def makestate(im, pos, rad, slab=None, mem_level='hi'):
"""
Workhorse for creating & optimizing states with an initial centroid
guess.
This is an example function that works for a particular microscope. For
your own microscope, you'll need to change particulars such as the psf
type and the orders of the background and illumination.
Parameters
----------
im : :class:`~peri.util.RawImage`
A RawImage of the data.
pos : [N,3] element numpy.ndarray.
The initial guess for the N particle positions.
rad : N element numpy.ndarray.
The initial guess for the N particle radii.
slab : :class:`peri.comp.objs.Slab` or None, optional
If not None, a slab corresponding to that in the image. Default
is None.
mem_level : {'lo', 'med-lo', 'med', 'med-hi', 'hi'}, optional
A valid memory level for the state to control the memory overhead
at the expense of accuracy. Default is `'hi'`
Returns
-------
:class:`~peri.states.ImageState`
An ImageState with a linked z-scale, a ConfocalImageModel, and
all the necessary components with orders at which are useful for
my particular test case.
"""
if slab is not None:
o = comp.ComponentCollection(
[
objs.PlatonicSpheresCollection(pos, rad, zscale=zscale),
slab
],
category='obj'
)
else:
o = objs.PlatonicSpheresCollection(pos, rad, zscale=zscale)
p = exactpsf.FixedSSChebLinePSF()
npts, iorder = _calc_ilm_order(im.get_image().shape)
i = ilms.BarnesStreakLegPoly2P1D(npts=npts, zorder=iorder)
b = ilms.LegendrePoly2P1D(order=(9 ,3, 5), category='bkg')
c = comp.GlobalScalar('offset', 0.0)
s = states.ImageState(im, [o, i, b, c, p])
runner.link_zscale(s)
if mem_level != 'hi':
s.set_mem_level(mem_level)
opt.do_levmarq(s, ['ilm-scale'], max_iter=1, run_length=6, max_mem=1e4)
return s
def table_psfs():
np.random.seed(12)
s = create_image()
sh = s.psf.shape
lpsfs = [
psfs.IdentityPSF(shape=sh, params=np.array([0.0])),
psfs.AnisotropicGaussian(shape=sh, params=(2.0, 1.0, 3.0)),
psfs.Gaussian4DLegPoly(shape=sh, order=(3, 3, 3)),
exactpsf.FixedSSChebLinePSF(
shape=sh,
zrange=(0, sh[0]),
cheb_degree=3,
cheb_evals=6,
support_size=FIXEDSS,
zslab=10.,
cutoffval=1. / 255,
measurement_iterations=3,
),
exactpsf.FixedSSChebLinePSF(
shape=sh,
zrange=(0, sh[0]),
cheb_degree=6,
cheb_evals=8,
support_size=FIXEDSS,
zslab=10.,
cutoffval=1. / 255,
measurement_iterations=3,
),
]
names = [
r'Identity',
r'Gaussian$(x,y)$',
r'Gaussian$(x,y,z,z^{\prime})$',
r'Cheby linescan (3,6)',
r'Cheby linescan (6,8)',
]
def vary_func(s, data):
s.set_psf(data)
return table(s, lpsfs, names, vary_func)
def create_img():
"""Creates an image, as a `peri.util.Image`, which is similar
to the image in the tutorial"""
# 1. particles + coverslip
rad = 0.5 * np.random.randn(POS.shape[0]) + 4.5 # 4.5 +- 0.5 px particles
part = objs.PlatonicSpheresCollection(POS, rad, zscale=0.89)
slab = objs.Slab(zpos=4.92, angles=(-4.7e-3, -7.3e-4))
objects = comp.ComponentCollection([part, slab], category='obj')
# 2. psf, ilm
p = exactpsf.FixedSSChebLinePSF(kfki=1.07, zslab=-29.3, alpha=1.17,
n2n1=0.98, sigkf=-0.33, zscale=0.89, laser_wavelength=0.45)
i = ilms.BarnesStreakLegPoly2P1D(npts=(16,10,8,4), zorder=8)
b = ilms.LegendrePoly2P1D(order=(7,2,2), category='bkg')
off = comp.GlobalScalar(name='offset', value=-2.11)
mdl = models.ConfocalImageModel()
st = states.ImageState(util.NullImage(shape=[48,64,64]),
[objects, p, i, b, off], mdl=mdl, model_as_data=True)
b.update(b.params, BKGVALS)
i.update(i.params, ILMVALS)
im = st.model + np.random.randn(*st.model.shape) * 0.03
return util.Image(im)
im_ilm = util.RawImage('./ilm_test.tif',
tile=util.Tile([48, 0, 0], [49, 100, 100]))
# also located in the scripts folder
# Looking at the image, the illlumination is very stripey, due to the line-scan
# nature of our confocal. To account for this, we use a stripe-based ilm:
ilm = ilms.BarnesStreakLegPoly2P1D(npts=(50, 30, 20, 13, 7, 7, 7), zorder=1)
