Automatic backup triggered by new deployment

.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/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 (
+       WebpageGenerator,
+      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:
@@ -778,7 +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()))
@@ -801,7 +811,8 @@ class FlomniSampleTransferMixin:
     def ftransfer_gripper_move(self, position: int):
         self.check_position_is_valid(position)
 
-        self._ftransfer_shiftx = -0.2
+        #this is not used for sample stage position!
+        self._ftransfer_shiftx = -0.15
         self._ftransfer_shiftz = -0.5
 
         fsamx_pos = dev.fsamx.readback.get()
@@ -821,7 +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,
@@ -966,8 +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__)
@@ -1208,6 +1217,76 @@ 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,
@@ -1230,14 +1309,14 @@ 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()
+        self._webpage_gen = WebpageGenerator(
+            bec_client=client,
+            output_dir="~/data/raw/webpage/",   # adjust to your staging path
+            verbosity=VERBOSITY_NORMAL,
+        )
+        self._webpage_gen.start()        
         self.OMNYTools = OMNYTools(self.client)
         self.reconstructor = PtychoReconstructor(self.ptycho_reconstruct_foldername)
         self.tomo_id_manager = TomoIDManager()
@@ -1293,6 +1372,42 @@ 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")
@@ -1479,21 +1594,11 @@ 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.")
@@ -1503,11 +1608,9 @@ class Flomni(
 
         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):
@@ -1519,7 +1622,6 @@ 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":
@@ -1533,24 +1635,27 @@ class Flomni(
 
                 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."
+            "\n\nAlignment scan finished. Please run SPEC_ptycho_align and load the new fit by flomni.read_alignment_offset() ."
         )
 
-    def _write_subtomo_to_scilog(self, subtomo_number):
-        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,
+        # 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):
         """
@@ -1559,18 +1664,6 @@ 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.")
@@ -1670,6 +1763,7 @@ class Flomni(
         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:
@@ -1713,9 +1807,9 @@ class Flomni(
             )
             if self.OMNYTools.yesno("Shall I continue?", "n"):
                 print("OK")
-        else:
-            print("Stopping.")
-            return
+            else:
+                print("Stopping.")
+                return
 
         self.flomnigui_show_progress()
 
@@ -1743,6 +1837,8 @@ 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:
@@ -1762,7 +1858,6 @@ 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
@@ -1810,7 +1905,6 @@ 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
@@ -1852,14 +1946,42 @@ class Flomni(
         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(
@@ -1883,7 +2005,6 @@ 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"""
@@ -1988,7 +2109,7 @@ 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,
@@ -2001,6 +2122,9 @@ class Flomni(
                     corridor_size=corridor_size,
                 )
 
+        self.tomo_reconstruct()
+
+
     def tomo_parameters(self):
         """print and update the tomo parameters"""
         print("Current settings:")
@@ -2139,19 +2263,21 @@ 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",
@@ -2160,20 +2286,38 @@ 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).add_text(content.replace("\n", "<br>")).add_tags("tomoscan").send()
 
 
 if __name__ == "__main__":

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

@@ -223,6 +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:
@@ -235,6 +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"
@@ -243,7 +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/webpage_generator.py

