def test_set_augmentation(self):
img_path = os.path.join(base_path, '../test_data/tiffconnector_1/im/')
label_path = os.path.join(base_path,
'../test_data/tiffconnector_1/labels/')
c = TiffConnector(img_path, label_path)
d = Dataset(c)
size = (1, 3, 4)
pad = (1, 2, 2)
m = TrainingBatch(d, size, padding_zxy=pad)
self.assertEqual(m.augmentation, {'flip'})
m.augment_by_rotation(True)
self.assertEqual(m.augmentation, {'flip', 'rotate'})
self.assertEqual(m.rotation_range, (-45, 45))
m.augment_by_shear(True)
self.assertEqual(m.augmentation, {'flip', 'rotate', 'shear'})
self.assertEqual(m.shear_range, (-5, 5))
m.augment_by_flipping(False)
self.assertEqual(m.augmentation, {'rotate', 'shear'})
def test_get_ilastik_weights2(self):
pth = os.path.join(base_path, '../test_data/ilastik/dimensionstest')
img_path = os.path.join(pth, 'images')
lbl_path = os.path.join(pth, 'x15_y10_z2_c4_classes2.ilp')
c = IlastikConnector(img_path, lbl_path)
d = Dataset(c)
size = (2, 15, 10) # this is the size of the whole image
pad = (0, 0, 0)
m = TrainingBatch(d, size, padding_zxy=pad)
m.augment_by_flipping(False)
mini = next(m)
weights = mini.weights()
print(weights[0, :, :, :, :])
# all samples of the batch should be identical,
# because tilesize=imsize
assert_array_equal(weights[0, :, :, :, :], weights[1, :, :, :, :])
# weight positions from labelvalue 1 and 2
pos = [[0, 0, 2, 1], [0, 0, 2, 1], [0, 0, 8, 6], [0, 0, 9, 6],
[0, 1, 4, 3], [1, 0, 2, 2], [1, 0, 3, 2], [1, 0, 8, 7],
[1, 0, 9, 7]]
for p in pos:
self.assertEqual(weights[0, p[0], p[1], p[2], p[3]], 1)
self.assertEqual(weights[1, p[0], p[1], p[2], p[3]], 1)
def test_get_ilastik_weights(self):
img_path = os.path.join(base_path, '../test_data/ilastik')
lbl_path = os.path.join(base_path,
'../test_data/ilastik/ilastik-1.2.ilp')
c = IlastikConnector(img_path, lbl_path)
d = Dataset(c)
size = (8, 2, 4)
pad = (0, 0, 0)
m = TrainingBatch(d, size, padding_zxy=pad)
m.augment_by_flipping(False)
mini = next(m)
weights = mini.weights()
# label 1 at position (4,1,3)
self.assertTrue(weights[0, 0, 4, 1, 3] == 1)
# label 2 at position (1,1,1)
self.assertTrue(weights[0, 1, 1, 1, 1] == 1)
# label 3 at position (1,1,1)
self.assertTrue(weights[0, 2, 7, 1, 1] == 1)