def deconv_plotter(*, sources=None, recons, iter):
"""Function that plots the deconvolved images as the iterations go.
Args:
sources (ndarray): 3d array of sources
recons (ndarray): 3d array of reconstructions
iter (int): current iteration number
"""
num_sources = recons.shape[0]
ssim1 = np.zeros(num_sources)
if sources is not None:
mse1 = np.mean((sources - recons)**2, axis=(1, 2))
psnr1 = 20 * np.log10(np.max(sources, axis=(1,2))/np.sqrt(mse1))
for i in range(num_sources):
ssim1[i] = compare_ssim(sources[i], recons[i],
data_range=np.max(recons[i])-np.min(recons[i]))
title = 'Iteration: {}\n Recon. SSIM={}\n Recon. PSNR={}'.format(iter+1, ssim1, psnr1)
else:
title = 'Iteration: {}'.format(iter+1)
plotter4d(recons,
cmap='gist_heat',
fignum=3,
figsize=(5.6,8),
title=title
)
plt.pause(0.01)
from mas import sse_cost
import numpy as np
import matplotlib.pyplot as plt
# %% psfs -----
ps = PhotonSieve()
wavelengths = np.array([33.4, 33.5]) * 1e-9
sources = sources[np.array((0, 1))].reshape((2, 1, 160, 160))
psfs = PSFs(
sieve=ps,
source_wavelengths=wavelengths,
measurement_wavelengths=wavelengths,
num_copies=1
)
# %% contributions -----
contributions = get_contributions(sources=sources[:, 0, :, :], psfs=psfs, real=True)
plt = plotter4d(
contributions,
title='measurement contributions',
column_labels=wavelengths,
sup_xlabel='source wavelengths',
row_labels=wavelengths,
sup_ylabel='measurement wavelengths',
scale=True
)
plt.savefig('contributions.png')
plt.show()
# patch_based
# TV
bm3d_pnp
# dncnn_pnp, model=model
),
recon_init=recon,
iternum=20,
periter=5,
nu=10**-1.5,
lam=[10**-3.8]*num_sources,
)
ssim_ = np.zeros(num_sources)
mse_ = np.mean((sources_ref - recon)**2, axis=(1, 2))
psnr_ = 20 * np.log10(np.max(sources_ref, axis=(1,2))/np.sqrt(mse_))
for i in range(num_sources):
ssim_[i] = ssim(sources_ref[i], recon[i],
data_range=np.max(recon[i])-np.min(recon[i]))
plotter4d(recon,
cmap='gist_heat',
figsize=(5.6,8),
title='Recon. SSIM={}\n Recon. PSNR={}'.format(ssim_, psnr_)
)
plotter4d(sources_ref,
cmap='gist_heat',
figsize=(5.6,8),
title='Original'
)
# csbs(psfs, sse_cost, 10, lam=1e-2, order=0)
# fourier_slices(psfs)
# %% ps -----
wavelengths = np.array([33.4e-9])
ps = PhotonSieve()
psfs_ps = PSFs(ps,
source_wavelengths=wavelengths,
measurement_wavelengths=49,
num_copies=5)
plotter4d(np.fft.fftshift(
np.abs(psfs.psf_dfts.reshape(7, 7, 301, 301)),
axes=(2, 3),
),
figsize=(5, 5),
scale=True)
plt.savefig('photonsieve_dfts.png', dpi=300)
# %% sq -----
wavelengths = np.array([33.4e-9])
ps = PhotonSieve()
psfs_sq = PSFs(ps,
source_wavelengths=wavelengths,
measurement_wavelengths=49,
num_copies=5)
def square(top, left, width, image_width=301, amplitude=1):
tikhonov_lam=1e-3)
recon_csbs = tikhonov(psfs=psfs_csbs,
measurements=meas_csbs,
tikhonov_lam=1e-3)
recon_focus -= np.mean(recon_focus, axis=(1, 2))[:, np.newaxis, np.newaxis]
recon_csbs -= np.mean(recon_csbs, axis=(1, 2))[:, np.newaxis, np.newaxis]
sources_comp = sources - np.mean(sources, axis=(1, 2))[:, np.newaxis,
np.newaxis]
