subtract background atom number, rather than background array

lib/imaging.py

@@ -165,6 +165,15 @@ class FluorescenceData(ImagingData):
         _dA = self.config.get("bin_size", 1)**2 \
                 * (DEF_DX**2 if dA is None else dA)
         if printflag: print("[imaging] Compute results")
+        N_bkgd = compute_mot_number(
+            self.arrays["background"].astype(np.float64),
+            0.40,
+            self.config["gain"],
+            self.config["exposure_time"] * 1e-6, # s
+            (0.0127**2 * np.pi) / (4 * np.pi * 0.125**2),
+            50e6 * 2 * np.pi,
+            1.0
+        ) if "background" in self.arrays else 0
         for label, array in self.arrays.items():
             if label == "background":
                 continue
@@ -172,18 +181,14 @@ class FluorescenceData(ImagingData):
             if array.max() >= (dtype_info.max - dtype_info.bits):
                 print(f"[imaging] WARNING: image '{label}' may contain clipping")
             N = compute_mot_number(
-                array if "background" not in self.arrays.keys() \
-                        else (
-                            array.astype(np.float64)
-                            - self.arrays["background"].astype(np.float64)
-                        ),
+                array,
                 0.40,
                 self.config["gain"], # dB
                 self.config["exposure_time"] * 1e-6, # s
                 (0.0127**2 * np.pi) / (4 * np.pi * 0.125**2),
                 50e6 * 2 * np.pi,
                 1.0
-            )
+            ) - N_bkgd
             sx, sy = lls_fit_gaussian(array, _dA)
             self.results = dict() if self.results is None else self.results
             self.results.update({
@@ -198,7 +203,7 @@ class FluorescenceData(ImagingData):
 def compute_mot_number(image, QE, gain, exposure_time, solid_angle,
         detuning, intensity_parameter):
     H, W = image.shape
-    im = image[H//5:4*H//5, W//5:4*W//5]
+    im = image[H//4:3*H//4, W//4:3*W//4]
     #pd.Plotter().imshow(im).savefig("img.png").close()
     electron_rate = im.astype(np.float64).sum()
     photon_rate \