def calc_stats(param):
n_pol = int(param[0])
ill_na = param[1]
det_na = 0.8
exp = multiframe.MultiFrameMicroscope(ill_thetas=[0],
det_thetas=[0],
ill_nas=[ill_na],
det_nas=[det_na],
ill_types=['wide'],
det_types=['lens'],
colors=['(1,0,0)'],
n_frames=n_pol,
n_pts=n_pts,
max_photons=4000 / n_pol,
n_samp=n)
exp.calc_estimation_stats()
data = exp.sa_uncert
med = np.median(data)
return med, np.median(np.abs(data - med))
def __init__(self,
multiframe=multiframe.MultiFrameMicroscope(),
data=None,
recon_type='tp',
recon_dx=1e-6,
recon_eps=1e-3,
recon_max_iter=1e2):
self.multiframe = multiframe
self.data = data
if len(self.multiframe.microscopes) != len(self.data):
print("Warning! Data size does not match multiframe model.")
self.recon_type = recon_type
self.recon_dx = recon_dx
self.recon_eps = recon_eps
self.recon_max_iter = recon_max_iter
self.recon_est_history = []
self.recon_norm_history = []
self.estimated_fluorophore = None
return True
else:
return False
pts_list = [pt for pt in pts if is_feasible(pt)]
pts = np.array(pts_list).T
na_ill = 0.6
na_det = 0.8
exp = multiframe.MultiFrameMicroscope(ill_thetas=[0],
det_thetas=[0],
ill_nas=[na_ill],
det_nas=[na_det],
ill_types=['wide'],
det_types=['lens'],
colors=['(1,0,0)'],
n_frames=4,
n_pts=n_pts_sphere,
max_photons=1000,
n_samp=1.33)
exp.calc_estimation_stats()
util.draw_scene(exp.scene_string(), my_ax=ax0, dpi=dpi)
util.draw_scene(exp.ellipse_string(n_pts=250), my_ax=ax1, dpi=dpi)
util.plot_sphere(directions=exp.directions,
data=exp.sa_uncert,
color_norm='log',
linthresh=1e-4,
color_min=1e-4,
color_max=1e1,
# Main input parameters
col_labels = ['Geometry', 'Uncertainty Ellipse', r'$\sigma_{\Omega}$']
row_labels = 6 * ['']
n_pts = 10000
n_rows = len(row_labels)
n_cols = 3
inch_fig = 5
dpi = 200
m1 = multiframe.MultiFrameMicroscope(ill_thetas=[0],
det_thetas=[0],
ill_nas=[0.01],
det_nas=[0.8],
ill_types=['sheet'],
det_types=['lens'],
colors=['(1,0,0)'],
n_frames=2,
n_pts=n_pts,
max_photons=4000 / 2,
n_samp=1.33)
m2 = multiframe.MultiFrameMicroscope(ill_thetas=[0],
det_thetas=[0],
ill_nas=[0.01],
det_nas=[0.8],
ill_types=['sheet'],
det_types=['lens'],
colors=['(1,0,0)'],
n_frames=3,
n_pts=n_pts,
edgecolor=c))
fig.colorbar(sc, cax=cax, orientation='vertical')
ax.set(xlim=[1.5, 10], ylim=[0, 1.33])
# Plot first two columns
n_pol = 2
ill_na = 0.2
det_na = 0.8
exp = multiframe.MultiFrameMicroscope(ill_thetas=[0],
det_thetas=[0],
ill_nas=[ill_na],
det_nas=[det_na],
ill_types=['wide'],
det_types=['lens'],
colors=['(1,0,0)'],
n_frames=n_pol,
n_pts=n_pts_sphere,
max_photons=4000 / n_pol,
n_samp=n)
exp.calc_estimation_stats()
# Make scene string
util.draw_scene(exp.scene_string(), my_ax=ax0, dpi=dpi)
util.draw_scene(exp.ellipse_string(n_pts=250), my_ax=ax1, dpi=dpi)
util.plot_sphere(directions=exp.directions,
data=exp.sa_uncert,
color_norm='log',
linthresh=1e-4,
edgecolor=c))
fig.colorbar(sc, cax=cax, orientation='vertical')
ax.set(xlim=[1.5, 10], ylim=[0, 1.33])
# Plot first two columns
n_pol = 3
ill_na = 0.2
det_na = 0.8
exp = multiframe.MultiFrameMicroscope(ill_thetas=[np.pi / 4, -np.pi / 4],
det_thetas=[-np.pi / 4, np.pi / 4],
ill_nas=2 * [ill_na],
det_nas=2 * [det_na],
ill_types=2 * ['wide'],
det_types=2 * ['lens'],
colors=['(1,0,0)', '(0,0,1)'],
n_frames=n_pol,
n_pts=n_pts,
max_photons=2000 / n_pol,
n_samp=1.33)
exp.calc_estimation_stats()
# Make scene string
util.draw_scene(exp.scene_string(), my_ax=ax0, dpi=dpi)
util.draw_scene(exp.ellipse_string(n_pts=250), my_ax=ax1, dpi=dpi)
util.plot_sphere(directions=exp.directions,
data=exp.sa_uncert,
color_norm='log',
NA_ill = np.linspace(0, 1.33, num=1000)
NA_det = NA_ill
pts = np.mgrid[n/n_grid_pts/2:n-n/n_grid_pts/2:n_grid_pts*1j,n/n_grid_pts/2:n-n/n_grid_pts/2:n_grid_pts*1j].reshape((2, n_grid_pts**2)).T.tolist()
def is_feasible(pt):
if pt[0] < pt[1] + 0.2:
return True
else:
return False
pts_list = [pt for pt in pts if is_feasible(pt)]
pts = np.array(pts_list).T
exp = multiframe.MultiFrameMicroscope(ill_thetas=[np.pi/4, -np.pi/4], det_thetas=[-np.pi/4, np.pi/4],
ill_nas=[0.8, 0.8], det_nas=[0.8, 0.8],
ill_types=2*['sheet'], det_types=2*['lens'],
colors=['(1,0,0)', '(0,0,1)'], n_frames=4,
n_pts=n_pts_sphere, max_photons=[1, 1], n_samp=1.33)
exp.calc_estimation_stats()
util.draw_scene(exp.scene_string(), my_ax=ax0, dpi=dpi)
util.draw_scene(exp.ellipse_string(n_pts=250), my_ax=ax1, dpi=dpi)
util.plot_sphere(directions=exp.directions, data=exp.sa_uncert,
color_norm='log', linthresh=1e-4,
color_min=1e-4, color_max=1e1,
my_ax=ax2, my_cax=cax2)
# Label axes and save
print('Saving final figure.')
fig.savefig('dual-view.pdf', dpi=1000)
