add handling for a background image in FluorescenceData

fluorescence_imaging.py

@@ -27,9 +27,17 @@ SEQ = SuperSequence(outdir, "sequence", {
         .digital_hilo(*C.dummy, 0.0, t0 + 100e-3)
         .with_color("k").with_stack_idx(0)
     ),
-    "Camera": (Sequence
-        .digital_pulse(*C.camera, t0, 12549.1e-6)
-        .with_color("C2").with_stack_idx(1)
+    "Coils": (Sequence
+        .digital_hilo(*C.coils, 0.0, t0 + 15e-3)
+        .with_color("C1").with_stack_idx(2)
+    ),
+    "Camera 1": (Sequence
+        .digital_pulse(*C.camera, t0, 12.5491e-3)
+        .with_color("C2").with_stack_idx(4)
+    ),
+    "Camera 2": (Sequence
+        .digital_pulse(*C.camera, t0 + 50e-3, 12.5491e-3)
+        .with_color("C2").with_stack_idx(4)
     ),
     "Push block": (Sequence
         .digital_lohi(*C.push_sh, t0 - 5e-3, t0 + 100e-3)
@@ -37,7 +45,7 @@ SEQ = SuperSequence(outdir, "sequence", {
     ),
     "Scope": (Sequence
         .digital_hilo(*C.scope, t0 - 25e-3, t0 + 100e-3)
-        .with_color("C7").with_stack_idx(2)
+        .with_color("C7").with_stack_idx(1)
     ),
 })
 
@@ -67,10 +75,10 @@ class FluorescenceImaging(Controller):
         SEQ.save()
 
     def run_camera(self, *args):
-        frames = self.cam.acquire_frames(1)
+        frames = self.cam.acquire_frames(2)
         data = FluorescenceData(
             outdir=outdir,
-            arrays={"image": frames[0]},
+            arrays={"image": frames[0], "background": frames[1]},
             config=camera_config,
             comments=comments
         )

lib/imaging.py

@@ -166,8 +166,11 @@ class FluorescenceData(ImagingData):
                 * (DEF_DX**2 if dA is None else dA)
         if printflag: print("[imaging] Compute results")
         for label, array in self.arrays.items():
+            if label == "background":
+                continue
             N = compute_mot_number(
-                array,
+                array if "background" not in self.arrays.keys() \
+                        else array - self.arrays["background"],
                 0.40,
                 self.config["gain"], # dB
                 self.config["exposure_time"] * 1e-6, # s