added tomo type 2 and 3, for golden ratio

csaxs_bec/bec_ipython_client/plugins/LamNI/lamni_optics_mixin.py

@@ -6,6 +6,8 @@ from rich.console import Console
 from rich.table import Table
 
 from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_put, fshclose
+from csaxs_bec.bec_ipython_client.plugins.omny.omny_general_tools import OMNYTools
+
 
 # import builtins to avoid linter errors
 dev = builtins.__dict__.get("dev")
@@ -18,25 +20,32 @@ class LamNIInitError(Exception):
 
 
 class LaMNIInitStagesMixin:
+    def __init__(self, client):
+        super().__init__()
+        self.client = client
+        self.OMNYTools = OMNYTools(self.client)
+
     def lamni_init_stages(self):
-        user_input = input("Starting initialization of LamNI stages. OK? [y/n]")
-        if user_input == "y":
+
+        if self.OMNYTools.yesno("Start initialization of LamNI stages. OK?"):
             print("staring...")
             dev.lsamrot.enabled = True
         else:
             return
 
+
+
+
         if self.check_all_axes_of_lamni_referenced():
-            user_input = input("Continue anyways? [y/n]")
-            if user_input == "y":
+            if self.OMNYTools.yesno("All axes are referenced. Continue anyways?"):
                 print("ok then...")
             else:
                 return
 
         axis_id_lsamrot = dev.lsamrot._config["deviceConfig"].get("axis_Id")
         if dev.lsamrot.controller.get_motor_limit_switch(axis_id_lsamrot)[1] == False:
-            user_input = input("The rotation stage will be moved to one limit [y/n]")
-            if user_input == "y":
+
+            if self.OMNYTools.yesno("The rotation stage will be moved to one limit"):
                 print("starting...")
             else:
                 return
@@ -47,10 +56,7 @@ class LaMNIInitStagesMixin:
             print("The controller will be disabled in bec. To enable dev.lsamrot.enabled=True")
             return
 
-        user_input = input(
-            "Init of loptz. Can the stage move to the upstream limit without collision?? [y/n]"
-        )
-        if user_input == "y":
+        if self.OMNYTools.yesno("Init of loptz. Can the stage move to the upstream limit without collision?"):
             print("ok then...")
         else:
             return
@@ -81,8 +87,7 @@ class LaMNIInitStagesMixin:
         time.sleep(0.1)
         self.find_reference_mark(dev.lsamrot)
 
-        user_input = input("Init of leye. Can the stage move to -x limit without collision? [y/n]")
-        if user_input == "y":
+        if self.OMNYTools.yesno("Init of leye. Can the stage move to -x limit without collision?"):
             print("starting...")
         else:
             return
@@ -134,8 +139,7 @@ class LaMNIInitStagesMixin:
         return ord(axis_id.lower()) - 97
 
     def _align_setup(self):
-        user_input = input("Start moving stages to default initial positions? [y/n]")
-        if user_input == "y":
+        if self.OMNYTools.yesno("Start moving stages to default initial positions?"):
             print("Start moving stages...")
         else:
             print("Stopping.")

csaxs_bec/bec_ipython_client/plugins/LamNI/x_ray_eye_align.py

@@ -15,13 +15,19 @@ from bec_lib.pdf_writer import PDFWriter
 from typeguard import typechecked
 
 from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_get, epics_put, fshopen
+from csaxs_bec.bec_ipython_client.plugins.omny.omny_general_tools import OMNYTools
 
 from .lamni_optics_mixin import LaMNIInitStagesMixin, LamNIOpticsMixin
 
 logger = bec_logger.logger
-bec = builtins.__dict__.get("bec")
 
 
+if builtins.__dict__.get("bec") is not None:
+    bec = builtins.__dict__.get("bec")
+    dev = builtins.__dict__.get("dev")
+    umv = builtins.__dict__.get("umv")
+    umvr = builtins.__dict__.get("umvr")
+
 class XrayEyeAlign:
     # pixel calibration, multiply to get mm
     # PIXEL_CALIBRATION = 0.2/209 #.2 with binning
@@ -510,8 +516,9 @@ class LamNI(LamNIOpticsMixin):
     def __init__(self, client):
         super().__init__()
         self.client = client
+        self.device_manager = client.device_manager
         self.align = XrayEyeAlign(client, self)
-        self.init = LaMNIInitStagesMixin()
+        self.init = LaMNIInitStagesMixin(client)
         self.check_shutter = True
         self.check_light_available = True
         self.check_fofb = True
@@ -524,6 +531,16 @@ class LamNI(LamNIOpticsMixin):
         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"
+        self.progress["subtomo"] = 0
+        self.progress["subtomo_projection"] = 0
+        self.progress["subtomo_total_projections"] = 1
+        self.progress["projection"] = 0
+        self.progress["total_projections"] = 1
+        self.progress["angle"] = 0
 
     def get_beamline_checks_enabled(self):
         print(
@@ -598,12 +615,12 @@ class LamNI(LamNIOpticsMixin):
         if val == 1:
             # equally spaced tomography with 8 sub tomograms
             self.client.set_global_var("tomo_type", val)
-        # elif val == 2:
-        #    # golden ratio tomography (sorted bunches)
-        #    self.client.set_global_var("tomo_type", val)
-        # elif val == 3:
-        #    # equally spaced tomography with starting angles shifted by golden ratio
-        #    self.client.set_global_var("tomo_type", val)
+        elif val == 2:
+            # golden ratio tomography (sorted bunches)
+            self.client.set_global_var("tomo_type", val)
+        elif val == 3:
+            # equally spaced tomography with starting angles shifted by golden ratio
+            self.client.set_global_var("tomo_type", val)
         else:
             raise ValueError("Unknown tomo_type.")
 
@@ -740,6 +757,41 @@ class LamNI(LamNIOpticsMixin):
     def tomo_stitch_overlap(self, val: float):
         self.client.set_global_var("tomo_stitch_overlap", val)
 
+    @property
+    def golden_max_number_of_projections(self):
+        val = self.client.get_global_var("golden_max_number_of_projections")
+        if val is None:
+            return 1000.0
+        return val
+
+    @golden_max_number_of_projections.setter
+    def golden_max_number_of_projections(self, val: float):
+        self.client.set_global_var("golden_max_number_of_projections", val)
+
+    @property
+    def golden_ratio_bunch_size(self):
+        val = self.client.get_global_var("golden_ratio_bunch_size")
+        if val is None:
+            return 20
+        return val
+
+    @golden_ratio_bunch_size.setter
+    def golden_ratio_bunch_size(self, val: float):
+        if val < 20:
+            raise ValueError("golden_ratio_bunch_size must be at least 20.")
+        self.client.set_global_var("golden_ratio_bunch_size", val)
+
+    @property
+    def golden_projections_at_0_deg_for_damage_estimation(self):
+        val = self.client.get_global_var("golden_projections_at_0_deg_for_damage_estimation")
+        if val is None:
+            return 0
+        return val
+
+    @golden_projections_at_0_deg_for_damage_estimation.setter
+    def golden_projections_at_0_deg_for_damage_estimation(self, val: float):
+        self.client.set_global_var("golden_projections_at_0_deg_for_damage_estimation", val)
+
     @property
     def sample_name(self):
         val = self.client.get_global_var("sample_name")
@@ -909,6 +961,49 @@ class LamNI(LamNIOpticsMixin):
         except Exception:
             logger.warning("Failed to send update to SciLog.")
 
+    def rt_off(self):
+        dev.rtx.enabled = False
+        dev.rty.enabled = False
+
+    def rt_on(self):
+        dev.rtx.enabled = True
+        dev.rty.enabled = True
+        if dev.rtx.enabled == True:
+            print("rt is enabled")
+        else:
+            print("failed to enable rt")
+
+    def feedback_enable_with_reset(self):
+        self.device_manager.devices.rtx.controller.feedback_enable_with_reset()
+        self.feedback_status()
+
+    def feedback_enable_without_reset(self):
+        self.device_manager.devices.rtx.controller.feedback_enable_without_reset()
+        self.feedback_status()
+
+    def feedback_disable(self):
+        self.device_manager.devices.rtx.controller.feedback_disable()
+        self.feedback_status()
+
+    def feedback_disable_and_reset_angle(self):
+        self.device_manager.devices.rtx.controller.feedback_disable_and_even_reset_lamni_angle_interferometer()
+        self.feedback_status()
+
+    def feedback_status(self):
+        if self.device_manager.devices.rtx.controller.feedback_is_running():
+            print("The rt feedback is \x1b[92mrunning\x1b[0m.")
+        else:
+            print("The rt feedback is \x1b[91mNOT\x1b[0m running.")
+
+    def show_interferometer_positions(self):
+        self.device_manager.devices.rtx.controller.show_interferometer_positions()
+
+    def show_signal_strength(self):
+        self.device_manager.devices.rtx.controller.show_signal_strength_interferometer()
+
+    def show_analog_signals(self):
+        return self.device_manager.devices.rtx.controller.show_analog_signals()
+
     def add_sample_database(
         self, samplename, date, eaccount, scan_number, setup, sample_additional_info, user
     ):
@@ -935,9 +1030,8 @@ class LamNI(LamNIOpticsMixin):
         # self.tomo_scan_projection(angle)
         # self.tomo_reconstruct()
 
-    def sub_tomo_scan(self, subtomo_number, start_angle=None):
-        """start a subtomo"""
-        dev = builtins.__dict__.get("dev")
+    def _write_subtomo_to_scilog(self, subtomo_number):
+        """Write subtomo start information to scilog."""
         bec = builtins.__dict__.get("bec")
         if self.tomo_id > 0:
             tags = ["BEC_subtomo", self.sample_name, f"tomo_id_{self.tomo_id}"]
@@ -948,6 +1042,10 @@ class LamNI(LamNIOpticsMixin):
             tags,
         )
 
+    def sub_tomo_scan(self, subtomo_number, start_angle=None):
+        """start a subtomo"""
+        self._write_subtomo_to_scilog(subtomo_number)
+
         if start_angle is None:
             if subtomo_number == 1:
                 start_angle = 0
@@ -980,13 +1078,14 @@ class LamNI(LamNIOpticsMixin):
         if not (subtomo_number % 2):
             angles = np.flip(angles)
         for angle in angles:
+            self.progress["tomo_type"] = "Equally spaced sub-tomograms"
             self.progress["subtomo"] = subtomo_number
-            self.progress["subtomo_projection"] = angles.index(angle)
-            self.progress["subtomo_total_projections"] = 180 / self.tomo_angle_stepsize
+            self.progress["subtomo_projection"] = np.where(angles == angle)[0][0]
+            self.progress["subtomo_total_projections"] = 360 / self.tomo_angle_stepsize
             self.progress["projection"] = (subtomo_number - 1) * self.progress[
                 "subtomo_total_projections"
             ] + self.progress["subtomo_projection"]
-            self.progress["total_projections"] = 180 / self.tomo_angle_stepsize * 8
+            self.progress["total_projections"] = 360 / self.tomo_angle_stepsize * 8
             self.progress["angle"] = angle
             self._tomo_scan_at_angle(angle, subtomo_number)
 
@@ -1049,6 +1148,11 @@ 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()
+
     def _write_tomo_scan_number(self, scan_number: int, angle: float, subtomo_number: int) -> None:
         tomo_scan_numbers_file = os.path.expanduser(
             "~/Data10/specES1/dat-files/tomography_scannumbers.txt"
@@ -1059,13 +1163,74 @@ class LamNI(LamNIOpticsMixin):
                 f"{scan_number} {angle} {dev.lsamrot.read()['lsamrot']['value']:.3f} {self.tomo_id} {subtomo_number} {0} {'lamni'}\n"
             )
 