# (we only use a zorder of 1 since we've truncated to 1 pixel in z).
# Our real model will use a point-spread function that will blur out the ilm
# field slightly more. So we check the fit with a model that includes the
# type of point-spread function that we will use. A model that blur with a
# point-spread function takes considerably more time to evaluate than a
# SmoothFieldModel, so if you're not sure if your ilm is high enough order
# you should first check with a faster SmoothFieldModel.
psf = exactpsf.FixedSSChebLinePSF()
st = states.ImageState(im_ilm, [ilm, psf], mdl=models.BlurredFieldModel())
opt.do_levmarq(st, st.params)
# Plotting the residuals shows that they're good, aside from scan noise
# inherent to the line CCD camera:
plot_averaged_residuals(st)
# Next, we include the coverslip slide. To do this we first re-set the tile on
# our raw image to the full image:
im_ilm.set_tile(util.Tile([0, 0, 0], [60, 100, 100]))
# We then create a coverslip object:
slab = objs.Slab(zpos=35.0, category='obj')
# We also need our illumination to have a z-dependence now. Since we already
particle_radii = 5.0
particles = objs.PlatonicSpheresCollection(particle_positions, particle_radii)
from peri.comp import comp
objects = comp.ComponentCollection([particles, coverslip], category='obj')
from peri.comp import ilms
illumination = ilms.BarnesStreakLegPoly2P1D(npts=(16, 10, 8, 4), zorder=8)
background = ilms.LegendrePoly2P1D(order=(7, 2, 2), category='bkg')
offset = comp.GlobalScalar(name='offset', value=0.)
from peri.comp import exactpsf
point_spread_function = exactpsf.FixedSSChebLinePSF()
from peri import models
model = models.ConfocalImageModel()
print(model)
from peri import states
st = states.ImageState(
im, [objects, illumination, background, point_spread_function, offset],
mdl=model)
def table():
s = create_image(identity=True)
lpoly = [0.0, 0.0, 0.01, 0.05, 0.10]
dnames = ['0.0', '0.0', '0.01', '0.05', '0.10']
lilms = [
ilms.LegendrePoly2P1D(shape=s.ilm.shape, order=(1, 1, 1)),
ilms.LegendrePoly2P1D(shape=s.ilm.shape, order=(3, 3, 3)),
ilms.BarnesStreakLegPoly2P1DX3(shape=s.ilm.shape,
order=(1, 1, 1),
npts=(10, 5)),
ilms.BarnesStreakLegPoly2P1DX3(shape=s.ilm.shape,
order=(1, 1, 2),
npts=(30, 10)),
ilms.BarnesStreakLegPoly2P1DX3(shape=s.ilm.shape,
order=s.ilm.order,
npts=(30, 10, 5)),
]
lnames = [
r'Legendre 2+1D (0,0,0)',
r'Legendre 2+1D (2,2,2)',
r'Barnes (10, 5), $N_z=1$',
r'Barnes (30, 10), $N_z=2$',
r'Barnes (30, 10, 5), $N_z=3$',
]
lpsfs = [
psfs.IdentityPSF(shape=s.psf.shape, params=np.array([0.0])),
psfs.AnisotropicGaussian(shape=s.psf.shape, params=(2.0, 1.0, 3.0)),
psfs.Gaussian4DLegPoly(shape=s.psf.shape, order=(3, 3, 3)),
exactpsf.FixedSSChebLinePSF(
shape=s.psf.shape,
zrange=(0, s.psf.shape[0]),
cheb_degree=3,
cheb_evals=6,
support_size=FIXEDSS,
zslab=10.,
cutoffval=1. / 255,
measurement_iterations=3,
),
exactpsf.FixedSSChebLinePSF(
shape=s.psf.shape,
zrange=(0, s.psf.shape[0]),
cheb_degree=6,
cheb_evals=8,
support_size=FIXEDSS,
zslab=10.,
cutoffval=1. / 255,
measurement_iterations=3,
),
]
pnames = [
r'Identity',
r'Gaussian$(x,y)$',
r'Gaussian$(x,y,z,z^{\prime})$',
r'Cheby linescan (3,6)',
r'Cheby linescan (6,8)',
]
results = OrderedDict()
for i in xrange(len(lpoly)):
print dnames[i], lnames[i], pnames[i]
poly = lpoly[i]
ilm = lilms[i]
psf = lpsfs[i]
s = create_image(polydispersity=poly)
s.set_ilm(ilm)
s.set_psf(psf)
if isinstance(s.ilm, ilms.BarnesStreakLegPoly2P1DX3):
s.ilm.randomize_parameters(ptp=0.4, vmax=1.0, fourier=False)
s.reset()
s.model_to_true_image()
pos1 = trackpy(s)
pos0 = s.obj.pos.copy()
s.obj.set_pos_rad(pos1, s.obj.rad.mean() * np.ones(pos1.shape[0]))
s.reset()
slicer = s.get_difference_image().shape[0] / 2
results[i] = (
dnames[i],
lnames[i],
pnames[i],
s.get_difference_image()[slicer].copy(),
pos0,
pos1,
)
return results