removed blchk from flomni

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 +11,12 @@ 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 (
+    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 +30,25 @@ 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.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"
@@ -56,105 +59,6 @@ class LamNI(LamNIOpticsMixin):
         self.progress["total_projections"] = 1
         self.progress["angle"] = 0
 
-    # ------------------------------------------------------------------
-    # Beamline checks
-    # ------------------------------------------------------------------
-
-    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,
-        }
-
-    @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()
-
-    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.")
 
     # ------------------------------------------------------------------
     # Special angles
@@ -212,7 +116,6 @@ 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 +125,12 @@ 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 +280,7 @@ 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 +401,22 @@ 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 +433,6 @@ 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 +470,11 @@ 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 +536,6 @@ 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()
                 if not self.special_angles:
                     self._current_special_angles = []
                 if self._current_special_angles:
@@ -662,10 +562,9 @@ 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:
-                    successful = True
-                else:
-                    self._wait_for_beamline_checks()
+                #todo here bl chk, if ok then successfull true
+                successful = True
+
 
     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 +908,4 @@ 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/flomni/flomni.py

@@ -15,7 +15,11 @@ from csaxs_bec.bec_ipython_client.plugins.cSAXS import cSAXSBeamlineChecks
 from csaxs_bec.bec_ipython_client.plugins.flomni.flomni_optics_mixin import FlomniOpticsMixin
 from csaxs_bec.bec_ipython_client.plugins.flomni.x_ray_eye_align import XrayEyeAlign
 from csaxs_bec.bec_ipython_client.plugins.flomni.gui_tools import flomniGuiTools
-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 (
+    OMNYTools,
+    PtychoReconstructor,
+    TomoIDManager,
+)
 
 logger = bec_logger.logger
 
@@ -65,9 +69,6 @@ class FlomniError(Exception):
 #                 print("Please expicitely confirm y or n.")
 
 
-
-
-
 class FlomniInitStagesMixin:
 
     def flomni_init_stages(self):
@@ -1159,18 +1160,12 @@ class Flomni(
         super().__init__()
         self.client = client
         self.device_manager = client.device_manager
-        self.check_shutter = False
-        self.check_light_available = False
-        self.check_fofb = False
-        self._check_msgs = []
         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.corr_pos_y = []
         self.corr_angle_y = []
         self.corr_pos_y_2 = []
@@ -1184,6 +1179,8 @@ class Flomni(
         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()
         self.align = XrayEyeAlign(self.client, self)
         self.set_client(client)
 
@@ -1215,27 +1212,6 @@ class Flomni(
     def axis_id_to_numeric(self, axis_id) -> int:
         return ord(axis_id.lower()) - 97
 
-    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,
-        }
-
-    @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()
-
     def set_special_angles(self, angles: list, repeats: int = 20, tolerance: float = 0.5):
         """Set the special angles for a tomo
 
@@ -1379,6 +1355,7 @@ class Flomni(
     @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):
@@ -1486,7 +1463,6 @@ class Flomni(
             if 0 <= angle < 180.05:
                 print(f"Starting flOMNI scan for angle {angle}")
                 while not successful:
-                    self._start_beam_check()
                     try:
                         start_scan_number = bec.queue.next_scan_number
                         self.tomo_scan_projection(angle)
@@ -1499,11 +1475,9 @@ class Flomni(
                             error_caught = True
                         else:
                             raise exc
-
-                    if self._was_beam_okay() and not error_caught:
-                        successful = True
-                    else:
-                        self._wait_for_beamline_checks()
+                    #todo here was if blchk success, then setting to success true
+                    successful = True
+                    
                 end_scan_number = bec.queue.next_scan_number
                 for scan_nr in range(start_scan_number, end_scan_number):
                     self._write_tomo_scan_number(scan_nr, angle, 0)
@@ -1592,7 +1566,7 @@ class Flomni(
             print(f"Starting flOMNI scan for angle {angle} in subtomo {subtomo_number}")
             self._print_progress()
             while not successful:
-                self._start_beam_check()
+                self.bl_chk._bl_chk_start()
                 if not self.special_angles:
                     self._current_special_angles = []
                 if self._current_special_angles:
@@ -1615,10 +1589,10 @@ class Flomni(
                     else:
                         raise exc
 
