feat: check all devices are enabled, if not try to enable

csaxs_bec/bec_ipython_client/plugins/LamNI/gui_tools.py

@@ -0,0 +1,188 @@
+import builtins
+
+from bec_widgets.cli.client import BECDockArea
+
+# from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_get, epics_put, fshopen, fshclose
+
+if builtins.__dict__.get("bec") is not None:
+    bec = builtins.__dict__.get("bec")
+    dev = builtins.__dict__.get("dev")
+    scans = builtins.__dict__.get("scans")
+
+def umv(*args):
+    return scans.umv(*args, relative=False)
+
+
+class LamniGuiToolsError(Exception):
+    pass
+
+
+class LamniGuiTools:
+
+    def __init__(self):
+        self.text_box = None
+        self.progressbar = None
+
+    def set_client(self, client):
+        self.client = client
+        self.gui = self.client.gui
+
+    def lamnigui_show_gui(self):
+        if "lamni" in self.gui.windows:
+            self.gui.lamni.show()
+        else:
+            self.gui.new("lamni")
+
+    def lamnigui_stop_gui(self):
+        self.gui.lamni.hide()
+
+    def lamnigui_raise(self):
+        self.gui.lamni.raise_window()
+
+    def lamnigui_show_xeyealign(self):
+        self.lamnigui_show_gui()
+        if self._lamnigui_check_attribute_not_exists("xeyegui"):
+            self.lamnigui_remove_all_docks()
+            self.xeyegui = self.gui.lamni.new("xeyegui").new("XRayEye")
+            # start live
+            if not dev.cam_xeye.live_mode:
+                dev.cam_xeye.live_mode = True
+
+
+    def _lamnigui_check_attribute_not_exists(self, attribute_name):
+        if hasattr(self.gui,"lamni"):
+            if hasattr(self.gui.lamni,attribute_name):
+                return False
+        return True
+
+    def lamnigui_remove_all_docks(self):
+        self.gui.lamni.delete_all() 
+        self.progressbar = None
+        self.text_box = None
+
+    def lamnigui_idle(self):
+        self.lamnigui_show_gui()
+        if self._lamnigui_check_attribute_not_exists("idle_text_box"):
+            self.lamnigui_remove_all_docks()
+            idle_text_box = self.gui.lamni.new("idle_textbox").new("TextBox")
+        text = (
+            "<pre>"
+            + "██████╗ ███████╗ ██████╗     ██╗      █████╗ ███╗   ███╗███╗   ██╗██╗\n"
+            + "██╔══██╗██╔════╝██╔════╝     ██║     ██╔══██╗████╗ ████║████╗  ██║██║\n"
+            + "██████╔╝█████╗  ██║          ██║     ███████║██╔████╔██║██╔██╗ ██║██║\n"
+            + "██╔══██╗██╔══╝  ██║          ██║     ██╔══██║██║╚██╔╝██║██║╚██╗██║██║\n"
+            + "██████╔╝███████╗╚██████╗     ███████╗██║  ██║██║ ╚═╝ ██║██║ ╚████║██║\n"
+            + "╚═════╝ ╚══════╝ ╚═════╝     ╚══════╝╚═╝  ╚═╝╚═╝     ╚═╝╚═╝  ╚═══╝╚═╝\n"
+            + "</pre>"
+        )
+        idle_text_box.set_html_text(text)
+
+    def lamnigui_docs(self, filename: str | None = None):
+        import csaxs_bec
+        from pathlib import Path
+
+        print("The general lamni documentation is at \nhttps://sls-csaxs.readthedocs.io/en/latest/user/ptychography/lamni.html#user-ptychography-lamni")
+
+        csaxs_bec_basepath = Path(csaxs_bec.__file__).parent
+        docs_folder = (
+            csaxs_bec_basepath /
+            "bec_ipython_client" / "plugins" / "lamni" / "docs"
+        )
+
+        if not docs_folder.is_dir():
+            raise NotADirectoryError(f"Docs folder not found: {docs_folder}")
+
+        pdfs = sorted(docs_folder.glob("*.pdf"))
+        if not pdfs:
+            raise FileNotFoundError(f"No PDF files found in {docs_folder}")
+
+        # --- Resolve PDF ------------------------------------------------------
+        if filename is not None:
+            pdf_file = docs_folder / filename
+            if not pdf_file.exists():
+                raise FileNotFoundError(f"Requested file not found: {filename}")
+        else:
+            print("\nAvailable lamni documentation PDFs:\n")
+            for i, pdf in enumerate(pdfs, start=1):
+                print(f"  {i:2d}) {pdf.name}")
+            print()
+
+            while True:
+                try:
+                    choice = int(input(f"Select a file (1–{len(pdfs)}): "))
+                    if 1 <= choice <= len(pdfs):
+                        pdf_file = pdfs[choice - 1]
+                        break
+                    print(f"Enter a number between 1 and {len(pdfs)}.")
+                except ValueError:
+                    print("Invalid input. Please enter a number.")
+
+        # --- GUI handling (active existence check) ----------------------------
+        self.lamnigui_show_gui()
+
+        if self._lamnigui_check_attribute_not_exists("PdfViewerWidget"):
+            self.lamnigui_remove_all_docks()
+            self.pdf_viewer = self.gui.lamni.new(widget="PdfViewerWidget")
+
+        # --- Load PDF ---------------------------------------------------------
+        self.pdf_viewer.PdfViewerWidget.load_pdf(str(pdf_file.resolve()))
+        print(f"\nLoaded: {pdf_file.name}\n")
+
+
+    def _lamnicam_check_device_exists(self, device):
+        try:
+            device
+        except:
+            return False
+        else:
+            return True
+
+    def lamnigui_show_progress(self):
+        self.lamnigui_show_gui()
+        if self._lamnigui_check_attribute_not_exists("progressbar"):
+            self.lamnigui_remove_all_docks()
+            # Add a new dock with a RingProgressBar widget
+            self.progressbar = self.gui.lamni.new("progressbar").new("RingProgressBar")
+            # Customize the size of the progress ring
+            self.progressbar.set_line_widths(20)
+            # Disable automatic updates and manually set the self.progressbar value
+            self.progressbar.enable_auto_updates(False)
+            # Set precision for the self.progressbar display
+            self.progressbar.set_precision(1)  # Display self.progressbar with one decimal places
+            # Setting multiple rigns with different values
+            self.progressbar.set_number_of_bars(3)
+            self.progressbar.rings[0].set_update("manual")
+            self.progressbar.rings[1].set_update("manual")
+            self.progressbar.rings[2].set_update("scan")
+            # Set the values of the rings to 50, 75, and 25 from outer to inner ring
+            # self.progressbar.set_value([50, 75])
+            # Add a new dock with a TextBox widget
+            self.text_box = self.gui.lamni.new(name="progress_text").new("TextBox")
+
+        self._lamnigui_update_progress()
+
+    def _lamnigui_update_progress(self):
+        if self.progressbar is not None:
+            progress = self.progress["projection"] / self.progress["total_projections"] * 100
+            subtomo_progress = (
+                self.progress["subtomo_projection"]
+                / self.progress["subtomo_total_projections"]
+                * 100
+            )
+            self.progressbar.set_value([progress, subtomo_progress, 0])
+            if self.text_box is not None:
+                text = f"Progress report:\n Tomo type: ....................... {self.progress['tomo_type']}\n Projection: ...................... {self.progress['projection']:.0f}\n Total projections expected ....... {self.progress['total_projections']}\n Angle: ........................... {self.progress['angle']}\n Current subtomo: ................. {self.progress['subtomo']}\n Current projection within subtomo: {self.progress['subtomo_projection']}\n Total projections per subtomo: ... {self.progress['subtomo_total_projections']}"
+                self.text_box.set_plain_text(text)
+
+
+if __name__ == "__main__":
+    from bec_lib.client import BECClient
+    from bec_widgets.cli.client_utils import BECGuiClient
+
+    client = BECClient()
+    client.start()
+    client.gui = BECGuiClient()
+
+    lamni_gui = LamniGuiTools(client)
+    lamni_gui.lamnigui_show_gui()
+    lamni_gui.lamnigui_show_progress()

