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constants.py
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constants.py
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# Dont forget the / at the end of the paths
# unzip data to these folders
CHEXPERT_DIR = '/cluster/projects/mcintoshgroup/CheXpert-v1.0-small/'
MIMIC_DIR = '/cluster/projects/mcintoshgroup/MIMIC-CXR/MIMIC-CXR/physionet.org/files/mimic-cxr/2.0.0/files/'
NIH_DIR = '/cluster/projects/mcintoshgroup/NIH-14/'
CXRAY_SZ = 320
CXRAY_DIS = ['No Finding','Enlarged Cardiomediastinum', 'Cardiomegaly', 'Lung Opacity','Lung Lesion', 'Edema', 'Consolidation', 'Pneumonia', 'Atelectasis','Pneumothorax', 'Pleural Effusion', 'Pleural Other', 'Fracture','Support Devices']
CXRAY_CL = [2,5,6,8,10]
COVID_KAGGLE_DIR = '/cluster/projects/mcintoshgroup/COVID-19_Radiography_Dataset/'
COVID_INT_DIR1 = '/cluster/projects/mcintoshgroup/COVID-PositiveOnly/'
COVID_INT_DIR2 = '/cluster/projects/mcintoshgroup/COVID-imaging/'
COVID_XRAY_SZ = 256
COVID_DIS = ['COVID','Normal','Lung_Opacity','Viral Pneumonia']
COVID_DIS_CL = [0,1]
JUST_DIR = '/cluster/projects/mcintoshgroup/BiasAnalysis/AudioBias/Test_Data/Audio/'
ICBHI_DIR = '/cluster/projects/mcintoshgroup/BiasAnalysis/AudioBias/ICBHI_final_database/'
PROCESSED_MEL_DIR = '/cluster/projects/mcintoshgroup/BiasAnalysis/AudioLungSounds/mel_spec/'
MEL_SPEC_SZ = 224
LUNG_DIS = ['Normal','Abnormal']
LUNG_DIS_CL = [0,1]
ILD_DIR = '/cluster/projects/mcintoshgroup/ILD/'
# ILD_DIS = ['Normal','Abnormal'] - # Changing since labels were originally flipped
ILD_DIS = ['Abnormal','Normal']
ILD_DIS_CL = [0,1]
PTBXL_DIR = '/cluster/projects/mcintoshgroup/Results/PTB-XL/'
PTBXL_DIS = ['CD','HYP','MI','STTC','NORM']
PTBXL_DIS_CL = [0,1,2,3,4]
LUDB_DIR = '/cluster/projects/mcintoshgroup/Results/LUDB/'
LUDB_DIS = ['CD','HYP']
LUDB_DIS_CL = [0,1]
# Save models here
BASE_DATA_DIR = '/cluster/projects/mcintoshgroup/BiasAnalysis/'
MODEL_DIR = '/cluster/projects/mcintoshgroup/BiasAnalysis/models_v1/'
# MODEL_DIR = '/cluster/projects/mcintoshgroup/BiasAnalysis/models/'
MEAN_STD = {
'chexpert_train':[[128.2121,],[74.0974,]],
'mimic_train':[[2477.1777,],[1103.6028,]],
'nih_train':[[128.9558,],[59.0587,]],
'covid_kaggle_train':[[129.5715,],[58.9904,]],
# OLD # 'covid_internal_train':[[2330.8491,],[776.7404,]],
'covid_internal_train':[[2347.5303,],[759.0811,]],
'ild_TR_train':[-584.2516,492.6476],
'ild_plan_train':[-749.2117,415.7507],
# OLD
# 'just_train': [[20.3834, 8.4188, 24.1917],[43.0854, 17.9024, 36.8831]],
# 'icbhi_train': [[54.8954, 20.1839, 61.6515],[55.9522, 24.3787, 39.3875]],
'just_train': [[24.7278, 9.9977, 27.5706],[50.5934, 22.3349, 39.7978]],
'icbhi_train': [[62.2622, 22.9156, 68.2407],[61.6764, 28.8834, 38.7871]],
# 12 Channel
'ptbxl_train':[
[-0.0020, -0.0015, 0.0006, 0.0018, -0.0012, -0.0004, 0.0002, -0.0009,-0.0016, -0.0014, -0.0008, -0.0024],
[0.1412, 0.1469, 0.1320, 0.1283, 0.1151, 0.1200, 0.1903, 0.2886, 0.2851,0.2653, 0.2386, 0.2012]
],
'ludb_train':[
[0.0005, 0.0004, 0.0005, 0.0005, 0.0005, 0.0005, 0.0004, 0.0003, 0.0002,0.0002, 0.0002, 0.0003],
[0.1167, 0.1142, 0.1054, 0.1187, 0.1065, 0.1097, 0.1198, 0.1180, 0.1162,0.1108, 0.1142, 0.1183]
]
}
DIS_CLASSES = {
'chexpert_80_20': CXRAY_DIS,
'mimic': CXRAY_DIS,
'combined': CXRAY_DIS,
'nih': CXRAY_DIS,
'combined_nihmimic': CXRAY_DIS,
'covid_kaggle': COVID_DIS,
'covid_internal': COVID_DIS,
}