def to_directory(self, directory):
if not os.path.isdir(directory):
os.mkdir(directory)
xdim, ydim, zdim = self.shape
num_digits = Image3D._num_digits(zdim-1)
for z in range(zdim):
num = str(z).zfill(num_digits)
fname = "z{}.png".format(num)
fpath = os.path.join(directory, fname)
with open(fpath, "wb") as fh:
im = Image.from_array(unique_color_array(self[:, :, z]))
fh.write(im.png())
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_unique_color_array(self):
from jicbioimage.core.util.array import unique_color_array
input_array = np.array([[0, 0, 0],
[1, 1, 1],
[16777215, 16777215, 16777215]])
c1 = [0, 0, 0]
c2 = [0, 0, 1]
c3 = [255, 255, 255]
expected_output = np.array([[c1, c1, c1],
[c2, c2, c2],
[c3, c3, c3]], dtype=np.uint8)
actual_output = unique_color_array(input_array)
self.assertTrue(np.array_equal(actual_output, expected_output))
def unique_color_image(self):
"""Return segmentation as a unique color image.
:returns: `jicbioimage.core.image.Image`
"""
return Image.from_array(unique_color_array(self))
