csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py

@@ -5,9 +5,11 @@ import subprocess
 import time
 from pathlib import Path
 
+import h5py
 import numpy as np
 from bec_lib import bec_logger
 from bec_lib.alarm_handler import AlarmBase
+from bec_lib.endpoints import MessageEndpoints
 from bec_lib.pdf_writer import PDFWriter
 from bec_lib.scan_repeat import scan_repeat
 from typeguard import typechecked
@@ -612,6 +614,8 @@ class FlomniSampleTransferMixin:
 
         print("The unmount process started.")
 
+        self.transfer_step = 0
+
         time.sleep(1)
         while True:
             in_progress = bool(
@@ -619,7 +623,7 @@ class FlomniSampleTransferMixin:
             )
             if not in_progress:
                 break
-            self.ftransfer_confirm()
+            self.ftransfer_confirm(step_name="get")
             time.sleep(1)
         self.ftransfer_controller_disable_mount_mode()
         self.ensure_gripper_up()
@@ -662,13 +666,15 @@ class FlomniSampleTransferMixin:
         print("The mount process started.")
 
         time.sleep(1)
+        self.transfer_step = 0
         while True:
             in_progress = bool(
                 float(dev.ftransy.controller.socket_put_and_receive("MG mntprgs").strip())
             )
             if not in_progress:
                 break
-            self.ftransfer_confirm()
+
+            self.ftransfer_confirm(step_name="put")
             time.sleep(1)
         self.ftransfer_controller_disable_mount_mode()
         self.ensure_gripper_up()
@@ -796,19 +802,35 @@ class FlomniSampleTransferMixin:
         )
         return in_mount_mode
 
-    def ftransfer_confirm(self):
+    def ftransfer_confirm(self, step_name: str = ""):
         confirm = int(float(dev.ftransy.controller.socket_put_and_receive("MG confirm").strip()))
 
         if confirm != -1:
             return
 
+        self.transfer_step += 1
         if self.OMNYTools.yesno("All OK? Continue?", "y"):
             print("OK. continue.")
+            data = self.client.connector.get_last(
+                MessageEndpoints.device_preview("cam_flomni_gripper", "preview")
+            )["data"].data
+            self.save_reference_image(data, file_suffix=f"{step_name}_{self.transfer_step}")
             dev.ftransy.controller.socket_put_confirmed("confirm=1")
         else:
             print("Stopping.")
             raise FlomniError("User abort sample transfer.")
 
+    def save_reference_image(self, image: np.ndarray, file_suffix: str = ""):
+        suffix = f"_{file_suffix}_" or "_"
+        # Save the reference image to a file
+        timestamp = time.strftime("%Y%m%d_%H%M%S")
+        file = os.path.expanduser(
+            f"~/data/raw/logs/sample_transfer_images/sample_transfer_reference_image{suffix}{timestamp}.h5"
+        )
+        os.makedirs(os.path.dirname(file), exist_ok=True)
+        with h5py.File(file, "w") as f:
+            f.create_dataset("reference_image", data=image)
+
     def ftransfer_gripper_is_open(self) -> bool:
         status = bool(float(dev.ftransy.controller.socket_put_and_receive("MG @OUT[9]").strip()))
         return status
@@ -2599,13 +2621,10 @@ class Flomni(
         if self.tomo_type == 1:
             print("\x1b[1mTomo type 1:\x1b[0m 8 equally spaced sub-tomograms")
             print(f"Angular range                    =  {self.tomo_angle_range} degrees")
-            # N, step, total_projections all come from the same helper
-            # sub_tomo_scan() effectively uses internally - see
-            # _tomo_type1_actual_grid() for why this can't just read
-            # self.tomo_angle_stepsize directly.
-            _, achievable_step, total_projections = self._tomo_type1_actual_grid()
-            print(f"Total number of projections: {total_projections}")
-            print(f"Angular step within sub-tomogram:   {achievable_step:.3f} degrees")
+            print(
+                f"Total number of projections: {(self.tomo_angle_range/self.tomo_angle_stepsize)*8}"
+            )
+            print(f"Angular step within sub-tomogram:   {self.tomo_angle_stepsize} degrees")
             print(
                 "Angular step of the final (combined) tomogram:"
                 f"   {self.tomo_angle_range / total_projections:.3f} degrees"

