Automatic backup triggered by new deployment

csaxs_bec/bec_ipython_client/plugins/cSAXS/test.yaml

@@ -0,0 +1,32 @@
+bpm1_settings:
+  readoutPriority: baseline
+  deviceClass: ...
+  deviceConfig:
+    gain_lsb: galil_rio_1.digital_out.ch0
+    gain_mid: galil_rio_1.digital_out.ch1
+    gain_msb: galil_rio_1.digital_out.ch2
+    coupling: galil_rio_1.digital_out.ch3
+    speed_mode: galil_rio_1.digital_out.ch4
+  enabled: true
+  readOnly: false
+  softwareTrigger: true
+  needs:
+    - galil_rio_1
+
+bpm1:
+  readoutPriority: baseline
+  deviceClass: ...
+  deviceConfig:
+    blade_t: galil_rio_1.analog_in.ch0
+    blade_r: galil_rio_1.analog_in.ch1
+    blade_b: galil_rio_1.analog_in.ch2
+    blade_l: galil_rio_1.analog_in.ch3
+  enabled: true
+  readOnly: false
+  softwareTrigger: true
+  needs:
+    - galil_rio_1
+
+
+
+    

csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py

@@ -778,7 +778,9 @@ class FlomniSampleTransferMixin:
             dev.ftransy.controller.socket_put_confirmed("confirm=1")
         else:
             print("Stopping.")
-            exit
+            raise FlomniError(
+                "User abort sample transfer."
+            )
 
     def ftransfer_gripper_is_open(self) -> bool:
         status = bool(float(dev.ftransy.controller.socket_put_and_receive("MG @OUT[9]").strip()))
@@ -801,7 +803,8 @@ class FlomniSampleTransferMixin:
     def ftransfer_gripper_move(self, position: int):
         self.check_position_is_valid(position)
 
-        self._ftransfer_shiftx = -0.2
+        #this is not used for sample stage position!
+        self._ftransfer_shiftx = -0.15
         self._ftransfer_shiftz = -0.5
 
         fsamx_pos = dev.fsamx.readback.get()
@@ -821,7 +824,7 @@ class FlomniSampleTransferMixin:
         self.check_tray_in()
 
         if position == 0:
-            umv(dev.ftransx, 10.715 + 0.2, dev.ftransz, 3.5950)
+            umv(dev.ftransx, 11, dev.ftransz, 3.5950)
         if position == 1:
             umv(
                 dev.ftransx,
@@ -1537,7 +1540,7 @@ class Flomni(
 
         umv(dev.fsamroy, 0)
         self.OMNYTools.printgreenbold(
-            "\n\nAlignment scan finished. Please run SPEC_ptycho_align and load the new fit."
+            "\n\nAlignment scan finished. Please run SPEC_ptycho_align and load the new fit by flomni.read_alignment_offset() ."
         )
 
     def _write_subtomo_to_scilog(self, subtomo_number):
@@ -1713,9 +1716,9 @@ class Flomni(
             )
             if self.OMNYTools.yesno("Shall I continue?", "n"):
                 print("OK")
-        else:
-            print("Stopping.")
-            return
+            else:
+                print("Stopping.")
+                return
 
         self.flomnigui_show_progress()
 
@@ -1743,6 +1746,7 @@ class Flomni(
             #     self.write_pdf_report()
             # else:
             self.tomo_id = 0
+            self.write_pdf_report()
 
