fix: flomni async readout

csaxs_bec/bec_ipython_client/plugins/LamNI/LamNI_webpage_generator.py

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

csaxs_bec/bec_ipython_client/plugins/cSAXS/cSAXSDLPCA200.py

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

csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py

@@ -21,14 +21,6 @@ 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:
@@ -786,9 +778,7 @@ class FlomniSampleTransferMixin:
             dev.ftransy.controller.socket_put_confirmed("confirm=1")
         else:
             print("Stopping.")
-            raise FlomniError(
-                "User abort sample transfer."
-            )
+            exit
 
     def ftransfer_gripper_is_open(self) -> bool:
         status = bool(float(dev.ftransy.controller.socket_put_and_receive("MG @OUT[9]").strip()))
@@ -811,8 +801,7 @@ class FlomniSampleTransferMixin:
     def ftransfer_gripper_move(self, position: int):
         self.check_position_is_valid(position)
 
-        #this is not used for sample stage position!
-        self._ftransfer_shiftx = -0.15
+        self._ftransfer_shiftx = -0.2
         self._ftransfer_shiftz = -0.5
 
         fsamx_pos = dev.fsamx.readback.get()
@@ -832,7 +821,7 @@ class FlomniSampleTransferMixin:
         self.check_tray_in()
 
         if position == 0:
-            umv(dev.ftransx, 11, dev.ftransz, 3.5950)
+            umv(dev.ftransx, 10.715 + 0.2, dev.ftransz, 3.5950)
         if position == 1:
             umv(
                 dev.ftransx,
@@ -977,6 +966,8 @@ 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__)
@@ -1217,76 +1208,6 @@ 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,
@@ -1309,20 +1230,14 @@ class Flomni(
         self.corr_angle_y = []
         self.corr_pos_y_2 = []
         self.corr_angle_y_2 = []
-        self._progress_proxy = _ProgressProxy(self.client)
-        self._progress_proxy.reset()
-        from csaxs_bec.bec_ipython_client.plugins.flomni.flomni_webpage_generator import (
-            FlomniWebpageGenerator,
-        )
-        self._webpage_gen = FlomniWebpageGenerator(
-            bec_client=client,
-            output_dir="~/data/raw/webpage/",
-            #upload_url="http://s1090968537.online.de/upload.php",   # optional
-            upload_url="https://v1p0zyg2w9n2k9c1.myfritz.net/upload.php",
-            local_port=8080
-        )
-        self._webpage_gen.start()
-
+        self.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.OMNYTools = OMNYTools(self.client)
         self.reconstructor = PtychoReconstructor(self.ptycho_reconstruct_foldername)
         self.tomo_id_manager = TomoIDManager()
@@ -1378,42 +1293,6 @@ 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")
@@ -1600,11 +1479,21 @@ 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.")
@@ -1614,9 +1503,11 @@ 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):
@@ -1628,6 +1519,7 @@ 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":
@@ -1641,27 +1533,24 @@ 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)
-                    alignment_scan_numbers.append(scan_nr)
+                    self._write_tomo_scan_number(scan_nr, angle, 0)
 
         umv(dev.fsamroy, 0)
         self.OMNYTools.printgreenbold(
-            "\n\nAlignment scan finished. Please run SPEC_ptycho_align and load the new fit by flomni.read_alignment_offset() ."
+            "\n\nAlignment scan finished. Please run SPEC_ptycho_align and load the new fit."
         )
 
-        # 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"
+    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,
         )
-        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):
         """
@@ -1670,6 +1559,18 @@ 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.")
@@ -1769,7 +1670,6 @@ 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:
@@ -1813,9 +1713,9 @@ class Flomni(
             )
             if self.OMNYTools.yesno("Shall I continue?", "n"):
                 print("OK")
-            else:
-                print("Stopping.")
-                return
+        else:
+            print("Stopping.")
+            return
 
         self.flomnigui_show_progress()
 
@@ -1829,22 +1729,20 @@ class Flomni(
             or (self.tomo_type == 3 and projection_number == None)
         ):
 
