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 annotate3D(microscopy_collection, series, segmentation3D, name):
for z in microscopy_collection.zslices(series):
image = microscopy_collection.image(s=series, z=z)
zslice = segmentation3D[:, :, z]
segmentation = SegmentedImage.from_array(zslice)
annotation = annotate(image, segmentation)
fname = "z{:03d}_{}.png".format(z, name)
fpath = os.path.join(AutoName.directory, fname)
with open(fpath, "wb") as fh:
fh.write(annotation.png())
def test_number_of_segments(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)
self.assertEqual(segmented_image.number_of_segments, 2)
def test_identifiers(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)
self.assertEqual(segmented_image.identifiers, set([1, 2]))
def test_unique_colour_image(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)
unique_color_image = segmented_image.unique_color_image
from jicbioimage.core.util.array import unique_color_array
self.assertTrue(np.array_equal(unique_color_image,
unique_color_array(input_array)))
def test_png(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)
png = segmented_image.png()
ar = np.asarray(PIL.Image.open(io.BytesIO(png)))
self.assertTrue(np.array_equal(ar, segmented_image.pretty_color_image))
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))
def test_merge_regions(self):
from jicbioimage.segment import SegmentedImage
input_array = np.array([[0, 0, 0],
[1, 1, 1],
[2, 2, 2]])
expected_output = np.array([[0, 0, 0],
[1, 1, 1],
[1, 1, 1]])
segmented_image = SegmentedImage.from_array(input_array)
segmented_image.merge_regions(1, 2)
self.assertTrue(np.array_equal(segmented_image, expected_output))