         with scans.dataset_id_on_hold:
             if self.tomo_type == 1:
@@ -2142,16 +2146,18 @@ class Flomni(
         fovxy = f"{self.fovx:.2f}/{self.fovy:.2f}"
         stitching = f"{self.stitch_x:.2f}/{self.stitch_y:.2f}"
         dataset_id = str(self.client.queue.next_dataset_number)
+        account = bec.active_account
         content = [
             f"{'Sample Name:':<{padding}}{self.sample_name:>{padding}}\n",
             f"{'Measurement ID:':<{padding}}{str(self.tomo_id):>{padding}}\n",
             f"{'Dataset ID:':<{padding}}{dataset_id:>{padding}}\n",
             f"{'Sample Info:':<{padding}}{'Sample Info':>{padding}}\n",
-            f"{'e-account:':<{padding}}{str(self.client.username):>{padding}}\n",
+            f"{'e-account:':<{padding}}{str(account):>{padding}}\n",
             f"{'Number of projections:':<{padding}}{int(180 / self.tomo_angle_stepsize * 8):>{padding}}\n",
             f"{'First scan number:':<{padding}}{self.client.queue.next_scan_number:>{padding}}\n",
             f"{'Last scan number approx.:':<{padding}}{self.client.queue.next_scan_number + int(180 / self.tomo_angle_stepsize * 8) + 10:>{padding}}\n",
-            f"{'Current photon energy:':<{padding}}{dev.mokev.read()['mokev']['value']:>{padding}.4f}\n",
+            f"{'Current photon energy:':<{padding}}To be implemented\n",
+            #f"{'Current photon energy:':<{padding}}{dev.mokev.read()['mokev']['value']:>{padding}.4f}\n",
             f"{'Exposure time:':<{padding}}{self.tomo_countingtime:>{padding}.2f}\n",
             f"{'Fermat spiral step size:':<{padding}}{self.tomo_shellstep:>{padding}.2f}\n",
             f"{'FOV:':<{padding}}{fovxy:>{padding}}\n",
@@ -2160,18 +2166,18 @@ class Flomni(
             f"{'Angular step within sub-tomogram:':<{padding}}{self.tomo_angle_stepsize:>{padding}.2f}\n",
         ]
         content = "".join(content)
-        user_target = os.path.expanduser(f"~/Data10/documentation/tomo_scan_ID_{self.tomo_id}.pdf")
+        user_target = os.path.expanduser(f"~/data/raw/documentation/tomo_scan_ID_{self.tomo_id}.pdf")
         with PDFWriter(user_target) as file:
             file.write(header)
             file.write(content)
-        subprocess.run(
-            "xterm /work/sls/spec/local/XOMNY/bin/upload/upload_last_pon.sh &", shell=True
-        )
+        # subprocess.run(
+        #     "xterm /work/sls/spec/local/XOMNY/bin/upload/upload_last_pon.sh &", shell=True
+        # )
         # status = subprocess.run(f"cp /tmp/spec-e20131-specES1.pdf {user_target}", shell=True)
         msg = bec.logbook.LogbookMessage()
         logo_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), "LamNI_logo.png")
         msg.add_file(logo_path).add_text("".join(content).replace("\n", "</p><p>")).add_tag(
-            ["BEC", "tomo_parameters", f"dataset_id_{dataset_id}", "LamNI", self.sample_name]
+            ["BEC", "tomo_parameters", f"dataset_id_{dataset_id}", "flOMNI", self.sample_name]
         )
         self.client.logbook.send_logbook_message(msg)
 

csaxs_bec/bec_ipython_client/plugins/flomni/flomni_optics_mixin.py

@@ -50,8 +50,6 @@ class FlomniOpticsMixin:
             # move both axes to the desired "in" positions
             umv(dev.feyex, feyex_in, dev.feyey, feyey_in)
 
-        self.xrayeye_update_frame()
-
     def _ffzp_in(self):
         foptx_in = self._get_user_param_safe("foptx", "in")
         fopty_in = self._get_user_param_safe("fopty", "in")

csaxs_bec/bec_ipython_client/plugins/flomni/x_ray_eye_align.py

@@ -253,6 +253,8 @@ 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()")
 
     def write_output(self):
         file = os.path.expanduser("~/Data10/specES1/internal/xrayeye_alignmentvalues")

csaxs_bec/device_configs/ptycho_flomni.yaml

@@ -395,6 +395,16 @@ rtz:
   readoutPriority: on_request
   connectionTimeout: 20
 
