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NSLS-II-FXI · Jan 17, 2025 · b679b39 · b679b39
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Showing 11 changed files with 2,078 additions and 396 deletions.
diff --git a/startup/10-area-detector.py b/startup/10-area-detector.py
@@ -416,12 +416,12 @@ def resume(self):
 CAM_RD_CFG = {
     "MARANA-4BV6X": {
         "rd_time": {
-            '12-bit (low noise)': 0.011, 
-            '16-bit (high dynamic rang': 0.014, 
-            '11-bit (high speed)': 0.007
+            '12-bit (low noise)': 0.02327893333333333, 
+            '16-bit (high dynamic rang': 0.013516799999999999, 
+            '11-bit (high speed)': 0.007351242105263158
         },
         "pxl_encoding": {
-            '12-bit (low noise)': 'Mono12', 
+            '12-bit (low noise)': 'Mono16', 
             '16-bit (high dynamic rang': 'Mono16', 
             '11-bit (high speed)': 'Mono12'},
         "image_mode": MaranaU.cam.image_mode.metadata["enum_strs"],

diff --git a/startup/18-zebra.py b/startup/18-zebra.py
@@ -24,7 +24,7 @@
 # will move this definition to motors.py
 ROT_BACK_VEL = 30
 
-BIN_FACS = {"Andor": {0: 1, 1: 2, 2: 3, 3: 4, 4: 8}, "MaranaU": {}, "Oryx": {}}
+BIN_FACS = {"Andor": {0: 1, 1: 2, 2: 3, 3: 4, 4: 8}, "MaranaU": {0: 1, 1: 2, 2: 3, 3: 4, 4: 8}, "Oryx": {}}
 
 
 class ZebraPositionCaptureData(Device):
@@ -286,6 +286,7 @@ class FXITomoFlyer(Device):
     }
 
     dft_pulse_wid = {"ms": 0.002, "s": 0.0005, "10s": 0.003}  # 0: ms  # 1: s  # 2: 10s
+    min_exp = {"MARANA-4BV6X": 0.001, "Neo": 0.001, "Oryx": 0.001}
     pc_trig_dir = {1: 0, -1: 1}  # 1: positive, -1: negative
     rot_var = 0.002
     scan_cfg = {}
@@ -959,8 +960,11 @@ def check_cam_acq_p(det, acq_p, bin_fac):
         acq_min = DET_MIN_AP[det.name] / BIN_FACS[det.name][bin_fac]
         if cam_model == "MARANA-4BV6X":
             full_acq_min = CAM_RD_CFG[cam_model]["rd_time"][det.pre_amp.enum_strs[det.pre_amp.value]]
-            acq_min = full_acq_min * (det.cam.size.size_y.value / 2048)
-            acq_p = max(acq_min + 0.002, acq_p) - FXITomoFlyer.rot_var  # accounting vel variation in rot vel 
+            acq_min = full_acq_min * (det.cam.size.size_y.value / 2046) + FXITomoFlyer.rot_var # add vel uncertainty tolerance
+        else:
+            acq_min = DET_MIN_AP[det.name] / BIN_FACS[det.name][bin_fac]
+        acq_p = max(acq_min + FXITomoFlyer.min_exp[cam_model], acq_p)  # add miminum exposure time
+        print(f"{full_acq_min=}\n{acq_min=}\n{acq_p=}\n{FXITomoFlyer.rot_var=}")
         return acq_p, acq_min
 
     @classmethod
@@ -1070,7 +1074,7 @@ def compose_scn_cfg(
         return scn_cfg
 
     @staticmethod
-    def do_prime(det):
+    def _prime_det(det):
         if CAM_RD_CFG[det.cam.model.value]["trigger_mode"][det.cam.trigger_mode.value] != "Internal":
             yield from abs_set(det.cam.trigger_mode, "Internal", timeout=5, settle_time=1, wait=True)
         if CAM_RD_CFG[det.cam.model.value]["image_mode"][det.cam.image_mode.value] != "Fixed":
@@ -1081,10 +1085,8 @@ def do_prime(det):
 
     @staticmethod
     def stop_det(det):
-        while det.cam.acquire.value != 0:
-            yield from abs_set(det.cam.acquire, 0, wait=True)
-        while det.hdf5.capture.value != 0:
-            yield from abs_set(det.hdf5.capture, 0, wait=True)
+        yield from abs_set_wait(det.cam.acquire, 0)
+        yield from abs_set_wait(det.hdf5.capture, 0)
 