-            #pylint: disable=undefined-variable
-            if bec.active_account != "":
-                self.tomo_id = self.add_sample_database(
-                    self.sample_name,
-                    str(datetime.date.today()),
-                    bec.active_account,
-                    bec.queue.next_scan_number,
-                    "flomni",
-                    "test additional info",
-                    "BEC",
-                )
-                self.write_pdf_report()
-            else:
-                self.tomo_id = 0
-            self.write_pdf_report()
-            self.progress["tomo_start_time"] = datetime.datetime.now().isoformat()
+            # pylint: disable=undefined-variable
+            # if bec.active_account != "":
+            #     self.tomo_id = self.add_sample_database(
+            #         self.sample_name,
+            #         str(datetime.date.today()),
+            #         bec.active_account,
+            #         bec.queue.next_scan_number,
+            #         "flomni",
+            #         "test additional info",
+            #         "BEC",
+            #     )
+            #     self.write_pdf_report()
+            # else:
+            self.tomo_id = 0
 
         with scans.dataset_id_on_hold:
             if self.tomo_type == 1:
@@ -1864,6 +1762,7 @@ 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
@@ -1911,6 +1810,7 @@ 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
@@ -1952,42 +1852,14 @@ 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']}")
-        print(f"Estimated remaining time: ........ {eta_str}\x1b[0m")
+        print(f"Current projection within subtomo: {self.progress['subtomo_projection']}\x1b[0m")
         self._flomnigui_update_progress()
 
     def add_sample_database(
@@ -2011,6 +1883,7 @@ 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"""
@@ -2115,7 +1988,7 @@ 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,
@@ -2128,9 +2001,6 @@ class Flomni(
                     corridor_size=corridor_size,
                 )
 
-        self.tomo_reconstruct()
-
-
     def tomo_parameters(self):
         """print and update the tomo parameters"""
         print("Current settings:")
@@ -2269,21 +2139,19 @@ class Flomni(
             + ' 888    888  "Y88888P"  888       888 888    Y888 8888888 \n'
         )
         padding = 20
-        fovxy = f"{self.fovx:.1f}/{self.fovy:.1f}"
-        stitching = f"{self.stitch_x:.0f}/{self.stitch_y:.0f}"
+        fovxy = f"{self.fovx:.2f}/{self.fovy:.2f}"
+        stitching = f"{self.stitch_x:.2f}/{self.stitch_y:.2f}"
         dataset_id = str(self.client.queue.next_dataset_number)
-        account = bec.active_account
         content = [
             f"{'Sample Name:':<{padding}}{self.sample_name:>{padding}}\n",
             f"{'Measurement ID:':<{padding}}{str(self.tomo_id):>{padding}}\n",
             f"{'Dataset ID:':<{padding}}{dataset_id:>{padding}}\n",
             f"{'Sample Info:':<{padding}}{'Sample Info':>{padding}}\n",
-            f"{'e-account:':<{padding}}{str(account):>{padding}}\n",
+            f"{'e-account:':<{padding}}{str(self.client.username):>{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}}To be implemented\n",
-            #f"{'Current photon energy:':<{padding}}{dev.mokev.read()['mokev']['value']:>{padding}.4f}\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",
@@ -2292,38 +2160,20 @@ 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"~/data/raw/documentation/tomo_scan_ID_{self.tomo_id}.pdf")
+        user_target = os.path.expanduser(f"~/Data10/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.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()
+        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)
 
 
 if __name__ == "__main__":

csaxs_bec/bec_ipython_client/plugins/flomni/flomni_optics_mixin.py

@@ -50,6 +50,8 @@ 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

@@ -223,14 +223,6 @@ 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:
@@ -243,31 +235,6 @@ 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"
@@ -276,9 +243,7 @@ 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'])}\n"
-                f" Scan started:  {start_display}\n"
-                f" Est. remaining:  {eta_display}"
+                f" Total projections per subtomo:  {int(self.progress['subtomo_total_projections'])}"
             )
             self.progressbar.set_center_label(text)
 

csaxs_bec/bec_ipython_client/plugins/flomni/x_ray_eye_align.py

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

csaxs_bec/bec_ipython_client/plugins/omny/omny_general_tools.py

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

csaxs_bec/bec_ipython_client/plugins/omny/omny_webpage_generator.py

@@ -1,96 +0,0 @@
-"""
-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/device_configs/bl_endstation.yaml