csaxs_bec/bec_ipython_client/plugins/flomni/x_ray_eye_align.py

@@ -5,9 +5,10 @@ import os
 import time
 from typing import TYPE_CHECKING
 
+import h5py
 import numpy as np
-
 from bec_lib import bec_logger
+from bec_lib.endpoints import MessageEndpoints
 
 # from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_get, epics_put, fshopen, fshclose
 
@@ -42,6 +43,7 @@ class XrayEyeAlign:
         self.device_manager = client.device_manager
         self.scans = client.scans
         self.alignment_values = {}
+        self.alignment_images = []
         # Deliberately NOT calling self.flomni.reset_correction() /
         # reset_tomo_alignment_fit() here: XrayEyeAlign is constructed every
         # time Flomni() is instantiated (i.e. every new client session, not
@@ -69,6 +71,14 @@ class XrayEyeAlign:
         # fit point instead of triggering another height correction.
         self._height_centered = False
 
+    def _save_alignment_data(self, file_path: str):
+        os.makedirs(os.path.dirname(file_path), exist_ok=True)
+        with h5py.File(os.path.expanduser(file_path), "w") as f:
+            f.create_dataset(
+                "alignment_values", data=np.array(list(self.alignment_values.values()))
+            )
+            f.create_dataset("alignment_images", data=np.array(self.alignment_images))
+
     def update_frame(self, keep_shutter_open=False):
         if self.flomni._flomnigui_check_attribute_not_exists("xeyegui"):
             self.flomni.flomnigui_show_xeyealign()
@@ -81,6 +91,8 @@ class XrayEyeAlign:
         dev.fsh.fshopen()
 
         time.sleep(1)
+        # store the image
+        self.alignment_images.append(dev.cam_xeye.get_last_image())
         # stop live view
         if not keep_shutter_open:
             self.gui.on_live_view_enabled(False)
@@ -135,6 +147,7 @@ class XrayEyeAlign:
                 "This routine can be called with paramter keep_shutter_open=True to keep the shutter always open"
             )
         self.send_message("Getting things ready. Please wait...")
+        self.alignment_images = []
 
         self.gui.enable_submit_button(False)
 
@@ -355,10 +368,14 @@ class XrayEyeAlign:
         umv(dev.rtx, 0)
         print("You are ready to remove the xray eye and start ptychography scans.")
         print("Fine alignment: flomni.tomo_parameters() , then flomni.tomo_alignment_scan()")
-        print("After that, run the fit in Matlab and load the new fit flomni.read_alignment_offset()")
+        print(
+            "After that, run the fit in Matlab and load the new fit flomni.read_alignment_offset()"
+        )
 
     def write_output(self):
-        file = os.path.expanduser("~/data/raw/logs/xrayeye_alignmentvalues")
+        file = os.path.expanduser("~/data/raw/logs/xrayeye_alignmentvalues/xrayeye_alignmentvalues")
+        timestamp = time.strftime("%Y%m%d_%H%M%S")
+        self._save_alignment_data(file + f"_image_data_{timestamp}.h5")
         if not os.path.exists(file):
             os.makedirs(os.path.dirname(file), exist_ok=True)
 

csaxs_bec/devices/omny/galil/fgalil_ophyd.py

@@ -7,7 +7,7 @@ from ophyd import Component as Cpt
 from ophyd import Device, PositionerBase, Signal
 from ophyd.status import wait as status_wait
 from ophyd.utils import LimitError
-from ophyd_devices.utils.controller import threadlocked
+from ophyd_devices.utils.controller import retry_once, threadlocked
 from ophyd_devices.utils.socket import SocketIO, raise_if_disconnected
 
