Issue with Plot label map
See original GitHub issueProblem Thank you for provide great library:) I have a problem about plotting LabelMap using plot().
To reproduce
def get_data(args):
print(f'> Getting {args.mode} data.... > Augmentation mode: {args.transform}')
data_path = os.path.join(args.data_dir, args.hospital)
dataset = MedicalDataset(root_dir=data_path, args=args)
for data in dataset.training_set:
one_subject = data
label = data['label'][tio.DATA]
print((data['label'][tio.DATA]== 1).nonzero(as_tuple=True))
one_subject.plot()
return dataset
class MedicalDataset(Dataset):
def __init__(self, root_dir, args):
self.root_dir = root_dir
self.image_size = args.image_size
self.subjects = []
dicom_list = os.listdir(os.path.join(self.root_dir, 'dicom'))
for dicom_dir in tqdm(dicom_list):
subject = tio.Subject(
input=tio.ScalarImage(os.path.join(root_dir, 'dicom', dicom_dir)),
label=tio.LabelMap(os.path.join(root_dir, 'label', dicom_dir+'.nii.gz')),
)
self.subjects.append(subject)
self.training_set = tio.SubjectsDataset(self.subjects)
print(f'{args.mode} dataset_size:', len(self.training_set), 'subjects')
Expected behavior Large size of segment is shown on plot but, small size of segment is not shown like "Actual behavior. So I check label category on nii.gz file by printing tensor, but there was no probelm. Does it originally working like this?
Actual behavior
System info
Output of python <(curl -s https://raw.githubusercontent.com/fepegar/torchio/main/print_system.py)
:
Platform: Windows-10-10.0.19043-SP0
torchio: 0.18.62
torch: 1.9.1+cu111
numpy: 1.21.2
Python: 3.9.6 | packaged by conda-forge | (default, Jul 11 2021, 03:37:25) [MSC v.1916 64 bit (AMD64)]
Issue Analytics
- State:
- Created 2 years ago
- Comments:15 (10 by maintainers)
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Top GitHub Comments
Thank you for your kind answering and fixing problem even though there was a problem talking with me. I wish you every happiness!!☺🌹
Alright. You discovered a bug. Thanks for reporting and for sharing your data! I will fix it in a second.