tomo id on private server added

.gitea/workflows/rtd_deploy.yml

@@ -0,0 +1,21 @@
+name: Read the Docs Deploy Trigger
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  trigger-rtd-webhook:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Trigger Read the Docs webhook
+        env:
+          RTD_TOKEN: ${{ secrets.RTD_TOKEN }}
+        run: |
+          curl --fail --show-error --silent \
+            -X POST \
+            -d "branches=${{ github.ref_name }}" \
+            -d "token=${RTD_TOKEN}" \
+            "https://readthedocs.org/api/v2/webhook/sls-csaxs/270162/"

.readthedocs.yaml

@@ -8,15 +8,14 @@ version: 2
 build:
   os: ubuntu-20.04
   tools:
-    python: "3.10"
+    python: "3.12"
   jobs:
     pre_install:
       - pip install .
 
-
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-   configuration: docs/conf.py
+  configuration: docs/conf.py
 
 # If using Sphinx, optionally build your docs in additional formats such as PDF
 # formats:
@@ -24,6 +23,5 @@ sphinx:
 
 # Optionally declare the Python requirements required to build your docs
 python:
-   install:
-   - requirements: docs/requirements.txt
-
+  install:
+    - requirements: docs/requirements.txt

csaxs_bec/bec_ipython_client/plugins/LamNI/LamNI_webpage_generator.py

@@ -0,0 +1,89 @@
+"""
+LamNI/webpage_generator.py
+===========================
+LamNI-specific webpage generator subclass.
+
+Integration (inside the LamNI __init__ / startup):
+---------------------------------------------------
+    from csaxs_bec.bec_ipython_client.plugins.LamNI.webpage_generator import (
+        LamniWebpageGenerator,
+    )
+    self._webpage_gen = LamniWebpageGenerator(
+        bec_client=client,
+        output_dir="~/data/raw/webpage/",
+    )
+    self._webpage_gen.start()
+
+Or use the factory (auto-selects by session name "lamni"):
+----------------------------------------------------------
+    from csaxs_bec.bec_ipython_client.plugins.flomni.webpage_generator import (
+        make_webpage_generator,
+    )
+    self._webpage_gen = make_webpage_generator(bec, output_dir="~/data/raw/webpage/")
+    self._webpage_gen.start()
+
+Interactive helpers:
+--------------------
+    lamni._webpage_gen.status()
+    lamni._webpage_gen.verbosity = 2
+    lamni._webpage_gen.stop()
+    lamni._webpage_gen.start()
+"""
+
+from pathlib import Path
+
+from csaxs_bec.bec_ipython_client.plugins.flomni.webpage_generator import (
+    WebpageGeneratorBase,
+    _safe_get,
+    _safe_float,
+    _gvar,
+)
+
+
+class LamniWebpageGenerator(WebpageGeneratorBase):
+    """
+    LamNI-specific webpage generator.
+    Logo: LamNI.png from the same directory as this file.
+
+    Override _collect_setup_data() to add LamNI-specific temperatures,
+    sample name, and measurement settings.
+    """
+
+    # TODO: fill in LamNI-specific device paths
+    # label -> dotpath under device_manager.devices
+    _TEMP_MAP = {
+        # "Sample":  "lamni_temphum.temperature_sample",
+        # "OSA":     "lamni_temphum.temperature_osa",
+    }
+
+    def _logo_path(self):
+        return Path(__file__).parent / "LamNI.png"
+
+    def _collect_setup_data(self) -> dict:
+        # ── LamNI-specific data goes here ─────────────────────────────
+        # Uncomment and adapt when device names are known:
+        #
+        # dm = self._bec.device_manager
+        # sample_name = _safe_get(dm, "lamni_samples.sample_names.sample0") or "N/A"
+        # temperatures = {
+        #     label: _safe_float(_safe_get(dm, path))
+        #     for label, path in self._TEMP_MAP.items()
+        # }
+        # settings = {
+        #     "Sample name":   sample_name,
+        #     "FOV x / y":     ...,
+        #     "Exposure time": _gvar(self._bec, "tomo_countingtime", ".3f", " s"),
+        #     "Angle step":    _gvar(self._bec, "tomo_angle_stepsize", ".2f", "\u00b0"),
+        # }
+        # return {
+        #     "type":         "lamni",
+        #     "sample_name":  sample_name,
+        #     "temperatures": temperatures,
+        #     "settings":     settings,
+        # }
+
+        # Placeholder — returns minimal info until implemented
+        return {
+            "type": "lamni",
+            # LamNI-specific data here
+        }

csaxs_bec/bec_ipython_client/plugins/cSAXS/cSAXSDLPCA200.py

@@ -70,7 +70,7 @@ DLPCA200_AMPLIFIER_CONFIG: dict[str, dict] = {
         "rio_device": "galilrioesxbox",
         "description": "Beam Position Monitor 4 current amplifier",
         "channels": {
-            "gain_lsb": 0,  # Pin 10 -> Galil ch0
+            "gain_lsb": rio_optics.analog_in.ch0,  # Pin 10 -> Galil ch0
             "gain_mid": 1,  # Pin 11 -> Galil ch1
             "gain_msb": 2,  # Pin 12 -> Galil ch2
             "coupling": 3,  # Pin 13 -> Galil ch3

csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py

@@ -21,6 +21,14 @@ from csaxs_bec.bec_ipython_client.plugins.omny.omny_general_tools import (
     TomoIDManager,
 )
 
+# from csaxs_bec.bec_ipython_client.plugins.flomni.webpage_generator import (
+#        FlomniWebpageGenerator,
+#       VERBOSITY_SILENT,   # 0 — no output
+#       VERBOSITY_NORMAL,   # 1 — startup / stop messages only  (default)
+#       VERBOSITY_VERBOSE,  # 2 — one-line summary per cycle
+#       VERBOSITY_DEBUG,    # 3 — full JSON payload per cycle
+#    )
+
 logger = bec_logger.logger
 
 if builtins.__dict__.get("bec") is not None:
@@ -28,6 +36,7 @@ if builtins.__dict__.get("bec") is not None:
     dev = builtins.__dict__.get("dev")
     scans = builtins.__dict__.get("scans")
 
+
 def umv(*args):
     return scans.umv(*args, relative=False)
 
@@ -35,12 +44,15 @@ def umv(*args):
 class FlomniToolsError(Exception):
     pass
 
+
 class FlomniInitError(Exception):
     pass
 
+
 class FlomniError(Exception):
     pass
 
+
 # class FlomniTools:
 #     def yesno(self, message: str, default="none", autoconfirm=0) -> bool:
 #         if autoconfirm and default == "y":
@@ -84,13 +96,16 @@ class FlomniInitStagesMixin:
             else:
                 return
 
-
         sensor_voltage_target = dev.ftransy.user_parameter.get("sensor_voltage")
         sensor_voltage = float(dev.ftransy.controller.socket_put_and_receive("MG@AN[1]").strip())
 
         if not np.isclose(sensor_voltage, sensor_voltage_target, 0.25):
-            print(f"Sensor voltage of the gripper is {sensor_voltage}, while target from config is {sensor_voltage_target}")
-            print("Verify that the value is acceptable and update config file. Reload config and start again.")
+            print(
+                f"Sensor voltage of the gripper is {sensor_voltage}, while target from config is {sensor_voltage_target}"
+            )
+            print(
+                "Verify that the value is acceptable and update config file. Reload config and start again."
+            )
             return
 
         print("Starting to drive ftransy to +y limit")
@@ -118,8 +133,9 @@ class FlomniInitStagesMixin:
         dev.feyex.limits = [-30, -1]
         print("done")
 
-
-        if self.OMNYTools.yesno("Init of foptz. Can the stage move to the upstream limit without collision?"):
+        if self.OMNYTools.yesno(
+            "Init of foptz. Can the stage move to the upstream limit without collision?"
+        ):
             print("OK. continue.")
         else:
             return
@@ -173,7 +189,9 @@ class FlomniInitStagesMixin:
         dev.fsamy.limits = [2, 3.1]
         print("done")
 
-        if self.OMNYTools.yesno("Init of tracking stages. Did you remove the outer laser flight tubes?"):
+        if self.OMNYTools.yesno(
+            "Init of tracking stages. Did you remove the outer laser flight tubes?"
+        ):
             print("OK. continue.")
         else:
             print("Stopping.")
@@ -206,7 +224,9 @@ class FlomniInitStagesMixin:
         print("done")
 
         print("Initializing UPR stage.")
-        if self.OMNYTools.yesno("To ensure that the end switches work, please check that they are currently not pushed. Is everything okay?"):
+        if self.OMNYTools.yesno(
+            "To ensure that the end switches work, please check that they are currently not pushed. Is everything okay?"
+        ):
             print("OK. continue.")
         else:
             print("Stopping.")
@@ -246,7 +266,9 @@ class FlomniInitStagesMixin:
         dev.fsamroy.limits = [-5, 365]
         print("done")
 
-        if self.OMNYTools.yesno("Init of foptx. Can the stage move to the positive limit without collision? Attention: tracker flight tube!"):
+        if self.OMNYTools.yesno(
+            "Init of foptx. Can the stage move to the positive limit without collision? Attention: tracker flight tube!"
+        ):
             print("OK. continue.")
         else:
             print("Stopping.")
@@ -425,7 +447,7 @@ class FlomniSampleTransferMixin:
     def ftransfer_flomni_stage_in(self):
         time.sleep(1)
         sample_in_position = dev.flomni_samples.is_sample_slot_used(0)
-        #bool(float(dev.flomni_samples.sample_placed.sample0.get()))
+        # bool(float(dev.flomni_samples.sample_placed.sample0.get()))
         if not sample_in_position:
             raise FlomniError("There is no sample in the sample stage. Aborting.")
         self.reset_correction()
@@ -440,7 +462,10 @@ class FlomniSampleTransferMixin:
 
         print("Moving X-ray eye in.")
 
-        if self.OMNYTools.yesno("Please confirm that this is ok with the flight tube. This check is to be removed after commissioning", "n"):
+        if self.OMNYTools.yesno(
+            "Please confirm that this is ok with the flight tube. This check is to be removed after commissioning",
+            "n",
+        ):
             print("OK. continue.")
         else:
             print("Stopping.")
@@ -451,7 +476,6 @@ class FlomniSampleTransferMixin:
         self.foptics_out()
         self.xrayeye_update_frame()
 
-
     def laser_tracker_show_all(self):
         dev.rtx.controller.laser_tracker_show_all()
 
@@ -554,7 +578,6 @@ class FlomniSampleTransferMixin:
 
         self.flomnigui_show_cameras()
 
-
         self.ftransfer_gripper_move(position)
 
         self.ftransfer_controller_enable_mount_mode()
@@ -594,7 +617,7 @@ class FlomniSampleTransferMixin:
         self.check_sensor_connected()
 
         sample_in_gripper = dev.flomni_samples.is_sample_in_gripper()
-        #bool(float(dev.flomni_samples.sample_in_gripper.get()))
+        # bool(float(dev.flomni_samples.sample_in_gripper.get()))
         if not sample_in_gripper:
             raise FlomniError("The gripper does not carry a sample.")
 
@@ -646,7 +669,7 @@ class FlomniSampleTransferMixin:
 
     def ftransfer_sample_change(self, new_sample_position: int):
         self.check_tray_in()
-#        sample_in_gripper = dev.flomni_samples.sample_in_gripper.get()
+        #        sample_in_gripper = dev.flomni_samples.sample_in_gripper.get()
         sample_in_gripper = dev.flomni_samples.is_sample_in_gripper()
         if sample_in_gripper:
             raise FlomniError("There is already a sample in the gripper. Aborting.")
@@ -654,28 +677,30 @@ class FlomniSampleTransferMixin:
         self.check_position_is_valid(new_sample_position)
 
         if new_sample_position == 0:
-            raise FlomniError("The new sample to place cannot be the sample in the sample stage. Aborting.")
+            raise FlomniError(
+                "The new sample to place cannot be the sample in the sample stage. Aborting."
+            )
 
-#        sample_placed = getattr(
-#            dev.flomni_samples.sample_placed, f"sample{new_sample_position}"
-#        ).get()
+        #        sample_placed = getattr(
+        #            dev.flomni_samples.sample_placed, f"sample{new_sample_position}"
+        #        ).get()
         sample_placed = dev.flomni_samples.is_sample_slot_used(new_sample_position)
         if not sample_placed:
             raise FlomniError(
                 f"There is currently no sample in position [{new_sample_position}]. Aborting."
             )
 
-#        sample_in_sample_stage = dev.flomni_samples.sample_placed.sample0.get()
+        #        sample_in_sample_stage = dev.flomni_samples.sample_placed.sample0.get()
         sample_in_sample_stage = dev.flomni_samples.is_sample_slot_used(0)
         if sample_in_sample_stage:
             # find a new home for the sample...
             empty_slots = []
-#            for name, val in dev.flomni_samples.read().items():
-#                if "flomni_samples_sample_placed_sample" not in name:
-#                    continue
-#                if val.get("value") == 0:
-#                    empty_slots.append(int(name.split("flomni_samples_sample_placed_sample")[1]))
-            for j in range(1,20):
+            #            for name, val in dev.flomni_samples.read().items():
+            #                if "flomni_samples_sample_placed_sample" not in name:
+            #                    continue
+            #                if val.get("value") == 0:
+            #                    empty_slots.append(int(name.split("flomni_samples_sample_placed_sample")[1]))
+            for j in range(1, 20):
                 if not dev.flomni_samples.is_sample_slot_used(j):
                     empty_slots.append(j)
             if not empty_slots:
@@ -761,7 +786,9 @@ 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()))
@@ -769,7 +796,7 @@ class FlomniSampleTransferMixin:
 
     def ftransfer_gripper_open(self):
         sample_in_gripper = dev.flomni_samples.is_sample_in_gripper()
-        #dev.flomni_samples.sample_in_gripper.get()
+        # dev.flomni_samples.sample_in_gripper.get()
         if sample_in_gripper:
             raise FlomniError(
                 "Cannot open gripper. There is still a sample in the gripper! Aborting."
@@ -784,13 +811,17 @@ 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()
         if position == 0 and fsamx_pos > -160:
 
-            if self.OMNYTools.yesno("May the flomni stage be moved out for the sample change? Feedback will be disabled and alignment will be lost!", "y"):
+            if self.OMNYTools.yesno(
+                "May the flomni stage be moved out for the sample change? Feedback will be disabled and alignment will be lost!",
+                "y",
+            ):
                 print("OK. continue.")
                 self.ftransfer_flomni_stage_out()
             else:
@@ -801,7 +832,7 @@ 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,
@@ -946,8 +977,6 @@ class FlomniSampleTransferMixin:
 
 class FlomniAlignmentMixin:
     import csaxs_bec
-    import os 
-    from pathlib import Path
 
     # Ensure this is a Path object, not a string
     csaxs_bec_basepath = Path(csaxs_bec.__file__)
@@ -956,10 +985,13 @@ class FlomniAlignmentMixin:
 
     # Build the absolute path correctly
     default_correction_file = (
-        csaxs_bec_basepath.parent / 'bec_ipython_client' / 'plugins' / 'flomni' / default_correction_file_rel
+        csaxs_bec_basepath.parent
+        / "bec_ipython_client"
+        / "plugins"
+        / "flomni"
+        / default_correction_file_rel
     ).resolve()
 
-
     def reset_correction(self, use_default_correction=True):
         """
         Reset the correction to the default values.
@@ -1031,12 +1063,12 @@ class FlomniAlignmentMixin:
         else:
             params = dev.omny_xray_gui.fit_params_x.get()
 
-            #amplitude
-            tomo_alignment_fit[0][0] = params['SineModel_0_amplitude']
-            #phase
-            tomo_alignment_fit[0][1] = params['SineModel_0_shift']
-            #offset
-            tomo_alignment_fit[0][2] = params['LinearModel_1_intercept']
+            # amplitude
+            tomo_alignment_fit[0][0] = params["SineModel_0_amplitude"]
+            # phase
+            tomo_alignment_fit[0][1] = params["SineModel_0_shift"]
+            # offset
+            tomo_alignment_fit[0][2] = params["LinearModel_1_intercept"]
             print("applying vertical default values from mirror calibration, not from fit!")
             tomo_alignment_fit[1][0] = 0
             tomo_alignment_fit[1][1] = 0
@@ -1045,7 +1077,6 @@ class FlomniAlignmentMixin:
             tomo_alignment_fit[1][4] = 0
             print("New alignment parameters loaded based on Xray eye alignment GUI:")
 
-
         print(
             f"X Amplitude {tomo_alignment_fit[0][0]}, "
             f"X Phase {tomo_alignment_fit[0][1]}, "
@@ -1186,13 +1217,83 @@ class FlomniAlignmentMixin:
         return additional_correction_shift
 
 
+class _ProgressProxy:
+    """Dict-like proxy that persists the flOMNI progress dict as a BEC global variable.
+
+    Every read (`proxy["key"]`) fetches the current dict from the global var store,
+    and every write (`proxy["key"] = val`) fetches, updates, and saves it back.
+    This makes the progress state visible to all BEC client sessions via
+    ``client.get_global_var("tomo_progress")``.
+    """
+
+    _GLOBAL_VAR_KEY = "tomo_progress"
+    _DEFAULTS: dict = {
+        "subtomo": 0,
+        "subtomo_projection": 0,
+        "subtomo_total_projections": 1,
+        "projection": 0,
+        "total_projections": 1,
+        "angle": 0,
+        "tomo_type": 0,
+        "tomo_start_time": None,
+        "estimated_remaining_time": None,
+        "heartbeat": None,
+    }
+
+    def __init__(self, client):
+        self._client = client
+
+    # ------------------------------------------------------------------
+    # Internal helpers
+    # ------------------------------------------------------------------
+    def _load(self) -> dict:
+        val = self._client.get_global_var(self._GLOBAL_VAR_KEY)
+        if val is None:
+            return dict(self._DEFAULTS)
+        return val
+
+    def _save(self, data: dict) -> None:
+        self._client.set_global_var(self._GLOBAL_VAR_KEY, data)
+
+    # ------------------------------------------------------------------
+    # Dict-like interface
+    # ------------------------------------------------------------------
+    def __getitem__(self, key):
+        return self._load()[key]
+
+    def __setitem__(self, key, value) -> None:
+        data = self._load()
+        data[key] = value
+        self._save(data)
+
+    def __repr__(self) -> str:
+        return f"{self.__class__.__name__}({self._load()!r})"
+
+    def get(self, key, default=None):
+        return self._load().get(key, default)
+
+    def update(self, *args, **kwargs) -> None:
+        """Update multiple fields in a single round-trip."""
+        data = self._load()
+        data.update(*args, **kwargs)
+        self._save(data)
+
+    def reset(self) -> None:
+        """Reset all progress fields to their default values."""
+        self._save(dict(self._DEFAULTS))
+
+    def as_dict(self) -> dict:
+        """Return a plain copy of the current progress state."""
+        return self._load()
+
+
 class Flomni(
     FlomniInitStagesMixin,
     FlomniSampleTransferMixin,
     FlomniAlignmentMixin,
     FlomniOpticsMixin,
     cSAXSBeamlineChecks,
-    flomniGuiTools
+    flomniGuiTools,
 ):
     def __init__(self, client):
         super().__init__()
@@ -1208,14 +1309,20 @@ class Flomni(
         self.corr_angle_y = []
         self.corr_pos_y_2 = []
         self.corr_angle_y_2 = []
-        self.progress = {}
-        self.progress["subtomo"] = 0
-        self.progress["subtomo_projection"] = 0
-        self.progress["subtomo_total_projections"] = 1
-        self.progress["projection"] = 0
-        self.progress["total_projections"] = 1
-        self.progress["angle"] = 0
-        self.progress["tomo_type"] = 0
+        self._progress_proxy = _ProgressProxy(self.client)
+        self._progress_proxy.reset()
+        from csaxs_bec.bec_ipython_client.plugins.flomni.flomni_webpage_generator import (
+            FlomniWebpageGenerator,
+        )
+        self._webpage_gen = FlomniWebpageGenerator(
+            bec_client=client,
+            output_dir="~/data/raw/webpage/",
+            #upload_url="http://s1090968537.online.de/upload.php",   # optional
+            upload_url="https://v1p0zyg2w9n2k9c1.myfritz.net/upload.php",
+            local_port=8080
+        )
+        self._webpage_gen.start()
+
         self.OMNYTools = OMNYTools(self.client)
         self.reconstructor = PtychoReconstructor(self.ptycho_reconstruct_foldername)
         self.tomo_id_manager = TomoIDManager()
@@ -1224,7 +1331,10 @@ class Flomni(
 
     def start_x_ray_eye_alignment(self, keep_shutter_open=False):
 
