POC: GUI layout for recOrder v1.0.0

examples/birefringence-and-phase.yml

@@ -5,27 +5,29 @@ input_channel_names:
 - State3
 time_indices: all
 reconstruction_dimension: 3
-birefringence:
-  transfer_function:
-    swing: 0.1
-  apply_inverse:
-    wavelength_illumination: 0.532
-    background_path: ''
-    remove_estimated_background: false
-    flip_orientation: false
-    rotate_orientation: false
-phase:
-  transfer_function:
-    wavelength_illumination: 0.532
-    yx_pixel_size: 0.325
-    z_pixel_size: 2.0
-    z_padding: 0
-    index_of_refraction_media: 1.3
-    numerical_aperture_detection: 1.2
-    numerical_aperture_illumination: 0.5
-    invert_phase_contrast: false
-  apply_inverse:
-    reconstruction_algorithm: Tikhonov
-    regularization_strength: 0.001
-    TV_rho_strength: 0.001
-    TV_iterations: 1
+reconstruction_type: Birefringence and Phase
+reconstruction_settings:
+  birefringence_settings:
+    transfer_function:
+      swing: 0.1
+    apply_inverse:
+      wavelength_illumination: 0.532
+      background_path: ''
+      remove_estimated_background: false
+      flip_orientation: false
+      rotate_orientation: false
+  phase_settings:
+    transfer_function:
+      wavelength_illumination: 0.532
+      yx_pixel_size: 0.325
+      z_pixel_size: 2.0
+      z_padding: 0
+      index_of_refraction_media: 1.3
+      numerical_aperture_detection: 1.2
+      numerical_aperture_illumination: 0.5
+      invert_phase_contrast: false
+    apply_inverse:
+      reconstruction_algorithm: Tikhonov
+      regularization_strength: 0.001
+      TV_rho_strength: 0.001
+      TV_iterations: 1

examples/birefringence.yml

@@ -5,7 +5,8 @@ input_channel_names:
 - State3
 time_indices: all
 reconstruction_dimension: 3
-birefringence:
+reconstruction_type: Birefringence
+reconstruction_settings:
   transfer_function:
     swing: 0.1
   apply_inverse:

examples/fluorescence.yml

@@ -2,7 +2,8 @@ input_channel_names:
 - GFP
 time_indices: all
 reconstruction_dimension: 3
-fluorescence:
+reconstruction_type: Fluorescence
+reconstruction_settings:
   transfer_function:
     yx_pixel_size: 0.325
     z_pixel_size: 2.0

examples/phase.yml

@@ -2,15 +2,16 @@ input_channel_names:
 - BF
 time_indices: all
 reconstruction_dimension: 3
-phase:
+reconstruction_type: Phase
+reconstruction_settings:
   transfer_function:
     wavelength_illumination: 0.532
     yx_pixel_size: 0.325
     z_pixel_size: 2.0
     z_padding: 0
     index_of_refraction_media: 1.3
-    numerical_aperture_detection: 1.2
-    numerical_aperture_illumination: 0.5
+    numerical_aperture_detection: 0.75
+    numerical_aperture_illumination: 0.55
     invert_phase_contrast: false
   apply_inverse:
     reconstruction_algorithm: Tikhonov

recOrder/cli/apply_inverse_transfer_function.py

@@ -39,26 +39,21 @@ def get_reconstruction_output_metadata(position_path: Path, config_path: Path):
     T, _, Z, Y, X = input_dataset.data.shape
 
     settings = utils.yaml_to_model(config_path, ReconstructionSettings)
-
-    # Simplify important settings names
-    recon_biref = settings.birefringence is not None
-    recon_phase = settings.phase is not None
-    recon_fluo = settings.fluorescence is not None
     recon_dim = settings.reconstruction_dimension
 