 from csaxs_bec.devices.omny.galil.galil_ophyd import (
@@ -19,7 +19,6 @@ from csaxs_bec.devices.omny.galil.galil_ophyd import (
     GalilMotorResolution,
     GalilSetpointSignal,
     GalilSignalRO,
-    retry_once,
 )
 
 logger = bec_logger.logger
@@ -41,6 +40,7 @@ class FlomniGalilController(GalilController):
         "all_axes_referenced",
         "lights_off",
         "lights_on",
+        "print_command_history",
     ]
 
     def is_axis_moving(self, axis_Id, axis_Id_numeric) -> bool:

csaxs_bec/devices/omny/galil/fupr_ophyd.py

@@ -7,7 +7,7 @@ from ophyd import Component as Cpt
 from ophyd import Device, PositionerBase, Signal
 from ophyd.status import wait as status_wait
 from ophyd.utils import LimitError
-from ophyd_devices.utils.controller import threadlocked
+from ophyd_devices.utils.controller import retry_once, threadlocked
 from ophyd_devices.utils.socket import SocketIO, raise_if_disconnected
 
 from csaxs_bec.devices.omny.galil.galil_ophyd import (
@@ -19,7 +19,6 @@ from csaxs_bec.devices.omny.galil.galil_ophyd import (
     GalilMotorResolution,
     GalilSetpointSignal,
     GalilSignalRO,
-    retry_once,
 )
 
 logger = bec_logger.logger

csaxs_bec/devices/omny/galil/galil_ophyd.py

@@ -8,7 +8,7 @@ from typing import Any
 
 from bec_lib import bec_logger
 from ophyd.utils import ReadOnlyError
-from ophyd_devices.utils.controller import Controller, threadlocked
+from ophyd_devices.utils.controller import Controller, retry_once, threadlocked
 from ophyd_devices.utils.socket import SocketSignal
 from prettytable import PrettyTable
 
@@ -27,20 +27,6 @@ class BECConfigError(Exception):
     pass
 
 
-def retry_once(fcn):
-    """Decorator to rerun a function in case a Galil communication error was raised. This may happen if the buffer was not empty."""
-
-    @functools.wraps(fcn)
-    def wrapper(self, *args, **kwargs):
-        try:
-            val = fcn(self, *args, **kwargs)
-        except (GalilCommunicationError, GalilError):
-            val = fcn(self, *args, **kwargs)
-        return val
-
-    return wrapper
-
-
 class GalilController(Controller):
     """
     Base class for Galil controllers. This class provides the basic functionality for Galil controllers and should be subclassed for specific devices.
@@ -59,6 +45,7 @@ class GalilController(Controller):
         "is_motor_on",
         "is_thread_active",
         "all_axes_referenced",
+        "print_command_history",
     ]
 
     OKBLUE = "\033[94m"
@@ -70,6 +57,7 @@ class GalilController(Controller):
 
     @threadlocked
     def socket_put(self, val: str) -> None:
+        self.command_history.append(f"[PUT]: {val}")
         self.sock.put(f"{val}\r".encode())
 
     @retry_once

csaxs_bec/devices/omny/galil/galil_rio.py

@@ -21,14 +21,10 @@ from ophyd import DynamicDeviceComponent as DDC
 from ophyd import Kind
 from ophyd.utils import ReadOnlyError
 from ophyd_devices import PSIDeviceBase
-from ophyd_devices.utils.controller import Controller, threadlocked
+from ophyd_devices.utils.controller import Controller, retry_once, threadlocked
 from ophyd_devices.utils.socket import SocketIO
 
