def create_state(image, pos, rad, slab=None, sigma=0.05, conf=conf_simple):
"""
Create a state from a blank image, set of pos and radii
Parameters:
-----------
image : `peri.util.Image` object
raw confocal image with which to compare.
pos : initial conditions for positions (in raw image coordinates)
rad : initial conditions for radii array (can be scalar)
sigma : float, noise level
slab : float
z-position of the microscope slide in the image (pixel units)
"""
# we accept radius as a scalar, so check if we need to expand it
if not hasattr(rad, '__iter__'):
rad = rad * np.ones(pos.shape[0])
model = models.models[conf.get('model')]()
# setup the components based on the configuration
components = []
for k, v in conf.get('comps', {}).iteritems():
args = conf.get('args').get(k, {})
comp = model.registry[k][v](**args)
components.append(comp)
sphs = objs.PlatonicSpheresCollection(pos, rad)
if slab is not None:
sphs = ComponentCollection([sphs, objs.Slab(zpos=slab + pad)],
category='obj')
components.append(sphs)
s = states.ImageState(image, components, sigma=sigma)
if isinstance(image, util.NullImage):
s.model_to_data()
return s
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)
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 # spent time updating the ilm parameters, we update the corresponding values # of the new ilm to the older ones: ilm_z = ilms.BarnesStreakLegPoly2P1D(npts=(50, 30, 20, 13, 7, 7, 7), zorder=7) ilm_z.set_values(ilm.params, ilm.values) # Keep in mind that setting the parameters only works for this certain # ilm classes. The BarnesStreakLegPoly2P1D (1) has the same named Barnes # parameters regardless of the z-order, and (2) these determine the ilm field # in the xy-plane in the same way when the number of points is the same and # the image shape is the same. In contrast, if we had fit the in-plane # illumination with a lower set of npts, just setting the parameters wouldn't # work. [This is because the BarnesStreakLegPoly2P1D barnes parameters are # labeled according to their distance from the leftmost edge of the image. So # ilm-b0-49 would be on the rightmost side of the image if npts=(50,...), but # it would be in the middle of the image if npts=(100,...).] We could get
from peri import util
from peri.viz.interaction import OrthoViewer
import matplotlib
im = util.RawImage('../../Downloads/small_confocal_image.tif')
import numpy
from peri.comp import objs
coverslip = objs.Slab(zpos=6)
particle_positions = numpy.load('../../Downloads/particle-positions.npy')
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
from peri import states, util, models
from peri.comp import psfs, objs, ilms, GlobalScalar, ComponentCollection
from peri.test import nbody
import peri.opt.optimize as opt
import peri.opt.addsubtract as addsub
im = util.NullImage(shape=(32, ) * 3)
pos, rad, tile = nbody.create_configuration(3, im.tile)
P = ComponentCollection(
[objs.PlatonicSpheresCollection(pos, rad),
objs.Slab(2)], category='obj')
H = psfs.AnisotropicGaussian()
I = ilms.BarnesStreakLegPoly2P1D(npts=(25, 13, 3),
zorder=2,
local_updates=False)
B = ilms.LegendrePoly2P1D(order=(3, 1, 1), category='bkg', constval=0.01)
C = GlobalScalar('offset', 0.0)
I.randomize_parameters()
s = states.ImageState(im, [B, I, H, P, C], pad=16, model_as_data=True)