     # Prepare output dataset
     channel_names = []
-    if recon_biref:
+    if "Birefringence" in settings.reconstruction_type:
         channel_names.append("Retardance")
         channel_names.append("Orientation")
         channel_names.append("BF")
         channel_names.append("Pol")
-    if recon_phase:
+    if "Phase" in settings.reconstruction_type:
         if recon_dim == 2:
             channel_names.append("Phase2D")
         elif recon_dim == 3:
             channel_names.append("Phase3D")
-    if recon_fluo:
+    if settings.reconstruction_type == "Fluorescence":
         fluor_name = settings.input_channel_names[0]
         if recon_dim == 2:
             channel_names.append(fluor_name + "_Density2D")
@@ -125,19 +120,20 @@ def apply_inverse_transfer_function_single_position(
             f"time_indices = {time_indices} includes a time index beyond the maximum index of the dataset = {time_ubound}"
         )
 
-    # Simplify important settings names
-    recon_biref = settings.birefringence is not None
-    recon_phase = settings.phase is not None
-    recon_fluo = settings.fluorescence is not None
-    recon_dim = settings.reconstruction_dimension
-
     # Prepare birefringence parameters
-    if settings.birefringence is not None:
+    if "Birefringence" in settings.reconstruction_type:
         # settings.birefringence has more parameters than waveorder needs,
         # so this section converts the settings to a dict and separates the
         # waveorder parameters (biref_inverse_dict) from the recorder
         # parameters (cyx_no_sample_data, and wavelength_illumination)
-        biref_inverse_dict = settings.birefringence.apply_inverse.dict()
+        if settings.reconstruction_type == "Birefringence":
+            biref_inverse_dict = (
+                settings.reconstruction_settings.apply_inverse.dict()
+            )
+        elif settings.reconstruction_type == "Birefringence and Phase":
+            biref_inverse_dict = (
+                settings.reconstruction_settings.birefringence_settings.apply_inverse.dict()
+            )
 
         # Resolve background path into array
         background_path = biref_inverse_dict.pop("background_path")
@@ -157,38 +153,42 @@ def apply_inverse_transfer_function_single_position(
     # Prepare the apply_inverse_model_function and its arguments
 
     # [biref only]
-    if recon_biref and (not recon_phase):
+    if settings.reconstruction_type == "Birefringence":
         echo_headline("Reconstructing birefringence with settings:")
-        echo_settings(settings.birefringence)
+        echo_settings(settings.reconstruction_settings)
 
         # Setup parameters for apply_inverse_to_zyx_and_save
         apply_inverse_model_function = apply_inverse_models.birefringence
         apply_inverse_args = {
             "cyx_no_sample_data": cyx_no_sample_data,
             "wavelength_illumination": biref_wavelength_illumination,
-            "recon_dim": recon_dim,
+            "recon_dim": settings.reconstruction_dimension,
             "biref_inverse_dict": biref_inverse_dict,
             "transfer_function_dataset": transfer_function_dataset,
         }
 
     # [phase only]
-    if recon_phase and (not recon_biref):
+    if settings.reconstruction_type == "Phase":
         echo_headline("Reconstructing phase with settings:")
-        echo_settings(settings.phase.apply_inverse)
+        echo_settings(settings.reconstruction_settings.apply_inverse)
 
         # Setup parameters for apply_inverse_to_zyx_and_save
         apply_inverse_model_function = apply_inverse_models.phase
         apply_inverse_args = {
-            "recon_dim": recon_dim,
-            "settings_phase": settings.phase,
+            "recon_dim": settings.reconstruction_dimension,
+            "settings_phase": settings.reconstruction_settings,
             "transfer_function_dataset": transfer_function_dataset,
         }
 
     # [biref and phase]
-    if recon_biref and recon_phase:
+    if settings.reconstruction_type == "Birefringence and Phase":
         echo_headline("Reconstructing birefringence and phase with settings:")
-        echo_settings(settings.birefringence.apply_inverse)
-        echo_settings(settings.phase.apply_inverse)
+        echo_settings(
+            settings.reconstruction_settings.birefringence_settings.apply_inverse
+        )
+        echo_settings(
+            settings.reconstruction_settings.phase_settings.apply_inverse
+        )
 
