def test_voi(self):
from cremi_tools.metrics import voi
shape = (64, 64, 64)
seg = np.random.randint(0, 100, size=shape, dtype='uint32')
gt = np.random.randint(0, 100, size=shape, dtype='uint32')
vis, vim = voi(seg, gt)
self.assertGreater(vis, 0)
self.assertGreater(vim, 0)
def test_vi_random_data(self):
print("Blub")
from elf.evaluation import rand_index
shape = (256, 256)
x = np.random.randint(0, 100, size=shape)
y = np.random.randint(0, 100, size=shape)
vi_s, vi_m = variation_of_information(x, y, ignore_gt=[0])
vi_s_exp, vi_m_exp = voi(x, y)
self.assertAlmostEqual(vi_s, vi_s_exp)
self.assertAlmostEqual(vi_m, vi_m_exp)
def test_vi(self):
from cluster_tools.utils.validation_utils import variation_of_information
f = z5py.File(self.path)
ds_gt = f[self.gt_key]
ds_gt.n_threads = 4
gt = ds_gt[self.bb]
ds_seg = f[self.seg_key]
ds_seg.n_threads = 4
seg = ds_seg[self.bb]
vi_s, vi_m = variation_of_information(seg, gt, ignore_gt=[0])
vi_s_exp, vi_m_exp = voi(seg, gt)
self.assertAlmostEqual(vi_s, vi_s_exp)
self.assertAlmostEqual(vi_m, vi_m_exp)
def test_cremi_score(self):
from cluster_tools.utils.validation_utils import cremi_score
f = z5py.File(self.path)
ds_gt = f[self.gt_key]
ds_gt.n_threads = 4
gt = ds_gt[self.bb]
ds_seg = f[self.seg_key]
ds_seg.n_threads = 4
seg = ds_seg[self.bb]
vis, vim, ari, cs = cremi_score(seg, gt, ignore_gt=[0])
ari_exp = adapted_rand(seg, gt)
vis_exp, vim_exp = voi(seg, gt)
cs_exp = np.sqrt(ari_exp * (vis_exp + vim_exp))
self.assertAlmostEqual(ari, ari_exp)
self.assertAlmostEqual(vis, vis_exp)
self.assertAlmostEqual(vim, vim_exp)
self.assertAlmostEqual(cs, cs_exp)
def get_scores(seg, gt):
rand = adapted_rand(seg, gt)
vis, vim = voi(seg, gt)
return {'rand': rand, 'vi-split': vis, 'vi-merge': vim}