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lwx aa72814955 | 1 year ago | |
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models | 1 year ago | |
utils | 1 year ago | |
LICENSE | 1 year ago | |
README-zh.md | 1 year ago | |
README.md | 1 year ago | |
data_function.py | 1 year ago | |
data_preprocessing.py | 1 year ago | |
hparam.py | 1 year ago | |
loss_function.py | 1 year ago | |
main.py | 1 year ago | |
metrics.py | 1 year ago | |
show_data.py | 1 year ago | |
train.py | 1 year ago |
Read Chinese Introduction:Here!
We are planning a major update to the code in the near future, so if you have any suggestions, please feel free to email me or mention them in the issue.
if your source dataset is :
source_dataset
├── source_1.mhd
├── source_1.zraw
├── source_2.mhd
├── source_2.zraw
├── source_3.mhd
├── source_3.zraw
├── source_4.mhd
├── source_4.zraw
└── ...
and your label dataset is :
label_dataset
├── label_1.mhd
├── label_1.zraw
├── label_2.mhd
├── label_2.zraw
├── label_3.mhd
├── label_3.zraw
├── label_4.mhd
├── label_4.zraw
└── ...
then your should modify fold_arch as *.mhd, source_train_dir as source_dataset and label_train_dir as label_dataset in hparam.py
if your source dataset is :
source_dataset
├── 1
├── source_1.mhd
├── source_1.zraw
├── 2
├── source_2.mhd
├── source_2.zraw
├── 3
├── source_3.mhd
├── source_3.zraw
├── 4
├── source_4.mhd
├── source_4.zraw
└── ...
and your label dataset is :
label_dataset
├── 1
├── label_1.mhd
├── label_1.zraw
├── 2
├── label_2.mhd
├── label_2.zraw
├── 3
├── label_3.mhd
├── label_3.zraw
├── 4
├── label_4.mhd
├── label_4.zraw
└── ...
then your should modify fold_arch as */*.mhd, source_train_dir as source_dataset and label_train_dir as label_dataset in hparam.py
set hparam.train_or_test to 'train'
python main.py
set hparam.train_or_test to 'train'
python main.py -k True
set hparam.train_or_test to 'test'
python main.py
This project is not perfect and there are still many problems. If you are using this project and would like to give the author some feedbacks, you can send Me an email.
This repository is an unoffical PyTorch implementation of Medical segmentation in 3D and 2D and highly based on MedicalZooPytorch and torchio. Thank you for the above repo. The project is done with the supervisions of Prof. Ruoxiu Xiao and Dr. Cheng Chen. Thank you to Youming Zhang, Daiheng Gao, Jie Zhang, Xing Tao, Weili Jiang and Shanshan Li for all the help I received.
If this code is helpful for you, you can cite these for us. Thank you.
[1] Chen C, Zhou K. An Effective Deep Neural Network for Lung Lesions Segmentation from COVID-19 CT Images[J]. IEEE Transactions on Industrial Informatics, 2021.
[2] Chen C, Zhang T, et al. Pathological lung segmentation in chest CT images based on improved random walker[J]. Computer Methods and Programs in Biomedicine, 2021, 200: 105864.
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