result_focus = np.sum(compare_ssim(sources_comp, recon_focus))
result_csbs = np.sum(compare_ssim(sources_comp, recon_csbs))
print('focused SSIM sum:', result_focus)
print('csbs SSIM sum:', result_csbs)
plotter4d(recon_focus)
plotter4d(recon_csbs)
# plt.imsave('meas_focus0.png', meas_focus[0], cmap='gist_heat')
# plt.imsave('meas_focus1.png', meas_focus[1], cmap='gist_heat')
# plt.imsave('meas_csbs0.png', meas_csbs[0], cmap='gist_heat')
# plt.imsave('meas_csbs1.png', meas_csbs[1], cmap='gist_heat')
# plt.imsave('recon_focus0.png', recon_focus[0], cmap='gist_heat')
# plt.imsave('recon_focus1.png', recon_focus[1], cmap='gist_heat')
# plt.imsave('recon_csbs0.png', recon_csbs[0], cmap='gist_heat')
# plt.imsave('recon_csbs1.png', recon_csbs[1], cmap='gist_heat')
noisy_nanoflare_list.append(noisy_nanoflare)
noisy_nanoflares.append(noisy_nanoflare_list)
# dimension: (num photon count, num measurements, X, Y)
noisy_nanoflares = np.array(noisy_nanoflares)
# %% plot -----
# single snapshot images
plt = plotter4d(
noisy_nanoflares[:, [0, -1]],
title='Noisy, single-snapshot measurements at ',
colorbar=False,
row_labels=max_photon_count_list,
column_labels=['t=0s', 't=19s'],
sup_ylabel='Max photon count',
figsize=(4.5, 10),
cmap='gist_heat'
)
plt.savefig('first_last_comparison.png', dpi=300)
plt.figure()
plt.imshow(measured_nanoflare_list[0], cmap='gist_heat')
plt.axis('off')
plt.title('Blurred, single-snapshot measurement')
plt.savefig('single_measured.png', dpi=300)
plt.figure()
plt.imshow(nanoflare_list[0], cmap='gist_heat')
plt.axis('off')
iterations=60,
lam=10**-6,
time_step=10**-2,
liveplot=True)
###### COMPUTE PERFORMANCE METRICS ######
ssim_ = np.zeros(num_sources)
mse_ = np.mean((sources_ref - recon)**2, axis=(1, 2))
psnr_ = 20 * np.log10(np.max(sources_ref, axis=(1, 2)) / np.sqrt(mse_))
for i in range(num_sources):
ssim_[i] = ssim(sources_ref[i],
recon[i],
data_range=np.max(recon[i]) - np.min(recon[i]))
plotter4d(recon,
cmap='gist_heat',
figsize=(5.6, 8),
title='Recon. SSIM={}\n Recon. PSNR={}'.format(ssim_, psnr_))
print('ssim:{:.3f}, psnr:{:.2f}'.format(np.mean(ssim_, axis=0),
np.mean(psnr_, axis=0)))
plotter4d(measured_noisy,
cmap='gist_heat',
figsize=(5.6, 8),
title='Noisy Meas')
# plotter4d(sources,
# title='Orig',
# figsize=(5.6,8),
# cmap='gist_heat'
# )
def get_ssim(source, recon):
return compare_ssim(recon, source)
get_ssim = np.vectorize(get_ssim, signature='(a,b),(c,d)->()')
csbs_modes = [
'CSBS grid', 'CSBS focus', 'Naive grid', 'Naive focus', 'Original'
]
recons[4] = sources
plotter4d(recons[:, 0],
cmap='gist_heat',
scale=True,
row_labels=csbs_modes,
column_labels=['33.4nm', '33.5nm'],
sup_xlabel='Source',
sup_ylabel='CSBS mode',
figsize=(5, 6))
plt.savefig('reconstructions.png', dpi=300)
plt.close()
# ssims = np.mean(get_ssim(sources, recons), axis=(1, 2))
ssims = np.mean(get_ssim(sources, recons), axis=(1, 2))
plt.plot(ssims, 'o')
plt.grid(True)
plt.xticks(np.arange(len(ssims)), csbs_modes)
plt.savefig('ssim_comparison.png', dpi=300)
plt.show()
tikhonov_order=order)