+rt_flyer:
+  deviceClass: csaxs_bec.devices.omny.rt.rt_flomni_ophyd.RtFlomniFlyer
+  deviceConfig:
+    host: mpc2844.psi.ch
+    port: 2222
+  readoutPriority: async
+  connectionTimeout: 20
+  enabled: true
+  readOnly: False
+
 ############################################################
 ####################### Cameras ############################
 ############################################################

csaxs_bec/devices/epics/mcs_card/mcs_card_csaxs.py

@@ -317,8 +317,6 @@ class MCSCardCSAXS(PSIDeviceBase, MCSCard):
         try:
             scan_done = bool(value == self._num_total_triggers)
             self.progress.put(value=value, max_value=self._num_total_triggers, done=scan_done)
-            if scan_done:
-                self._scan_done_event.set()
         except Exception:
             content = traceback.format_exc()
             logger.info(f"Device {self.name}  error: {content}")
@@ -393,6 +391,7 @@ class MCSCardCSAXS(PSIDeviceBase, MCSCard):
         self._current_data_index = 0
 
         # NOTE Make sure that the signal that omits mca callbacks is cleared
+        # DO NOT REMOVE!!
         self._omit_mca_callbacks.clear()
 
         # For a fly scan we need to start the mcs card ourselves
@@ -563,8 +562,9 @@ class MCSCardCSAXS(PSIDeviceBase, MCSCard):
 
     def on_stop(self) -> None:
         """Hook called when the device is stopped. In addition, any status that is registered through cancel_on_stop will be cancelled here."""
-        self.stop_all.put(1)
-        self.erase_all.put(1)
+        with suppress_mca_callbacks(self):
+            self.stop_all.put(1)
+            self.erase_all.put(1)
 
     def mcs_recovery(self, timeout: int = 1) -> None:
         """

csaxs_bec/devices/omny/rt/rt_flomni_ophyd.py

@@ -1,20 +1,18 @@
 import threading
 import time
-from typing import List
 
 import numpy as np
-from bec_lib import bec_logger, messages
-from bec_lib.endpoints import MessageEndpoints
+from bec_lib import bec_logger
 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 import AsyncMultiSignal, DeviceStatus, ProgressSignal
 from ophyd_devices.utils.controller import Controller, threadlocked
 from ophyd_devices.utils.socket import SocketIO, raise_if_disconnected
 from prettytable import PrettyTable
 
 from csaxs_bec.devices.omny.rt.rt_ophyd import (
-    BECConfigError,
     RtCommunicationError,
     RtError,
     RtReadbackSignal,
@@ -432,27 +430,6 @@ class RtFlomniController(Controller):
             t.add_row([i, self.read_ssi_interferometer(i)])
         print(t)
 
-    def _get_signals_from_table(self, return_table) -> dict:
-        self.average_stdeviations_x_st_fzp += float(return_table[4])
-        self.average_stdeviations_y_st_fzp += float(return_table[7])
-        signals = {
-            "target_x": {"value": float(return_table[2])},
-            "average_x_st_fzp": {"value": float(return_table[3])},
-            "stdev_x_st_fzp": {"value": float(return_table[4])},
-            "target_y": {"value": float(return_table[5])},
-            "average_y_st_fzp": {"value": float(return_table[6])},
-            "stdev_y_st_fzp": {"value": float(return_table[7])},
-            "average_rotz": {"value": float(return_table[8])},
-            "stdev_rotz": {"value": float(return_table[9])},
-            "average_stdeviations_x_st_fzp": {
-                "value": self.average_stdeviations_x_st_fzp / (int(return_table[0]) + 1)
-            },
-            "average_stdeviations_y_st_fzp": {
-                "value": self.average_stdeviations_y_st_fzp / (int(return_table[0]) + 1)
-            },
-        }
-        return signals
-
     @threadlocked
     def start_scan(self):
         if not self.feedback_is_running():
@@ -492,91 +469,6 @@ class RtFlomniController(Controller):
         current_position_in_scan = int(float(return_table[2]))
         return (mode, number_of_positions_planned, current_position_in_scan)
 
