIRECTORY")
root_dir = tempfile.mkdtemp() if directory is None else os.path.expanduser(directory)
print(root_dir)
task = "Task09_Spleen"
resource = "https://msd-for-monai.s3-us-west-2.amazonaws.com/" + task + ".tar"
compressed_file = os.path.join(root_dir, task + ".tar")
data_dir = os.path.join(root_dir, task)
download_and_extract(resource, compressed_file, root_dir)
# get images
images = sorted(glob(os.path.join(data_dir, "imagesTr", "*.nii.gz")))
labels = sorted(glob(os.path.join(data_dir, "labelsTr", "*.nii.gz")))
data_dicts = [{"image": image, "label": label}
for image, label in zip(images, labels)]
# transforms
transform = Compose([
<transforms>
])
ds = CacheDataset(data=data_dicts, transform=transforms, ...) # any other args
dl = DataLoader(ds, batch_size=?, shuffle=?, num_workers=?)
for _ in dl:
pass |
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2 replies
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Thanks very much for your reply! I figured it out using the code that you provided. Turns out I was missing LoadImaged from my transforms... I'm so sorry. At some point I think the LoadNiftid transform was removed and I never replaced it properly. Thanks again for the support, much appreciated! More details in case it's helpful to anyone else: The code rijobro provided, with my parameters: ds loads with Dataset, but not with CacheDataset. The error code when using CacheDataset without LoadImaged in transform: Using CacheDataset with transforms |
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Ok that makes sense. I guess the error message here wasn't very helpful, maybe that's something we can improve! @wyli? |
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Answer selected by
ctpn
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Do you think you could create a minimum example that demonstrates your problem? You can use one of the freely available datasets, something like this: