def test_dda_fit():
s = Sphere(n=1.59, r=.2, center=(5, 5, 5))
o = Optics(wavelen=.66, index=1.33, pixel_scale=.1)
schema = ImageSchema(optics=o, shape=100)
h = Mie.calc_holo(s, schema)
def make_scatterer(r, x, y, z):
local_s = Sphere(r=r, center=(x, y, z))
return Scatterer(local_s.indicators, n=s.n)
parameters = [
par(.18, [.1, .3], name='r', step=.1),
par(5, [4, 6], 'x'),
par(5, [4, 6], 'y'),
par(5.2, [4, 6], 'z')
]
p = Parametrization(make_scatterer, parameters)
model = Model(p, DDA.calc_holo)
res = fit(model, h)
assert_parameters_allclose(res.parameters,
dict([('r', 0.2003609439787491),
('x', 5.0128083665603995),
('y', 5.0125252883133617),
('z', 4.9775097284878775)]),
rtol=1e-3)
def calculateHologram(self): #calculate hologram with current settings
self.warning.setText('Calculating...')
#self.compute.setChecked(True)
scale = self.scale
sender = self.sender()
######## hologram calculation (4x big to allow scrolling)
start = time.time()
sphere = Sphere(n = self.lcd5.value()+.0001j,
r = self.lcd4.value(),
center = (256*self.scale,256*self.scale,self.lcd3.value()))
sphere2 = Sphere(n = self.lcd5.value()+.0001j,
r = self.lcd4.value(),
center = (self.lcd.value(),self.lcd2.value(),self.lcd3.value()))
self.sphObject.setText(repr(sphere2))
schema = ImageSchema(shape = 512, spacing = float(self.pxsizeText.text()),
optics = Optics(wavelen = float(self.waveText.text()),
index = float(self.mindexText.text()), polarization = [1,0]))
schema2 = ImageSchema(shape = 256, spacing = float(self.pxsizeText.text()),
optics = Optics(wavelen = float(self.waveText.text()),
index = float(self.mindexText.text()), polarization = [1,0]))
self.schemaObject.setText(str(repr(schema2)))
self.holo = Mie.calc_holo(sphere, schema)
self.lastholo = self.holo
self.lastZ = self.lcd3.value()
end = time.time()
#now take only the part that you want to display
x = round(self.sld.value())
y = round(self.sld2.value())
im = toimage(self.holo[256-x:512-x,256-y:512-y]) #PIL image
#https://github.com/shuge/Enjoy-Qt-Python-Binding/blob/master/image/display_img/pil_to_qpixmap.py
#myQtImage = ImageQt(im)
#qimage = QtGui.QImage(myQtImage)
if im.mode == "RGB":
pass
elif im.mode == "L":
im = im.convert("RGBA")
data = im.tostring('raw',"RGBA")
qim = QtGui.QImage(data, 256, 256, QtGui.QImage.Format_ARGB32)
pixmap = QtGui.QPixmap.fromImage(qim)
myScaledPixmap = pixmap.scaled(QtCore.QSize(400,400))
self.warning.setText('')
self.hologram.setPixmap(myScaledPixmap)
#self.hologram.setScaledContents(True)
#myScaledPixmap.scaledToWidth(True)
self.timer.setText('Calc. Time: '+str(round(end-start,4))+' s')
self.timer.setAlignment(QtCore.Qt.AlignBottom | QtCore.Qt.AlignCenter)
def test_serialization():
par_s = Sphere(center=(par(.567e-5, [0, 1e-5]), par(.576e-6, [0, 1e-5]),
par(15e-6, [1e-5, 2e-5])),
r=par(8.5e-7, [1e-8, 1e-5]),
n=par(1.59, [1, 2]))
alpha = par(.6, [.1, 1], 'alpha')
schema = ImageSchema(shape=100,
spacing=.1151e-6,
optics=Optics(.66e-6, 1.33))
model = Model(par_s, Mie.calc_holo, alpha=alpha)
holo = Mie.calc_holo(model.scatterer.guess, schema, model.alpha.guess)
result = fit(model, holo)