psnr_focus.append(compare_psnr(sources, recon_focus))
psnr_csbs.append(compare_psnr(sources, recon_csbs))
ssim_focus.append(np.sum(compare_ssim(sources, recon_focus)))
ssim_csbs.append(np.sum(compare_ssim(sources, recon_csbs)))
print('psnr_focus:{} \npsnr_csbs:{} \nssim_focus:{} \nssim_csbs:{}'.format(
np.array(psnr_focus).mean(),
np.array(psnr_csbs).mean(),
np.array(ssim_focus).mean(),
np.array(ssim_csbs).mean()))
plotter4d(recon_focus,
title='recon_focus \n ssim:{} psnr:{}'.format(
np.array(ssim_focus).mean(),
np.array(psnr_focus).mean()),
colorbar=True)
plotter4d(recon_csbs,
title='recon_csbs \n ssim:{} psnr:{}'.format(
np.array(ssim_csbs).mean(),
np.array(psnr_csbs).mean()),
colorbar=True)
plotter4d(sources, title='sources')
# %% plotting
z = np.zeros((160, 160, 3))
z[:, :, 0] = sources[0]
z[:, :, 1] = sources[1]
# plt.imsave('figures/sources.png', z)
sources = size_equalizer(sources, meas_size)
# take multiple measurements with different noise
measured_noisy_instances = np.zeros((num_instances, ) + measured.shape)
for i in range(num_instances):
for j in range(measured.shape[0]):
measured_noisy_instances[i, j, 0] = np.fft.fftshift(
add_noise(measured[j, 0],
dbsnr=10,
max_count=500,
model='Poisson'
# dbsnr=20, no_noise=no_noise, model='Gaussian'
))
if len(measured_noisy_instances.shape) == 4:
measured_noisy_instances = measured_noisy_instances[np.newaxis]
plotter4d(sources, title='Orig', figsize=(5.6, 8), cmap='gist_heat')
[k, num_sources, aa, bb] = psfs.selected_psfs.shape[:2] + sources.shape[2:]
LAM = get_LAM(rows=aa, cols=bb, order=tikhonov_order)
ssim = np.zeros((len(tikhonov_lam), num_instances, num_sources))
psnr = np.zeros((len(tikhonov_lam), num_instances, num_sources))
for i in range(len(tikhonov_lam)):
SIG_inv = block_inv(psfs.selected_GAM + tikhonov_lam[i] *
np.einsum('ij,kl', np.eye(num_sources), LAM))
for j in range(num_instances):
# DFT of the kernel corresponding to (D^TD)
recon = np.real(
np.fft.ifft2(
block_mul(
SIG_inv,
block_mul(psfs.selected_psf_dfts_h,
noise_level[1]).conj()
# preview the correlation map computed by register_translation
coarse_correlation = np.fft.fftshift(np.fft.ifft2(image_product))
# preview the correlation map computed by register_translation
fine_correlation = _upsampled_dft(image_product, image_product.shape[0],
100, (offset * 100) +
image_product.shape[0] // 2).conj()
correlations.append([coarse_correlation, fine_correlation])
correlations = np.array(correlations)
# %% plot -----
plt = plotter4d(noisy_list,
title='Original and shifted images at various noise levels',
colorbar=False,
row_labels=max_photon_count_list,
column_labels=['original', 'shifted'],
sup_ylabel='max photon count',
figsize=(4.5, 10),
cmap='gist_heat')
plt.savefig('images.png', dpi=300)
plt = plotter4d(np.abs(correlations),
title='Correlation stages',
colorbar=False,
row_labels=max_photon_count_list,
column_labels=['coarse', 'fine'],
sup_ylabel='max photon count',
sup_xlabel='correlations',
figsize=(4.5, 10),
cmap='gist_heat')
plt.savefig('correlations.png', dpi=300)