Comments (3)
askerlee
commented on July 30, 2024
You mean test3d.py right?
Previously I suggested you to insert a structure like below to use brats 2020 dataset. But seems brats 2020 folders are already included in this structure:
'brats': {
'num_classes': 4,
'bce_weight': [0., 3, 1, 1.75], # bg, ET, WT, TC
'ds_class': 'BratsSet',
'train_ds_names': '2019train',
'test_ds_name': '2019valid',
'chosen_modality': -1,
'xyz_permute': None, # (1, 2, 0),
'orig_input_size': None,
# each dim of the orig_patch_size should always be multiply of 8.
'orig_patch_size': (112, 112, 96),
'input_scale': (1, 1, 1),
'D_pool_K': 2,
'has_mask': { '2019train': True, '2019valid': False,
'2020train': True, '2020valid': False },
'weight': { '2019train': 1, '2019valid': 1,
'2020train': 1, '2020valid': 1 }
},
But you need to name the names of the training and validation folders to 2020train and 2020valid, respectively.
Then the test command line will be like:
python3 test3d.py --task brats --split all --bs 5 --ds 2020valid --net segtran --attractors 1024 --translayers 1 --cpdir ../model/segtran-brats-2019train-01170142 --iters 8000
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bhralzz
commented on July 30, 2024
but still getting below error in test3d.py
TypeError: init() got an unexpected keyword argument 'mask_num_classes'
when running the command
python3 test3d.py --task brats --split all --bs 5 --ds BraTS20_Valid --net segtran --attractors 1024 --translayers 1 --cpdir ../model/segtran-brats-BraTS20_Train-09211348 --iters 1000
as the train and validation folder path as below:
BraTS20_Train & BraTS20_Valid
and the train3d.py worked correctly in this setting
by removing such keywords worked!
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askerlee
commented on July 30, 2024
Thank you! Yes it's because I updated datasets3d.py but forgot to update test3d.py. So some useless variables were still there. I've fixed the code.
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