         # Setup parameters for apply_inverse_to_zyx_and_save
         apply_inverse_model_function = (
@@ -197,22 +197,22 @@ def apply_inverse_transfer_function_single_position(
         apply_inverse_args = {
             "cyx_no_sample_data": cyx_no_sample_data,
             "wavelength_illumination": biref_wavelength_illumination,
-            "recon_dim": recon_dim,
+            "recon_dim": settings.reconstruction_dimension,
             "biref_inverse_dict": biref_inverse_dict,
-            "settings_phase": settings.phase,
+            "settings_phase": settings.reconstruction_settings.phase_settings,
             "transfer_function_dataset": transfer_function_dataset,
         }
 
     # [fluo]
-    if recon_fluo:
+    if settings.reconstruction_type == "Fluorescence":
         echo_headline("Reconstructing fluorescence with settings:")
-        echo_settings(settings.fluorescence.apply_inverse)
+        echo_settings(settings.reconstruction_settings.apply_inverse)
 
         # Setup parameters for apply_inverse_to_zyx_and_save
         apply_inverse_model_function = apply_inverse_models.fluorescence
         apply_inverse_args = {
-            "recon_dim": recon_dim,
-            "settings_fluorescence": settings.fluorescence,
+            "recon_dim": settings.reconstruction_dimension,
+            "settings_fluorescence": settings.reconstruction_settings,
             "transfer_function_dataset": transfer_function_dataset,
         }
 

recOrder/cli/compute_transfer_function.py

@@ -16,11 +16,17 @@
     output_dirpath,
 )
 from recOrder.cli.printing import echo_headline, echo_settings
-from recOrder.cli.settings import ReconstructionSettings
+from recOrder.cli.settings import (
+    ReconstructionSettings,
+    PhaseSettings,
+    BirefringenceSettings,
+)
 from recOrder.io import utils
 
 
-def generate_and_save_birefringence_transfer_function(settings, dataset):
+def generate_and_save_birefringence_transfer_function(
+    settings: ReconstructionSettings, dataset
+):
     """Generates and saves the birefringence transfer function to the dataset, based on the settings.
 
     Parameters
@@ -30,13 +36,13 @@ def generate_and_save_birefringence_transfer_function(settings, dataset):
         The dataset that will be updated.
     """
     echo_headline("Generating birefringence transfer function with settings:")
-    echo_settings(settings.birefringence.transfer_function)
+    echo_settings(settings.reconstruction_settings.transfer_function)
 
     # Calculate transfer functions
     intensity_to_stokes_matrix = (
         inplane_oriented_thick_pol3d.calculate_transfer_function(
             scheme=str(len(settings.input_channel_names)) + "-State",
-            **settings.birefringence.transfer_function.dict(),
+            **settings.reconstruction_settings.transfer_function.dict(),
         )
     )
     # Save
@@ -45,7 +51,9 @@ def generate_and_save_birefringence_transfer_function(settings, dataset):
     ] = intensity_to_stokes_matrix.cpu().numpy()[None, None, None, ...]
 
 
-def generate_and_save_phase_transfer_function(settings, dataset, zyx_shape):
+def generate_and_save_phase_transfer_function(
+    settings: ReconstructionSettings, dataset, zyx_shape
+):
     """Generates and saves the phase transfer function to the dataset, based on the settings.
 
     Parameters
@@ -57,11 +65,13 @@ def generate_and_save_phase_transfer_function(settings, dataset, zyx_shape):
         A tuple of integers specifying the input data's shape in (Z, Y, X) order
     """
     echo_headline("Generating phase transfer function with settings:")
-    echo_settings(settings.phase.transfer_function)
+    echo_settings(settings.reconstruction_settings.transfer_function)
 