-    def tomo_scan(self, subtomo_start=1, start_angle=None):
-        """start a tomo scan"""
+    def _golden(self, ii, howmany_sorted, maxangle=360, reverse=False):
+        """Return the ii-th golden ratio angle within sorted bunches of size howmany_sorted,
+        and its subtomo number. Operates over maxangle degrees (360 for LamNI)."""
+        golden = []
+        for iji in range(
+            (ii - (ii % howmany_sorted)), (ii - (ii % howmany_sorted)) + howmany_sorted, 1
+        ):
+            golden.append(
+                ((iji * maxangle * (1 + pow(5, 0.5)) / 2) * 1000 % (maxangle * 1000)) / 1000
+            )
+        golden.sort()
+        subtomo_number = int(ii / howmany_sorted) + 1
+        if reverse and not subtomo_number % 2:
+            golden.reverse()
+        return (golden[ii % howmany_sorted], subtomo_number)
+
+    def _golden_equally_spaced(self, ii, number_of_projections_per_subtomo, maxangle=360, reverse=True, verbose=False):
+        """Return angles for equally spaced tomography with sub-tomogram starting angles
+        shifted according to the golden ratio. Operates over maxangle degrees (360 for LamNI).
+        ii is the projection number starting at 0."""
+        angular_step = maxangle / number_of_projections_per_subtomo
+        subtomo_number = int(((ii) * angular_step) / maxangle) + 1
+        start_angle = self._golden(subtomo_number - 1, 1, angular_step)[0]
+        projection_number_of_subtomo = (
+            ii - (subtomo_number - 1) * number_of_projections_per_subtomo
+        )
+
+        if reverse:
+            if subtomo_number % 2:
+                angle = start_angle + projection_number_of_subtomo * angular_step
+            else:
+                angle = (
+                    start_angle
+                    + (number_of_projections_per_subtomo - 1) * angular_step
+                    - projection_number_of_subtomo * angular_step
+                )
+        else:
+            angle = start_angle + projection_number_of_subtomo * angular_step
+
+        if verbose:
+            print(
+                f"Equally spaced golden ratio tomography.\n"
+                f"Angular step: {angular_step}\n"
+                f"Subtomo Number: {subtomo_number}\n"
+                f"Angle: {angle}"
+            )
+
+        return angle, subtomo_number
+
+    def tomo_scan(self, subtomo_start=1, start_angle=None, projection_number=None):
+        """Start a tomo scan.
+
+        Args:
+            subtomo_start (int): For tomo_type 1, the sub-tomogram number to start from. Defaults to 1.
+            start_angle (float, optional): Override the starting angle of the first sub-tomogram. Defaults to None.
+            projection_number (int, optional): For tomo_types 2 and 3, resume from this projection index. Defaults to None.
+        """
         bec = builtins.__dict__.get("bec")
         scans = builtins.__dict__.get("scans")
         self._current_special_angles = self.special_angles.copy()
 
-        if self.tomo_type == 1 and subtomo_start == 1 and start_angle is None:
+        # Register a new tomo scan in the database and write the PDF report
+        # only when starting fresh (not resuming mid-scan)
+        if (
+            (self.tomo_type == 1 and subtomo_start == 1 and start_angle is None)
+            or (self.tomo_type == 2 and projection_number is None)
+            or (self.tomo_type == 3 and projection_number is None)
+        ):
             # pylint: disable=undefined-variable
             self.tomo_id = self.add_sample_database(
                 self.sample_name,
@@ -1077,10 +1242,108 @@ class LamNI(LamNIOpticsMixin):
                 "BEC",
             )
             self.write_pdf_report()
+
         with scans.dataset_id_on_hold:
-            for ii in range(subtomo_start, 9):
-                self.sub_tomo_scan(ii, start_angle=start_angle)
-                start_angle = None
+            if self.tomo_type == 1:
+                # 8 equally spaced sub-tomograms over 360 degrees
+                self.progress["tomo_type"] = "Equally spaced sub-tomograms"
+                for ii in range(subtomo_start, 9):
+                    self.sub_tomo_scan(ii, start_angle=start_angle)
+                    start_angle = None
+
+            elif self.tomo_type == 2:
+                # Golden ratio tomography (sorted bunches) over 360 degrees
+                self.progress["tomo_type"] = "Golden ratio tomography"
+                previous_subtomo_number = -1
+                ii = 0 if projection_number is None else projection_number
+                while True:
+                    angle, subtomo_number = self._golden(
+                        ii, self.golden_ratio_bunch_size, maxangle=360, reverse=True
+                    )
+                    if previous_subtomo_number != subtomo_number:
+                        self._write_subtomo_to_scilog(subtomo_number)
+                        if (
+                            subtomo_number % 2 == 1
+                            and ii > 10
+                            and self.golden_projections_at_0_deg_for_damage_estimation == 1
+                        ):
+                            self._tomo_scan_at_angle(0, subtomo_number)
+                        previous_subtomo_number = subtomo_number
+
+                    self.progress["subtomo"] = subtomo_number
+                    self.progress["projection"] = ii
+                    self.progress["angle"] = angle
+                    if self.golden_ratio_bunch_size > 0:
+                        self.progress["subtomo_total_projections"] = self.golden_ratio_bunch_size
+                        self.progress["subtomo_projection"] = (
+                            ii - (subtomo_number - 1) * self.golden_ratio_bunch_size
+                        )
+                    else:
+                        self.progress["subtomo_total_projections"] = 0
+                        self.progress["subtomo_projection"] = 0
+                    self.progress["total_projections"] = (
+                        self.golden_max_number_of_projections
+                        if self.golden_max_number_of_projections > 0
+                        else 0
+                    )
+
+                    self._tomo_scan_at_angle(angle, subtomo_number)
+                    ii += 1
+                    if (
+                        self.golden_max_number_of_projections > 0
+                        and ii > self.golden_max_number_of_projections
+                    ):
+                        print(
+                            f"Golden ratio tomography stopped automatically after the requested"
+                            f" {self.golden_max_number_of_projections} projections."
+                        )
+                        break
+
+            elif self.tomo_type == 3:
+                # Equally spaced tomography with golden ratio starting angles over 360 degrees
+                self.progress["tomo_type"] = "Equally spaced, golden ratio starting angles"
+                previous_subtomo_number = -1
+                ii = 0 if projection_number is None else projection_number
+                while True:
+                    angle, subtomo_number = self._golden_equally_spaced(
+                        ii, int(360 / self.tomo_angle_stepsize), maxangle=360, reverse=True
+                    )
+                    if previous_subtomo_number != subtomo_number:
+                        self._write_subtomo_to_scilog(subtomo_number)
+                        if (
+                            subtomo_number % 2 == 1
+                            and ii > 10
+                            and self.golden_projections_at_0_deg_for_damage_estimation == 1
+                        ):
+                            self._tomo_scan_at_angle(0, subtomo_number)
+                        previous_subtomo_number = subtomo_number
+
+                    self.progress["subtomo"] = subtomo_number
+                    self.progress["projection"] = ii
+                    self.progress["angle"] = angle
+                    self.progress["subtomo_total_projections"] = 360 / self.tomo_angle_stepsize
+                    self.progress["subtomo_projection"] = (
+                        ii - (subtomo_number - 1) * self.progress["subtomo_total_projections"]
+                    )
+                    self.progress["total_projections"] = (
+                        self.golden_max_number_of_projections
+                        if self.golden_max_number_of_projections > 0
+                        else 0
+                    )
+
+                    self._tomo_scan_at_angle(angle, subtomo_number)
+                    ii += 1
+                    if (
+                        self.golden_max_number_of_projections > 0
+                        and ii > self.golden_max_number_of_projections
+                    ):
+                        print(
+                            f"Golden ratio tomography stopped automatically after the requested"
+                            f" {self.golden_max_number_of_projections} projections."
+                        )
+                        break
+            else:
+                raise ValueError(f"Unknown tomo_type: {self.tomo_type}.")
 
     def tomo_parameters(self):
         """print and update the tomo parameters"""
@@ -1103,9 +1366,37 @@ class LamNI(LamNIOpticsMixin):
         print(f"   _tomo_fovy_offset       <mm>  =  {self.align.tomo_fovy_offset}")
         print(f"   _manual_shift_x         <mm>  =  {self.manual_shift_x}")
         print(f"   _manual_shift_y         <mm>  =  {self.manual_shift_y}")
-        print(f"Angular step within sub-tomogram:   {self.tomo_angle_stepsize} degrees")
-        print(f"Resulting in number of projections: {360/self.tomo_angle_stepsize*8}")
-        print(f"Sample name: {self.sample_name}\n")
+        print("")
+        if self.tomo_type == 1:
+            print("\x1b[1mTomo type 1:\x1b[0m 8 equally spaced sub-tomograms")
+            print(f"Angular step within sub-tomogram:   {self.tomo_angle_stepsize} degrees")
+            print(f"Resulting in number of projections: {360/self.tomo_angle_stepsize*8}")
+        elif self.tomo_type == 2:
+            print("\x1b[1mTomo type 2:\x1b[0m Golden ratio tomography")
+            print(f"Sorted in bunches of: {self.golden_ratio_bunch_size}")
+            if self.golden_max_number_of_projections > 0:
+                print(f"Ending after {self.golden_max_number_of_projections} projections.")
+            else:
+                print("Ending by manual interruption.")
+            if self.golden_projections_at_0_deg_for_damage_estimation == 1:
+                print(
+                    "Repeating projections at 0 degrees at the beginning of every second subtomogram."
+                )
+        elif self.tomo_type == 3:
+            print(
+                "\x1b[1mTomo type 3:\x1b[0m Equally spaced tomography, golden ratio starting angle"
+            )
+            print(f"Angular step within sub-tomogram:   {self.tomo_angle_stepsize} degrees")
+            print(f"Number of projections per sub-tomogram: {360/self.tomo_angle_stepsize}")
+            if self.golden_max_number_of_projections > 0:
+                print(f"Ending after {self.golden_max_number_of_projections} projections.")
+            else:
+                print("Ending by manual interruption.")
+            if self.golden_projections_at_0_deg_for_damage_estimation == 1:
+                print(
+                    "Repeating projections at 0 degrees at the beginning of every second subtomogram."
+                )
+        print(f"\nSample name: {self.sample_name}\n")
 
         user_input = input("Are these parameters correctly set for your scan? ")
         if user_input == "y":
@@ -1125,13 +1416,61 @@ class LamNI(LamNIOpticsMixin):
             self.ptycho_reconstruct_foldername = self._get_val(
                 "Reconstruction queue ", self.ptycho_reconstruct_foldername, str
             )
-            tomo_numberofprojections = self._get_val(
-                "Number of projections", 360 / self.tomo_angle_stepsize * 8, int
-            )
 
-            print(f"The angular step will be {360/tomo_numberofprojections}")
-            self.tomo_angle_stepsize = 360 / tomo_numberofprojections * 8
-            print(f"The angular step in a subtomogram it will be {self.tomo_angle_stepsize}")
+            print("Tomography type:")
+            print("  1: 8 equally spaced sub-tomograms (360 deg)")
+            print("  2: Golden ratio tomography")
+            print("  3: Equally spaced tomography, golden ratio starting angle")
+            self.tomo_type = self._get_val("Tomography type", self.tomo_type, int)
+
+            if self.tomo_type == 1:
+                tomo_numberofprojections = self._get_val(
+                    "Number of projections", 360 / self.tomo_angle_stepsize * 8, int
+                )
+                print(f"The angular step will be {360/tomo_numberofprojections}")
+                self.tomo_angle_stepsize = 360 / tomo_numberofprojections * 8
+                print(f"The angular step in a subtomogram it will be {self.tomo_angle_stepsize}")
+
+            elif self.tomo_type == 2:
+                while True:
+                    bunch_size = self._get_val(
+                        "Number of projections sorted per bunch (minimum 20)",
+                        self.golden_ratio_bunch_size,
+                        int,
+                    )
+                    if bunch_size >= 20:
+                        self.golden_ratio_bunch_size = bunch_size
+                        break
+                    print("Bunch size must be at least 20. Please try again.")
+                self.golden_max_number_of_projections = self._get_val(
+                    "Stop after number of projections (0 for endless)",
+                    self.golden_max_number_of_projections,
+                    int,
+                )
+                self.golden_projections_at_0_deg_for_damage_estimation = self._get_val(
+                    "Repeat projections at 0 deg every second subtomo 1/0?",
+                    self.golden_projections_at_0_deg_for_damage_estimation,
+                    int,
+                )
+
+            elif self.tomo_type == 3:
+                numprj = self._get_val(
+                    "Number of projections per sub-tomogram",
+                    int(360 / self.tomo_angle_stepsize),
+                    int,
+                )
+                self.tomo_angle_stepsize = 360 / numprj
+                self.golden_max_number_of_projections = self._get_val(
+                    "Stop after number of projections (0 for endless)",
+                    self.golden_max_number_of_projections,
+                    int,
+                )
+                self.golden_projections_at_0_deg_for_damage_estimation = self._get_val(
+                    "Repeat projections at 0 deg every second subtomo 1/0?",
+                    self.golden_projections_at_0_deg_for_damage_estimation,
+                    int,
+                )
+
             self.sample_name = self._get_val("sample name", self.sample_name, str)
 
