adjustments to fluorescence imaging

fluorescence_imaging.py

@@ -7,13 +7,13 @@ outdir = DATADIRS.fluorescence_imaging.joinpath(get_timestamp())
 comments = """
 Fluorescence imaging
 ====================
-62 MHz/26.41 dBm AOM, 4.00 A dispenser, 120.5 A MOT coil
+62 MHz/26.41 dBm AOM, 3.75 A dispenser, 120.5 A MOT coil
 """[1:-1]
 
 # CAMERA OPTIONS
 camera_config = {
     "exposure_time": 12549.1,
-    "gain": 0.0,
+    "gain": 20.0,
     "gamma": 1.25,
     "black_level": 5.0,
     "bin_size": 1,
@@ -31,6 +31,10 @@ SEQ = SuperSequence(outdir, "sequence", {
         .digital_pulse(*C.camera, t0, 12549.1e-6)
         .with_color("C2").with_stack_idx(1)
     ),
+    "Push block": (Sequence
+        .digital_lohi(*C.push_sh, t0 - 5e-3, t0 + 100e-3)
+        .with_color("C3").with_stack_idx(3)
+    ),
     "Scope": (Sequence
         .digital_hilo(*C.scope, t0 - 25e-3, t0 + 100e-3)
         .with_color("C7").with_stack_idx(2)

lib/imaging.py

@@ -191,8 +191,9 @@ def compute_mot_number(image, QE, gain, exposure_time, solid_angle,
     if image.max() >= np.iinfo(image.dtype).max:
         print("[imaging] WARNING: image may contain clipping")
     H, W = image.shape
-    im = image[H//3:2*H//3, W//3:2*W//3].astype(np.float64)
-    electron_rate = im.sum() / 16 # get to 12-bit values
+    im = image[H//3:2*H//3, W//3:2*W//3]
+    pd.Plotter().imshow(im).savefig("img.png").close()
+    electron_rate = im.astype(np.float64).sum() / 16 # get to 12-bit values
     photon_rate \
             = electron_rate \
             / 10**(gain / 10) \