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root bbbab74552 | 2 years ago | |
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imgs | 2 years ago | |
scripts | 2 years ago | |
src | 2 years ago | |
README.md | 2 years ago | |
UNet2d.ckpt | 2 years ago | |
eval.py | 2 years ago | |
eval_log.txt | 2 years ago | |
requirements.txt | 2 years ago | |
suwen-1.0.1-py3-none-any.whl | 2 years ago | |
train.py | 2 years ago | |
train_log.txt | 2 years ago |
2DUNet was proposed in 2015, it is a typoe of neural network that directly consumes 2D images. The u-net archiecture ahiceves very good performance on very different biomedical segmentation applications. Without strong data augmentations, it only needs very few annotated images and has a ver reasonable trainning time.
Paper: Ronneberger, O., Fischer, P. and Brox, T., 2015, October. U-net: Convolutional networks for biomedical image segmentation. In International Conference on Medical image computing and computer-assisted intervention (pp. 234-241). Springer, Cham.
Paper: Hofmanninger J, Prayer F, Pan J, Röhrich S, Prosch H, Langs G. Automatic lung segmentation in routine imaging is primarily a data diversity problem, not a methodology problem. European Radiology Experimental. 2020 Dec;4(1):1-3.
The 2DUNet segementation network takes n 2D images as input, applies input and feature transformations. BN is introdued before each ReLU.
2d-Covid-segmentaiton
Dataset size: 1.2G
suwen package
pip install -r requirements.txt
pip install ./suwen-1.0.1-py3-none-any.whl
After installing MindSpore via the official website, you can start training and evaluation as follows:
# enter script dir, train PointNet
sh run_train_ascend.sh
# enter script dir, evaluate PointNet
sh run_eval.sh
.
├── README.md
├── UNet2d.ckpt
├── eval.py
├── eval_log.txt
├── imgs
│ └── 2dUNet.png
├── requirements.txt
├── scripts
│ ├── run_eval.sh
│ └── run_train_ascend.sh
├── src
│ ├── __pycache__
│ │ ├── cross_entropy_with_logits.cpython-37.pyc
│ │ ├── dataset.cpython-37.pyc
│ │ ├── dice_loss.cpython-37.pyc
│ │ └── dice_metric.cpython-37.pyc
│ ├── cross_entropy_with_logits.py
│ ├── dataset.py
│ ├── dice_loss.py
│ └── dice_metric.py
├── suwen-1.0.1-py3-none-any.whl
├── train.py
└── train_log.txt
4 directories, 19 files
Major parameters in train.py are as follows:
--data_path: The absolute full path to the train and evaluation datasets.
--seg_path : The absolute full path to the train and evaluation segmentation labels.
--ckpt_path: The absolute full path to the checkpoint file saved after training.
More hyperparamteters can be modified in src/config.py.
running on Ascend
sh run_train_ascend.sh
After training, the loss value will be achieved as what in train_log.txt
The model checkpoint will be saved in the current ckpt directory.
Before running the command below, please check the checkpoint path used for evaluation.
running on Ascend
sh scripts/run_eval.sh
You can view the results through the file "eval_log". The accuracy of the test dataset will be as what in eval_log.txt.
Parameters | |
---|---|
Resource | Ascend 910; CPU 2.60GHz, 24cores; Memory, 96G |
uploaded Date | 11/22/2021 (month/day/year) |
MindSpore Version | 1.3.0 |
Dataset | MM-WHS |
Training Parameters | epoch=600 |
Optimizer | Adam |
Loss Function | Softmax Cross Entropy |
outputs | probability |
Loss | SoftmaxCrossEntropyWithLogits |
Speed | -ms/step- |
Total time | -ms |
Checkpoint for Fine tuning | 23M (.ckpt file) |
Parameters | |
---|---|
Resource | Ascend 910; CPU 2.60GHz, 24cores; Memory, 96G |
uploaded Date | 11/22/2021 (month/day/year) |
MindSpore Version | 1.3.0 |
Dataset | MM-WHS |
batch_size | 1 |
outputs | probability |
Dice | 75.86% |
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