     @staticmethod
@@ -1197,6 +1536,7 @@ class LamNI(LamNIOpticsMixin):
             (
                 f"{'Angular step within sub-tomogram:':<{padding}}{self.tomo_angle_stepsize:>{padding}.2f}\n"
             ),
+            f"{'Tomo type:':<{padding}}{self.tomo_type:>{padding}}\n",
         ]
         content = "".join(content)
         user_target = os.path.expanduser(f"~/Data10/documentation/tomo_scan_ID_{self.tomo_id}.pdf")
@@ -1389,3 +1729,4 @@ class DataDrivenLamNI(LamNI):
             shapes.append(data.shape)
         if len(set(shapes)) > 1:
             raise ValueError(f"Tomo data file has entries of inconsistent lengths: {shapes}.")
+        

csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py

@@ -35,32 +35,32 @@ class FlomniInitError(Exception):
 class FlomniError(Exception):
     pass
 
-class FlomniTools:
-    def yesno(self, message: str, default="none", autoconfirm=0) -> bool:
-        if autoconfirm and default == "y":
-            self.printgreen(message + " Automatically confirming default: yes")
-            return True
-        elif autoconfirm and default == "n":
-            self.printgreen(message + " Automatically confirming default: no")
-            return False
-        if default == "y":
-            message_ending = " [Y]/n? "
-        elif default == "n":
-            message_ending = " y/[N]? "
-        else:
-            message_ending = " y/n? "
-        while True:
-            user_input = input(self.OKBLUE + message + message_ending + self.ENDC)
-            if (
-                user_input == "Y" or user_input == "y" or user_input == "yes" or user_input == "Yes"
-            ) or (default == "y" and user_input == ""):
-                return True
-            if (
-                user_input == "N" or user_input == "n" or user_input == "no" or user_input == "No"
-            ) or (default == "n" and user_input == ""):
-                return False
-            else:
-                print("Please expicitely confirm y or n.")
+# class FlomniTools:
+#     def yesno(self, message: str, default="none", autoconfirm=0) -> bool:
+#         if autoconfirm and default == "y":
+#             self.printgreen(message + " Automatically confirming default: yes")
+#             return True
+#         elif autoconfirm and default == "n":
+#             self.printgreen(message + " Automatically confirming default: no")
+#             return False
+#         if default == "y":
+#             message_ending = " [Y]/n? "
+#         elif default == "n":
+#             message_ending = " y/[N]? "
+#         else:
+#             message_ending = " y/n? "
+#         while True:
+#             user_input = input(self.OKBLUE + message + message_ending + self.ENDC)
+#             if (
+#                 user_input == "Y" or user_input == "y" or user_input == "yes" or user_input == "Yes"
+#             ) or (default == "y" and user_input == ""):
+#                 return True
+#             if (
+#                 user_input == "N" or user_input == "n" or user_input == "no" or user_input == "No"
+#             ) or (default == "n" and user_input == ""):
+#                 return False
+#             else:
+#                 print("Please expicitely confirm y or n.")
 
 
 

csaxs_bec/device_configs/bl_detectors.yaml

@@ -9,6 +9,17 @@ eiger_1_5:
   readoutPriority: async
   softwareTrigger: False
 
+eiger_9:
+  description: Eiger 9M detector 
+  deviceClass: csaxs_bec.devices.jungfraujoch.eiger_9m.Eiger9M
+  deviceConfig:
+    detector_distance: 100
+    beam_center: [0, 0]
+  onFailure: raise
+  enabled: true
+  readoutPriority: async
+  softwareTrigger: False
+
 ids_cam:
   description: IDS camera for live image acquisition
   deviceClass: csaxs_bec.devices.ids_cameras.IDSCamera

csaxs_bec/devices/epics/mcs_card/mcs_card_csaxs.py

@@ -317,10 +317,14 @@ class MCSCardCSAXS(PSIDeviceBase, MCSCard):
             old_value: Previous value of the signal.
             value: New value of the signal.
         """
-        scan_done = bool(value == self._num_total_triggers)
-        self.progress.put(value=value, max_value=self._num_total_triggers, done=scan_done)
-        if scan_done:
-            self._scan_done_event.set()
+        try:
+            scan_done = bool(value == self._num_total_triggers)
+            self.progress.put(value=value, max_value=self._num_total_triggers, done=scan_done)
+            if scan_done:
+                self._scan_done_event.set()
+        except Exception:
+            content = traceback.format_exc()
+            logger.info(f"Device {self.name}  error: {content}")
 
     def on_stage(self) -> None:
         """

csaxs_bec/devices/jungfraujoch/README.MD

@@ -0,0 +1,48 @@
+# Overview
+Integration module for Eiger detectors at the cSAXS beamline with JungfrauJoch backend.
+There are currently two supported Eiger detectors:
+- EIGER 1.5M
+- EIGER 9M
+
+This module provides a base integration for both detectors. A short list of useful
+information is also provided below.
+
+## JungfrauJoch Service
+The JungfrauJoch WEB UI is available on http://sls-jfjoch-001:8080. This is an interface
+to the broker which runs on sls-jfjoch-001.psi.ch. The writer service runs on
+xbl-daq-34.psi.ch. Permissions to get access to these machines and run systemctl or
+journalctl commands can be requested with the Infrastructure and Services group in AWI.
+Beamline scientists need to check if they have the necessary permissions to connect
+to these machines and run the commands below.
+
+Useful commands for the broker service on sls-jfjoch-001.psi.ch:
+- sudo systemctl status jfjoch_broker # Check status
+- sudo systemctl start jfjoch_broker # Start service
+- sudo systemctl stop jfjoch_broker # Stop service
+- sudo systemctl restart jfjoch_broker # Restart service
+
+For the writer service on xbl-daq-34.psi.ch:
+- sudo journalctl -u jfjoch_writer -f # streams live logs
+- sudo systemctl status jfjoch_writer # Check status
+- sudo systemctl start jfjoch_writer # Start service
+- sudo systemctl stop jfjoch_writer # Stop service
+- sudo systemctl restart jfjoch_writer # Restart service
+
+More information about the JungfrauJoch and API client can be found at: (https://jungfraujoch.readthedocs.io/en/latest/index.html)
+
+### JungfrauJoch API Client
+A thin wrapper for the JungfrauJoch API client is provided in the [jungfrau_joch_client](./jungfrau_joch_client.py). 
+Details about the specific integration are provided in the code. 
+
+
+## Eiger implementation
+The Eiger detector integration is provided in the [eiger.py](./eiger.py) module. It provides a base integration for both Eiger 1.5M and Eiger 9M detectors.
+Logic specific to each detector is implemented in the respective modules:
+- [eiger_1_5m.py](./eiger_1_5m.py)
+- [eiger_9m.py](./eiger_9m.py)
+
+With the current implementation, the detector initialization should be done by a beamline scientist through the JungfrauJoch WEB UI by choosing the 
+appropriate detector (1.5M or 9M) before loading the device config with BEC. BEC will check upon connecting if the selected detector matches the expected one.
+A preview stream for images is also provided which is forwarded and accessible through the `preview_image` signal.
+
+For more specific details, please check the code documentation. 

csaxs_bec/devices/jungfraujoch/eiger.py

@@ -1,34 +1,23 @@
 """
-Generic integration of JungfrauJoch backend with Eiger detectors
-for the cSAXS beamline at the Swiss Light Source.
 
-The WEB UI is available on http://sls-jfjoch-001:8080
+Integration module for Eiger detectors at the cSAXS beamline with JungfrauJoch backend.
 
-NOTE: this may not be the best place to store this information. It should be migrated to
-beamline documentation for debugging of Eiger & JungfrauJoch.
+A few notes on setup and operation of the Eiger detectors through the JungfrauJoch broker:
 
-The JungfrauJoch server for cSAXS runs on sls-jfjoch-001.psi.ch
-User with sufficient rights may use:
-- sudo systemctl restart jfjoch_broker
-- sudo systemctl status jfjoch_broker
-to check and/or restart the broker for the JungfrauJoch server.
-
-Some extra notes for setting up the detector:
 - If the energy on JFJ is set via DetectorSettings, the variable in DatasetSettings will be ignored
 - Changes in energy may take time,  good to implement logic that only resets energy if needed.
 - For the Eiger, the frame_time_us in DetectorSettings is ignored, only the frame_time_us in
   the DatasetSettings is relevant
 - The bit_depth will be adjusted automatically based on the exp_time. Here, we need to ensure
-  that subsequent triggers properly
-  consider the readout_time of the boards. For Jungfrau detectors, the difference between
-  count_time_us and frame_time_us is the readout_time of the boards. For the Eiger, this needs
-  to be taken into account during the integration.
+  that subsequent triggers properly consider the readout_time of the boards. For the Eiger detectors
+  at cSAXS, a readout time of 20us is configured through the JungfrauJoch deployment config. This
+  setting is sufficiently large for the detectors if they run in parallel mode.
 - beam_center and detector settings are required input arguments, thus, they may be set to wrong
   values for acquisitions to start. Please keep this in mind.
 
 Hardware related notes:
 - If there is an HW issue with the detector, power cycling may help.
-- The sls_detector package is available on console on /sls/X12SA/data/gac-x12sa/erik/micromamba
+- The sls_detector package is available on console on /sls/x12sa/applications/erik/micromamba
     - Run: source setup_9m.sh # Be careful, this connects to the detector, so it should not be
       used during operation
     - Useful commands:
@@ -39,9 +28,6 @@ Hardware related notes:
         - cd power_control_user/
         - ./on
         - ./off
-
-Further information that may be relevant for debugging:
-JungfrauJoch - one needs to connect to the jfj-server (sls-jfjoch-001)
 """
 
 from __future__ import annotations
@@ -84,10 +70,19 @@ class EigerError(Exception):
 
 class Eiger(PSIDeviceBase):
     """
-    Base integration of the Eiger1.5M and Eiger9M at cSAXS. All relevant
+    Base integration of the Eiger1.5M and Eiger9M at cSAXS.
+
+    Args:
+        name (str) : Name of the device
+        detector_name (str): Name of the detector. Supports ["EIGER 9M", "EIGER 8.5M (tmp)", "EIGER 1.5M"]
+        host (str): Hostname of the Jungfrau Joch server.
+        port (int): Port of the Jungfrau Joch server.
+        scan_info (ScanInfo): The scan info to use.
+        device_manager (DeviceManagerDS): The device manager to use.
+        **kwargs: Additional keyword arguments.
     """
 
-    USER_ACCESS = ["detector_distance", "beam_center"]
+    USER_ACCESS = ["set_detector_distance", "set_beam_center"]
 
     file_event = Cpt(FileEventSignal, name="file_event")
     preview_image = Cpt(PreviewSignal, name="preview_image", ndim=2)
@@ -105,23 +100,12 @@ class Eiger(PSIDeviceBase):
         device_manager=None,
         **kwargs,
     ):
-        """
-        Initialize the PSI Device Base class.
-
-        Args:
-            name (str) : Name of the device
-            detector_name (str): Name of the detector. Supports ["EIGER 9M", "EIGER 8.5M (tmp)", "EIGER 1.5M"]
-            host (str): Hostname of the Jungfrau Joch server.
-            port (int): Port of the Jungfrau Joch server.
-            scan_info (ScanInfo): The scan info to use.
-            device_manager (DeviceManagerDS): The device manager to use.
-            **kwargs: Additional keyword arguments.
-        """
         super().__init__(name=name, scan_info=scan_info, device_manager=device_manager, **kwargs)
         self._host = f"{host}:{port}"
         self.jfj_client = JungfrauJochClient(host=self._host, parent=self)
+        # NOTE: fetch this information from JungfrauJochClient during on_connected!
         self.jfj_preview_client = JungfrauJochPreview(
-            url="tcp://129.129.95.114:5400", cb=self.preview_image.put
+            url="tcp://129.129.95.114:5400", cb=self._preview_callback
         )  # IP of sls-jfjoch-001.psi.ch on port 5400 for ZMQ stream
         self.device_manager = device_manager
         self.detector_name = detector_name
@@ -129,53 +113,102 @@ class Eiger(PSIDeviceBase):
         self._beam_center = beam_center
         self._readout_time = readout_time
         self._full_path = ""
+        self._num_triggers = 0
+        self._wait_for_on_complete = 20  # seconds
         if self.device_manager is not None:
             self.device_manager: DeviceManagerDS
 
+    def _preview_callback(self, message: dict) -> None:
+        """
+        Callback method for handling preview messages as received from the JungfrauJoch preview stream.
+        These messages are dictionary dumps as described in the JFJ ZMQ preview stream documentation.
+        (https://jungfraujoch.readthedocs.io/en/latest/ZEROMQ_STREAM.html#preview-stream).
+
+        Args:
+            message (dict): The message received from the preview stream.
+        """
+        if message.get("type", "") == "image":
+            data = message.get("data", {}).get("default", None)
+            if data is None:
+                logger.error(f"Received image message on device {self.name} without data.")
+                return
+            logger.info(f"Received preview image on device {self.name}")
+            self.preview_image.put(data)
+
+    # pylint: disable=missing-function-docstring
     @property
     def detector_distance(self) -> float:
-        """The detector distance in mm."""
         return self._detector_distance
 
     @detector_distance.setter
     def detector_distance(self, value: float) -> None:
-        """Set the detector distance in mm."""
         if value <= 0:
             raise ValueError("Detector distance must be a positive value.")
         self._detector_distance = value
 
+    def set_detector_distance(self, distance: float) -> None:
+        """
+        Set the detector distance in mm.
+
+        Args:
+            distance (float): The detector distance in mm.
+        """
+        self.detector_distance = distance
+
+    # pylint: disable=missing-function-docstring
     @property
     def beam_center(self) -> tuple[float, float]:
-        """The beam center in pixels. (x,y)"""
         return self._beam_center
 
     @beam_center.setter
     def beam_center(self, value: tuple[float, float]) -> None:
-        """Set the beam center in pixels. (x,y)"""
+        if any(coord < 0 for coord in value):
+            raise ValueError("Beam center coordinates must be non-negative.")
         self._beam_center = value
 
-    def on_init(self) -> None:
+    def set_beam_center(self, x: float, y: float) -> None:
         """
-        Called when the device is initialized.
+        Set the beam center coordinates in pixels.
 
