tedbang/deeplung

Detection

This is a refine version of DeepLung repo with dependecies:

• python 3.7
• pytorch 1.10

Reference:

https://github.com/wentaozhu/DeepLung.git

https://github.com/uci-cbcl/DeepLung.git

Preprare data

1. Download the luna16 data and put all them in folder luna16
2. change path variable in file config_training.py and config_training9.py to your data folder. (change f variable in run_training.sh to choose another config file)
3. run prepare.py to preproess all data.

Start running detection

1. use the cmd

sh run_training.sh 

Done

• torch version problem
• data path
• numpy version problem (1.21.5 with problem of np.asarray(metrics))

Classification

• fix the error loading file with xlrd : /data/yangqinzhu/ctLung/DeepLung-master/nodcls/data/list3.2.csv

PrepareData

1. change .dcm file name, such as 1-001.dcm to 0000001.dcm
2. run ./nodcls/data/extclsshpinfo.py
3. run /data/yangqinzhu/ctLung/DeepLung-master/nodcls/data/dataconverter.py to get file annotationdetclsconv_v3.csv
4. run /data/yangqinzhu/ctLung/DeepLung-master/nodcls/data/nodclsgbt.py to generate folder /luna16/cls/crop_v3/

Train

1. run main_nodcls.py to train the based classify model.(/data/yangqinzhu/ctLung/DeepLung-master/checkpoint-9/ckpt.t7)
2. run bash run_test_getTrainData.sh to get pbb train data before runing file det2cls.py.
3. run det2cls.py to train classify.
4. run testdet2cls.py.

you can change the path as you need, I have listed them it front of the function in each python file