@@ -0,0 +1,892 @@
+"""
+webpage_generator.py
+====================
+Background thread that reads the flOMNI tomo progress from the BEC global
+variable store and writes a self-contained status.json + status.html to a
+configurable output directory.  A separate upload process can copy those
+files to the web host.
+
+Usage (inside Flomni.__init__, after self._progress_proxy.reset()):
+--------------------------------------------------------------------
+    self._webpage_gen = WebpageGenerator(
+        bec_client=client,
+        output_dir="~/data/raw/webpage/",
+    )
+    self._webpage_gen.start()
+
+Interactive commands (optional, in the iPython session):
+---------------------------------------------------------
+    flomni._webpage_gen.status()          # print current status
+    flomni._webpage_gen.verbosity = 2     # switch to VERBOSE mid-session
+    flomni._webpage_gen.stop()            # release lock, let another session take over
+    flomni._webpage_gen.start()           # restart after stop()
+"""
+
+import datetime
+import json
+import os
+import socket
+import threading
+import time
+from pathlib import Path
+
+from bec_lib import bec_logger
+
+logger = bec_logger.logger
+
+# ---------------------------------------------------------------------------
+# Constants
+# ---------------------------------------------------------------------------
+
+# BEC global-var key used as a distributed singleton lock
+_LOCK_VAR_KEY = "webpage_generator_lock"
+
+# Heartbeat must be refreshed at least this often (seconds) or the lock
+# is considered stale and another session may take over.
+_LOCK_STALE_AFTER_S = 45
+
+# How long between generator cycles (seconds)
+_CYCLE_INTERVAL_S = 15
+
+# If the tomo progress heartbeat has not been updated for this long we
+# consider the tomo loop no longer actively running.
+_TOMO_HEARTBEAT_STALE_S = 90
+
+# After finishing normally, stay in IDLE_SHORT for this long before
+# switching to IDLE_LONG (which triggers the audio warning).
+_IDLE_SHORT_WINDOW_S = 300  # 5 minutes
+
+# Verbosity levels
+VERBOSITY_SILENT = 0   # no output at all
+VERBOSITY_NORMAL = 1   # startup/stop messages only
+VERBOSITY_VERBOSE = 2  # each cycle summary
+VERBOSITY_DEBUG = 3    # full detail each cycle
+
+
+# ---------------------------------------------------------------------------
+# Helpers
+# ---------------------------------------------------------------------------
+
+def _now_iso() -> str:
+    return datetime.datetime.now().isoformat(timespec="seconds")
+
+
+def _epoch() -> float:
+    return time.time()
+
+
+def _heartbeat_age_s(iso_str) -> float:
+    """Return seconds since the ISO-format heartbeat string, or infinity."""
+    if iso_str is None:
+        return float("inf")
+    try:
+        ts = datetime.datetime.fromisoformat(iso_str)
+        return (datetime.datetime.now() - ts).total_seconds()
+    except Exception:
+        return float("inf")
+
+
+def _format_duration(seconds) -> str:
+    if seconds is None:
+        return "N/A"
+    try:
+        seconds = int(float(seconds))
+    except (TypeError, ValueError):
+        return "N/A"
+    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 _check_account_match(bec_client) -> bool:
+    """Return True if the BEC active account matches the system user."""
+    try:
+        active = bec_client.active_account          # e.g. "p23092"
+        system_user = os.getenv("USER") or os.getlogin()   # e.g. "e23092"
+        return active[1:] == system_user[1:]
+    except Exception:
+        return True   # don't block on unknown accounts
+
+
+# ---------------------------------------------------------------------------
+# Status derivation
+# ---------------------------------------------------------------------------
+
+def _derive_status(progress: dict, queue_has_active_scan: bool, idle_since) -> str:
+    """
+    Derive a simple status string from available signals.
+
+    Returns one of:
+        "scanning"      - tomo heartbeat is fresh (tomo loop actively running)
+        "running"       - a scan is active but outside the tomo heartbeat window
+                          (alignment, other tasks, or brief inter-scan gap)
+        "idle_short"    - recently finished, within IDLE_SHORT_WINDOW_S
+        "idle_long"     - idle longer than IDLE_SHORT_WINDOW_S (trigger warning)
+        "unknown"       - cannot determine yet
+    """
+    hb_age = _heartbeat_age_s(progress.get("heartbeat"))
+    tomo_active = hb_age < _TOMO_HEARTBEAT_STALE_S
+
+    if tomo_active:
+        return "scanning"
+
+    if queue_has_active_scan:
+        return "running"
+
+    if idle_since is not None:
+        idle_s = _epoch() - idle_since
+        return "idle_short" if idle_s < _IDLE_SHORT_WINDOW_S else "idle_long"
+
+    return "unknown"
+
+
+# ---------------------------------------------------------------------------
+# Main generator class
+# ---------------------------------------------------------------------------
+
+class WebpageGenerator:
