update visualization script

examples/models/inplane_oriented_thick_pol3d_vector.py

@@ -9,7 +9,7 @@
 # Parameters
 # all lengths must use consistent units e.g. um
 oversample_factor = 2
-zyx_shape = (100, 256, 256)
+zyx_shape = (50, 128, 128) # (100, 256, 256)
 swing = 0.1
 scheme = "5-State"
 yx_pixel_size = 0.325 / oversample_factor  # 0.325
@@ -26,7 +26,7 @@
 )
 
 # Calculate transfer function
-sfZYX_transfer_function, intensity_to_stokes_matrix = (
+singular_system, sfZYX_transfer_function, intensity_to_stokes_matrix = (
     inplane_oriented_thick_pol3d_vector.calculate_transfer_function(
         swing,
         scheme,
@@ -49,7 +49,7 @@
     zyx_scale=(z_pixel_size, yx_pixel_size, yx_pixel_size),
 )
 
-# input("Showing transfer functions. Press <enter> to continue...")
+input("Showing transfer functions. Press <enter> to continue...")
 viewer.layers.select_all()
 viewer.layers.remove_selected()
 
@@ -64,7 +64,7 @@
 fzyx_object_recon = (
     inplane_oriented_thick_pol3d_vector.apply_inverse_transfer_function(
         szyx_data,
-        sfZYX_transfer_function,
+        singular_system,
         intensity_to_stokes_matrix,
         regularization_strength=1e-1,
     )

waveorder/models/inplane_oriented_thick_pol3d_vector.py

@@ -177,15 +177,16 @@ def calculate_transfer_function(
 
     # transfer function
     return (
-        singular_system,
+        singular_system, # (3 stokes, 3 object, Z, Y, X)
+        sfZYX_transfer_function, 
         intensity_to_stokes_matrix,
-    )  # (3 stokes, 3 object, Z, Y, X)
-
+    )  
 
 def visualize_transfer_function(viewer, sfZYX_transfer_function, zyx_scale):
     shift_dims = (-3, -2, -1)
     lim = torch.max(torch.abs(sfZYX_transfer_function)) * 0.9
 
+
     viewer.add_image(
         torch.fft.ifftshift(
             torch.real(sfZYX_transfer_function), dim=shift_dims