-        if self.OMNYTools.yesno("Starting Xrayeye alignment. Deleting any potential existing alignment for this sample.", "y"):
+        if self.OMNYTools.yesno(
+            "Starting Xrayeye alignment. Deleting any potential existing alignment for this sample.",
+            "y",
+        ):
             self.align = XrayEyeAlign(self.client, self)
             try:
                 self.align.align(keep_shutter_open)
@@ -1236,7 +1346,7 @@ class Flomni(
                     umv(dev.fsamx, fsamx_in)
                 raise exc
 
-    def xrayeye_update_frame(self,keep_shutter_open=False):
+    def xrayeye_update_frame(self, keep_shutter_open=False):
         self.align.update_frame(keep_shutter_open)
 
     def xrayeye_alignment_start(self, keep_shutter_open=False):
@@ -1268,6 +1378,42 @@ class Flomni(
         self.special_angles = []
         self.special_angle_repeats = 1
 
+    @property
+    def progress(self) -> _ProgressProxy:
+        """Proxy dict backed by the BEC global variable ``tomo_progress``.
+
+        Readable from any BEC client session via::
+
+            client.get_global_var("tomo_progress")
+
+        Individual fields can be read and written just like a regular dict::
+
+            flomni.progress["projection"]          # read
+            flomni.progress["projection"] = 42     # write (persists immediately)
+
+        To update multiple fields atomically use :py:meth:`_ProgressProxy.update`::
+
+            flomni.progress.update(projection=42, angle=90.0)
+
+        To reset all fields to their defaults::
+
+            flomni.progress.reset()
+        """
+        return self._progress_proxy
+
+    @progress.setter
+    def progress(self, val: dict) -> None:
+        """Replace the entire progress dict.
+
+        Accepts a plain :class:`dict` and persists it to the global var store.
+        Example::
+
+            flomni.progress = {"projection": 0, "total_projections": 100, ...}
+        """
+        if not isinstance(val, dict):
+            raise TypeError(f"progress must be a dict, got {type(val).__name__!r}")
+        self._progress_proxy._save(val)
+
     @property
     def tomo_shellstep(self):
         val = self.client.get_global_var("tomo_shellstep")
@@ -1454,21 +1600,11 @@ class Flomni(
     def sample_name(self):
         return self.sample_get_name(0)
 
-    def write_to_scilog(self, content, tags: list = None):
-        try:
-            if tags is not None:
-                tags.append("BEC")
-            else:
-                tags = ["BEC"]
-            msg = bec.logbook.LogbookMessage()
-            msg.add_text(content).add_tag(tags)
-            self.client.logbook.send_logbook_message(msg)
-        except Exception:
-            logger.warning("Failed to write to scilog.")
-
     def tomo_alignment_scan(self):
         """
         Performs a tomogram alignment scan.
+        Collects all scan numbers acquired during the alignment, prints them at the end,
+        and creates a BEC scilog text entry summarising the alignment scan numbers.
         """
         if self.get_alignment_offset(0) == (0, 0, 0):
             print("It appears that the xrayeye alignemtn was not performend or loaded. Aborting.")
@@ -1476,14 +1612,11 @@ class Flomni(
         dev = builtins.__dict__.get("dev")
         bec = builtins.__dict__.get("bec")
 
-
         self.feye_out()
         tags = ["BEC_alignment_tomo", self.sample_name]
-        self.write_to_scilog(
-            f"Starting alignment scan. First scan number: {bec.queue.next_scan_number}.", tags
-        )
-    
+
         start_angle = 0
+        alignment_scan_numbers = []
 
         angle_end = start_angle + 180
         for angle in np.linspace(start_angle, angle_end, num=int(180 / 45) + 1, endpoint=True):
@@ -1495,7 +1628,6 @@ class Flomni(
                     try:
                         start_scan_number = bec.queue.next_scan_number
                         self.tomo_scan_projection(angle)
-                        self.tomo_reconstruct()
                         error_caught = False
                     except AlarmBase as exc:
                         if exc.alarm_type == "TimeoutError":
@@ -1504,28 +1636,33 @@ class Flomni(
                             error_caught = True
                         else:
                             raise exc
-                    #todo here was if blchk success, then setting to success true
+                    # todo here was if blchk success, then setting to success true
                     successful = True
-                    
+
                 end_scan_number = bec.queue.next_scan_number
                 for scan_nr in range(start_scan_number, end_scan_number):
-                    self._write_tomo_scan_number(scan_nr, angle, 0)
+                    #self._write_tomo_scan_number(scan_nr, angle, 0)
+                    alignment_scan_numbers.append(scan_nr)
 
         umv(dev.fsamroy, 0)
-        self.OMNYTools.printgreenbold("\n\nAlignment scan finished. Please run SPEC_ptycho_align and load the new fit.")
-
-    def _write_subtomo_to_scilog(self, subtomo_number):
-        dev = builtins.__dict__.get("dev")
-        bec = builtins.__dict__.get("bec")
-        if self.tomo_id > 0:
-            tags = ["BEC_subtomo", self.sample_name, f"tomo_id_{self.tomo_id}"]
-        else:
-            tags = ["BEC_subtomo", self.sample_name]
-        self.write_to_scilog(
-            f"Starting subtomo: {subtomo_number}. First scan number: {bec.queue.next_scan_number}.",
-            tags,
+        self.OMNYTools.printgreenbold(
+            "\n\nAlignment scan finished. Please run SPEC_ptycho_align and load the new fit by flomni.read_alignment_offset() ."
         )
 
+        # summary of alignment scan numbers
+        scan_list_str = ", ".join(str(s) for s in alignment_scan_numbers)
+        #print(f"\nAlignment scan numbers ({len(alignment_scan_numbers)} total): {scan_list_str}")
+
+        # BEC scilog entry (no logo)
+        scilog_content = (
+            f"Alignment scan finished.\n"
+            f"Sample: {self.sample_name}\n"
+            f"Number of alignment scans: {len(alignment_scan_numbers)}\n"
+            f"Alignment scan numbers: {scan_list_str}\n"
+        )
+        print(scliog_content)
+        bec.messaging.scilog.new().add_text(scilog_content.replace("\n", "<br>")).add_tags("alignmentscan").send()
+
     def sub_tomo_scan(self, subtomo_number, start_angle=None):
         """
         Performs a sub tomogram scan.
@@ -1533,18 +1670,6 @@ class Flomni(
             subtomo_number (int): The sub tomogram number.
             start_angle (float, optional): The start angle of the scan. Defaults to None.
         """
-        #        dev = builtins.__dict__.get("dev")
-        #        bec = builtins.__dict__.get("bec")
-        #        if self.tomo_id > 0:
-        #            tags = ["BEC_subtomo", self.sample_name, f"tomo_id_{self.tomo_id}"]
-        #        else:
-        #            tags = ["BEC_subtomo", self.sample_name]
-        #        self.write_to_scilog(
-        #            f"Starting subtomo: {subtomo_number}. First scan number: {bec.queue.next_scan_number}.",
-        #            tags,
-        #        )
-
-        self._write_subtomo_to_scilog(subtomo_number)
 
         if start_angle is not None:
             print(f"Sub tomo scan with start angle {start_angle} requested.")
@@ -1567,20 +1692,19 @@ class Flomni(
             elif subtomo_number == 8:
                 start_angle = self.tomo_angle_stepsize / 8.0 * 7
 
-
         # _tomo_shift_angles (potential global variable)
         _tomo_shift_angles = 0
         # compute number of projections
 
         start = start_angle + _tomo_shift_angles
 
-        if subtomo_number % 2:    # odd = forward
+        if subtomo_number % 2:  # odd = forward
             max_allowed_angle = 180.05 + self.tomo_angle_stepsize
             proposed_end = start + 180
             angle_end = min(proposed_end, max_allowed_angle)
             span = angle_end - start
 
-        else:                     # even = reverse
+        else:  # even = reverse
             min_allowed_angle = 0
             proposed_end = start - 180
             angle_end = max(proposed_end, min_allowed_angle)
@@ -1589,38 +1713,23 @@ class Flomni(
         # number of projections needed to maintain step size
         N = int(span / self.tomo_angle_stepsize) + 1
 
-        angles = np.linspace(
-            start,
-            angle_end,
-            num=N,
-            endpoint=True,
-        )
+        angles = np.linspace(start, angle_end, num=N, endpoint=True)
 
-        if subtomo_number % 2:    # odd subtomos → forward direction
+        if subtomo_number % 2:  # odd subtomos → forward direction
             # clamp end angle to max allowed
             max_allowed_angle = 180.05 + self.tomo_angle_stepsize
             proposed_end = start + 180
             angle_end = min(proposed_end, max_allowed_angle)
 
-            angles = np.linspace(
-                start,
-                angle_end,
-                num=N,
-                endpoint=True,
-            )
+            angles = np.linspace(start, angle_end, num=N, endpoint=True)
 
-        else:                     # even subtomos → reverse direction
+        else:  # even subtomos → reverse direction
             # go FROM start_angle down toward 0
             min_allowed_angle = 0
             proposed_end = start - 180
             angle_end = max(proposed_end, min_allowed_angle)
 
-            angles = np.linspace(
-                start,
-                angle_end,
-                num=N,
-                endpoint=True,
-            )
+            angles = np.linspace(start, angle_end, num=N, endpoint=True)
 
         for i, angle in enumerate(angles):
 
@@ -1636,9 +1745,9 @@ class Flomni(
                     self._subtomo_offset = 0
 
                 else:
-                    if subtomo_number % 2:    # odd = forward direction
+                    if subtomo_number % 2:  # odd = forward direction
                         self._subtomo_offset = round(sa / step)
-                    else:                     # even = reverse direction
+                    else:  # even = reverse direction
                         self._subtomo_offset = round((180 - sa) / step)
 
             # progress index must always increase
@@ -1647,22 +1756,24 @@ class Flomni(
 
             # existing progress fields
             self.progress["subtomo_total_projections"] = int(180 / self.tomo_angle_stepsize)
-            self.progress["projection"] = (subtomo_number - 1) * self.progress["subtomo_total_projections"] + self.progress["subtomo_projection"]
+            self.progress["projection"] = (subtomo_number - 1) * self.progress[
+                "subtomo_total_projections"
+            ] + self.progress["subtomo_projection"]
             self.progress["total_projections"] = 180 / self.tomo_angle_stepsize * 8
             self.progress["angle"] = angle
 
             # finally do the scan at this angle
             self._tomo_scan_at_angle(angle, subtomo_number)
 
-
     def _tomo_scan_at_angle(self, angle, subtomo_number):
         successful = False
         error_caught = False
         if 0 <= angle < 180.05:
+            self.progress["heartbeat"] = datetime.datetime.now().isoformat()
             print(f"Starting flOMNI scan for angle {angle} in subtomo {subtomo_number}")
             self._print_progress()
             while not successful:
-                #self.bl_chk._bl_chk_start()
+                # self.bl_chk._bl_chk_start()
                 if not self.special_angles:
                     self._current_special_angles = []
                 if self._current_special_angles:
@@ -1697,12 +1808,14 @@ class Flomni(
         """start a tomo scan"""
 
         if not self._check_eye_out_and_optics_in():
-            print("Attention: The setup is not in measurement condition.\nXray eye might be IN or the Xray optics OUT.")
+            print(
+                "Attention: The setup is not in measurement condition.\nXray eye might be IN or the Xray optics OUT."
+            )
             if self.OMNYTools.yesno("Shall I continue?", "n"):
-            print("OK")
-        else:
-            print("Stopping.")
-            return
+                print("OK")
+            else:
+                print("Stopping.")
+                return
 
         self.flomnigui_show_progress()
 
@@ -1716,20 +1829,22 @@ class Flomni(
             or (self.tomo_type == 3 and projection_number == None)
         ):
 
-            # pylint: disable=undefined-variable
-            # if bec.active_account != "":
-            #     self.tomo_id = self.add_sample_database(
-            #         self.sample_name,
-            #         str(datetime.date.today()),
-            #         bec.active_account,
-            #         bec.queue.next_scan_number,
-            #         "flomni",
-            #         "test additional info",
-            #         "BEC",
-            #     )
-            #     self.write_pdf_report()
-            # else:
-            self.tomo_id = 0
+            #pylint: disable=undefined-variable
+            if bec.active_account != "":
+                self.tomo_id = self.add_sample_database(
+                    self.sample_name,
+                    str(datetime.date.today()),
+                    bec.active_account,
+                    bec.queue.next_scan_number,
+                    "flomni",
+                    "test additional info",
+                    "BEC",
+                )
+                self.write_pdf_report()
+            else:
+                self.tomo_id = 0
+            self.write_pdf_report()
+            self.progress["tomo_start_time"] = datetime.datetime.now().isoformat()
 
         with scans.dataset_id_on_hold:
             if self.tomo_type == 1:
@@ -1738,7 +1853,7 @@ class Flomni(
                 for ii in range(subtomo_start, 9):
                     self.sub_tomo_scan(ii, start_angle=start_angle)
                     start_angle = None
-    
+
             elif self.tomo_type == 2:
                 # Golden ratio tomography
                 previous_subtomo_number = -1
@@ -1749,7 +1864,6 @@ class Flomni(
                 while True:
                     angle, subtomo_number = self._golden(ii, self.golden_ratio_bunch_size, 180, 1)
                     if previous_subtomo_number != subtomo_number:
-                        self._write_subtomo_to_scilog(subtomo_number)
                         if (
                             subtomo_number % 2 == 1
                             and ii > 10
@@ -1797,7 +1911,6 @@ class Flomni(
                         ii, int(180 / self.tomo_angle_stepsize), 180, 1, 0
                     )
                     if previous_subtomo_number != subtomo_number:
-                        self._write_subtomo_to_scilog(subtomo_number)
                         if (
                             subtomo_number % 2 == 1
                             and ii > 10
@@ -1834,19 +1947,47 @@ class Flomni(
             else:
                 raise FlomniError("undefined tomo type")
 
-        self.progress['projection'] = self.progress['total_projections']
+        self.progress["projection"] = self.progress["total_projections"]
         self.progress["subtomo_projection"] = self.progress["subtomo_total_projections"]
-        self._print_progress()             
+        self._print_progress()
         self.OMNYTools.printgreenbold("Tomoscan finished")
 
+    @staticmethod
+    def _format_duration(seconds: float) -> str:
+        """Format a duration in seconds as a human-readable string, e.g. '2h 03m 15s'."""
+        seconds = int(seconds)
+        h, remainder = divmod(seconds, 3600)
+        m, s = divmod(remainder, 60)
+        if h > 0:
+            return f"{h}h {m:02d}m {s:02d}s"
+        if m > 0:
+            return f"{m}m {s:02d}s"
+        return f"{s}s"
+
     def _print_progress(self):
+        # --- compute and store estimated remaining time -----------------------
+        start_str = self.progress.get("tomo_start_time")
+        projection = self.progress["projection"]
+        total = self.progress["total_projections"]
+        if start_str is not None and total > 0 and projection > 9:
+            elapsed = (
+                datetime.datetime.now() - datetime.datetime.fromisoformat(start_str)
+            ).total_seconds()
+            rate = projection / elapsed  # projections per second
+            remaining_s = (total - projection) / rate
+            self.progress["estimated_remaining_time"] = remaining_s
+            eta_str = self._format_duration(remaining_s)
+        else:
+            eta_str = "N/A"
+        # ----------------------------------------------------------------------
         print("\x1b[95mProgress report:")
         print(f"Tomo type: ....................... {self.progress['tomo_type']}")
         print(f"Projection: ...................... {self.progress['projection']:.0f}")
         print(f"Total projections expected ....... {self.progress['total_projections']}")
         print(f"Angle: ........................... {self.progress['angle']}")
         print(f"Current subtomo: ................. {self.progress['subtomo']}")
-        print(f"Current projection within subtomo: {self.progress['subtomo_projection']}\x1b[0m")
+        print(f"Current projection within subtomo: {self.progress['subtomo_projection']}")
+        print(f"Estimated remaining time: ........ {eta_str}\x1b[0m")
         self._flomnigui_update_progress()
 
     def add_sample_database(
@@ -1870,7 +2011,6 @@ class Flomni(
             return
 
         self.tomo_scan_projection(angle)
-        self.tomo_reconstruct()
 
     def _golden(self, ii, howmany_sorted, maxangle, reverse=False):
         """returns the iis golden ratio angle of sorted bunches of howmany_sorted and its subtomo number"""
@@ -1930,9 +2070,7 @@ class Flomni(
         )
 
     def _write_tomo_scan_number(self, scan_number: int, angle: float, subtomo_number: int) -> None:
-        tomo_scan_numbers_file = os.path.expanduser(
-            "~/data/raw/logs/tomography_scannumbers.txt"
-        )
+        tomo_scan_numbers_file = os.path.expanduser("~/data/raw/logs/tomography_scannumbers.txt")
         with open(tomo_scan_numbers_file, "a+") as out_file:
             # pylint: disable=undefined-variable
             out_file.write(
@@ -1943,7 +2081,6 @@ class Flomni(
 
         dev.rtx.controller.laser_tracker_check_signalstrength()
 
-
         scans = builtins.__dict__.get("scans")
 
         # additional_correction = self.align.compute_additional_correction(angle)
@@ -1978,7 +2115,7 @@ class Flomni(
                     f"{str(datetime.datetime.now())}: flomni scan projection at angle {angle}, scan"
                     f" number {bec.queue.next_scan_number}.\n"
                 )
-                # self.write_to_scilog(log_message, ["BEC_scans", self.sample_name])
+
                 scans.flomni_fermat_scan(
                     fovx=self.fovx,
                     fovy=self.fovy,
@@ -1991,6 +2128,9 @@ class Flomni(
                     corridor_size=corridor_size,
                 )
 
+        self.tomo_reconstruct()
+
+
     def tomo_parameters(self):
         """print and update the tomo parameters"""
         print("Current settings:")
@@ -2033,7 +2173,6 @@ class Flomni(
                 )
         print(f"\nSample name: {self.sample_name}\n")
 
-
         if self.OMNYTools.yesno("Are these parameters correctly set for your scan?", "y"):
             print("... excellent!")
         else:
@@ -2130,19 +2269,21 @@ class Flomni(
             + ' 888    888  "Y88888P"  888       888 888    Y888 8888888 \n'
         )
         padding = 20
-        fovxy = f"{self.fovx:.2f}/{self.fovy:.2f}"
-        stitching = f"{self.stitch_x:.2f}/{self.stitch_y:.2f}"
+        fovxy = f"{self.fovx:.1f}/{self.fovy:.1f}"
+        stitching = f"{self.stitch_x:.0f}/{self.stitch_y:.0f}"
         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",
@@ -2151,20 +2292,38 @@ 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]
-        )
-        self.client.logbook.send_logbook_message(msg)
+        # msg = bec.tomo_progress.tomo_progressMessage()
+        # 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}", "flOMNI", self.sample_name]
+        # )
+        # self.client.tomo_progress.send_tomo_progress_message("~/data/raw/documentation/tomo_scan_ID_{self.tomo_id}.pdf").send()
+        import csaxs_bec
+
+
+        # Ensure this is a Path object, not a string
+        csaxs_bec_basepath = Path(csaxs_bec.__file__)
+
+        logo_file_rel = "flOMNI.png"
+
+        # Build the absolute path correctly
+        logo_file = (
+            csaxs_bec_basepath.parent
+            / "bec_ipython_client"
+            / "plugins"
+            / "flomni"
+            / logo_file_rel
+        ).resolve()
+        print(logo_file)
+        bec.messaging.scilog.new().add_attachment(logo_file, width=200).add_text(content.replace("\n", "<br>")).add_tags("tomoscan").send()
 
 
 if __name__ == "__main__":
@@ -2181,4 +2340,4 @@ if __name__ == "__main__":
     builtins.__dict__["bec"] = bec
     builtins.__dict__["umv"] = umv
     flomni = Flomni(bec)
-    flomni.start_x_ray_eye_alignment()
+    flomni.start_x_ray_eye_alignment()

