fix(file_writer): Fix file_writer format method.

.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/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 +1309,18 @@ 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
+        )
+        self._webpage_gen.start()
+
         self.OMNYTools = OMNYTools(self.client)
         self.reconstructor = PtychoReconstructor(self.ptycho_reconstruct_foldername)
         self.tomo_id_manager = TomoIDManager()
@@ -1224,7 +1329,10 @@ 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 +1344,7 @@ 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 +1376,42 @@ 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 +1598,11 @@ 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 +1610,11 @@ 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 +1626,6 @@ 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 +1634,33 @@ 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 +1668,6 @@ 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 +1690,19 @@ 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 +1711,23 @@ 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 +1743,9 @@ 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 +1754,24 @@ 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 +1806,14 @@ 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()
 
@@ -1730,6 +1841,8 @@ class Flomni(
             #     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 +1851,7 @@ 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 +1862,6 @@ 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 +1909,6 @@ 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 +1945,47 @@ 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 +2009,6 @@ 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 +2068,7 @@ 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 +2079,6 @@ class Flomni(
 
         dev.rtx.controller.laser_tracker_check_signalstrength()
 
-
         scans = builtins.__dict__.get("scans")
 
         # additional_correction = self.align.compute_additional_correction(angle)
@@ -1978,7 +2113,7 @@ 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 +2126,9 @@ class Flomni(
                     corridor_size=corridor_size,
                 )
 
+        self.tomo_reconstruct()
+
+
     def tomo_parameters(self):
         """print and update the tomo parameters"""
         print("Current settings:")
@@ -2033,7 +2171,6 @@ 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 +2267,21 @@ 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 +2290,38 @@ 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 +2338,4 @@ 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_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
@@ -558,7 +558,7 @@ xbimtrx:
     # precision: 3
     # tolerance: 0.005
   enabled: true
-  onFailure: buffer
+  onFailure: retry
   readOnly: false
   readoutPriority: baseline
   connectionTimeout: 20
@@ -581,7 +581,7 @@ xbimtry:
     # precision: 3
     # tolerance: 0.005
   enabled: true
-  onFailure: buffer
+  onFailure: retry
   readOnly: false
   readoutPriority: baseline
   connectionTimeout: 20
@@ -589,3 +589,237 @@ 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

csaxs_bec/device_configs/bl_optics_hutch.yaml

@@ -68,91 +68,106 @@ ccmx:
   - cSAXS
   - optics
 
+# ccm_energy:
+#   readoutPriority: baseline
+#   deviceClass: ophyd_devices.devices.simple_positioner.PSIPositionerBase
+#     prefix: "X12SA-OP-CCM1:"
+#     override_suffixes:
+#       user_readback: "ENERGY-GET"
+#       user_setpoint: "ENERGY-SET"
+#       velocity: "ROTY:VELO"
+#   deviceTags:
+#   - user motors
+#   enabled: true
+#   readOnly: 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

@@ -10,8 +10,8 @@
 endstation:
   - !include ./bl_endstation.yaml
 
-detectors:
-  - !include ./bl_detectors.yaml
+# detectors:
+#   - !include ./bl_detectors.yaml
 
 #sastt:
 #  - !include ./sastt.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 +522,18 @@ 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
   deviceTags:
     - detector
   enabled: true

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/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 +1,472 @@
 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.
-
-    Args:
-        data (dict): Scan data
-        name (str): Entry name
-        default (Any, optional): Default value. Defaults to None.
+    NeXus file format for cSAXS beamline. This format is based on the default NeXus format, but with some additional entries specific to the cSAXS beamline. The structure of the file is based on the NeXus standard, but with some additional groups and datasets specific to the cSAXS beamline.
     """
-    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)
+    def format(self) -> None:
+        """
+        Prepare the NeXus file format.
+        Override this method in file writer plugins to customize the HDF5 file format.
 
+        The class provides access to the following attributes:
+        - self.storage: The HDF5Storage object.
+        - self.data: The data dictionary.
+        - self.file_references: The file references dictionary, which has the link to external data.
+        - self.device_manager: The DeviceManagerBase object.
+        - self.get_entry(name, default=None): Helper method to get an entry from the data dictionary.
 