temp = tempfile.NamedTemporaryFile()
save(temp, result)
temp.flush()
temp.seek(0)
loaded = load(temp)
assert_obj_close(result, loaded, context='serialized_result')
def test_layered():
s = Sphere(n = (1,2), r = (1, 2), center = (2, 2, 2))
sch = ImageSchema((10, 10), .2, Optics(.66, 1, (1, 0)))
hs = Mie.calc_holo(s, sch)
guess = hp.scattering.scatterer.sphere.LayeredSphere((1,2), (par(1.01), par(.99)), (2, 2, 2))
model = Model(guess, Mie.calc_holo)
res = fit(model, hs)
assert_allclose(res.scatterer.t, (1, 1), rtol = 1e-12)
def test_layered():
s = Sphere(n = (1,2), r = (1, 2), center = (2, 2, 2))
sch = ImageSchema((10, 10), .2, Optics(.66, 1, (1, 0)))
hs = Mie.calc_holo(s, sch)
guess = hp.scattering.scatterer.sphere.LayeredSphere((1,2), (par(1.01), par(.99)), (2, 2, 2))
model = Model(guess, Mie.calc_holo)
res = fit(model, hs)
assert_allclose(res.scatterer.t, (1, 1), rtol = 1e-12)
def test_fit_superposition():
"""
Fit Mie superposition to a calculated hologram from two spheres
"""
# Make a test hologram
optics = Optics(wavelen=6.58e-07,
index=1.33,
polarization=[0.0, 1.0],
divergence=0,
spacing=None,
train=None,
mag=None,
pixel_scale=[2 * 2.302e-07, 2 * 2.302e-07])
s1 = Sphere(n=1.5891 + 1e-4j, r=.65e-6, center=(1.56e-05, 1.44e-05, 15e-6))
s2 = Sphere(n=1.5891 + 1e-4j, r=.65e-6, center=(3.42e-05, 3.17e-05, 10e-6))
sc = Spheres([s1, s2])
alpha = .629
theory = Mie(optics, 100)
holo = theory.calc_holo(sc, alpha)
# Now construct the model, and fit
parameters = [
Parameter(name='x0', guess=1.6e-5, limit=[0, 1e-4]),
Parameter('y0', 1.4e-5, [0, 1e-4]),
Parameter('z0', 15.5e-6, [0, 1e-4]),
Parameter('r0', .65e-6, [0.6e-6, 0.7e-6]),
Parameter('nr', 1.5891, [1, 2]),
Parameter('x1', 3.5e-5, [0, 1e-4]),
Parameter('y1', 3.2e-5, [0, 1e-4]),
Parameter('z1', 10.5e-6, [0, 1e-4]),
Parameter('r1', .65e-6, [0.6e-6, 0.7e-6])
]
def make_scatterer(x0, x1, y0, y1, z0, z1, r0, r1, nr):
s = Spheres([
Sphere(center=(x0, y0, z0), r=r0, n=nr + 1e-4j),
Sphere(center=(x1, y1, z1), r=r1, n=nr + 1e-4j)
])
return s
model = Model(parameters,
Mie,
make_scatterer=make_scatterer,
alpha=Parameter('alpha', .63, [.5, 0.8]))
result = fit(model, holo)
assert_obj_close(result.scatterer, sc)
assert_approx_equal(result.alpha, alpha, significant=4)
assert_equal(result.model, model)
assert_read_matches_write(result)
def test_n():
sph = Sphere(par(.5), 1.6, (5,5,5))
sch = ImageSchema(shape=[100, 100], spacing=[0.1, 0.1],
optics=Optics(wavelen=0.66,
index=1.33,
polarization=[1, 0],
divergence=0.0),
origin=[0.0, 0.0, 0.0])
model = Model(sph, Mie.calc_holo, alpha=1)
holo = Mie.calc_holo(model.scatterer.guess, sch)
coster = CostComputer(holo, model, random_subset=.1)
assert_allclose(coster.flattened_difference({'n' : .5}), 0)
def test_integer_correctness():
# we keep having bugs where the fitter doesn't
schema = ImageSchema(shape = 100, spacing = .1,
optics = Optics(wavelen = .660, index = 1.33, polarization = (1, 0)))
s = Sphere(center = (10.2, 9.8, 10.3), r = .5, n = 1.58)
holo = Mie.calc_holo(s, schema)
par_s = Sphere(center = (par(guess = 10, limit = [5,15]), par(10, [5, 15]), par(10, [5, 15])),
