def test_region_by_identifier(self):
from jicbioimage.segment import SegmentedImage
input_array = np.array([[0, 0, 0],
[1, 1, 1],
[2, 2, 2]])
segmented_image = SegmentedImage.from_array(input_array)
with self.assertRaises(ValueError):
segmented_image.region_by_identifier(0)
with self.assertRaises(ValueError):
segmented_image.region_by_identifier(0.5)
with self.assertRaises(ValueError):
segmented_image.region_by_identifier(-1)
from jicbioimage.segment import Region
selected_region = segmented_image.region_by_identifier(1)
self.assertTrue(isinstance(selected_region, Region))
expected_output = Region.select_from_array(input_array, 1)
self.assertTrue(np.array_equal(selected_region,
expected_output))
def test_dilate(self):
from jicbioimage.segment import Region
test_array = np.array([[0, 0, 0, 0, 0],
[0, 0, 1, 1, 0],
[0, 1, 1, 0, 0],
[0, 1, 0, 0, 0],
[0, 0, 0, 0, 0]])
region = Region(test_array)
dilate_array = np.array([[0, 0, 1, 1, 0],
[0, 1, 1, 1, 1],
[1, 1, 1, 1, 0],
[1, 1, 1, 0, 0],
[0, 1, 0, 0, 0]], dtype=bool)
self.assertTrue(np.array_equal(region.dilate(),
dilate_array))
def test_region_select_from_array(self):
from jicbioimage.segment import Region
id_array = np.array([[0, 0, 0],
[1, 1, 1],
[2, 2, 2]])
region_1 = Region.select_from_array(id_array, 1)
self.assertFalse(region_1[0, 0])
self.assertTrue(region_1[1, 0])
self.assertFalse(region_1[2, 0])
self.assertEqual(region_1.area, 3)
def test_background(self):
from jicbioimage.segment import SegmentedImage
input_array = np.array([[0, 0, 0],
[1, 1, 1],
[2, 2, 2]])
segmented_image = SegmentedImage.from_array(input_array)
from jicbioimage.segment import Region
background = segmented_image.background
expected_output = Region.select_from_array(input_array, 0)
self.assertTrue(np.array_equal(background,
expected_output))