-                if self._was_beam_okay() and not error_caught:
+                if self.bl_chk._bl_chk_stop() and not error_caught:
                     successful = True
                 else:
-                    self._wait_for_beamline_checks()
+                    self.bl_chk._bl_chk_wait_until_recovered()
             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, subtomo_number)
@@ -1770,13 +1744,15 @@ class Flomni(
         self, samplename, date, eaccount, scan_number, setup, sample_additional_info, user
     ):
         """Add a sample to the omny sample database. This also retrieves the tomo id."""
-        subprocess.run(
-            f"wget --user=omny --password=samples -q -O /tmp/currsamplesnr.txt 'https://omny.web.psi.ch/samples/newmeasurement.php?sample={samplename}&date={date}&eaccount={eaccount}&scannr={scan_number}&setup={setup}&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
 
     def _at_each_angle(self, angle: float) -> None:
         if "flomni_at_each_angle" in builtins.__dict__:
@@ -1838,19 +1814,11 @@ class Flomni(
     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)
-
-        # pylint: disable=undefined-variable
-        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 _write_tomo_scan_number(self, scan_number: int, angle: float, subtomo_number: int) -> None:
         tomo_scan_numbers_file = os.path.expanduser(
@@ -2101,4 +2069,4 @@ if __name__ == "__main__":
     builtins.__dict__["bec"] = bec
     builtins.__dict__["umv"] = umv
     flomni = Flomni(bec)
-    flomni.start_x_ray_eye_alignment()
+    flomni.start_x_ray_eye_alignment()

csaxs_bec/bec_ipython_client/plugins/flomni/gui_tools.py

@@ -107,11 +107,12 @@ class flomniGuiTools:
             idle_text_box = self.gui.flomni.new("idle_textbox").new("TextBox")
         text = (
             "<pre>"
-            + " ,---.,--. ,-----. ,--.   ,--.,--.  ,--.,--. \n"
-            + "/  .-'|  |'  .-.  '|   `.'   ||  ,'.|  ||  | \n"
-            + "|  `-,|  ||  | |  ||  |'.'|  ||  |' '  ||  | \n"
-            + "|  .-'|  |'  '-'  '|  |   |  ||  | `   ||  | \n"
-            + "`--'  `--' `-----' `--'   `--'`--'  `--'`--' \n"
+            + "██████╗ ███████╗ ██████╗     ███████╗██╗      ██████╗ ███╗   ███╗███╗   ██╗██╗\n"
+            + "██╔══██╗██╔════╝██╔════╝     ██╔════╝██║     ██╔═══██╗████╗ ████║████╗  ██║██║\n"
+            + "██████╔╝█████╗  ██║          █████╗  ██║     ██║   ██║██╔████╔██║██╔██╗ ██║██║\n"
+            + "██╔══██╗██╔══╝  ██║          ██╔══╝  ██║     ██║   ██║██║╚██╔╝██║██║╚██╗██║██║\n"
+            + "██████╔╝███████╗╚██████╗     ██║     ███████╗╚██████╔╝██║ ╚═╝ ██║██║ ╚████║██║\n"
+            + "╚═════╝ ╚══════╝ ╚═════╝     ╚═╝     ╚══════╝ ╚═════╝ ╚═╝     ╚═╝╚═╝  ╚═══╝╚═╝\n"
             + "</pre>"
         )
         idle_text_box.set_html_text(text)

csaxs_bec/bec_ipython_client/plugins/omny/gui_tools.py

@@ -83,16 +83,12 @@ class OMNYGuiTools:
                 pass
         text = (
             "<pre>"
-            + "    ,o888888o.           ,8.       ,8.          b.             8 `8.`8888.      ,8' \n"
-            + " . 8888     `88.        ,888.     ,888.         888o.          8  `8.`8888.    ,8'  \n"
-            + ",8 8888       `8b      .`8888.   .`8888.        Y88888o.       8   `8.`8888.  ,8'   \n"
-            + "88 8888        `8b    ,8.`8888. ,8.`8888.       .`Y888888o.    8    `8.`8888.,8'    \n"
-            + "88 8888         88   ,8'8.`8888,8^8.`8888.      8o. `Y888888o. 8     `8.`88888'     \n"
-            + "88 8888         88  ,8' `8.`8888' `8.`8888.     8`Y8o. `Y88888o8      `8. 8888      \n"
-            + "88 8888        ,8P ,8'   `8.`88'   `8.`8888.    8   `Y8o. `Y8888       `8 8888      \n"
-            + "`8 8888       ,8P ,8'     `8.`'     `8.`8888.   8      `Y8o. `Y8        8 8888      \n"
-            + " ` 8888     ,88' ,8'       `8        `8.`8888.  8         `Y8o.`        8 8888      \n"
-            + "    `8888888P'  ,8'         `         `8.`8888. 8            `Yo        8 8888      \n"
+            + "██████╗ ███████╗ ██████╗      ██████╗ ███╗   ███╗███╗   ██╗██╗   ██╗\n"
+            + "██╔══██╗██╔════╝██╔════╝     ██╔═══██╗████╗ ████║████╗  ██║╚██╗ ██╔╝\n"
+            + "██████╔╝█████╗  ██║          ██║   ██║██╔████╔██║██╔██╗ ██║ ╚████╔╝ \n"
+            + "██╔══██╗██╔══╝  ██║          ██║   ██║██║╚██╔╝██║██║╚██╗██║  ╚██╔╝  \n"
+            + "██████╔╝███████╗╚██████╗     ╚██████╔╝██║ ╚═╝ ██║██║ ╚████║   ██║   \n"
+            + "╚═════╝ ╚══════╝ ╚═════╝      ╚═════╝ ╚═╝     ╚═╝╚═╝  ╚═══╝   ╚═╝   \n"
             + "</pre>"
         )
         self.idle_text_box.set_html_text(text)