+    """
+    Singleton-safe background thread that generates the experiment status
+    page by reading BEC global variables.
+
+    Parameters
+    ----------
+    bec_client : BECClient
+        The active BEC client instance (``bec`` in the iPython session).
+    output_dir : str | Path
+        Directory where ``status.json`` and ``status.html`` are written.
+        Created if it does not exist.
+    cycle_interval : float
+        Seconds between update cycles.  Default: 15 s.
+    verbosity : int
+        VERBOSITY_SILENT / VERBOSITY_NORMAL / VERBOSITY_VERBOSE / VERBOSITY_DEBUG.
+        Default: VERBOSITY_NORMAL.
+    """
+
+    def __init__(
+        self,
+        bec_client,
+        output_dir: str = "~/data/raw/webpage/",
+        cycle_interval: float = _CYCLE_INTERVAL_S,
+        verbosity: int = VERBOSITY_NORMAL,
+    ):
+        self._bec = bec_client
+        self._output_dir = Path(output_dir).expanduser().resolve()
+        self._cycle_interval = cycle_interval
+        self._verbosity = verbosity
+
+        self._thread = None
+        self._stop_event = threading.Event()
+
+        # Rolling state kept between cycles
+        self._idle_since = None
+        self._owner_id = f"{socket.gethostname()}:{os.getpid()}"
+
+    # ------------------------------------------------------------------
+    # Public API
+    # ------------------------------------------------------------------
+
+    def start(self) -> bool:
+        """
+        Start the generator thread if this session wins the singleton lock.
+        Returns True if started, False if another session already owns it.
+        """
+        if not _check_account_match(self._bec):
+            self._log(
+                VERBOSITY_NORMAL,
+                "WebpageGenerator: BEC account does not match system user. "
+                "Not starting to avoid writing data to the wrong account.",
+                level="warning",
+            )
+            return False
+
+        if self._thread is not None and self._thread.is_alive():
+            self._log(VERBOSITY_NORMAL, "WebpageGenerator already running in this session.")
+            return True
+
+        if not self._acquire_lock():
+            return False
+
+        self._output_dir.mkdir(parents=True, exist_ok=True)
+        self._stop_event.clear()
+        self._thread = threading.Thread(
+            target=self._run,
+            name="WebpageGenerator",
+            daemon=True,
+        )
+        self._thread.start()
+        self._log(
+            VERBOSITY_NORMAL,
+            f"WebpageGenerator started (owner: {self._owner_id}, "
+            f"output: {self._output_dir}, interval: {self._cycle_interval}s)",
+        )
+        return True
+
+    def stop(self) -> None:
+        """Stop the generator thread and release the singleton lock."""
+        self._stop_event.set()
+        if self._thread is not None:
+            self._thread.join(timeout=self._cycle_interval + 5)
+        self._release_lock()
+        self._log(VERBOSITY_NORMAL, "WebpageGenerator stopped.")
+
+    @property
+    def verbosity(self) -> int:
+        return self._verbosity
+
+    @verbosity.setter
+    def verbosity(self, val: int) -> None:
+        self._verbosity = val
+        self._log(VERBOSITY_NORMAL, f"WebpageGenerator verbosity set to {val}.")
+
+    def status(self) -> None:
+        """Print a human-readable status summary to the console."""
+        lock = self._read_lock()
+        running = self._thread is not None and self._thread.is_alive()
+        print(
+            f"WebpageGenerator\n"
+            f"  This session running : {running}\n"
+            f"  Lock owner           : {lock.get('owner_id', 'none')}\n"
+            f"  Lock heartbeat       : {lock.get('heartbeat', 'never')}\n"
+            f"  Output dir           : {self._output_dir}\n"
+            f"  Cycle interval       : {self._cycle_interval}s\n"
+            f"  Verbosity            : {self._verbosity}\n"
+        )
+
+    # ------------------------------------------------------------------
+    # Singleton lock helpers
+    # ------------------------------------------------------------------
+
+    def _acquire_lock(self) -> bool:
+        lock = self._read_lock()
+        if lock:
+            age = _heartbeat_age_s(lock.get("heartbeat"))
+            if age < _LOCK_STALE_AFTER_S:
+                self._log(
+                    VERBOSITY_NORMAL,
+                    f"WebpageGenerator already owned by "
+                    f"'{lock.get('owner_id')}' "
+                    f"(heartbeat {age:.0f}s ago). Not starting.",
+                )
+                return False
+            self._log(
+                VERBOSITY_NORMAL,
+                f"Stale lock found (owner: '{lock.get('owner_id')}', "
+                f"{age:.0f}s ago). Taking over.",
+            )
+
+        self._write_lock()
+        return True
+
+    def _write_lock(self) -> None:
+        self._bec.set_global_var(
+            _LOCK_VAR_KEY,