r = .5, n = 1.58)
model = Model(par_s, Mie.calc_holo, alpha = par(.6, [.1, 1]))
result = fit(model, holo)
assert_allclose(result.scatterer.center, [10.2, 9.8, 10.3])
def test_n():
sph = Sphere(par(.5), 1.6, (5,5,5))
sch = ImageSchema(shape=[100, 100], spacing=[0.1, 0.1],
optics=Optics(wavelen=0.66,
index=1.33,
polarization=[1, 0],
divergence=0.0),
origin=[0.0, 0.0, 0.0])
model = Model(sph, Mie.calc_holo, alpha=1)
holo = Mie.calc_holo(model.scatterer.guess, sch)
coster = CostComputer(holo, model, use_random_fraction=.1)
assert_allclose(coster.flattened_difference({'n' : .5}), 0)
def test_integer_correctness():
# we keep having bugs where the fitter doesn't
schema = ImageSchema(shape = 100, spacing = .1,
optics = Optics(wavelen = .660, index = 1.33, polarization = (1, 0)))
s = Sphere(center = (10.2, 9.8, 10.3), r = .5, n = 1.58)
holo = Mie.calc_holo(s, schema)
par_s = Sphere(center = (par(guess = 10, limit = [5,15]), par(10, [5, 15]), par(10, [5, 15])),
r = .5, n = 1.58)
model = Model(par_s, Mie.calc_holo, alpha = par(.6, [.1, 1]))
result = fit(model, holo)
assert_allclose(result.scatterer.center, [10.2, 9.8, 10.3])
def test_fit_superposition():
"""
Fit Mie superposition to a calculated hologram from two spheres
"""
# Make a test hologram
optics = Optics(wavelen=6.58e-07, index=1.33, polarization=[0.0, 1.0],
divergence=0, spacing=None, train=None, mag=None,
pixel_scale=[2*2.302e-07, 2*2.302e-07])
s1 = Sphere(n=1.5891+1e-4j, r = .65e-6,
center=(1.56e-05, 1.44e-05, 15e-6))
s2 = Sphere(n=1.5891+1e-4j, r = .65e-6,
center=(3.42e-05, 3.17e-05, 10e-6))
sc = Spheres([s1, s2])
alpha = .629
theory = Mie(optics, 100)
holo = theory.calc_holo(sc, alpha)
# Now construct the model, and fit
parameters = [Parameter(name = 'x0', guess = 1.6e-5, limit = [0, 1e-4]),
Parameter('y0', 1.4e-5, [0, 1e-4]),
Parameter('z0', 15.5e-6, [0, 1e-4]),
Parameter('r0', .65e-6, [0.6e-6, 0.7e-6]),
Parameter('nr', 1.5891, [1, 2]),
Parameter('x1', 3.5e-5, [0, 1e-4]),
Parameter('y1', 3.2e-5, [0, 1e-4]),
Parameter('z1', 10.5e-6, [0, 1e-4]),
Parameter('r1', .65e-6, [0.6e-6, 0.7e-6])]
def make_scatterer(x0, x1, y0, y1, z0, z1, r0, r1, nr):
s = Spheres([
Sphere(center = (x0, y0, z0), r=r0, n = nr+1e-4j),
Sphere(center = (x1, y1, z1), r=r1, n = nr+1e-4j)])
return s
model = Model(parameters, Mie, make_scatterer=make_scatterer, alpha =
Parameter('alpha', .63, [.5, 0.8]))
result = fit(model, holo)
assert_obj_close(result.scatterer, sc)
assert_approx_equal(result.alpha, alpha, significant=4)
assert_equal(result.model, model)
assert_read_matches_write(result)
def test_dda_fit():
s = Sphere(n = 1.59, r = .2, center = (5, 5, 5))
o = Optics(wavelen = .66, index=1.33, pixel_scale=.1)
schema = ImageSchema(optics = o, shape = 100)
h = Mie.calc_holo(s, schema)
def make_scatterer(r, x, y, z):
local_s = Sphere(r = r, center = (x, y, z))
return Scatterer(local_s.indicators, n = s.n)
parameters = [par(.18, [.1, .3], name='r', step=.1), par(5, [4, 6], 'x'),
par(5, [4,6], 'y'), par(5.2, [4, 6], 'z')]
p = Parametrization(make_scatterer, parameters)
model = Model(p, DDA.calc_holo)