csaxs_bec/bec_ipython_client/plugins/LamNI/lamni.py

@@ -2,7 +2,6 @@ import builtins
 import datetime
 import os
 import subprocess
-import threading
 import time
 from pathlib import Path
 
@@ -12,7 +11,13 @@ from bec_lib.alarm_handler import AlarmBase
 from bec_lib.pdf_writer import PDFWriter
 from typeguard import typechecked
 
-from csaxs_bec.bec_ipython_client.plugins.omny.omny_general_tools import OMNYTools
+from csaxs_bec.bec_ipython_client.plugins.omny.omny_general_tools import (
+    BeamlineChecker,
+    OMNYTools,
+    PtychoReconstructor,
+    TomoIDManager,
+)
+from csaxs_bec.bec_ipython_client.plugins.LamNI.gui_tools import LamniGuiTools
 
 from .alignment import XrayEyeAlign
 from .lamni_optics_mixin import LaMNIInitStages, LamNIOpticsMixin
@@ -26,26 +31,26 @@ if builtins.__dict__.get("bec") is not None:
     umvr = builtins.__dict__.get("umvr")
 
 
-class LamNI(LamNIOpticsMixin):
+class LamNI(LamNIOpticsMixin, LamniGuiTools):
     def __init__(self, client):
         super().__init__()
         self.client = client
         self.device_manager = client.device_manager
         self.align = XrayEyeAlign(client, self)
         self.init = LaMNIInitStages(client)
-        self.check_shutter = True
-        self.check_light_available = True
-        self.check_fofb = True
-        self._check_msgs = []
+
+        # Extracted collaborators
+        self.bl_chk = BeamlineChecker(client)
+        self.reconstructor = PtychoReconstructor(self.ptycho_reconstruct_foldername)
+        self.tomo_id_manager = TomoIDManager()
+        self.OMNYTools = OMNYTools(self.client)
+
         self.tomo_id = -1
         self.special_angles = []
         self.special_angle_repeats = 20
         self.special_angle_tolerance = 20
         self._current_special_angles = []
-        self._beam_is_okay = True
-        self._stop_beam_check_event = None
-        self.beam_check_thread = None
-        self.OMNYTools = OMNYTools(self.client)
+
         # Progress tracking
         self.progress = {}
         self.progress["tomo_type"] = "Equally spaced sub-tomograms"
@@ -57,104 +62,19 @@ class LamNI(LamNIOpticsMixin):
         self.progress["angle"] = 0
 