+            {
+                "owner_id": self._owner_id,
+                "heartbeat": _now_iso(),
+                "pid": os.getpid(),
+                "hostname": socket.gethostname(),
+            },
+        )
+
+    def _read_lock(self) -> dict:
+        val = self._bec.get_global_var(_LOCK_VAR_KEY)
+        return val if isinstance(val, dict) else {}
+
+    def _release_lock(self) -> None:
+        lock = self._read_lock()
+        if lock.get("owner_id") == self._owner_id:
+            self._bec.delete_global_var(_LOCK_VAR_KEY)
+
+    # ------------------------------------------------------------------
+    # Main loop
+    # ------------------------------------------------------------------
+
+    def _run(self) -> None:
+        while not self._stop_event.is_set():
+            cycle_start = _epoch()
+            try:
+                self._cycle()
+            except Exception as exc:
+                self._log(
+                    VERBOSITY_NORMAL,
+                    f"WebpageGenerator cycle error: {exc}",
+                    level="warning",
+                )
+            # Refresh the singleton heartbeat
+            try:
+                self._write_lock()
+            except Exception:
+                pass
+            # Sleep for the remainder of the interval
+            elapsed = _epoch() - cycle_start
+            sleep_time = max(0.0, self._cycle_interval - elapsed)
+            self._stop_event.wait(sleep_time)
+
+    def _cycle(self) -> None:
+        """One generator cycle: read state -> derive status -> write outputs."""
+
+        # --- Read progress from global var (readable from any session) -------
+        progress = self._bec.get_global_var("tomo_progress") or {}
+
+        # --- Read queue status -----------------------------------------------
+        # NOTE: queue status is always 'RUNNING' while BEC is alive.
+        # An actual scan is executing only when info is non-empty AND
+        # active_request_block is set on the first entry.
+        try:
+            queue_info = self._bec.queue.queue_storage.current_scan_queue
+            primary = queue_info.get("primary")
+            queue_status = primary.status if primary is not None else "unknown"
+            queue_has_active_scan = (
+                primary is not None
+                and len(primary.info) > 0
+                and primary.info[0].active_request_block is not None
+            )
+        except Exception:
+            queue_status = "unknown"
+            queue_has_active_scan = False
+
+        # --- Track idle onset ------------------------------------------------
+        # Use both the tomo heartbeat and the queue active-scan flag.
+        # This handles the brief COMPLETED gap between individual scans
+        # while a tomo is still running.
+        hb_age = _heartbeat_age_s(progress.get("heartbeat"))
+        tomo_active = hb_age < _TOMO_HEARTBEAT_STALE_S
+
+        if tomo_active or queue_has_active_scan:
+            self._idle_since = None
+        elif self._idle_since is None:
+            self._idle_since = _epoch()
+
+        # --- Derive experiment status ----------------------------------------
+        exp_status = _derive_status(progress, queue_has_active_scan, self._idle_since)
+
+        # --- Build payload ---------------------------------------------------
+        idle_for_s = None if self._idle_since is None else (_epoch() - self._idle_since)
+
+        payload = {
+            "generated_at": _now_iso(),
+            "generated_at_epoch": _epoch(),
+            "experiment_status": exp_status,
+            "queue_status": queue_status,
+            "queue_has_active_scan": queue_has_active_scan,
+            "idle_for_s": idle_for_s,
+            "idle_for_human": _format_duration(idle_for_s),
+            "progress": {
+                "tomo_type": progress.get("tomo_type", "N/A"),
+                "projection": progress.get("projection", 0),
+                "total_projections": progress.get("total_projections", 0),
+                "subtomo": progress.get("subtomo", 0),
+                "subtomo_projection": progress.get("subtomo_projection", 0),
+                "subtomo_total_projections": progress.get("subtomo_total_projections", 1),
+                "angle": progress.get("angle", 0),
+                "tomo_start_time": progress.get("tomo_start_time"),
+                "estimated_remaining_s": progress.get("estimated_remaining_time"),
+                "estimated_remaining_human": _format_duration(
+                    progress.get("estimated_remaining_time")
+                ),
+                "heartbeat": progress.get("heartbeat"),
+                "heartbeat_age_s": round(hb_age, 1) if hb_age != float("inf") else None,
+            },
+            "generator": {
+                "owner_id": self._owner_id,
+                "cycle_interval_s": self._cycle_interval,
+            },
+        }
+
+        # --- Write outputs ---------------------------------------------------