-def NeXus_format(
-    storage: HDF5Storage, data: dict, file_references: dict, device_manager: DeviceManagerBase
-) -> HDF5Storage:
-    """
-    Prepare the NeXus file format.
+        See also: :class:`bec_server.file_writer.file_writer.HDF5Storage`.
 
-    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.
+        """
 
-    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
+        # entry = self.storage.create_group("entry")
 
-    # /entry/collection
-    collection = entry.create_group("collection")
-    collection.attrs["NX_class"] = "NXcollection"
-    bec_collection = collection.create_group("bec")
+        # # /entry/control
+        # control = entry.create_group("control")
+        # control.attrs["NX_class"] = "NXmonitor"
+        # control.create_dataset(name="mode", data="monitor")
 
-    # /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"))
+        # #########
+        # # EXAMPLE for soft link
+        # #########
+        # # /entry/data
+        # if "eiger_4" in self.device_manager.devices:
+        #     entry.create_soft_link(name="data", target="/entry/instrument/eiger_4")
 
-    # /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")
+        # ########
+        # # EXAMPLE for external link
+        # ########
+        # # control = entry.create_group("sample")
+        # # control.create_ext_link("data", self.file_references["eiger9m"]["path"], "EG9M/data")
 
-    # /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"
+        # # /entry/sample
+        # control = entry.create_group("sample")
+        # control.attrs["NX_class"] = "NXsample"
+        # control.create_dataset(name="name", data=self.data.get("samplename"))
+        # control.create_dataset(name="description", data=self.data.get("sample_description"))
 
-    # /entry/instrument
-    instrument = entry.create_group("instrument")
-    instrument.attrs["NX_class"] = "NXinstrument"
-    instrument.create_dataset(name="name", data="cSAXS beamline")
+        # # /entry/instrument
+        # instrument = entry.create_group("instrument")
+        # instrument.attrs["NX_class"] = "NXinstrument"
 
-    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"
+        # 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")
 
-    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
+        # entry = self.storage.create_group("entry")
+        # entry.attrs["NX_class"] = "NXentry"
+        # entry.attrs["definition"] = "NXsas"
+        # entry.attrs["start_time"] = self.data.get("start_time")
+        # entry.attrs["end_time"] = self.data.get("end_time")
+        # entry.attrs["version"] = 1.0
 
-    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/control
+        # control = entry.create_group("control")
+        # control.attrs["NX_class"] = "NXmonitor"
+        # control.create_dataset(name="mode", data="monitor")
+        # control.create_dataset(name="integral", data=self.get_entry("bpm4i"))
 
-    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"
+        # # /entry/data
+        # main_data = entry.create_group("data")
+        # main_data.attrs["NX_class"] = "NXdata"
+        # if "eiger_4" in self.device_manager.devices:
+        #     main_data.create_soft_link(name="data", target="/entry/instrument/eiger_4/data")
+        # elif "eiger9m" in self.device_manager.devices:
+        #     main_data.create_soft_link(name="data", target="/entry/instrument/eiger9m/data")
+        # elif "pilatus_2" in self.device_manager.devices:
+        #     main_data.create_soft_link(name="data", target="/entry/instrument/pilatus_2/data")
 
-    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)
-        )
-        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"
+        # # /entry/sample
+        # control = entry.create_group("sample")
+        # control.attrs["NX_class"] = "NXsample"
+        # control.create_dataset(name="name", data=self.get_entry("samplename"))
+        # control.create_dataset(name="description", data=self.data.get("sample_description"))
+        # x_translation = control.create_dataset(name="x_translation", data=self.get_entry("samx"))
+        # x_translation.attrs["units"] = "mm"
+        # y_translation = control.create_dataset(name="y_translation", data=self.get_entry("samy"))
+        # y_translation.attrs["units"] = "mm"
+        # temperature_log = control.create_dataset(
+        #     name="temperature_log", data=self.get_entry("temp")
+        # )
+        # temperature_log.attrs["units"] = "K"
 
