def test_basic(self):
class NS(object):
def __init__(self, dict):
self.__dict__.update(dict)
segmentation_param=NS({'evaluation_units':'foreground,cc',
'num_classes':2,
'output_prob':False})
eval_param=NS({'evaluations':'Dice'})
mask = np.reshape(np.abs(np.linspace(0.,2.,64)-1)>.8,[4,4,4,1,1])
data_dict = {'label':mask,'inferred':mask}
interp_orders = {'label':0,'inferred':0}
image_folder = '.'
e = SegmentationEvaluator(None, segmentation_param, eval_param)
def generator():
yield ('test',data_dict,interp_orders)
result_dict = e.evaluate_from_generator(generator())
self.assertIn(('subject_id', 'label'), result_dict)
self.assertIn(('subject_id', 'cc_id'), result_dict)
self.assertEqual(tuple(result_dict[('subject_id', 'label')].index.names),
('subject_id', 'label'))
self.assertEqual(tuple(result_dict[('subject_id', 'cc_id')].index.names),
('subject_id', 'cc_id'))
print(result_dict[('subject_id', 'cc_id')].to_dict('index'))
self.assertEqual(result_dict[('subject_id', 'label')].to_dict('index'),
{('test', 1): {'dice': 1.}})
self.assertEqual(result_dict[('subject_id', 'cc_id')].to_dict('index'),
{('test', 'r1_s1'): {'dice': 1.},
('test', 'r2_s2'): {'dice': 1.}})
def test_basic(self):
class NS(object):
def __init__(self, dict):
self.__dict__.update(dict)
segmentation_param=NS({'evaluation_units':'foreground,cc',
'num_classes':2,
'output_prob':False})
eval_param=NS({'evaluations':'Dice'})
mask = np.reshape(np.abs(np.linspace(0.,2.,64)-1)>.8,[4,4,4,1,1])
data_dict = {'label':mask,'inferred':mask}
interp_orders = {'label':0,'inferred':0}
image_folder = '.'
e = SegmentationEvaluator(None, segmentation_param, eval_param)
def generator():
yield ('test',data_dict,interp_orders)
result_dict = e.evaluate_from_generator(generator())
self.assertIn(('subject_id', 'label'), result_dict)
self.assertIn(('subject_id', 'cc_id'), result_dict)
self.assertEqual(tuple(result_dict[('subject_id', 'label')].index.names),
('subject_id', 'label'))
self.assertEqual(tuple(result_dict[('subject_id', 'cc_id')].index.names),
('subject_id', 'cc_id'))
print(result_dict[('subject_id', 'cc_id')].to_dict('index'))
self.assertEqual(result_dict[('subject_id', 'label')].to_dict('index'),
{('test', 1): {'dice': 1.}})
self.assertEqual(result_dict[('subject_id', 'cc_id')].to_dict('index'),
{('test', 'r1_s1'): {'dice': 1.},
('test', 'r2_s2'): {'dice': 1.}})
def test_segmentation_evaluator(self):
app_param = Namespace(evaluation_units='label,cc',output_prob=False,
num_classes=2)
eval_param = Namespace(evaluations='Dice,Jaccard,average_distance')
evalu = SegmentationEvaluator(SegmentationEvaluatorTests.ReaderStub(),
app_param, eval_param)
result_dict = evalu.evaluate()
self.assertIn(('subject_id', 'cc_id'), result_dict)
self.assertIn(('subject_id', 'label'), result_dict)
group_cc = result_dict[('subject_id', 'cc_id')]
group_l = result_dict[('subject_id', 'label')]
self.assertIn('jaccard', list(group_l.columns))
self.assertIn('dice', list(group_l.columns))
self.assertIn('jaccard', list(group_cc.columns))
self.assertIn('dice', list(group_cc.columns))
self.assertIn('average_distance', list(group_cc.columns))
self.assertIn(('foo','r1_s1'), list(group_cc.index))
self.assertIn(('bar','r1_s1'), list(group_cc.index))
self.assertIn(('foo',1), list(group_l.index))
self.assertIn(('bar',1), list(group_l.index))
def test_segmentation_evaluator(self):
app_param = Namespace(evaluation_units='label,cc',output_prob=False,
num_classes=2)
eval_param = Namespace(evaluations='Dice,Jaccard,average_distance')
evalu = SegmentationEvaluator(SegmentationEvaluatorTests.ReaderStub(),
app_param, eval_param)
result_dict = evalu.evaluate()
self.assertIn(('subject_id', 'cc_id'), result_dict)
self.assertIn(('subject_id', 'label'), result_dict)
group_cc = result_dict[('subject_id', 'cc_id')]
group_l = result_dict[('subject_id', 'label')]
self.assertIn('jaccard', list(group_l.columns))
self.assertIn('dice', list(group_l.columns))
self.assertIn('jaccard', list(group_cc.columns))
self.assertIn('dice', list(group_cc.columns))
self.assertIn('average_distance', list(group_cc.columns))
self.assertIn(('foo','r1_s1'), list(group_cc.index))
self.assertIn(('bar','r1_s1'), list(group_cc.index))
self.assertIn(('foo',1), list(group_l.index))
self.assertIn(('bar',1), list(group_l.index))
def initialise_evaluator(self, eval_param):
self.eval_param = eval_param
self.evaluator = SegmentationEvaluator(self.readers[0],
self.segmentation_param,
eval_param)