+        json_path = self._output_dir / "status.json"
+        json_path.write_text(json.dumps(payload, indent=2, default=str))
+
+        html_path = self._output_dir / "status.html"
+        html_path.write_text(_render_html())
+
+        # --- Console feedback ------------------------------------------------
+        self._log(
+            VERBOSITY_VERBOSE,
+            f"[{_now_iso()}] status={exp_status}  active_scan={queue_has_active_scan}  "
+            f"proj={payload['progress']['projection']}/"
+            f"{payload['progress']['total_projections']}  "
+            f"hb_age={payload['progress']['heartbeat_age_s']}s  "
+            f"idle={_format_duration(idle_for_s)}",
+        )
+        self._log(
+            VERBOSITY_DEBUG,
+            f"  full payload:\n{json.dumps(payload, indent=4, default=str)}",
+        )
+
+    # ------------------------------------------------------------------
+    # Logging helper
+    # ------------------------------------------------------------------
+
+    def _log(self, min_verbosity: int, msg: str, level: str = "info") -> None:
+        if self._verbosity < min_verbosity:
+            return
+        if level == "warning":
+            logger.warning(msg)
+        elif level == "error":
+            logger.error(msg)
+        else:
+            print(msg)
+
+
+# ---------------------------------------------------------------------------
+# HTML template (static shell - the page fetches status.json on load/refresh)
+# ---------------------------------------------------------------------------
+
+def _render_html() -> str:
+    """Return the full HTML for the status page."""
+    return r"""<!DOCTYPE html>
+<html lang="en">
+<head>
+  <meta charset="UTF-8">
+  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+  <title>flOMNI - Experiment Status</title>
+  <style>
+    @import url('https://fonts.googleapis.com/css2?family=Space+Mono:wght@400;700&family=DM+Sans:wght@300;400;600&display=swap');
+
+    :root {
+      --bg:           #0d0f14;
+      --surface:      #161a23;
+      --surface2:     #1e2330;
+      --border:       #2a3045;
+      --text:         #cdd6f4;
+      --text-dim:     #6c7a9c;
+      --mono:         'Space Mono', monospace;
+      --sans:         'DM Sans', sans-serif;
+      --c-scanning:   #89dceb;
+      --c-running:    #a6e3a1;
+      --c-idle-short: #f9e2af;
+      --c-idle-long:  #fab387;
+      --c-error:      #f38ba8;
+      --c-unknown:    #6c7a9c;
+      --status-color: var(--c-unknown);
+    }
+
+    body.scanning   { --status-color: var(--c-scanning);  }
+    body.running    { --status-color: var(--c-running);   }
+    body.idle_short { --status-color: var(--c-idle-short);}
+    body.idle_long  { --status-color: var(--c-idle-long); }
+    body.error      { --status-color: var(--c-error);     }
+    body.unknown    { --status-color: var(--c-unknown);   }
+
+    * { box-sizing: border-box; margin: 0; padding: 0; }
+
+    body {
+      background: var(--bg);
+      color: var(--text);
+      font-family: var(--sans);
+      font-weight: 300;
+      min-height: 100vh;
+      padding: 2rem;
+      transition: background 0.6s ease;
+    }
+
+    body::before {
+      content: '';
+      position: fixed; inset: 0;
+      background: radial-gradient(ellipse 80% 50% at 50% -10%,
+                    color-mix(in srgb, var(--status-color) 8%, transparent), transparent);
+      pointer-events: none;
+      transition: background 0.8s ease;
+      z-index: 0;
+    }
+
+    .layout {
+      position: relative; z-index: 1;
+      max-width: 860px;
+      margin: 0 auto;
+      display: grid;
+      gap: 1.5rem;
+    }
+
+    header {
+      display: flex;
+      align-items: baseline;
+      justify-content: space-between;
+      gap: 1rem;
+      padding-bottom: 1rem;
+      border-bottom: 1px solid var(--border);
+    }
+    .logo {
+      font-family: var(--mono);
+      font-size: 1.1rem;
+      font-weight: 700;
+      letter-spacing: 0.15em;
+      color: var(--text-dim);
+    }
+    .logo span { color: var(--status-color); transition: color 0.6s; }
+    #last-update { font-family: var(--mono); font-size: 0.7rem; color: var(--text-dim); }
+
+    .status-card {
+      background: var(--surface);
+      border: 1px solid var(--border);
+      border-left: 3px solid var(--status-color);
+      border-radius: 8px;
+      padding: 1.5rem 2rem;
+      display: flex;
+      align-items: center;
+      gap: 2rem;
+      transition: border-color 0.6s;
+    }
+    .status-pill {
+      font-family: var(--mono);
+      font-size: 0.75rem;
+      font-weight: 700;
+      letter-spacing: 0.12em;
+      text-transform: uppercase;
+      color: var(--bg);
+      background: var(--status-color);
+      padding: 0.3rem 0.9rem;
+      border-radius: 100px;
+      white-space: nowrap;
+      transition: background 0.6s;
+    }
+    .status-detail { flex: 1; font-size: 0.9rem; color: var(--text-dim); line-height: 1.6; }
