Connect background corrections

recOrder/acq/acquisition_workers.py

@@ -96,7 +96,9 @@ def _generate_transfer_function_config(
 
 def _generate_apply_inverse_config(apply_inverse_settings_path, calib_window):
     birefringence_apply_inverse_settings = (
-        settings._BirefringenceApplyInverseSettings()
+        settings._BirefringenceApplyInverseSettings(
+            background_path=calib_window.acq_bg_directory
+        )
     )
 
     phase_apply_inverse_settings = settings._PhaseApplyInverseSettings()

recOrder/cli/apply_inverse_transfer_function.py

@@ -143,7 +143,7 @@ def apply_inverse_transfer_function_cli(
         # Resolve background path into array
         background_path = biref_inverse_dict["background_path"]
         biref_inverse_dict.pop("background_path")
-        if background_path is not None:
+        if background_path != "":
             cyx_no_sample_data = utils.new_load_background(background_path)
             _check_background_consistency(
                 cyx_no_sample_data.shape, input_dataset.data.shape
@@ -338,8 +338,10 @@ def apply_inverse_transfer_function_cli(
                     **biref_inverse_dict,
                 )
 
+                brightfield_3d = reconstructed_parameters_3d[2]
+
                 zyx_phase = phase_thick_3d.apply_inverse_transfer_function(
-                    tczyx_data[time_index, 0],
+                    brightfield_3d,
                     real_potential_transfer_function,
                     imaginary_potential_transfer_function,
                     z_padding=settings.phase_transfer_function_settings.z_padding,

recOrder/cli/settings.py

@@ -1,3 +1,4 @@
+import os
 from pydantic import BaseModel, DirectoryPath, validator
 from typing import Literal, List
 
@@ -110,13 +111,21 @@ class TransferFunctionSettings(BaseModel):
 
 
 class _BirefringenceApplyInverseSettings(BaseModel):
-    background_path: str = (
-        None  # I'd DirectoryPath but it's not JSON serializable?
-    )
+    background_path: str = ""
     remove_estimated_background: bool = False
     orientation_flip: bool = False
     orientation_rotate: bool = False
 
+    @validator("background_path")
+    def check_background_path(cls, v):
+        if v == "":
+            return v
+
+        raw_dir = r"{}".format(v)
+        if not os.path.isdir(raw_dir):
+            raise ValueError(f"{v} is not a existing directory")
+        return raw_dir
+
 
 class _PhaseApplyInverseSettings(BaseModel):
     reconstruction_algorithm: Literal["Tikhonov", "TV"] = "Tikhonov"

recOrder/plugin/main_widget.py

@@ -303,7 +303,7 @@ def __init__(self, napari_viewer: Viewer):
         self.orientation_offset = False
         self.pad_z = 0
         self.phase_reconstructor = None
-        self.acq_bg_directory = None
+        self.acq_bg_directory = ""
         self.auto_shutter = True
         self.lca_dac = None
         self.lcb_dac = None