res = fit(model, h)
assert_parameters_allclose(res.parameters, OrderedDict([('r',
0.2003609439787491), ('x', 5.0128083665603995), ('y', 5.0125252883133617),
('z', 4.9775097284878775)]), rtol=1e-3)
def test_serialization():
par_s = Sphere(center = (par(.567e-5, [0, 1e-5]), par(.576e-6, [0, 1e-5]),
par(15e-6, [1e-5,
2e-5])),
r = par(8.5e-7, [1e-8, 1e-5]), n = par(1.59, [1,2]))
alpha = par(.6, [.1, 1], 'alpha')
schema = ImageSchema(shape = 100, spacing = .1151e-6, optics = Optics(.66e-6, 1.33))
model = Model(par_s, Mie.calc_holo, alpha=alpha)
holo = Mie.calc_holo(model.scatterer.guess, schema, model.alpha.guess)
result = fit(model, holo)
temp = tempfile.NamedTemporaryFile()
save(temp, result)
temp.flush()
temp.seek(0)
loaded = load(temp)
assert_obj_close(result, loaded, context = 'serialized_result')
import scipy
from holopy.scattering.scatterer import Sphere, Spheres
from holopy.core import ImageSchema, Optics
from holopy.scattering.theory import Mie
import matplotlib.pyplot as plt
sphere = Sphere(n = 1.59+.0001j, r = .5, center = (4, 3, 5))
schema = ImageSchema(shape = 100, spacing = .1,
optics = Optics(wavelen = .660, index = 1.33,
polarization = [1,0]))
s1 = Sphere(center=(5, 5, 5), n = 1.59, r = .5)
s2 = Sphere(center=(4, 4, 5), n = 1.59, r = .5)
collection = Spheres([s1, s2])
holo = Mie.calc_holo(collection, schema)
scipy.misc.imsave('holoTest.png',holo)
plt.imshow(holo)
plt.show()
import holopy as hp
from holopy.scattering.theory import Mie
from holopy.scattering.scatterer import Sphere, Spheres
from holopy.core import ImageSchema, Optics
schema = ImageSchema(shape=100,
spacing=.1,
optics=Optics(wavelen=.660,
index=1.33,
polarization=[1, 0]))
s1 = Sphere(center=(5, 5, 5), n=1.59, r=.5)
s2 = Sphere(center=(4, 4, 5), n=1.59, r=.5)
collection = Spheres([s1, s2])
holo = Mie.calc_holo(collection, schema)
hp.show(holo)
import holopy as hp
from holopy.scattering.scatterer import Sphere
from holopy.scattering.theory import Mie
from holopy.core import ImageSchema, Optics
schema = ImageSchema(shape = 100, spacing = .1,
optics = Optics(wavelen = .660, index = 1.33,
polarization = [1,0]))
cs = Sphere(center=(2.5, 5, 5), n = (1.59, 1.42),\
r = (0.3, 0.6))
holo = Mie.calc_holo(cs, schema)
hp.show(holo)
import holopy as hp
from holopy.scattering.scatterer import Sphere
from holopy.core import ImageSchema, Optics
from holopy.scattering.theory import Mie
sphere = Sphere(n=1.59 + .0001j, r=.5, center=(4, 3, 5))
schema = ImageSchema(shape=100,
spacing=.1,
optics=Optics(wavelen=.660,
index=1.33,
polarization=[1, 0]))
holo = Mie.calc_holo(sphere, schema)
hp.show(holo)
import holopy as hp
from holopy.scattering.scatterer import Sphere
from holopy.core import ImageSchema, Optics
from holopy.scattering.theory import Mie
sphere = Sphere(n = 1.59+.0001j, r = .5, center = (4, 3, 5))
schema = ImageSchema(shape = 100, spacing = .1,
optics = Optics(wavelen = .660, index = 1.33,
polarization = [1,0]))
holo = Mie.calc_holo(sphere, schema)
hp.show(holo)
def calculateHologram(self): # calculate hologram with current settings
self.warning.setText("Calculating...")