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/gui_tools.py

@@ -18,10 +18,17 @@ class flomniGuiToolsError(Exception):
 
 
 class flomniGuiTools:
+    GUI_RPC_TIMEOUT = 20
 
     def __init__(self):
         self.text_box = None
         self.progressbar = None
+        self.flomni_window = None
+        self.xeyegui = None
+        self.pdf_viewer = None
+        self.idle_text_box = None
+        self.camera_gripper_image = None
+        self.camera_overview_image = None
 
     def set_client(self, client):
         self.client = client
@@ -29,9 +36,10 @@ class flomniGuiTools:
 
     def flomnigui_show_gui(self):
         if "flomni" in self.gui.windows:
+            self.flomni_window = self.gui.windows["flomni"]
             self.gui.flomni.raise_window()
         else:
-            self.gui.new("flomni")
+            self.flomni_window = self.gui.new("flomni", timeout=self.GUI_RPC_TIMEOUT)
             time.sleep(1)
 
     def flomnigui_stop_gui(self):
@@ -42,9 +50,11 @@ class flomniGuiTools:
 
     def flomnigui_show_xeyealign(self):
         self.flomnigui_show_gui()
-        if self._flomnigui_check_attribute_not_exists("xeyegui"):
+        if self._flomnigui_is_missing("xeyegui"):
             self.flomnigui_remove_all_docks()
-            self.xeyegui = self.gui.flomni.new("XRayEye", object_name="xrayeye")
+            self.xeyegui = self.gui.flomni.new(
+                "XRayEye", object_name="xrayeye", timeout=self.GUI_RPC_TIMEOUT
+            )
         # start live
         if not dev.cam_xeye.live_mode_enabled.get():
             dev.cam_xeye.live_mode_enabled.put(True)
@@ -52,9 +62,11 @@ class flomniGuiTools:
 
     def flomnigui_show_xeyealign_fittab(self):
         self.flomnigui_show_gui()
-        if self._flomnigui_check_attribute_not_exists("xeyegui"):
+        if self._flomnigui_is_missing("xeyegui"):
             self.flomnigui_remove_all_docks()
-            self.xeyegui = self.gui.flomni.new("XRayEye")
+            self.xeyegui = self.gui.flomni.new(
+                "XRayEye", object_name="xrayeye", timeout=self.GUI_RPC_TIMEOUT
+            )
         self.xeyegui.switch_tab("fit")
 
     def _flomnigui_check_attribute_not_exists(self, attribute_name):
@@ -70,31 +82,39 @@ class flomniGuiTools:
                     return False
         return True
 
+    def _flomnigui_is_missing(self, attribute_name):
+        widget = getattr(self, attribute_name, None)
+        if widget is None:
+            return True
+        if hasattr(widget, "_is_deleted") and widget._is_deleted():
+            return True
+        return False
+
     def flomnigui_show_cameras(self):
         self.flomnigui_show_gui()
         if self._flomnigui_check_attribute_not_exists(
             "cam_flomni_gripper"
         ) or self._flomnigui_check_attribute_not_exists("cam_flomni_overview"):
             self.flomnigui_remove_all_docks()
-            camera_gripper_image = self.gui.flomni.new("Image")
+            self.camera_gripper_image = self.gui.flomni.new("Image")
             if self._flomnicam_check_device_exists(dev.cam_flomni_gripper):
-                camera_gripper_image.image(device="cam_flomni_gripper", signal="preview")
-                camera_gripper_image.lock_aspect_ratio = True
-                camera_gripper_image.enable_fps_monitor = True
-                camera_gripper_image.enable_toolbar = False
-                camera_gripper_image.outer_axes = False
-                camera_gripper_image.inner_axes = False
+                self.camera_gripper_image.image(device="cam_flomni_gripper", signal="preview")
+                self.camera_gripper_image.lock_aspect_ratio = True
+                self.camera_gripper_image.enable_fps_monitor = True
+                self.camera_gripper_image.enable_toolbar = False
+                self.camera_gripper_image.outer_axes = False
+                self.camera_gripper_image.inner_axes = False
                 dev.cam_flomni_gripper.start_live_mode()
             else:
                 print("Cannot open camera_gripper. Device does not exist.")
-            camera_overview_image = self.gui.flomni.new("Image")
+            self.camera_overview_image = self.gui.flomni.new("Image")
             if self._flomnicam_check_device_exists(dev.cam_flomni_overview):
-                camera_overview_image.image(device="cam_flomni_overview", signal="preview")
-                camera_overview_image.lock_aspect_ratio = True
-                camera_overview_image.enable_fps_monitor = True
-                camera_overview_image.enable_toolbar = False
-                camera_overview_image.outer_axes = False
-                camera_overview_image.inner_axes = False
+                self.camera_overview_image.image(device="cam_flomni_overview", signal="preview")
+                self.camera_overview_image.lock_aspect_ratio = True
+                self.camera_overview_image.enable_fps_monitor = True
+                self.camera_overview_image.enable_toolbar = False
+                self.camera_overview_image.outer_axes = False
+                self.camera_overview_image.inner_axes = False
                 dev.cam_flomni_overview.start_live_mode()
             else:
                 print("Cannot open camera_overview. Device does not exist.")
@@ -104,15 +124,20 @@ class flomniGuiTools:
         # dev.cam_flomni_gripper.stop_live_mode()
         # dev.cam_xeye.live_mode = False
         if hasattr(self.gui, "flomni"):
-            self.gui.flomni.delete_all()
+            self.gui.flomni.delete_all(timeout=self.GUI_RPC_TIMEOUT)
         self.progressbar = None
         self.text_box = None
+        self.xeyegui = None
+        self.pdf_viewer = None
+        self.idle_text_box = None
+        self.camera_gripper_image = None
+        self.camera_overview_image = None
 
     def flomnigui_idle(self):
         self.flomnigui_show_gui()
-        if self._flomnigui_check_attribute_not_exists("idle_text_box"):
+        if self._flomnigui_is_missing("idle_text_box"):
             self.flomnigui_remove_all_docks()
-            idle_text_box = self.gui.flomni.new("TextBox")
+            self.idle_text_box = self.gui.flomni.new("TextBox")
         text = (
             "<pre>"
             + "██████╗ ███████╗ ██████╗     ███████╗██╗      ██████╗ ███╗   ███╗███╗   ██╗██╗\n"
@@ -123,7 +148,7 @@ class flomniGuiTools:
             + "╚═════╝ ╚══════╝ ╚═════╝     ╚═╝     ╚══════╝ ╚═════╝ ╚═╝     ╚═╝╚═╝  ╚═══╝╚═╝\n"
             + "</pre>"
         )
-        idle_text_box.set_html_text(text)
+        self.idle_text_box.set_html_text(text)
 
     def flomnigui_docs(self, filename: str | None = None):
         import csaxs_bec
@@ -167,7 +192,7 @@ class flomniGuiTools:
         # --- GUI handling (active existence check) ----------------------------
         self.flomnigui_show_gui()
 
-        if self._flomnigui_check_attribute_not_exists("PdfViewerWidget"):
+        if self._flomnigui_is_missing("pdf_viewer"):
             self.flomnigui_remove_all_docks()
             self.pdf_viewer = self.gui.flomni.new(widget="PdfViewerWidget")
 
@@ -185,7 +210,7 @@ class flomniGuiTools:
 
     def flomnigui_show_progress(self):
         self.flomnigui_show_gui()
-        if self._flomnigui_check_attribute_not_exists("progressbar"):
+        if self._flomnigui_is_missing("progressbar"):
             self.flomnigui_remove_all_docks()
             # Add a new dock with a RingProgressBar widget
             self.progressbar = self.gui.flomni.new("RingProgressBar")
@@ -198,6 +223,14 @@ class flomniGuiTools:
         self._flomnigui_update_progress()
 
     def _flomnigui_update_progress(self):
+        """Update the progress ring bar and center label from the current progress state.
+
+        ``self.progress`` is backed by the BEC global variable ``tomo_progress``
+        (see :class:`_ProgressProxy` in ``flomni.py``), so this method reflects
+        the live state that is also accessible from other BEC client sessions via::
+
+            client.get_global_var("tomo_progress")
+        """
         main_progress_ring = self.progressbar.rings[0]
         subtomo_progress_ring = self.progressbar.rings[1]
         if self.progressbar is not None:
@@ -210,6 +243,31 @@ class flomniGuiTools:
             main_progress_ring.set_value(progress)
             subtomo_progress_ring.set_value(subtomo_progress)
 
+            # --- format start time for display --------------------------------
+            start_str = self.progress.get("tomo_start_time")
+            if start_str is not None:
+                import datetime as _dt
+                start_display = _dt.datetime.fromisoformat(start_str).strftime("%Y-%m-%d %H:%M:%S")
+            else:
+                start_display = "N/A"
+
+            # --- format estimated remaining time ------------------------------
+            remaining_s = self.progress.get("estimated_remaining_time")
+            if remaining_s is not None and remaining_s >= 0:
+                import datetime as _dt
+                remaining_s = int(remaining_s)
+                h, rem = divmod(remaining_s, 3600)
+                m, s = divmod(rem, 60)
+                if h > 0:
+                    eta_display = f"{h}h {m:02d}m {s:02d}s"
+                elif m > 0:
+                    eta_display = f"{m}m {s:02d}s"
+                else:
+                    eta_display = f"{s}s"
+            else:
+                eta_display = "N/A"
+            # ------------------------------------------------------------------
+
             text = (
                 f"Progress report:\n"
                 f" Tomo type:  {self.progress['tomo_type']}\n"
@@ -218,7 +276,9 @@ class flomniGuiTools:
                 f" Angle:  {self.progress['angle']:.1f}\n"
                 f" Current subtomo:  {self.progress['subtomo']}\n"
                 f" Current projection within subtomo: {self.progress['subtomo_projection']}\n"
-                f" Total projections per subtomo:  {int(self.progress['subtomo_total_projections'])}"
+                f" Total projections per subtomo:  {int(self.progress['subtomo_total_projections'])}\n"
+                f" Scan started:  {start_display}\n"
+                f" Est. remaining:  {eta_display}"
             )
             self.progressbar.set_center_label(text)
 

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/bec_ipython_client/plugins/omny/omny_general_tools.py

@@ -234,9 +234,10 @@ class TomoIDManager:
         )
     """
 
-    OMNY_URL = "https://omny.web.psi.ch/samples/newmeasurement.php"
-    OMNY_USER = "omny"
-    OMNY_PASSWORD = "samples"
+    #OMNY_URL = "https://omny.web.psi.ch/samples/newmeasurement.php"
+    OMNY_URL = "https://v1p0zyg2w9n2k9c1.myfritz.net/samples/newmeasurement.php"
+    OMNY_USER = ""
+    OMNY_PASSWORD = ""
     TMP_FILE = "/tmp/currsamplesnr.txt"
 
     def register(
@@ -273,9 +274,14 @@ class TomoIDManager:
             f"&additional={additional_info}"
             f"&user={user}"
         )
+        # subprocess.run(
+        #     f"wget --user={self.OMNY_USER} --password={self.OMNY_PASSWORD}"
+        #     f" -q -O {self.TMP_FILE} '{url}'",
+        #     shell=True,
+        # )
+        #print(url)
         subprocess.run(
-            f"wget --user={self.OMNY_USER} --password={self.OMNY_PASSWORD}"
-            f" -q -O {self.TMP_FILE} '{url}'",
+            f"wget -q -O {self.TMP_FILE} '{url}'",
             shell=True,
         )
         with open(self.TMP_FILE) as f:

csaxs_bec/bec_ipython_client/plugins/omny/omny_webpage_generator.py

@@ -0,0 +1,96 @@
+"""
+omny/webpage_generator.py
+==========================
+OMNY-specific webpage generator subclass.
+
+Integration (inside the OMNY __init__ / startup):
+--------------------------------------------------
+    from csaxs_bec.bec_ipython_client.plugins.omny.webpage_generator import (
+        OmnyWebpageGenerator,
+    )
+    self._webpage_gen = OmnyWebpageGenerator(
+        bec_client=client,
+        output_dir="~/data/raw/webpage/",
+    )
+    self._webpage_gen.start()
+
+Or use the factory (auto-selects by session name "omny"):
+---------------------------------------------------------
+    from csaxs_bec.bec_ipython_client.plugins.flomni.webpage_generator import (
+        make_webpage_generator,
+    )
+    self._webpage_gen = make_webpage_generator(bec, output_dir="~/data/raw/webpage/")
+    self._webpage_gen.start()
+
+Interactive helpers:
+--------------------
+    omny._webpage_gen.status()
+    omny._webpage_gen.verbosity = 2
+    omny._webpage_gen.stop()
+    omny._webpage_gen.start()
+"""
+
+from pathlib import Path
+
+from csaxs_bec.bec_ipython_client.plugins.flomni.webpage_generator import (
+    WebpageGeneratorBase,
+    _safe_get,
+    _safe_float,
+    _gvar,
+)
+
+
+class OmnyWebpageGenerator(WebpageGeneratorBase):
+    """
+    OMNY-specific webpage generator.
+    Logo: OMNY.png from the same directory as this file.
+
+    Override _collect_setup_data() to add OMNY-specific temperatures,
+    sample name, and measurement settings.
+
+    The old OMNY spec webpage showed:
+        - Cryo temperatures (XOMNY-TEMP-CRYO-A/B)
+        - Per-channel temperatures (XOMNY-TEMP1..48)
+        - Dewar pressure / LN2 flow
+        - Interferometer strengths (OINTERF)
+    Map these to BEC device paths below once available.
+    """
+
+    # TODO: fill in OMNY-specific device paths
+    # label -> dotpath under device_manager.devices
+    _TEMP_MAP = {
+        # "Sample (cryo A)": "omny_temp.cryo_a",
+        # "Cryo head (B)":   "omny_temp.cryo_b",
+    }
+
+    def _logo_path(self):
+        return Path(__file__).parent / "OMNY.png"
+
+    def _collect_setup_data(self) -> dict:
+        # ── OMNY-specific data goes here ──────────────────────────────
+        # Uncomment and adapt when device names are known:
+        #
+        # dm = self._bec.device_manager
+        # sample_name = _safe_get(dm, "omny_samples.sample_names.sample0") or "N/A"
+        # temperatures = {
+        #     label: _safe_float(_safe_get(dm, path))
+        #     for label, path in self._TEMP_MAP.items()
+        # }
+        # settings = {
+        #     "Sample name":   sample_name,
+        #     "FOV x / y":     ...,
+        #     "Exposure time": _gvar(self._bec, "tomo_countingtime", ".3f", " s"),
+        #     "Angle step":    _gvar(self._bec, "tomo_angle_stepsize", ".2f", "\u00b0"),
+        # }
+        # return {
+        #     "type":         "omny",
+        #     "sample_name":  sample_name,
+        #     "temperatures": temperatures,
+        #     "settings":     settings,
+        # }
+
+        # Placeholder — returns minimal info until implemented
+        return {
+            "type": "omny",
+            # OMNY-specific data here
+        }

csaxs_bec/bec_widgets/widgets/client.py

@@ -38,12 +38,14 @@ class XRayEye(RPCBase):
         None
         """
 
+    @rpc_timeout(20)
     @rpc_call
     def on_live_view_enabled(self, enabled: "bool"):
         """
         None
         """
 
+    @rpc_timeout(20)
     @rpc_call
     def on_motors_enable(self, x_enable: "bool", y_enable: "bool"):
         """
@@ -54,6 +56,7 @@ class XRayEye(RPCBase):
             y_enable(bool): enable y motor controls
         """
 
+    @rpc_timeout(20)
     @rpc_call
     def enable_submit_button(self, enable: "bool"):
         """
@@ -90,12 +93,14 @@ class XRayEye(RPCBase):
         None
         """
 
+    @rpc_timeout(20)
     @rpc_call
     def switch_tab(self, tab: "str"):
         """
         None
         """
 
+    @rpc_timeout(20)
     @rpc_call
     def submit_fit_array(self, fit_array):
         """

csaxs_bec/bec_widgets/widgets/xray_eye/x_ray_eye.py

@@ -4,6 +4,7 @@ from bec_lib import bec_logger
 from bec_lib.endpoints import MessageEndpoints
 from bec_qthemes import material_icon
 from bec_widgets import BECWidget, SafeProperty, SafeSlot
+from bec_widgets.utils.rpc_decorator import rpc_timeout
 from bec_widgets.widgets.plots.image.image import Image
 from bec_widgets.widgets.plots.waveform.waveform import Waveform
 from bec_widgets.widgets.plots.image.setting_widgets.image_roi_tree import ROIPropertyTree
@@ -367,6 +368,7 @@ class XRayEye(BECWidget, QWidget):
         return self.message_line_edit.toPlainText()
 
     @user_message.setter
+    @rpc_timeout(20)
     def user_message(self, message: str):
         self.message_line_edit.setText(message)
 
@@ -375,6 +377,7 @@ class XRayEye(BECWidget, QWidget):
         return self.sample_name_line_edit.text()
 
     @sample_name.setter
+    @rpc_timeout(20)
     def sample_name(self, message: str):
         self.sample_name_line_edit.setText(message)
 
@@ -395,6 +398,7 @@ class XRayEye(BECWidget, QWidget):
     ################################################################################
 
     @SafeSlot(str)
+    @rpc_timeout(20)
     def switch_tab(self, tab: str):
         if tab == "fit":
             self.tab_widget.setCurrentIndex(1)
@@ -412,6 +416,7 @@ class XRayEye(BECWidget, QWidget):
         return roi.get_coordinates()
 
     @SafeSlot(bool)
+    @rpc_timeout(20)
     def on_live_view_enabled(self, enabled: bool):
         logger.info(f"Live view is enabled: {enabled}")
         self.live_preview_toggle.blockSignals(True)
@@ -460,6 +465,7 @@ class XRayEye(BECWidget, QWidget):
         self.shutter_toggle.blockSignals(False)
 
     @SafeSlot(bool, bool)
+    @rpc_timeout(20)
     def on_motors_enable(self, x_enable: bool, y_enable: bool):
         """
         Enable/Disable motor controls
@@ -472,6 +478,7 @@ class XRayEye(BECWidget, QWidget):
         self.motor_control_2d.enable_controls_ver(y_enable)
 
     @SafeSlot(bool)
+    @rpc_timeout(20)
     def enable_submit_button(self, enable: bool):
         """
         Enable/disable submit button.
@@ -509,6 +516,7 @@ class XRayEye(BECWidget, QWidget):
         print(f"meta: {meta}")
 