-    def read_positions_from_sampler(self):
-        # this was for reading after the scan completed
-        number_of_samples_to_read = 1  # self.get_scan_status()[1]  #number of valid samples, will be updated upon first data read
-
-        read_counter = 0
-
-        self.average_stdeviations_x_st_fzp = 0
-        self.average_stdeviations_y_st_fzp = 0
-        self.average_lamni_angle = 0
-
-        mode, number_of_positions_planned, current_position_in_scan = self.get_scan_status()
-
-        # if not (mode==2 or mode==3):
-        #    error
-        self.device_manager.connector.set(
-            MessageEndpoints.device_status("rt_scan"),
-            messages.DeviceStatusMessage(
-                device="rt_scan", status=1, metadata=self.readout_metadata
-            ),
-        )
-        # while scan is running
-        while mode > 0:
-
-            # TODO here?: scan abortion if no progress in scan *raise error
-
-            # logger.info(f"Current scan position {current_position_in_scan} out of {number_of_positions_planned}")
-            mode, number_of_positions_planned, current_position_in_scan = self.get_scan_status()
-            time.sleep(0.01)
-            if current_position_in_scan > 5:
-                while current_position_in_scan > read_counter + 1:
-                    return_table = (self.socket_put_and_receive(f"r{read_counter}")).split(",")
-                    # logger.info(f"{return_table}")
-                    logger.info(f"Read {read_counter} out of {number_of_positions_planned}")
-
-                    read_counter = read_counter + 1
-
-                    signals = self._get_signals_from_table(return_table)
-
-                    self.publish_device_data(signals=signals, point_id=int(return_table[0]))
-
-        time.sleep(0.05)
-
-        # read the last samples even though scan is finished already
-        while number_of_positions_planned > read_counter:
-            return_table = (self.socket_put_and_receive(f"r{read_counter}")).split(",")
-            logger.info(f"Read {read_counter} out of {number_of_positions_planned}")
-            # logger.info(f"{return_table}")
-            read_counter = read_counter + 1
-
-            signals = self._get_signals_from_table(return_table)
-            self.publish_device_data(signals=signals, point_id=int(return_table[0]))
-
-        self.device_manager.connector.set(
-            MessageEndpoints.device_status("rt_scan"),
-            messages.DeviceStatusMessage(
-                device="rt_scan", status=0, metadata=self.readout_metadata
-            ),
-        )
-
-        logger.info(
-            "Flomni statistics: Average of all standard deviations: x"
-            f" {self.average_stdeviations_x_st_fzp/read_counter*1000:.1f}, y"
-            f" {self.average_stdeviations_y_st_fzp/read_counter*1000:.1f}"
-        )
-
-    def publish_device_data(self, signals, point_id):
-        self.device_manager.connector.set_and_publish(
-            MessageEndpoints.device_read("rt_flomni"),
-            messages.DeviceMessage(
-                signals=signals, metadata={"point_id": point_id, **self.readout_metadata}
-            ),
-        )
-
-    def start_readout(self):
-        readout = threading.Thread(target=self.read_positions_from_sampler)
-        readout.start()
-
-    def kickoff(self, metadata):
-        self.readout_metadata = metadata
-        while not self._min_scan_buffer_reached:
-            time.sleep(0.001)
-        self.start_scan()
-        time.sleep(0.1)
-        self.start_readout()
-
 
 class RtFlomniReadbackSignal(RtReadbackSignal):
     @retry_once
@@ -844,6 +736,185 @@ class RtFlomniMotor(Device, PositionerBase):
         return super().stop(success=success)
 