     @staticmethod
     def bin_det(det, bin_fac):
@@ -1093,15 +1095,30 @@ def bin_det(det, bin_fac):
             if bin_fac is None:
                 bin_fac = 0
             if int(bin_fac) not in [0, 1, 2, 3, 4]:
+                print('b4')
                 raise ValueError("binnng must be in [0, 1, 2, 3, 4]")
             yield from abs_set(det.binning, bin_fac, wait=True)
             return bin_fac
-            # FXITomoFlyer.do_prime(det)
+        else:
+            return bin_fac
 
     @staticmethod
     def prime_det(det):
         if (det.cam.array_size.array_size_x.value != det.hdf5.array_size.width.value) or (det.cam.array_size.array_size_y.value != det.hdf5.array_size.height.value):
-            yield from FXITomoFlyer.do_prime(det)
+            yield from FXITomoFlyer._prime_det(det)
+
+    @staticmethod
+    def set_roi_det(det, roi):
+        if roi is None:
+            yield from abs_set_wait(det.cam.size.size_x, det.cam.max_size.max_size_x.value)
+            yield from abs_set_wait(det.cam.min_x, 1)
+            yield from abs_set_wait(det.cam.size.size_y, det.cam.max_size.max_size_y.value)
+            yield from abs_set_wait(det.cam.min_y, 1)
+        else:
+            yield from abs_set_wait(det.cam.size.size_x, roi["size_x"])
+            yield from abs_set_wait(det.cam.min_x, roi["min_x"])
+            yield from abs_set_wait(det.cam.size.size_y, roi["size_y"])
+            yield from abs_set_wait(det.cam.min_y, roi["min_y"])
 
     @staticmethod
     def def_abs_out_pos(
@@ -1161,21 +1178,26 @@ def set_mot_r_step_for_scan(scn_cfg):
 
     @staticmethod
     def set_cam_mode(cam, stage="pre-scan"):
+        # if stage == "pre-scan":
+        #     yield from abs_set_wait(cam.cam.image_mode, CAM_RD_CFG[cam.cam.model.value]["image_mode"].index("Fixed"), timeout=5, settle_time=0.5)
+        #     yield from abs_set_wait(cam.cam.trigger_mode, CAM_RD_CFG[cam.cam.model.value]["trigger_mode"].index("External"), timeout=5, settle_time=0.5)
+        # elif stage == "ref-scan":
+        #     yield from abs_set_wait(cam.cam.image_mode, CAM_RD_CFG[cam.cam.model.value]["image_mode"].index("Fixed"), timeout=5, settle_time=0.5)
+        #     yield from abs_set_wait(cam.cam.trigger_mode, CAM_RD_CFG[cam.cam.model.value]["trigger_mode"].index("Internal"), timeout=5, settle_time=0.5)
+        # elif stage == "post-scan":
+        #     yield from abs_set_wait(cam.cam.image_mode, CAM_RD_CFG[cam.cam.model.value]["image_mode"].index("Continuous"), timeout=5, settle_time=0.5)
+        #     yield from abs_set_wait(cam.cam.trigger_mode, CAM_RD_CFG[cam.cam.model.value]["trigger_mode"].index("Internal"), timeout=5, settle_time=0.5)
+        # return
         if stage == "pre-scan":
-            while CAM_RD_CFG[cam.cam.model.value]["image_mode"][cam.cam.image_mode.value] != "Fixed":
-                yield from abs_set(cam.cam.image_mode, "Fixed", timeout=5, settle_time=0.5, wait=True)
-            while CAM_RD_CFG[cam.cam.model.value]["trigger_mode"][cam.cam.trigger_mode.value] != "External":
-                yield from abs_set(cam.cam.trigger_mode, "External", timeout=5, settle_time=0.5, wait=True)
+            yield from abs_set_wait(cam.cam.image_mode, 0, timeout=5, settle_time=0.5)
+            yield from abs_set_wait(cam.cam.trigger_mode, 2, timeout=5, settle_time=0.5)
         elif stage == "ref-scan":
-            while CAM_RD_CFG[cam.cam.model.value]["image_mode"][cam.cam.image_mode.value] != "Fixed":
-                yield from abs_set(cam.cam.image_mode, "Fixed", timeout=5, settle_time=0.5, wait=True)
-            while CAM_RD_CFG[cam.cam.model.value]["trigger_mode"][cam.cam.trigger_mode.value] != "Internal":
-                yield from abs_set(cam.cam.trigger_mode, "Internal", timeout=5, settle_time=0.5, wait=True)
+            yield from abs_set_wait(cam.cam.image_mode, 0, timeout=5, settle_time=0.5)
+            yield from abs_set_wait(cam.cam.trigger_mode, 0, timeout=5, settle_time=0.5)
         elif stage == "post-scan":
-            while CAM_RD_CFG[cam.cam.model.value]["image_mode"][cam.cam.image_mode.value] != "Continuous":
-                yield from abs_set(cam.cam.image_mode, "Continuous", timeout=5, settle_time=0.5, wait=True)
-            while CAM_RD_CFG[cam.cam.model.value]["trigger_mode"][cam.cam.trigger_mode.value] != "Internal":
-                yield from abs_set(cam.cam.trigger_mode, "Internal", timeout=5, settle_time=0.5, wait=True)
+            yield from abs_set_wait(cam.cam.image_mode, 1, timeout=5, settle_time=0.5)
+            yield from abs_set_wait(cam.cam.trigger_mode, 0, timeout=5, settle_time=0.5)
+        return
 