     @SafeSlot()
+    @rpc_timeout(20)
     def submit_fit_array(self, fit_array):
         self.tab_widget.setCurrentIndex(1)
         # self.fix_x.title = " got fit array"

csaxs_bec/device_configs/bl_endstation.yaml

@@ -72,7 +72,7 @@ xbpm3x:
     # precision: 3
     # tolerance: 0.005
   enabled: true
-  onFailure: buffer
+  onFailure: retry
   readOnly: false
   readoutPriority: baseline
   connectionTimeout: 20
@@ -95,7 +95,7 @@ xbpm3y:
     # precision: 3
     # tolerance: 0.005
   enabled: true
-  onFailure: buffer
+  onFailure: retry
   readOnly: false
   readoutPriority: baseline
   connectionTimeout: 20
@@ -118,7 +118,7 @@ sl3trxi:
     # precision: 3
     # tolerance: 0.005
   enabled: true
-  onFailure: buffer
+  onFailure: retry
   readOnly: false
   readoutPriority: baseline
   connectionTimeout: 20
@@ -141,7 +141,7 @@ sl3trxo:
     # precision: 3
     # tolerance: 0.005
   enabled: true
-  onFailure: buffer
+  onFailure: retry
   readOnly: false
   readoutPriority: baseline
   connectionTimeout: 20
@@ -164,7 +164,7 @@ sl3trxb:
     # precision: 3
     # tolerance: 0.005
   enabled: true
-  onFailure: buffer
+  onFailure: retry
   readOnly: false
   readoutPriority: baseline
   connectionTimeout: 20
@@ -187,7 +187,7 @@ sl3trxt:
     # precision: 3
     # tolerance: 0.005
   enabled: true
-  onFailure: buffer
+  onFailure: retry
   readOnly: false
   readoutPriority: baseline
   connectionTimeout: 20
@@ -210,7 +210,7 @@ fast_shutter_n1_x:
     # precision: 3
     # tolerance: 0.005
   enabled: true
-  onFailure: buffer
+  onFailure: retry
   readOnly: false
   readoutPriority: baseline
   connectionTimeout: 20
@@ -234,7 +234,7 @@ fast_shutter_o1_x:
     # precision: 3
     # tolerance: 0.005
   enabled: true
-  onFailure: buffer
+  onFailure: retry
   readOnly: false
   readoutPriority: baseline
   connectionTimeout: 20
@@ -257,7 +257,7 @@ fast_shutter_o2_x:
     # precision: 3
     # tolerance: 0.005
   enabled: true
-  onFailure: buffer
+  onFailure: retry
   readOnly: false
   readoutPriority: baseline
   connectionTimeout: 20
@@ -280,7 +280,7 @@ filter_array_1_x:
     # precision: 3
     # tolerance: 0.005
   enabled: true
-  onFailure: buffer
+  onFailure: retry
   readOnly: false
   readoutPriority: baseline
   connectionTimeout: 20
@@ -303,7 +303,7 @@ filter_array_2_x:
     # precision: 3
     # tolerance: 0.005
   enabled: true
-  onFailure: buffer
+  onFailure: retry
   readOnly: false
   readoutPriority: baseline
   connectionTimeout: 20
@@ -326,7 +326,7 @@ filter_array_3_x:
     # precision: 3
     # tolerance: 0.005
   enabled: true
-  onFailure: buffer
+  onFailure: retry
   readOnly: false
   readoutPriority: baseline
   connectionTimeout: 20
@@ -349,7 +349,7 @@ filter_array_4_x:
     # precision: 3
     # tolerance: 0.005
   enabled: true
-  onFailure: buffer
+  onFailure: retry
   readOnly: false
   readoutPriority: baseline
   connectionTimeout: 20
@@ -372,7 +372,7 @@ sl4trxi:
     # precision: 3
     # tolerance: 0.005
   enabled: true
-  onFailure: buffer
+  onFailure: retry
   readOnly: false
   readoutPriority: baseline
   connectionTimeout: 20
@@ -395,7 +395,7 @@ sl4trxo:
     # precision: 3
     # tolerance: 0.005
   enabled: true
-  onFailure: buffer
+  onFailure: retry
   readOnly: false
   readoutPriority: baseline
   connectionTimeout: 20
@@ -418,7 +418,7 @@ sl4trxb:
     # precision: 3
     # tolerance: 0.005
   enabled: true
-  onFailure: buffer
+  onFailure: retry
   readOnly: false
   readoutPriority: baseline
   connectionTimeout: 20
@@ -441,7 +441,7 @@ sl4trxt:
     # precision: 3
     # tolerance: 0.005
   enabled: true
-  onFailure: buffer
+  onFailure: retry
   readOnly: false
   readoutPriority: baseline
   connectionTimeout: 20
@@ -466,7 +466,7 @@ sl5trxi:
     # precision: 3
     # tolerance: 0.005
   enabled: true
-  onFailure: buffer
+  onFailure: retry
   readOnly: false
   readoutPriority: baseline
   connectionTimeout: 20
@@ -489,7 +489,7 @@ sl5trxo:
     # precision: 3
     # tolerance: 0.005
   enabled: true
-  onFailure: buffer
+  onFailure: retry
   readOnly: false
   readoutPriority: baseline
   connectionTimeout: 20
@@ -512,7 +512,7 @@ sl5trxb:
     # precision: 3
     # tolerance: 0.005
   enabled: true
-  onFailure: buffer
+  onFailure: retry
   readOnly: false
   readoutPriority: baseline
   connectionTimeout: 20
@@ -535,7 +535,7 @@ sl5trxt:
     # precision: 3
     # tolerance: 0.005
   enabled: true
-  onFailure: buffer
+  onFailure: retry
   readOnly: false
   readoutPriority: baseline
   connectionTimeout: 20
@@ -544,6 +544,66 @@ sl5trxt:
     # bl_smar_stage to use csaxs reference method. assign number according to axis channel
     bl_smar_stage: 5
 
+sl5ch:
+  description: ESbox1 slit 5 center horizontal
+  deviceClass: ophyd_devices.devices.virtual_slit.VirtualSlitCenter
+  deviceConfig:
+    left_slit: sl5trxi
+    right_slit: sl5trxo
+    offset: 0
+  enabled: true
+  onFailure: retry
+  readOnly: false
+  readoutPriority: baseline
+  needs:
+    - sl5trxi
+    - sl5trxo
+
+sl5wh:
+  description: ESbox1 slit 5 width horizontal
+  deviceClass: ophyd_devices.devices.virtual_slit.VirtualSlitWidth
+  deviceConfig:
+    left_slit: sl5trxi
+    right_slit: sl5trxo
+    offset: 0
+  enabled: true
+  onFailure: retry
+  readOnly: false
+  readoutPriority: baseline
+  needs:
+    - sl5trxi
+    - sl5trxo
+
+sl5cv:
+  description: ESbox1 slit 5 center vertical
+  deviceClass: ophyd_devices.devices.virtual_slit.VirtualSlitCenter
+  deviceConfig:
+    left_slit: sl5trxb
+    right_slit: sl5trxt
+    offset: 0
+  enabled: true
+  onFailure: retry
+  readOnly: false
+  readoutPriority: baseline
+  needs:
+    - sl5trxb
+    - sl5trxt
+
+sl5wv:
+  description: ESbox1 slit 5 width vertical
+  deviceClass: ophyd_devices.devices.virtual_slit.VirtualSlitWidth
+  deviceConfig:
+    left_slit: sl5trxb
+    right_slit: sl5trxt
+    offset: 0
+  enabled: true
+  onFailure: retry
+  readOnly: false
+  readoutPriority: baseline
+  needs:
+    - sl5trxb
+    - sl5trxt
+
 xbimtrx:
   description: ESbox2 beam intensity monitor x movement
   deviceClass: csaxs_bec.devices.smaract.smaract_ophyd.SmaractMotor
@@ -558,7 +618,7 @@ xbimtrx:
     # precision: 3
     # tolerance: 0.005
   enabled: true
-  onFailure: buffer
+  onFailure: retry
   readOnly: false
   readoutPriority: baseline
   connectionTimeout: 20
@@ -581,7 +641,7 @@ xbimtry:
     # precision: 3
     # tolerance: 0.005
   enabled: true
-  onFailure: buffer
+  onFailure: retry
   readOnly: false
   readoutPriority: baseline
   connectionTimeout: 20
@@ -589,3 +649,295 @@ xbimtry:
     init_position: 0
     # bl_smar_stage to use csaxs reference method. assign number according to axis channel
     bl_smar_stage: 1
+
+
+
+################### XBOX related ###################
+# we assue the epics settings for resolution, velocity etc. are correct
+# we do not overwrite from here
+
+aptrx:
+  description: Aperture pinhole X
+  deviceClass: ophyd_devices.devices.psi_motor.EpicsUserMotorVME
+  deviceConfig:
+    prefix: X12SA-ES1-PIN1:TRX1
+  deviceTags:
+    - cSAXS_ES
+  onFailure: retry
+  enabled: true
+  readoutPriority: baseline
+  softwareTrigger: false
+
+aptry:
+  description: Aperture pinhole Y
+  deviceClass: ophyd_devices.devices.psi_motor.EpicsUserMotorVME
+  deviceConfig:
+    prefix: X12SA-ES1-PIN1:TRY1
+  deviceTags:
+    - cSAXS_ES
+  onFailure: retry
+  enabled: true
+  readoutPriority: baseline
+  softwareTrigger: false
+
+ebtrx:
+  description: Exposure box aperture X
+  deviceClass: ophyd_devices.devices.psi_motor.EpicsUserMotorVME
+  deviceConfig:
+    prefix: X12SA-ES1-EB:TRX1
+  deviceTags:
+    - cSAXS_ES
+  onFailure: retry
+  enabled: true
+  readoutPriority: baseline
+  softwareTrigger: false
+
+ebtry:
+  description: Exposure box aperture Y
+  deviceClass: ophyd_devices.devices.psi_motor.EpicsUserMotorVME
+  deviceConfig:
+    prefix: X12SA-ES1-EB:TRY1
+  deviceTags:
+    - cSAXS_ES
+  onFailure: retry
+  enabled: true
+  readoutPriority: baseline
+  softwareTrigger: false
+
+ebtrz:
+  description: Exposure box aperture Z
+  deviceClass: ophyd_devices.devices.psi_motor.EpicsUserMotorVME
+  deviceConfig:
+    prefix: X12SA-ES1-EB:TRZ1
+  deviceTags:
+    - cSAXS_ES
+  onFailure: retry
+  enabled: true
+  readoutPriority: baseline
+  softwareTrigger: false
+
+ebsupport:
+  description: Exposure box granite support Y
+  deviceClass: ophyd_devices.devices.psi_motor.EpicsUserMotorVME
+  deviceConfig:
+    prefix: X12SA-EH1-EB:TRY1
+  deviceTags:
+    - cSAXS_ES
+  onFailure: retry
+  enabled: true
+  readoutPriority: baseline
+  softwareTrigger: false
+
+fttrx1:
+  description: FTS1 translation X
+  deviceClass: ophyd_devices.devices.psi_motor.EpicsUserMotorVME
+  deviceConfig:
+    prefix: X12SA-ES1-FTS1:TRX1
+  deviceTags:
+    - cSAXS_ES
+  onFailure: retry
+  enabled: true
+  readoutPriority: baseline
+  softwareTrigger: false
+
+fttry1:
+  description: FTS1 translation Y
+  deviceClass: ophyd_devices.devices.psi_motor.EpicsUserMotorVME
+  deviceConfig:
+    prefix: X12SA-ES1-FTS1:TRY1
+  deviceTags:
+    - cSAXS_ES
+  onFailure: retry
+  enabled: true
+  readoutPriority: baseline
+  softwareTrigger: false
+
+fttrx2:
+  description: FTS2 translation X
+  deviceClass: ophyd_devices.devices.psi_motor.EpicsUserMotorVME
+  deviceConfig:
+    prefix: X12SA-ES1-FTS2:TRX1
+  deviceTags:
+    - cSAXS_ES
+  onFailure: retry
+  enabled: true
+  readoutPriority: baseline
+  softwareTrigger: false
+
+fttry2:
+  description: FTS2 translation Y
+  deviceClass: ophyd_devices.devices.psi_motor.EpicsUserMotorVME
+  deviceConfig:
+    prefix: X12SA-ES1-FTS2:TRY1
+  deviceTags:
+    - cSAXS_ES
+  onFailure: retry
+  enabled: true
+  readoutPriority: baseline
+  softwareTrigger: false
+
+fttrz:
+  description: FTS1 translation Z
+  deviceClass: ophyd_devices.devices.psi_motor.EpicsUserMotorVME
+  deviceConfig:
+    prefix: X12SA-ES1-FTS1:TRZ1
+  deviceTags:
+    - cSAXS_ES
+  onFailure: retry
+  enabled: true
+  readoutPriority: baseline
+  softwareTrigger: false
+
+bs1x:
+  description: Beamstop 1 X
+  deviceClass: ophyd_devices.devices.psi_motor.EpicsUserMotorVME
+  deviceConfig:
+    prefix: X12SA-ES1-BS1:TRX1
+  deviceTags:
+    - cSAXS_ES
+  onFailure: retry
+  enabled: true
+  readoutPriority: baseline
+  softwareTrigger: false
+
+bs1y:
+  description: Beamstop 1 Y
+  deviceClass: ophyd_devices.devices.psi_motor.EpicsUserMotorVME
+  deviceConfig:
+    prefix: X12SA-ES1-BS1:TRY1
+  deviceTags:
+    - cSAXS_ES
+  onFailure: retry
+  enabled: true
+  readoutPriority: baseline
+  softwareTrigger: false
+
+bs2x:
+  description: Beamstop 2 X
+  deviceClass: ophyd_devices.devices.psi_motor.EpicsUserMotorVME
+  deviceConfig:
+    prefix: X12SA-ES1-BS2:TRX1
+  deviceTags:
+    - cSAXS_ES
+  onFailure: retry
+  enabled: true
+  readoutPriority: baseline
+  softwareTrigger: false
+
+bs2y:
+  description: Beamstop 2 Y
+  deviceClass: ophyd_devices.devices.psi_motor.EpicsUserMotorVME
+  deviceConfig:
+    prefix: X12SA-ES1-BS2:TRY1
+  deviceTags:
+    - cSAXS_ES
+  onFailure: retry
+  enabled: true
+  readoutPriority: baseline
+  softwareTrigger: false
+
+dttrx:
+  description: Detector table X
+  deviceClass: ophyd_devices.devices.psi_motor.EpicsUserMotorVME
+  deviceConfig:
+    prefix: X12SA-ES1-DETT:TRX1
+  deviceTags:
+    - cSAXS_ES
+  onFailure: retry
+  enabled: true
+  readoutPriority: baseline
+  softwareTrigger: false
+
+dttry:
+  description: Detector table Y
+  deviceClass: ophyd_devices.devices.psi_motor.EpicsUserMotorVME
+  deviceConfig:
+    prefix: X12SA-ES1-DETT:TRY1
+  deviceTags:
+    - cSAXS_ES
+  onFailure: retry
+  enabled: true
+  readoutPriority: baseline
+  softwareTrigger: false
+
+dttrz:
+  description: Detector table Z
+  deviceClass: ophyd_devices.devices.psi_motor.EpicsUserMotorVME
+  deviceConfig:
+    prefix: X12SA-ES1-DETT:TRZ1
+  deviceTags:
+    - cSAXS_ES
+  onFailure: retry
+  enabled: true
+  readoutPriority: baseline
+  softwareTrigger: false
+
+dettrx:
+  description: Detector 1 X
+  deviceClass: ophyd_devices.devices.psi_motor.EpicsUserMotorVME
+  deviceConfig:
+    prefix: X12SA-ES1-DET1:TRX1
+  deviceTags:
+    - cSAXS_ES
+  onFailure: retry
+  enabled: true
+  readoutPriority: baseline
+  softwareTrigger: false
+
+
+####################
+### Beamstop diode control for flight tube
+####################
+
+beamstop_gain_control:
+  description: Gain control for beamstop flightube
+  deviceClass: csaxs_bec.devices.pseudo_devices.bpm_control.BPMControl
+  deviceConfig:
+    gain_lsb: galilrioesft.digital_out.ch0  # Pin 10 -> Galil ch0
+    gain_mid: galilrioesft.digital_out.ch1  # Pin 11 -> Galil ch1
+    gain_msb: galilrioesft.digital_out.ch2  # Pin 12 -> Galil ch2
+    coupling: galilrioesft.digital_out.ch3  # Pin 13 -> Galil ch3
+    speed_mode: galilrioesft.digital_out.ch4  # Pin 14 -> Galil ch4
+  enabled: true
+  readoutPriority: baseline
+  onFailure: retry
+  needs:
+    - galilrioesft
+
+galilrioesft:
+  description: Galil RIO for remote gain switching and slow reading FlightTube
+  deviceClass: csaxs_bec.devices.omny.galil.galil_rio.GalilRIO
+  deviceConfig:
+    host: galilrioesft.psi.ch
+  enabled: true
+  onFailure: retry
+  readOnly: false
+  readoutPriority: baseline
+  connectionTimeout: 20
+
+beamstop_dummy_bpm:
+  description: BPM Xbox 2 (First Xbox in ES hutch)
+  deviceClass: csaxs_bec.devices.pseudo_devices.bpm.BPM
+  deviceConfig:
+    left_top:  galilrioesft.analog_in.ch0
+    right_top: galilrioesft.analog_in.ch1
+    right_bot: galilrioesft.analog_in.ch2
+    left_bot:  galilrioesft.analog_in.ch3
+  enabled: true
+  readoutPriority: baseline
+  onFailure: retry
+  needs:
+    - galilrioesft
+
+beamstop_intensity:
+  description: Beamstop intensity from Galil analog input ch6
+  deviceClass: csaxs_bec.devices.pseudo_devices.signal_forwarder.SignalForwarder
+  deviceConfig:
+    signal: galilrioesft.analog_in.ch6
+  enabled: true
+  readoutPriority: baseline
+  onFailure: retry
+  needs:
+    - galilrioesft
+
+

csaxs_bec/device_configs/bl_frontend.yaml

@@ -199,6 +199,25 @@ xbpm1c4:
   readOnly: true
   softwareTrigger: false
 
+bpm1:
+  description: 'XBPM1 (frontend)'
+  deviceClass: csaxs_bec.devices.pseudo_devices.bpm.BPM
+  deviceConfig:
+    left_top: xbpm1c1
+    right_top: xbpm1c2
+    right_bot: xbpm1c3
+    left_bot: xbpm1c4
+  onFailure: raise
+  enabled: true
+  readoutPriority: monitored
+  readOnly: true
+  softwareTrigger: false
+  needs:
+    - xbpm1c1
+    - xbpm1c2
+    - xbpm1c3
+    - xbpm1c4
+
 ############################################
 ######### End of xbpm sub devices ##########
 ############################################

csaxs_bec/device_configs/bl_optics_hutch.yaml

@@ -68,91 +68,110 @@ ccmx:
   - cSAXS
   - optics
 
+# TO BE REVIEWED, REMOVE VELOCITY WITH NEW CLASS!
+ccm_energy:
+  description: 'test'
+  deviceClass: ophyd_devices.devices.simple_positioner.PSISimplePositioner
+  deviceConfig: 
+    prefix: 'X12SA-OP-CCM1:'
+    override_suffixes:
+      user_readback: "ENERGY-GET"
+      user_setpoint: "ENERGY-SET"
+      velocity: "ROTY.VELO"
+      motor_done_move: "ROTY.DMOV"
+  onFailure: buffer
+  enabled: true
+  readoutPriority: baseline
+  readOnly: false
+  softwareTrigger: false
+
 
 
 ##########################################################################
 ######################## SMARACT STAGES ##################################
 ##########################################################################
 
-xbpm2x:
-  description: X-ray beam position monitor 1 in OPbox
-  deviceClass: csaxs_bec.devices.smaract.smaract_ophyd.SmaractMotor
-  deviceConfig:
-    axis_Id: A
-    host: x12sa-eb-smaract-mcs-03.psi.ch
-    limits:
-    - -200
-    - 200
-    port: 5000
-    sign: 1
-  enabled: true
-  onFailure: buffer
-  readOnly: false
-  readoutPriority: baseline
-  connectionTimeout: 20
-  userParameter:
-    # bl_smar_stage to use csaxs reference method. assign number according to axis channel
-    bl_smar_stage: 0
+# xbpm2x:
+#   description: X-ray beam position monitor 1 in OPbox
+#   deviceClass: csaxs_bec.devices.smaract.smaract_ophyd.SmaractMotor
+#   deviceConfig:
+#     axis_Id: A
+#     host: x12sa-eb-smaract-mcs-03.psi.ch
+#     limits:
+#     - -200
+#     - 200
+#     port: 5000
+#     sign: 1
+#   enabled: true
+#   onFailure: buffer
+#   readOnly: false
+#   readoutPriority: baseline
+#   connectionTimeout: 20
+#   userParameter:
+#     # bl_smar_stage to use csaxs reference method. assign number according to axis channel
+#     bl_smar_stage: 0
 
-xbpm2y:
-  description: X-ray beam position monitor 1 in OPbox
-  deviceClass: csaxs_bec.devices.smaract.smaract_ophyd.SmaractMotor
-  deviceConfig:
-    axis_Id: B
-    host: x12sa-eb-smaract-mcs-03.psi.ch
-    limits:
-    - -200
-    - 200
-    port: 5000
-    sign: 1
-  enabled: true
-  onFailure: buffer
-  readOnly: false
-  readoutPriority: baseline
-  connectionTimeout: 20
-  userParameter:
-    # bl_smar_stage to use csaxs reference method. assign number according to axis channel
-    bl_smar_stage: 1
+# xbpm2y:
+#   description: X-ray beam position monitor 1 in OPbox
+#   deviceClass: csaxs_bec.devices.smaract.smaract_ophyd.SmaractMotor
+#   deviceConfig:
+#     axis_Id: B
+#     host: x12sa-eb-smaract-mcs-03.psi.ch
+#     limits:
+#     - -200
+#     - 200
+#     port: 5000
+#     sign: 1
+#   enabled: true
+#   onFailure: buffer
+#   readOnly: false
+#   readoutPriority: baseline
+#   connectionTimeout: 20
+#   userParameter:
+#     # bl_smar_stage to use csaxs reference method. assign number according to axis channel
+#     bl_smar_stage: 1
+
+# cu_foilx:
+#   description: Cu foil in OPbox
+#   deviceClass: csaxs_bec.devices.smaract.smaract_ophyd.SmaractMotor
+#   deviceConfig:
+#     axis_Id: C
+#     host: x12sa-eb-smaract-mcs-03.psi.ch
+#     limits:
+#     - -200
+#     - 200
+#     port: 5000
+#     sign: 1
+#   enabled: true
+#   onFailure: buffer
+#   readOnly: false
+#   readoutPriority: baseline
+#   connectionTimeout: 20
+#   userParameter:
+#     # bl_smar_stage to use csaxs reference method. assign number according to axis channel
+#     bl_smar_stage: 2
+
+# scinx:
+#   description: scintillator in OPbox
+#   deviceClass: csaxs_bec.devices.smaract.smaract_ophyd.SmaractMotor
+#   deviceConfig:
+#     axis_Id: D
+#     host: x12sa-eb-smaract-mcs-03.psi.ch
+#     limits:
+#     - -200
+#     - 200
+#     port: 5000
+#     sign: 1
+#   enabled: true
+#   onFailure: buffer
+#   readOnly: false
+#   readoutPriority: baseline
+#   connectionTimeout: 20
+#   userParameter:
+#     # bl_smar_stage to use csaxs reference method. assign number according to axis channel
+#     bl_smar_stage: 3
 