 
+class RtFlomniFlyer(Device):
+    USER_ACCESS = ["controller"]
+    data = Cpt(
+        AsyncMultiSignal,
+        name="data",
+        signals=[
+            "target_x",
+            "average_x_st_fzp",
+            "stdev_x_st_fzp",
+            "target_y",
+            "average_y_st_fzp",
+            "stdev_y_st_fzp",
+            "average_rotz",
+            "stdev_rotz",
+            "average_stdeviations_x_st_fzp",
+            "average_stdeviations_y_st_fzp",
+        ],
+        ndim=1,
+        async_update={"type": "add", "max_shape": [None]},
+        max_size=1000,
+    )
+    progress = Cpt(
+        ProgressSignal, doc="ProgressSignal indicating the progress of the device during a scan."
+    )
+
+    def __init__(
+        self,
+        prefix="",
+        *,
+        name,
+        kind=None,
+        read_attrs=None,
+        configuration_attrs=None,
+        parent=None,
+        host="mpc2844.psi.ch",
+        port=2222,
+        socket_cls=SocketIO,
+        device_manager=None,
+        **kwargs,
+    ):
+        super().__init__(prefix=prefix, name=name, parent=parent, **kwargs)
+        self.shutdown_event = threading.Event()
+        self.controller = RtFlomniController(
+            socket_cls=socket_cls, socket_host=host, socket_port=port, device_manager=device_manager
+        )
+        self.average_stdeviations_x_st_fzp = 0
+        self.average_stdeviations_y_st_fzp = 0
+        self.average_lamni_angle = 0
+        self.readout_thread = None
+        self.scan_done_event = threading.Event()
+        self.scan_done_event.set()
+
+    def read_positions_from_sampler(self, status: DeviceStatus):
+        """
+        Read the positions from the sampler and update the data signal.
+        This function runs in a separate thread and continuously checks the
+        scan status.
+
+        Args:
+            status (DeviceStatus): The status object to update when the readout is complete.
+        """
+        read_counter = 0
+        self.average_stdeviations_x_st_fzp = 0
+        self.average_stdeviations_y_st_fzp = 0
+        self.average_lamni_angle = 0
+
+        mode, number_of_positions_planned, current_position_in_scan = (
+            self.controller.get_scan_status()
+        )
+
+        # while scan is running
+        while mode > 0 and not self.shutdown_event.wait(0.01):
+            # logger.info(f"Current scan position {current_position_in_scan} out of {number_of_positions_planned}")
+            mode, number_of_positions_planned, current_position_in_scan = (
+                self.controller.get_scan_status()
+            )
+            if current_position_in_scan > 5:
+                while current_position_in_scan > read_counter + 1:
+                    return_table = (
+                        self.controller.socket_put_and_receive(f"r{read_counter}")
+                    ).split(",")
+                    logger.info(f"Read {read_counter} out of {number_of_positions_planned}")
+                    self.progress.put(
+                        value=read_counter, max_value=number_of_positions_planned, done=False
+                    )
+                    read_counter = read_counter + 1
+                    signals = self._get_signals_from_table(return_table)
+                    self.data.set(signals)
+
+        if self.shutdown_event.wait(0.05):
+            logger.info("Shutdown event set, stopping readout.")
+            # if we are here, the shutdown_event is set. We can exit the readout loop.
+            status.set_finished()
+            return
+
+        # read the last samples even though scan is finished already
+        while number_of_positions_planned > read_counter and not self.shutdown_event.is_set():
