updates on 2024_06_18

startup/10-area-detector.py

@@ -20,7 +20,11 @@
 from ophyd.areadetector.cam import AreaDetectorCam
 from ophyd.areadetector.detectors import DetectorBase
 from nslsii.ad33 import StatsPluginV33, CamV33Mixin
-#from nslsii.ad33 import SingleTriggerV33
+
+
+from nslsii.ad33 import SingleTriggerV33
+
+
 from ophyd.areadetector.trigger_mixins import TriggerBase, ADTriggerStatus
 from ophyd.device import Staged
 from ophyd.status import SubscriptionStatus
@@ -44,7 +48,7 @@ def describe(self):
         )
         return res
 
-
+'''
 class SingleTriggerV33(TriggerBase):
     _status_type = ADTriggerStatus
 
@@ -68,7 +72,7 @@ def acquire_complete(*args, old_value, value, **kwargs):
         self.dispatch(self._image_name, ttime.time())
         return status
 
-
+'''
 class AndorCam(CamV33Mixin, AreaDetectorCam):
     def __init__(self, *args, **kwargs):
         AreaDetectorCam.__init__(self, *args, **kwargs)
@@ -219,7 +223,7 @@ def resume(self):
         self.hdf5._generate_resource(res_kwargs)
         return super().resume()
 
-    @timing
+    #@timing
     def stage(self):
         import itertools
         if self.cam.detector_state.get() != 0:
@@ -237,7 +241,7 @@ def stage(self):
                 else:
                     raise
 
-    @timing
+    #@timing
     def unstage(self, *args, **kwargs):
         import itertools
         #self._acquisition_signal.put(0, wait=True)
@@ -275,9 +279,12 @@ class Manta(SingleTrigger, AreaDetector):
         HDF5PluginWithFileStore,
         suffix="HDF1:",
         # write_path_template="/nsls2/data/fxi-new/legacy/Andor/%Y/%m/%d/",
-        write_path_template="/nsls2/data/fxi-new/legacy/Andor//%Y/%m/%d/",
-        # write_path_template = '/dev/shm/',
-        root="/nsls2/data/fxi-new/legacy/Andor/",
+        write_path_template="/nsls2/data/fxi-new/legacy/Oryx/%Y/%m/%d/",
+        # write_path_template='/tmp/test_2022/%Y/%m/%d/' ,
+        # write_path_template="/nsls2/data/fxi-new/assets/default/%Y/%m/%d/",
+        # write_path_template="/nsls2/data/fxi-new/legacy/Andor//%Y/%m/%d/",
+        # root="/nsls2/data/fxi-new/assets/default",
+        root="/nsls2/data/fxi-new/legacy/Oryx",
         # write_path_template='/tmp/',
         # root='/',
     )
@@ -362,6 +369,9 @@ def resume(self):
     getattr(Andor, k).ensure_nonblocking()
 Andor.hdf5.time_stamp.name = "Andor_timestamps"
 
+#########################################
+''' comment away this section when Marana is disconnected 
+
 # added by XH
 Marana = AndorKlass("XF:18IDB-ES{Det:Marana1}", name="Andor")
 Marana.cam.ensure_nonblocking()
@@ -378,6 +388,8 @@ def resume(self):
     getattr(Marana, k).ensure_nonblocking()
 Marana.hdf5.time_stamp.name = "Andor_timestamps"
 
+'''
+#############################################
 # vlm = Manta("XF:18IDB-BI{VLM:1}", name="vlm")
 # detA1.read_attrs = ['hdf5', 'stats1', 'stats5']
 # detA1.read_attrs = ['hdf5']
@@ -387,6 +399,16 @@ def resume(self):
 # vlm.hdf5.read_attrs = []
 