     # ------------------------------------------------------------------
-    # Beamline checks
+    # Beamline checks — delegated to BeamlineChecker
     # ------------------------------------------------------------------
 
-    def get_beamline_checks_enabled(self):
-        print(
-            f"Shutter: {self.check_shutter}\nFOFB: {self.check_fofb}\nLight available:"
-            f" {self.check_light_available}"
-        )
-
     @property
     def beamline_checks_enabled(self):
-        return {
-            "shutter": self.check_shutter,
-            "fofb": self.check_fofb,
-            "light available": self.check_light_available,
-        }
+        return self.bl_chk.checks_enabled
 
     @beamline_checks_enabled.setter
     def beamline_checks_enabled(self, val: bool):
-        self.check_shutter = val
-        self.check_light_available = val
-        self.check_fofb = val
-        self.get_beamline_checks_enabled()
+        self.bl_chk.checks_enabled = val
 
-    def _run_beamline_checks(self):
-        msgs = []
-        dev = builtins.__dict__.get("dev")
-        try:
-            if self.check_shutter:
-                shutter_val = dev.x12sa_es1_shutter_status.read(cached=True)
-                if shutter_val["value"].lower() != "open":
-                    self._beam_is_okay = False
-                    msgs.append("Check beam failed: Shutter is closed.")
-            if self.check_light_available:
-                machine_status = dev.sls_machine_status.read(cached=True)
-                if machine_status["value"] not in ["Light Available", "Light-Available"]:
-                    self._beam_is_okay = False
-                    msgs.append("Check beam failed: Light not available.")
-            if self.check_fofb:
-                fast_orbit_feedback = dev.sls_fast_orbit_feedback.read(cached=True)
-                if fast_orbit_feedback["value"] != "running":
-                    self._beam_is_okay = False
-                    msgs.append("Check beam failed: Fast orbit feedback is not running.")
-        except Exception:
-            logger.warning("Failed to check beam.")
-        return msgs
-
-    def _check_beam(self):
-        while not self._stop_beam_check_event.is_set():
-            self._check_msgs = self._run_beamline_checks()
-            if not self._beam_is_okay:
-                self._stop_beam_check_event.set()
-            time.sleep(1)
-
-    def _start_beam_check(self):
-        self._beam_is_okay = True
-        self._stop_beam_check_event = threading.Event()
-        self.beam_check_thread = threading.Thread(target=self._check_beam, daemon=True)
-        self.beam_check_thread.start()
-
-    def _was_beam_okay(self):
-        self._stop_beam_check_event.set()
-        self.beam_check_thread.join()
-        return self._beam_is_okay
-
-    def _print_beamline_checks(self):
-        for msg in self._check_msgs:
-            logger.warning(msg)
-
-    def _wait_for_beamline_checks(self):
-        self._print_beamline_checks()
-        try:
-            msg = bec.logbook.LogbookMessage()
-            msg.add_text(
-                "<p><mark class='pen-red'><strong>Beamline checks failed at"
-                f" {str(datetime.datetime.now())}: {''.join(self._check_msgs)}</strong></mark></p>"
-            ).add_tag(["BEC", "beam_check"])
-            self.client.logbook.send_logbook_message(msg)
-        except Exception:
-            logger.warning("Failed to send update to SciLog.")
-
-        while True:
-            self._beam_is_okay = True
-            self._check_msgs = self._run_beamline_checks()
-            if self._beam_is_okay:
-                break
-            self._print_beamline_checks()
-            time.sleep(1)
-
-        try:
-            msg = bec.logbook.LogbookMessage()
-            msg.add_text(
-                "<p><mark class='pen-red'><strong>Operation resumed at"
-                f" {str(datetime.datetime.now())}.</strong></mark></p>"
-            ).add_tag(["BEC", "beam_check"])
-            self.client.logbook.send_logbook_message(msg)
-        except Exception:
-            logger.warning("Failed to send update to SciLog.")
+    def get_beamline_checks_enabled(self):
+        self.bl_chk.print_status()
 
     # ------------------------------------------------------------------
     # Special angles
@@ -212,7 +132,6 @@ class LamNI(LamNIOpticsMixin):
     def feedback_status(self):
         self.device_manager.devices.rtx.controller.show_feedback_status()
 
-
     def show_interferometer_positions(self):
         self.device_manager.devices.rtx.controller.show_feedback_status()
 
@@ -222,6 +141,12 @@ class LamNI(LamNIOpticsMixin):
     def show_analog_signals(self):
         return self.device_manager.devices.rtx.controller.show_analog_signals()
 
+    def lights_off(self):
+        self.device_manager.devices.lsamx.controller.lights_off()
+
+    def lights_on(self):
+        self.device_manager.devices.lsamx.controller.lights_on()
+
     # ------------------------------------------------------------------
     # Global parameters (backed by BEC global vars)
     # ------------------------------------------------------------------
@@ -371,6 +296,7 @@ class LamNI(LamNIOpticsMixin):
     @ptycho_reconstruct_foldername.setter
     def ptycho_reconstruct_foldername(self, val: str):
         self.client.set_global_var("ptycho_reconstruct_foldername", val)
+        self.reconstructor.folder_name = val  # keep reconstructor in sync
 
     @property
     def tomo_angle_stepsize(self):
@@ -491,23 +417,22 @@ class LamNI(LamNIOpticsMixin):
             )
 