-from csaxs_bec.devices.omny.galil.galil_ophyd import (
-    GalilCommunicationError,
-    GalilSignalBase,
-    retry_once,
-)
+from csaxs_bec.devices.omny.galil.galil_ophyd import GalilCommunicationError, GalilSignalBase
 
 if TYPE_CHECKING:  # pragma: no cover
     from bec_lib.devicemanager import ScanInfo
@@ -43,6 +39,7 @@ class GalilRIOController(Controller):
     @threadlocked
     def socket_put(self, val: str) -> None:
         """Socker put method."""
+        self.command_history.append(f"[PUT]: {val}")
         self.sock.put(f"{val}\r".encode())
 
     @retry_once

csaxs_bec/devices/omny/galil/lgalil_ophyd.py

@@ -7,7 +7,7 @@ from ophyd import Component as Cpt
 from ophyd import Device, PositionerBase, Signal
 from ophyd.status import wait as status_wait
 from ophyd.utils import LimitError
-from ophyd_devices.utils.controller import threadlocked
+from ophyd_devices.utils.controller import retry_once, threadlocked
 from ophyd_devices.utils.socket import SocketIO, raise_if_disconnected
 
 from csaxs_bec.devices.omny.galil.galil_ophyd import (
@@ -17,7 +17,6 @@ from csaxs_bec.devices.omny.galil.galil_ophyd import (
     GalilMotorIsMoving,
     GalilSetpointSignal,
     GalilSignalRO,
-    retry_once,
 )
 
 logger = bec_logger.logger
@@ -29,15 +28,19 @@ class GalilMotorResolution(GalilSignalRO):
     def _socket_get(self):
         if self.parent.axis_Id_numeric < 6:
             return float(
-                self.controller.socket_put_and_receive(f"MG encpermm[{self.parent.axis_Id_numeric}]")
+                self.controller.socket_put_and_receive(
+                    f"MG encpermm[{self.parent.axis_Id_numeric}]"
+                )
             )
         else:
             return float(
-                self.controller.socket_put_and_receive(f"MG stppermm[{self.parent.axis_Id_numeric}]")
+                self.controller.socket_put_and_receive(
+                    f"MG stppermm[{self.parent.axis_Id_numeric}]"
+                )
             )
 
-class LamniGalilController(GalilController):
 
+class LamniGalilController(GalilController):
 
     # ============================================================
     # Error status
@@ -51,7 +54,7 @@ class LamniGalilController(GalilController):
         0x10: "Cap1 exceeded allowed left-stop boundary during movement",
         0x20: "Cap2 exceeded allowed left-stop boundary during movement (disabled in code)",
         0x40: "Cap1 did not respond to test movement",
-        0x80: "Cap2 did not respond to test movement"
+        0x80: "Cap2 did not respond to test movement",
     }
 
     allaxrer_table = {
@@ -61,10 +64,9 @@ class LamniGalilController(GalilController):
         4: "Pressure valve mismatch (OUT13=0 but IN13=1)",
         5: "Capacitive sensor boundary violations (caperr > 0)",
         6: "Emergency Stop triggered (IN[5]=0)",
-        7: "Following error detected on one or more axes"
+        7: "Following error detected on one or more axes",
     }
 
-
     USER_ACCESS = [
         "describe",
         "show_running_threads",
@@ -78,7 +80,8 @@ class LamniGalilController(GalilController):
         "is_motor_on",
         "all_axes_referenced",
         "lamni_lights_off",
-        "lamni_lights_on"
+        "lamni_lights_on",
+        "print_command_history",
     ]
 
     def show_status_other(self):
@@ -107,7 +110,9 @@ class LamniGalilController(GalilController):
         if allaxref == 1:
             print(f"Allaxref = 1, all OK.")
         else:
-            print(f"Allaxref = {allaxref}. Not all axes are referenced or error introduced preventing motion.")
+            print(
+                f"Allaxref = {allaxref}. Not all axes are referenced or error introduced preventing motion."
+            )
             allaxrer = int(float(self.socket_put_and_receive("MGallaxrer")))
             print("\nallaxrer =", allaxrer)
             print(self.decode_allaxrer(allaxrer))
@@ -143,7 +148,6 @@ class LamniGalilController(GalilController):
 
         print("\n==================================\n")
 