-cu_foilx:
-  description: Cu foil in OPbox
-  deviceClass: csaxs_bec.devices.smaract.smaract_ophyd.SmaractMotor
-  deviceConfig:
-    axis_Id: C
-    host: x12sa-eb-smaract-mcs-03.psi.ch
-    limits:
-    - -200
-    - 200
-    port: 5000
-    sign: 1
-  enabled: true
-  onFailure: buffer
-  readOnly: false
-  readoutPriority: baseline
-  connectionTimeout: 20
-  userParameter:
-    # bl_smar_stage to use csaxs reference method. assign number according to axis channel
-    bl_smar_stage: 2
 
-scinx:
-  description: scintillator in OPbox
-  deviceClass: csaxs_bec.devices.smaract.smaract_ophyd.SmaractMotor
-  deviceConfig:
-    axis_Id: D
-    host: x12sa-eb-smaract-mcs-03.psi.ch
-    limits:
-    - -200
-    - 200
-    port: 5000
-    sign: 1
-  enabled: true
-  onFailure: buffer
-  readOnly: false
-  readoutPriority: baseline
-  connectionTimeout: 20
-  userParameter:
-    # bl_smar_stage to use csaxs reference method. assign number according to axis channel
-    bl_smar_stage: 3
 
 
 # dmm1_trx_readback_example: # This is the same template as for i.e. bpm4i 

csaxs_bec/device_configs/main.yaml

@@ -1,8 +1,8 @@
 # This is the main configuration file that is
 # commented or uncommented according to the type of experiment
 
-# optics:
-#   - !include ./bl_optics_hutch.yaml
+optics:
+  - !include ./bl_optics_hutch.yaml
 
 # frontend:
 #   - !include ./bl_frontend.yaml

csaxs_bec/device_configs/ptycho_flomni.yaml

@@ -395,6 +395,16 @@ rtz:
   readoutPriority: on_request
   connectionTimeout: 20
 
+rt_positions:
+  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 ############################
 ############################################################
@@ -512,6 +522,19 @@ omny_panda:
       FMC_IN.VAL2.Min: cap_voltage_fzp_x_min
       FMC_IN.VAL2.Max: cap_voltage_fzp_x_max
       FMC_IN.VAL2.Mean: cap_voltage_fzp_x_mean
+      INENC1.VAL.Max: interf_st_fzp_y_max
+      INENC1.VAL.Mean: interf_st_fzp_y_mean
+      INENC1.VAL.Min: interf_st_fzp_y_min
+      INENC2.VAL.Max: interf_st_fzp_x_max
+      INENC2.VAL.Mean: interf_st_fzp_x_mean
+      INENC2.VAL.Min: interf_st_fzp_x_min
+      INENC3.VAL.Max: interf_st_rotz_max
+      INENC3.VAL.Mean: interf_st_rotz_mean
+      INENC3.VAL.Min: interf_st_rotz_min
+      INENC4.VAL.Max: interf_st_rotx_max
+      INENC4.VAL.Mean: interf_st_rotx_mean
+      INENC4.VAL.Min: interf_st_rotx_min
+      PCAP.GATE_DURATION.Value: pcap_gate_duration_value
   deviceTags:
     - detector
   enabled: true

csaxs_bec/device_configs/test_config.yaml

@@ -0,0 +1,24 @@
+galilrioesxbox:
+  description: Galil RIO for remote gain switching and slow reading ES XBox
+  deviceClass: csaxs_bec.devices.omny.galil.galil_rio.GalilRIO
+  deviceConfig:
+    host: galilrioesft.psi.ch
+  enabled: true
+  onFailure: raise
+  readOnly: false
+  readoutPriority: baseline
+  connectionTimeout: 20
+bpm1:
+  readoutPriority: baseline
+  deviceClass: csaxs_bec.devices.pseudo_devices.bpm.BPM
+  deviceConfig:
+    blade_t: galilrioesxbox.analog_in.ch0
+    blade_r: galilrioesxbox.analog_in.ch1
+    blade_b: galilrioesxbox.analog_in.ch2
+    blade_l: galilrioesxbox.analog_in.ch3
+  enabled: true
+  readOnly: false
+  softwareTrigger: true
+  needs:
+    - galilrioesxbox
+

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/devices/omny/shutter.py

@@ -13,6 +13,14 @@ from ophyd_devices import PSIDeviceBase
 logger = bec_logger.logger
 
 
+class MonitorSignal(Signal):
+    """A simple wrapper around ophyd Signal that automatically monitors the signal for changes."""
+
+    def __init__(self, *, name, auto_monitor=False, **kwargs):
+        super().__init__(name=name, **kwargs)
+        self.auto_monitor = auto_monitor
+
+
 class OMNYFastShutter(PSIDeviceBase, Device):
     """
     Fast Shutter control for OMNY setup. If started with at the beamline, it will expose
@@ -26,7 +34,7 @@ class OMNYFastShutter(PSIDeviceBase, Device):
     SUB_VALUE = "value"
     _default_sub = SUB_VALUE
 
-    shutter = Cpt(Signal, name="shutter")
+    shutter = Cpt(MonitorSignal, name="shutter", auto_monitor=True)
 
     # -----------------------------------------------------
     # User-facing shutter control functions
@@ -48,7 +56,6 @@ class OMNYFastShutter(PSIDeviceBase, Device):
     def fshopen(self):
         """Open the fast shutter."""
         if self._check_if_cSAXS_shutter_exists_in_config():
-            self.shutter.put(1)
             return self.device_manager.devices["fsh"].fshopen()
         else:
             self.shutter.put(1)
@@ -56,7 +63,6 @@ class OMNYFastShutter(PSIDeviceBase, Device):
     def fshclose(self):
         """Close the fast shutter."""
         if self._check_if_cSAXS_shutter_exists_in_config():
-            self.shutter.put(0)
             return self.device_manager.devices["fsh"].fshclose()
         else:
             self.shutter.put(0)

csaxs_bec/devices/pseudo_devices/bpm.py

@@ -0,0 +1,172 @@
+"""Module for a BPM pseudo device that computes the position and intensity from the blade signals."""
+
+from ophyd import Component as Cpt
+from ophyd import Kind, Signal
+from ophyd_devices.interfaces.base_classes.psi_pseudo_device_base import PSIPseudoDeviceBase
+from ophyd_devices.utils.bec_processed_signal import BECProcessedSignal
+
+
+class BPM(PSIPseudoDeviceBase):
+    """BPM positioner pseudo device."""
+
+    # Blade signals, a,b,c,d
+    left_top = Cpt(
+        BECProcessedSignal,
+        name="left_top",
+        model_config=None,
+        kind=Kind.config,
+        doc="BPM left_top blade",
+    )
+    right_top = Cpt(
+        BECProcessedSignal,
+        name="right_top",
+        model_config=None,
+        kind=Kind.config,
+        doc="BPM right_top blade",
+    )
+    right_bot = Cpt(
+        BECProcessedSignal,
+        name="right_bot",
+        model_config=None,
+        kind=Kind.config,
+        doc="BPM right_bottom blade",
+    )
+    left_bot = Cpt(
+        BECProcessedSignal,
+        name="left_bot",
+        model_config=None,
+        kind=Kind.config,
+        doc="BPM left_bot blade",
+    )
+
+    # Virtual signals
+    pos_x = Cpt(
+        BECProcessedSignal,
+        name="pos_x",
+        model_config=None,
+        kind=Kind.config,
+        doc="BPM X position, -1 fully left, 1 fully right",
+    )
+    pos_y = Cpt(
+        BECProcessedSignal,
+        name="pos_y",
+        model_config=None,
+        kind=Kind.config,
+        doc="BPM Y position, -1 fully bottom, 1 fully top",
+    )
+    diagonal = Cpt(
+        BECProcessedSignal,
+        name="diagonal",
+        model_config=None,
+        kind=Kind.config,
+        doc="BPM diagonal, -1 fully diagonal left_top-right_bot, 1 fully diagonal right_top-left_bot",
+    )
+    intensity = Cpt(
+        BECProcessedSignal,
+        name="intensity",
+        model_config=None,
+        kind=Kind.config,
+        doc="BPM intensity",
+    )
+
+    def __init__(
+        self,
+        name,
+        left_top: str,
+        right_top: str,
+        right_bot: str,
+        left_bot: str,
+        device_manager=None,
+        scan_info=None,
+        **kwargs,
+    ):
+        super().__init__(name=name, device_manager=device_manager, scan_info=scan_info, **kwargs)
+        # Get all blade signal objects from utility method
+        signal_t = self.left_top.get_device_object_from_bec(
+            object_name=left_top, signal_name=self.name, device_manager=device_manager
+        )
+        signal_r = self.right_top.get_device_object_from_bec(
+            object_name=right_top, signal_name=self.name, device_manager=device_manager
+        )
+        signal_b = self.right_bot.get_device_object_from_bec(
+            object_name=right_bot, signal_name=self.name, device_manager=device_manager
+        )
+        signal_l = self.left_bot.get_device_object_from_bec(
+            object_name=left_bot, signal_name=self.name, device_manager=device_manager
+        )
+
+        # Set compute methods for blade signals and virtual signals
+        self.left_top.set_compute_method(self._compute_blade_signal, signal=signal_t)
+        self.right_top.set_compute_method(self._compute_blade_signal, signal=signal_r)
+        self.right_bot.set_compute_method(self._compute_blade_signal, signal=signal_b)
+        self.left_bot.set_compute_method(self._compute_blade_signal, signal=signal_l)
+
+        self.intensity.set_compute_method(
+            self._compute_intensity,
+            left_top=self.left_top,
+            right_top=self.right_top,
+            right_bot=self.right_bot,
+            left_bot=self.left_bot,
+        )
+        self.pos_x.set_compute_method(
+            self._compute_pos_x,
+            left_bot=self.left_bot,
+            left_top=self.left_top,
+            right_top=self.right_top,
+            right_bot=self.right_bot,
+        )
+        self.pos_y.set_compute_method(
+            self._compute_pos_y,
+            left_bot=self.left_bot,
+            left_top=self.left_top,
+            right_top=self.right_top,
+            right_bot=self.right_bot,
+        )
+        self.diagonal.set_compute_method(
+            self._compute_diagonal,
+            left_bot=self.left_bot,
+            left_top=self.left_top,
+            right_top=self.right_top,
+            right_bot=self.right_bot,
+        )
+
+    def _compute_blade_signal(self, signal: Signal) -> float:
+        return signal.get()
+
+    def _compute_intensity(
+        self, left_top: Signal, right_top: Signal, right_bot: Signal, left_bot: Signal
+    ) -> float:
+        intensity = left_top.get() + right_top.get() + right_bot.get() + left_bot.get()
+        return intensity
+
+    def _compute_pos_x(
+        self, left_bot: Signal, left_top: Signal, right_top: Signal, right_bot: Signal
+    ) -> float:
+        """X position from -1 to 1, where -1 means beam fully on the left side, 1 means beam fully on the right side."""
+        sum_left = left_bot.get() + left_top.get()
+        sum_right = right_top.get() + right_bot.get()
+        sum_total = sum_left + sum_right
+        if sum_total == 0:
+            return 0.0
+        return (sum_right - sum_left) / sum_total
+
+    def _compute_pos_y(
+        self, left_bot: Signal, left_top: Signal, right_top: Signal, right_bot: Signal
+    ) -> float:
+        """Y position from -1 to 1, where -1 means beam fully on the bottom side, 1 means beam fully on the top side."""
+        sum_top = left_top.get() + right_top.get()
+        sum_bot = right_bot.get() + left_bot.get()
+        sum_total = sum_top + sum_bot
+        if sum_total == 0:
+            return 0.0
+        return (sum_top - sum_bot) / sum_total
+
+    def _compute_diagonal(
+        self, left_bot: Signal, left_top: Signal, right_top: Signal, right_bot: Signal
+    ) -> float:
+        sum_diag1 = left_bot.get() + right_top.get()
+        sum_diag2 = left_top.get() + right_bot.get()
+        sum_total = sum_diag1 + sum_diag2
+        if sum_total == 0:
+            return 0.0
+        return (sum_diag1 - sum_diag2) / sum_total

csaxs_bec/devices/pseudo_devices/bpm_control.py

@@ -0,0 +1,189 @@
+"""
+Module for controlling the BPM amplifier settings, such as gain and coupling.
+"""
+
+from __future__ import annotations
+
+from typing import TYPE_CHECKING, Literal
+
+from ophyd import Component as Cpt
+from ophyd import Kind
+from ophyd_devices.interfaces.base_classes.psi_pseudo_device_base import PSIPseudoDeviceBase
+from ophyd_devices.utils.bec_processed_signal import BECProcessedSignal
+
+if TYPE_CHECKING:  # pragma: no cover
+    from bec_lib.devicemanager import ScanInfo
+    from bec_server.device_server.devices.devicemanager import DeviceManagerDS
+    from ophyd import Signal
+
+_GAIN_BITS_LOW_NOISE: dict[tuple, int] = {
+    (0, 0, 0): int(1e3),
+    (0, 0, 1): int(1e4),
+    (0, 1, 0): int(1e5),
+    (0, 1, 1): int(1e6),
+    (1, 0, 0): int(1e7),
+    (1, 0, 1): int(1e8),
+    (1, 1, 0): int(1e9),
+}
+
+_GAIN_BITS_HIGH_SPEED: dict[tuple, int] = {
+    (0, 0, 0): int(1e5),
+    (0, 0, 1): int(1e6),
+    (0, 1, 0): int(1e7),
+    (0, 1, 1): int(1e8),
+    (1, 0, 0): int(1e9),
+    (1, 0, 1): int(1e10),
+    (1, 1, 0): int(1e11),
+}
+
+_GAIN_TO_BITS: dict[int, tuple] = {}
+for _bits, _gain in _GAIN_BITS_LOW_NOISE.items():
+    _GAIN_TO_BITS[_gain] = (*_bits, True)
+for _bits, _gain in _GAIN_BITS_HIGH_SPEED.items():
+    if _gain not in _GAIN_TO_BITS:  # low-noise takes priority
+        _GAIN_TO_BITS[_gain] = (*_bits, False)
+
+VALID_GAINS = sorted(_GAIN_TO_BITS.keys())
+
+
+class BPMControl(PSIPseudoDeviceBase):
+    """
+    BPM amplifier control pseudo device. It is responsible for controlling the
+    gain and coupling for the BPM amplifier. It relies on signals from a device
+    in BEC to be available. For cSAXS, these are most liikely to be from the
+    GalilRIO device that controls the BPM amplifier.
+
+    Args:
+        name (str): Name of the pseudo device.
+        gain_lsb (str): Name of the signal in BEC that controls the LSB
+            of the gain setting.
+        gain_mid (str): Name of the signal in BEC that controls the MID
+            bit of the gain setting.
+        gain_msb (str): Name of the signal in BEC that controls the MSB
+            of the gain setting.
+        coupling (str): Name of the signal in BEC that controls the coupling
+            setting.
+        speed_mode (str): Name of the signal in BEC that controls the speed mode
+            (low-noise vs high-speed) of the amplifier.
+    """
+
+    USER_ACCESS = ["set_gain", "set_coupling"]
+
+    gain = Cpt(
+        BECProcessedSignal,
+        name="gain",
+        model_config=None,
+        kind=Kind.config,
+        doc="Gain of the amplifier",
+    )
+    coupling = Cpt(
+        BECProcessedSignal,
+        name="coupling",
+        model_config=None,
+        kind=Kind.config,
+        doc="Coupling of the amplifier",
+    )
+    speed = Cpt(
+        BECProcessedSignal,
+        name="speed",
+        model_config=None,
+        kind=Kind.config,
+        doc="Speed of the amplifier",
+    )
+
+    def __init__(
+        self,
+        name: str,
+        gain_lsb: str,
+        gain_mid: str,
+        gain_msb: str,
+        coupling: str,
+        speed_mode: str,
+        device_manager: DeviceManagerDS | None = None,
+        scan_info: ScanInfo | None = None,
+        **kwargs,
+    ):
+        super().__init__(name=name, device_manager=device_manager, scan_info=scan_info, **kwargs)
+
+        # First we get all signal objects from BEC using the utility method provided by the BECProcessedSignal class.
+        self._gain_lsb = self.gain.get_device_object_from_bec(
+            object_name=gain_lsb, signal_name=self.name, device_manager=device_manager
+        )
+        self._gain_mid = self.gain.get_device_object_from_bec(
+            object_name=gain_mid, signal_name=self.name, device_manager=device_manager
+        )
+        self._gain_msb = self.gain.get_device_object_from_bec(
+            object_name=gain_msb, signal_name=self.name, device_manager=device_manager
+        )
+        self._coupling = self.gain.get_device_object_from_bec(
+            object_name=coupling, signal_name=self.name, device_manager=device_manager
+        )
+        self._speed_mode = self.gain.get_device_object_from_bec(
+            object_name=speed_mode, signal_name=self.name, device_manager=device_manager
+        )
+
+        # Set the compute methods for the virtual signals.
+        self.gain.set_compute_method(
+            self._compute_gain,
+            msb=self._gain_msb,
+            mid=self._gain_mid,
+            lsb=self._gain_lsb,
+            speed_mode=self._speed_mode,
+        )
+        self.coupling.set_compute_method(self._compute_coupling, coupling=self._coupling)
+        self.speed.set_compute_method(self._compute_speed, speed=self._speed_mode)
+
+    def set_gain(
+        self,
+        gain: Literal[
+            1000, 10000, 100000, 1000000, 10000000, 100000000, 1000000000, 10000000000, 100000000000
+        ],
+    ) -> None:
+        """
+        Set the gain of the amplifier.
+
+        Args:
+            gain (Literal): Must be one of 1000, 10000, 100000, 1000000, 10000000, 100000000, 1000000000, 10000000000.
+        """
+        gain_int = int(gain)
+        if gain_int not in VALID_GAINS:
+            raise ValueError(
+                f"{self.name} received invalid gain {gain_int}, must be in {VALID_GAINS}"
+            )
+
+        msb, mid, lsb, use_low_noise = _GAIN_TO_BITS[gain_int]
+
+        self._gain_msb.set(bool(msb)).wait(timeout=2)
+        self._gain_lsb.set(bool(lsb)).wait(timeout=2)
+        self._gain_mid.set(bool(mid)).wait(timeout=2)
+        self._speed_mode.set(bool(use_low_noise))
+
+    def set_coupling(self, coupling: Literal["AC", "DC"]) -> None:
+        """
+        Set the coupling of the amplifier.
+
+        Args:
+            coupling (Literal): Must be either "AC" or "DC".
+        """
+        if coupling not in ["AC", "DC"]:
+            raise ValueError(
+                f"{self.name} received invalid coupling value {coupling}, please use 'AC' or 'DC'"
+            )
+        self._coupling.set(coupling == "DC").wait(timeout=2)
+
+    def _compute_gain(self, msb: Signal, mid: Signal, lsb: Signal, speed_mode: Signal) -> int:
+        """Compute the gain based on the bits and speed mode."""
+        bits = (msb.get(), mid.get(), lsb.get())
+        speed_mode = speed_mode.get()
+        if speed_mode:
+            return _GAIN_BITS_LOW_NOISE.get(bits)
+        else:
+            return _GAIN_BITS_HIGH_SPEED.get(bits)
+
+    def _compute_coupling(self, coupling: Signal) -> str:
+        """Compute the coupling based on the signal."""
+        return "DC" if coupling.get() else "AC"
+
+    def _compute_speed(self, speed: Signal) -> str:
+        """Compute the speed based on the signal."""
+        return "low_speed" if speed.get() else "high_speed"

csaxs_bec/devices/pseudo_devices/dlpca200_settings.py

@@ -0,0 +1 @@
+# from ophyd 

csaxs_bec/devices/pseudo_devices/signal_forwarder.py

@@ -0,0 +1,41 @@
+"""
+Pseudo device that forwards a single BEC signal 1:1.
+"""
+
+from ophyd import Component as Cpt
+from ophyd import Kind, Signal
+from ophyd_devices.interfaces.base_classes.psi_pseudo_device_base import PSIPseudoDeviceBase
+from ophyd_devices.utils.bec_processed_signal import BECProcessedSignal
+
+
+class SignalForwarder(PSIPseudoDeviceBase):
+    """Forward one signal unchanged."""
+
+    signal = Cpt(
+        BECProcessedSignal,
+        name="signal",
+        model_config=None,
+        kind=Kind.config,
+        doc="Forwarded signal",
+    )
+
+    def __init__(
+        self,
+        name,
+        signal: str,
+        device_manager=None,
+        scan_info=None,
+        **kwargs,
+    ):
+        super().__init__(name=name, device_manager=device_manager, scan_info=scan_info, **kwargs)
+
+        src = self.signal.get_device_object_from_bec(
+            object_name=signal,
+            signal_name=self.name,
+            device_manager=device_manager,
+        )
+
+        self.signal.set_compute_method(self._compute_signal, signal=src)
+
+    def _compute_signal(self, signal: Signal) -> float:
+        return signal.get()

csaxs_bec/file_writer/__init__.py

@@ -1 +1 @@
-from .csaxs_nexus import NeXus_format as cSAXS_NeXus_format
+from .csaxs_nexus import cSAXSNeXusFormat

csaxs_bec/file_writer/csaxs_nexus.py

@@ -1,445 +1,470 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Any
-
 import numpy as np
-
-if TYPE_CHECKING:
-    from bec_lib.devicemanager import DeviceManagerBase
-    from bec_server.file_writer.file_writer import HDF5Storage
+from bec_server.file_writer.default_writer import DefaultFormat
 
 
-def get_entry(data: dict, name: str, default=None) -> Any:
+class cSAXSNeXusFormat(DefaultFormat):
     """
-    Get an entry from the scan data assuming a <device>.<device>.value structure.
+    NeXus file format for the cSAXS beamline (BEC era).
 
