Install covid19ct3d using pip `(for Python >=3.6)`
git clone https://github.com/reshalfahsi/covid19ct3d
cd covid19ct3d
pip install .
Training
import covid19ct3d
# set training parameters
epoch = 30 # epoch number
lr = 1e-2 # learning rate
augmentation = True # choose to do data augmentation
batchsize = 2 # training batch size
trainsize = "128 128 64" # training dataset size
train_path = "./dataset" # path to train dataset
train_save = "./model" # path to saved model
step_lr = 2 # set the epoch to drop learning rate
# perform training
covid19ct3d.train(epoch=epoch,
lr=lr,
augmentation=augmentation,
batchsize=batchsize,
trainsize=trainsize,
train_path=train_path,
train_save=train_save,
step_lr=step_lr
)
Prediction
import covid19ct3d
# set prediction parameters
predict_size = "128 128 64" # predict size
pth_path = './model/COVID19CT3D.pth' # path to the trained model
data_path = './dataset/CT-0/study_0100.nii.gz' # path to the dataset
# perform prediction
covid19ct3d.predict(predict_size=predict_size,
pth_path=pth_path,
data_path=data_path
)
Model Information
import covid19ct3d
covid19ct3d.info()
Training
covid19ct3d train \
--epoch 30 \
--lr 1e-2 \
--batchsize 2 \
--trainsize "128 128 64" \
--train_path "./dataset" \
--train_save "./model" \
--augmentation
Prediction
covid19ct3d predict \
--predict_size "128 128 64" \
--pth_path "./model/COVID19CT3D.pth" \
--data_path "./dataset/CT-23/study_0982.nii.gz"
Model Information
covid19ct3d info