-    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"
+        # # /entry/instrument
+        # instrument = entry.create_group("instrument")
+        # instrument.attrs["NX_class"] = "NXinstrument"
+        # instrument.create_dataset(name="name", data="cSAXS beamline")
 
-    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"
+        # 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(self.get_entry("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=self.get_entry("curr"))
+        # current.attrs["units"] = "mA"
 
-    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."
-    )
+        # 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=self.get_entry("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"
 
-    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"
+        # 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=self.get_entry("sl0wh"))
+        # x_gap.attrs["units"] = "mm"
+        # x_translation = source.create_dataset(name="x_translation", data=self.get_entry("sl0ch"))
+        # x_translation.attrs["units"] = "mm"
+        # distance = source.create_dataset(
+        #     name="distance", data=-21700 - np.asarray(self.get_entry("samz", 0))
+        # )
+        # distance.attrs["units"] = "mm"
 
-    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_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=self.get_entry("sl1wh"))
+        # x_gap.attrs["units"] = "mm"
+        # y_gap = source.create_dataset(name="y_gap", data=self.get_entry("sl1wv"))
+        # y_gap.attrs["units"] = "mm"
+        # x_translation = source.create_dataset(name="x_translation", data=self.get_entry("sl1ch"))
+        # x_translation.attrs["units"] = "mm"
+        # height = source.create_dataset(name="x_translation", data=self.get_entry("sl1ch"))
+        # height.attrs["units"] = "mm"
+        # distance = source.create_dataset(
+        #     name="distance", data=-7800 - np.asarray(self.get_entry("samz", 0))
+        # )
+        # distance.attrs["units"] = "mm"
 
-    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"
+        # mono = instrument.create_group("monochromator")
+        # mono.attrs["NX_class"] = "NXmonochromator"
+        # mokev = self.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)
+        #     )
+        #     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(self.get_entry("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"
+        # 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=self.get_entry("moth1"))
+        # bragg_angle.attrs["units"] = "degrees"
 
-    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"
+        # 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=self.get_entry("moth1"))
+        # bragg_angle.attrs["units"] = "degrees"
+        # bend_x = crystal_2.create_dataset(name="bend_x", data=self.get_entry("mobd"))
+        # bend_x.attrs["units"] = "degrees"
 
-    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"
+        # 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=self.get_entry("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=self.get_entry("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=self.get_entry("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=self.get_entry("bpm4z"))
+        # xbpm4_skew_data.attrs["units"] = "NX_DIMENSIONLESS"
+        # xbpm4_skew.create_dataset(
+        #     name="description", data="Normalized difference of counts between diagonal quadrants."
+        # )
 
-    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"
+        # 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=self.get_entry("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(self.get_entry("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"
+        # 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=self.get_entry("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=self.get_entry("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=self.get_entry("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=self.get_entry("bpm5z"))
+        # xbpm5_skew_data.attrs["units"] = "NX_DIMENSIONLESS"
+        # xbpm5_skew.create_dataset(
+        #     name="description", data="Normalized difference of counts between diagonal quadrants."
+        # )
 
-    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"
+        # 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=self.get_entry("sl2wh"))
+        # x_gap.attrs["units"] = "mm"
+        # y_gap = source.create_dataset(name="y_gap", data=self.get_entry("sl2wv"))
+        # y_gap.attrs["units"] = "mm"
+        # x_translation = source.create_dataset(name="x_translation", data=self.get_entry("sl2ch"))
+        # x_translation.attrs["units"] = "mm"
+        # height = source.create_dataset(name="x_translation", data=self.get_entry("sl2cv"))
+        # height.attrs["units"] = "mm"
+        # distance = source.create_dataset(
+        #     name="distance", data=-3140 - np.asarray(self.get_entry("samz", 0))
+        # )
+        # distance.attrs["units"] = "mm"
 