+            return_table = (self.controller.socket_put_and_receive(f"r{read_counter}")).split(",")
+            logger.info(f"Read {read_counter} out of {number_of_positions_planned}")
+            self.progress.put(value=read_counter, max_value=number_of_positions_planned, done=False)
+            read_counter = read_counter + 1
+
+            signals = self._get_signals_from_table(return_table)
+            self.data.set(signals)
+
+        # NOTE: No need to set the status to failed if the shutdown_event is set.
+        # The stop() method will take care of that.
+        status.set_finished()
+        self.progress.put(value=read_counter, max_value=number_of_positions_planned, done=True)
+
+        logger.info(
+            "Flomni statistics: Average of all standard deviations: x"
+            f" {self.average_stdeviations_x_st_fzp/read_counter*1000:.1f}, y"
+            f" {self.average_stdeviations_y_st_fzp/read_counter*1000:.1f}"
+        )
+
+    def _get_signals_from_table(self, return_table) -> dict:
+        self.average_stdeviations_x_st_fzp += float(return_table[4])
+        self.average_stdeviations_y_st_fzp += float(return_table[7])
+        signals = {
+            "target_x": {"value": float(return_table[2])},
+            "average_x_st_fzp": {"value": float(return_table[3])},
+            "stdev_x_st_fzp": {"value": float(return_table[4])},
+            "target_y": {"value": float(return_table[5])},
+            "average_y_st_fzp": {"value": float(return_table[6])},
+            "stdev_y_st_fzp": {"value": float(return_table[7])},
+            "average_rotz": {"value": float(return_table[8])},
+            "stdev_rotz": {"value": float(return_table[9])},
+            "average_stdeviations_x_st_fzp": {
+                "value": self.average_stdeviations_x_st_fzp / (int(return_table[0]) + 1)
+            },
+            "average_stdeviations_y_st_fzp": {
+                "value": self.average_stdeviations_y_st_fzp / (int(return_table[0]) + 1)
+            },
+        }
+        return signals
+
+    def stage(self):
+        self.shutdown_event.clear()
+        self.scan_done_event.set()
+        return super().stage()
+
+    def start_readout(self, status: DeviceStatus):
+        self.readout_thread = threading.Thread(
+            target=self.read_positions_from_sampler, args=(status,)
+        )
+        self.readout_thread.start()
+
+    def kickoff(self) -> DeviceStatus:
+        self.shutdown_event.clear()
+        self.scan_done_event.clear()
+        while not self.controller._min_scan_buffer_reached and not self.shutdown_event.wait(0.001):
+            ...
+        self.controller.start_scan()
+        self.shutdown_event.wait(0.1)
+        status = DeviceStatus(self)
+        status.set_finished()
+        return status
+
+    def complete(self) -> DeviceStatus:
+        """Wait until the flyer is done."""
+        if self.scan_done_event.is_set():
+            # if the scan_done_event is already set, we can return a finished status immediately
+            status = DeviceStatus(self)
+            status.set_finished()
+            return status
+        status = DeviceStatus(self)
+        self.start_readout(status)
+        status.add_callback(lambda *args, **kwargs: self.scan_done_event.set())
+        return status
+
+    def stop(self, *, success=False):
+        self.shutdown_event.set()
+        self.scan_done_event.set()
+        if self.readout_thread is not None:
+            self.readout_thread.join()
+        return super().stop(success=success)
+
+
 if __name__ == "__main__":
     rtcontroller = RtFlomniController(
         socket_cls=SocketIO, socket_host="mpc2844.psi.ch", socket_port=2222, device_manager=None

