new scripts for imaging the MOT with the EMCCD

blue_fluorescence_green_mot.py

+from lib import *
+from lib import CONNECTIONS as C
+import datetime, sys, pathlib
+
+outdir = DATADIRS.fluorescence_imaging.joinpath(get_timestamp())
+
+comments = """
+Fluorescence imaging
+====================
+"""[1:-1]
+
+# CAMERA OPTIONS
+camera_config = {
+    "exposure_time": 100,
+    "gain": 45.49,
+    "gamma": 1.25,
+    "black_level": 5.0,
+    "bin_size": 1,
+}
+
+# BUILD SEQUENCE
+t0 = 1.0 # take the picture
+tau = 50e-3
+SEQ = SuperSequence(outdir, "sequence", {
+    "Sequence": (Sequence
+        .digital_hilo(*C.dummy, 0.0, t0 + 800e-3)
+        .with_color("k").with_stack_idx(0)
+    ),
+    "Camera 1": (Sequence
+        .digital_pulse(*C.flir_trig, t0 - 5e-3, 0.2985e-3)
+        .with_color("C2").with_stack_idx(4)
+    ),
+    "Camera 2": (Sequence
+        .digital_pulse(*C.flir_trig, t0 + 300e-3, 0.2985e-3)
+        .with_color("C2").with_stack_idx(4)
+    ),
+    "Push shutter": (Sequence
+        .digital_lohi(*C.push_sh, t0 - 10e-3, t0 + 800e-3)
+        .with_color("C3").with_stack_idx(3)
+    ),
+    "Push aom": (Sequence
+        .digital_lohi(*C.push_aom, t0 - 10e-3, t0 + 800e-3)
+        .with_color("C3").with_stack_idx(3)
+    ),
+    "MOT coils 1": (Sequence
+        .digital_hilo(*C.mot3_coils_igbt, 0.0, t0 - 0.5e-3)
+    ).with_color("C1").with_stack_idx(2),
+    "MOT coils recapture": (Sequence
+        .digital_pulse(*C.mot3_coils_igbt, t0 + tau, 700e-3)
+    ).with_color("C1").with_stack_idx(2),
+    "Blue beams ": (Sequence
+        .digital_hilo(*C.mot3_blue_sh, 0.0, t0 - 4e-3)
+    ).with_color("C0").with_stack_idx(5),
+    "Blue beams recapture": (Sequence
+        .digital_pulse(*C.mot3_blue_sh, t0 + tau, 700e-3)
+    ).with_color("C0").with_stack_idx(5),
+    "MOT shims": (Sequence
+        .digital_hilo(*C.mot3_shims_onoff, t0 - 0.5e-3, t0 + tau)
+    ).with_color("C1").with_stack_idx(3),
+    "Green beams AOM": (Sequence
+        .digital_hilo(*C.mot3_green_aom, t0 - 1.8e-3, t0  + tau -0*700e-6)
+    ).with_color("C6").with_stack_idx(6),
+    "Green beams shutter": (Sequence
+        .digital_hilo(*C.mot3_green_sh, t0 - 10e-3, t0 + tau)
+    ).with_color("C6").with_stack_idx(7),
+    "Blue imaging shutter": (Sequence
+        .digital_pulse(*C.probe_sh, t0 - 5e-3 + 30e-3, 15e-3)
+        .with_color("C4").with_stack_idx(3)
+    ),
+    "Blue imaging aom": (Sequence
+        .digital_pulse(*C.probe_aom, t0  + 30e-3 , 10e-3)
+        .with_color("C4").with_stack_idx(3)
+    ),
+    "EMCCD": (Sequence
+        .digital_pulse(*C.andor_trig, t0 - 27e-3 + 30e-3, 10e-3)
+        .with_color("C2").with_stack_idx(4)
+    ),
+    "Scope": (Sequence
+        .digital_hilo(*C.scope_trig, t0 - 50e-3, t0 + 800e-3)
+        .with_color("C7").with_stack_idx(1)
+    ),
+}, C)
+
+seq_bkgd = SuperSequence(outdir.joinpath("sequences"), f"background", {
+    "Sequence": (Sequence
+        .digital_hilo(*C.dummy, 0.0, 100e-3)
+    ),
+    "Push": (Sequence
+        .digital_lohi(*C.push_sh, 0.0, 100e-3)
+    ),
+    "MOT beams": (Sequence
+        .digital_lohi(*C.mot3_blue_sh, 0.0, 50e-3)
+    ),
+    "MOT coils": (Sequence
+        .digital_hilo(*C.mot3_coils_igbt, 0.0, 100e-3)
+        .digital_hilo(*C.mot3_coils_onoff, 0.0, 100e-3)
+    ),
+    "Camera": (Sequence
+        .digital_pulse(*C.flir_trig, 80e-3, camera_config["exposure_time"] * 1e-6)
+    ),
+    "Scope": (Sequence
+        .digital_hilo(*C.scope_trig, 0.0, 100e-3)
+    ),
+}, C)
+