     # ------------------------------------------------------------------
-    # Sample database
+    # Sample database — delegated to TomoIDManager in omny general tools
     # ------------------------------------------------------------------
 
     def add_sample_database(
         self, samplename, date, eaccount, scan_number, setup, sample_additional_info, user
     ):
         """Add a sample to the OMNY sample database and retrieve the tomo id."""
-        subprocess.run(
-            "wget --user=omny --password=samples -q -O /tmp/currsamplesnr.txt"
-            f" 'https://omny.web.psi.ch/samples/newmeasurement.php?sample={samplename}"
-            f"&date={date}&eaccount={eaccount}&scannr={scan_number}&setup={setup}"
-            f"&additional={sample_additional_info}&user={user}'",
-            shell=True,
+        return self.tomo_id_manager.register(
+            sample_name=samplename,
+            date=date,
+            eaccount=eaccount,
+            scan_number=scan_number,
+            setup=setup,
+            additional_info=sample_additional_info,
+            user=user,
         )
-        with open("/tmp/currsamplesnr.txt") as tomo_number_file:
-            tomo_number = int(tomo_number_file.read())
-        return tomo_number
 
     # ------------------------------------------------------------------
     # Scan projection
@@ -524,7 +449,6 @@ class LamNI(LamNIOpticsMixin):
 
         for stitch_x in range(-self.lamni_stitch_x, self.lamni_stitch_x + 1):
             for stitch_y in range(-self.lamni_stitch_y, self.lamni_stitch_y + 1):
-                # pylint: disable=undefined-variable
                 self._current_scan_list.append(bec.queue.next_scan_number)
                 log_message = (
                     f"{str(datetime.datetime.now())}: LamNI scan projection at angle {angle},"
@@ -562,18 +486,11 @@ class LamNI(LamNIOpticsMixin):
     def tomo_reconstruct(self, base_path="~/Data10/specES1"):
         """Write the tomo reconstruct file for the reconstruction queue."""
         bec = builtins.__dict__.get("bec")
-        base_path = os.path.expanduser(base_path)
-        ptycho_queue_path = Path(os.path.join(base_path, self.ptycho_reconstruct_foldername))
-        ptycho_queue_path.mkdir(parents=True, exist_ok=True)
-
-        last_scan_number = bec.queue.next_scan_number - 1
-        ptycho_queue_file = os.path.abspath(
-            os.path.join(ptycho_queue_path, f"scan_{last_scan_number:05d}.dat")
+        self.reconstructor.write(
+            scan_list=self._current_scan_list,
+            next_scan_number=bec.queue.next_scan_number,
+            base_path=base_path,
         )
-        with open(ptycho_queue_file, "w") as queue_file:
-            scans = " ".join([str(scan) for scan in self._current_scan_list])
-            queue_file.write(f"p.scan_number {scans}\n")
-            queue_file.write("p.check_nextscan_started 1\n")
 
     def _at_each_angle(self, angle: float) -> None:
         self.tomo_scan_projection(angle)
@@ -635,7 +552,7 @@ class LamNI(LamNIOpticsMixin):
             print(f"Starting LamNI scan for angle {angle} in subtomo {subtomo_number}")
             self._print_progress()
             while not successful:
-                self._start_beam_check()
+                self.bl_chk.start()
                 if not self.special_angles:
                     self._current_special_angles = []
                 if self._current_special_angles:
@@ -662,10 +579,10 @@ class LamNI(LamNIOpticsMixin):
                 for scan_nr in range(start_scan_number, end_scan_number):
                     self._write_tomo_scan_number(scan_nr, angle, subtomo_number)
 
-                if self._was_beam_okay() and not error_caught:
+                if self.bl_chk.stop() and not error_caught:
                     successful = True
                 else:
-                    self._wait_for_beamline_checks()
+                    self.bl_chk.wait_until_recovered()
 
     def _golden(self, ii, howmany_sorted, maxangle=360, reverse=False):
         """Return the ii-th golden ratio angle within sorted bunches and its subtomo number."""
@@ -1009,5 +926,4 @@ class LamNI(LamNIOpticsMixin):
         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)
-
+        self.client.logbook.send_logbook_message(msg)

csaxs_bec/bec_ipython_client/plugins/LamNI/lamni_optics_mixin.py

@@ -51,7 +51,7 @@ class LaMNIInitStages:
             self.drive_axis_to_limit(dev.lsamrot, "forward")
             dev.lsamrot.enabled = False
             print("Now hard reboot the controller and run the initialization routine again.")
-            print("The controller will be disabled in bec. To enable dev.lsamrot.enabled=True")
+            print("Remark: The controller will be disabled in bec. It will be enabled by running the init route, \nbut in case needed, to enable manually set dev.lsamrot.enabled=True")
             return
 
