def test_Sequence(self):
optics = Fluorescence(
NA=0.6,
magnification=10,
resolution=1e-6,
wavelength=633e-9,
output_region=(0, 0, 32, 32),
)
ellipse = Ellipse(
position_unit="pixel",
position=(16, 16),
intensity=1,
radius=(1.5e-6, 1e-6),
rotation=0, # This will be the value at time 0.
upsample=2,
)
def get_rotation(sequence_length, previous_value):
return previous_value + 2 * np.pi / sequence_length
rotating_ellipse = sequences.Sequential(ellipse, rotation=get_rotation)
imaged_rotating_ellipse = optics(rotating_ellipse)
imaged_rotating_ellipse_sequence = sequences.Sequence(
imaged_rotating_ellipse, sequence_length=50)
self.assertIsInstance(imaged_rotating_ellipse_sequence,
sequences.Sequence)
def test_Generator(self):
optics = Fluorescence(
NA=0.7,
wavelength=680e-9,
resolution=1e-6,
magnification=10,
output_region=(0, 0, 128, 128),
)
scatterer = PointParticle(
intensity=100,
position_unit="pixel",
position=lambda: np.random.rand(2) * 128,
)
imaged_scatterer = optics(scatterer)
def get_particle_position(result):
for property in result.properties:
if "position" in property:
return property["position"]
generator = generators.Generator()
particle_generator = generator.generate(imaged_scatterer,
get_particle_position,
batch_size=4)
particles, positions = next(particle_generator)
for particle, position in zip(particles, positions):
self.assertEqual(particle.shape, (128, 128, 1))
self.assertTrue(np.all(position >= 0))
self.assertTrue(np.all(position <= 128))
def testDefocus(self):
aberrated_optics = Fluorescence(
NA=0.3,
resolution=1e-6,
magnification=10,
wavelength=530e-9,
output_region=(0, 0, 64, 64),
padding=(64, 64, 64, 64),
aberration=aberrations.Defocus(coefficient=1))
aberrated_particle = aberrated_optics(self.particle)
for z in (-100, 0, 100):
im = aberrated_particle.resolve(z=z)
self.assertIsInstance(im, Image)
self.assertEqual(im.shape, (64, 64, 1))
def test_Sphere(self):
optics = Fluorescence(NA=0.7,
wavelength=680e-9,
resolution=1e-6,
magnification=10,
output_region=(0, 0, 64, 64))
scatterer = scatterers.Sphere(intensity=100,
position_unit="pixel",
position=(32, 32),
radius=1e-6,
upsample=4)
imaged_scatterer = optics(scatterer)
output_image = imaged_scatterer.resolve()
self.assertIsInstance(output_image, Image)
self.assertEqual(output_image.shape, (64, 64, 1))
def test_Ellipsoid(self):
optics = Fluorescence(
NA=0.7,
wavelength=680e-9,
resolution=1e-6,
magnification=10,
output_region=(0, 0, 64, 64),
)
scatterer = scatterers.Ellipsoid(
intensity=100,
position_unit="pixel",
position=(32, 32),
radius=(1e-6, 0.5e-6, 0.25e-6),
rotation=(np.pi / 4, 0, 0),
upsample=4,
)
imaged_scatterer = optics(scatterer)
output_image = imaged_scatterer.resolve()
self.assertIsInstance(output_image, Image)
self.assertEqual(output_image.shape, (64, 64, 1))