def test_IlluminationGradient(self):
illumination_gradient = optics.IlluminationGradient(gradient=(5e-5,
5e-5))
microscope = optics.Brightfield(
NA=0.7,
wavelength=660e-9,
resolution=1e-6,
magnification=10,
refractive_index_medium=1.33,
upscale=2,
output_region=(0, 0, 64, 64),
padding=(10, 10, 10, 10),
aberration=None,
illumination=illumination_gradient,
)
scatterer = PointParticle(
refractive_index=1.45 + 0.1j,
position_unit="pixel",
position=(32, 32),
)
imaged_scatterer = microscope(scatterer)
output_image = imaged_scatterer.resolve()
self.assertIsInstance(output_image, Image)
self.assertEqual(output_image.shape, (64, 64, 1))
self.assertEqual(
output_image.get_property("pupil_at_focus").shape, (128, 128))
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 test_Brightfield(self):
microscope = optics.Brightfield(NA=0.7,
wavelength=660e-9,
resolution=1e-6,
magnification=10,
refractive_index_medium=1.33,
upscale=2,
output_region=(0, 0, 64, 64),
padding=(10, 10, 10, 10),
aberration=None)
scatterer = PointParticle(
refractive_index=1.45 + 0.1j,
position_unit="pixel",
position=(32, 32),
)
imaged_scatterer = microscope(scatterer)
output_image = imaged_scatterer.resolve()
self.assertIsInstance(output_image, Image)
self.assertEqual(output_image.shape, (64, 64, 1))
def test_Fluorescence(self):
microscope = optics.Fluorescence(NA=0.7,
wavelength=660e-9,
resolution=1e-6,
magnification=10,
refractive_index_medium=1.33,
upscale=2,
padding=(10, 10, 10, 10),
output_region=(0, 0, 64, 64),
aberration=None)
scatterer = PointParticle(
intensity=100, # Squared magnitude of the field.
position_unit="pixel", # Units of position (default meter)
position=(32, 32), # Position of the particle
)
imaged_scatterer = microscope(scatterer)
output_image = imaged_scatterer.resolve()
self.assertIsInstance(output_image, Image)
self.assertEqual(output_image.shape, (64, 64, 1))
class TestAberrations(unittest.TestCase):
particle = PointParticle(position=(32, 32), position_unit="pixel", intensity=1)
def testGaussianApodization(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.GaussianApodization(sigma=0.5),
)
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 testPiston(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.Piston(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 testVerticalTilt(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.VerticalTilt(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 testHorizontalTilt(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.HorizontalTilt(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 testObliqueAstigmatism(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.ObliqueAstigmatism(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 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 testAstigmatism(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.Astigmatism(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 testObliqueTrefoil(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.ObliqueTrefoil(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 testVerticalComa(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.VerticalComa(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 testHorizontalComa(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.HorizontalComa(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 testTrefoil(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.Trefoil(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 testSphericalAberration(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.SphericalAberration(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))