 
+Oryx = Manta("XF:18IDB-ES{Det:Oryx1}", name="Oryx")
+#Oryx.cam.ensure_nonblocking()
+Oryx.read_attrs = ["hdf5"]
+#Oryx.stats1.read_attrs = ["total"]
+Oryx.hdf5.read_attrs = ["time_stamp"]
+Oryx.stage_sigs["cam.image_mode"] = 1
+for k in ("image", ):
+    getattr(Oryx, k).ensure_nonblocking()
+Oryx.hdf5.time_stamp.name = "Oryx_timestamps"
+
 #for det in [detA1, Andor]:
 for det in [detA1]:
     det.stats1.total.kind = "hinted"

startup/11-txm_motor.py

@@ -140,15 +140,16 @@ class BetrandLens(Device):
     x = Cpt(MyEpicsMotor, "{BLens:1-Ax:X}Mtr")
     #y = Cpt(MyEpicsMotor, "{BLens:1-Ax:Y}Mtr")
     y = Cpt(MyEpicsMotor, "{ZP:1-Ax:Y}Mtr")
-    z = Cpt(MyBaseMotor, "{BLens:1-Ax:Z}Mtr")
+    #z = Cpt(MyBaseMotor, "{BLens:1-Ax:Z}Mtr")
 
 
 class TXMSampleStage(Device):
     sx = Cpt(MyEpicsMotor, "{Env:1-Ax:Xl}Mtr")
     sy = Cpt(MyEpicsMotor, "{Env:1-Ax:Yl}Mtr")
     sz = Cpt(MyEpicsMotor, "{Env:1-Ax:Zl}Mtr")
-    pi_x = Cpt(MyBaseMotor, "{TXM:1-Ax:X}Mtr")
+   # pi_x = Cpt(MyBaseMotor, "{TXM:1-Ax:X}Mtr")
     pi_r = Cpt(MyEpicsMotor, "{TXM:2-Ax:R}Mtr")
+    #pi_r = Cpt(MyEpicsMotor, "{TXM:1-Ax:R}Mtr")
 
 
 class DetSupport(Device):
@@ -243,11 +244,11 @@ class Scint(Device):
     #phase_ring.z,
     betr.x,
     betr.y,
-    betr.z,
+    #betr.z,
     zps.sx,
     zps.sy,
     zps.sz,
-    zps.pi_x,
+    #zps.pi_x,
     zps.pi_r,
     DetU.x,
     DetU.y,

startup/18-zebra.py

@@ -665,9 +665,6 @@ def complete(self):
         whether that is true, so it will obligingly stop immediately. It is
         up to the caller to ensure that the motion is actually complete.
         """
-
-        print("\nin complet: complete starts")
-
         # Our acquisition complete PV is: XF:05IDD-ES:1{Dev:Zebra1}:ARRAY_ACQ
         t0 = ttime.monotonic()
         while self._encoder.pc.data_in_progress.get() == 1:
@@ -744,10 +741,10 @@ def get_zebra_data():
             self._last_bulk["timestamps"].update(
                 {k: v["timestamp"] for k, v in reading.items()}
             )
-        print(
-            f"\nin complete: {type(self._last_bulk)=}\n{type(self._document_cache)=}\n"
-        )
-        print(f"\nin complete: {(self._last_bulk)=}\n{(self._document_cache)=}\n")
+        # print(
+        #     f"\nin complete: {type(self._last_bulk)=}\n{type(self._document_cache)=}\n"
+        # )
+        # print(f"\nin complete: {(self._last_bulk)=}\n{(self._document_cache)=}\n")
 
         return NullStatus()
 