 
 Zebra = FXIZebra(

diff --git a/startup/40-scan_pre_define.py b/startup/40-scan_pre_define.py
@@ -56,7 +56,9 @@ def _take_image(detectors, motor, num, stream_name="primary"):
 def _set_Andor_chunk_size(detectors, chunk_size):
     for detector in detectors:
         yield from unstage(detector)
-    yield from abs_set(MaranaU.cam.num_images, chunk_size, wait=True)
+    yield from abs_set_wait(MaranaU.cam.acquire, 0)
+    yield from abs_set_wait(MaranaU.cam.image_mode, 0)
+    yield from abs_set_wait(MaranaU.cam.num_images, chunk_size, wait=True)
     for detector in detectors:
         yield from stage(detector)
 
@@ -94,16 +96,17 @@ def _take_bkg_image(
 
 
 def _set_andor_param(exposure_time=0.1, period=0.1, chunk_size=1, binning=[1, 1]):
-    yield from mv(MaranaU.cam.acquire, 0)
-    yield from mv(MaranaU.cam.acquire, 0)
-    yield from mv(MaranaU.cam.image_mode, 0)
-    yield from mv(MaranaU.cam.num_images, chunk_size)
-    period_cor = max(period, exposure_time+0.013)    
+    for i in range(2):
+        yield from abs_set_wait(MaranaU.cam.acquire, 0)
+        yield from bps.sleep(0.2)
+    for i in range(2):
+        yield from abs_set_wait(MaranaU.cam.image_mode, 0)
+        yield from bps.sleep(0.5)
+    yield from abs_set_wait(MaranaU.cam.num_images, chunk_size)
+    period_cor = max(period, exposure_time+0.024)    
 
-    yield from mv(MaranaU.cam.acquire_time, exposure_time)
-    yield from bps.sleep(1)
-    yield from abs_set(MaranaU.cam.acquire_period, period_cor)
-    yield from bps.sleep(1)
+    yield from abs_set_wait(MaranaU.cam.acquire_time, exposure_time)
+    yield from abs_set_wait(MaranaU.cam.acquire_period, period_cor)
 
 
 def _xanes_per_step(
@@ -152,8 +155,8 @@ def _close_shutter(simu=False):
         i = 0
         reading = yield from bps.rd(shutter_status)
         while not reading:  # if 1:  closed; if 0: open
-            yield from abs_set(shutter_close, 1, wait=True)
-            yield from bps.sleep(3)
+            yield from abs_set_wait(shutter_close, 1, wait=True)
+            yield from bps.sleep(1)
             i += 1
             print(f"try closing {i} time(s) ...")
             if i > 20:
@@ -171,7 +174,7 @@ def _open_shutter(simu=False):
         i = 0
         reading = yield from bps.rd(shutter_status)
         while reading:  # if 1:  closed; if 0: open
-            yield from abs_set(shutter_open, 1, wait=True)
+            yield from abs_set_wait(shutter_open, 1, wait=True)
             print(f"try opening {i} time(s) ...")
             yield from bps.sleep(1)
             i += 1
@@ -183,9 +186,7 @@ def _open_shutter(simu=False):
 
 
 def _set_rotation_speed(rs=30):
-    yield from abs_set(zps.pi_r.velocity, rs)
-    yield from bps.sleep(0.5)
-    yield from abs_set(zps.pi_r.velocity, rs)
+    yield from abs_set_wait(zps.pi_r.velocity, rs)
 
 
 def _move_sample(x_pos, y_pos, z_pos, r_pos, repeat=1):