+class FluorescenceImaging(Controller):
+    def precmd(self, *args):
+        self.comp = MAIN.connect()
+        (self.comp
+            .def_digital(*C.mot3_coils_onoff, 1)
+            .def_digital(*C.mot3_blue_sh, 1)
+            .def_digital(*C.push_aom, 1)
+            .def_digital(*C.push_sh, 1)
+            .enqueue(SEQ.to_sequence())
+        )
+
+        self.cam = FLIR.connect()
+        (self.cam
+            .configure_capture(**camera_config)
+            .configure_trigger()
+        )
+
+    def postcmd(self, *args):
+        self.comp.clear().disconnect()
+        self.cam.disconnect()
+
+    def run_sequence(self, *args):
+        self.comp.run()
+        SEQ.save()
+
+    def run_camera(self, *args):
+        frames = self.cam.acquire_frames(2)
+        data = FluorescenceData(
+            outdir=outdir,
+            arrays={"image": frames[0], "background": frames[1]},
+            config=camera_config,
+            comments=comments
+        )
+        data.compute_results()
+        data.save()
+        data.render_arrays()
+
+    def cmd_visualize(self, *args):
+        SEQ.draw_detailed().show().close()
+        sys.exit(0)
+
+if __name__ == "__main__":
+    FluorescenceImaging().RUN()
\ No newline at end of file

fluorescence_imaging_emccd.py

+from lib import *
+from lib import CONNECTIONS as C
+import datetime, sys, pathlib
+
+outdir = DATADIRS.fluorescence_imaging.joinpath(get_timestamp())
+
+comments = """
+Fluorescence imaging
+====================
+"""[1:-1]
+
+# CAMERA OPTIONS
+camera_config = {
+    "exposure_time": 1000,
+    "gain": 45.49,
+    "gamma": 1.25,
+    "black_level": 5.0,
+    "bin_size": 1,
+}
+
+# BUILD SEQUENCE
+t0 = 1.0 # take the picture
+
+SEQ = SuperSequence(outdir, "sequence", {
+    "Sequence": (Sequence
+        .digital_hilo(*C.dummy, 0.0, t0 + 800e-3)
+        .with_color("k").with_stack_idx(0)
+    ),
+    # "Camera 1": (Sequence
+    #     .digital_pulse(*C.flir_trig, t0, 12.5491e-3)
+    #     .with_color("C2").with_stack_idx(4)
+    # ),
+    "Camera 1": (Sequence
+        .digital_pulse(*C.flir_trig, t0 + 107e-3, 0.2985e-3)
+        .with_color("C2").with_stack_idx(4)
+    ),
+    "Camera 2": (Sequence
+        .digital_pulse(*C.flir_trig, t0 + 700e-3, 0.2985e-3)
+        .with_color("C2").with_stack_idx(4)
+    ),
+    "EMCCD": (Sequence
+        .digital_pulse(*C.andor_trig, t0 + 77e-3, 10e-3)
+        .with_color("C2").with_stack_idx(4)
+    ),
+    "Push beam": (Sequence
+        .digital_lohi(*C.push_sh, t0 - 10e-3, t0 + 800e-3)
+        .with_color("C3").with_stack_idx(3)
+    ),
+    # "Green imaging pulse": (Sequence
+    #     .digital_pulse(*C.raman_green, t0 + 104e-3, 10e-3)
+    #     .with_color("C3").with_stack_idx(3)
+    # ),
+    "MOT beams": (Sequence
+        .digital_pulse(*C.mot3_blue_sh, t0 + 100e-3 , 3e-3,  invert=True)
+        .with_color("C4").with_stack_idx(2)
+    ),
+    "Blue imaging pulse": (Sequence
+        .digital_pulse(*C.mot3_blue_sh, t0 + 109e-3, 491e-3,  invert=True)
+        .with_color("C4").with_stack_idx(3)
+    ),
+    # "MOT beams": (Sequence
+    #     .digital_pulse(*C.mot3_blue_sh, t0 + 100e-3 , 500e-3, invert=True)
+    #     .with_color("C4").with_stack_idx(2)
+    # ),
+    "MOT coils": (Sequence
+        .digital_pulse(*C.mot3_coils_igbt, t0 + 104e-3 , 500e-3, invert=True)
+        .with_color("C4").with_stack_idx(2)
+    ),
+    "Scope": (Sequence
+        .digital_hilo(*C.scope_trig, t0 - 25e-3, t0 + 800e-3)
+        .with_color("C7").with_stack_idx(1)
