correct phase recon regression, legacy recon assumes axially even gre…

…en's function

waveorder/models/phase_thick_3d.py

@@ -72,6 +72,7 @@ def calculate_transfer_function(
  det_pupil,
  wavelength_illumination / index_of_refraction_media,
  z_position_list,
+ axially_even=False,
  )
 
  (

waveorder/optics.py

@@ -422,7 +422,8 @@ def generate_propagation_kernel(
 
 
 def generate_greens_function_z(
- radial_frequencies, pupil_support, wavelength_illumination, z_position_list
+ radial_frequencies, pupil_support, wavelength_illumination, z_position_list, 
+ axially_even=True,
 ):
  """
 
@@ -439,9 +440,14 @@ def generate_greens_function_z(
  wavelength_illumination : float
  wavelength of the light in the immersion media
 
- z_position_list  : torch.tensor or list
+ z_position_list : torch.tensor or list
  1D array of defocused z position with the size of (Z,)
 
+ axially_even : bool
+ For backwards compatibility with legacy phase reconstruction.
+ Ideally the legacy phase reconstruction should be unified with 
+ the new reconstructions, and this parameter should be removed.
+
  Returns
  -------
  greens_function_z : torch.tensor
@@ -454,18 +460,17 @@ def generate_greens_function_z(
  * pupil_support
  ) ** (1 / 2) / wavelength_illumination
 
+ if axially_even:
+ z_positions = torch.abs(torch.tensor(z_position_list)[:, None, None])
+ else:
+ z_positions = torch.tensor(z_position_list)[:, None, None]
+
  greens_function_z = (
  -1j
  / 4
  / np.pi
  * pupil_support[None, :, :]
- * torch.exp(
- 1j
- * 2
- * np.pi
- * torch.abs(torch.tensor(z_position_list)[:, None, None])
- * oblique_factor[None, :, :]
- )
+ * torch.exp(1j * 2 * np.pi * z_positions * oblique_factor[None, :, :])
  / (oblique_factor[None, :, :] + 1e-15)
  )