# self.compute.setChecked(True)
scale = self.scale
sender = self.sender()
######## hologram calculation (4x big to allow scrolling)
start = time.time()
sphere = Sphere(
n=self.lcd5.value() + 0.0001j,
r=self.lcd4.value(),
center=(256 * self.scale, 256 * self.scale, self.lcd3.value()),
)
sphere2 = Sphere(
n=self.lcd5.value() + 0.0001j,
r=self.lcd4.value(),
center=(self.lcd.value(), self.lcd2.value(), self.lcd3.value()),
)
self.sphObject.setText(repr(sphere2))
schema = ImageSchema(
shape=512,
spacing=float(self.pxsizeText.text()),
optics=Optics(
wavelen=float(self.waveText.text()), index=float(self.mindexText.text()), polarization=[1, 0]
),
)
schema2 = ImageSchema(
shape=256,
spacing=float(self.pxsizeText.text()),
optics=Optics(
wavelen=float(self.waveText.text()), index=float(self.mindexText.text()), polarization=[1, 0]
),
)
self.schemaObject.setText(str(repr(schema2)))
self.holo = Mie.calc_holo(sphere, schema)
self.lastholo = self.holo
self.lastZ = self.lcd3.value()
end = time.time()
# now take only the part that you want to display
x = round(self.sld.value())
y = round(self.sld2.value())
im = toimage(self.holo[256 - x : 512 - x, 256 - y : 512 - y]) # PIL image
# https://github.com/shuge/Enjoy-Qt-Python-Binding/blob/master/image/display_img/pil_to_qpixmap.py
# myQtImage = ImageQt(im)
# qimage = QtGui.QImage(myQtImage)
if im.mode == "RGB":
pass
elif im.mode == "L":
im = im.convert("RGBA")
data = im.tostring("raw", "RGBA")
qim = QtGui.QImage(data, 256, 256, QtGui.QImage.Format_ARGB32)
pixmap = QtGui.QPixmap.fromImage(qim)
myScaledPixmap = pixmap.scaled(QtCore.QSize(400, 400))
self.warning.setText("")
self.hologram.setPixmap(myScaledPixmap)
# self.hologram.setScaledContents(True)
# myScaledPixmap.scaledToWidth(True)
self.timer.setText("Calc. Time: " + str(round(end - start, 4)) + " s")
self.timer.setAlignment(QtCore.Qt.AlignBottom | QtCore.Qt.AlignCenter)
import holopy as hp
from holopy.scattering.scatterer import Sphere
from holopy.scattering.theory import Mie
from holopy.core import ImageSchema, Optics
schema = ImageSchema(shape=100,
spacing=.1,
optics=Optics(wavelen=.660,
index=1.33,
polarization=[1, 0]))
cs = Sphere(center=(2.5, 5, 5), n = (1.59, 1.42),\
r = (0.3, 0.6))
holo = Mie.calc_holo(cs, schema)
hp.show(holo)
def calculateHologram(self): #calculate hologram with current settings
#schema is generic to all scattering theories
schema = ImageSchema(shape = [int(self.heightText.text()),int(self.widthText.text())], spacing = float(self.pxsizeText.text()),
optics = Optics(wavelen = float(self.waveText.text()),
index = float(self.mindexText.text()), polarization = [1.0,0.0]))
self.schemaObject.setText(str(repr(schema)))
#first sphere is general for both single sphere and two sphere cases
sphere = Sphere(n = self.lcd5.value()+.0001j,
r = self.lcd4.value(),
center = (self.lcd.value(),self.lcd2.value(),self.lcd3.value()))
if self.reconstruct.isChecked():
self.slideZ(sphere, schema)
start = end = 0 #fake time since reconstruction time is odd to keep track of here
else:
scale = self.scale
sender = self.sender()
start = time.time()
if self.onesphere.checkState() == 2:
self.sphObject.setText(repr(sphere))
#we have two theories to choose from for computing single sphere holograms
if sphere.parameters != self.oldscattererparameters:
#when changing parameters, always use GPU because it's fast enough
self.gpu.toggle()
if self.cpu.isChecked():
if sphere.parameters == self.oldMieCPUparameters and repr(schema) == repr(self.oldMieCPUschema):
self.holo = self.oldMieCPUHolo
print 'loaded cached mie hologram'
else:
self.holo = Mie.calc_holo(sphere,schema)
print 'freshly calculated mie hologram'