         if self.OMNYTools.yesno(

csaxs_bec/bec_ipython_client/plugins/cSAXS/smaract.py

@@ -37,6 +37,92 @@ class cSAXSInitSmaractStages:
     # ------------------------------
     # Internal helpers (runtime-based)
     # ------------------------------
+
+    def _ensure_all_session_devices_enabled(self, selection: set | None = None, try_enable: bool = True):
+        """
+        Ensure all session devices (or a selection) that define 'bl_smar_stage' are enabled.
+
+        Parameters
+        ----------
+        selection : set | None
+            If provided, only devices in this set are considered.
+        try_enable : bool
+            If True, attempt to set device.enabled = True for devices that expose 'enabled' and are False.
+            If False, only report status without changing it.
+
+        Returns
+        -------
+        dict
+            {
+                "enabled_now": [device_names enabled by this call],
+                "already_enabled": [device_names already enabled or without 'enabled' attr],
+                "failed": [device_names that could not be enabled],
+                "inaccessible": [device_names not accessible]
+            }
+        """
+        enabled_now = []
+        already_enabled = []
+        failed = []
+        inaccessible = []
+
+        # Build axis map to restrict to SmarAct-based devices (same logic as other helpers)
+        axis_map = self._build_session_axis_map(selection=selection)
+
+        for dev_name in sorted(axis_map.keys()):
+            try:
+                d = self._get_device_object(dev_name)
+                if d is None:
+                    inaccessible.append(dev_name)
+                    logger.warning(f"[cSAXS] Device {dev_name} not accessible.")
+                    continue
+
+                # If device has no 'enabled' attribute, treat as already enabled/usable
+                if not hasattr(d, "enabled"):
+                    already_enabled.append(dev_name)
+                    continue
+
+                # If already enabled
+                try:
+                    if getattr(d, "enabled"):
+                        already_enabled.append(dev_name)
+                        continue
+                except Exception:
+                    # If reading enabled fails, treat as inaccessible for safety
+                    failed.append(dev_name)
+                    logger.warning(f"[cSAXS] Could not read 'enabled' for {dev_name}.")
+                    continue
+
+                # Device exists and is disabled
+                if try_enable:
+                    try:
+                        logger.info(f"[cSAXS] Enabling device {dev_name} (was disabled).")
+                        setattr(d, "enabled", True)
+                        # small delay to let device initialize if needed
+                        time.sleep(0.05)
+                        if getattr(d, "enabled"):
+                            enabled_now.append(dev_name)
+                            logger.info(f"[cSAXS] Device {dev_name} enabled.")
+                        else:
+                            failed.append(dev_name)
+                            logger.warning(f"[cSAXS] Device {dev_name} still disabled after enabling attempt.")
+                    except Exception as exc:
+                        failed.append(dev_name)
+                        logger.error(f"[cSAXS] Failed to enable {dev_name}: {exc}")
+                else:
+                    # Not trying to enable, just report
+                    failed.append(dev_name)
+            except Exception as exc:
+                failed.append(dev_name)
+                logger.error(f"[cSAXS] _ensure_all_session_devices_enabled error for {dev_name}: {exc}")
+
+        return {
+            "enabled_now": enabled_now,
+            "already_enabled": already_enabled,
+            "failed": failed,
+            "inaccessible": inaccessible,
+        }
+
+
     def _yesno(self, question: str, default: str = "y") -> bool:
         """
         Use OMNYTools.yesno if available; otherwise default to 'yes' (or fallback to input()).
@@ -107,6 +193,7 @@ class cSAXSInitSmaractStages:
     # ------------------------------
     # Public API
     # ------------------------------
+
     def smaract_reference_stages(self, force: bool = False, devices_to_reference=None):
         """
         Reference SmarAct stages using runtime discovery.
@@ -167,6 +254,19 @@ class cSAXSInitSmaractStages:
             devices_to_reference = [devices_to_reference]
         selection = set(devices_to_reference) if devices_to_reference else None
 
+        # First: ensure all relevant devices are enabled before attempting referencing
+        enable_report = self._ensure_all_session_devices_enabled(selection=selection, try_enable=True)
+        if enable_report["failed"]:
+            logger.warning(
+                "[cSAXS] Some devices could not be enabled before referencing: "
+                + ", ".join(sorted(enable_report["failed"]))
+            )
+        if enable_report["inaccessible"]:
+            logger.warning(
+                "[cSAXS] Some devices were inaccessible before referencing: "
+                + ", ".join(sorted(enable_report["inaccessible"]))
+            )
+
         # Build axis map for selected devices (or all devices present)
         axis_map = self._build_session_axis_map(selection=selection)
         if selection:
@@ -174,7 +274,6 @@ class cSAXSInitSmaractStages:
             if unknown:
                 print(f"Unknown devices requested or missing 'bl_smar_stage' (ignored): {unknown}")
 
-
         newly_referenced = []
         already_referenced = []
         failed = []
@@ -191,6 +290,17 @@ class cSAXSInitSmaractStages:
                 failed.append(dev_name)
                 continue
 
+            # If device exposes 'enabled' and is False, skip (we already tried enabling above)
+            try:
+                if hasattr(d, "enabled") and not getattr(d, "enabled"):
+                    print(f"{dev_name}: device disabled, skipping.")
+                    failed.append(dev_name)
+                    continue
+            except Exception:
+                print(f"{dev_name}: could not read enabled state, skipping.")
+                failed.append(dev_name)
+                continue
+
             try:
                 is_ref = d.controller.axis_is_referenced(ch)
 