-    Args:
-        data (dict): Scan data
-        name (str): Entry name
-        default (Any, optional): Default value. Defaults to None.
+    Mirrors the old SPEC layout.xml hierarchy and adds the flOMNI instrument
+    group for the nano-positioning stage used in ptychography.
+
+    Device resilience
+    -----------------
+    Every device read (self.get_entry / device call) is wrapped in try/except.
+    If a device is removed from the BEC config file between sessions it simply
+    disappears from the device_manager — the corresponding dataset or link is
+    silently omitted from the HDF5 file without raising an error. This means
+    the file structure is additive: re-add the device to the config and the
+    field reappears automatically on the next scan.
+
+    Top-level HDF5 structure
+    ────────────────────────
+    /entry                        NXentry  (definition = NXptycho)
+      /sample                     NXsample  ← primary sample group
+      /entry_ptycho               NXentry   ← generic ptycho entry
+      /data_soft                  NXentry   ← convenience Eiger frame links
+      /control                    NXmonitor
+      /instrument                 NXinstrument
+          /source
+          /insertion_device
+          /monochromator
+          /XBPM3
+          /slit_3 … slit_5
+          /filter_set
+          /beam_stop_1 … beam_stop_2
+          /eiger_1_5              NXdetector
+          /mcs                    NXdetector
+          /flOMNI                 NXpositioner
+
+    Device name mapping (old SPEC → current BEC)
+    ────────────────────────────────────────────
+    samx / samy    →  samx / samy     (generic; kept for non-flOMNI configs)
+    sl3wh/wv/ch/cv →  sl3trxi/o/b/t  (individual blade motors; gap/centre TODO)
+    sl4wh/wv/ch/cv →  sl4trxi/o/b/t
+    sl5wh/wv/ch/cv →  sl5trxi/o/b/t
+    bs1x / bs1y    →  bs1x / bs1y
+    bs2x / bs2y    →  bs2x / bs2y
+    dettrx         →  dettrx
+    eiger_4        →  eiger_1_5
+    mcs            →  mcs
+    filter_array   →  filter_array_1_x … filter_array_4_x
+    xbpm3          →  xbpm3x / xbpm3y  (stage positions; signal readouts TODO)
+    energy         →  ccm_energy
+
+    TODO (devices not yet in BEC list)
+    ───────────────────────────────────
+    curr, idgap                   ring current, undulator gap
+    moth1, mobd                   monochromator crystal angles
+    mith, mibd, mirror_coating    mirror
+    bpm3s/x/y/z                   XBPM3 signal readouts
+    sl0 / sl1 / sl2               upstream optics-hutch slits
+    slit gap / centre             derived from blade pairs + calibration offset
     """
-    if isinstance(data.get(name), list) and isinstance(data.get(name)[0], dict):
-        return [sub_data.get(name, {}).get("value", default) for sub_data in data.get(name)]
 
-    return data.get(name, {}).get(name, {}).get("value", default)
+    # -------------------------------------------------------------------------
+    # Helpers
+    # -------------------------------------------------------------------------
+
+    def _safe_dataset(self, group, name: str, device: str,
+                      units: str | None = None,
+                      description: str | None = None) -> None:
+        """
+        Write a dataset from the BEC scan data dictionary.
+        Silently skips if the device was not recorded in this scan
+        (e.g. removed from config, readoutPriority=on_request and not triggered,
+        or the scan finished before the device responded).
+        """
+        try:
+            value = self.get_entry(device)
+            ds = group.create_dataset(name, data=value)
+            if units:
+                ds.attrs["units"] = units
+            if description:
+                ds.attrs["description"] = description
+        except Exception:
+            pass
+
+    def _safe_soft_link(self, group, name: str, target: str) -> None:
+        """Create a soft link; silently skip on any error."""
+        try:
+            group.create_soft_link(name, target)
+        except Exception:
+            pass
+
+    def _slit_blades(self, group, prefix: str) -> None:
+        """
+        Store individual blade motor positions for a 4-blade slit set.
+        Derived quantities (gap, centre) require a per-slit calibration offset
+        and will be added in a later update.
+        """
+        for blade, motor in [
+            ("inner_x",  f"{prefix}trxi"),
+            ("outer_x",  f"{prefix}trxo"),
+            ("bottom_y", f"{prefix}trxb"),
+            ("top_y",    f"{prefix}trxt"),
+        ]:
+            self._safe_dataset(group, blade, motor, units="mm")
 
 
-def NeXus_format(
-    storage: HDF5Storage, data: dict, file_references: dict, device_manager: DeviceManagerBase
-) -> HDF5Storage:
-    """
-    Prepare the NeXus file format.
+    # -------------------------------------------------------------------------
+    # Main format method
+    # -------------------------------------------------------------------------
 
-    Args:
-        storage (HDF5Storage): HDF5 storage. Pseudo hdf5 file container that will be written to disk later.
-        data (dict): scan data
-        file_references (dict): File references. Can be used to add external files to the HDF5 file. The path is given relative to the HDF5 file.
-        device_manager (DeviceManagerBase): Device manager. Can be used to check if devices are available.
+    def format(self) -> None:
+        """Build the NeXus/HDF5 layout for a cSAXS scan."""
 
-    Returns:
-        HDF5Storage: Updated HDF5 storage
-    """
-    # /entry
-    entry = storage.create_group("entry")
-    entry.attrs["NX_class"] = "NXentry"
-    entry.attrs["definition"] = "NXsas"
-    entry.attrs["start_time"] = data.get("start_time")
-    entry.attrs["end_time"] = data.get("end_time")
-    entry.attrs["version"] = 1.0
+        # Canonical paths referenced by multiple groups
+        RT_POS_PATH = "/entry/instrument/flOMNI/rt_positions"
+        EIGER_COLL  = "/entry/collection/file_references/eiger_1_5"
 
-    # /entry/collection
-    collection = entry.create_group("collection")
-    collection.attrs["NX_class"] = "NXcollection"
-    bec_collection = collection.create_group("bec")
+        # ── Root entry ────────────────────────────────────────────────────────
+        entry = self.storage.create_group("entry")
+        entry.attrs["NX_class"]   = "NXentry"
+        entry.attrs["definition"] = "NXptycho"
 
-    # /entry/control
-    control = entry.create_group("control")
-    control.attrs["NX_class"] = "NXmonitor"
-    control.create_dataset(name="mode", data="monitor")
-    control.create_dataset(name="integral", data=get_entry(data, "bpm4i"))
+        # ── /entry/sample ─────────────────────────────────────────────────────
+        # Primary sample group. Contains the name of the mounted sample and a
+        # link to the real-time scan positions. Generic samx/samy are recorded
+        # here so the group is meaningful for non-flOMNI configurations too.
+        sample = entry.create_group("sample")
+        sample.attrs["NX_class"] = "NXsample"
+        # Soft-link name directly to the value BEC recorded in the collection.
+        # Only written when flomni_samples is present; other configs leave name absent.
+        if "flomni_samples" in self.device_manager.devices:
+            self._safe_soft_link(
+                sample, "name",
+                "/entry/collection/devices/flomni_samples"
+                "/flomni_samples_sample_names_sample0/value",
+            )
+        # Generic coarse stage positions (meaningful in non-flOMNI setups)
+        self._safe_dataset(sample, "x_translation", "samx", units="mm")
+        self._safe_dataset(sample, "y_translation", "samy", units="mm")
+        # Real-time encoder positions — the primary scan coordinate
+        self._safe_soft_link(sample, "positions", RT_POS_PATH)
 
-    # /entry/data
-    main_data = entry.create_group("data")
-    main_data.attrs["NX_class"] = "NXdata"
-    if "eiger_4" in device_manager.devices:
-        main_data.create_soft_link(name="data", target="/entry/instrument/eiger_4/data")
-    elif "eiger9m" in device_manager.devices:
-        main_data.create_soft_link(name="data", target="/entry/instrument/eiger9m/data")
-    elif "pilatus_2" in device_manager.devices:
-        main_data.create_soft_link(name="data", target="/entry/instrument/pilatus_2/data")
+        # ── /entry/entry_ptycho ───────────────────────────────────────────────
+        # Generic ptychography entry. Detector data and scan positions are
+        # linked in from the instrument groups so this entry is self-contained
+        # for downstream reconstruction codes.
+        entry_ptycho = entry.create_group("entry_ptycho")
+        entry_ptycho.attrs["NX_class"]   = "NXentry"
+        entry_ptycho.attrs["definition"] = "NXptycho"
 
-    # /entry/sample
-    control = entry.create_group("sample")
-    control.attrs["NX_class"] = "NXsample"
-    control.create_dataset(name="name", data=get_entry(data, "samplename"))
-    control.create_dataset(name="description", data=data.get("sample_description"))
-    x_translation = control.create_dataset(name="x_translation", data=get_entry(data, "samx"))
-    x_translation.attrs["units"] = "mm"
-    y_translation = control.create_dataset(name="y_translation", data=get_entry(data, "samy"))
-    y_translation.attrs["units"] = "mm"
-    temperature_log = control.create_dataset(name="temperature_log", data=get_entry(data, "temp"))
-    temperature_log.attrs["units"] = "K"
+        nxdata = entry_ptycho.create_group("data")
+        nxdata.attrs["NX_class"] = "NXdata"
+        nxdata.attrs["signal"]   = "data"
+        # Detector frames
+        try:
+            for k in self.file_references["eiger_1_5"].hinted_h5_entries.keys():
+                self._safe_soft_link(nxdata, k, f"{EIGER_COLL}/{k}")
+        except Exception:
+            pass
+        # Scan positions
+        self._safe_soft_link(nxdata, "positions", RT_POS_PATH)
 
-    # /entry/instrument
-    instrument = entry.create_group("instrument")
-    instrument.attrs["NX_class"] = "NXinstrument"
-    instrument.create_dataset(name="name", data="cSAXS beamline")
+        # Link to the primary sample group
+        self._safe_soft_link(entry_ptycho, "sample", "/entry/sample")
 
-    source = instrument.create_group("source")
-    source.attrs["NX_class"] = "NXsource"
-    source.create_dataset(name="type", data="Synchrotron X-ray Source")
-    source.create_dataset(name="name", data="Swiss Light Source")
-    source.create_dataset(name="probe", data="x-ray")
-    distance = source.create_dataset(
-        name="distance", data=-33800 - np.asarray(get_entry(data, "samz", 0))
-    )
-    distance.attrs["units"] = "mm"
-    sigma_x = source.create_dataset(name="sigma_x", data=0.202)
-    sigma_x.attrs["units"] = "mm"
-    sigma_y = source.create_dataset(name="sigma_y", data=0.018)
-    sigma_y.attrs["units"] = "mm"
-    divergence_x = source.create_dataset(name="divergence_x", data=0.000135)
-    divergence_x.attrs["units"] = "radians"
-    divergence_y = source.create_dataset(name="divergence_y", data=0.000025)
-    divergence_y.attrs["units"] = "radians"
-    current = source.create_dataset(name="current", data=get_entry(data, "curr"))
-    current.attrs["units"] = "mA"
+        # ── /entry/data_soft ──────────────────────────────────────────────────
+        # Convenience group mirroring the old /entry/data hardlink from layout.xml.
+        data_soft = entry.create_group("data_soft")
+        data_soft.attrs["NX_class"] = "NXentry"
+        try:
+            for k in self.file_references["eiger_1_5"].hinted_h5_entries.keys():
+                self._safe_soft_link(data_soft, k, f"{EIGER_COLL}/{k}")
+        except Exception:
+            pass
 
-    insertion_device = instrument.create_group("insertion_device")
-    insertion_device.attrs["NX_class"] = "NXinsertion_device"
-    source.create_dataset(name="type", data="undulator")
-    gap = source.create_dataset(name="gap", data=get_entry(data, "idgap"))
-    gap.attrs["units"] = "mm"
-    k = source.create_dataset(name="k", data=2.46)
-    k.attrs["units"] = "NX_DIMENSIONLESS"
-    length = source.create_dataset(name="length", data=1820)
-    length.attrs["units"] = "mm"
+        # ── /entry/control ────────────────────────────────────────────────────
+        control = entry.create_group("control")
+        control.attrs["NX_class"] = "NXmonitor"
+        control.create_dataset("mode", data="monitor")
+        # TODO: beam intensity integral — add device when available
+        # self._safe_dataset(control, "integral", "bpm_sum", units="NX_DIMENSIONLESS")
 
-    slit_0 = instrument.create_group("slit_0")
-    slit_0.attrs["NX_class"] = "NXslit"
-    source.create_dataset(name="material", data="OFHC Cu")
-    source.create_dataset(name="description", data="Horizontal secondary source slit")
-    x_gap = source.create_dataset(name="x_gap", data=get_entry(data, "sl0wh"))
-    x_gap.attrs["units"] = "mm"
-    x_translation = source.create_dataset(name="x_translation", data=get_entry(data, "sl0ch"))
-    x_translation.attrs["units"] = "mm"
-    distance = source.create_dataset(
-        name="distance", data=-21700 - np.asarray(get_entry(data, "samz", 0))
-    )
-    distance.attrs["units"] = "mm"
+        # ── /entry/instrument ─────────────────────────────────────────────────
+        instrument = entry.create_group("instrument")
+        instrument.attrs["NX_class"] = "NXinstrument"
+        instrument.create_dataset("name", data="cSAXS beamline")
 
-    slit_1 = instrument.create_group("slit_1")
-    slit_1.attrs["NX_class"] = "NXslit"
-    source.create_dataset(name="material", data="OFHC Cu")
-    source.create_dataset(name="description", data="Horizontal secondary source slit")
-    x_gap = source.create_dataset(name="x_gap", data=get_entry(data, "sl1wh"))
-    x_gap.attrs["units"] = "mm"
-    y_gap = source.create_dataset(name="y_gap", data=get_entry(data, "sl1wv"))
-    y_gap.attrs["units"] = "mm"
-    x_translation = source.create_dataset(name="x_translation", data=get_entry(data, "sl1ch"))
-    x_translation.attrs["units"] = "mm"
-    height = source.create_dataset(name="x_translation", data=get_entry(data, "sl1ch"))
-    height.attrs["units"] = "mm"
-    distance = source.create_dataset(
-        name="distance", data=-7800 - np.asarray(get_entry(data, "samz", 0))
-    )
-    distance.attrs["units"] = "mm"
+        # ── Source ────────────────────────────────────────────────────────────
+        # Numerical values are currently unknown and stored as 0.
+        # Will be updated once the corresponding devices are in BEC.
+        source = instrument.create_group("source")
+        source.attrs["NX_class"] = "NXsource"
+        source.create_dataset("type",  data="Synchrotron X-ray Source")
+        source.create_dataset("name",  data="Swiss Light Source")
+        source.create_dataset("probe", data="x-ray")
+        source.create_dataset("sigma_x",      data=0.0).attrs["units"] = "mm"
+        source.create_dataset("sigma_y",      data=0.0).attrs["units"] = "mm"
+        source.create_dataset("divergence_x", data=0.0).attrs["units"] = "radians"
+        source.create_dataset("divergence_y", data=0.0).attrs["units"] = "radians"
+        # TODO: current — add device when available
+        # self._safe_dataset(source, "current", "curr", units="mA")
 
