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Add option for axial flip of phase_thick_3d transfer function #124

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Jun 13, 2023
Merged

Add option for axial flip of phase_thick_3d transfer function #124

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87619e3
`illumination_wavelength` -> `wavelength_illumination`
talonchandler Jun 8, 2023
754ebc2
add option for axial flip of transfer function
talonchandler Jun 9, 2023
7e99291
test axial flip
ziw-liu Jun 9, 2023
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5 changes: 4 additions & 1 deletion tests/models/test_phase_thick_3d.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,9 @@
import pytest
from waveorder.models import phase_thick_3d


def test_calculate_transfer_function():
@pytest.mark.parametrize("axial_flip", (True, False))
def test_calculate_transfer_function(axial_flip):
z_padding = 5
H_re, H_im = phase_thick_3d.calculate_transfer_function(
zyx_shape=(20, 100, 101),
Expand All @@ -12,6 +14,7 @@ def test_calculate_transfer_function():
index_of_refraction_media=1.0,
numerical_aperture_illumination=0.45,
numerical_aperture_detection=0.55,
axial_flip=axial_flip
)

assert H_re.shape == (20 + 2 * z_padding, 100, 101)
Expand Down
6 changes: 3 additions & 3 deletions waveorder/models/inplane_anisotropic_thin_pol3d.py
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Expand Up @@ -50,7 +50,7 @@ def apply_transfer_function(
def apply_inverse_transfer_function(
czyx_data,
intensity_to_stokes_matrix,
illumination_wavelength, # TOOD: MOVE THIS PARAM TO OTF? (leaky param)
wavelength_illumination, # TOOD: MOVE THIS PARAM TO OTF? (leaky param)
cyx_no_sample_data=None, # if not None, use this data for background correction
project_stokes_to_2d=False,
remove_estimated_background=False, # if True estimate background from czyx_data and remove it
Expand Down Expand Up @@ -97,7 +97,7 @@ def apply_inverse_transfer_function(
*background_corrected_stokes
)

# Return retardance in distance units (matching illumination_wavelength)
retardance = adr_parameters[0] * illumination_wavelength / (2 * np.pi)
# Return retardance in distance units (matching wavelength_illumination)
retardance = adr_parameters[0] * wavelength_illumination / (2 * np.pi)

return retardance, adr_parameters[1], adr_parameters[2], adr_parameters[3]
7 changes: 5 additions & 2 deletions waveorder/models/phase_thick_3d.py
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,7 @@ def calculate_transfer_function(
index_of_refraction_media,
numerical_aperture_illumination,
numerical_aperture_detection,
axial_flip=False,
):
radial_frequencies = util.generate_radial_frequencies(
zyx_shape[1:], yx_pixel_size
Expand All @@ -46,6 +47,8 @@ def calculate_transfer_function(
z_position_list = torch.fft.ifftshift(
(torch.arange(z_total) - z_total // 2) * z_pixel_size
)
if axial_flip:
z_position_list = torch.flip(z_position_list, dims=(0,))

ill_pupil = optics.generate_pupil(
radial_frequencies,
Expand Down Expand Up @@ -143,7 +146,7 @@ def apply_inverse_transfer_function(
imaginary_potential_transfer_function,
z_padding,
z_pixel_size, # TODO: MOVE THIS PARAM TO OTF? (leaky param)
illumination_wavelength, # TOOD: MOVE THIS PARAM TO OTF? (leaky param)
wavelength_illumination, # TOOD: MOVE THIS PARAM TO OTF? (leaky param)
absorption_ratio=0.0,
method="Tikhonov",
reg_re=1e-3,
Expand Down Expand Up @@ -194,4 +197,4 @@ def apply_inverse_transfer_function(
if z_padding != 0:
f_real = f_real[z_padding:-z_padding]

return f_real * z_pixel_size / 4 / np.pi * illumination_wavelength
return f_real * z_pixel_size / 4 / np.pi * wavelength_illumination
8 changes: 4 additions & 4 deletions waveorder/optics.py
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Expand Up @@ -326,7 +326,7 @@ def generate_propagation_kernel(


def generate_greens_function_z(
radial_frequencies, pupil_support, illumination_wavelength, z_position_list
radial_frequencies, pupil_support, wavelength_illumination, z_position_list
):
"""

Expand All @@ -340,7 +340,7 @@ def generate_greens_function_z(
pupil_support : torch.tensor
the array that defines the support of the pupil function with the size of (Y, X)

illumination_wavelength : float
wavelength_illumination : float
wavelength of the light in the immersion media

z_position_list : torch.tensor or list
Expand All @@ -354,9 +354,9 @@ def generate_greens_function_z(
"""

oblique_factor = (
(1 - illumination_wavelength**2 * radial_frequencies**2)
(1 - wavelength_illumination**2 * radial_frequencies**2)
* pupil_support
) ** (1 / 2) / illumination_wavelength
) ** (1 / 2) / wavelength_illumination

greens_function_z = (
-1j
Expand Down