-
     def lamni_lights_off(self):
         self.socket_put_confirmed("SB1")
 
@@ -170,14 +174,16 @@ class LamniGalilReadbackSignal(GalilSignalRO):
             current_pos = float(self.controller.socket_put_and_receive(f"TP{self.parent.axis_Id}"))
             current_pos *= self.parent.sign
             encoder_resolution = self.parent.motor_resolution.get()
-            logger.info(f"Read galil encoder position of axis {self.parent.axis_Id_numeric} to be TP {current_pos} with resolution {encoder_resolution}")
+            logger.info(
+                f"Read galil encoder position of axis {self.parent.axis_Id_numeric} to be TP {current_pos} with resolution {encoder_resolution}"
+            )
             return current_pos / encoder_resolution
         else:
             current_pos = float(self.controller.socket_put_and_receive(f"TD{self.parent.axis_Id}"))
             current_pos *= self.parent.sign
             step_mm = self.parent.motor_resolution.get()
             return current_pos / step_mm
-        
+
     def read(self):
         self._metadata["timestamp"] = time.time()
         val = super().read()

csaxs_bec/devices/omny/galil/ogalil_ophyd.py

@@ -10,15 +10,13 @@ from ophyd import Component as Cpt
 from ophyd import Device, PositionerBase, Signal
 from ophyd.status import wait as status_wait
 from ophyd.utils import LimitError
-from ophyd_devices.utils.controller import threadlocked
+from ophyd_devices.utils.controller import retry_once, threadlocked
 from ophyd_devices.utils.socket import SocketIO, raise_if_disconnected
 
 from csaxs_bec.devices.omny.galil.galil_ophyd import (
     BECConfigError,
     GalilAxesReferenced,
-    GalilCommunicationError,
     GalilController,
-    GalilError,
     GalilMotorIsMoving,
     GalilSetpointSignal,
     GalilSignalRO,
@@ -27,20 +25,6 @@ from csaxs_bec.devices.omny.galil.galil_ophyd import (
 logger = bec_logger.logger
 
 
-def retry_once(fcn):
-    """Decorator to rerun a function in case a Galil communication error was raised. This may happen if the buffer was not empty."""
-
-    @functools.wraps(fcn)
-    def wrapper(self, *args, **kwargs):
-        try:
-            val = fcn(self, *args, **kwargs)
-        except (GalilCommunicationError, GalilError):
-            val = fcn(self, *args, **kwargs)
-        return val
-
-    return wrapper
-
-
 class GalilMotorResolution(GalilSignalRO):
     @retry_once
     @threadlocked
@@ -130,6 +114,7 @@ class OMNYGalilController(GalilController):
         "get_motor_limit_switch",
         "is_motor_on",
         "all_axes_referenced",
+        "print_command_history",
         "_ogalil_switchsocket",
         "_ogalil_switchsocket_switch_all_on",
         "_ogalil_switchsocket_status",

csaxs_bec/devices/omny/galil/sgalil_ophyd.py

@@ -8,7 +8,7 @@ from ophyd import Component as Cpt
 from ophyd import Device, DeviceStatus, PositionerBase, Signal
 from ophyd.status import wait as status_wait
 from ophyd.utils import LimitError, ReadOnlyError
-from ophyd_devices.utils.controller import Controller, threadlocked
+from ophyd_devices.utils.controller import Controller, retry_once, threadlocked
 from ophyd_devices.utils.socket import SocketIO, SocketSignal, raise_if_disconnected
 from prettytable import PrettyTable
 
