def main(args):
testing = [
'001', '017', '020', '022', '043', '082', '094', '115', '120', '137',
'173', '174', '205'
]
testing = [
'019', '023', '054', '093', '096', '123', '127', '136', '141', '153',
'188', '191', '201'
]
#testing = ['173', '002', '068', '133', '155', '114', '090', '105', '112', '175', '183', '208', '029', '065', '157', '162', '141', '062', '031', '156', '189', '135', '020', '077', '000', '009', '198', '036']
testing = [
'001', '017', '020', '022', '043', '082', '094', '115', '120', '137',
'173', '174', '205', '019', '023', '054', '093', '096', '123', '127',
'136', '141', '153', '188', '191', '201'
]
wholeDICE = []
kidneyDICE = []
cancerDICE = []
for x in tqdm(testing, desc="Caluculating DICE...", ncols=60):
trueLabel = os.path.expanduser(
args.trueLabel) + '/case_00' + x + '/segmentation.nii.gz'
resultLabel = os.path.expanduser(
args.resultLabel) + '/case_00' + x + '/label.mha'
true = sitk.ReadImage(trueLabel)
result = sitk.ReadImage(resultLabel)
trueArray = sitk.GetArrayFromImage(true)
resultArray = sitk.GetArrayFromImage(result)
wholeDICE.append(DICE(trueArray, resultArray))
trueKid = np.where(trueArray == 1, 1, 0)
trueCan = np.where(trueArray == 2, 2, 0)
resultKid = np.where(resultArray == 1, 1, 0)
resultCan = np.where(resultArray == 2, 2, 0)
kidneyDICE.append(DICE(trueKid, resultKid))
cancerDICE.append(DICE(trueCan, resultCan))
print('case_00' + x)
print("Average whole: {} ".format(DICE(trueArray, resultArray)))
print("Average kidney: {} ".format(DICE(trueKid, resultKid)))
print("Average cancer: {} ".format(DICE(trueCan, resultCan)))
print("Average whole: {} ".format(caluculateAVG(wholeDICE)))
print("Average kidney: {} ".format(caluculateAVG(kidneyDICE)))
print("Average cancer: {} ".format(caluculateAVG(cancerDICE)))
print()
def main(args):
testing = [
'019', '023', '054', '093', '096', '123', '127', '136', '141', '153',
'188', '191', '201'
]
# testing = ['173', '002', '068', '133', '155', '114', '090', '105', '112', '175', '183', '208', '029', '065', '157', '162', '141', '062', '031', '156', '189', '135', '020', '077', '000', '009', '198', '036']
wholeDICE = []
kidneyDICE = []
cancerDICE = []
for x in testing:
trueLabelLeft = os.path.expanduser(
args.trueLabel) + '/case_00' + x + '/label_left.nii.gz'
resultLabelLeft = os.path.expanduser(
args.resultLabel) + '/case_00' + x + '/segmentation_left.mha'
trueLabelRight = os.path.expanduser(
args.trueLabel) + '/case_00' + x + '/label_right.nii.gz'
resultLabelRight = os.path.expanduser(
args.resultLabel) + '/case_00' + x + '/segmentation_right.mha'
trueLeft = sitk.ReadImage(trueLabelLeft)
resultLeft = sitk.ReadImage(resultLabelLeft)
trueRight = sitk.ReadImage(trueLabelRight)
resultRight = sitk.ReadImage(resultLabelRight)
trueArrayLeft = sitk.GetArrayFromImage(trueLeft)
resultArrayLeft = sitk.GetArrayFromImage(resultLeft)
trueArrayRight = sitk.GetArrayFromImage(trueRight)
resultArrayRight = sitk.GetArrayFromImage(resultRight)
whole = DICEVersion2(trueArrayLeft, resultArrayLeft, trueArrayRight,
resultArrayRight)
wholeDICE.append(whole)
trueKidLeft = np.where(trueArrayLeft == 1, 1, 0)
trueCanLeft = np.where(trueArrayLeft == 2, 2, 0)