-        No siganls are connected at this point,
-        thus should not be set here but in on_connected instead.
+        Args:
+            x (float): The x coordinate of the beam center in pixels.
+            y (float): The y coordinate of the beam center in pixels.
         """
+        self.beam_center = (x, y)
+
+    def on_init(self) -> None:
+        """Hook called during device initialization."""
+
+    # pylint: disable=arguments-differ
+    def wait_for_connection(self, timeout: float = 10) -> None:
+        """
+        Wait for the device to be connected to the JungfrauJoch backend.
+
+        Args:
+            timeout (float): Timeout in seconds to wait for the connection.
+        """
+        self.jfj_client.api.status_get(_request_timeout=timeout)  # If connected, this responds
 
     def on_connected(self) -> None:
         """
+        Hook called after the device is connected to through the device server.
+
         Called after the device is connected and its signals are connected.
-        Default values for signals should be set here.
+        Default values for signals should be set here. Currently, the detector needs to be
+        initialised manually through the WEB UI of JungfrauJoch. Once agreed upon, the automated
+        initialisation can be re-enabled here (code commented below).
         """
+        start_time = time.time()
         logger.debug(f"On connected called for {self.name}")
         self.jfj_client.stop(request_timeout=3)
         # Check which detector is selected
 
         # Get available detectors
         available_detectors = self.jfj_client.api.config_select_detector_get(_request_timeout=5)
+        logger.debug(f"Available detectors {available_detectors}")
         # Get current detector
         current_detector_name = ""
-        if available_detectors.current_id:
+        if available_detectors.current_id is not None:
             detector_selection = [
                 det.description
                 for det in available_detectors.detectors
@@ -190,8 +223,9 @@ class Eiger(PSIDeviceBase):
             raise RuntimeError(
                 f"Detector {self.detector_name} is not in IDLE state, current state: {self.jfj_client.detector_state}. Please initialize the detector in the WEB UI: {self._host}."
             )
-        # TODO - check again once Eiger should be initialized automatically, currently human initialization is expected
-        # # Once the automation should be enabled, we may use here
+
+        # TODO - Currently the initialisation of the detector is done manually through the WEB UI. Once adjusted
+        # this can be automated here again.
         # detector_selection = [
         #     det for det in available_detectors.detectors if det.id == self.detector_name
         # ]
@@ -207,41 +241,51 @@ class Eiger(PSIDeviceBase):
 
         # Setup Detector settings, here we may also set the energy already as this might be time consuming
         settings = DetectorSettings(frame_time_us=int(500), timing=DetectorTiming.TRIGGER)
-        self.jfj_client.set_detector_settings(settings, timeout=10)
+        self.jfj_client.set_detector_settings(settings, timeout=5)
+
         # Set the file writer to the appropriate output for the HDF5 file
         file_writer_settings = FileWriterSettings(overwrite=True, format=FileWriterFormat.NXMXVDS)
         logger.debug(
             f"Setting writer_settings: {yaml.dump(file_writer_settings.to_dict(), indent=4)}"
         )
+
+        # Setup the file writer settings
         self.jfj_client.api.config_file_writer_put(
             file_writer_settings=file_writer_settings, _request_timeout=10
         )
+
         # Start the preview client
         self.jfj_preview_client.connect()
         self.jfj_preview_client.start()
-        logger.info(f"Connected to JungfrauJoch preview stream at {self.jfj_preview_client.url}")
+        logger.info(
+            f"Device {self.name} initialized after {time.time()-start_time:.2f}s. Preview stream connected on url: {self.jfj_preview_client.url}"
+        )
 
     def on_stage(self) -> DeviceStatus | None:
         """
-        Called while staging the device.
-
-        Information about the upcoming scan can be accessed from the scan_info object.
+        Hook called when staging the device. Information about the upcoming scan can be accessed from the scan_info object.
+        scan_msg = self.scan_info.msg
         """
         start_time = time.time()
         scan_msg = self.scan_info.msg
-        # Set acquisition parameter
-        # TODO add check of mono energy, this can then also be passed to DatasetSettings
+
+        # TODO: Check mono energy from device in BEC
+        # Setting incident energy in keV
         incident_energy = 12.0
+        # Setting up exp_time and num_triggers acquisition parameter
         exp_time = scan_msg.scan_parameters.get("exp_time", 0)
-        if exp_time <= self._readout_time:
+        if exp_time <= self._readout_time:  # Exp_time must be at least the readout time
             raise ValueError(
-                f"Receive scan request for scan {scan_msg.scan_name} with exp_time {exp_time}s, which must be larger than the readout time {self._readout_time}s of the detector {self.detector_name}."
+                f"Value error on device {self.name}: Exposure time {exp_time}s is less than readout time {self._readout_time}s."
             )
-        frame_time_us = exp_time  #
-        ntrigger = int(scan_msg.num_points * scan_msg.scan_parameters["frames_per_trigger"])
-        # Fetch file path
+        self._num_triggers = int(
+            scan_msg.num_points * scan_msg.scan_parameters["frames_per_trigger"]
+        )
+
+        # Setting up the full path for file writing
         self._full_path = get_full_path(scan_msg, name=f"{self.name}_master")
         self._full_path = os.path.abspath(os.path.expanduser(self._full_path))
+
         # Inform BEC about upcoming file event
         self.file_event.put(
             file_path=self._full_path,
@@ -249,11 +293,14 @@ class Eiger(PSIDeviceBase):
             successful=False,
             hinted_h5_entries={"data": "entry/data/data"},
         )
+
         # JFJ adds _master.h5 automatically
         path = os.path.relpath(self._full_path, start="/sls/x12sa/data").removesuffix("_master.h5")
+
+        # Create dataset settings for API call.
         data_settings = DatasetSettings(
-            image_time_us=int(frame_time_us * 1e6),  # This is currently ignored
-            ntrigger=ntrigger,
+            image_time_us=int(exp_time * 1e6),
+            ntrigger=self._num_triggers,
             file_prefix=path,
             beam_x_pxl=int(self._beam_center[0]),
             beam_y_pxl=int(self._beam_center[1]),
@@ -261,11 +308,15 @@ class Eiger(PSIDeviceBase):
             incident_energy_ke_v=incident_energy,
         )
         logger.debug(f"Setting data_settings: {yaml.dump(data_settings.to_dict(), indent=4)}")
-        prep_time = start_time - time.time()
-        logger.debug(f"Prepared information for eiger to start acquisition in {prep_time:.2f}s")
-        self.jfj_client.wait_for_idle(timeout=10, request_timeout=10)  # Ensure we are in IDLE state
+        prep_time = time.time()
+        self.jfj_client.wait_for_idle(timeout=10)  # Ensure we are in IDLE state
         self.jfj_client.start(settings=data_settings)  # Takes around ~0.6s
-        logger.debug(f"Wait for IDLE and start call took {time.time()-start_time-prep_time:.2f}s")
+
+        # Time the stage process
+        logger.info(
+            f"Device {self.name} staged for scan. Time spent {time.time()-start_time:.2f}s,"
+            f" with {time.time()-prep_time:.2f}s spent with communication to JungfrauJoch."
+        )
 
     def on_unstage(self) -> DeviceStatus:
         """Called while unstaging the device."""
@@ -278,7 +329,9 @@ class Eiger(PSIDeviceBase):
 
     def _file_event_callback(self, status: DeviceStatus) -> None:
         """Callback to update the file_event signal when the acquisition is done."""
-        logger.info(f"Acquisition done callback called for {self.name} for status {status.success}")
+        logger.debug(
+            f"File event callback on complete status for device {self.name}: done={status.done}, successful={status.success}"
+        )
         self.file_event.put(
             file_path=self._full_path,
             done=status.done,
@@ -287,19 +340,44 @@ class Eiger(PSIDeviceBase):
         )
 
     def on_complete(self) -> DeviceStatus:
-        """Called to inquire if a device has completed a scans."""
+        """
+        Called at the end of the scan. The method should implement an asynchronous wait for the
+        device to complete the acquisition. A callback to update the file_event signal is
+        attached that resolves the file event when the acquisition is done.
+
+        Returns:
+            DeviceStatus: The status object representing the completion of the acquisition.
+        """
 
         def wait_for_complete():
             start_time = time.time()
-            timeout = 10
-            for _ in range(timeout):
-                if self.jfj_client.wait_for_idle(timeout=1, request_timeout=10):
+            # NOTE: This adjust the time (s) that should be waited for completion of the scan.
+            timeout = self._wait_for_on_complete
+            while time.time() - start_time < timeout:
+                if self.jfj_client.wait_for_idle(timeout=1, raise_on_timeout=False):
+                    # TODO: Once available, add check for
+                    statistics: MeasurementStatistics = (
+                        self.jfj_client.api.statistics_data_collection_get(_request_timeout=5)
+                    )
+                    if statistics.images_collected < self._num_triggers:
+                        raise EigerError(
+                            f"Device {self.name} acquisition incomplete. "
+                            f"Expected {self._num_triggers} triggers, "
+                            f"but only {statistics.images_collected} were collected."
+                        )
                     return
+                logger.info(
+                    f"Waiting for device {self.name} to finish complete, time elapsed: "
+                    f"{time.time() - start_time}."
+                )
             statistics: MeasurementStatistics = self.jfj_client.api.statistics_data_collection_get(
                 _request_timeout=5
             )
+            broker_status = self.jfj_client.jfj_status
             raise TimeoutError(
-                f"Timeout after waiting for detector {self.name} to complete for {time.time()-start_time:.2f}s, measurement statistics: {yaml.dump(statistics.to_dict(), indent=4)}"
+                f"Timeout after waiting for device {self.name} to complete for {time.time()-start_time:.2f}s \n \n"
+                f"Broker status: \n{yaml.dump(broker_status.to_dict(), indent=4)} \n \n"
+                f"Measurement statistics: \n{yaml.dump(statistics.to_dict(), indent=4)}"
             )
 
         status = self.task_handler.submit_task(wait_for_complete, run=True)
@@ -312,7 +390,11 @@ class Eiger(PSIDeviceBase):
 
     def on_stop(self) -> None:
         """Called when the device is stopped."""
-        self.jfj_client.stop(
-            request_timeout=0.5
-        )  # Call should not block more than 0.5 seconds to stop all devices...
+        self.jfj_client.stop(request_timeout=0.5)
         self.task_handler.shutdown()
+
+    def on_destroy(self):
+        """Called when the device is destroyed."""
+        self.jfj_preview_client.stop()
+        self.on_stop()
+        return super().on_destroy()

csaxs_bec/devices/jungfraujoch/eiger_9m.py

@@ -21,18 +21,18 @@ if TYPE_CHECKING:  # pragma no cover
     from bec_server.device_server.device_server import DeviceManagerDS
 
 EIGER9M_READOUT_TIME_US = 500e-6  # 500 microseconds in s
-DETECTOR_NAME = "EIGER 8.5M (tmp)"  # "EIGER 9M""
+DETECTOR_NAME = "EIGER 9M"  # "EIGER 9M""
 
 
 # pylint:disable=invalid-name
 class Eiger9M(Eiger):
     """
-    Eiger 1.5M specific integration for the in-vaccum Eiger.
+    EIGER 9M specific integration for the in-vaccum Eiger.
 