@@ -829,7 +826,7 @@ def resume(self):
     def preset_flyer(self, scn_cfg):
         yield from FXITomoFlyer.bin_det(self.detectors[0], scn_cfg["bin_fac"])
         yield from FXITomoFlyer.init_mot_r(scn_cfg)
-        yield from FXITomoFlyer.set_cam_mode(self.detectors[0], stage="pre-scan")
+        # yield from FXITomoFlyer.set_cam_mode(self.detectors[0], stage="pre-scan")
         scn_cfg = FXITomoFlyer.cal_cam_rot_params(self.detectors[0], scn_cfg)
         pc_cfg = FXITomoFlyer.cal_zebra_pc_params(scn_cfg)
         yield from self.preset_zebra(pc_cfg)
@@ -1075,15 +1072,22 @@ def prime_det(det):
             yield from abs_set(det.cam.num_images, 5, wait=True)
             yield from abs_set(det.cam.acquire, 1, wait=False)
 
+    @staticmethod
+    def stop_det(det):
+        for _ in range(5):
+            yield from abs_set(det.cam.acquire, 0, wait=True)
+        yield from abs_set(det.hdf5.capture, 0, wait=True)
+
     @staticmethod
     def bin_det(det, bin_fac):
-        yield from abs_set(det.cam.acquire, 0, wait=False)
-        if bin_fac is None:
-            bin_fac = 0
-        if int(bin_fac) not in [0, 1, 2, 3, 4]:
-            raise ValueError("binnng must be in [0, 1, 2, 3, 4]")
-        yield from abs_set(det.binning, bin_fac, wait=True)
-        FXITomoFlyer.prime_det(det)
+        if det.binning.value != bin_fac:
+            yield from abs_set(det.cam.acquire, 0, wait=False)
+            if bin_fac is None:
+                bin_fac = 0
+            if int(bin_fac) not in [0, 1, 2, 3, 4]:
+                raise ValueError("binnng must be in [0, 1, 2, 3, 4]")
+            yield from abs_set(det.binning, bin_fac, wait=True)
+            FXITomoFlyer.prime_det(det)
 
     @staticmethod
     def def_abs_out_pos(

startup/20-global_param.py

@@ -24,3 +24,8 @@
 CALIBER_FLAG = 1
 
 CALIBER = {}
+
+ZP_8keV = {"D": 244,
+           "dr": 30}
+ZP_9keV = {"D": 550, 
+           "dr": 50}

startup/40-scan_pre_define.py

@@ -210,3 +210,9 @@ def _take_ref_image(
     yield from _set_Andor_chunk_size(cams, chunk_size)
     yield from _take_image(cams, [], num, stream_name=stream_name)
 
+
+def _prime_cam(cam=Andor):
+    yield from abs_set(cam.cam.image_mode, 0, wait=True)
+    yield from abs_set(cam.cam.num_images, 5, wait=True)
+    yield from abs_set(cam.cam.acquire, 1, wait=True)
+

startup/41-scans.py

@@ -317,12 +317,12 @@ def fly_scan(
     @bpp.monitor_during_decorator([zps.pi_r])
     @run_decorator(md=_md)
     def fly_inner_scan():
-        '''
+
         for flt in filters:
             yield from mv(flt, 1)
             yield from mv(flt, 1)
         yield from bps.sleep(1)
-        '''
+
         # close shutter, dark images: numer=chunk_size (e.g.20)
         print("\nshutter closed, taking dark images...")
         yield from _take_dark_image(
@@ -622,9 +622,11 @@ def xanes_scan2(
     filters=[],
     rot_first_flag=1,
     simu=False,
+    return_ini=True,
     md=None,
 ):
     """
+    changed something
     Different from xanes_scan:  In xanes_scan2, it moves out sample and take background image at each energy
 