@@ -246,7 +356,17 @@ class cSAXSInitSmaractStages:
     def smaract_check_all_referenced(self):
         """
         Check reference state for all SmarAct devices that define 'bl_smar_stage'.
+        This now enables all relevant devices first (attempt), then performs the checks.
         """
+        # Attempt to enable all relevant devices first (do not force enabling if you prefer)
+        enable_report = self._ensure_all_session_devices_enabled(selection=None, try_enable=True)
+        if enable_report["enabled_now"]:
+            print("Now enabled devices which were disabled before: " + ", ".join(sorted(enable_report["enabled_now"])))
+        if enable_report["failed"]:
+            print("Could not enable: " + ", ".join(sorted(enable_report["failed"])))
+        if enable_report["inaccessible"]:
+            print("Inaccessible: " + ", ".join(sorted(enable_report["inaccessible"])))
+
         axis_map = self._build_session_axis_map(selection=None)
         for dev_name in sorted(axis_map.keys()):
             ch = axis_map[dev_name]
@@ -254,6 +374,16 @@ class cSAXSInitSmaractStages:
             if d is None:
                 print(f"{dev_name}: device not accessible or unsupported.")
                 continue
+
+            # Skip devices that expose 'enabled' and are False
+            try:
+                if hasattr(d, "enabled") and not getattr(d, "enabled"):
+                    print(f"{dev_name} (axis {ch}) is disabled; skipping reference check.")
+                    continue
+            except Exception:
+                print(f"{dev_name} (axis {ch}) enabled-state unknown; skipping.")
+                continue
+
             try:
                 if d.controller.axis_is_referenced(ch):
                     print(f"{dev_name} (axis {ch}) is referenced.")
@@ -262,6 +392,7 @@ class cSAXSInitSmaractStages:
             except Exception as e:
                 print(f"Error checking {dev_name} (axis {ch}): {e}")
 
+
     def smaract_components_to_initial_position(self, devices_to_move=None):
         """
         Move selected (or all) SmarAct-based components to their configured init_position.

csaxs_bec/bec_ipython_client/plugins/omny/omny_general_tools.py

@@ -1,23 +1,29 @@
-import time
-import numpy as np
-import sys
-import termios
-import tty
+import builtins
+import datetime
 import fcntl
 import os
-import builtins
+import subprocess
+import sys
+import termios
+import threading
+import time
+import tty
+from pathlib import Path
 
+import numpy as np
+from bec_lib import bec_logger
 from rich import box
 from rich.console import Console
 from rich.table import Table
 
-# from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_get, epics_put, fshopen, fshclose
+logger = bec_logger.logger
 
 if builtins.__dict__.get("bec") is not None:
     bec = builtins.__dict__.get("bec")
     dev = builtins.__dict__.get("dev")
     scans = builtins.__dict__.get("scans")
 
+
 def umv(*args):
     return scans.umv(*args, relative=False)
 
@@ -110,24 +116,20 @@ class OMNYTools:
                         next1, next2 = sys.stdin.read(2)
                         if next1 == "[":
                             if next2 == "A":
-                                # print("up")
                                 if dev2 != "none":
                                     umvr(dev2, step2)
                                     if special_command != "none":
                                         special_command()
                             elif next2 == "B":
-                                # print(" down")
                                 if dev2 != "none":
                                     umvr(dev2, -step2)
                                     if special_command != "none":
                                         special_command()
                             elif next2 == "C":
-                                # print("right")
                                 umvr(dev1, step1)
                                 if special_command != "none":
                                     special_command()
                             elif next2 == "D":
-                                # print("left")
                                 umvr(dev1, -step1)
                                 if special_command != "none":
                                     special_command()
@@ -143,13 +145,324 @@ class OMNYTools:
                             step2 = step2 / 2
                         print(f"\rHalf step size. New step size: {step1}, {step2}\r")
                 except IOError:
-                    # No input available, keep looping
                     pass
 
-                # Sleep for a short period to avoid high CPU usage
                 time.sleep(0.02)
 