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

csaxs_bec/device_configs/bl_frontend.yaml

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

csaxs_bec/device_configs/bl_optics_hutch.yaml

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

csaxs_bec/device_configs/main.yaml

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

csaxs_bec/device_configs/ptycho_flomni.yaml

@@ -395,7 +395,7 @@ rtz:
   readoutPriority: on_request
   connectionTimeout: 20
 
-rt_positions:
+rt_flyer:
   deviceClass: csaxs_bec.devices.omny.rt.rt_flomni_ophyd.RtFlomniFlyer
   deviceConfig:
     host: mpc2844.psi.ch
@@ -522,19 +522,6 @@ omny_panda:
       FMC_IN.VAL2.Min: cap_voltage_fzp_x_min
       FMC_IN.VAL2.Max: cap_voltage_fzp_x_max
       FMC_IN.VAL2.Mean: cap_voltage_fzp_x_mean
-      INENC1.VAL.Max: interf_st_fzp_y_max
-      INENC1.VAL.Mean: interf_st_fzp_y_mean
-      INENC1.VAL.Min: interf_st_fzp_y_min
-      INENC2.VAL.Max: interf_st_fzp_x_max
-      INENC2.VAL.Mean: interf_st_fzp_x_mean
-      INENC2.VAL.Min: interf_st_fzp_x_min
-      INENC3.VAL.Max: interf_st_rotz_max
-      INENC3.VAL.Mean: interf_st_rotz_mean
-      INENC3.VAL.Min: interf_st_rotz_min
-      INENC4.VAL.Max: interf_st_rotx_max
-      INENC4.VAL.Mean: interf_st_rotx_mean
-      INENC4.VAL.Min: interf_st_rotx_min
-      PCAP.GATE_DURATION.Value: pcap_gate_duration_value
   deviceTags:
     - detector
   enabled: true

csaxs_bec/device_configs/test_config.yaml

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

csaxs_bec/devices/epics/mcs_card/mcs_card_csaxs.py

@@ -317,6 +317,8 @@ 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}")
@@ -391,7 +393,6 @@ 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
@@ -562,9 +563,8 @@ 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."""
-        with suppress_mca_callbacks(self):
-            self.stop_all.put(1)
-            self.erase_all.put(1)
+        self.stop_all.put(1)
+        self.erase_all.put(1)
 
     def mcs_recovery(self, timeout: int = 1) -> None:
         """

csaxs_bec/devices/omny/shutter.py

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

csaxs_bec/devices/pseudo_devices/bpm.py

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

csaxs_bec/devices/pseudo_devices/bpm_control.py

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

csaxs_bec/devices/pseudo_devices/dlpca200_settings.py

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

csaxs_bec/devices/pseudo_devices/signal_forwarder.py

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

csaxs_bec/file_writer/__init__.py

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

csaxs_bec/file_writer/csaxs_nexus.py

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

csaxs_bec/scans/flomni_fermat_scan.py

@@ -105,11 +105,11 @@ class FlomniFermatScan(AsyncFlyScanBase):
 
     def scan_report_instructions(self):
         """Scan report instructions for the progress bar"""
-        yield from self.stubs.scan_report_instruction({"device_progress": ["rt_positions"]})
+        yield from self.stubs.scan_report_instruction({"device_progress": ["rt_flyer"]})
 
     @property
     def monitor_sync(self) -> str:
-        return "rt_positions"
+        return "rt_flyer"
 
     def initialize(self):
         self.scan_motors = []
@@ -294,10 +294,10 @@ class FlomniFermatScan(AsyncFlyScanBase):
 
     def scan_core(self):
         # send off the flyer
-        yield from self.stubs.kickoff(device="rt_positions")
+        yield from self.stubs.kickoff(device="rt_flyer")
 
         # start the readout loop of the flyer
-        status = yield from self.stubs.complete(device="rt_positions", wait=False)
+        status = yield from self.stubs.complete(device="rt_flyer", wait=False)
 
         # read the monitors until the flyer is done
         while not status.done:

tests/tests_devices/test_mcs_card.py

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

tests/tests_devices/test_omny_shutter.py

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

tests/tests_devices/test_pseudo_devices.py

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