+    .status-detail strong { color: var(--text); font-weight: 600; }
+
+    .progress-card {
+      background: var(--surface);
+      border: 1px solid var(--border);
+      border-radius: 8px;
+      padding: 1.5rem 2rem;
+      display: grid;
+      grid-template-columns: auto 1fr;
+      gap: 1.5rem 2.5rem;
+      align-items: center;
+    }
+
+    .rings-wrap { position: relative; width: 120px; height: 120px; flex-shrink: 0; }
+    .rings-wrap svg { width: 100%; height: 100%; transform: rotate(-90deg); }
+    .ring-track { fill: none; stroke: var(--surface2); }
+    .ring-outer {
+      fill: none; stroke: var(--status-color); stroke-linecap: round; opacity: 0.9;
+      transition: stroke-dashoffset 0.8s cubic-bezier(.4,0,.2,1), stroke 0.6s;
+    }
+    .ring-inner {
+      fill: none;
+      stroke: color-mix(in srgb, var(--status-color) 55%, var(--surface2));
+      stroke-linecap: round;
+      transition: stroke-dashoffset 0.8s cubic-bezier(.4,0,.2,1), stroke 0.6s;
+    }
+    .ring-label {
+      position: absolute; inset: 0;
+      display: flex; flex-direction: column;
+      align-items: center; justify-content: center;
+      font-family: var(--mono);
+    }
+    .ring-label .pct    { font-size: 1.3rem; font-weight: 700; color: var(--text); }
+    .ring-label .sublbl { font-size: 0.6rem; color: var(--text-dim); letter-spacing: 0.06em; }
+
+    .progress-info { display: grid; grid-template-columns: 1fr 1fr; gap: 0.75rem 2rem; }
+    .info-item { display: flex; flex-direction: column; gap: 0.15rem; }
+    .info-item .label {
+      font-family: var(--mono); font-size: 0.65rem; color: var(--text-dim);
+      letter-spacing: 0.08em; text-transform: uppercase;
+    }
+    .info-item .value { font-size: 0.95rem; font-weight: 600; color: var(--text); }
+
+    .bar-wrap { grid-column: 1 / -1; display: flex; flex-direction: column; gap: 0.4rem; }
+    .bar-label {
+      display: flex; justify-content: space-between;
+      font-family: var(--mono); font-size: 0.65rem; color: var(--text-dim);
+      letter-spacing: 0.06em; text-transform: uppercase;
+    }
+    .bar-track { height: 6px; background: var(--surface2); border-radius: 99px; overflow: hidden; }
+    .bar-fill {
+      height: 100%;
+      background: color-mix(in srgb, var(--status-color) 70%, var(--surface2));
+      border-radius: 99px;
+      transition: width 0.8s cubic-bezier(.4,0,.2,1), background 0.6s;
+    }
+
+    .audio-card {
+      background: var(--surface); border: 1px solid var(--border); border-radius: 8px;
+      padding: 1.25rem 2rem; display: flex; align-items: center;
+      justify-content: space-between; gap: 1rem; flex-wrap: wrap;
+    }
+    .audio-info { display: flex; align-items: center; gap: 0.75rem; }
+    .audio-dot { width: 8px; height: 8px; border-radius: 50%; background: var(--text-dim); transition: background 0.3s; }
+    .audio-dot.active { background: var(--c-scanning); box-shadow: 0 0 6px var(--c-scanning); }
+    .audio-text { font-size: 0.85rem; color: var(--text-dim); }
+    .audio-controls { display: flex; gap: 0.75rem; }
+
+    button {
+      font-family: var(--mono); font-size: 0.7rem; font-weight: 700;
+      letter-spacing: 0.1em; text-transform: uppercase;
+      border: 1px solid var(--border); background: var(--surface2); color: var(--text);
+      padding: 0.4rem 1rem; border-radius: 6px; cursor: pointer;
+      transition: background 0.2s, border-color 0.2s, color 0.2s;
+    }
+    button:hover { background: var(--border); }
+    button.active { background: var(--status-color); border-color: var(--status-color); color: var(--bg); }
+
+    footer {
+      font-family: var(--mono); font-size: 0.65rem; color: var(--text-dim);
+      border-top: 1px solid var(--border); padding-top: 1rem;
+      display: flex; justify-content: space-between; gap: 1rem; flex-wrap: wrap;
+    }
+
+    #audio-gate {
+      position: fixed; inset: 0; background: rgba(13,15,20,0.85);
+      backdrop-filter: blur(6px); display: flex; align-items: center;
+      justify-content: center; z-index: 100; cursor: pointer;
+    }
+    #audio-gate.hidden { display: none; }
+    .gate-box {
+      background: var(--surface); border: 1px solid var(--border); border-radius: 12px;
+      padding: 2.5rem 3rem; text-align: center; max-width: 400px;
+    }
+    .gate-box h2 { font-size: 1.1rem; font-weight: 600; margin-bottom: 0.5rem; }
+    .gate-box p  { font-size: 0.85rem; color: var(--text-dim); margin-bottom: 1.5rem; }
+    .gate-btn {
+      font-family: var(--mono); font-size: 0.8rem; font-weight: 700;
+      letter-spacing: 0.1em; text-transform: uppercase;
+      background: var(--status-color); color: var(--bg); border: none;
+      padding: 0.7rem 2rem; border-radius: 8px; cursor: pointer;
+    }
+  </style>
+</head>
+<body class="unknown">
+
+<div id="audio-gate">
+  <div class="gate-box">
+    <h2>flOMNI Status Page</h2>
+    <p>Click to enable the page. Audio warnings require a user interaction to activate.</p>