     The logic implemented here is coupled to the DelayGenerator integration,
     repsonsible for the global triggering of all devices through a single Trigger logic.
     Please check the eiger.py class for more details about the integration of relevant backend
-    services. The detector_name must be set to "EIGER 1.5M:
+    services. The detector_name must be set to "EIGER 9M":
     """
 
     USER_ACCESS = Eiger.USER_ACCESS + []  # Add more user_access methods here.

csaxs_bec/devices/jungfraujoch/jungfrau_joch_client.py

@@ -1,13 +1,15 @@
-"""Module with client interface for the Jungfrau Joch detector API"""
+"""Module with a thin client wrapper around the Jungfrau Joch detector API"""
 
 from __future__ import annotations
 
 import enum
+import threading
 import time
 import traceback
 from typing import TYPE_CHECKING
 
 import requests
+import yaml
 from bec_lib.logger import bec_logger
 from jfjoch_client.api.default_api import DefaultApi
 from jfjoch_client.api_client import ApiClient
@@ -18,7 +20,7 @@ from jfjoch_client.models.detector_settings import DetectorSettings
 
 logger = bec_logger.logger
 
-if TYPE_CHECKING:
+if TYPE_CHECKING:  # pragma: no cover
     from ophyd import Device
 
 
@@ -29,7 +31,10 @@ class JungfrauJochClientError(Exception):
 
 
 class DetectorState(str, enum.Enum):
-    """Possible Detector states for Jungfrau Joch detector"""
+    """
+    Enum states of the BrokerStatus state. The pydantic model validates in runtime,
+    thus we keep the possible states here for a convenient overview and access.
+    """
 
     INACTIVE = "Inactive"
     IDLE = "Idle"
@@ -40,13 +45,15 @@ class DetectorState(str, enum.Enum):
 
 
 class JungfrauJochClient:
-    """Thin wrapper around the Jungfrau Joch API client.
+    """
+    Jungfrau Joch API client wrapper. It provides a thin wrapper methods around the API client,
+    that allow to connect, initialise, wait for state changes, set settings, start and stop
+    acquisitions.
 
-    sudo systemctl restart jfjoch_broker
-    sudo systemctl status jfjoch_broker
-
-    It looks as if the detector is not being stopped properly.
-    One module remains running, how can we restart the detector?
+    Args:
+        host (str): Hostname of the Jungfrau Joch broker service.
+                    Default is "http://sls-jfjoch-001:8080"
+        parent (Device, optional): Parent ophyd device, used for logging purposes.
     """
 
     def __init__(
@@ -59,50 +66,63 @@ class JungfrauJochClient:
         self._parent_name = parent.name if parent else self.__class__.__name__
 
     @property
-    def jjf_state(self) -> BrokerStatus:
-        """Get the status of JungfrauJoch"""
+    def jfj_status(self) -> BrokerStatus:
+        """Broker status of JungfrauJoch."""
         response = self.api.status_get()
         return BrokerStatus(**response.to_dict())
 
+    # pylint: disable=missing-function-docstring
     @property
     def initialised(self) -> bool:
-        """Check if jfj is connected and ready to receive commands"""
         return self._initialised
 
     @initialised.setter
     def initialised(self, value: bool) -> None:
-        """Set the connected status"""
         self._initialised = value
 
-    # TODO this is not correct, as it may be that the state in INACTIVE. Models are not in sync...
-    # REMOVE all model enums as most of the validation takes place in the Pydantic models, i.e. BrokerStatus here..
+    # pylint: disable=missing-function-docstring
     @property
     def detector_state(self) -> DetectorState:
-        """Get the status of JungfrauJoch"""
-        return DetectorState(self.jjf_state.state)
+        return DetectorState(self.jfj_status.state)
 
-    def connect_and_initialise(self, timeout: int = 10, **kwargs) -> None:
-        """Check if JungfrauJoch is connected and ready to receive commands"""
+    def connect_and_initialise(self, timeout: int = 10) -> None:
+        """
+        Connect and initialise the JungfrauJoch detector. The detector must be in
+        IDLE state to become initialised. This is a blocking call, the timeout parameter
+        will be passed to the HTTP requests timeout method of the wait_for_idle method.
+
+        Args:
+            timeout (int): Timeout in seconds for the initialisation and waiting for IDLE state.
+        """
         status = self.detector_state
+        # TODO: #135 Check if the detector has to be in INACTIVE state before initialisation
         if status != DetectorState.IDLE:
-            self.api.initialize_post()  # This is a blocking call....
-            self.wait_for_idle(timeout, request_timeout=timeout)  # Blocking call
+            self.api.initialize_post()
+            self.wait_for_idle(timeout)
         self.initialised = True
 
     def set_detector_settings(self, settings: dict | DetectorSettings, timeout: int = 10) -> None:
-        """Set the detector settings. JungfrauJoch must be in IDLE, Error or Inactive state.
-        Note, the full settings have to be provided, otherwise the settings will be overwritten with default values.
+        """
+        Set the detector settings. The state of JungfrauJoch must be in IDLE,
+        Error or Inactive state. Please note: a full set of setttings has to be provided,
+        otherwise the settings will be overwritten with default values.
 
         Args:
             settings (dict): dictionary of settings
+            timeout (int): Timeout in seconds for the HTTP request to set the settings.
         """
         state = self.detector_state
         if state not in [DetectorState.IDLE, DetectorState.ERROR, DetectorState.INACTIVE]:
+            logger.info(
+                f"JungfrauJoch backend fo device {self._parent_name} is not in IDLE state,"
+                " waiting 1s before retrying..."
+            )
             time.sleep(1)  # Give the detector 1s to become IDLE, retry
             state = self.detector_state
             if state not in [DetectorState.IDLE, DetectorState.ERROR, DetectorState.INACTIVE]:
                 raise JungfrauJochClientError(
-                    f"Error in {self._parent_name}. Detector must be in IDLE, ERROR or INACTIVE state to set settings. Current state: {state}"
+                    f"Error on {self._parent_name}. Detector must be in IDLE, ERROR or INACTIVE"
+                    " state to set settings. Current state: {state}"
                 )
 
         if isinstance(settings, dict):
@@ -110,28 +130,36 @@ class JungfrauJochClient:
         try:
             self.api.config_detector_put(detector_settings=settings, _request_timeout=timeout)
         except requests.exceptions.Timeout:
-            raise TimeoutError(f"Timeout while setting detector settings for {self._parent_name}")
+            raise TimeoutError(
+                f"Timeout on device {self._parent_name} while setting detector settings:\n "
+                f"{yaml.dump(settings, indent=4)}."
+            )
         except Exception:
             content = traceback.format_exc()
+            logger.error(
+                f"Error on device {self._parent_name} while setting detector settings:\n "
+                f"{yaml.dump(settings, indent=4)}. Error traceback: {content}"
+            )
             raise JungfrauJochClientError(
-                f"Error while setting detector settings for {self._parent_name}: {content}"
+                f"Error on device {self._parent_name} while setting detector settings:\n "
+                f"{yaml.dump(settings, indent=4)}. Full traceback: {content}."
             )
 
     def start(self, settings: dict | DatasetSettings, request_timeout: float = 10) -> None:
-        """Start the mesaurement. DatasetSettings must be provided, and JungfrauJoch must be in IDLE state.
-        The method call is blocking and JungfrauJoch will be ready to measure after the call resolves.
+        """
+        Start the acquisition with the provided dataset settings.
+        The detector must be in IDLE state. Settings must always provide a full set of
+        parameters, missing parameters will be set to default values.
 
         Args:
-            settings (dict): dictionary of settings
-
-        Please check the DataSettings class for the available settings. Minimum required settings are
-        beam_x_pxl, beam_y_pxl, detector_distance_mm, incident_energy_keV.
-
+            settings (dict | DatasetSettings): Dataset settings to start the acquisition with.
+            request_timeout (float): Timeout in sec for the HTTP request to start the acquisition.
         """
         state = self.detector_state
         if state != DetectorState.IDLE:
             raise JungfrauJochClientError(
-                f"Error in {self._parent_name}. Detector must be in IDLE state to set settings. Current state: {state}"
+                f"Error on device {self._parent_name}. "
+                f"Detector must be in IDLE state to start acquisition. Current state: {state}"
             )
 
         if isinstance(settings, dict):
@@ -141,46 +169,80 @@ class JungfrauJochClient:
                 dataset_settings=settings, _request_timeout=request_timeout
             )
         except requests.exceptions.Timeout:
+            content = traceback.format_exc()
+            logger.error(
+                f"Timeout error after {request_timeout} seconds on device {self._parent_name} "
+                f"during 'start' call with dataset settings: {yaml.dump(settings, indent=4)}. \n"
+                f"Traceback: {content}"
+            )
             raise TimeoutError(
-                f"TimeoutError in JungfrauJochClient for parent device {self._parent_name} for 'start' call"
+                f"Timeout error after {request_timeout} seconds on device {self._parent_name} "
+                f"during 'start' call with dataset settings: {yaml.dump(settings, indent=4)}."
             )
         except Exception:
             content = traceback.format_exc()
+            logger.error(
+                f"Error on device {self._parent_name} during 'start' post with dataset settings: \n"
+                f"{yaml.dump(settings, indent=4)}. \nTraceback: {content}"
+            )
             raise JungfrauJochClientError(
-                f"Error in JungfrauJochClient for parent device {self._parent_name} during 'start' call: {content}"
+                f"Error on device {self._parent_name} during 'start' post with dataset settings: \n"
+                f"{yaml.dump(settings, indent=4)}. \nTraceback: {content}."
             )
 
     def stop(self, request_timeout: float = 0.5) -> None:
         """Stop the acquisition, this only logs errors and is not raising."""
-        try:
-            self.api.cancel_post_with_http_info(_request_timeout=request_timeout)
-        except requests.exceptions.Timeout:
-            content = traceback.format_exc()
-            logger.error(
-                f"Timeout in JungFrauJochClient for device {self._parent_name} during stop: {content}"
-            )
-        except Exception:
-            content = traceback.format_exc()
-            logger.error(
-                f"Error in JungFrauJochClient for device {self._parent_name} during stop: {content}"
-            )
 
-    def wait_for_idle(self, timeout: int = 10, request_timeout: float | None = None) -> bool:
-        """Wait for JungfrauJoch to be in Idle state. Blocking call with timeout.
+        def _stop_call(self):
+            try:
+                self.api.cancel_post_with_http_info()  # (_request_timeout=request_timeout)
+            except requests.exceptions.Timeout:
+                content = traceback.format_exc()
+                logger.error(
+                    f"Timeout error after {request_timeout} seconds on device {self._parent_name} "
+                    f"during stop: {content}"
+                )
+            except Exception:
+                content = traceback.format_exc()
+                logger.error(f"Error on device {self._parent_name} during stop: {content}")
+
+        thread = threading.Thread(
+            target=_stop_call, daemon=True, args=(self,), name="stop_jungfraujoch_thread"
+        )
+        thread.start()
+
+    def wait_for_idle(self, timeout: int = 10, raise_on_timeout: bool = True) -> bool:
+        """
+        Method to wait until the detector is in IDLE state. This is a blocking call with a
+        timeout that can be specified. The additional parameter raise_on_timeout can be used to
+        raise an exception on timeout instead of returning boolean True/False.
 