csaxs_bec/bec_ipython_client/plugins/omny/omny_general_tools.py

@@ -1,26 +1,35 @@
-import time
-import numpy as np
-import sys
-import termios
-import tty
+import builtins
+import datetime
 import fcntl
 import os
-import builtins
+import socket
+import subprocess
+import sys
+import termios
+import threading
+import time
+import tty
+from pathlib import Path
 
+import epics
+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)
-
+def umvr(*args):
+    return scans.umv(*args, relative=True)
 
 class OMNYToolsError(Exception):
     pass
@@ -110,24 +119,20 @@ 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 +148,135 @@ 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 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.
+        """
+        if not self._accounts_match():
+            logger.warning("Active BEC account does not match system user — skipping queue file write.")
+            return
+        
+        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()

csaxs_bec/device_configs/ptycho_lamni.yaml

@@ -271,4 +271,20 @@ rty:
   enabled: true
   readOnly: False
 
-
+############################################################
+######################### Cameras ##########################
+############################################################
+cam_xeye:
+  description: Camera LamNI Xray eye ID15
+  deviceClass: csaxs_bec.devices.ids_cameras.ids_camera.IDSCamera
+  deviceConfig:
+    camera_id: 15
+    bits_per_pixel: 24
+    num_rotation_90: 3
+    transpose: false
+    force_monochrome: true
+    m_n_colormode: 1
+  enabled: true
+  onFailure: buffer
+  readOnly: false
+  readoutPriority: async

csaxs_bec/devices/omny/galil/lgalil_ophyd.py

@@ -15,7 +15,6 @@ from csaxs_bec.devices.omny.galil.galil_ophyd import (
     GalilAxesReferenced,
     GalilController,
     GalilMotorIsMoving,
-    GalilMotorResolution,
     GalilSetpointSignal,
     GalilSignalRO,
     retry_once,
@@ -24,6 +23,19 @@ from csaxs_bec.devices.omny.galil.galil_ophyd import (
 logger = bec_logger.logger
 
 
+class GalilMotorResolution(GalilSignalRO):
+    @retry_once
+    @threadlocked
+    def _socket_get(self):
+        if self.parent.axis_Id_numeric < 6:
+            return float(
+                self.controller.socket_put_and_receive(f"MG encpermm[{self.parent.axis_Id_numeric}]")
+            )
+        else:
+            return float(
+                self.controller.socket_put_and_receive(f"MG stppermm[{self.parent.axis_Id_numeric}]")
+            )
+
 class LamniGalilController(GalilController):
 
 
@@ -154,11 +166,18 @@ class LamniGalilReadbackSignal(GalilSignalRO):
         Returns:
             float: Readback value after adjusting for sign and motor resolution.
         """
-        current_pos = float(self.controller.socket_put_and_receive(f"TD{self.parent.axis_Id}"))
-        current_pos *= self.parent.sign
-        step_mm = self.parent.motor_resolution.get()
-        return current_pos / step_mm
-
+        if self.parent.axis_Id_numeric < 6:
+            current_pos = float(self.controller.socket_put_and_receive(f"TP{self.parent.axis_Id}"))
+            current_pos *= self.parent.sign
+            encoder_resolution = self.parent.motor_resolution.get()
+            logger.info(f"Read galil encoder position of axis {self.parent.axis_Id_numeric} to be TP {current_pos} with resolution {encoder_resolution}")
+            return current_pos / encoder_resolution
+        else:
+            current_pos = float(self.controller.socket_put_and_receive(f"TD{self.parent.axis_Id}"))
+            current_pos *= self.parent.sign
+            step_mm = self.parent.motor_resolution.get()
+            return current_pos / step_mm
+        
     def read(self):
         self._metadata["timestamp"] = time.time()
         val = super().read()

