def setUp(self):
ins = Instrument(magnification=.048, wavelength=.447, n_m=1.335)
p1 = Sphere(r_p=[150, 150, 200], a_p=1., n_p=1.45)
p2 = Sphere(r_p=[75, 75, 150], a_p=1.25, n_p=1.61)
coords = coordinates((201, 201))
self.model = GeneralizedLorenzMie(coords, [p1, p2], ins)
self.fast_model = FastGeneralizedLorenzMie(coords, [p1, p2], ins)
self.cuda_model = CudaGeneralizedLorenzMie(coords, [p1, p2], ins)
def feature_extent(sphere, config, nfringes=20):
'''Radius of holographic feature in pixels'''
s = Sphere()
s.a_p = sphere.a_p
s.n_p = sphere.n_p
s.z_p = sphere.z_p
h = LMHologram(coordinates=np.arange(300))
h.instrument.properties = config['instrument']
h.particle = sphere
# roughly estimate radii of zero crossings
b = h.hologram() - 1.
ndx = np.where(np.diff(np.sign(b)))[0] + 1
return float(ndx[nfringes])
def make_sample(config):
'''Returns an array of Sphere objects'''
particle = config['particle']
nrange = particle['nspheres']
mpp = config['instrument']['magnification']
if nrange[0] == nrange[1]:
nspheres = nrange[0]
else:
nspheres = np.random.randint(nrange[0], nrange[1])
sample = []
for n in range(nspheres):
np.random.seed()
sphere = Sphere()
for prop in ('a_p', 'n_p', 'k_p', 'z_p'):
setattr(sphere, prop, make_value(particle[prop]))
##Making sure separation between particles is large enough##
close = True
aval = sphere.a_p
zval = sphere.z_p
while close:
close = False
xval = make_value(particle['x_p'])
yval = make_value(particle['y_p'])
for s in sample:
xs, ys, zs = s.x_p, s.y_p, s.z_p
atest = s.a_p
dist = np.sqrt((xs - xval)**2 + (ys - yval)**2 +
(zs - zval)**2)
threshold = (atest + aval) / mpp
if dist < threshold:
close = True
setattr(sphere, 'x_p', xval)
setattr(sphere, 'y_p', yval)
sample.append(sphere)
return sample
def __init__(self,
a_p=None,
n_p=None,
r_p=None,
particle=None,
**kwargs):
'''
Parameters
----------
a_p : float or numpy.ndarray, optional
Starting radius of sphere. Alternatively, can be
an array of radii of concentric shells within the sphere
n_p : complex or numpy.ndarray, optional
Starting refractive index of sphere. Alternatively,
can be an array of refractive indexes of the shells.
r_p : numpy.ndarray or list, optional
coordinates of sphere center: (x_p, y_p, z_p)
'''
super(LorenzMie, self).__init__(**kwargs)
self.particle = Sphere()
if a_p is not None:
self.particle.a_p = a_p
if n_p is not None:
self.particle.n_p = n_p
if r_p is not None:
self.particle.r_p = r_p
def make_sample(config):
'''Returns an array of Sphere objects'''
particle = config['particle']
nrange = particle['nspheres']
nspheres = np.random.randint(nrange[0], nrange[1])
sample = []
for n in range(nspheres):
sphere = Sphere()
for prop in ('a_p', 'n_p', 'k_p', 'x_p', 'y_p', 'z_p'):
setattr(sphere, prop, make_value(particle[prop]))
sample.append(sphere)
return sample
def setUp(self):
self.particle = Sphere()
self.fast_particle = FastSphere()
self.particle.r_p = (100, 200, 300)
self.fast_particle.r_p = (100, 200, 300)
class TestSphere(unittest.TestCase):
def setUp(self):
self.particle = Sphere()
self.fast_particle = FastSphere()
self.particle.r_p = (100, 200, 300)
self.fast_particle.r_p = (100, 200, 300)
def test_set_ap(self):
value = 1.
self.particle.a_p = value
self.assertEqual(value, self.particle.a_p)
value = [1., 1.5]
self.particle.a_p = value
self.assertSequenceEqual(value, self.particle.a_p.tolist())
def test_set_np(self):
value = 1.5
self.particle.n_p = value
self.assertEqual(value, self.particle.n_p)
value = [1.5, 1.51]
self.particle.n_p = value
self.assertSequenceEqual(value, self.particle.n_p.tolist())
def test_fast(self):
self.particle.a_p = 1.
self.particle.n_p = 1.45
self.fast_particle.a_p = 1.
self.fast_particle.n_p = 1.45
n_m = 1.34
wavelength = 0.447
ab = self.particle.ab(n_m, wavelength)
fast_ab = self.fast_particle.ab(n_m, wavelength)
self.assertTrue(np.allclose(ab[0:20, :], fast_ab[0:20, :]))
def test_coefficients(self):
self.particle.a_p = 1.
