generate example settings with revised model

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

@@ -2,7 +2,8 @@ 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

recOrder/cli/settings.py

@@ -1,12 +1,11 @@
 import os
-from typing import Literal, Optional, Union
+from typing import Literal, Union
 from pydantic import (
     BaseModel,
     Extra,
     NonNegativeFloat,
     NonNegativeInt,
     PositiveFloat,
-    root_validator,
     validator,
 )
 
@@ -138,8 +137,8 @@ class PhaseSettings(MyBaseModel):
 
 
 class BirefringenceAndPhaseSettings(MyBaseModel):
-    birefringence_settings: BirefringenceSettings
-    phase_settings: PhaseSettings
+    birefringence_settings: BirefringenceSettings = BirefringenceSettings()
+    phase_settings: PhaseSettings = PhaseSettings()
 
 
 class FluorescenceSettings(MyBaseModel):
@@ -149,16 +148,36 @@ class FluorescenceSettings(MyBaseModel):
     apply_inverse: FourierApplyInverseSettings = FourierApplyInverseSettings()
 
 
+OPTION_TO_MODEL_DICT = {
+    "Birefringence": BirefringenceSettings,
+    "Phase": PhaseSettings,
+    "Birefringence and Phase": BirefringenceAndPhaseSettings,
+    "Fluorescence": FluorescenceSettings,
+}
+
+RECONSTRUCTION_TYPES = Literal[tuple(OPTION_TO_MODEL_DICT.keys())]
+
+
 # Top level settings
 class ReconstructionSettings(MyBaseModel):
     input_channel_names: list[str] = [f"State{i}" for i in range(4)]
     time_indices: Union[
         NonNegativeInt, list[NonNegativeInt], Literal["all"]
     ] = "all"
     reconstruction_dimension: Literal[2, 3] = 3
-    reconstruction_type: Union[
+    reconstruction_type: RECONSTRUCTION_TYPES = "Birefringence"
+    reconstruction_settings: Union[
         BirefringenceSettings,
         PhaseSettings,
         BirefringenceAndPhaseSettings,
         FluorescenceSettings,
     ] = BirefringenceSettings()
+
+    @validator("reconstruction_settings")
+    def validate_reconstruction_settings(cls, v, values):
+        recon_type = values.get("reconstruction_type")
+        if OPTION_TO_MODEL_DICT[recon_type] != type(v):
+            raise ValueError(
+                f"reconstruction_type = {recon_type} needs to match reconstruction_settings = {type(v)}"
+            )
+        return v

recOrder/plugin/_widget.py

@@ -22,19 +22,11 @@
 from superqt import QCollapsible, QLabeledSlider
 
 from recOrder.cli import settings
+from recOrder.cli.settings import OPTION_TO_MODEL_DICT, RECONSTRUCTION_TYPES
 
 if TYPE_CHECKING:
     from napari import Viewer
 
-OPTION_TO_MODEL_DICT = {
-    "Birefringence": settings.BirefringenceSettings,
-    "Phase": settings.PhaseSettings,
-    "Birefringence and Phase": settings.BirefringenceAndPhaseSettings,
-    "Fluorescence": settings.FluorescenceSettings,
-}
-
-RECONSTRUCTION_TYPES = Literal[tuple(OPTION_TO_MODEL_DICT.keys())]
-
 
 class QHLine(QFrame):
     def __init__(self):

recOrder/tests/cli_tests/test_settings.py

@@ -91,19 +91,22 @@ def test_generate_example_settings():
     example_path = "./examples/"
 
     s0 = settings.ReconstructionSettings(
-        birefringence=settings.BirefringenceSettings(),
-        phase=settings.PhaseSettings(),
+        reconstruction_type="Birefringence and Phase",
+        reconstruction_settings=settings.BirefringenceAndPhaseSettings(),
     )
     s1 = settings.ReconstructionSettings(
         input_channel_names=["BF"],
-        phase=settings.PhaseSettings(),
+        reconstruction_type="Phase",
+        reconstruction_settings=settings.PhaseSettings(),
     )
     s2 = settings.ReconstructionSettings(
-        birefringence=settings.BirefringenceSettings(),
+        reconstruction_type="Birefringence",
+        reconstruction_settings=settings.BirefringenceSettings(),
     )
     s3 = settings.ReconstructionSettings(
         input_channel_names=["GFP"],
-        fluorescence=settings.FluorescenceSettings(),
+        reconstruction_type="Fluorescence",
+        reconstruction_settings=settings.FluorescenceSettings(),
     )
     file_names = [
         "birefringence-and-phase.yml",