         Args:
             timeout (int): timeout in seconds
+            raise_on_timeout (bool): If True, raises an exception on timeout. Default is True.
         Returns:
             bool: True if the detector is in IDLE state, False if timeout occurred
         """
-        if request_timeout is None:
-            request_timeout = timeout
         try:
-            self.api.wait_till_done_post(timeout=timeout, _request_timeout=request_timeout)
+            self.api.wait_till_done_post(timeout=timeout, _request_timeout=timeout)
         except requests.exceptions.Timeout:
-            raise TimeoutError(f"HTTP request timeout in wait_for_idle for {self._parent_name}")
-        except Exception:
             content = traceback.format_exc()
-            logger.debug(f"Waiting for device {self._parent_name} to become IDLE: {content}")
+            logger.info(
+                f"Timeout after {timeout} seconds on device {self._parent_name} in wait_for_idle: {content}"
+            )
+            if raise_on_timeout:
+                raise TimeoutError(
+                    f"Timeout after {timeout} seconds on device {self._parent_name} in wait_for_idle."
+                )
+            return False
+        except Exception as exc:
+            content = traceback.format_exc()
+            logger.info(
+                f"Error on device {self._parent_name} in wait_for_idle. Full traceback: {content}"
+            )
+            if raise_on_timeout:
+                raise JungfrauJochClientError(
+                    f"Error on device {self._parent_name} in wait_for_idle: {content}"
+                ) from exc
             return False
         return True

csaxs_bec/devices/jungfraujoch/jungfraujoch_preview.py

@@ -1,22 +1,136 @@
-"""Module for the Eiger preview ZMQ stream."""
+"""
+Module for the JungfrauJoch preview ZMQ stream for the Eiger detector at cSAXS.
+The Preview client is implemented for the JungfrauJoch ZMQ PUB-SUB interface, and
+should be independent of the EIGER detector type.
+
+The client connects to the ZMQ PUB-SUB preview stream and calls a user provided callback
+function with the decompressed messages received from the stream. The callback needs to be
+able to deal with the different message types sent by the JungfrauJoch server ("start",
+"image", "end") as described in the JungfrauJoch ZEROMQ preview stream documentation.
+(https://jungfraujoch.readthedocs.io/en/latest/ZEROMQ_STREAM.html#preview-stream).
+"""
 
 from __future__ import annotations
 
-import json
 import threading
 import time
 from typing import Callable
 
+import cbor2
 import numpy as np
 import zmq
 from bec_lib.logger import bec_logger
+from dectris.compression import decompress
 
 logger = bec_logger.logger
 
-ZMQ_TOPIC_FILTER = b""
+###############################
+###### CBOR TAG DECODERS ######
+###############################
+# Dectris specific CBOR tags and decoders for Jungfrau data
+# Reference:
+# https://github.com/dectris/documentation/blob/main/stream_v2/examples/client.py
+
+
+def decode_multi_dim_array(tag: cbor2.CBORTag, column_major: bool = False):
+    """Decode a multi-dimensional array from a CBOR tag."""
+    dimensions, contents = tag.value
+    if isinstance(contents, list):
+        array = np.empty((len(contents),), dtype=object)
+        array[:] = contents
+    elif isinstance(contents, (np.ndarray, np.generic)):
+        array = contents
+    else:
+        raise cbor2.CBORDecodeValueError("expected array or typed array")
+    return array.reshape(dimensions, order="F" if column_major else "C")
+
+
+def decode_typed_array(tag: cbor2.CBORTag, dtype: str):
+    """Decode a typed array from a CBOR tag."""
+    if not isinstance(tag.value, bytes):
+        raise cbor2.CBORDecodeValueError("expected byte string in typed array")
+    return np.frombuffer(tag.value, dtype=dtype)
+
+
+def decode_dectris_compression(tag: cbor2.CBORTag):
+    """Decode a Dectris compressed array from a CBOR tag."""
+    algorithm, elem_size, encoded = tag.value
+    return decompress(encoded, algorithm, elem_size=elem_size)
+
+
+#########################################
+#### Dectris CBOR TAG Extensions ########
+#########################################
+
+# Mapping of various additional CBOR tags from Dectris to decoder functions
+tag_decoders = {
+    40: lambda tag: decode_multi_dim_array(tag, column_major=False),
+    64: lambda tag: decode_typed_array(tag, dtype="u1"),
+    65: lambda tag: decode_typed_array(tag, dtype=">u2"),
+    66: lambda tag: decode_typed_array(tag, dtype=">u4"),
+    67: lambda tag: decode_typed_array(tag, dtype=">u8"),
+    68: lambda tag: decode_typed_array(tag, dtype="u1"),
+    69: lambda tag: decode_typed_array(tag, dtype="<u2"),
+    70: lambda tag: decode_typed_array(tag, dtype="<u4"),
+    71: lambda tag: decode_typed_array(tag, dtype="<u8"),
+    72: lambda tag: decode_typed_array(tag, dtype="i1"),
+    73: lambda tag: decode_typed_array(tag, dtype=">i2"),
+    74: lambda tag: decode_typed_array(tag, dtype=">i4"),
+    75: lambda tag: decode_typed_array(tag, dtype=">i8"),
+    77: lambda tag: decode_typed_array(tag, dtype="<i2"),
+    78: lambda tag: decode_typed_array(tag, dtype="<i4"),
+    79: lambda tag: decode_typed_array(tag, dtype="<i8"),
+    80: lambda tag: decode_typed_array(tag, dtype=">f2"),
+    81: lambda tag: decode_typed_array(tag, dtype=">f4"),
+    82: lambda tag: decode_typed_array(tag, dtype=">f8"),
+    83: lambda tag: decode_typed_array(tag, dtype=">f16"),
+    84: lambda tag: decode_typed_array(tag, dtype="<f2"),
+    85: lambda tag: decode_typed_array(tag, dtype="<f4"),
+    86: lambda tag: decode_typed_array(tag, dtype="<f8"),
+    87: lambda tag: decode_typed_array(tag, dtype="<f16"),
+    1040: lambda tag: decode_multi_dim_array(tag, column_major=True),
+    56500: lambda tag: decode_dectris_compression(tag),  # pylint: disable=unnecessary-lambda
+}
+
+
+def tag_hook(decoder, tag: int):
+    """
+    Tag hook for the cbor2.loads method. Both arguments "decoder" and "tag" mus be present.
+    We use the tag to choose the respective decoder from the tag_decoders registry if available.
+    """
+    tag_decoder = tag_decoders.get(tag.tag)
+    return tag_decoder(tag) if tag_decoder else tag
+
+
+######################
+#### ZMQ Settings ####
+######################
+
+ZMQ_TOPIC_FILTER = b""  # Subscribe to all topics
+ZMQ_CONFLATE_SETTING = 1  # Keep only the most recent message
+ZMQ_RCVHWM_SETTING = 1  # Set high water mark to 1, this configures the max number of queue messages
+
+
+#################################
+#### Jungfrau Preview Client ####
+#################################
 
 
 class JungfrauJochPreview:
+    """
+    Preview client for the JungfrauJoch ZMQ preview stream. The client is started with
+    a URL to receive the data from the JungfrauJoch PUB-SUB preview interface, and a
+    callback function that is called with messages received from the preview stream.
+    The callback needs to be able to deal with the different message types sent
+    by the JungfrauJoch server ("start", "image", "end") as described in the
+    JungfrauJoch ZEROMQ preview stream documentation. Messages are dictionary dumps.
+    (https://jungfraujoch.readthedocs.io/en/latest/ZEROMQ_STREAM.html#preview-stream).
+
+    Args:
+        url (str): ZMQ PUB-SUB preview stream URL.
+        cb (Callable): Callback function called with messages received from the stream.
+    """
+
     USER_ACCESS = ["start", "stop"]
 
     def __init__(self, url: str, cb: Callable):
@@ -27,16 +141,18 @@ class JungfrauJochPreview:
         self._on_update_callback = cb
 
     def connect(self):
-        """Connect to the JungfrauJoch PUB-SUB streaming interface
-
-        JungfrauJoch may reject connection for a few seconds when it restarts,
-        so if it fails, wait a bit and try to connect again.
+        """
+        Connect to the JungfrauJoch PUB-SUB streaming interface. If the connection is refused
+        it will reattempt a second time after a one second delay.
         """
         # pylint: disable=no-member
 
         context = zmq.Context()
         self._socket = context.socket(zmq.SUB)
+        self._socket.setsockopt(zmq.CONFLATE, ZMQ_CONFLATE_SETTING)
         self._socket.setsockopt(zmq.SUBSCRIBE, ZMQ_TOPIC_FILTER)
+        self._socket.setsockopt(zmq.RCVHWM, ZMQ_RCVHWM_SETTING)
+
         try:
             self._socket.connect(self.url)
         except ConnectionRefusedError:
@@ -44,17 +160,26 @@ class JungfrauJochPreview:
             self._socket.connect(self.url)
 
     def start(self):
+        """Start the ZMQ update loop in a background thread."""
         self._zmq_thread = threading.Thread(
             target=self._zmq_update_loop, daemon=True, name="JungfrauJoch_live_preview"
         )
         self._zmq_thread.start()
 
     def stop(self):
+        """Stop the ZMQ update loop and wait for the thread to finish."""
         self._shutdown_event.set()
         if self._zmq_thread:
-            self._zmq_thread.join()
+            self._zmq_thread.join(timeout=1.0)
 
-    def _zmq_update_loop(self):
+    def _zmq_update_loop(self, poll_interval: float = 0.2):
+        """
+        ZMQ update loop running in a background thread. The polling is throttled by
+        the poll_interval parameter.
+
+        Args:
+            poll_interval (float): Time in seconds to wait between polling attempts.
+        """
         while not self._shutdown_event.is_set():
             if self._socket is None:
                 self.connect()
@@ -64,18 +189,21 @@ class JungfrauJochPreview:
                 # Happens when ZMQ partially delivers the multipart message
                 pass
             except zmq.error.Again:
-                # Happens when receive queue is empty
-                time.sleep(0.1)
+                logger.debug(
+                    f"ZMQ Again exception, receive queue is empty for JFJ preview at {self.url}."
+                )
+            finally:
+                # We throttle the polling to avoid heavy load on the device server
+                time.sleep(poll_interval)
 
     def _poll(self):
         """
-        Poll the ZMQ socket for new data. It will throttle the data update and
-        only subscribe to the topic for a single update. This is not very nice
-        but it seems like there is currently no option to set the update rate on
-        the backend.
+        Poll the ZMQ socket for new data. We are currently subscribing and unsubscribing
+        for each poll loop to avoid receiving too many messages. Throttling of the update
+        loop is handled in the _zmq_update_loop method.
         """
 
-        if self._shutdown_event.wait(0.2):
+        if self._shutdown_event.is_set():
             return
 
         try:
@@ -90,7 +218,19 @@ class JungfrauJochPreview:
             # Unsubscribe from the topic
             self._socket.setsockopt(zmq.UNSUBSCRIBE, ZMQ_TOPIC_FILTER)
 
-    def _parse_data(self, data):
-        # TODO decode and parse the data
-        # self._on_update_callback(data)
-        pass
+    def _parse_data(self, bytes_list: list[bytes]):
+        """
+        Parse the received ZMQ data from the JungfrauJoch preview stream.
+        We will call the _on_update_callback with the decompressed messages as a dictionary.
+
+        The callback needs to be able to deal with the different message types sent
+        by the JungfrauJoch server ("start", "image", "end") as described in the
+        JungfrauJoch ZEROMQ preview stream documentation. Messages are dictionary dumps.
+        (https://jungfraujoch.readthedocs.io/en/latest/ZEROMQ_STREAM.html#preview-stream).
+
+        Args:
+            bytes_list (list[bytes]): List of byte messages received from ZMQ recv_multipart.
+        """
+        for byte_msg in bytes_list:
+            msg = cbor2.loads(byte_msg, tag_hook=tag_hook)
+            self._on_update_callback(msg)

csaxs_bec/devices/omny/galil/galil_ophyd.py

@@ -4,6 +4,7 @@ This module contains the base class for Galil controllers as well as the signals
 
 import functools
 import time
+from typing import Any
 
 from bec_lib import bec_logger
 from ophyd.utils import ReadOnlyError
@@ -347,7 +348,7 @@ class GalilSignalBase(SocketSignal):
     def __init__(self, signal_name, **kwargs):
         self.signal_name = signal_name
         super().__init__(**kwargs)
-        self.controller = self.parent.controller
+        self.controller = self.root.controller if hasattr(self.root, "controller") else None
 
 
 class GalilSignalRO(GalilSignalBase):

csaxs_bec/devices/omny/galil/galil_rio.py

@@ -6,24 +6,26 @@ Link to the Galil RIO vendor page:
 https://www.galil.com/plcs/remote-io/rio-471xx
 
 This module provides the GalilRIOController for communication with the RIO controller
-over TCP/IP. It also provides a device integration that interfaces to these
-8 analog channels.
+over TCP/IP. It also provides a device integration that interfaces to its
+8 analog channels, and 16 digital output channels. Some PLCs may have 24 digital output channels,
+which can be easily supported by changing the _NUM_DIGITAL_OUTPUT_CHANNELS variable.
 """
 
 from __future__ import annotations
 
-import time
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Literal
 
 from bec_lib.logger import bec_logger
-from ophyd import Component as Cpt
+from ophyd import DynamicDeviceComponent as DDC
+from ophyd import Kind
+from ophyd.utils import ReadOnlyError
 from ophyd_devices import PSIDeviceBase
 from ophyd_devices.utils.controller import Controller, threadlocked
 from ophyd_devices.utils.socket import SocketIO
 
 from csaxs_bec.devices.omny.galil.galil_ophyd import (
     GalilCommunicationError,
-    GalilSignalRO,
+    GalilSignalBase,
     retry_once,
 )
 
@@ -35,15 +37,11 @@ logger = bec_logger.logger
 
 
 class GalilRIOController(Controller):
-    """
-    Controller Class for Galil RIO controller communication.
-
-    Multiple controllers are in use at the cSAXS beamline:
-    - 129.129.98.64 (port 23)
-    """
+    """Controller Class for Galil RIO controller communication."""
 
