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inference_synapse.py
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import glob
import os
import SimpleITK as sitk
import numpy as np
import argparse
from medpy import metric
def read_nii(path):
return sitk.GetArrayFromImage(sitk.ReadImage(path))
def dice(pred, label):
if (pred.sum() + label.sum()) == 0:
return 1
else:
return 2. * np.logical_and(pred, label).sum() / (pred.sum() + label.sum())
def hd(pred,gt):
if pred.sum() > 0 and gt.sum()>0:
hd95 = metric.binary.hd95(pred, gt)
return hd95
else:
return 0
def process_label(label):
spleen = label == 1
right_kidney = label == 2
left_kidney = label == 3
gallbladder = label == 4
liver = label == 6
stomach = label == 7
aorta = label == 8
pancreas = label == 11
return spleen,right_kidney,left_kidney,gallbladder,liver,stomach,aorta,pancreas
def test(fold):
path='./'
label_list=sorted(glob.glob(os.path.join(path,'labelsTs','*nii.gz')))
infer_list=sorted(glob.glob(os.path.join(path,'inferTs',fold,'*nii.gz')))
print("loading success...")
print(label_list)
print(infer_list)
Dice_spleen=[]
Dice_right_kidney=[]
Dice_left_kidney=[]
Dice_gallbladder=[]
Dice_liver=[]
Dice_stomach=[]
Dice_aorta=[]
Dice_pancreas=[]
hd_spleen=[]
hd_right_kidney=[]
hd_left_kidney=[]
hd_gallbladder=[]
hd_liver=[]
hd_stomach=[]
hd_aorta=[]
hd_pancreas=[]
file=path + 'inferTs/'+fold
if not os.path.exists(file):
os.makedirs(file)
fw = open(file+'/dice_pre.txt', 'a')
for label_path,infer_path in zip(label_list,infer_list):
print(label_path.split('/')[-1])
print(infer_path.split('/')[-1])
label,infer = read_nii(label_path),read_nii(infer_path)
label_spleen,label_right_kidney,label_left_kidney,label_gallbladder,label_liver,label_stomach,label_aorta,label_pancreas=process_label(label)
infer_spleen,infer_right_kidney,infer_left_kidney,infer_gallbladder,infer_liver,infer_stomach,infer_aorta,infer_pancreas=process_label(infer)
Dice_spleen.append(dice(infer_spleen,label_spleen))
Dice_right_kidney.append(dice(infer_right_kidney,label_right_kidney))
Dice_left_kidney.append(dice(infer_left_kidney,label_left_kidney))
Dice_gallbladder.append(dice(infer_gallbladder,label_gallbladder))
Dice_liver.append(dice(infer_liver,label_liver))
Dice_stomach.append(dice(infer_stomach,label_stomach))
Dice_aorta.append(dice(infer_aorta,label_aorta))
Dice_pancreas.append(dice(infer_pancreas,label_pancreas))
hd_spleen.append(hd(infer_spleen,label_spleen))
hd_right_kidney.append(hd(infer_right_kidney,label_right_kidney))
hd_left_kidney.append(hd(infer_left_kidney,label_left_kidney))
hd_gallbladder.append(hd(infer_gallbladder,label_gallbladder))
hd_liver.append(hd(infer_liver,label_liver))
hd_stomach.append(hd(infer_stomach,label_stomach))
hd_aorta.append(hd(infer_aorta,label_aorta))
hd_pancreas.append(hd(infer_pancreas,label_pancreas))
fw.write('*'*20+'\n',)
fw.write(infer_path.split('/')[-1]+'\n')
fw.write('Dice_spleen: {:.4f}\n'.format(Dice_spleen[-1]))
fw.write('Dice_right_kidney: {:.4f}\n'.format(Dice_right_kidney[-1]))
fw.write('Dice_left_kidney: {:.4f}\n'.format(Dice_left_kidney[-1]))
