From f71bc4e88c0562a8176ce4703673ac4df4f2f0bd Mon Sep 17 00:00:00 2001
From: Talon Chandler <talonchandler@gmail.com>
Date: Tue, 25 Apr 2023 10:27:32 -0700
Subject: [PATCH] connect background corrections

---
 recOrder/acq/acquisition_workers.py             |  4 +++-
 recOrder/cli/apply_inverse_transfer_function.py |  6 ++++--
 recOrder/cli/settings.py                        | 15 ++++++++++++---
 recOrder/plugin/main_widget.py                  |  2 +-
 4 files changed, 20 insertions(+), 7 deletions(-)

diff --git a/recOrder/acq/acquisition_workers.py b/recOrder/acq/acquisition_workers.py
index 7b66bdd1..5b5e0b97 100644
--- a/recOrder/acq/acquisition_workers.py
+++ b/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()
diff --git a/recOrder/cli/apply_inverse_transfer_function.py b/recOrder/cli/apply_inverse_transfer_function.py
index d892a3f5..2b86a745 100644
--- a/recOrder/cli/apply_inverse_transfer_function.py
+++ b/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,
diff --git a/recOrder/cli/settings.py b/recOrder/cli/settings.py
index d6f0c003..5187954b 100644
--- a/recOrder/cli/settings.py
+++ b/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"
diff --git a/recOrder/plugin/main_widget.py b/recOrder/plugin/main_widget.py
index 985d3b2e..8149a98b 100644
--- a/recOrder/plugin/main_widget.py
+++ b/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