Rename model from anisotropic_thin to oriented_thick

examples/models/inplane_oriented_thick_pol3D.py

@@ -0,0 +1,63 @@
+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...")

tests/models/test_inplane_anisotropic_thin_pol3D.py → tests/models/test_inplane_oriented_thick_pol3D.py

@@ -1,12 +1,12 @@
 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",
         )