     if settings.reconstruction_dimension == 2:
         # Convert zyx_shape and z_pixel_size into yx_shape and z_position_list
-        settings_dict = settings.phase.transfer_function.dict()
+        settings_dict = (
+            settings.reconstruction_settings.transfer_function.dict()
+        )
         settings_dict["yx_shape"] = [zyx_shape[1], zyx_shape[2]]
         settings_dict["z_position_list"] = list(
             -(np.arange(zyx_shape[0]) - zyx_shape[0] // 2)
@@ -95,7 +105,7 @@ def generate_and_save_phase_transfer_function(settings, dataset, zyx_shape):
             imaginary_potential_transfer_function,
         ) = phase_thick_3d.calculate_transfer_function(
             zyx_shape=zyx_shape,
-            **settings.phase.transfer_function.dict(),
+            **settings.reconstruction_settings.transfer_function.dict(),
         )
         # Save
         dataset[
@@ -108,8 +118,44 @@ def generate_and_save_phase_transfer_function(settings, dataset, zyx_shape):
         ]
 
 
+def generate_and_save_birefringence_and_phase_transfer_function(
+    settings: ReconstructionSettings, dataset, zyx_shape
+):
+    """Generates and saves the birefringence and phase transfer functions to the dataset, based on the settings.
+
+    Parameters
+    ----------
+    settings: ReconstructionSettings
+    dataset: NGFF Node
+        The dataset that will be updated.
+    zyx_shape : tuple
+        A tuple of integers specifying the input data's shape in (Z, Y, X) order
+    """
+    phase_only_settings = ReconstructionSettings(
+        input_channel_names=settings.input_channel_names,
+        time_indices=settings.time_indices,
+        reconstruction_dimension=settings.reconstruction_dimension,
+        reconstruction_type="Phase",
+        reconstruction_settings=settings.reconstruction_settings.phase_settings,
+    )
+    generate_and_save_phase_transfer_function(
+        phase_only_settings, dataset, zyx_shape
+    )
+
+    biref_only_settings = ReconstructionSettings(
+        input_channel_names=settings.input_channel_names,
+        time_indices=settings.time_indices,
+        reconstruction_dimension=settings.reconstruction_dimension,
+        reconstruction_type="Birefringence",
+        reconstruction_settings=settings.reconstruction_settings.birefringence_settings,
+    )
+    generate_and_save_birefringence_transfer_function(
+        biref_only_settings, dataset
+    )
+
+
 def generate_and_save_fluorescence_transfer_function(
-    settings, dataset, zyx_shape
+    settings: ReconstructionSettings, dataset, zyx_shape
 ):
     """Generates and saves the fluorescence transfer function to the dataset, based on the settings.
 
@@ -122,7 +168,7 @@ def generate_and_save_fluorescence_transfer_function(
         A tuple of integers specifying the input data's shape in (Z, Y, X) order
     """
     echo_headline("Generating fluorescence transfer function with settings:")
-    echo_settings(settings.fluorescence.transfer_function)
+    echo_settings(settings.reconstruction_settings.transfer_function)
 
     if settings.reconstruction_dimension == 2:
         raise NotImplementedError
@@ -131,7 +177,7 @@ def generate_and_save_fluorescence_transfer_function(
         optical_transfer_function = (
             isotropic_fluorescent_thick_3d.calculate_transfer_function(
                 zyx_shape=zyx_shape,
-                **settings.fluorescence.transfer_function.dict(),
+                **settings.reconstruction_settings.transfer_function.dict(),
             )
         )
         # Save
@@ -176,15 +222,19 @@ def compute_transfer_function_cli(
     )
 
     # Pass settings to appropriate calculate_transfer_function and save
-    if settings.birefringence is not None:
+    if settings.reconstruction_type == "Birefringence":
         generate_and_save_birefringence_transfer_function(
             settings, output_dataset
         )
-    if settings.phase is not None:
+    elif settings.reconstruction_type == "Phase":
         generate_and_save_phase_transfer_function(
             settings, output_dataset, zyx_shape
         )
-    if settings.fluorescence is not None:
+    elif settings.reconstruction_type == "Birefringence and Phase":
+        generate_and_save_birefringence_and_phase_transfer_function(
+            settings, output_dataset, zyx_shape
+        )
+    elif settings.reconstruction_type == "Fluorescence":
         generate_and_save_fluorescence_transfer_function(
             settings, output_dataset, zyx_shape
         )