update timings (update not complete) and add option for subtracting background...

update timings (update not complete) and add option for subtracting background from numbers reported in results.toml

fluorescence_imaging_multi.py

@@ -112,7 +112,7 @@ class FluorescenceImaging(Controller):
             config=camera_config,
             comments=comments
         )
-        data.compute_results()
+        data.compute_results(subtract_bkgd=False)
         data.save()
         data.render_arrays()
 

lib/imaging.py

@@ -161,7 +161,8 @@ class FluorescenceData(ImagingData):
         return FluorescenceData(
             data.outdir, data.arrays, data.config, data.comments, data.results)
 
-    def compute_results(self, dA=3.45**2, printflag: bool=True):
+    def compute_results(self, subtract_bkgd: bool=True, dA: float=3.45**2,
+            printflag: bool=True):
         _dA = self.config.get("bin_size", 1)**2 \
                 * (DEF_DX**2 if dA is None else dA)
         if printflag: print("[imaging] Compute results")
@@ -177,13 +178,12 @@ class FluorescenceData(ImagingData):
             self.arrays["background"].astype(np.float64),
             **compute_mot_number_params,
             k=0
-        ) if "background" in self.arrays.keys() else 0.0
+        ) if subtract_bkgd and "background" in self.arrays.keys() else 0.0
         for label, array in self.arrays.items():
-            if label == "background":
-                continue
             dtype_info = np.iinfo(array.dtype)
             if array.max() >= (dtype_info.max - dtype_info.bits):
-                print(f"[imaging] WARNING: image '{label}' may contain clipping")
+                print(
+                    f"[imaging] WARNING: image '{label}' may contain clipping")
             N = compute_mot_number(
                 array.astype(np.float64),
                 **compute_mot_number_params,

mot_transfer.py

@@ -3,11 +3,15 @@ from lib import *
 from lib import CONNECTIONS as C
 import sys, pathlib
 
-outdir = DATADIRS.mot_transfer.joinpath(get_timestamp())
+timestamp = get_timestamp()
+print(timestamp)
+outdir = DATADIRS.mot_transfer.joinpath(timestamp)
 
 comments = """
 MOT transfer
 ============
+71.40 MHz PDH RF
+3 A shims
 """[1:-1]
 
 # CAMERA OPTIONS
@@ -16,13 +20,13 @@ camera_config = {
     "gain": 5.0,
     "gamma": 1.25,
     "black_level": 5.0,
-    "bin_size": 2,
+    "bin_size": 1,
 }
 
 # CONSTRUCT SEQUENCE
-t0 = 2.25 # big coils start turning off at t0
+t0 = 2.5 # big coils start turning off at t0
 R = 3 # repetition for each tau
-tau_ = np.array([np.linspace(5.0e-3, 500.0e-3, 21) for k in range(R)]).T.flatten()
+tau_ = np.array([np.linspace(6.5e-3, 86.5e-3, 11) for k in range(R)]).T.flatten()
 z = int(np.ceil(np.log10(tau_.shape[0])))
 
 def make_sequence(tau, name=None):
@@ -46,7 +50,7 @@ def make_sequence(tau, name=None):
 
         "MOT coils 2": (Sequence
             .digital_hilo(*C.mot3_coils_igbt,
-                t0 + tau - 4.5e-3, t0 + tau + 100e-3)
+                t0 + tau - 6.8e-3, t0 + tau + 100e-3)
         ).with_color("C1").with_stack_idx(2),
 
         "Blue beams 1": (Sequence
@@ -54,15 +58,15 @@ def make_sequence(tau, name=None):
         ).with_color("C0").with_stack_idx(5),
 
         "Blue beams 2": (Sequence
-            .digital_hilo(*C.mot3_blue_sh, t0 + tau - 1e-3, t0 + tau + 100e-3)
+            .digital_hilo(*C.mot3_blue_sh, t0 + tau - 3e-3, t0 + tau + 100e-3)
         ).with_color("C0").with_stack_idx(5),
 
         "MOT shims": (Sequence
-            .digital_hilo(*C.mot3_shims_onoff, t0 - 1e-3, t0 + tau - 1e-3)
+            .digital_hilo(*C.mot3_shims_onoff, t0 - 0.5e-3, t0 + tau)
         ).with_color("C1").with_stack_idx(3),
 
         "Green beams": (Sequence
-            .digital_hilo(*C.mot3_green_aom, t0 - 1e-3, t0 + tau - 1e-3)
+            .digital_hilo(*C.mot3_green_aom, t0, t0 + tau)
         ).with_color("C6").with_stack_idx(6),
 
         "Camera": (Sequence
@@ -74,23 +78,23 @@ def make_sequence(tau, name=None):
 
 sseq_bkgd = SuperSequence(outdir.joinpath("sequences"), f"background", {
     "Sequence": (Sequence
-        .digital_hilo(*C.dummy, 0.0, 100e-3)
+        .digital_hilo(*C.dummy, 0.0, 200e-3)
     ),
     "Push": (Sequence
-        .digital_lohi(*C.push_sh, 0.0, 100e-3)
+        .digital_lohi(*C.push_sh, 0.0, 200e-3)
     ),
     "MOT beams": (Sequence
-        .digital_lohi(*C.mot3_blue_sh, 0.0, 50e-3)
+        .digital_lohi(*C.mot3_blue_sh, 0.0, 150e-3)
     ),
     "MOT coils": (Sequence
-        .digital_hilo(*C.mot3_coils_igbt, 0.0, 100e-3)
-        .digital_hilo(*C.mot3_coils_onoff, 0.0, 100e-3)
+        .digital_hilo(*C.mot3_coils_igbt, 0.0, 200e-3)
+        .digital_hilo(*C.mot3_coils_onoff, 0.0, 200e-3)
     ),
     "Camera": (Sequence
-        .digital_pulse(*C.flir_trig, 80e-3, camera_config["exposure_time"] * 1e-6)
+        .digital_pulse(*C.flir_trig, 180e-3, camera_config["exposure_time"] * 1e-6)
     ),
     "Scope": (Sequence
-        .digital_hilo(*C.scope_trig, 0.0, 100e-3)
+        .digital_hilo(*C.scope_trig, 0.0, 200e-3)
     ),
 }, C)
 
@@ -146,7 +150,7 @@ class MOTTransfer(Controller):
             config=camera_config,
             comments=comments
         )
-        data.compute_results()
+        data.compute_results(subtract_bkgd=False)
         data.save()
         data.render_arrays()
 

mot_transfer_temperature.py

@@ -3,6 +3,8 @@ from lib import *
 from lib import CONNECTIONS as C
 import sys, pathlib
 
+raise Exception("This script is outdated: needs timing updates")
+
 outdir = DATADIRS.mot_transfer.joinpath(get_timestamp())
 
 comments = """
@@ -16,7 +18,7 @@ camera_config = {
     "gain": 5.0,
     "gamma": 1.25,
     "black_level": 5.0,
-    "bin_size": 2,
+    "bin_size": 1,
 }
 
 # CONSTRUCT SEQUENCE
@@ -148,7 +150,7 @@ class MOTTransferTemperature(Controller):
             config=camera_config,
             comments=comments
         )
-        data.compute_results()
+        data.compute_results(subtract_bkgd=False)
         data.save()
         data.render_arrays()