Skip to content

Commit

Permalink
fix mean/differential permittivity mistake
Browse files Browse the repository at this point in the history
  • Loading branch information
@talonchandler
talonchandler committed Mar 12, 2024
1 parent 6c0adf9 commit ebe7bf2
Showing 1 changed file with 38 additions and 38 deletions.
76 changes: 38 additions & 38 deletions examples/documentation/PTI_experiment/PTI_Experiment_Recon3D_anisotropic_target_small.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -203,8 +203,8 @@
# It is good to set the regularization such that (1c, 1s), (2c, 2s) have the same regularization
reg_inc = np.array([2.5, 5, 1, 1, 3, 3, 3]) * 1

# regulairzation for estimating mean permittivity
reg_mean_permittivity = 1e-2
# regulairzation for estimating differential permittivity
reg_differential_permittivity = 1e-2

# reconstruct components of scattering potential tensor
f_tensor = setup.scattering_potential_tensor_recon_3D_vec(
Expand Down Expand Up @@ -237,12 +237,12 @@
# "negative" -> only solution of negatively uniaxial material
# "unknown" -> both solutions of positively and negatively uniaxial material + optic sign estimation

mean_permittivity, azimuth, theta, mat_map = (
differential_permittivity, azimuth, theta, mat_map = (
setup.scattering_potential_tensor_to_3D_orientation(
f_tensor,
S_image_tm,
material_type="unknown",
reg_ret_pr=reg_mean_permittivity,
reg_ret_pr=reg_differential_permittivity,
itr=10,
fast_gpu_mode=True,
)
Expand All @@ -251,19 +251,19 @@
# %%
p_mat_map = optics.optic_sign_probability(mat_map, mat_map_thres=0.2)
phase = optics.phase_inc_correction(
f_tensor[0], mean_permittivity[1], theta[1]
f_tensor[0], differential_permittivity[1], theta[1]
)
phase_PT, absorption_PT, mean_permittivity_PT = [
phase_PT, absorption_PT, differential_permittivity_PT = [
optics.unit_conversion_from_scattering_potential_to_permittivity(
SP_array, lambda_illu, n_media=n_media, imaging_mode="3D"
)
for SP_array in [phase, f_tensor[1].copy(), mean_permittivity]
for SP_array in [phase, f_tensor[1].copy(), differential_permittivity]
]
mean_permittivity_PT = np.array(
differential_permittivity_PT = np.array(
[
((-1) ** i)
* util.wavelet_softThreshold(
((-1) ** i) * mean_permittivity_PT[i], "db8", 0.00303, level=1
((-1) ** i) * differential_permittivity_PT[i], "db8", 0.00303, level=1
)
for i in range(2)
]
Expand All @@ -283,11 +283,11 @@
np.stack(
[
phase_PT,
mean_permittivity_PT[0],
differential_permittivity_PT[0],
azimuth[0],
theta[0],
absorption_PT,
mean_permittivity_PT[1],
differential_permittivity_PT[1],
azimuth[1],
theta[1],
]
Expand All @@ -299,11 +299,11 @@
set_title=True,
titles=[
r"phase",
r"mean permittivity (+)",
r"differential permittivity (+)",
r"$\omega$ (+)",
r"$\theta$ (+)",
r"absorption",
r"mean permittivity (-)",
r"differential permittivity (-)",
r"$\omega$ (-)",
r"$\theta$ (-)",
],
Expand All @@ -328,7 +328,7 @@
"f_3",
"phase",
"absorption",
"mean_permittivity (-)",
"differential_permittivity (-)",
"azimuth (-)",
"theta (-)",
]
Expand Down Expand Up @@ -356,7 +356,7 @@
array[0, :7] = np.transpose(f_tensor, (0, 3, 1, 2))
array[0, 7] = np.transpose(phase_PT, (2, 1, 0))
array[0, 8] = np.transpose(absorption_PT, (2, 1, 0))
array[0, 9] = np.transpose(mean_permittivity_PT[1], (2, 1, 0))
array[0, 9] = np.transpose(differential_permittivity_PT[1], (2, 1, 0))
array[0, 10] = np.transpose(azimuth[1], (2, 1, 0))
array[0, 11] = np.transpose(theta[1], (2, 1, 0))

Expand All @@ -373,35 +373,35 @@

# compute the physical properties from the scattering potential tensor

mean_permittivity_p, azimuth_p, theta_p = (
differential_permittivity_p, azimuth_p, theta_p = (
optics.scattering_potential_tensor_to_3D_orientation_PN(
f_tensor, material_type="positive", reg_ret_pr=reg_mean_permittivity
f_tensor, material_type="positive", reg_ret_pr=reg_differential_permittivity
)
)
mean_permittivity_n, azimuth_n, theta_n = (
differential_permittivity_n, azimuth_n, theta_n = (
optics.scattering_potential_tensor_to_3D_orientation_PN(
f_tensor, material_type="negative", reg_ret_pr=reg_mean_permittivity
f_tensor, material_type="negative", reg_ret_pr=reg_differential_permittivity
)
)
mean_permittivity = np.array([mean_permittivity_p, mean_permittivity_n])
differential_permittivity = np.array([differential_permittivity_p, differential_permittivity_n])
azimuth = np.array([azimuth_p, azimuth_n])
theta = np.array([theta_p, theta_n])