+    <button class="gate-btn" onclick="unlockAudio()">Open Status Page</button>
+  </div>
+</div>
+
+<div class="layout">
+
+  <header>
+    <div class="logo">fl<span>OMNY</span> &middot; STATUS</div>
+    <div id="last-update">updating&hellip;</div>
+  </header>
+
+  <div class="status-card">
+    <div class="status-pill" id="status-pill">-</div>
+    <div class="status-detail" id="status-detail">Loading&hellip;</div>
+  </div>
+
+  <div class="progress-card">
+    <div class="rings-wrap">
+      <svg viewBox="0 0 120 120">
+        <circle class="ring-track" cx="60" cy="60" r="50" stroke-width="8"/>
+        <circle class="ring-outer" id="ring-outer"
+                cx="60" cy="60" r="50" stroke-width="8"
+                stroke-dasharray="314.16" stroke-dashoffset="314.16"/>
+        <circle class="ring-track" cx="60" cy="60" r="37" stroke-width="7"/>
+        <circle class="ring-inner" id="ring-inner"
+                cx="60" cy="60" r="37" stroke-width="7"
+                stroke-dasharray="232.48" stroke-dashoffset="232.48"/>
+      </svg>
+      <div class="ring-label">
+        <span class="pct" id="ring-pct">0%</span>
+        <span class="sublbl">OVERALL</span>
+      </div>
+    </div>
+
+    <div class="progress-info">
+      <div class="info-item">
+        <span class="label">Projection</span>
+        <span class="value" id="pi-proj">-</span>
+      </div>
+      <div class="info-item">
+        <span class="label">Sub-tomo</span>
+        <span class="value" id="pi-subtomo">-</span>
+      </div>
+      <div class="info-item">
+        <span class="label">Angle</span>
+        <span class="value" id="pi-angle">-</span>
+      </div>
+      <div class="info-item">
+        <span class="label">Tomo type</span>
+        <span class="value" id="pi-type">-</span>
+      </div>
+      <div class="info-item">
+        <span class="label">ETA</span>
+        <span class="value" id="pi-eta">-</span>
+      </div>
+      <div class="info-item">
+        <span class="label">Started</span>
+        <span class="value" id="pi-start">-</span>
+      </div>
+    </div>
+
+    <div class="bar-wrap">
+      <div class="bar-label">
+        <span>Sub-tomo progress</span>
+        <span id="bar-sub-label">-</span>
+      </div>
+      <div class="bar-track">
+        <div class="bar-fill" id="bar-sub-fill" style="width:0%"></div>
+      </div>
+    </div>
+  </div>
+
+  <div class="audio-card">
+    <div class="audio-info">
+      <div class="audio-dot" id="audio-dot"></div>
+      <span class="audio-text" id="audio-text">Audio warnings: initialising&hellip;</span>
+    </div>
+    <div class="audio-controls">
+      <button id="btn-toggle-audio" onclick="toggleAudio()">Enable</button>
+      <button onclick="testSound()">Test sound</button>
+    </div>
+  </div>
+
+  <footer>
+    <span id="footer-gen">generator: -</span>
+    <span id="footer-queue">queue active: -</span>
+    <span id="footer-hb">heartbeat: -</span>
+  </footer>
+
+</div>
+
+<script>
+const STATUS_JSON   = 'status.json';
+const POLL_INTERVAL = 15000;
+const WARN_STATUSES = new Set(['idle_long', 'error', 'unknown']);
+
+// Audio
+let audioCtx     = null;
+let audioEnabled = (localStorage.getItem('audioEnabled') !== 'false');
+let warningTimer = null;
+
+function getCtx() {
+  if (!audioCtx) audioCtx = new (window.AudioContext || window.webkitAudioContext)();
+  return audioCtx;
+}
+
+function beep(freq, dur, vol) {
+  try {
+    const ctx = getCtx(), osc = ctx.createOscillator(), gain = ctx.createGain();
+    osc.connect(gain); gain.connect(ctx.destination);
+    osc.type = 'sine';
+    osc.frequency.setValueAtTime(freq, ctx.currentTime);
+    gain.gain.setValueAtTime(vol, ctx.currentTime);
+    gain.gain.exponentialRampToValueAtTime(0.001, ctx.currentTime + dur);
+    osc.start(ctx.currentTime); osc.stop(ctx.currentTime + dur);
+  } catch(e) { console.warn('Audio:', e); }
+}
+
+function warningChime() { beep(660, 0.3, 0.4); setTimeout(() => beep(440, 0.4, 0.4), 350); }
+function testSound()    { beep(880,0.15,0.4); setTimeout(()=>beep(1100,0.15,0.4),180); setTimeout(()=>beep(880,0.3,0.4),360); }
+
+function toggleAudio() {
+  audioEnabled = !audioEnabled;
+  localStorage.setItem('audioEnabled', audioEnabled);
+  updateAudioUI();
+  if (!audioEnabled) stopWarning();
+}
+
+function updateAudioUI() {
+  const btn = document.getElementById('btn-toggle-audio');
+  const dot = document.getElementById('audio-dot');
+  const txt = document.getElementById('audio-text');
+  if (audioEnabled) {
+    btn.textContent = 'Disable'; btn.classList.add('active');
+    dot.classList.add('active'); txt.textContent = 'Audio warnings: enabled';
+  } else {
+    btn.textContent = 'Enable'; btn.classList.remove('active');
+    dot.classList.remove('active'); txt.textContent = 'Audio warnings: disabled';
+  }
+}
+
+function startWarning() {
+  if (warningTimer) return;
+  if (audioEnabled) warningChime();
+  warningTimer = setInterval(() => { if (audioEnabled) warningChime(); }, 30000);