     Scan the energy and take 2D image
@@ -736,10 +738,12 @@ def xanes_scan2(
     @stage_decorator(list(detectors) + motor)
     @run_decorator(md=_md)
     def xanes_inner_scan():
+        '''
         if len(filters):
             for filt in filters:
                 yield from mv(filt, 1)
                 yield from bps.sleep(0.5)
+        '''
         yield from _set_rotation_speed(rs=30)
         # take dark image
         print(f"\ntake {chunk_size} dark images...")
@@ -753,6 +757,10 @@ def xanes_inner_scan():
         yield from _open_shutter(simu)
 
         for eng in eng_list:
+            if len(filters):
+                for filt in filters:
+                    yield from mv(filt, 0)
+                    yield from bps.sleep(0.5)
             yield from _xanes_per_step(
                 eng,
                 detectors,
@@ -762,7 +770,10 @@ def xanes_inner_scan():
                 info_flag=0,
                 stream_name="primary",
             )
-
+            if len(filters):
+                for filt in filters:
+                    yield from mv(filt, 1)
+                    yield from bps.sleep(0.5)
             yield from _take_bkg_image(
                 motor_x_out,
                 motor_y_out,
@@ -784,13 +795,20 @@ def xanes_inner_scan():
                 repeat=2,
                 trans_first_flag=rot_first_flag,
             )
+        '''        
         if len(filters):
             for filt in filters:
                 yield from mv(filt, 0)
                 yield from bps.sleep(0.5)
-        yield from move_zp_ccd(eng_ini, move_flag=1, info_flag=0)
+        '''
+        if return_ini:
+            yield from move_zp_ccd(eng_ini, move_flag=1, info_flag=0)
         print("closing shutter")
         yield from _close_shutter(simu=simu)
+        if len(filters):
+            for filt in filters:
+                yield from mv(filt, 0)
+                yield from bps.sleep(0.5)
 
     yield from xanes_inner_scan()
     yield from mv(Andor.cam.image_mode, 1)
@@ -963,6 +981,8 @@ def xanes_inner_scan():
             repeat=2,
             rot_first_flag=rot_first_flag,
         )
+        yield from move_zp_ccd(eng_list[0])
+        yield from bps.sleep(5)
         print(f"\ntake bkg image after xanes scan, {chunk_size} per each energy...")
         for eng in eng_list:
             yield from _xanes_per_step(
@@ -1836,11 +1856,7 @@ def raster_2D_scan(
     @stage_decorator(list(detectors) + motor)
     @run_decorator(md=_md)
     def raster_2D_inner():
-
-        if len(filters):
-            for filt in filters:
-                yield from mv(filt, 1)
-                yield from bps.sleep(0.5)
+        select_filters(filters)
 
         # take dark image
         print("take 5 dark image")
@@ -1890,12 +1906,9 @@ def raster_2D_inner():
             repeat=1,
             trans_first_flag=1 - rot_first_flag,
         )
-        if len(filters):
-            for filt in filters:
-                yield from mv(filt, 0)
-                yield from bps.sleep(0.5)
+        select_filters([])
         print("closing shutter")
-        yield from _close_shutter(simu)
+        yield from _close_shutter(simu=simu)
 
     yield from raster_2D_inner()
     txt = get_scan_parameter()
@@ -2391,7 +2404,6 @@ def multipos_2D_xanes_scan2(
     out_y=None,
     out_z=None,
     out_r=None,
-    repeat_num=1,
     exposure_time=0.2,
     sleep_time=1,
     chunk_size=5,
@@ -2459,6 +2471,7 @@ def multipos_2D_xanes_scan2(
     note: string
 
     """
+    repeat_num = 1
     print(eng_list)
     print(x_list)
     print(y_list)
@@ -3106,6 +3119,7 @@ def xanes_3D(
     simu=False,
     relative_move_flag=1,
     rot_first_flag=1,
+    filters=[],
     note="",
     binning=[2, 2],
 ):
@@ -3129,6 +3143,7 @@ def xanes_3D(
             out_r=out_r,
             rs=rs,
             relative_move_flag=relative_move_flag,
+            filters=filters,
             note=my_note,
             simu=simu,
             rot_first_flag=rot_first_flag,
@@ -3363,5 +3378,3 @@ def tomo_mosaic_scan(
     txt = txt1 + txt4 + txt3
     insert_text(txt)
 
-
-#