csaxs_bec/scans/flomni_fermat_scan.py

@@ -27,20 +27,19 @@ from bec_lib import bec_logger, messages
 from bec_lib.alarm_handler import Alarms
 from bec_lib.endpoints import MessageEndpoints
 from bec_server.scan_server.errors import ScanAbortion
-from bec_server.scan_server.scans import SyncFlyScanBase
+from bec_server.scan_server.scans import AsyncFlyScanBase
 
 from csaxs_bec.devices.epics.delay_generator_csaxs.delay_generator_csaxs import TRIGGERSOURCE
 
 logger = bec_logger.logger
 
 
-class FlomniFermatScan(SyncFlyScanBase):
+class FlomniFermatScan(AsyncFlyScanBase):
     scan_name = "flomni_fermat_scan"
     scan_type = "fly"
     required_kwargs = ["fovx", "fovy", "exp_time", "step", "angle"]
     arg_input = {}
     arg_bundle_size = {"bundle": len(arg_input), "min": None, "max": None}
-    use_scan_progress_report = True
 
     def __init__(
         self,
@@ -104,6 +103,14 @@ class FlomniFermatScan(SyncFlyScanBase):
             self.zshift = -100
         self.flomni_rotation_status = None
 
+    def scan_report_instructions(self):
+        """Scan report instructions for the progress bar"""
+        yield from self.stubs.scan_report_instruction({"device_progress": ["rt_flyer"]})
+
+    @property
+    def monitor_sync(self) -> str:
+        return "rt_flyer"
+
     def initialize(self):
         self.scan_motors = []
         self.update_readout_priority()
@@ -113,10 +120,6 @@ class FlomniFermatScan(SyncFlyScanBase):
             self.positions, corridor_size=self.optim_trajectory_corridor
         )
 
-    @property
-    def monitor_sync(self):
-        return "rt_flomni"
-
     def reverse_trajectory(self):
         """
         Reverse the trajectory. Every other scan should be reversed to
@@ -290,26 +293,18 @@ class FlomniFermatScan(SyncFlyScanBase):
         return np.array(positions)
 
     def scan_core(self):
-        # use a device message to receive the scan number and
-        # scan ID before sending the message to the device server
-        yield from self.stubs.kickoff(device="rtx")
-        while True:
-            yield from self.stubs.read(group="monitored")
-            status = self.connector.get(MessageEndpoints.device_status("rt_scan"))
-            if status:
-                status_id = status.content.get("status", 1)
-                request_id = status.metadata.get("RID")
-                if status_id == 0 and self.metadata.get("RID") == request_id:
-                    break
-                if status_id == 2 and self.metadata.get("RID") == request_id:
-                    raise ScanAbortion(
-                        "An error occured during the flomni readout:"
-                        f" {status.metadata.get('error')}"
-                    )
+        # send off the flyer
+        yield from self.stubs.kickoff(device="rt_flyer")
 
+        # start the readout loop of the flyer
+        status = yield from self.stubs.complete(device="rt_flyer", wait=False)
+
+        # read the monitors until the flyer is done
+        while not status.done:
+            yield from self.stubs.read(group="monitored", point_id=self.point_id)
+            self.point_id += 1
             time.sleep(1)
             logger.debug("reading monitors")
-        # yield from self.device_rpc("rtx", "controller.kickoff")
 
     def move_to_start(self):
         """return to the start position"""
@@ -336,6 +331,7 @@ class FlomniFermatScan(SyncFlyScanBase):
         yield from self.read_scan_motors()
         self.prepare_positions()
         yield from self._prepare_setup()
+        yield from self.scan_report_instructions()
         yield from self.open_scan()
         yield from self.stage()
         yield from self.run_baseline_reading()

tests/tests_devices/test_mcs_card.py

@@ -217,6 +217,16 @@ def test_mcs_card_csaxs_complete_and_stop(mock_mcs_csaxs: MCSCardCSAXS):
     assert not mcs._start_monitor_async_data_emission.is_set()
 
 
+def test_mcs_on_stop(mock_mcs_csaxs: MCSCardCSAXS):
+    """Test that on stop sets the omit_mca_callbacks flag. Also test that on stage clears the omit_mca_callbacks flag."""
+    mcs = mock_mcs_csaxs
+    assert mcs._omit_mca_callbacks.is_set() is False
+    mcs.stop()
+    assert mcs._omit_mca_callbacks.is_set() is True
+    mcs.stage()
+    assert mcs._omit_mca_callbacks.is_set() is False
+
+
 def test_mcs_recovery(mock_mcs_csaxs: MCSCardCSAXS):
     mcs = mock_mcs_csaxs
     # Simulate ongoing acquisition