@@ -27,20 +27,6 @@ class BECConfigError(Exception):
     pass
 
 
-def retry_once(fcn):
-    """Decorator to rerun a function in case a Galil communication error was raised. This may happen if the buffer was not empty."""
-
-    @functools.wraps(fcn)
-    def wrapper(self, *args, **kwargs):
-        try:
-            val = fcn(self, *args, **kwargs)
-        except (GalilCommunicationError, GalilError):
-            val = fcn(self, *args, **kwargs)
-        return val
-
-    return wrapper
-
-
 class GalilController(Controller):
     USER_ACCESS = [
         "describe",
@@ -51,6 +37,7 @@ class GalilController(Controller):
         "sgalil_reference",
         "fly_grid_scan",
         "read_encoder_position",
+        "print_command_history",
     ]
     _axes_per_controller = 8
 
@@ -84,19 +71,22 @@ class GalilController(Controller):
     @threadlocked
     def socket_put(self, val: str) -> None:
         time.sleep(0.01)
+        self.command_history.append(f"[PUT]: {val}")
         self.sock.put(f"{val}\r".encode())
 
     @threadlocked
     def socket_get(self) -> str:
         time.sleep(0.01)
-        return self.sock.receive().decode()
+        response = self.sock.receive().decode()
+        self.command_history.append(f"[GET]: {response}")
+        return response
 
     @retry_once
     @threadlocked
     def socket_put_and_receive(self, val: str, remove_trailing_chars=True) -> str:
         self.socket_put(val)
         if remove_trailing_chars:
-            return self._remove_trailing_characters(self.sock.receive().decode())
+            return self._remove_trailing_characters(self.socket_get())
         return self.socket_get()
 
     @retry_once

csaxs_bec/devices/omny/rt/rt_flomni_ophyd.py

@@ -8,7 +8,7 @@ from ophyd import Device, PositionerBase, Signal
 from ophyd.status import wait as status_wait
 from ophyd.utils import LimitError
 from ophyd_devices import AsyncMultiSignal, DeviceStatus, ProgressSignal
-from ophyd_devices.utils.controller import Controller, threadlocked
+from ophyd_devices.utils.controller import Controller, retry_once, threadlocked
 from ophyd_devices.utils.socket import SocketIO, raise_if_disconnected
 from prettytable import PrettyTable
 
@@ -18,7 +18,6 @@ from csaxs_bec.devices.omny.rt.rt_ophyd import (
     RtReadbackSignal,
     RtSetpointSignal,
     RtSignalRO,
-    retry_once,
 )
 
 logger = bec_logger.logger

csaxs_bec/devices/omny/rt/rt_lamni_ophyd.py

@@ -9,7 +9,7 @@ from ophyd import Device, DeviceStatus, PositionerBase, Signal
 from ophyd.status import wait as status_wait
 from ophyd.utils import LimitError, ReadOnlyError
 from ophyd_devices.utils.bec_signals import AsyncMultiSignal, ProgressSignal
-from ophyd_devices.utils.controller import Controller, threadlocked
+from ophyd_devices.utils.controller import Controller, retry_once, threadlocked
 from ophyd_devices.utils.socket import SocketIO, SocketSignal, raise_if_disconnected
 from prettytable import PrettyTable
 
@@ -30,20 +30,6 @@ class BECConfigError(Exception):
     pass
 
 
-def retry_once(fcn):
-    """Decorator to rerun a function in case a CommunicationError was raised. This may happen if the buffer was not empty."""
-
-    @functools.wraps(fcn)
-    def wrapper(self, *args, **kwargs):
-        try:
-            val = fcn(self, *args, **kwargs)
-        except (RtLamniCommunicationError, RtLamniError):
-            val = fcn(self, *args, **kwargs)
-        return val
-
-    return wrapper
-
-
 class RtLamniController(Controller):
     """
     RT-Lamni controller class for all rt devices.
@@ -133,7 +119,7 @@ class RtLamniController(Controller):
 
