Hi,
I am trying to use the software using the myself dataset. While following the guides on github,I got a training exception error during training stage.
The data should be organized as follows:
├── /base/path
│ ├── raw_data
│ │ ├── tomo03.coords
│ │ └── tomo03.mrc
│ │ └── tomo04.coords
│ │ └── tomo04.mrc
│ │ └── tomo05.mrc
│ │ └── tomo06.mrc
│ │ └── ...
the preprocessing configs as follow:
pre_config={"dset_name": "preprocess",
"base_path": "/home/user/other_method/DeepETPicker",
"coord_path": "/home/user/other_method/DeepETPicker/raw_data",
"coord_format": ".coords",
"tomo_path": "/home/user/other_method/DeepETPicker/raw_data",
"tomo_format": ".mrc",
"num_cls": 1,
"label_type": "sphere",
"label_diameter": 10,
"ocp_type": "sphere",
"ocp_diameter": "20",
"norm_type": "standardization"}
and the train_configs as follows:
train_configs={"dset_name": "train",
"base_path": "/home/user/other_method/DeepETPicker",
"coord_path": "/home/user/other_method/DeepETPicker/coords",
"coord_format": ".coords",
"tomo_path": "/home/user/other_method/DeepETPicker/data_std",
"tomo_format": ".mrc",
"num_cls": 1,
"label_name": "sphere11",
"label_path": "/home/user/other_method/DeepETPicker/sphere11",
"label_type": "sphere",
"label_diameter": 11,
"ocp_type": "sphere",
"ocp_diameter": "23",
"ocp_name": "data_ocp",
"ocp_path": "/home/user/other_method/DeepETPicker/data_ocp",
"norm_type": "standardization",
"model_name": "ResUNet",
"train_set_ids": "0",
"val_set_ids": "1",
"batch_size": 8,
"patch_size": 64,
"padding_size": 12,
"lr": 0.0005,
"max_epochs": 100,
"seg_thresh": 0.5,
"gpu_ids": "0"}
But when I was training, I encountered the 'Training Exception' error.Could you provide any explanations on why this is occurring?
Thank you!
Hi,
I am trying to use the software using the myself dataset. While following the guides on github,I got a training exception error during training stage.
The data should be organized as follows:
├── /base/path
│ ├── raw_data
│ │ ├── tomo03.coords
│ │ └── tomo03.mrc
│ │ └── tomo04.coords
│ │ └── tomo04.mrc
│ │ └── tomo05.mrc
│ │ └── tomo06.mrc
│ │ └── ...
the preprocessing configs as follow:
pre_config={"dset_name": "preprocess",
"base_path": "/home/user/other_method/DeepETPicker",
"coord_path": "/home/user/other_method/DeepETPicker/raw_data",
"coord_format": ".coords",
"tomo_path": "/home/user/other_method/DeepETPicker/raw_data",
"tomo_format": ".mrc",
"num_cls": 1,
"label_type": "sphere",
"label_diameter": 10,
"ocp_type": "sphere",
"ocp_diameter": "20",
"norm_type": "standardization"}
and the train_configs as follows:
train_configs={"dset_name": "train",
"base_path": "/home/user/other_method/DeepETPicker",
"coord_path": "/home/user/other_method/DeepETPicker/coords",
"coord_format": ".coords",
"tomo_path": "/home/user/other_method/DeepETPicker/data_std",
"tomo_format": ".mrc",
"num_cls": 1,
"label_name": "sphere11",
"label_path": "/home/user/other_method/DeepETPicker/sphere11",
"label_type": "sphere",
"label_diameter": 11,
"ocp_type": "sphere",
"ocp_diameter": "23",
"ocp_name": "data_ocp",
"ocp_path": "/home/user/other_method/DeepETPicker/data_ocp",
"norm_type": "standardization",
"model_name": "ResUNet",
"train_set_ids": "0",
"val_set_ids": "1",
"batch_size": 8,
"patch_size": 64,
"padding_size": 12,
"lr": 0.0005,
"max_epochs": 100,
"seg_thresh": 0.5,
"gpu_ids": "0"}
But when I was training, I encountered the 'Training Exception' error.Could you provide any explanations on why this is occurring?
Thank you!