+}
+function stopWarning() { if (warningTimer) { clearInterval(warningTimer); warningTimer = null; } }
+
+function unlockAudio() {
+  getCtx().resume();
+  document.getElementById('audio-gate').classList.add('hidden');
+  updateAudioUI();
+  poll();
+}
+
+// Rendering
+const LABELS = {
+  scanning:   'SCANNING',
+  running:    'RUNNING',
+  idle_short: 'IDLE',
+  idle_long:  'IDLE - CHECK',
+  error:      'STOPPED',
+  unknown:    'UNKNOWN',
+};
+const DETAILS = {
+  scanning:   d => 'Tomo scan in progress &middot; projection ' + d.progress.projection + ' of ' + d.progress.total_projections + ' &middot; ' + d.progress.tomo_type,
+  running:    d => 'Queue active &middot; outside tomo heartbeat window (alignment or inter-scan gap)',
+  idle_short: d => 'Finished normally &middot; idle for <strong>' + d.idle_for_human + '</strong>',
+  idle_long:  d => 'Idle for <strong>' + d.idle_for_human + '</strong> &mdash; no tomo scan running',
+  error:      d => 'Queue stopped unexpectedly &middot; idle for <strong>' + (d.idle_for_human || '?') + '</strong>',
+  unknown:    d => 'Status unknown &middot; waiting for first data&hellip;',
+};
+
+function setRing(id, circ, pct) {
+  document.getElementById(id).style.strokeDashoffset = circ * (1 - Math.min(pct, 1));
+}
+function fmtAngle(v) { const n = parseFloat(v); return isNaN(n) ? '-' : n.toFixed(2) + '\u00b0'; }
+function fmtTime(iso) {
+  if (!iso) return '-';
+  try { return new Date(iso).toLocaleTimeString([], {hour:'2-digit', minute:'2-digit'}); }
+  catch { return iso; }
+}
+
+function render(d) {
+  const s = d.experiment_status || 'unknown';
+  const p = d.progress || {};
+
+  document.body.className = s;
+  document.getElementById('status-pill').textContent  = LABELS[s] || s.toUpperCase();
+  document.getElementById('status-detail').innerHTML  = (DETAILS[s] || (()=>s))(d);
+
+  const oPct = p.total_projections > 0 ? p.projection / p.total_projections : 0;
+  const sPct = p.subtomo_total_projections > 0 ? p.subtomo_projection / p.subtomo_total_projections : 0;
+  setRing('ring-outer', 314.16, oPct);
+  setRing('ring-inner', 232.48, sPct);
+  document.getElementById('ring-pct').textContent = Math.round(oPct * 100) + '%';
+
+  document.getElementById('pi-proj').textContent    = (p.projection || 0) + ' / ' + (p.total_projections || 0);
+  document.getElementById('pi-subtomo').textContent = p.subtomo || '-';
+  document.getElementById('pi-angle').textContent   = fmtAngle(p.angle);
+  document.getElementById('pi-type').textContent    = p.tomo_type || '-';
+  document.getElementById('pi-eta').textContent     = p.estimated_remaining_human || '-';
+  document.getElementById('pi-start').textContent   = fmtTime(p.tomo_start_time);
+
+  document.getElementById('bar-sub-label').textContent = (p.subtomo_projection || 0) + ' / ' + (p.subtomo_total_projections || 0);
+  document.getElementById('bar-sub-fill').style.width  = (sPct * 100).toFixed(1) + '%';
+
+  document.getElementById('last-update').textContent  = 'updated ' + new Date(d.generated_at).toLocaleTimeString();
+  document.getElementById('footer-gen').textContent   = 'generator: '   + (d.generator && d.generator.owner_id || '-');
+  document.getElementById('footer-queue').textContent = 'queue active: ' + d.queue_has_active_scan;
+  document.getElementById('footer-hb').textContent    = 'heartbeat: '   + (p.heartbeat_age_s != null ? p.heartbeat_age_s + 's ago' : 'none');
+
+  WARN_STATUSES.has(s) ? startWarning() : stopWarning();
+}
+
+async function poll() {
+  try {
+    const r = await fetch(STATUS_JSON + '?t=' + Date.now());
+    if (!r.ok) throw new Error('HTTP ' + r.status);
+    render(await r.json());
+  } catch(e) {
+    console.warn('Fetch failed:', e);
+    document.getElementById('last-update').textContent = 'fetch failed - retrying...';
+  }
+}
+
+updateAudioUI();
+setInterval(poll, POLL_INTERVAL);
+// First poll triggered by unlockAudio() after the gate is dismissed
+</script>
+</body>
+</html>
+"""

csaxs_bec/bec_ipython_client/plugins/flomni/x_ray_eye_align.py

@@ -253,6 +253,8 @@ class XrayEyeAlign:
 
         umv(dev.rtx, 0)
         print("You are ready to remove the xray eye and start ptychography scans.")
+        print("Fine alignment: flomni.tomo_parameters() , then flomni.tomo_alignment_scan()")
+        print("After that, run the fit in Matlab and load the new fit flomni.read_alignment_offset()")
 
     def write_output(self):
         file = os.path.expanduser("~/Data10/specES1/internal/xrayeye_alignmentvalues")

csaxs_bec/device_configs/ptycho_flomni.yaml

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

csaxs_bec/devices/epics/mcs_card/mcs_card_csaxs.py

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

csaxs_bec/devices/omny/rt/rt_flomni_ophyd.py

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

csaxs_bec/scans/flomni_fermat_scan.py

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

tests/tests_devices/test_mcs_card.py

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