-    mono = instrument.create_group("monochromator")
-    mono.attrs["NX_class"] = "NXmonochromator"
-    mokev = data.get("mokev", {})
-    if mokev:
-        if isinstance(mokev, list):
-            mokev = mokev[0]
-        wavelength = mono.create_dataset(
-            name="wavelength", data=12.3984193 / (mokev.get("mokev").get("value") + 1e-9)
+        # ── Insertion device ──────────────────────────────────────────────────
+        insertion_device = instrument.create_group("insertion_device")
+        insertion_device.attrs["NX_class"] = "NXinsertion_device"
+        insertion_device.create_dataset("type",   data="undulator")
+        insertion_device.create_dataset("k",      data=0.0)
+        insertion_device.create_dataset("length", data=0.0).attrs["units"] = "mm"
+        # TODO: gap — add device when available
+        # self._safe_dataset(insertion_device, "gap", "idgap", units="mm")
+
+        # ── Monochromator ─────────────────────────────────────────────────────
+        # ccm_energy is a baseline device and is recorded in the scan data.
+        mono = instrument.create_group("monochromator")
+        mono.attrs["NX_class"] = "NXmonochromator"
+        mono.create_dataset("type", data="Double crystal fixed exit monochromator.")
+        try:
+            energy_kev = self.get_entry("ccm_energy")
+            energy_arr = np.asarray(energy_kev, dtype=float)
+            en_ds = mono.create_dataset("energy", data=energy_arr)
+            en_ds.attrs["units"] = "keV"
+            with np.errstate(divide="ignore", invalid="ignore"):
+                wavelength = np.where(energy_arr != 0, 12.3984193 / energy_arr, 0.0)
+            wl_ds = mono.create_dataset("wavelength", data=wavelength)
+            wl_ds.attrs["units"] = "Angstrom"
+        except Exception:
+            pass
+        # TODO: crystal angles — add moth1 / mobd when available
+        # crystal_1 = mono.create_group("crystal_1")
+        # crystal_1.attrs["NX_class"] = "NXcrystal"
+        # crystal_1.create_dataset("usage",      data="Bragg")
+        # crystal_1.create_dataset("type",       data="Si")
+        # crystal_1.create_dataset("order_no",   data=1.0)
+        # crystal_1.create_dataset("reflection", data="[1 1 1]")
+        # self._safe_dataset(crystal_1, "bragg_angle", "moth1", units="degrees")
+        # crystal_2 = mono.create_group("crystal_2")
+        # crystal_2.attrs["NX_class"] = "NXcrystal"
+        # crystal_2.create_dataset("usage",      data="Bragg")
+        # crystal_2.create_dataset("type",       data="Si")
+        # crystal_2.create_dataset("order_no",   data=2.0)
+        # crystal_2.create_dataset("reflection", data="[1 1 1]")
+        # self._safe_dataset(crystal_2, "bragg_angle", "moth1", units="degrees")
+        # self._safe_dataset(crystal_2, "bend_x",      "mobd",  units="degrees")
+
+        # ── Mirror ────────────────────────────────────────────────────────────
+        # TODO: mith, mibd, mirror_coating not yet in device list
+        # mirror = instrument.create_group("mirror")
+        # mirror.attrs["NX_class"] = "NXmirror"
+        # mirror.create_dataset("type", data="single")
+        # mirror.create_dataset(
+        #     "description",
+        #     data=(
+        #         "Grazing incidence mirror to reject high-harmonic wavelengths. "
+        #         "Three coating options: no coating (SiO2), rhodium (Rh), platinum (Pt)."
+        #     ),
+        # )
+        # mirror.create_dataset("substrate_material", data="SiO2")
+        # self._safe_dataset(mirror, "incident_angle",   "mith",          units="degrees")
+        # self._safe_dataset(mirror, "coating_material", "mirror_coating", units="NX_CHAR")
+        # self._safe_dataset(mirror, "bend_y",           "mibd",           units="NX_DIMENSIONLESS")
+
+        # ── Upstream slits (optics hutch) ─────────────────────────────────────
+        # TODO: slit_0 / slit_1 / slit_2 motors not yet in BEC device list
+        # slit_0 = instrument.create_group("slit_0")
+        # ...
+        # slit_1 = instrument.create_group("slit_1")
+        # ...
+        # slit_2 = instrument.create_group("slit_2")
+        # ...
+
+        # ── XBPM3 ─────────────────────────────────────────────────────────────
+        # xbpm3x/xbpm3y are stage motor positions for aligning the monitor.
+        # Signal readouts (sum/x/y/skew) are TODO once MCS channels are mapped.
+        xbpm3 = instrument.create_group("XBPM3")
+        xbpm3.attrs["NX_class"]    = "NXdetector"
+        xbpm3.attrs["description"] = "X-ray beam position monitor 3, experimental hutch"
+        self._safe_dataset(xbpm3, "x_stage", "xbpm3x", units="mm",
+                           description="XBPM3 stage x-translation")
+        self._safe_dataset(xbpm3, "y_stage", "xbpm3y", units="mm",
+                           description="XBPM3 stage y-translation")
+        # TODO: signal readout sub-groups once MCS channels are configured
+        # for suffix, entry_name, desc in [
+        #     ("sum",  "bpm3s", "Sum of counts for the four quadrants."),
+        #     ("x",    "bpm3x", "Normalized diff, left vs right quadrants."),
+        #     ("y",    "bpm3y", "Normalized diff, high vs low quadrants."),
+        #     ("skew", "bpm3z", "Normalized diff, diagonal quadrants."),
+        # ]:
+        #     g = xbpm3.create_group(f"XBPM3_{suffix}")
+        #     self._safe_dataset(g, "data", entry_name, units="NX_DIMENSIONLESS")
+        #     g.create_dataset("description", data=desc)
+
+        # ── Slit 3 (experimental hutch, exposure box) ─────────────────────────
+        slit_3 = instrument.create_group("slit_3")
+        slit_3.attrs["NX_class"] = "NXslit"
+        slit_3.create_dataset("material",    data="Si")
+        slit_3.create_dataset("description", data="Slit 3, experimental hutch, exposure box")
+        # TODO: gap / centre require per-slit calibration offset — add later
+        self._slit_blades(slit_3, "sl3")
+
+        # ── Filter set ────────────────────────────────────────────────────────
+        filter_set = instrument.create_group("filter_set")
+        filter_set.attrs["NX_class"] = "NXattenuator"
+        filter_set.create_dataset("material", data="Si")
+        filter_set.create_dataset(
+            "description",
+            data=(
+                "Four linear filter stages (filter_array_1_x … filter_array_4_x). "
+                "Each stage has five filter positions plus an 'out' position."
+            ),
         )
-        wavelength.attrs["units"] = "Angstrom"
-        energy = mono.create_dataset(name="energy", data=mokev.get("mokev").get("value"))
-        energy.attrs["units"] = "keV"
-    mono.create_dataset(name="type", data="Double crystal fixed exit monochromator.")
-    distance = mono.create_dataset(
-        name="distance", data=-5220 - np.asarray(get_entry(data, "samz", 0))
-    )
-    distance.attrs["units"] = "mm"
+        for i in range(1, 5):
+            self._safe_dataset(filter_set, f"stage_{i}_x",
+                               f"filter_array_{i}_x", units="mm")
+        # TODO: attenuator_transmission = 10^(ftrans) once device is available
 
-    crystal_1 = mono.create_group("crystal_1")
-    crystal_1.attrs["NX_class"] = "NXcrystal"
-    crystal_1.create_dataset(name="usage", data="Bragg")
-    crystal_1.create_dataset(name="order_no", data="1")
-    crystal_1.create_dataset(name="reflection", data="[1 1 1]")
-    bragg_angle = crystal_1.create_dataset(name="bragg_angle", data=get_entry(data, "moth1"))
-    bragg_angle.attrs["units"] = "degrees"
+        # ── Slit 4 (experimental hutch, exposure box) ─────────────────────────
+        slit_4 = instrument.create_group("slit_4")
+        slit_4.attrs["NX_class"] = "NXslit"
+        slit_4.create_dataset("material",    data="Ge")
+        slit_4.create_dataset("description", data="Slit 4, experimental hutch, exposure box")
+        self._slit_blades(slit_4, "sl4")
 
-    crystal_2 = mono.create_group("crystal_2")
-    crystal_2.attrs["NX_class"] = "NXcrystal"
-    crystal_2.create_dataset(name="usage", data="Bragg")
-    crystal_2.create_dataset(name="order_no", data="2")
-    crystal_2.create_dataset(name="reflection", data="[1 1 1]")
-    bragg_angle = crystal_2.create_dataset(name="bragg_angle", data=get_entry(data, "moth1"))
-    bragg_angle.attrs["units"] = "degrees"
-    bend_x = crystal_2.create_dataset(name="bend_x", data=get_entry(data, "mobd"))
-    bend_x.attrs["units"] = "degrees"
+        # ── Slit 5 (experimental hutch, exposure box) ─────────────────────────
+        slit_5 = instrument.create_group("slit_5")
+        slit_5.attrs["NX_class"] = "NXslit"
+        slit_5.create_dataset("material",    data="Si")
+        slit_5.create_dataset("description", data="Slit 5, experimental hutch, exposure box")
+        self._slit_blades(slit_5, "sl5")
 
-    xbpm4 = instrument.create_group("XBPM4")
-    xbpm4.attrs["NX_class"] = "NXdetector"
-    xbpm4_sum = xbpm4.create_group("XBPM4_sum")
-    xbpm4_sum_data = xbpm4_sum.create_dataset(name="data", data=get_entry(data, "bpm4s"))
-    xbpm4_sum_data.attrs["units"] = "NX_DIMENSIONLESS"
-    xbpm4_sum.create_dataset(name="description", data="Sum of counts for the four quadrants.")
-    xbpm4_x = xbpm4.create_group("XBPM4_x")
-    xbpm4_x_data = xbpm4_x.create_dataset(name="data", data=get_entry(data, "bpm4x"))
-    xbpm4_x_data.attrs["units"] = "NX_DIMENSIONLESS"
-    xbpm4_x.create_dataset(
-        name="description", data="Normalized difference of counts between left and right quadrants."
-    )
-    xbpm4_y = xbpm4.create_group("XBPM4_y")
-    xbpm4_y_data = xbpm4_y.create_dataset(name="data", data=get_entry(data, "bpm4y"))
-    xbpm4_y_data.attrs["units"] = "NX_DIMENSIONLESS"
-    xbpm4_y.create_dataset(
-        name="description", data="Normalized difference of counts between high and low quadrants."
-    )
-    xbpm4_skew = xbpm4.create_group("XBPM4_skew")
-    xbpm4_skew_data = xbpm4_skew.create_dataset(name="data", data=get_entry(data, "bpm4z"))
-    xbpm4_skew_data.attrs["units"] = "NX_DIMENSIONLESS"
-    xbpm4_skew.create_dataset(
-        name="description", data="Normalized difference of counts between diagonal quadrants."
-    )
+        # ── Beam stop 1 ────────────────────────────────────────────────────────
+        beam_stop_1 = instrument.create_group("beam_stop_1")
+        beam_stop_1.attrs["NX_class"] = "NXbeam_stop"
+        beam_stop_1.create_dataset("description", data="circular")
+        beam_stop_1.create_dataset("size", data=3.0).attrs["units"] = "mm"
+        self._safe_dataset(beam_stop_1, "x", "bs1x", units="mm")
+        self._safe_dataset(beam_stop_1, "y", "bs1y", units="mm")
+        # TODO: diode signal behind beam stop 1 when device is available
 
-    mirror = instrument.create_group("mirror")
-    mirror.attrs["NX_class"] = "NXmirror"
-    mirror.create_dataset(name="type", data="single")
-    mirror.create_dataset(
-        name="description",
-        data="Grazing incidence mirror to reject high-harmonic wavelengths from the monochromator. There are three coating options available that are used depending on the X-ray energy, no coating (SiO2), rhodium (Rh) or platinum (Pt).",
-    )
-    incident_angle = mirror.create_dataset(name="incident_angle", data=get_entry(data, "mith"))
-    incident_angle.attrs["units"] = "degrees"
-    substrate_material = mirror.create_dataset(name="substrate_material", data="SiO2")
-    substrate_material.attrs["units"] = "NX_CHAR"
-    coating_material = mirror.create_dataset(name="coating_material", data="SiO2")
-    coating_material.attrs["units"] = "NX_CHAR"
-    bend_y = mirror.create_dataset(name="bend_y", data="mibd")
-    bend_y.attrs["units"] = "NX_DIMENSIONLESS"
-    distance = mirror.create_dataset(
-        name="distance", data=-4370 - np.asarray(get_entry(data, "samz", 0))
-    )
-    distance.attrs["units"] = "mm"
+        # ── Beam stop 2 ────────────────────────────────────────────────────────
+        beam_stop_2 = instrument.create_group("beam_stop_2")
+        beam_stop_2.attrs["NX_class"] = "NXbeam_stop"
+        beam_stop_2.create_dataset("description", data="rectangular")
+        beam_stop_2.create_dataset("size_x", data=5.0).attrs["units"]  = "mm"
+        beam_stop_2.create_dataset("size_y", data=2.25).attrs["units"] = "mm"
+        self._safe_dataset(beam_stop_2, "x", "bs2x", units="mm")
+        self._safe_dataset(beam_stop_2, "y", "bs2y", units="mm")
+        # TODO: diode (transmitted signal) when device is available
 
-    xbpm5 = instrument.create_group("XBPM5")
-    xbpm5.attrs["NX_class"] = "NXdetector"
-    xbpm5_sum = xbpm5.create_group("XBPM5_sum")
-    xbpm5_sum_data = xbpm5_sum.create_dataset(name="data", data=get_entry(data, "bpm5s"))
-    xbpm5_sum_data.attrs["units"] = "NX_DIMENSIONLESS"
-    xbpm5_sum.create_dataset(name="description", data="Sum of counts for the four quadrants.")
-    xbpm5_x = xbpm5.create_group("XBPM5_x")
-    xbpm5_x_data = xbpm5_x.create_dataset(name="data", data=get_entry(data, "bpm5x"))
-    xbpm5_x_data.attrs["units"] = "NX_DIMENSIONLESS"
-    xbpm5_x.create_dataset(
-        name="description", data="Normalized difference of counts between left and right quadrants."
-    )
-    xbpm5_y = xbpm5.create_group("XBPM5_y")
-    xbpm5_y_data = xbpm5_y.create_dataset(name="data", data=get_entry(data, "bpm5y"))
-    xbpm5_y_data.attrs["units"] = "NX_DIMENSIONLESS"
-    xbpm5_y.create_dataset(
-        name="description", data="Normalized difference of counts between high and low quadrants."
-    )
-    xbpm5_skew = xbpm5.create_group("XBPM5_skew")
-    xbpm5_skew_data = xbpm5_skew.create_dataset(name="data", data=get_entry(data, "bpm5z"))
-    xbpm5_skew_data.attrs["units"] = "NX_DIMENSIONLESS"
-    xbpm5_skew.create_dataset(
-        name="description", data="Normalized difference of counts between diagonal quadrants."
-    )
-
-    slit_2 = instrument.create_group("slit_2")
-    slit_2.attrs["NX_class"] = "NXslit"
-    source.create_dataset(name="material", data="Ag")
-    source.create_dataset(name="description", data="Slit 2, optics hutch")
-    x_gap = source.create_dataset(name="x_gap", data=get_entry(data, "sl2wh"))
-    x_gap.attrs["units"] = "mm"
-    y_gap = source.create_dataset(name="y_gap", data=get_entry(data, "sl2wv"))
-    y_gap.attrs["units"] = "mm"
-    x_translation = source.create_dataset(name="x_translation", data=get_entry(data, "sl2ch"))
-    x_translation.attrs["units"] = "mm"
-    height = source.create_dataset(name="x_translation", data=get_entry(data, "sl2cv"))
-    height.attrs["units"] = "mm"
-    distance = source.create_dataset(
-        name="distance", data=-3140 - np.asarray(get_entry(data, "samz", 0))
-    )
-    distance.attrs["units"] = "mm"
-
-    slit_3 = instrument.create_group("slit_3")
-    slit_3.attrs["NX_class"] = "NXslit"
-    source.create_dataset(name="material", data="Si")
-    source.create_dataset(name="description", data="Slit 3, experimental hutch, exposure box")
-    x_gap = source.create_dataset(name="x_gap", data=get_entry(data, "sl3wh"))
-    x_gap.attrs["units"] = "mm"
-    y_gap = source.create_dataset(name="y_gap", data=get_entry(data, "sl3wv"))
-    y_gap.attrs["units"] = "mm"
-    x_translation = source.create_dataset(name="x_translation", data=get_entry(data, "sl3ch"))
-    x_translation.attrs["units"] = "mm"
-    height = source.create_dataset(name="x_translation", data=get_entry(data, "sl3cv"))
-    height.attrs["units"] = "mm"
-    # distance = source.create_dataset(name="distance", data=-3140 - get_entry(data, "samz", 0))
-    # distance.attrs["units"] = "mm"
-
-    filter_set = instrument.create_group("filter_set")
-    filter_set.attrs["NX_class"] = "NXattenuator"
-    filter_set.create_dataset(name="material", data="Si")
-    filter_set.create_dataset(
-        name="description",
-        data="The filter set consists of 4 linear stages, each with five filter positions. Additionally, each one allows for an out position to allow 'no filtering'.",
-    )
-    attenuator_transmission = filter_set.create_dataset(
-        name="attenuator_transmission", data=10 ** get_entry(data, "ftrans", 0)
-    )
-    attenuator_transmission.attrs["units"] = "NX_DIMENSIONLESS"
-
-    slit_4 = instrument.create_group("slit_4")
-    slit_4.attrs["NX_class"] = "NXslit"
-    source.create_dataset(name="material", data="Si")
-    source.create_dataset(name="description", data="Slit 4, experimental hutch, exposure box")
-    x_gap = source.create_dataset(name="x_gap", data=get_entry(data, "sl4wh"))
-    x_gap.attrs["units"] = "mm"
-    y_gap = source.create_dataset(name="y_gap", data=get_entry(data, "sl4wv"))
-    y_gap.attrs["units"] = "mm"
-    x_translation = source.create_dataset(name="x_translation", data=get_entry(data, "sl4ch"))
-    x_translation.attrs["units"] = "mm"
-    height = source.create_dataset(name="x_translation", data=get_entry(data, "sl4cv"))
-    height.attrs["units"] = "mm"
-    # distance = source.create_dataset(name="distance", data=-3140 - get_entry(data, "samz", 0))
-    # distance.attrs["units"] = "mm"
-
-    slit_5 = instrument.create_group("slit_5")
-    slit_5.attrs["NX_class"] = "NXslit"
-    source.create_dataset(name="material", data="Si")
-    source.create_dataset(name="description", data="Slit 5, experimental hutch, exposure box")
-    x_gap = source.create_dataset(name="x_gap", data=get_entry(data, "sl5wh"))
-    x_gap.attrs["units"] = "mm"
-    y_gap = source.create_dataset(name="y_gap", data=get_entry(data, "sl5wv"))
-    y_gap.attrs["units"] = "mm"
-    x_translation = source.create_dataset(name="x_translation", data=get_entry(data, "sl5ch"))
-    x_translation.attrs["units"] = "mm"
-    height = source.create_dataset(name="x_translation", data=get_entry(data, "sl5cv"))
-    height.attrs["units"] = "mm"
-    # distance = source.create_dataset(name="distance", data=-3140 - get_entry(data, "samz", 0))
-    # distance.attrs["units"] = "mm"
-
-    beam_stop_1 = instrument.create_group("beam_stop_1")
-    beam_stop_1.attrs["NX_class"] = "NX_beamstop"
-    beam_stop_1.create_dataset(name="description", data="circular")
-    bms1_size = beam_stop_1.create_dataset(name="size", data=3)
-    bms1_size.attrs["units"] = "mm"
-    bms1_x = beam_stop_1.create_dataset(name="size", data=get_entry(data, "bs1x"))
-    bms1_x.attrs["units"] = "mm"
-    bms1_y = beam_stop_1.create_dataset(name="size", data=get_entry(data, "bs1y"))
-    bms1_y.attrs["units"] = "mm"
-
-    beam_stop_2 = instrument.create_group("beam_stop_2")
-    beam_stop_2.attrs["NX_class"] = "NX_beamstop"
-    beam_stop_2.create_dataset(name="description", data="rectangular")
-    bms2_size_x = beam_stop_2.create_dataset(name="size_x", data=5)
-    bms2_size_x.attrs["units"] = "mm"
-    bms2_size_y = beam_stop_2.create_dataset(name="size_y", data=2.25)
-    bms2_size_y.attrs["units"] = "mm"
-    bms2_x = beam_stop_2.create_dataset(name="size", data=get_entry(data, "bs2x"))
-    bms2_x.attrs["units"] = "mm"
-    bms2_y = beam_stop_2.create_dataset(name="size", data=get_entry(data, "bs2y"))
-    bms2_y.attrs["units"] = "mm"
-    bms2_data = beam_stop_2.create_dataset(name="data", data=get_entry(data, "diode"))
-    bms2_data.attrs["units"] = "NX_DIMENSIONLESS"
-
-    if "eiger1p5m" in device_manager.devices and device_manager.devices.eiger1p5m.enabled:
-        eiger_4 = instrument.create_group("eiger_4")
-        eiger_4.attrs["NX_class"] = "NXdetector"
-        x_pixel_size = eiger_4.create_dataset(name="x_pixel_size", data=75)
-        x_pixel_size.attrs["units"] = "um"
-        y_pixel_size = eiger_4.create_dataset(name="y_pixel_size", data=75)
-        y_pixel_size.attrs["units"] = "um"
-        polar_angle = eiger_4.create_dataset(name="polar_angle", data=0)
-        polar_angle.attrs["units"] = "degrees"
-        azimuthal_angle = eiger_4.create_dataset(name="azimuthal_angle", data=0)
-        azimuthal_angle.attrs["units"] = "degrees"
-        rotation_angle = eiger_4.create_dataset(name="rotation_angle", data=0)
-        rotation_angle.attrs["units"] = "degrees"
-        description = eiger_4.create_dataset(
-            name="description", data="Single-photon counting detector, 320 micron-thick Si chip"
-        )
-        orientation = eiger_4.create_group("orientation")
-        orientation.attrs["description"] = (
-            "Orientation defines the number of counterclockwise rotations by 90 deg followed by a transposition to reach the 'cameraman orientation', that is looking towards the beam."
-        )
-        orientation.create_dataset(name="transpose", data=1)
-        orientation.create_dataset(name="rot90", data=3)
-
-    if (
-        "eiger9m" in device_manager.devices
-        and device_manager.devices.eiger9m.enabled
-        and "eiger9m" in file_references
-    ):
-        eiger9m = instrument.create_group("eiger9m")
-        eiger9m.attrs["NX_class"] = "NXdetector"
-        x_pixel_size = eiger9m.create_dataset(name="x_pixel_size", data=75)
-        x_pixel_size.attrs["units"] = "um"
-        y_pixel_size = eiger9m.create_dataset(name="y_pixel_size", data=75)
-        y_pixel_size.attrs["units"] = "um"
-        polar_angle = eiger9m.create_dataset(name="polar_angle", data=0)
-        polar_angle.attrs["units"] = "degrees"
-        azimuthal_angle = eiger9m.create_dataset(name="azimuthal_angle", data=0)
-        azimuthal_angle.attrs["units"] = "degrees"
-        rotation_angle = eiger9m.create_dataset(name="rotation_angle", data=0)
-        rotation_angle.attrs["units"] = "degrees"
-        description = eiger9m.create_dataset(
-            name="description", data="Eiger9M detector, in-house developed, Paul Scherrer Institute"
-        )
-        orientation = eiger9m.create_group("orientation")
-        orientation.attrs["description"] = (
-            "Orientation defines the number of counterclockwise rotations by 90 deg followed by a transposition to reach the 'cameraman orientation', that is looking towards the beam."
-        )
-        orientation.create_dataset(name="transpose", data=1)
-        orientation.create_dataset(name="rot90", data=3)
-        data = eiger9m.create_ext_link("data", file_references["eiger9m"]["path"], "EG9M/data")
-        status = eiger9m.create_ext_link(
-            "status", file_references["eiger9m"]["path"], "EG9M/status"
+        # ── Detector translation ───────────────────────────────────────────────
+        self._safe_dataset(
+            instrument, "detector_translation_x", "dettrx",
+            units="mm", description="Detector x-translation stage",
         )
 