fw.write('Dice_gallbladder: {:.4f}\n'.format(Dice_gallbladder[-1]))
fw.write('Dice_liver: {:.4f}\n'.format(Dice_liver[-1]))
fw.write('Dice_stomach: {:.4f}\n'.format(Dice_stomach[-1]))
fw.write('Dice_aorta: {:.4f}\n'.format(Dice_aorta[-1]))
fw.write('Dice_pancreas: {:.4f}\n'.format(Dice_pancreas[-1]))
fw.write('hd_spleen: {:.4f}\n'.format(hd_spleen[-1]))
fw.write('hd_right_kidney: {:.4f}\n'.format(hd_right_kidney[-1]))
fw.write('hd_left_kidney: {:.4f}\n'.format(hd_left_kidney[-1]))
fw.write('hd_gallbladder: {:.4f}\n'.format(hd_gallbladder[-1]))
fw.write('hd_liver: {:.4f}\n'.format(hd_liver[-1]))
fw.write('hd_stomach: {:.4f}\n'.format(hd_stomach[-1]))
fw.write('hd_aorta: {:.4f}\n'.format(hd_aorta[-1]))
fw.write('hd_pancreas: {:.4f}\n'.format(hd_pancreas[-1]))
dsc=[]
HD=[]
dsc.append(Dice_spleen[-1])
dsc.append((Dice_right_kidney[-1]))
dsc.append(Dice_left_kidney[-1])
dsc.append(np.mean(Dice_gallbladder[-1]))
dsc.append(np.mean(Dice_liver[-1]))
dsc.append(np.mean(Dice_stomach[-1]))
dsc.append(np.mean(Dice_aorta[-1]))
dsc.append(np.mean(Dice_pancreas[-1]))
fw.write('DSC:'+str(np.mean(dsc))+'\n')
HD.append(hd_spleen[-1])
HD.append(hd_right_kidney[-1])
HD.append(hd_left_kidney[-1])
HD.append(hd_gallbladder[-1])
HD.append(hd_liver[-1])
HD.append(hd_stomach[-1])
HD.append(hd_aorta[-1])
HD.append(hd_pancreas[-1])
fw.write('hd:'+str(np.mean(HD))+'\n')
fw.write('*'*20+'\n')
fw.write('Mean_Dice\n')
fw.write('Dice_spleen'+str(np.mean(Dice_spleen))+'\n')
fw.write('Dice_right_kidney'+str(np.mean(Dice_right_kidney))+'\n')
fw.write('Dice_left_kidney'+str(np.mean(Dice_left_kidney))+'\n')
fw.write('Dice_gallbladder'+str(np.mean(Dice_gallbladder))+'\n')
fw.write('Dice_liver'+str(np.mean(Dice_liver))+'\n')
fw.write('Dice_stomach'+str(np.mean(Dice_stomach))+'\n')
fw.write('Dice_aorta'+str(np.mean(Dice_aorta))+'\n')
fw.write('Dice_pancreas'+str(np.mean(Dice_pancreas))+'\n')
fw.write('Mean_hd\n')
fw.write('hd_spleen'+str(np.mean(hd_spleen))+'\n')
fw.write('hd_right_kidney'+str(np.mean(hd_right_kidney))+'\n')
fw.write('hd_left_kidney'+str(np.mean(hd_left_kidney))+'\n')
fw.write('hd_gallbladder'+str(np.mean(hd_gallbladder))+'\n')
fw.write('hd_liver'+str(np.mean(hd_liver))+'\n')
fw.write('hd_stomach'+str(np.mean(hd_stomach))+'\n')
fw.write('hd_aorta'+str(np.mean(hd_aorta))+'\n')
fw.write('hd_pancreas'+str(np.mean(hd_pancreas))+'\n')
fw.write('*'*20+'\n')
dsc=[]
dsc.append(np.mean(Dice_spleen))
dsc.append(np.mean(Dice_right_kidney))
dsc.append(np.mean(Dice_left_kidney))
dsc.append(np.mean(Dice_gallbladder))
dsc.append(np.mean(Dice_liver))
dsc.append(np.mean(Dice_stomach))
dsc.append(np.mean(Dice_aorta))
dsc.append(np.mean(Dice_pancreas))
fw.write('dsc:'+str(np.mean(dsc))+'\n')
HD=[]
HD.append(np.mean(hd_spleen))
HD.append(np.mean(hd_right_kidney))
HD.append(np.mean(hd_left_kidney))
HD.append(np.mean(hd_gallbladder))
HD.append(np.mean(hd_liver))
HD.append(np.mean(hd_stomach))
HD.append(np.mean(hd_aorta))
HD.append(np.mean(hd_pancreas))
fw.write('hd:'+str(np.mean(HD))+'\n')
print('done')
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument("fold", help="fold name")
args = parser.parse_args()
fold=args.fold
test(fold)