From ed801319cf7aaa16e3125cd24c0d1a6860f22c70 Mon Sep 17 00:00:00 2001
From: acorrao <95718914+AdamCorrao@users.noreply.github.com>
Date: Fri, 12 Apr 2024 12:03:26 -0400
Subject: [PATCH] fix: normalize then bkg sub

---
 pdf_agents/agents.py | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/pdf_agents/agents.py b/pdf_agents/agents.py
index 19f13b4..0c5cea6 100644
--- a/pdf_agents/agents.py
+++ b/pdf_agents/agents.py
@@ -102,8 +102,6 @@ def measurement_plan(self, point: ArrayLike) -> Tuple[str, List, Dict]:
     def unpack_run(self, run) -> Tuple[Union[float, ArrayLike], Union[float, ArrayLike]]:
         """Subtracts background and returns motor positions and data"""
         y = run.primary.data[self.data_key].read().flatten()
-        if self.background is not None:
-            y = y - self.background[1]
 
         ordinate = np.array(run.primary.data[self.roi_key]).flatten()
         if self.norm_region is not None:
@@ -127,11 +125,16 @@ def unpack_run(self, run) -> Tuple[Union[float, ArrayLike], Union[float, ArrayLi
                 if len(np.where(self.background[0] > self.norm_region[1])[0])
                 else None
             )
-            scale_factor = np.sum(self.background[1][bkg_idx_min:bkg_idx_max]) / np.sum(y[idx_min:idx_max])
+
+            scale_bkg = 1 / np.sum(self.background[1][bkg_idx_min:bkg_idx_max])
+            scale_y = 1 / np.sum(y[idx_min:idx_max])
+
         else:
-            scale_factor = 1
+            scale_bkg = 1
+            scale_y = 1
 
-        y = y * scale_factor
+        if self.background is not None:
+            y = (y * scale_y) - (self.background[1] * scale_bkg)
 
         if self.roi is not None:
             ordinate = np.array(run.primary.data[self.roi_key]).flatten()