update readme

README.md

@@ -88,38 +88,43 @@ We used 10k CT volumes from public datasets and 98k private CT volumes for pretr
 
 **Main Requirements**  
 > torch==1.10.2  
-> pymic 
+> PyMIC 
 
-**Installation**
-```bash
-pip install DDD
-```
+To use [PyMIC](https://github.com/HiLab-git/PyMIC), please download the latest code in the master branch, and add the path of pymic source code to `PYTHONPATH` environmental variable. See `bash.sh` for example.
 
-**Download Model**
 
+**Demo data**
+In this demo, we show using PCT-Net for left atrial segmentation. The dataset can be downloaded from [PYMIC_data](https://drive.google.com/file/d/1eZakSEBr_zfIHFTAc96OFJix8cUBf-KR/view?usp=sharing).
 
-**Preprocess**
-```bash
-python DDD
-```
+The dataset, network and training/testing settings can be found in configuration files: `demo/pctnet_scratch.cfg` and `demo/pctnet_pretrain.cfg` for training from scratch and using the pretrained weights, respectively.
 
+After downloading the data, edit the value of `root_dir` in the configuration files, and make sure the path to the images are correct.
 
 **Training**
 ```bash
-python DDD
+python train.py demo/pctnet_scratch.cfg
 ```
+or 
 
+```bash
+python train.py demo/pctnet_pretrain.cfg
+```
 
-**Validation**
+**Inference**
 ```bash
-python DDD
+python predict.py demo/pctnet_scratch.cfg
 ```
+or 
 
+```bash
+python predict.py demo/pctnet_pretrain.cfg
+```
 
-**Testing**
+**Evaluation**
 ```bash
-python DDD
+python $PyMIC_path/pymic/util/evaluation_seg.py -cfg demo/evaluation.cfg
 ```
+You may need to edit `demo/evaluation.cfg` to specify the path of segmented results before evaluating the performance.
 
 ## 🙋‍♀️ Feedback and Contact
 

bash.sh

@@ -1,4 +1,3 @@
-# PyMIC_path=/home/x/projects/PyMIC_project/PyMIC
 PyMIC_path=/home/x/projects/PyMIC_project/PyMIC_release/PyMIC-master
 export PYTHONPATH=$PYTHONPATH:$PyMIC_path