-    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)
+        # 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=self.get_entry("sl3wh"))
+        # x_gap.attrs["units"] = "mm"
+        # y_gap = source.create_dataset(name="y_gap", data=self.get_entry("sl3wv"))
+        # y_gap.attrs["units"] = "mm"
+        # x_translation = source.create_dataset(name="x_translation", data=self.get_entry("sl3ch"))
+        # x_translation.attrs["units"] = "mm"
+        # height = source.create_dataset(name="x_translation", data=self.get_entry("sl3cv"))
+        # height.attrs["units"] = "mm"
+        # # distance = source.create_dataset(name="distance", data=-3140 - self.get_entry("samz", 0))
+        # # distance.attrs["units"] = "mm"
 
-    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"
-        )
+        # 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 ** self.get_entry("ftrans", 0)
+        # )
+        # attenuator_transmission.attrs["units"] = "NX_DIMENSIONLESS"
 
-    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"
-        )
+        # 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=self.get_entry("sl4wh"))
+        # x_gap.attrs["units"] = "mm"
+        # y_gap = source.create_dataset(name="y_gap", data=self.get_entry("sl4wv"))
+        # y_gap.attrs["units"] = "mm"
+        # x_translation = source.create_dataset(name="x_translation", data=self.get_entry("sl4ch"))
+        # x_translation.attrs["units"] = "mm"
+        # height = source.create_dataset(name="x_translation", data=self.get_entry("sl4cv"))
+        # height.attrs["units"] = "mm"
+        # # distance = source.create_dataset(name="distance", data=-3140 - self.get_entry("samz", 0))
+        # # distance.attrs["units"] = "mm"
 
-    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"
-        )
+        # 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=self.get_entry("sl5wh"))
+        # x_gap.attrs["units"] = "mm"
+        # y_gap = source.create_dataset(name="y_gap", data=self.get_entry("sl5wv"))
+        # y_gap.attrs["units"] = "mm"
+        # x_translation = source.create_dataset(name="x_translation", data=self.get_entry("sl5ch"))
+        # x_translation.attrs["units"] = "mm"
+        # height = source.create_dataset(name="x_translation", data=self.get_entry("sl5cv"))
+        # height.attrs["units"] = "mm"
+        # # distance = source.create_dataset(name="distance", data=-3140 - self.get_entry("samz", 0))
+        # # distance.attrs["units"] = "mm"
 
-    return storage
+        # 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=self.get_entry("bs1x"))
+        # bms1_x.attrs["units"] = "mm"
+        # bms1_y = beam_stop_1.create_dataset(name="size", data=self.get_entry("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=self.get_entry("bs2x"))
+        # bms2_x.attrs["units"] = "mm"
+        # bms2_y = beam_stop_2.create_dataset(name="size", data=self.get_entry("bs2y"))
+        # bms2_y.attrs["units"] = "mm"
+        # bms2_data = beam_stop_2.create_dataset(name="data", data=self.get_entry("diode"))
+        # bms2_data.attrs["units"] = "NX_DIMENSIONLESS"
+
+        # if (
+        #     "eiger1p5m" in self.device_manager.devices
+        #     and self.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 self.device_manager.devices
+        #     and self.device_manager.devices.eiger9m.enabled
+        #     and "eiger9m" in self.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", self.file_references["eiger9m"]["path"], "EG9M/data"
+        #     )
+        #     status = eiger9m.create_ext_link(
+        #         "status", self.file_references["eiger9m"]["path"], "EG9M/status"
+        #     )
+
+        # if (
+        #     "pilatus_2" in self.device_manager.devices
+        #     and self.device_manager.devices.pilatus_2.enabled
+        #     and "pilatus_2" in self.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", self.file_references["pilatus_2"]["path"], "entry/instrument/pilatus_2/data"
+        #     )
+
+        # if (
+        #     "falcon" in self.device_manager.devices
+        #     and self.device_manager.devices.falcon.enabled
+        #     and "falcon" in self.file_references
+        # ):
+        #     falcon = instrument.create_ext_link(
+        #         "falcon", self.file_references["falcon"]["path"], "entry/instrument/FalconX1"
+        #     )

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