csaxs_bec/scans/LamNIFermatScan.py

@@ -169,6 +169,9 @@ class LamNIMixin:
 
         self.device_manager.devices.lsamx.read_only = True
         self.device_manager.devices.lsamy.read_only = True
+        
+        #update angle readback before start of the scan
+        yield from self.stubs.send_rpc_and_wait("lsamrot", "readback.get")
 
         yield from self.stubs.send_rpc_and_wait("rtx", "controller.feedback_enable_without_reset")
 

docs/user/ptychography/flomni.md

@@ -108,12 +108,17 @@ The nano-positioning is controlled by a feedback loop running on a real-time lin
 
 Once the loop has started, it is possible to start bec with the flOMNI configuration file.
 
+Starting bec with session will load the scripts
+`bec --session flomni`
+
+The flOMNI scripts can be loaded manually by  
+`from csaxs_bec.bec_ipython_client.plugins.flomni import Flomni`  
+`flomni =  Flomni(bec)`
+
 Loading the flOMNI configuration (this command will load the OMNY configuration only - isolated from the beamline)  
 `bec.config.update_session_with_file("/bec/csaxs_bec/csaxs_bec/device_configs/flomni_config.yaml")`
 
-Loading the flOMNI scripts  
-`from csaxs_bec.bec_ipython_client.plugins.flomni import Flomni`  
-`flomni =  Flomni(bec)`
+
 
 If the realtime system is restarted, bec will lose communication. To restart:  
 `flomni.rt_off()` … then wait a few seconds  
@@ -138,10 +143,14 @@ This script will first verify that the stages are not in an initialized state, a
 The positions of the optics stages are stored as stage parameters and are thus linked to the configuration file.  
 Example: The OSAx “in” position can be reviewed by `dev.fosax.user_parameter`  
 Update the value by (example "fosax", "in") by `dev.fosax.update_user_parameter({"in":value})`
+Important note: if these values are changed, they are not automatically stored to the config file and will only be available in the current session.
 
 `flomni.ffzp_info()` shows info about the available FZPs at the current energy of the beamline. Optional parameter is the photon _energy_ in keV.  
 Example: `flomni.ffzp_info(6.2)`
 
+Documents about availabe optics can be accessed by
+`flomni.flomnigui_docs`
+
 The [laser feedback](user.ptychography.flomni.laser_feedback) will be disabled and fine alignment lost if foptx/y are moved!
 
 Following functions exist to move the optics in and out, with self-explaining naming.

docs/user/ptychography/lamni.md

@@ -102,13 +102,16 @@ The nano-positioning is controlled by a feedback loop running on a real-time lin
 
 Once the loop has started, it is possible to start bec with the LamNI configuration file.
 
-Loading the LamNI configuration (this command will load the LamNI configuration only - isolated from the beamline)  
-`bec.config.update_session_with_file("/bec/csaxs_bec/csaxs_bec/device_configs/lamni_config.yaml")`
+Loading the LamNI scripts is done by starting bec as
+`bec --session lamni`
 
-Loading the LamNI scripts  
+The scripts can alternatively manually be loaded by  
 `from csaxs_bec.bec_ipython_client.plugins.LamNI import LamNI`
 `lamni = LamNI(bec)`
 
+Loading the LamNI configuration (this command will load the LamNI configuration only - isolated from the beamline)  
+`bec.config.update_session_with_file("/bec/csaxs_bec/csaxs_bec/device_configs/lamni_config.yaml")`
+
 If the realtime system is restarted, BEC will lose communication. To restart:  
 `lamni.rt_off()` … then wait a 10 seconds  
 `lamni.rt_on()`
@@ -152,6 +155,12 @@ The underlying scan function can be called as
 
 Use `scans.lamni_fermat_scan?`for detailed information. A prerequisite for scanning is a running feedback system.
 
+### GUI tools
+
+During operation the BEC GUI will show the relevant cameras or progress information. To manually switch view TAB completion on 'lamni.lamnigui_' will show all options to control the GUI. Most useful
+'lamni.lamnigui_show_progress()' will show the measurement progress GUI
+'lamnigui_show_xeyealign()' will show the XrayEye alignment GUI
+
 ### X-ray optics alignment
 
 The positions of the optics stages are stored as stage parameters and are thus linked to the configuration file.