+    ),
+}, C)
+
+seq_bkgd = SuperSequence(outdir.joinpath("sequences"), f"background", {
+    "Sequence": (Sequence
+        .digital_hilo(*C.dummy, 0.0, 100e-3)
+    ),
+    "Push": (Sequence
+        .digital_lohi(*C.push_sh, 0.0, 100e-3)
+    ),
+    "MOT beams": (Sequence
+        .digital_lohi(*C.mot3_blue_sh, 0.0, 50e-3)
+    ),
+    "MOT coils": (Sequence
+        .digital_hilo(*C.mot3_coils_igbt, 0.0, 100e-3)
+        .digital_hilo(*C.mot3_coils_onoff, 0.0, 100e-3)
+    ),
+    "Camera": (Sequence
+        .digital_pulse(*C.flir_trig, 80e-3, camera_config["exposure_time"] * 1e-6)
+    ),
+    "Scope": (Sequence
+        .digital_hilo(*C.scope_trig, 0.0, 100e-3)
+    ),
+}, C)
+
+class FluorescenceImaging(Controller):
+    def precmd(self, *args):
+        self.comp = MAIN.connect()
+        (self.comp
+            .def_digital(*C.mot3_coils_onoff, 1)
+            .def_digital(*C.mot3_blue_sh, 1)
+            .def_digital(*C.push_aom, 1)
+            .def_digital(*C.push_sh, 1)
+            .enqueue(SEQ.to_sequence())
+        )
+
+        self.cam = FLIR.connect()
+        (self.cam
+            .configure_capture(**camera_config)
+            .configure_trigger()
+        )
+
+    def postcmd(self, *args):
+        self.comp.clear().disconnect()
+        self.cam.disconnect()
+
+    def run_sequence(self, *args):
+        self.comp.run()
+        SEQ.save()
+
+    def run_camera(self, *args):
+        frames = self.cam.acquire_frames(2)
+        data = FluorescenceData(
+            outdir=outdir,
+            arrays={"image": frames[0], "background": frames[1]},
+            config=camera_config,
+            comments=comments
+        )
+        data.compute_results()
+        data.save()
+        data.render_arrays()
+
+    def cmd_visualize(self, *args):
+        SEQ.draw_detailed().show().close()
+        sys.exit(0)
+
+if __name__ == "__main__":
+    FluorescenceImaging().RUN()
+

mot_transfer_FastDetection.py

+import numpy as np
+from lib import *
+from lib import CONNECTIONS as C
+import sys, pathlib
+
+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
+camera_config = {
+    "exposure_time": 100,
+    "gain": 5,
+    "gamma": 1.25,
+    "black_level": 5.0,
+    "bin_size": 1,
+}
+
+# CONSTRUCT SEQUENCE
+t0 = 1.8 # big coils start turning off at t0
+R = 3 # repetition for each tau
+#TAU = np.array([np.linspace(6.5e-3, 126.5e-3, 5) for k in range(R)]).T.flatten()
+TAU = np.array([
+    [
+        6.5e-3, 10e-3, 20e-3, 30e-3, 50e-3, 100e-3, 200e-3, 400e-3
+    ] for k in range(R)
+]).T.flatten()
+#TAU = np.array(R * [6.5e-3, 100e-3, 200e-3]).T.flatten()
+z = int(np.ceil(np.log10(R)))
+
+def make_sequence(tau, name=None):
+    name = f"tau={tau:.5f}" if name is None else name
+    return SuperSequence(outdir.joinpath("sequences"), name, {
+        "Sequence": (Sequence
+            .digital_hilo(*C.dummy, 0.0, t0 + tau + 100e-3)
+        ).with_color("k").with_stack_idx(0),
+
+        "Scope": (Sequence
+            .digital_hilo(*C.scope_trig, t0 - 25e-3, t0 + tau + 100e-3)
+        ).with_color("C7").with_stack_idx(1),
+
+        "Push beam": (Sequence
+            .digital_hilo(*C.push_sh, 0.0, t0 - 10e-3)
+        ).with_color("C3").with_stack_idx(4),
+
+        "MOT coils 1": (Sequence
+            .digital_hilo(*C.mot3_coils_igbt, 0.0, t0 - 0.5e-3)
+        ).with_color("C1").with_stack_idx(2),
+
+        "MOT coils 2": (Sequence
+            .digital_hilo(*C.mot3_coils_igbt,
+                t0 + tau - 6.8e-3 , t0 + tau + 100e-3)
