num_patches_per_image missing in the default config file for swinunetr

[aryaabdi]

I am trying to run auto3Dseg with swinunetr backbone. I follow the toy example, however, I am getting the following error:

Traceback (most recent call last):
File "/home/z004br3h/projects/rg_segmentation/exp/pretrain_headneck_rev_3_swinunetr/swinunetr_0/scripts/train.py", line 850, in
fire.Fire()
File "/home/z004br3h/python/pyenv/pt2/lib/python3.10/site-packages/fire/core.py", line 143, in Fire
component_trace = _Fire(component, args, parsed_flag_args, context, name)
File "/home/z004br3h/python/pyenv/pt2/lib/python3.10/site-packages/fire/core.py", line 477, in _Fire
component, remaining_args = _CallAndUpdateTrace(
File "/home/z004br3h/python/pyenv/pt2/lib/python3.10/site-packages/fire/core.py", line 693, in _CallAndUpdateTrace
component = fn(*varargs, **kwargs)
File "/home/z004br3h/projects/rg_segmentation/exp/pretrain_headneck_rev_3_swinunetr/swinunetr_0/scripts/train.py", line 192, in run
train_transforms = parser.get_parsed_content("transforms_train")
File "/home/z004br3h/python/pyenv/pt2/lib/python3.10/site-packages/monai/bundle/config_parser.py", line 290, in get_parsed_content
return self.ref_resolver.get_resolved_content(id=id, **kwargs)
File "/home/z004br3h/python/pyenv/pt2/lib/python3.10/site-packages/monai/bundle/reference_resolver.py", line 193, in get_resolved_content
return self._resolve_one_item(id=id, **kwargs)
File "/home/z004br3h/python/pyenv/pt2/lib/python3.10/site-packages/monai/bundle/reference_resolver.py", line 163, in _resolve_one_item
self._resolve_one_item(id=d, waiting_list=waiting_list, **kwargs)
File "/home/z004br3h/python/pyenv/pt2/lib/python3.10/site-packages/monai/bundle/reference_resolver.py", line 163, in _resolve_one_item
self._resolve_one_item(id=d, waiting_list=waiting_list, **kwargs)
File "/home/z004br3h/python/pyenv/pt2/lib/python3.10/site-packages/monai/bundle/reference_resolver.py", line 159, in _resolve_one_item
raise ValueError(msg) from err
ValueError: the referring item @num_patches_per_image is not defined in the config content.

The variable num_patches_per_image is not defined in the default hyperparameter.yaml. Does this variable need to be set manually?

[KumoLiu]

Hi @aryaabdi, I didn't see the usage for this arg in swinunetr's algorithm.
https://github.com/Project-MONAI/research-contributions/tree/main/auto3dseg/algorithm_templates/swinunetr
Can you run the hello world successfully?
https://github.com/Project-MONAI/tutorials/blob/main/auto3dseg/notebooks/auto3dseg_hello_world.ipynb