     @threadlocked
     def _position_sampling_single_read(self):
-        (number_of_samples, sum0, sum0_2, sum1, sum1_2, sum2, sum2_2) = self.socket_put_and_receive(
+        number_of_samples, sum0, sum0_2, sum1, sum1_2, sum2, sum2_2 = self.socket_put_and_receive(
             f"Sr"
         ).split(",")
         avg_x = float(sum1) / int(number_of_samples)
@@ -187,7 +173,7 @@ class RtLamniController(Controller):
             parent._min_scan_buffer_reached = False
             for pos_index, pos in enumerate(positions):
                 cmd = f"s{pos[0]:.05f},{pos[1]:.05f},0"
-                parent.socket_put_and_receive(cmd)                
+                parent.socket_put_and_receive(cmd)
                 if pos_index > 100:
                     parent._min_scan_buffer_reached = True
             parent._min_scan_buffer_reached = True
@@ -224,7 +210,7 @@ class RtLamniController(Controller):
                 "Cannot start scan because feedback loop is not running or there is an interferometer error."
             )
             # here exception
-        (mode, number_of_positions_planned, current_position_in_scan) = self.get_scan_status()
+        mode, number_of_positions_planned, current_position_in_scan = self.get_scan_status()
 
         if number_of_positions_planned == 0:
             logger.error("Cannot start scan because no target positions are planned.")
@@ -241,24 +227,25 @@ class RtLamniController(Controller):
         if self.feedback_is_running():
             print("Loop is running, no error on interferometer.")
         else:
-            print("Loop is not running, either it is turned off or an interferometer error occurred.")
-
+            print(
+                "Loop is not running, either it is turned off or an interferometer error occurred."
+            )
 
     def show_analog_signals(self) -> dict:
         self.socket_put("As")  # start sampling
         time.sleep(0.01)
         return_table = (self.socket_put_and_receive("Ar")).split(",")
-        
+
         number_of_samples = int(float(return_table[0]))
         signals = {
-            "number_of_samples":    number_of_samples,
-            "piezo_0":              float(return_table[1]),
-            "piezo_1":              float(return_table[2]),
-            "cap_0":                float(return_table[3]),
-            "cap_1":                float(return_table[4]),
-            "cap_2":                float(return_table[5]),
-            "cap_3":                float(return_table[6]),
-            "cap_4":                float(return_table[7]),
+            "number_of_samples": number_of_samples,
+            "piezo_0": float(return_table[1]),
+            "piezo_1": float(return_table[2]),
+            "cap_0": float(return_table[3]),
+            "cap_1": float(return_table[4]),
+            "cap_2": float(return_table[5]),
+            "cap_3": float(return_table[6]),
+            "cap_4": float(return_table[7]),
         }
 
         t = PrettyTable()
@@ -294,8 +281,8 @@ class RtLamniController(Controller):
         t = PrettyTable()
         t.title = "Interferometer signal strength"
         t.field_names = ["Axis", "Description", "Value", "Running"]
-        t.add_row([0, "ST FZP horizontal",   ssi_0,        "-"])
-        t.add_row([1, "ST FZP vertical",     ssi_1,        "-"])
+        t.add_row([0, "ST FZP horizontal", ssi_0, "-"])
+        t.add_row([1, "ST FZP vertical", ssi_1, "-"])
         t.add_row([2, "Angle interferometer", angle_signal, angle_running])
         print(t)
 
@@ -318,7 +305,7 @@ class RtLamniController(Controller):
         print(t)
         print(f"Feedback loop running: {loop_status}")
 
-        return {"x": pos_x, "y": pos_y, "loop_running": loop_status}    
+        return {"x": pos_x, "y": pos_y, "loop_running": loop_status}
 
     def feedback_enable_with_reset(self):
         if not self.feedback_status_angle_lamni():

csaxs_bec/devices/omny/rt/rt_omny_ophyd.py

@@ -10,7 +10,7 @@ from ophyd import Device, DeviceStatus, PositionerBase, Signal
 from ophyd.status import wait as status_wait
 from ophyd.utils import LimitError
 from ophyd_devices import AsyncMultiSignal, ProgressSignal
-from ophyd_devices.utils.controller import Controller, threadlocked
+from ophyd_devices.utils.controller import Controller, retry_once, threadlocked
 from ophyd_devices.utils.socket import SocketIO, raise_if_disconnected
 from prettytable import PrettyTable
 
