diff --git a/recOrder/cli/apply_inverse_transfer_function.py b/recOrder/cli/apply_inverse_transfer_function.py index 9c566466..e68c4269 100644 --- a/recOrder/cli/apply_inverse_transfer_function.py +++ b/recOrder/cli/apply_inverse_transfer_function.py @@ -15,7 +15,7 @@ ) from recOrder.io import utils from waveorder.models import ( - inplane_anisotropic_thin_pol3d, + inplane_oriented_thick_pol3d, isotropic_thin_3d, phase_thick_3d, ) @@ -168,7 +168,7 @@ def apply_inverse_transfer_function_cli( for time_index in range(t_shape): # Apply reconstructed_parameters = ( - inplane_anisotropic_thin_pol3d.apply_inverse_transfer_function( + inplane_oriented_thick_pol3d.apply_inverse_transfer_function( tczyx_data[time_index], intensity_to_stokes_matrix, wavelength, @@ -277,7 +277,7 @@ def apply_inverse_transfer_function_cli( for time_index in range(t_shape): # Apply - reconstructed_parameters_2d = inplane_anisotropic_thin_pol3d.apply_inverse_transfer_function( + reconstructed_parameters_2d = inplane_oriented_thick_pol3d.apply_inverse_transfer_function( tczyx_data[time_index], intensity_to_stokes_matrix, wavelength, @@ -286,7 +286,7 @@ def apply_inverse_transfer_function_cli( **biref_inverse_dict, ) - reconstructed_parameters_3d = inplane_anisotropic_thin_pol3d.apply_inverse_transfer_function( + reconstructed_parameters_3d = inplane_oriented_thick_pol3d.apply_inverse_transfer_function( tczyx_data[time_index], intensity_to_stokes_matrix, wavelength, @@ -339,7 +339,7 @@ def apply_inverse_transfer_function_cli( # Apply for time_index in range(t_shape): - reconstructed_parameters_3d = inplane_anisotropic_thin_pol3d.apply_inverse_transfer_function( + reconstructed_parameters_3d = inplane_oriented_thick_pol3d.apply_inverse_transfer_function( tczyx_data[time_index], intensity_to_stokes_matrix, wavelength, diff --git a/recOrder/cli/compute_transfer_function.py b/recOrder/cli/compute_transfer_function.py index ffe6cbc8..78b5b61f 100644 --- a/recOrder/cli/compute_transfer_function.py +++ b/recOrder/cli/compute_transfer_function.py @@ -6,7 +6,7 @@ from recOrder.cli.settings import TransferFunctionSettings from recOrder.cli.parsing import config_path_option, output_dataset_options from waveorder.models import ( - inplane_anisotropic_thin_pol3d, + inplane_oriented_thick_pol3d, isotropic_thin_3d, phase_thick_3d, ) @@ -41,7 +41,7 @@ def compute_transfer_function_cli(config_path, output_path): # Calculate transfer functions intensity_to_stokes_matrix = ( - inplane_anisotropic_thin_pol3d.calculate_transfer_function( + inplane_oriented_thick_pol3d.calculate_transfer_function( **settings.birefringence_transfer_function_settings.dict() ) )