-    if (
-        "pilatus_2" in device_manager.devices
-        and device_manager.devices.pilatus_2.enabled
-        and "pilatus_2" in file_references
-    ):
-        pilatus_2 = instrument.create_group("pilatus_2")
-        pilatus_2.attrs["NX_class"] = "NXdetector"
-        x_pixel_size = pilatus_2.create_dataset(name="x_pixel_size", data=172)
-        x_pixel_size.attrs["units"] = "um"
-        y_pixel_size = pilatus_2.create_dataset(name="y_pixel_size", data=172)
-        y_pixel_size.attrs["units"] = "um"
-        polar_angle = pilatus_2.create_dataset(name="polar_angle", data=0)
-        polar_angle.attrs["units"] = "degrees"
-        azimuthal_angle = pilatus_2.create_dataset(name="azimuthal_angle", data=0)
-        azimuthal_angle.attrs["units"] = "degrees"
-        rotation_angle = pilatus_2.create_dataset(name="rotation_angle", data=0)
-        rotation_angle.attrs["units"] = "degrees"
-        description = pilatus_2.create_dataset(
-            name="description", data="Pilatus 300K detector, Dectris, Switzerland"
-        )
-        orientation = pilatus_2.create_group("orientation")
-        orientation.attrs["description"] = (
-            "Orientation defines the number of counterclockwise rotations by 90 deg followed by a transposition to reach the 'cameraman orientation', that is looking towards the beam."
-        )
-        orientation.create_dataset(name="transpose", data=1)
-        orientation.create_dataset(name="rot90", data=2)
-        data = pilatus_2.create_ext_link(
-            "data", file_references["pilatus_2"]["path"], "entry/instrument/pilatus_2/data"
-        )
+        # ── Eiger 1.5M detector ───────────────────────────────────────────────
+        if (
+            "eiger_1_5" in self.device_manager.devices
+            and self.device_manager.devices.eiger_1_5.enabled
+            and "eiger_1_5" in self.file_references
+        ):
+            eiger = instrument.create_group("eiger_1_5")
+            eiger.attrs["NX_class"] = "NXdetector"
+            eiger.create_dataset("x_pixel_size",    data=75.0).attrs["units"] = "um"
+            eiger.create_dataset("y_pixel_size",    data=75.0).attrs["units"] = "um"
+            eiger.create_dataset("polar_angle",     data=0.0).attrs["units"]  = "degrees"
+            eiger.create_dataset("azimuthal_angle", data=0.0).attrs["units"]  = "degrees"
+            eiger.create_dataset("rotation_angle",  data=0.0).attrs["units"]  = "degrees"
+            eiger.create_dataset(
+                "description",
+                data="Eiger 1.5M detector, in-house developed, Paul Scherrer Institute",
+            )
+            eiger.create_dataset(
+                "type",
+                data="Single-photon counting detector, 320 micron-thick Si chip",
+            )
+            orientation = eiger.create_group("orientation")
+            orientation.attrs["description"] = (
+                "Orientation defines the number of counterclockwise rotations by 90 deg "
+                "followed by a transposition to reach the 'cameraman orientation', "
+                "looking towards the beam."
+            )
+            orientation.create_dataset("transpose", data=1)
+            orientation.create_dataset("rot90",     data=3)
+            # Soft-link recorded frame data from the BEC collection
+            try:
+                for k in self.file_references["eiger_1_5"].hinted_h5_entries.keys():
+                    self._safe_soft_link(eiger, k, f"{EIGER_COLL}/{k}")
+            except Exception:
+                pass
+            # External link to pixel mask in the Eiger master file
+            try:
+                eiger.create_ext_link(
+                    "pixel_mask",
+                    self.file_references["eiger_1_5"].file_path,
+                    "/entry/instrument/detector/pixel_mask",
+                )
+            except Exception:
+                pass
 
-    if (
-        "falcon" in device_manager.devices
-        and device_manager.devices.falcon.enabled
-        and "falcon" in file_references
-    ):
-        falcon = instrument.create_ext_link(
-            "falcon", file_references["falcon"]["path"], "entry/instrument/FalconX1"
-        )
+        # ── MCS (multi-channel scaler) ─────────────────────────────────────────
+        if (
+            "mcs" in self.device_manager.devices
+            and self.device_manager.devices.mcs.enabled
+        ):
+            mcs_group = instrument.create_group("mcs")
+            mcs_group.attrs["NX_class"]    = "NXdetector"
+            mcs_group.attrs["description"] = "MCS card cSAXS — multi-channel scaler"
+            self._safe_soft_link(mcs_group, "data", "/entry/collection/devices/mcs")
 
-    return storage
+        # ── flOMNI ────────────────────────────────────────────────────────────
+        # flomni_samples is used as the sentinel for the entire flOMNI setup.
+        # If it is absent from the device_manager (removed from config) the
+        # whole group is omitted. Individual datasets inside are still each
+        # guarded by _safe_dataset / _safe_soft_link in case a specific motor
+        # is temporarily disabled without removing the full setup.
+        if "flomni_samples" in self.device_manager.devices:
+            flomni = instrument.create_group("flOMNI")
+            flomni.attrs["NX_class"]    = "NXpositioner"
+            flomni.attrs["description"] = "flOMNI flexible tOMography Nano Imaging"
+
+            # Galil motors — coarse sample stage
+            self._safe_dataset(flomni, "fsamx",   "fsamx",   units="mm",      description="Sample coarse X")
+            self._safe_dataset(flomni, "fsamy",   "fsamy",   units="mm",      description="Sample coarse Y")
+            self._safe_dataset(flomni, "fsamroy", "fsamroy", units="degrees",  description="Sample rotation")
+
+            # Galil motors — sample transfer / tray
+            self._safe_dataset(flomni, "ftransx", "ftransx", units="mm", description="Sample transfer X")
+            self._safe_dataset(flomni, "ftransy", "ftransy", units="mm", description="Sample transfer Y")
+            self._safe_dataset(flomni, "ftransz", "ftransz", units="mm", description="Sample transfer Z")
+            self._safe_dataset(flomni, "ftray",   "ftray",   units="mm", description="Sample transfer tray")
+
+            # Galil motors — laser tracker
+            self._safe_dataset(flomni, "ftracky", "ftracky", units="mm", description="Laser tracker coarse Y")
+            self._safe_dataset(flomni, "ftrackz", "ftrackz", units="mm", description="Laser tracker coarse Z")
+
+            # Galil motors — X-ray eye
+            self._safe_dataset(flomni, "feyex", "feyex", units="mm", description="X-ray eye X")
+            self._safe_dataset(flomni, "feyey", "feyey", units="mm", description="X-ray eye Y")
+
+            # Galil motors — optics (zone plate)
+            self._safe_dataset(flomni, "foptx", "foptx", units="mm", description="Optics X")
+            self._safe_dataset(flomni, "fopty", "fopty", units="mm", description="Optics Y")
+            self._safe_dataset(flomni, "foptz", "foptz", units="mm", description="Optics Z")
+
+            # Galil motor — heater
+            self._safe_dataset(flomni, "fheater", "fheater", units="mm", description="Heater Y")
+
+            # Smaract motors — OSA (order-sorting aperture)
+            self._safe_dataset(flomni, "fosax", "fosax", units="mm", description="OSA X")
+            self._safe_dataset(flomni, "fosay", "fosay", units="mm", description="OSA Y")
+            self._safe_dataset(flomni, "fosaz", "fosaz", units="mm", description="OSA Z")
+
+            # Temperature and humidity sensor (soft link to BEC collection entry)
+            self._safe_soft_link(
+                flomni, "flomni_temphum",
+                "/entry/collection/devices/flomni_temphum",
+            )
+
+            # Real-time encoder positions (RtFlomniFlyer)
+            # Single soft link to the entire rt_positions folder in the BEC
+            # collection. This is the primary scan coordinate for ptychography.
+            self._safe_soft_link(
+                flomni, "rt_positions",
+                "/entry/collection/devices/rt_positions",
+            )

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_positions"]})
+
+    @property
+    def monitor_sync(self) -> str:
+        return "rt_positions"
+
     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_positions")
 
+        # start the readout loop of the flyer
+        status = yield from self.stubs.complete(device="rt_positions", 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

tests/tests_devices/test_omny_shutter.py

@@ -0,0 +1,69 @@
+import pytest
+from bec_server.device_server.tests.utils import DMMock
+
+from csaxs_bec.devices.omny.shutter import MonitorSignal, OMNYFastShutter
+
+
+@pytest.mark.parametrize("auto_monitor", [False, True])
+def test_monitor_signal_stores_auto_monitor(auto_monitor):
+    signal = MonitorSignal(name="signal", auto_monitor=auto_monitor)
+
+    assert signal.auto_monitor is auto_monitor
+
+
+def test_monitor_signal_put_propagates_value_to_readback_callback():
+    signal = MonitorSignal(name="signal", auto_monitor=True)
+    initial_value = signal.read()[signal.name]["value"]
+    callback_values = []
+    callback_reads = []
+
+    def _test_cb(value, old_value, **kwargs):
+        callback_values.append((value, old_value))
+        callback_reads.append(kwargs["obj"].read())
+
+    signal.subscribe(_test_cb, event_type=signal.SUB_VALUE, run=False)
+
+    signal.put(1)
+
+    assert callback_values == [(1, initial_value)]
+    assert len(callback_reads) == 1
+    assert callback_reads[0][signal.name]["value"] == 1
+    assert signal.read()[signal.name]["value"] == 1
+
+    signal.put(0)
+    assert callback_values == [(1, initial_value), (0, 1)]
+    assert len(callback_reads) == 2
+    assert callback_reads[1][signal.name]["value"] == 0
+    assert signal.read()[signal.name]["value"] == 0
+
+
+@pytest.fixture
+def omny_fast_shutter():
+    shutter = OMNYFastShutter(name="omny_fast_shutter", device_manager=DMMock())
+
+    try:
+        yield shutter
+    finally:
+        shutter.destroy()
+
+
+def test_omny_fast_shutter_uses_monitor_signal_with_auto_monitor(omny_fast_shutter):
+    assert isinstance(omny_fast_shutter.shutter, MonitorSignal)
+    assert omny_fast_shutter.shutter.auto_monitor is True
+
+
+def test_omny_fast_shutter_propagates_signal_changes_to_device_readback(omny_fast_shutter):
+    signal_name = omny_fast_shutter.shutter.name
+    callback_reads = []
+
+    def _test_cb(**kwargs):
+        callback_reads.append(omny_fast_shutter.read())
+
+    omny_fast_shutter.shutter.subscribe(_test_cb, event_type=omny_fast_shutter.shutter.SUB_VALUE, run=False)
+
+    omny_fast_shutter.shutter.put(1)
+
+    assert len(callback_reads) == 1
+    assert callback_reads[0][signal_name]["value"] == 1
+    assert omny_fast_shutter.read()[signal_name]["value"] == 1
+    assert omny_fast_shutter.fshstatus() == 1

tests/tests_devices/test_pseudo_devices.py

@@ -0,0 +1,241 @@
+"""Module to test the pseudo_device module."""
+
+import pytest
+from bec_lib.atlas_models import Device
+from ophyd_devices.sim.sim_signals import SetableSignal
+
+from csaxs_bec.devices.pseudo_devices.bpm import BPM
+from csaxs_bec.devices.pseudo_devices.bpm_control import _GAIN_TO_BITS, BPMControl
+
+
+@pytest.fixture
+def patched_dm(dm_with_devices):
+    # Patch missing current_session attribute in the device manager
+    dm = dm_with_devices
+    setattr(dm, "current_session", dm._session)
+    #
+    signal_lsb = SetableSignal(name="gain_lsb", value=0, kind="config")
+    signal_mid = SetableSignal(name="gain_mid", value=0, kind="config")
+    signal_msb = SetableSignal(name="gain_msb", value=0, kind="config")
+    signal_coupling = SetableSignal(name="coupling", value=0, kind="config")
+    signal_speed = SetableSignal(name="speed_mode", value=0, kind="config")
+    for signal in [signal_lsb, signal_mid, signal_msb, signal_coupling, signal_speed]:
+        dev_cfg = Device(
+            name=signal.name,
+            deviceClass="ophyd_devices.sim.sim_signals.SetableSignal",
+            enabled=True,
+            readoutPriority="baseline",
+        )
+        dm._session["devices"].append(dev_cfg.model_dump())
+        dm.devices._add_device(signal.name, signal)
+    return dm
+
+
+@pytest.fixture
+def bpm_control(patched_dm):
+    name = "bpm_control"
+    control_config = Device(
+        name=name,
+        deviceClass="csaxs_bec.devices.pseudo_devices.bpm_control.BPMControl",
+        enabled=True,
+        readoutPriority="baseline",
+        deviceConfig={
+            "gain_lsb": "gain_lsb",
+            "gain_mid": "gain_mid",
+            "gain_msb": "gain_msb",
+            "coupling": "coupling",
+            "speed_mode": "speed_mode",
+        },
+        needs=["gain_lsb", "gain_mid", "gain_msb", "coupling", "speed_mode"],
+    )
+    patched_dm._session["devices"].append(control_config.model_dump())
+    try:
+        control = BPMControl(
+            name=name,
+            gain_lsb="gain_lsb",
+            gain_mid="gain_mid",
+            gain_msb="gain_msb",
+            coupling="coupling",
+            speed_mode="speed_mode",
+            device_manager=patched_dm,
+        )
+        patched_dm.devices._add_device(control.name, control)
+        control.wait_for_connection()
+        yield control
+    finally:
+        control.destroy()
+
+
+def test_bpm_control_set_gain(bpm_control):
+    gain_lsb = bpm_control.device_manager.devices["gain_lsb"]
+    gain_mid = bpm_control.device_manager.devices["gain_mid"]
+    gain_msb = bpm_control.device_manager.devices["gain_msb"]
+    coupling = bpm_control.device_manager.devices["coupling"]
+    speed_mode = bpm_control.device_manager.devices["speed_mode"]
+    gain_lsb.put(0)
+    gain_mid.put(0)
+    gain_msb.put(0)
+    coupling.put(0)
+    speed_mode.put(1)
+
+    gain = bpm_control.gain.get()
+    assert _GAIN_TO_BITS.get(gain) == (0, 0, 0, speed_mode.get() == 1)
+
+    gain_val = 10000000
+    bpm_control.set_gain(gain_val)
+    assert _GAIN_TO_BITS.get(gain_val, ()) == (
+        gain_msb.get(),
+        gain_mid.get(),
+        gain_lsb.get(),
+        speed_mode.get(),
+    )
+
+    gain_val = 100000000000
+    bpm_control.set_gain(gain_val)
+    assert _GAIN_TO_BITS.get(gain_val, ()) == (
+        gain_msb.get(),
+        gain_mid.get(),
+        gain_lsb.get(),
+        speed_mode.get(),
+    )
+
+    with pytest.raises(ValueError):
+        bpm_control.set_gain(1005.0)
+
+
+def test_bpm_control_set_coupling(bpm_control):
+    coupling = bpm_control.device_manager.devices["coupling"]
+    coupling.put(0)
+
+    bpm_control.coupling.get() == "AC"
+    coupling.put(1)
+    bpm_control.coupling.get() == "DC"
+
+    bpm_control.set_coupling("AC")
+    assert coupling.get() == 0
+
+    with pytest.raises(ValueError):
+        bpm_control.set_coupling("wrong")
+
+
+@pytest.fixture
+def patched_dm_bpm(dm_with_devices):
+    # Patch missing current_session attribute in the device manager
+    dm = dm_with_devices
+    setattr(dm, "current_session", dm._session)
+    #
+    left_top = SetableSignal(name="left_top", value=0, kind="config")
+    right_top = SetableSignal(name="right_top", value=0, kind="config")
+    right_bot = SetableSignal(name="right_bot", value=0, kind="config")
+    left_bot = SetableSignal(name="left_bot", value=0, kind="config")
+    for signal in [left_top, right_top, right_bot, left_bot]:
+
+        dev_cfg = Device(
+            name=signal.name,
+            deviceClass="ophyd_devices.sim.sim_signals.SetableSignal",
+            enabled=True,
+            readoutPriority="baseline",
+        )
+        dm._session["devices"].append(dev_cfg.model_dump())
+        dm.devices._add_device(signal.name, signal)
+    return dm
+
+
+@pytest.fixture
+def bpm(patched_dm_bpm):
+    name = "bpm"
+    bpm_config = Device(
+        name=name,
+        deviceClass="csaxs_bec.devices.pseudo_devices.bpm.BPM",
+        enabled=True,
+        readoutPriority="baseline",
+        deviceConfig={
+            "left_top": "left_top",
+            "right_top": "right_top",
+            "right_bot": "right_bot",
+            "left_bot": "left_bot",
+        },
+        needs=["left_top", "right_top", "right_bot", "left_bot"],
+    )
+    patched_dm_bpm._session["devices"].append(bpm_config.model_dump())
+    try:
+        bpm = BPM(
+            name=name,
+            left_top="left_top",
+            right_top="right_top",
+            right_bot="right_bot",
+            left_bot="left_bot",
+            device_manager=patched_dm_bpm,
+        )
+        patched_dm_bpm.devices._add_device(bpm.name, bpm)
+        bpm.wait_for_connection()
+        yield bpm
+    finally:
+        bpm.destroy()
+
+
+def test_bpm_positions(bpm):
+    left_top = bpm.device_manager.devices["left_top"]
+    right_top = bpm.device_manager.devices["right_top"]
+    right_bot = bpm.device_manager.devices["right_bot"]
+    left_bot = bpm.device_manager.devices["left_bot"]
+
+    # Test center position
+    for signal in [left_top, right_top, right_bot, left_bot]:
+        signal.put(1)
+    assert bpm.pos_x.get() == 0
+    assert bpm.pos_y.get() == 0
+
+    # Test fully left
+    left_top.put(1)
+    right_top.put(0)
+    right_bot.put(0)
+    left_bot.put(1)
+    assert bpm.pos_x.get() == -1
+    assert bpm.pos_y.get() == 0
+    assert bpm.diagonal.get() == 0
+    assert bpm.intensity.get() == 2
+
+    # Test fully right
+    left_top.put(0)
+    right_top.put(1)
+    right_bot.put(1)
+    left_bot.put(0)
+    assert bpm.pos_x.get() == 1
+    assert bpm.pos_y.get() == 0
+    assert bpm.diagonal.get() == 0
+
+    # Test fully top
+    left_top.put(1)
+    right_top.put(1)
+    right_bot.put(0)
+    left_bot.put(0)
+    assert bpm.pos_x.get() == 0
+    assert bpm.pos_y.get() == 1
+    assert bpm.diagonal.get() == 0
+
+    # Test fully bottom
+    left_top.put(0)
+    right_top.put(0)
+    right_bot.put(1)
+    left_bot.put(1)
+    assert bpm.pos_x.get() == 0
+    assert bpm.pos_y.get() == -1
+    assert bpm.diagonal.get() == 0
+
+    # Diagonal beam
+    left_top.put(1)
+    right_top.put(0)
+    right_bot.put(1)
+    left_bot.put(0)
+    assert bpm.pos_x.get() == 0
+    assert bpm.pos_y.get() == 0
+    assert bpm.diagonal.get() == -1
+
+    left_top.put(0)
+    right_top.put(1)
+    right_bot.put(0)
+    left_bot.put(1)
+    assert bpm.pos_x.get() == 0
+    assert bpm.pos_y.get() == 0
+    assert bpm.diagonal.get() == 1