     @threadlocked
     def socket_put(self, val: str) -> None:
+        """Socker put method."""
         self.sock.put(f"{val}\r".encode())
 
     @retry_once
@@ -64,21 +62,95 @@ class GalilRIOController(Controller):
             )
 
 
-class GalilRIOSignalRO(GalilSignalRO):
+class GalilRIOAnalogSignalRO(GalilSignalBase):
     """
-    Read-only Signal for reading a single analog input channel from the Galil RIO controller.
-    It always read all 8 analog channels at once, and updates the reabacks of all channels.
-    New readbacks are only fetched from the controller if the last readback is older than
-    _READ_TIMEOUT seconds, otherwise the last cached readback is returned to reduce network traffic.
+    Signal for reading analog input channels of the Galil RIO controller. This signal is read-only, so
+    the set method raises a ReadOnlyError. The get method retrieves the values of all analog
+    channels in a single socket command. The readback values of all channels are updated based
+    on the response, and subscriptions are run for all channels. Readings are cached as implemented
+    in the SocketSignal class, so that multiple reads of the same channel within an update cycle do
+    not result in multiple socket calls.
 
     Args:
-        signal_name (str): Name of the signal.
-        channel (int): Analog channel number (0-7).
-        parent (GalilRIO): Parent GalilRIO device.
+        signal_name (str): The name of the signal, e.g. "ch0", "ch1", ..., "ch7"
+        channel (int): The channel number corresponding to the signal, e.g. 0 for "ch0", 1 for "ch1", ...
+        parent (GalilRIO): The parent device instance that this signal belongs to.
     """
 
     _NUM_ANALOG_CHANNELS = 8
-    _READ_TIMEOUT = 0.1  # seconds
+
+    def __init__(self, signal_name: str, channel: int, parent: GalilRIO, **kwargs):
+        super().__init__(signal_name=signal_name, parent=parent, **kwargs)
+        self._channel = channel
+        self._metadata["connected"] = False
+        self._metadata["write_access"] = False
+
+    def _socket_set(self, val):
+        """Read-only signal, so set method raises an error."""
+        raise ReadOnlyError(f"Signal {self.name} is read-only.")
+
+    def _socket_get(self) -> float:
+        """Get command for the readback signal"""
+        cmd = "MG@" + ", @".join([f"AN[{ii}]" for ii in range(self._NUM_ANALOG_CHANNELS)])
+        ret = self.controller.socket_put_and_receive(cmd)
+        values = [float(val) for val in ret.strip().split(" ")]
+        # Run updates for all channels. This also updates the _readback and metadata timestamp
+        # value of this channel.
+        self._update_all_channels(values)
+        return self._readback
+
+    # pylint: disable=protected-access
+    def _update_all_channels(self, values: list[float]) -> None:
+        """
+        Method to receive a list of readback values for channels 0 to 7. Updates for each channel idx
+        are applied to the corresponding GalilRIOAnalogSignalRO signal with matching attr_name "ch{idx}".
+
+        We also update the _last_readback attribute of each of the signals, to avoid multiple socket calls,
+        but rather use the cached value of the combined reading for all channels.
+
+        Args:
+            values (list[float]): List of new readback values for all channels, where the
+                index corresponds to the channel number (0-7).
+        """
+        updates: dict[str, tuple[float, float]] = {}  # attr_name -> (new_val, old_val)
+        # Update all readbacks first
+        for walk in self.parent.walk_signals():
+            if isinstance(walk.item, GalilRIOAnalogSignalRO):
+                idx = int(walk.item.attr_name[-1])
+                if 0 <= idx < len(values):
+                    old_val = walk.item._readback
+                    new_val = values[idx]
+                    walk.item._metadata["timestamp"] = self._last_readback
+                    walk.item._last_readback = self._last_readback
+                    walk.item._readback = new_val
+                    if (
+                        idx != self._channel
+                    ):  # Only run subscriptions on other channels, not on itself
+                        # as this is handled by the SocketSignal and we want to avoid running multiple
+                        # subscriptions for the same channel update
+                        updates[walk.item.attr_name] = (new_val, old_val)
+                else:
+                    logger.warning(
+                        f"Received {len(values)} values but found channel index {idx} in signal {walk.item.name}. Skipping update for this signal."
+                    )
+
+        # Run subscriptions after all readbacks have been updated
+        # on all channels except the one that triggered the update
+        for walk in self.parent.walk_signals():
+            if walk.item.attr_name in updates:
+                new_val, old_val = updates[walk.item.attr_name]
+                walk.item._run_subs(
+                    sub_type=walk.item.SUB_VALUE,
+                    old_value=old_val,
+                    value=new_val,
+                    timestamp=self._last_readback,
+                )
+
+
+class GalilRIODigitalOutSignal(GalilSignalBase):
+    """Signal for controlling digital outputs of the Galil RIO controller."""
+
+    _NUM_DIGITAL_OUTPUT_CHANNELS = 16
 
     def __init__(self, signal_name: str, channel: int, parent: GalilRIO, **kwargs):
         super().__init__(signal_name, parent=parent, **kwargs)
@@ -87,81 +159,83 @@ class GalilRIOSignalRO(GalilSignalRO):
 
     def _socket_get(self) -> float:
         """Get command for the readback signal"""
-        cmd = "MG@" + ",@".join([f"AN[{ii}]" for ii in range(self._NUM_ANALOG_CHANNELS)])
+        cmd = f"MG@OUT[{self._channel}]"
         ret = self.controller.socket_put_and_receive(cmd)
-        values = [float(val) for val in ret.strip().split(" ")]
-        # This updates all channels' readbacks, including self._readback
-        self._update_all_channels(values)
+        self._readback = float(ret.strip())
         return self._readback
 
-    def get(self):
-        """Get current analog channel values from the Galil RIO controller."""
-        # If the last readback has happend more than _READ_TIMEOUT seconds ago, read all channels again
-        if time.monotonic() - self.parent.last_readback > self._READ_TIMEOUT:
-            self._readback = self._socket_get()
-        return self._readback
+    def _socket_set(self, val: Literal[0, 1]) -> None:
+        """Set command for the digital output signal. Value should be 0 or 1."""
 
-    # pylint: disable=protected-access
-    def _update_all_channels(self, values: list[float]) -> None:
-        """
-        Update all analog channel readbacks based on the provided list of values.
-        List of values must be in order from an_ch0 to an_ch7.
+        if val not in (0, 1):
+            raise ValueError("Digital output value must be 0 or 1.")
+        cmd = f"SB{self._channel}" if val == 1 else f"CB{self._channel}"
+        self.controller.socket_put_confirmed(cmd)
 
-        We first have to update the _last_readback timestamp of the GalilRIO parent device.
-        Then we update all readbacks of all an_ch channels, before we run any subscriptions.
-        This ensures that all readbacks are updated before any subscriptions are run, which
-        may themselves read other channels.
 
-        Args:
-            values (list[float]): List of 8 float values corresponding to the analog channels.
-                                  They must be in order from an_ch0 to an_ch7.
-        """
-        timestamp = time.time()
-        # Update parent's last readback before running subscriptions!!
-        self.parent._last_readback = time.monotonic()
-        updates: dict[str, tuple[float, float]] = {}  # attr_name -> (new_val, old_val)
-        # Update all readbacks first
-        for walk in self.parent.walk_signals():
-            if walk.item.attr_name.startswith("an_ch"):
-                idx = int(walk.item.attr_name[-1])
-                if 0 <= idx < len(values):
-                    old_val = walk.item._readback
-                    new_val = values[idx]
-                    walk.item._metadata["timestamp"] = timestamp
-                    walk.item._readback = new_val
-                    updates[walk.item.attr_name] = (new_val, old_val)
+def _create_analog_channels(num_channels: int) -> dict[str, tuple]:
+    """
+    Helper method to create a dictionary of analog channel definitions for the DynamicDeviceComponent.
 
-        # Run subscriptions after all readbacks have been updated
-        for walk in self.parent.walk_signals():
-            if walk.item.attr_name in updates:
-                new_val, old_val = updates[walk.item.attr_name]
-                walk.item._run_subs(
-                    sub_type=walk.item.SUB_VALUE,
-                    old_value=old_val,
-                    value=new_val,
-                    timestamp=timestamp,
-                )
+    Args:
+        num_channels (int): The number of analog channels to create.
+    """
+    an_channels = {}
+    for i in range(0, num_channels):
+        an_channels[f"ch{i}"] = (
+            GalilRIOAnalogSignalRO,
+            f"ch{i}",
+            {"kind": Kind.normal, "notify_bec": True, "channel": i, "doc": f"Analog channel {i}."},
+        )
+    return an_channels
+
+
+def _create_digital_output_channels(num_channels: int) -> dict[str, tuple]:
+    """
+    Helper method to create a dictionary of digital output channel definitions for the DynamicDeviceComponent.
+
+    Args:
+        num_channels (int): The number of digital output channels to create.
+    """
+    di_out_channels = {}
+    for i in range(0, num_channels):
+        di_out_channels[f"ch{i}"] = (
+            GalilRIODigitalOutSignal,
+            f"ch{i}",
+            {
+                "kind": Kind.config,
+                "notify_bec": True,
+                "channel": i,
+                "doc": f"Digital output channel {i}.",
+            },
+        )
+    return di_out_channels
 
 
 class GalilRIO(PSIDeviceBase):
     """
-    Galil RIO controller integration with 8 analog input channels. To implement the device,
-    please provide the appropriate host and port (default port is 23).
+    Galil RIO controller integration with 16 digital output channels and 8 analog input channels.
+    The default port for the controller is 23.
 
     Args:
         host (str): Hostname or IP address of the Galil RIO controller.
+        port (int, optional): Port number for the TCP/IP connection. Defaults to 23.
+        socket_cls (type[SocketIO], optional): Socket class to use for communication. Defaults to SocketIO.
+        scan_info (ScanInfo, optional): ScanInfo object for the device.
+        device_manager (DeviceManagerDS): The device manager instance that manages this device.
+        **kwargs: Additional keyword arguments passed to the PSIDeviceBase constructor.
     """
 
     SUB_CONNECTION_CHANGE = "connection_change"
 
-    an_ch0 = Cpt(GalilRIOSignalRO, signal_name="an_ch0", channel=0, doc="Analog input channel 0")
-    an_ch1 = Cpt(GalilRIOSignalRO, signal_name="an_ch1", channel=1, doc="Analog input channel 1")
-    an_ch2 = Cpt(GalilRIOSignalRO, signal_name="an_ch2", channel=2, doc="Analog input channel 2")
-    an_ch3 = Cpt(GalilRIOSignalRO, signal_name="an_ch3", channel=3, doc="Analog input channel 3")
-    an_ch4 = Cpt(GalilRIOSignalRO, signal_name="an_ch4", channel=4, doc="Analog input channel 4")
-    an_ch5 = Cpt(GalilRIOSignalRO, signal_name="an_ch5", channel=5, doc="Analog input channel 5")
-    an_ch6 = Cpt(GalilRIOSignalRO, signal_name="an_ch6", channel=6, doc="Analog input channel 6")
-    an_ch7 = Cpt(GalilRIOSignalRO, signal_name="an_ch7", channel=7, doc="Analog input channel 7")
+    #############################
+    ### Analog input channels ###
+    #############################
+
+    analog_in = DDC(_create_analog_channels(GalilRIOAnalogSignalRO._NUM_ANALOG_CHANNELS))
+    digital_out = DDC(
+        _create_digital_output_channels(GalilRIODigitalOutSignal._NUM_DIGITAL_OUTPUT_CHANNELS)
+    )
 
     def __init__(
         self,
@@ -177,19 +251,18 @@ class GalilRIO(PSIDeviceBase):
         if port is None:
             port = 23  # Default port for Galil RIO controller
         self.controller = GalilRIOController(
-            socket_cls=socket_cls, socket_host=host, socket_port=port, device_manager=device_manager
+            name=f"GalilRIOController_{name}",
+            socket_cls=socket_cls,
+            socket_host=host,
+            socket_port=port,
+            device_manager=device_manager,
         )
-        self._last_readback: float = time.monotonic()
+        self._readback_metadata: dict[str, float] = {"last_readback": 0.0}
         super().__init__(name=name, device_manager=device_manager, scan_info=scan_info, **kwargs)
         self.controller.subscribe(
             self._update_connection_state, event_type=self.SUB_CONNECTION_CHANGE
         )
 