self.particle.n_p = 1.45
n_m = 1.34
wavelength = 0.447
ab = self.particle.ab(n_m, wavelength)
# supposed ground truth from IDL implementation
gt = np.array(
[[0.j, 0.j],
[0.99922907 - 0.027754991j, 0.99913551 - 0.029389456j],
[0.99798931 - 0.044795570j, 0.99922896 - 0.027756943j],
[0.99912817 - 0.029513850j, 0.99536713 - 0.067907302j],
[0.99113427 - 0.093739712j, 0.99898631 - 0.031822280j],
[0.99745408 - 0.050392869j, 0.98372746 - 0.12652173j],
[0.97954507 - 0.14155044j, 0.99484334 - 0.071624499j],
[0.98344449 - 0.12759869j, 0.97377732 - 0.15979691j],
[0.97295236 - 0.16222228j, 0.96333549 - 0.18793674j],
[0.94122462 - 0.23520381j, 0.97203532 - 0.16487164j],
[0.93923397 - 0.23890065j, 0.90827363 - 0.28863930j],
[0.90681965 - 0.29068501j, 0.89369866 - 0.30822291j],
[0.85285635 - 0.35424906j, 0.90527481 - 0.29283498j],
[0.80640888 - 0.39511213j, 0.79527030 - 0.40350397j],
[0.74158827 - 0.43776147j, 0.67754233 - 0.46741707j],
[0.67568826 - 0.46811712j, 0.68941667 - 0.46273246j],
[0.58974388 - 0.49188010j, 0.67362393 - 0.46888669j],
[0.39208775 - 0.48821609j, 0.44840396 - 0.49733072j],
[0.13651257 - 0.34333204j, 0.11909958 - 0.32390565j],
[0.023845866 - 0.15256881j, 0.014321099 - 0.11881079j],
[0.0027834357 - 0.052684800j, 0.0012329865 - 0.035092254j],
[0.00025087072 - 0.015836912j, 8.5639136e-05 - 0.0092537453j],
[1.7963837e-05 - 0.0042383386j, 4.8214299e-06 - 0.0021957702j],
[1.0259636e-06 - 0.0010128981j, 2.1937314e-07 - 0.00046837281j],
[4.6954175e-08 - 0.00021668912j, 8.0932302e-09 - 8.9962382e-05j],
[1.7358544e-09 - 4.1663586e-05j, 2.4393269e-10 - 1.5618345e-05j],
[5.2348010e-11 - 7.2351925e-06j, 6.0618245e-12 - 2.4620773e-06j],
[1.3008375e-12 - 1.1405426e-06j, 1.2536060e-13 - 3.5406299e-07j],
[2.6896048e-14 - 1.6400015e-07j, 2.1766243e-15 - 4.6654306e-08j],
[4.6687756e-16 - 2.1607350e-08j, 3.1991070e-17 - 5.6560648e-09j],
[6.8604036e-18 - 2.6192371e-09j, 4.0101716e-19 - 6.3325905e-10j],
[8.5980970e-20 - 2.9322501e-10j, 4.3169528e-21 - 6.5703417e-11j],
[9.2545268e-22 - 3.0421149e-11j, 4.0162615e-23 - 6.3372936e-12j],
[8.6092607e-24 - 2.9340497e-12j, 3.2488696e-25 - 5.6988406e-13j],
[6.9664134e-26 - 2.6383515e-13j, 2.3050348e-27 - 4.7906383e-14j],
[4.9651027e-28 - 2.2178247e-14j, 1.5031287e-29 - 3.7739203e-15j],
[3.4175377e-30 - 1.7471016e-15j, 1.3633875e-31 - 2.7923729e-16j],
[4.3729724e-32 - 1.2926869e-16j, 4.4429448e-33 - 1.9447037e-17j],
[1.9627507e-33 - 9.0026403e-18j, 2.6860514e-34 - 1.2772834e-18j],
[1.2393948e-34 - 5.9129145e-19j, 1.6573650e-35 - 7.9263326e-20j],
[7.6708376e-36 - 3.6693179e-20j, 9.7307317e-37 - 4.6553744e-21j],
[4.5045616e-37 - 2.1550971e-21j, 5.4177177e-38 - 2.5919978e-22j],
[2.5080037e-38 - 1.1999046e-22j, 2.8639380e-39 - 1.3701950e-23j],
[1.3258143e-39 - 6.3430989e-24j, 1.4400608e-40 - 6.8896892e-25j],
[6.6679424e-41 - 3.1901465e-25j, 6.9378818e-42 - 3.3192937e-26j],
[3.2184201e-42 - 1.5397901e-26j, 3.4506417e-43 - 1.6508920e-27j],
[1.5867090e-43 - 7.5912988e-28j, 2.7763127e-44 - 1.3282725e-28j]])
self.assertTrue(np.allclose(ab[0:20, :], gt[0:20, :]))
if __name__ == '__main__':
from pylorenzmie.theory.Instrument import Instrument
from pylorenzmie.theory.Sphere import Sphere
import matplotlib.pyplot as plt
# Create coordinate grid for image
x = np.arange(0, 201)
y = np.arange(0, 201)
xv, yv = np.meshgrid(x, y)
xv = xv.flatten()
yv = yv.flatten()
zv = np.zeros_like(xv)
coordinates = np.stack((xv, yv, zv))
# Place a sphere in the field of view, above the focal plane
particle = Sphere()
particle.r_p = [125, 75, 100]
particle.a_p = 0.5
particle.n_p = 1.45
# Form image with default instrument
instrument = Instrument()
instrument.magnification = 0.135
instrument.wavelength = 0.447
instrument.n_m = 1.335
k = instrument.wavenumber()
# Use Generalized Lorenz-Mie theory to compute field
kernel = CudaGeneralizedLorenzMie(coordinates=coordinates,
particle=particle,
instrument=instrument)
field = kernel.field()
# Compute hologram from field and show it