         finally:
             # Restore the terminal to its original state
             termios.tcsetattr(fd, termios.TCSADRAIN, old_term)
             fcntl.fcntl(fd, fcntl.F_SETFL, old_flags)
+
+import socket
+
+class BeamlineChecker:
+    """Monitors beamline health during scans.
+
+    Runs checks in a background thread and blocks scan progress
+    until beam conditions are restored if they fail.
+
+    Usage:
+        checker = BeamlineChecker(client)
+        checker._bl_chk_start()
+        # ... run scan ...
+        beam_was_ok = checker._bl_chk_stop()
+        if not beam_was_ok:
+            checker._bl_chk_wait_until_recovered()
+    """
+
+    def __init__(self, client):
+        self.client = client
+        self.check_shutter = True
+        self.check_light_available = True
+        self.check_fofb = True
+        self._beam_is_okay = True
+        self._stop_event = None
+        self._thread = None
+        self._local_network_warned = False
+        self._check_msgs = []
+
+    # ------------------------------------------------------------------
+    # Public control interface
+    # ------------------------------------------------------------------
+
+    def bl_chk_status(self):
+        """Print and return the current enabled/disabled state of all checks."""
+        if self._is_local_network():
+            print("Beamline checks cannot be performed on this network (129.129.98.x) — skipping.")
+            return {}
+        status = {
+            "shutter": self.check_shutter,
+            "fofb": self.check_fofb,
+            "light available": self.check_light_available,
+        }
+        print(
+            f"Shutter: {self.check_shutter}\n"
+            f"FOFB: {self.check_fofb}\n"
+            f"Light available: {self.check_light_available}"
+        )
+        return status
+
+    def bl_chk_enable_all(self):
+        """Enable all beamline checks."""
+        self.check_shutter = True
+        self.check_light_available = True
+        self.check_fofb = True
+        self.bl_chk_status()
+
+    def bl_chk_disable_all(self):
+        """Disable all beamline checks."""
+        self.check_shutter = False
+        self.check_light_available = False
+        self.check_fofb = False
+        self.bl_chk_status()
+
+    def bl_chk_enable_shutter(self):
+        """Enable the shutter check."""
+        self.check_shutter = True
+        self.bl_chk_status()
+
+    def bl_chk_disable_shutter(self):
+        """Disable the shutter check."""
+        self.check_shutter = False
+        self.bl_chk_status()
+
+    def bl_chk_enable_fofb(self):
+        """Enable the fast orbit feedback check."""
+        self.check_fofb = True
+        self.bl_chk_status()
+
+    def bl_chk_disable_fofb(self):
+        """Disable the fast orbit feedback check."""
+        self.check_fofb = False
+        self.bl_chk_status()
+
+    def bl_chk_enable_light(self):
+        """Enable the light available check."""
+        self.check_light_available = True
+        self.bl_chk_status()
+
+    def bl_chk_disable_light(self):
+        """Disable the light available check."""
+        self.check_light_available = False
+        self.bl_chk_status()
+
+    def _bl_chk_start(self):
+        """Start the background beam check thread."""
+        self._beam_is_okay = True
+        self._stop_event = threading.Event()
+        self._thread = threading.Thread(target=self._poll, daemon=True)
+        self._thread.start()
+
+    def _bl_chk_stop(self) -> bool:
+        """Stop the background thread and return whether beam was okay throughout."""
+        self._stop_event.set()
+        self._thread.join()
+        return self._beam_is_okay
+
+    def _bl_chk_wait_until_recovered(self):
+        """Block until all beamline checks pass again, logging to SciLog."""
+        self._log_failure_to_scilog()
+        while True:
+            self._beam_is_okay = True
+            self._check_msgs = self._run_checks()
+            if self._beam_is_okay:
+                break
+            self._print_msgs()
+            time.sleep(1)
+        self._log_recovery_to_scilog()
+
+    # ------------------------------------------------------------------
+    # Internal
+    # ------------------------------------------------------------------
+
+    def _is_local_network(self) -> bool:
+        """Return True if running on the 129.129.98.x subnet."""
+        try:
+            hostname = socket.gethostname()
+            ip = socket.gethostbyname(hostname)
+            return ip.startswith("129.129.98.")
+        except Exception:
+            return False
+
+    def _run_checks(self) -> list:
+        if self._is_local_network():
+            if not self._local_network_warned:
+                print("Beamline checks cannot be performed on this network (129.129.98.x) — skipping.")
+                self._local_network_warned = True
+            return []
+        msgs = []
+        dev = builtins.__dict__.get("dev")
+        try:
+            if self.check_shutter:
+                val = dev.x12sa_es1_shutter_status.read(cached=True)
+                if val["value"].lower() != "open":
+                    self._beam_is_okay = False
+                    msgs.append("Check beam failed: Shutter is closed.")
+            if self.check_light_available:
+                val = dev.sls_machine_status.read(cached=True)
+                if val["value"] not in ["Light Available", "Light-Available"]:
+                    self._beam_is_okay = False
+                    msgs.append("Check beam failed: Light not available.")
+            if self.check_fofb:
+                val = dev.sls_fast_orbit_feedback.read(cached=True)
+                if val["value"] != "running":
+                    self._beam_is_okay = False
+                    msgs.append("Check beam failed: Fast orbit feedback is not running.")
+        except Exception:
+            logger.warning("Failed to check beam.")
+        return msgs
+
+    def _poll(self):
+        while not self._stop_event.is_set():
+            self._check_msgs = self._run_checks()
+            if not self._beam_is_okay:
+                self._stop_event.set()
+            time.sleep(1)
+
+    def _print_msgs(self):
+        for msg in self._check_msgs:
+            logger.warning(msg)
+
+    def _log_failure_to_scilog(self):
+        self._print_msgs()
+        try:
+            bec = builtins.__dict__.get("bec")
+            msg = bec.logbook.LogbookMessage()
+            msg.add_text(
+                "<p><mark class='pen-red'><strong>Beamline checks failed at"
+                f" {str(datetime.datetime.now())}: {''.join(self._check_msgs)}</strong></mark></p>"
+            ).add_tag(["BEC", "beam_check"])
+            self.client.logbook.send_logbook_message(msg)
+        except Exception:
+            logger.warning("Failed to send beam failure update to SciLog.")
+
+    def _log_recovery_to_scilog(self):
+        try:
+            bec = builtins.__dict__.get("bec")
+            msg = bec.logbook.LogbookMessage()
+            msg.add_text(
+                "<p><mark class='pen-red'><strong>Operation resumed at"
+                f" {str(datetime.datetime.now())}.</strong></mark></p>"
+            ).add_tag(["BEC", "beam_check"])
+            self.client.logbook.send_logbook_message(msg)
+        except Exception:
+            logger.warning("Failed to send beam recovery update to SciLog.")
+
+class PtychoReconstructor:
+    """Writes ptychography reconstruction queue files after each scan projection.
+
+    An external reconstruction engine monitors the queue folder and picks
+    up .dat files as they are written.
+
+    Usage:
+        reconstructor = PtychoReconstructor(folder_name="reconstruction_queue")
+        reconstructor.write(
+            scan_list=[1023, 1024],
+            next_scan_number=1025,
+            base_path="~/data/raw",
+        )
+    """
+
+    def __init__(self, folder_name: str = "reconstruction_queue"):
+        self.folder_name = folder_name
+
+    def _accounts_match(self) -> bool:
+        """Check if bec.active_account matches the current system user (p vs e prefix)."""
+        try:
+            bec = builtins.__dict__.get("bec")
+            active = bec.active_account  # e.g. "p23092"
+            system_user = os.getenv("USER") or os.getlogin()  # e.g. "e23092"
+            print(f"Active server account {active}, BEC client account {system_user}.")
+            return active[1:] == system_user[1:]
+        except Exception:
+            logger.warning("Failed to compare active account to system user.")
+            return False
+
+    def write(self, scan_list: list, next_scan_number: int, base_path: str = "~/data/raw/analysis/"):
+        """Write a reconstruction queue file for the given scan list.
+
+        Args:
+            scan_list (list): Scan numbers belonging to this projection
+                              (may contain multiple entries when stitching).
+            next_scan_number (int): The current next scan number, used to
+                                    name the queue file.
+            base_path (str): Root path under which the queue folder lives.
+        """
+        base_path = os.path.expanduser(base_path)
+        queue_path = Path(os.path.join(base_path, self.folder_name))
+        queue_path.mkdir(parents=True, exist_ok=True)
+
+        last_scan_number = next_scan_number - 1
+        queue_file = os.path.abspath(
+            os.path.join(queue_path, f"scan_{last_scan_number:05d}.dat")
+        )
+        with open(queue_file, "w") as f:
+            scans = " ".join(str(s) for s in scan_list)
+            f.write(f"p.scan_number {scans}\n")
+            f.write("p.check_nextscan_started 1\n")
+
+
+class TomoIDManager:
+    """Registers a tomography measurement in the OMNY sample database
+    and returns its assigned tomo ID.
+
+    Usage:
+        id_manager = TomoIDManager()
+        tomo_id = id_manager.register(
+            sample_name="my_sample",
+            date="2024-03-08",
+            eaccount="e12345",
+            scan_number=1001,
+            setup="lamni",
+            additional_info="test info",
+            user="BEC",
+        )
+    """
+
+    OMNY_URL = "https://omny.web.psi.ch/samples/newmeasurement.php"
+    OMNY_USER = "omny"
+    OMNY_PASSWORD = "samples"
+    TMP_FILE = "/tmp/currsamplesnr.txt"
+
+    def register(
+        self,
+        sample_name: str,
+        date: str,
+        eaccount: str,
+        scan_number: int,
+        setup: str,
+        additional_info: str,
+        user: str,
+    ) -> int:
+        """Register a new measurement and return the assigned tomo ID.
+
+        Args:
+            sample_name (str): Name of the sample.
+            date (str): Date string (e.g. "2024-03-08").
+            eaccount (str): E-account identifier.
+            scan_number (int): First scan number of the measurement.
+            setup (str): Setup name (e.g. "lamni").
+            additional_info (str): Any additional sample information.
+            user (str): User name.
+
+        Returns:
+            int: The tomo ID assigned by the OMNY database.
+        """
+        url = (
+            f"{self.OMNY_URL}"
+            f"?sample={sample_name}"
+            f"&date={date}"
+            f"&eaccount={eaccount}"
+            f"&scannr={scan_number}"
+            f"&setup={setup}"
+            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,
+        )
+        with open(self.TMP_FILE) as f:
+            return int(f.read())

