def test_valid_MR_dataset(self):
"""
valid MRI dataset
"""
P13 = MRAnalysis(13, './testing')
self.assertFalse(P13.valid)
P11 = MRAnalysis(11, './testing')
self.assertTrue(P11.valid)
P14 = MRAnalysis(14, './testing')
self.assertTrue(P14.valid)
def test_established_ece_match(self):
"""
MRI ECE : Histology ECE for if ECE present in entire patient
"""
P10 = MRAnalysis(10, './testing')
self.assertTrue(P10.ece_match['established_match'] == 'True_Positive')
P11 = MRAnalysis(11, './testing')
self.assertTrue(P11.ece_match['established_match'] == 'False_Negative')
P14 = MRAnalysis(14, './testing')
self.assertTrue(P14.ece_match['established_match'] == 'True_Negative')
def test_histology_ECE(self):
"""
Histology JSON ECE parsing
"""
P10 = LesionAnalysis(10, './testing')
self.assertTrue(P10.histology['index']['Staging'] == 'T3a')
self.assertTrue(P10.histology['index']['ECE_extent'] == 'Established')
P10 = MRAnalysis(10, './testing')
self.assertTrue(P10.histology['index']['Staging'] == 'T3a')
self.assertTrue(P10.histology['index']['ECE_extent'] == 'Established')
P11 = MRAnalysis(11, './testing')
self.assertTrue(P11.histology['index']['Staging'] == 'T3b')
self.assertTrue(P11.histology['index']['ECE_extent'] == 'Established')
def test_mri_lesion(self):
"""
MRI file parsing for index lesion
"""
P11 = MRAnalysis(11, './testing')
self.assertTrue(P11.mri['index']['region'] == '9p')
self.assertTrue(P11.mri['index']['IOS'] == 3)
# these tests depend on Prostate27, but I'll include them too
self.assertTrue(P11.mri['index']['location'] == 'posterior')
self.assertTrue(P11.mri['index']['zone'] == 'peripheral zone')
# these tests are only relevant for MRI data
self.assertTrue(P11.mri['index']['Gleason'] == 7)
self.assertTrue(P11.mri['index']['diameter_mm'] == 8)
self.assertTrue(P11.mri['index']['ECE'] == False)
self.assertTrue(P11.mri['index']['lesion_number'] == 1)
# test for case with multiple IOS3 lesions (top line in text file is index)
P14 = MRAnalysis(14, './testing')
self.assertTrue(P14.mri['index']['region'] == '10p')
self.assertTrue(P14.mri['index']['IOS'] == 3)
self.assertFalse(P14.mri['index']['region'] == '3p')
def test_histology_mri_index_match(self):
"""
histology / MRI index match
"""
P11 = MRAnalysis(11, './testing')
self.assertFalse(P11.index_match['exact'])
self.assertTrue(P11.index_match['nn'])
P14 = MRAnalysis(14, './testing')
self.assertFalse(P14.index_match['exact'])
self.assertTrue(P14.index_match['nn'])
P13 = MRAnalysis(13, './testing')
self.assertFalse(P13.valid)
P11 = MRAnalysis(11, './testing')
self.assertTrue(P11.valid)
P14 = MRAnalysis(14, './testing')
self.assertTrue(P14.valid)
def test_index_ece_match(self):
"""
MRI ECE : Histology ECE for index lesions
"""
P11 = MRAnalysis(11, './testing')
self.assertFalse(P11.ece_match['index']['False_Positive'])
self.assertFalse(P11.ece_match['index']['Established'])
self.assertFalse(P11.ece_match['index']['Focal'])
self.assertFalse(P11.ece_match['index']['True_Negative'])
P10 = MRAnalysis(10, './testing')
self.assertFalse(P10.ece_match['index']['False_Positive'])
self.assertTrue(P10.ece_match['index']['Established'])
self.assertFalse(P10.ece_match['index']['Focal'])
self.assertFalse(P10.ece_match['index']['True_Negative'])
P14 = MRAnalysis(14, './testing')
self.assertFalse(P14.ece_match['index']['False_Positive'])
self.assertFalse(P14.ece_match['index']['Established'])
self.assertFalse(P14.ece_match['index']['Focal'])
self.assertFalse(P14.ece_match['index']['True_Negative'])
def test_MR_no_index_match(self):
"""
no histology index lesion using MRAnalysis class
"""
P13 = MRAnalysis(13, './testing')
self.assertFalse(P13.check_index_match())
def test_MR_no_index_match(self):
"""
no histology index lesion using MRAnalysis class
"""
P13 = MRAnalysis(13, './testing')
self.assertFalse(P13.check_index_match())
Pece_index_TN = []
Pece_index_FP = []
Pece_index_miss = []
# check ECE for patient-level matches
Pece_pm_TP = []
Pece_pm_FN = []
Pece_pm_TN = []
Pece_pm_FP = []
# check ECE for patient level matches only on Established focal extent lesions
Pece_em_TP = []
Pece_em_FN = []
Pece_em_TN = []
Pece_em_FP = []
for p in range(56, 107):
P = MRAnalysis(p)
if P.valid:
Ptotal.append(p)
if P.index_match['exact']:
Pexact.append(p)
if P.index_match['nn']:
Pnn.append(p)
else:
Pmiss.append(p)
if P.benign_match['atrophy']:
Patrophy.append(p)
if P.benign_match['bph']:
Pbph.append(p)
Pclinsig.append(P.clin_sig_match)
Pclinsigsens.append(P.clin_sig_sensitivity)