@@ -27,7 +27,6 @@ from csaxs_bec.devices.omny.rt.rt_ophyd import (
     RtReadbackSignal,
     RtSetpointSignal,
     RtSignalRO,
-    retry_once,
 )
 
 logger = bec_logger.logger
@@ -853,7 +852,7 @@ class RtOMNYController(Controller):
                 " interferometer error."
             )
             # here exception
-        (mode, number_of_positions_planned, current_position_in_scan) = self.get_scan_status()
+        mode, number_of_positions_planned, current_position_in_scan = self.get_scan_status()
 
         if number_of_positions_planned == 0:
             logger.error("Cannot start scan because no target positions are planned.")

csaxs_bec/devices/omny/rt/rt_ophyd.py

@@ -1,5 +1,5 @@
 """
-This module contains base signals for RT devices. Controller and motors are implemented in the 
+This module contains base signals for RT devices. Controller and motors are implemented in the
 bespoke modules such as `rt_flomni_ophyd.py` or `rt_lamni_ophyd.py`.
 """
 
@@ -8,7 +8,7 @@ import time
 
 from bec_lib import bec_logger
 from ophyd.utils import ReadOnlyError
-from ophyd_devices.utils.controller import ControllerCommunicationError, threadlocked
+from ophyd_devices.utils.controller import ControllerCommunicationError, retry_once, threadlocked
 from ophyd_devices.utils.socket import SocketSignal
 
 logger = bec_logger.logger
@@ -26,20 +26,6 @@ class BECConfigError(Exception):
     pass
 
 
-def retry_once(fcn):
-    """Decorator to rerun a function in case a CommunicationError was raised. This may happen if the buffer was not empty."""
-
-    @functools.wraps(fcn)
-    def wrapper(self, *args, **kwargs):
-        try:
-            val = fcn(self, *args, **kwargs)
-        except (RtCommunicationError, RtError):
-            val = fcn(self, *args, **kwargs)
-        return val
-
-    return wrapper
-
-
 class RtSignalBase(SocketSignal):
     def __init__(self, signal_name, **kwargs):
         self.signal_name = signal_name

csaxs_bec/devices/smaract/smaract_controller.py

@@ -6,7 +6,7 @@ import os
 import time
 
 import numpy as np
-from ophyd_devices.utils.controller import Controller, axis_checked, threadlocked
+from ophyd_devices.utils.controller import Controller, axis_checked, retry_once, threadlocked
 from prettytable import PrettyTable
 from typeguard import typechecked
 
@@ -20,20 +20,6 @@ class SmaractCommunicationMode(enum.Enum):
     ASYNC = 1
 
 
-def retry_once(fcn):
-    """Decorator to rerun a function in case a SmaractCommunicationError was raised. This may happen if the buffer was not empty."""
-
-    @functools.wraps(fcn)
-    def wrapper(self, *args, **kwargs):
-        try:
-            val = fcn(self, *args, **kwargs)
-        except (SmaractCommunicationError, SmaractErrorCode):
-            val = fcn(self, *args, **kwargs)
-        return val
-
-    return wrapper
-
-
 class SmaractChannelStatus(enum.Enum):
     STOPPED = 0
     STEPPING = 1
@@ -82,6 +68,7 @@ class SmaractController(Controller):
         "all_axes_referenced",
         "set_closed_loop_move_speed",
         "is_axis_moving",
+        "print_command_history",
     ]
 
     def __init__(
@@ -113,6 +100,7 @@ class SmaractController(Controller):
 
     @threadlocked
     def socket_put(self, val: str):
+        self.command_history.append(f"[PUT]: {val}")
         self.sock.put(f":{val}\n".encode())
 
     @threadlocked