def arfi_lesions(self):
"""
characterize all ARFI lesions and define ARFI index lesion
"""
if self.arfi.values()[0] != 'no lesions read':
try:
from prostate27 import Prostate27
p = Prostate27()
index = {}
for lesion in self.arfi['lesions']:
if lesion['index'] is True:
index['IOS'] = lesion['IOS']
index['region'] = lesion['region']
index['location'] = \
p.anterior_posterior([lesion['region']])
index['zone'] = p.zone(lesion['region'])
self.arfi['index'] = index
break
except ValueError:
self.arfi['index'] = None
# specify location and zone for each lesion
for n, lesion in enumerate(self.arfi['lesions']):
self.arfi['lesions'][n].update({
'location':
p.anterior_posterior([lesion['region']]),
'zone':
p.zone(lesion['region'])
})
def check_hist_clin_sig_sensitivity(self):
"""
check if ARFI detected clinically-significant lesions
"""
from prostate27 import Prostate27
p = Prostate27()
self.clin_sig_sensitivity = []
try:
for lesion in self.histology['pca']:
if lesion['Clinically Significant']:
nnset = p.nearest_neighbors([lesion['region']])
for arfi in self.arfi['lesions']:
lesion_region = arfi['region']
if ('index' not in lesion_region) and \
('read' not in lesion_region):
if lesion_region in nnset:
self.clin_sig_sensitivity.append([
True,
p.anterior_posterior([lesion['region']])
])
else:
self.clin_sig_sensitivity.append([
False,
p.anterior_posterior([lesion['region']])
])
except KeyError:
self.clin_sig_sensitivity = None
def check_benign_match(self):
"""
check if atrophy or bph is present in the exact or nearest neighbor
region to an ARFI lesion
"""
from prostate27 import Prostate27
p = Prostate27()
self.benign_match = {}
for benign in ['atrophy', 'bph']:
try:
if self.histology['index'] is None:
self.benign_match[benign] = False
else:
benign_regions = self.histology[benign]['regions']
arfi_regions_nn = p.nearest_neighbors(
[x['region'] for x in self.arfi['lesions']])
if (any([x in benign_regions for x in arfi_regions_nn])) \
and (self.histology['index']['region'] not in
benign_regions):
self.benign_match[benign] = True
else:
self.benign_match[benign] = False
except KeyError:
self.benign_match[benign] = False
def mri_lesions(self):
"""
characterize all MRI lesions and define MRI index lesion
"""
if self.mri.values()[0] != 'no lesions read':
try:
from prostate27 import Prostate27
p = Prostate27()
index = {}
for lesion in self.mri['lesions']:
if lesion['index'] is True:
index['IOS'] = lesion['IOS']
index['region'] = lesion['region']
index['location'] = p.anterior_posterior(
[lesion['region']])
index['zone'] = p.zone(lesion['region'])
index['Gleason'] = lesion['Gleason']
index['diameter_mm'] = lesion['diameter_mm']
index['ECE'] = lesion['extracap']
index['lesion_number'] = lesion['lesion_number']
self.mri['index'] = index
break
except ValueError:
self.mri['index'] = None
for n, lesion in enumerate(self.mri['lesions']):
self.mri['lesions'][n].update({
'location':
p.anterior_posterior([lesion['region']]),
'zone':
p.zone(lesion['region'])
})
def test_location(self):
"""
indices corresponding to region
"""
p = Prostate27()
self.assertTrue(p.location(['12a']) == (2, 1, 3))
self.assertTrue(p.location(['1a']) == (0, 1, 1))
self.assertTrue(p.location(['5a']) == (2, 1, 1))
def test_anterior_posterior(self):
"""
anterior / posterior assignment
"""
p = Prostate27()
self.assertTrue(p.anterior_posterior(['14as']) == 'anterior')
self.assertTrue(p.anterior_posterior(['1p']) == 'posterior')
self.assertTrue(p.anterior_posterior(['5a']) == 'anterior')
def test_nn_ranges(self):
"""
27 region index bounds not exceeded; AS regions pull all mid-gland
"""
p = Prostate27()
self.assertTrue(p.nn_ranges((1, 2, 3)) == [[0, 1, 2], [1, 2], [2, 3]])
self.assertTrue(
p.nn_ranges((0, 0, 0)) == [[0, 1], [0, 1], [0, 1, 2, 3]])
def test_zone(self):
"""
peripheral zone / central gland assignment
"""
p = Prostate27()
self.assertTrue(p.zone('9a') == 'central gland')
self.assertTrue(p.zone('11a') == 'central gland')
self.assertTrue(p.zone('4a') == 'peripheral zone')
self.assertTrue(p.zone('14as') == 'peripheral zone')
def histology_lesions(self):
"""
characterize all histology lesions in dict, including index, nearest
neighbors, clinical significance, location and zone
"""
from prostate27 import Prostate27
p = Prostate27()
try:
index = {}
for lesion in self.histology['pca']:
if lesion['index'] is True:
index['region'] = lesion['region']
index['Gleason'] = lesion['Gleason']
index['volume'] = lesion['volume_cc']
index['nn'] = p.nearest_neighbors([lesion['region']])
index['location'] = p.anterior_posterior(
[lesion['region']])
index['Staging'] = lesion['Staging']
index['ECE_extent'] = lesion['ECE_extent']
index['zone'] = p.zone(lesion['region'])
self.histology['index'] = index
break
for n, les in enumerate(self.histology['pca']):
if self.clin_sig(les['volume_cc'], les['Gleason']):
self.histology['pca'][n].update(
{'Clinically Significant': True})
else:
self.histology['pca'][n].update(
{'Clinically Significant': False})
self.histology['pca'][n].update(
{'location': p.anterior_posterior([les['region']])})
self.histology['pca'][n].update(
{'zone': p.zone(les['region'])})
except ValueError:
print "No PCA lesion"
self.histology['index'] = None
if 'index' in self.histology:
pass
else:
print "No Histology Index Lesion, P%i" % self.pnum
self.histology['index'] = None
def check_clin_sig_match(self):
"""
check if ARFI reads are clinically-significant lesions
"""
from prostate27 import Prostate27
p = Prostate27()
hist_nnset = set()
histnonsigset = set()
self.clin_sig_match = []
# find histology nearest neighbors for all clinically sig lesions
for i in self.histology['pca']:
if i['Clinically Significant']:
hist_nnset.update(p.nearest_neighbors([i['region']]))
else:
histnonsigset.update(p.nearest_neighbors([i['region']]))
self.false_positive = []
try:
for lesion in self.arfi['lesions']:
lesion_region = lesion['region']
if lesion_region in hist_nnset:
self.clin_sig_match.append(
[True, lesion['location'], lesion['IOS']])
else:
self.clin_sig_match.append(
[False, lesion['location'], lesion['IOS']])
# check if something else exists in this region, including:
# non-clinically significant PCA, atrophy, BPH
if lesion_region in histnonsigset:
self.false_positive.append('pca')
elif self.histology['atrophy']:
if lesion_region in self.histology['atrophy'][
'regions']:
self.false_positive.append('atrophy')
elif self.histology['bph']:
if lesion_region in self.histology['bph']['regions']:
self.false_positive.append('bph')
else:
self.false_positive.append('no lesion')
except KeyError:
self.clin_sig_match = None
self.false_positive = None
def test_nearest_neighbor(self):
"""
nearest neighbors are found for individual or list of regions
"""
p = Prostate27()
self.assertIn('6a', p.nearest_neighbors(['5a']))