+        ).with_color("C1").with_stack_idx(2),
+
+        "Blue beams 1": (Sequence
+            .digital_hilo(*C.mot3_blue_sh, 0.0, t0 - 4e-3)
+        ).with_color("C0").with_stack_idx(5),
+
+        "Blue beams 2": (Sequence
+            .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 - 0.5e-3, t0 + tau)
+        ).with_color("C1").with_stack_idx(3),
+
+        "Green beams AOM": (Sequence
+            .digital_hilo(*C.mot3_green_aom, t0, t0 + tau -0*700e-6)
+        ).with_color("C6").with_stack_idx(6),
+
+        "Green beams shutter": (Sequence
+            .digital_hilo(*C.mot3_green_sh, t0 - 10e-3, t0 + tau)
+        ).with_color("C6").with_stack_idx(7),
+
+        "Camera": (Sequence
+            .digital_pulse(*C.flir_trig, t0 + tau - 0*600e-6 + 100e-6,
+                camera_config["exposure_time"] / 1e6
+            )
+        ).with_color("C2").with_stack_idx(7),
+    }, C)
+
+sseq_bkgd = SuperSequence(outdir.joinpath("sequences"), f"background", {
+    "Sequence": (Sequence
+        .digital_hilo(*C.dummy, 0.0, 200e-3)
+    ),
+    "Push": (Sequence
+        .digital_lohi(*C.push_sh, 0.0, 200e-3)
+    ),
+    "MOT beams": (Sequence
+        .digital_lohi(*C.mot3_blue_sh, 0.0, 150e-3)
+    ),
+    "MOT coils": (Sequence
+        .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, 180e-3, camera_config["exposure_time"] * 1e-6)
+    ),
+    "Scope": (Sequence
+        .digital_hilo(*C.scope_trig, 0.0, 200e-3)
+    ),
+}, C)
+
+class MOTTransfer(Controller):
+    def precmd(self, *args):
+        self.comp = MAIN.connect()
+        (self.comp
+            .def_digital(*C.mot3_coils_onoff, 1)
+            .def_analog(*C.mot3_coils_cur, 3.45)
+            .def_analog(*C.mot3_coils_vol, 7.00)
+            .def_digital(*C.mot3_shims_onoff, 0)
+            .def_digital(*C.mot3_blue_sh, 1)
+            .def_digital(*C.push_aom, 1)
+            .def_digital(*C.push_sh, 1)
+            .def_digital(*C.mot3_green_aom, 0)
+            .def_digital(*C.mot3_green_sh, 0)
+        )
+
+        self.cam = FLIR.connect()
+        (self.cam
+            .configure_capture(**camera_config)
+            .configure_trigger()
+        )
+
+    def postcmd(self, *args):
+        self.comp.disconnect()
+        self.cam.disconnect()
+
+    def run_sequence(self, *args):
+        for k, tau in enumerate(TAU):
+            sseq = make_sequence(tau, f"tau={tau:.5f}_{str(k % R).zfill(z):s}")
+            (self.comp
+                .enqueue(sseq.to_sequence())
+                .run()
+                .clear()
+            )
+            sseq.save()
+        (self.comp
+            .enqueue(sseq_bkgd.to_sequence())
+            .run()
+            .clear()
+        )
+        sseq_bkgd.save()
+
+    def run_camera(self, *args):
+        frames = self.cam.acquire_frames(len(TAU) + 1)
+        arrays = {
+            f"tau={TAU[k]:.5f}_{str(k % R).zfill(z):s}": frame
+            for k, frame in enumerate(frames[:-1])
+        }
+        arrays.update({"background": frames[-1]})
+        data = FluorescenceData(
+            outdir=outdir,
+            arrays=arrays,
+            config=camera_config,
+            comments=comments
+        )
+        data.compute_results(subtract_bkgd=True)
+        data.save()
+        data.render_arrays()
+
+    def cmd_visualize(self, *args):
+        (make_sequence(float(args[0]) if len(args) > 0 else TAU.max())
+            .draw_detailed().show().close()
+        )
+        sys.exit(0)
+
+if __name__ == "__main__":
+    MOTTransfer().RUN()
+