csaxs_bec/bec_ipython_client/startup/post_startup.py

@@ -111,3 +111,34 @@ bec._beamline_mixin._bl_info_register(OperatorInfo)
 # SETUP PROMPTS
 bec._ip.prompts.session_name = _session_name
 bec._ip.prompts.status = 1
+
+# ACCOUNT MISMATCH CHECK
+import os
+
+def _check_account_mismatch():
+    try:
+        active = bec.active_account  # e.g. "p23092"
+        system_user = os.getenv("USER") or os.getlogin()  # e.g. "e23092"
+        if active[1:] != system_user[1:]:
+            print(f"""
+\033[91m\033[1m
+    ██╗    ██╗ █████╗ ██████╗ ███╗   ██╗██╗███╗   ██╗ ██████╗ 
+    ██║    ██║██╔══██╗██╔══██╗████╗  ██║██║████╗  ██║██╔════╝ 
+    ██║ █╗ ██║███████║██████╔╝██╔██╗ ██║██║██╔██╗ ██║██║  ███╗
+    ██║███╗██║██╔══██║██╔══██╗██║╚██╗██║██║██║╚██╗██║██║   ██║
+    ╚███╔███╔╝██║  ██║██║  ██║██║ ╚████║██║██║ ╚████║╚██████╔╝
+    ╚══╝╚══╝ ╚═╝  ╚═╝╚═╝  ╚═╝╚═╝  ╚═══╝╚═╝╚═╝  ╚═══╝ ╚═════╝ 
+
+    ACCOUNT MISMATCH DETECTED!
+    BEC active account : {active}
+    System user        : {system_user}
+
+    Data read and written by the BEC client does not match the data account!
+    Please verify you are logged in with the correct account.
+\033[0m""")
+    except Exception:
+        logger.warning("Failed to verify account match.")
+
+
+if _args.session.lower() == "lamni" or _args.session.lower() == "flomni" or _args.session.lower() == "omny":
+    _check_account_mismatch()