diff --git a/startup/41-scans.py b/startup/41-scans.py
@@ -389,6 +389,134 @@ def fly_inner_scan():
     print(txt)
     return uid
 '''
+def radiography_scan(
+    exposure_time=0.1,
+    period_time=0.1,
+    out_x=-100,
+    out_y=-100,
+    out_z=0,
+    out_r=0,
+    num_img=10,
+    take_dark_img=True,
+    relative_move_flag=1,
+    rot_first_flag=1, 
+    note="",
+    simu=False,
+    md=None,
+):
+    """
+    Take multiple images (MaranaU camera)
+
+    Input:
+    ------------
+    exposure_time: float, exposure time for each image
+
+    out_x: float(int), relative sample out position for zps.sx
+
+    out_y: float(int), relative sampel out position for zps.sy
+
+    out_z: float(int), relative sampel out position for zps.sz
+
+    out_r: float(int), relative sampel out position for zps.pi_r
+
+    num_img: int, number of images to take
+    """
+
+    yield from _set_andor_param(exposure_time, period_time, 1)
+
+    detectors = [MaranaU]
+    motor_x_ini = zps.sx.position
+    motor_y_ini = zps.sy.position
+    motor_z_ini = zps.sz.position
+    motor_r_ini = zps.pi_r.position
+
+    if relative_move_flag:
+        motor_x_out = motor_x_ini + out_x if not (out_x is None) else motor_x_ini
+        motor_y_out = motor_y_ini + out_y if not (out_y is None) else motor_y_ini
+        motor_z_out = motor_z_ini + out_z if not (out_z is None) else motor_z_ini
+        motor_r_out = motor_r_ini + out_r if not (out_r is None) else motor_r_ini
+    else:
+        motor_x_out = out_x if not (out_x is None) else motor_x_ini
+        motor_y_out = out_y if not (out_y is None) else motor_y_ini
+        motor_z_out = out_z if not (out_z is None) else motor_z_ini
+        motor_r_out = out_r if not (out_r is None) else motor_r_ini
+
+
+    motors = [zps.sx, zps.sy, zps.sz, zps.pi_r]
+
+    _md = {
+        "detectors": ["MaranaU"],
+        "motors": [mot.name for mot in motors],
+        "XEng": XEng.position,
+        "plan_args": {
+            "exposure_time": exposure_time,
+            "out_x": out_x,
+            "out_y": out_y,
+            "out_z": out_z,
+            "out_r": out_r,
+            "num_img": num_img,
+            "num_bkg": 20,
+            "note": note if note else "None",
+        },
+        "plan_name": "radiography_scan",
+        "plan_pattern": "linspace",
+        "plan_pattern_module": "numpy",
+        "hints": {},
+        "operator": "FXI",
+        "note": note if note else "None",
+        # "motor_pos": wh_pos(print_on_screen=0),
+    }
+    _md.update(md or {})
+    _md["hints"].setdefault("dimensions", [(("time",), "primary")])
+
+    @stage_decorator(list(detectors) + motors)
+    @run_decorator(md=_md)
+    def inner_scan():
+
+        # close shutter, dark images: numer=chunk_size (e.g.20)
+        if take_dark_img:
+            print("\nshutter closed, taking dark images...")
+            yield from _take_dark_image(detectors, motors, num=1, chunk_size=20, stream_name="dark", simu=simu)
+
+        yield from _open_shutter(simu=simu)
+        yield from _set_Andor_chunk_size(detectors, chunk_size=num_img)
+        yield from _take_image(detectors, motors, num=1, stream_name="primary")
+
+
+        # taking out sample and take background image
+        print("\nTaking background images...")
+        yield from _take_bkg_image(
+            motor_x_out,
+            motor_y_out,
+            motor_z_out,
+            motor_r_out,
+            detectors,
+            [],
+            num=1,
+            chunk_size=20,
+            rot_first_flag=rot_first_flag,
+            stream_name="flat",
+            simu=simu,
+        )
+        if take_dark_img:
+            yield from _close_shutter(simu=simu)
+        yield from _move_sample_in(
+            motor_x_ini,
+            motor_y_ini,
+            motor_z_ini,
+            motor_r_ini,
+            trans_first_flag=rot_first_flag,
+            repeat=3,
+        )
+
+    uid = yield from inner_scan()
+    yield from mv(MaranaU.cam.image_mode, 1)
+    #yield from _close_shutter(simu=simu)
+    txt = get_scan_parameter()
+    insert_text(txt)
+    print(txt)
+    return uid
+
 
 def fly_scan(
     exposure_time=0.05,