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Rename model from anisotropic_thin to oriented_thick (#127)
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`anisotropic_thin` -> `oriented_thick`
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talonchandler authored Jun 14, 2023
1 parent 1943167 commit c645c84
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Showing 4 changed files with 65 additions and 67 deletions.
65 changes: 0 additions & 65 deletions examples/models/inplane_anisotropic_thin_pol3D.py

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63 changes: 63 additions & 0 deletions examples/models/inplane_oriented_thick_pol3D.py
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import napari
import numpy as np
from waveorder import util
from waveorder.models import inplane_oriented_thick_pol3d

# Parameters
# all lengths must use consistent units e.g. um
simulation_arguments = {"yx_shape": (256, 256)}
transfer_function_arguments = {"swing": 0.1, "scheme": "5-State"}

# Create a phantom
inplane_oriented_parameters = (
inplane_oriented_thick_pol3d.generate_test_phantom(**simulation_arguments)
)

# Calculate transfer function
intensity_to_stokes_matrix = (
inplane_oriented_thick_pol3d.calculate_transfer_function(
**transfer_function_arguments
)
)

# Display transfer function
viewer = napari.Viewer()
inplane_oriented_thick_pol3d.visualize_transfer_function(
viewer, intensity_to_stokes_matrix
)
input("Showing transfer functions. Press <enter> to continue...")
viewer.layers.select_all()
viewer.layers.remove_selected()

# Simulate
czyx_data = inplane_oriented_thick_pol3d.apply_transfer_function(
*inplane_oriented_parameters,
intensity_to_stokes_matrix,
)

# Reconstruct
inplane_oriented_parameters_recon = (
inplane_oriented_thick_pol3d.apply_inverse_transfer_function(
czyx_data, intensity_to_stokes_matrix
)
)

# Display
arrays = [
(inplane_oriented_parameters_recon[3], "Depolarization - recon"),
(inplane_oriented_parameters_recon[2], "Transmittance - recon"),
(inplane_oriented_parameters_recon[1], "Orientation - recon"),
(inplane_oriented_parameters_recon[0], "Retardance - recon"),
(czyx_data, "Data"),
(inplane_oriented_parameters[3], "Depolarization"),
(inplane_oriented_parameters[2], "Transmittance"),
(inplane_oriented_parameters[1], "Orientation"),
(inplane_oriented_parameters[0], "Retardance"),
]

for array in arrays:
viewer.add_image(array[0].cpu().numpy(), name=array[1])

viewer.grid.enabled = True
viewer.grid.shape = (2, 5)
input("Showing object, data, and recon. Press <enter> to quit...")
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import pytest
import torch
from waveorder import stokes
from waveorder.models import inplane_anisotropic_thin_pol3d
from waveorder.models import inplane_oriented_thick_pol3d


def test_calculate_transfer_function():
intensity_to_stokes_matrix = (
inplane_anisotropic_thin_pol3d.calculate_transfer_function(
inplane_oriented_thick_pol3d.calculate_transfer_function(
swing=0.1,
scheme="5-State",
)
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