self.oldMieCPUHolo = self.holo
self.oldMieCPUparameters = sphere.parameters
self.oldMieCPUschema = schema
else:
if sphere.parameters == self.oldscattererparameters and repr(schema) == repr(self.oldMieGPUschema):
self.holo = self.oldMieGPUHolo
print 'loaded cached GPU hologram'
else:
self.holo = gpuMie.calc_holo(sphere, schema)
self.oldMieGPUHolo = self.holo
self.oldscattererparameters = sphere.parameters
self.oldMieGPUschema = schema
self.oldscatterer = sphere
self.oldschema = schema
else:
#we have three theories to choose from for computing single sphere holograms
s1 = sphere
s2 = Sphere(n = self.lcd5.value()+.0001j,
r = self.lcd4.value(),
center = (self.lcd7.value(),self.lcd8.value(),self.lcd9.value()))
cluster = Spheres([s1, s2])
self.sphObject.setText(repr(cluster))
if cluster.parameters != self.oldscatterer.parameters:
self.gpu.toggle()
if self.cpu.isChecked():
if cluster.parameters == self.oldMieCPUparameters and repr(schema) == repr(self.oldMieCPUschema):
self.holo = self.oldMieCPUHolo
print 'loaded cached CPU superposition hologram'
else:
self.holo = Mie.calc_holo(cluster, schema)
self.oldMieCPUHolo = self.holo
self.oldMieCPUschema = schema
self.oldMieCPUparameters = cluster.parameters
if self.multisphere.isChecked():
if cluster.parameters == self.oldMultiparameters and repr(schema) == repr(self.oldMultischema):
self.holo = self.oldMultiHolo
print 'loaded cached CPU multisphere hologram'
else:
self.holo = Multisphere.calc_holo(cluster, schema)
self.oldtheory = 'multi'
self.oldMultiHolo = self.holo
self.oldMultiparameters = cluster.parameters
self.oldMultischema = schema
print 'multisphere calculation done'
if self.gpu.isChecked():
if cluster.parameters == self.oldscattererparameters and repr(schema) == repr(self.oldschema):
self.holo = self.oldMieGPUHolo
print 'loaded cached GPU hologram'
else:
self.holo = gpuMie.calc_holo(cluster, schema)
self.oldMieGPUHolo = self.holo
self.oldschema = schema
self.oldscatterer = cluster
self.oldscattererparameters = cluster.parameters
end = time.time()
#display the hologram
im = scipy.misc.toimage(self.holo) #PIL image
#https://github.com/shuge/Enjoy-Qt-Python-Binding/blob/master/image/display_img/pil_to_qpixmap.py
if im.mode == "RGB":
pass
elif im.mode == "L":
im = im.convert("RGBA")
data = im.tostring('raw',"RGBA")
qim = QtGui.QImage(data, float(self.widthText.text()), float(self.heightText.text()), QtGui.QImage.Format_ARGB32)
pixmap = QtGui.QPixmap.fromImage(qim)
#set size of displayed image with max width or height = 500 px
if float(self.widthText.text()) == float(self.heightText.text()):
scaledsize = [500,500]
else:
if float(self.widthText.text()) > float(self.heightText.text()):
scaledsize = [500,500/float(self.widthText.text())*float(self.heightText.text())]
else:
scaledsize = [500/float(self.heightText.text())*float(self.widthText.text()),500]
myScaledPixmap = pixmap.scaled(QtCore.QSize(scaledsize[0],scaledsize[1]))
self.warning.setText('')
self.label.setPixmap(myScaledPixmap)
if end-start > 0.03:
self.timer.setText('Calc. Time: '+str(round(end-start,4))+' s')
else:
self.timer.setText('')
if self.lcd3.value()<2*self.lcd4.value() or self.lcd9.value()<2*self.lcd4.value():
self.warning.setText('z < sphere diameter')
if self.lcd.value() > float(self.heightText.text())*float(self.pxsizeText.text()):
self.warning.setText('x out of range, move slider or increase height')
if self.lcd2.value() > float(self.widthText.text())*float(self.pxsizeText.text()):
self.warning.setText('y out of range, move slider or increase width')
if float(self.pxsizeText.text()) <= 0:
self.warning.setText('pixel scale must be greater than 0')