p_mat_map = optics.optic_sign_probability(mat_map, mat_map_thres=0.09)
phase = optics.phase_inc_correction(
f_tensor[0], mean_permittivity[1], theta[1]
f_tensor[0], differential_permittivity[1], theta[1]
)
phase_PT, absorption_PT, mean_permittivity_PT = [
phase_PT, absorption_PT, differential_permittivity_PT = [
optics.unit_conversion_from_scattering_potential_to_permittivity(
SP_array, lambda_illu, n_media=n_media, imaging_mode="3D"
)
for SP_array in [phase, f_tensor[1].copy(), mean_permittivity]
for SP_array in [phase, f_tensor[1].copy(), differential_permittivity]
]
mean_permittivity_PT = np.array(
differential_permittivity_PT = np.array(
[
((-1) ** i)
* util.wavelet_softThreshold(
((-1) ** i) * mean_permittivity_PT[i], "db8", 0.00303, level=1
((-1) ** i) * differential_permittivity_PT[i], "db8", 0.00303, level=1
)
for i in range(2)
]
Expand Down Expand Up @@ -472,24 +472,24 @@
plt.colorbar(sub_ax, ax=ax[1, 1])

sub_ax = ax[2, 0].imshow(
np.abs(mean_permittivity_PT[0, :, :, z_layer]),
np.abs(differential_permittivity_PT[0, :, :, z_layer]),
cmap="gray",
origin="lower",
vmin=ret_min,
vmax=ret_max,
)
ax[2, 0].set_title("mean permittivity (+) (xy)")
ax[2, 0].set_title("differential permittivity (+) (xy)")
plt.colorbar(sub_ax, ax=ax[2, 0])

sub_ax = ax[2, 1].imshow(
np.transpose(np.abs(mean_permittivity_PT[0, y_layer, :, :])),
np.transpose(np.abs(differential_permittivity_PT[0, y_layer, :, :])),
cmap="gray",
origin="lower",
vmin=ret_min,
vmax=ret_max,
aspect=z_step / ps,
)
ax[2, 1].set_title("mean permittivity (+) (xz)")
ax[2, 1].set_title("differential permittivity (+) (xz)")
plt.colorbar(sub_ax, ax=ax[2, 1])

sub_ax = ax[3, 0].imshow(
Expand Down Expand Up @@ -550,7 +550,7 @@
np.transpose(
[
np.clip(phase_PT, phase_min, phase_max),
np.clip(np.abs(mean_permittivity_PT[1]), ret_min, ret_max),
np.clip(np.abs(differential_permittivity_PT[1]), ret_min, ret_max),
],
(3, 0, 1, 2),
),
Expand All @@ -574,7 +574,7 @@
theta[1],
(
np.clip(
np.abs(mean_permittivity_PT[1]),
np.abs(differential_permittivity_PT[1]),
ret_min_color,
ret_max_color,
)
Expand Down Expand Up @@ -615,10 +615,10 @@
np.array(
[
(azimuth[1]) % np.pi / np.pi,
np.ones_like(mean_permittivity_PT[1]),
np.ones_like(differential_permittivity_PT[1]),
(
np.clip(
np.abs(mean_permittivity_PT[1]),
np.abs(differential_permittivity_PT[1]),
ret_min_color,
ret_max_color,
)
Expand Down Expand Up @@ -655,10 +655,10 @@
+ threshold_inc
)
/ np.pi,
np.ones_like(mean_permittivity_PT[1]),
np.ones_like(differential_permittivity_PT[1]),
(
np.clip(
np.abs(mean_permittivity_PT[1]),
np.abs(differential_permittivity_PT[1]),
ret_min_color,
ret_max_color,
)
Expand Down Expand Up @@ -687,10 +687,10 @@
fig, ax = plt.subplots(1, 1, figsize=(15, 15))

visual.plot3DVectorField(
np.abs(mean_permittivity_PT[1, :, :, z_layer]),
np.abs(differential_permittivity_PT[1, :, :, z_layer]),
azimuth[1, :, :, z_layer],
theta[1, :, :, z_layer],
anisotropy=40 * np.abs(mean_permittivity_PT[1, :, :, z_layer]),
anisotropy=40 * np.abs(differential_permittivity_PT[1, :, :, z_layer]),
cmapImage="gray",
clim=[ret_min, ret_max],
aspect=1,
Expand All @@ -703,7 +703,7 @@
)

# %%
ret_mask = np.abs(mean_permittivity_PT[1]).copy()
ret_mask = np.abs(differential_permittivity_PT[1]).copy()
ret_mask[ret_mask < 0.0075] = 0
ret_mask[ret_mask > 0.0075] = 1

Expand Down

0 comments on commit ebe7bf2

Please sign in to comment.