trueKidRight = np.where(trueArrayRight == 1, 1, 0)
trueCanRight = np.where(trueArrayRight == 2, 2, 0)
resultKidLeft = np.where(resultArrayLeft == 1, 1, 0)
resultCanLeft = np.where(resultArrayLeft == 2, 2, 0)
resultKidRight = np.where(resultArrayRight == 1, 1, 0)
resultCanRight = np.where(resultArrayRight == 2, 2, 0)
# if (trueCanLeft != 2).all() and (resultCanLeft != 2).all():
# cancer =
kidney = DICEVersion2(trueKidLeft, resultKidLeft, trueKidRight,
resultKidRight)
cancer = DICEVersion2(trueCanLeft, resultCanLeft, trueCanRight,
resultCanRight)
kidneyDICE.append(kidney)
cancerDICE.append(cancer)
print('case_00' + x)
print("Average whole: {} ".format(whole))
print("Average kidney: {} ".format(kidney))
print("Average cancer: {} ".format(cancer))
print("Average whole: {} ".format(caluculateAVG(wholeDICE)))
print("Average kidney: {} ".format(caluculateAVG(kidneyDICE)))
print("Average cancer: {} ".format(caluculateAVG(cancerDICE)))
print()
def main(args):
testing = [
'019', '023', '054', '093', '096', '123', '127', '136', '141', '153',
'188', '191', '201'
]
wholeDICE = []
kidneyDICE = []
cancerDICE = []
for x in testing:
trueLabelLeft = os.path.expanduser(
args.trueLabel) + '/case_00' + x + '/label_left.nii.gz'
resultLabelLeft = os.path.expanduser(
args.resultLabel) + '/case_00' + x + '/segmentation_left.mha'
trueLabelRight = os.path.expanduser(
args.trueLabel) + '/case_00' + x + '/label_right.nii.gz'
resultLabelRight = os.path.expanduser(
args.resultLabel) + '/case_00' + x + '/segmentation_right.mha'
trueLeft = sitk.ReadImage(trueLabelLeft)
resultLeft = sitk.ReadImage(resultLabelLeft)
trueRight = sitk.ReadImage(trueLabelRight)
resultRight = sitk.ReadImage(resultLabelRight)
trueArrayLeft = sitk.GetArrayFromImage(trueLeft)
resultArrayLeft = sitk.GetArrayFromImage(resultLeft)
trueArrayRight = sitk.GetArrayFromImage(trueRight)
resultArrayRight = sitk.GetArrayFromImage(resultRight)
wholeLeft = DICE(trueArrayLeft, resultArrayLeft)
wholeRight = DICE(trueArrayRight, resultArrayRight)
wholeDICE.append(wholeLeft)
wholeDICE.append(wholeRight)
trueKidLeft = np.where(trueArrayLeft == 1, 1, 0)
trueCanLeft = np.where(trueArrayLeft == 2, 2, 0)
trueKidRight = np.where(trueArrayRight == 1, 1, 0)
trueCanRight = np.where(trueArrayRight == 2, 2, 0)
resultKidLeft = np.where(resultArrayLeft == 1, 1, 0)
resultCanLeft = np.where(resultArrayLeft == 2, 2, 0)
resultKidRight = np.where(resultArrayRight == 1, 1, 0)
resultCanRight = np.where(resultArrayRight == 2, 2, 0)
kidneyLeft = DICE(trueKidLeft, resultKidLeft)
kidneyRight = DICE(trueKidRight, resultKidRight)
cancerLeft = DICE(trueCanLeft, resultCanLeft)
cancerRight = DICE(trueCanRight, resultCanRight)
kidneyDICE.append(kidneyLeft)
kidneyDICE.append(kidneyRight)
cancerDICE.append(cancerLeft)
cancerDICE.append(cancerRight)
print('case_00' + x)
print("Average whole: {} {} ".format(wholeLeft, wholeRight))
print("Average kidney: {} {} ".format(kidneyLeft, kidneyRight))
print("Average cancer: {} {} ".format(cancerLeft, cancerRight))
print("Average whole: {} ".format(caluculateAVG(wholeDICE)))
print("Average kidney: {} ".format(caluculateAVG(kidneyDICE)))
print("Average cancer: {} ".format(caluculateAVG(cancerDICE)))
print()