-    @property
-    def last_readback(self) -> float:
-        """Return the time of the last readback from the controller."""
-        return self._last_readback
-
     # pylint: disable=arguments-differ
     def wait_for_connection(self, timeout: float = 30.0) -> None:
         """Wait for the RIO controller to be connected within timeout period."""
@@ -207,7 +280,7 @@ class GalilRIO(PSIDeviceBase):
 
 
 if __name__ == "__main__":
-    HOST_NAME = "129.129.98.64"
+    HOST_NAME = "129.129.122.14"
     from bec_server.device_server.tests.utils import DMMock
 
     dm = DMMock()

csaxs_bec/devices/omny/galil/lgalil_ophyd.py

@@ -25,6 +25,34 @@ logger = bec_logger.logger
 
 
 class LamniGalilController(GalilController):
+
+
+    # ============================================================
+    # Error status
+    # ============================================================
+
+    caperr_bits = {
+        0x01: "Cap1 outside expected left-stop range (early check)",
+        0x02: "Cap2 outside expected left-stop range (early check)",
+        0x04: "Cap1 too low during pressure-off check (near right boundary)",
+        0x08: "Cap2 too low during pressure-off check (near right boundary)",
+        0x10: "Cap1 exceeded allowed left-stop boundary during movement",
+        0x20: "Cap2 exceeded allowed left-stop boundary during movement (disabled in code)",
+        0x40: "Cap1 did not respond to test movement",
+        0x80: "Cap2 did not respond to test movement"
+    }
+
+    allaxrer_table = {
+        1: "Not all axes referenced after reference search",
+        2: "Pressure-loss emergency stop (pressure 14/15 active while motor C off)",
+        3: "Unexpected pressure OFF while soft-limits not yet set",
+        4: "Pressure valve mismatch (OUT13=0 but IN13=1)",
+        5: "Capacitive sensor boundary violations (caperr > 0)",
+        6: "Emergency Stop triggered (IN[5]=0)",
+        7: "Following error detected on one or more axes"
+    }
+
+
     USER_ACCESS = [
         "describe",
         "show_running_threads",
@@ -37,6 +65,8 @@ class LamniGalilController(GalilController):
         "get_motor_limit_switch",
         "is_motor_on",
         "all_axes_referenced",
+        "lamni_lights_off",
+        "lamni_lights_on"
     ]
 
     def show_status_other(self):
@@ -60,6 +90,47 @@ class LamniGalilController(GalilController):
             print("There is air pressure at the outer rotation radial.")
         swver = float(self.socket_put_and_receive("MGswver"))
         print(f"Lgalil LAMNI firmware version {swver:2.0f}.")
+        allaxref = int(float(self.socket_put_and_receive("MGallaxref")))
+        print(f"Error statuts:")
+        if allaxref == 1:
+            print(f"Allaxref = 1, all OK.")
+        else:
+            print(f"Allaxref = {allaxref}. Not all axes are referenced or error introduced preventing motion.")
+            allaxrer = int(float(self.socket_put_and_receive("MGallaxrer")))
+            print("\nallaxrer =", allaxrer)
+            print(self.decode_allaxrer(allaxrer))
+            caperr = int(float(self.socket_put_and_receive("MGcaperr")))
+            print("\nDecoding caperr =", caperr)
+            self.visualize_caperr(caperr)
+
+    def decode_allaxrer(self, code: int) -> str:
+        """Return human-readable meaning of allaxrer code."""
+        return self.allaxrer_table.get(code, "Unknown allaxrer code")
+
+    def visualize_caperr(self, mask: int):
+        """Pretty-print a bitmask visualization for caperr."""
+        print("\n=== CAPERR BITMASK VISUALIZER ===")
+        print(f"Raw value: {mask}   (0x{mask:02X})")
+        print("----------------------------------\n")
+
+        print("Bit | Hex  | Active | Meaning")
+        print("----------------------------------")
+
+        for bit, meaning in self.caperr_bits.items():
+            active = "YES" if mask & bit else "no"
+            print(f"{bit:3d} | 0x{bit:02X} | {active:6} | {meaning}")
+
+        print("\nActive flags:")
+        active_flags = [meaning for bit, meaning in self.caperr_bits.items() if mask & bit]
+
+        if active_flags:
+            for f in active_flags:
+                print("  ✓", f)
+        else:
+            print("  (none)")
+
+        print("\n==================================\n")
+
 
     def lamni_lights_off(self):
         self.socket_put_confirmed("SB1")
@@ -93,7 +164,7 @@ class LamniGalilReadbackSignal(GalilSignalRO):
         val = super().read()
         if self.parent.axis_Id_numeric == 2:
             try:
-                rt = self.parent.device_manager.devices[self.parent.rtx]
+                rt = self.parent.device_manager.devices[self.parent.rt]
                 if rt.enabled:
                     rt.obj.controller.set_rotation_angle(val[self.parent.name]["value"])
             except KeyError:
@@ -147,7 +218,7 @@ class LamniGalilMotor(Device, PositionerBase):
             raise BECConfigError(
                 "device_mapping has been specified but the device_manager cannot be accessed."
             )
-        self.rt = self.device_mapping.get("rt")
+        self.rt = self.device_mapping.get("rt", "rtx")
 
         super().__init__(
             prefix,

csaxs_bec/devices/omny/rt/rt_lamni_ophyd.py

@@ -11,6 +11,7 @@ from ophyd.status import wait as status_wait
 from ophyd.utils import LimitError, ReadOnlyError
 from ophyd_devices.utils.controller import Controller, threadlocked
 from ophyd_devices.utils.socket import SocketIO, SocketSignal, raise_if_disconnected
+from prettytable import PrettyTable
 
 from csaxs_bec.devices.omny.rt.rt_ophyd import RtCommunicationError, RtError
 
@@ -51,6 +52,7 @@ class RtLamniController(Controller):
     _axes_per_controller = 3
     USER_ACCESS = [
         "socket_put_and_receive",
+        "socket_put",
         "set_rotation_angle",
         "feedback_disable",
         "feedback_enable_without_reset",
@@ -62,6 +64,11 @@ class RtLamniController(Controller):
         "_set_axis_velocity_maximum_speed",
         "_position_sampling_single_read",
         "_position_sampling_single_reset_and_start_sampling",
+        "show_signal_strength_interferometer",
+        "show_interferometer_positions",
+        "show_analog_signals",
+        "show_feedback_status",
+
     ]
 
     def __init__(
@@ -208,8 +215,9 @@ class RtLamniController(Controller):
 
     @threadlocked
     def start_scan(self):
-        interferometer_feedback_not_running = int((self.socket_put_and_receive("J2")).split(",")[0])
-        if interferometer_feedback_not_running == 1:
+        # interferometer_feedback_not_running = int((self.socket_put_and_receive("J2")).split(",")[0])
+        # if interferometer_feedback_not_running == 1:
+        if not self.feedback_is_running():    
             logger.error(
                 "Cannot start scan because feedback loop is not running or there is an interferometer error."
             )
@@ -270,6 +278,44 @@ class RtLamniController(Controller):
             "average_lamni_angle": {"value": self.average_lamni_angle / (int(return_table[0]) + 1)},
         }
         return signals
+    
+    def feedback_is_running(self) -> bool:
+        status = int(float((self.socket_put_and_receive("J2")).split(",")[0]))
+        return status == 0  # 0 means running, 1 means error/disabled
+
+    def show_feedback_status(self):
+        if self.feedback_is_running():
+            print("Loop is running, no error on interferometer.")
+        else:
+            print("Loop is not running, either it is turned off or an interferometer error occurred.")
+
+
+    def show_analog_signals(self) -> dict:
+        self.socket_put("As")  # start sampling
+        time.sleep(0.01)
+        return_table = (self.socket_put_and_receive("Ar")).split(",")
+        
+        number_of_samples = int(float(return_table[0]))
+        signals = {
+            "number_of_samples":    number_of_samples,
+            "piezo_0":              float(return_table[1]),
+            "piezo_1":              float(return_table[2]),
+            "cap_0":                float(return_table[3]),
+            "cap_1":                float(return_table[4]),
+            "cap_2":                float(return_table[5]),
+            "cap_3":                float(return_table[6]),
+            "cap_4":                float(return_table[7]),
+        }
+
+        t = PrettyTable()
+        t.title = f"LamNI Analog Signals ({number_of_samples} samples)"
+        t.field_names = ["Signal", "Value"]
+        for key, val in signals.items():
+            if key != "number_of_samples":
+                t.add_row([key, f"{val:.4f}"])
+        print(t)
+
+        return
 
     def read_positions_from_sampler(self):
         # this was for reading after the scan completed
@@ -347,6 +393,48 @@ class RtLamniController(Controller):
         )
         return bool(return_table[0])
 
+    def show_signal_strength_interferometer(self):
+        # trigger SSI averaging before reading
+        self.socket_put("J3")
+        time.sleep(0.05)
+        return_table = (self.socket_put_and_receive("J2")).split(",")
+        ssi_0 = float(return_table[1])
+        ssi_1 = float(return_table[2])
+
+        return_table_angle = (self.socket_put_and_receive("J7")).split(",")
+        angle_running = bool(int(float(return_table_angle[0])))
+        angle_position = float(return_table_angle[1])
+        angle_signal = float(return_table_angle[2])
+
+        t = PrettyTable()
+        t.title = "Interferometer signal strength"
+        t.field_names = ["Axis", "Description", "Value", "Running"]
+        t.add_row([0, "ST FZP horizontal",   ssi_0,        "-"])
+        t.add_row([1, "ST FZP vertical",     ssi_1,        "-"])
+        t.add_row([2, "Angle interferometer", angle_signal, angle_running])
+        print(t)
+
+        if angle_running:
+            print(f"Angle interferometer position: {angle_position:.4f} um")
+        else:
+            print("Warning: angle interferometer is not running.")
+
+    def show_interferometer_positions(self) -> dict:
+        return_table = (self.socket_put_and_receive("J4")).split(",")
+        loop_status = bool(int(float(return_table[0])))
+        pos_y = float(return_table[1])
+        pos_x = float(return_table[2])
+
+        t = PrettyTable()
+        t.title = "LamNI Interferometer Positions"
+        t.field_names = ["Axis", "Description", "Position (um)"]
+        t.add_row([0, "X", f"{pos_x:.4f}"])
+        t.add_row([1, "Y", f"{pos_y:.4f}"])
+        print(t)
+        print(f"Feedback loop running: {loop_status}")
+
+        return {"x": pos_x, "y": pos_y, "loop_running": loop_status}    
+
     def feedback_enable_with_reset(self):
         if not self.feedback_status_angle_lamni():
             self.feedback_disable_and_even_reset_lamni_angle_interferometer()

pyproject.toml

@@ -25,6 +25,8 @@ dependencies = [
     "bec_widgets",
     "zmq",
     "opencv-python",
+    "dectris-compression", # for JFJ preview stream decompression
+    "cbor2",
 ]
 
 [project.optional-dependencies]

tests/conftest.py

@@ -1,14 +0,0 @@
-"""
-Conftest runs for all tests in this directory and subdirectories. Thereby, we know for
-certain that the SocketSignal.READBACK_TIMEOUT is set to 0 for all tests, which prevents
-hanging tests when a readback is attempted on a non-connected socket.
-"""
-
-# conftest.py
-import pytest
-from ophyd_devices.utils.socket import SocketSignal
-
-
-@pytest.fixture(autouse=True)
-def patch_socket_timeout(monkeypatch):
-    monkeypatch.setattr(SocketSignal, "READBACK_TIMEOUT", 0.0)

tests/tests_devices/test_eiger.py

@@ -5,6 +5,7 @@ from time import time
 from typing import TYPE_CHECKING, Generator
 from unittest import mock
 
+import numpy as np
 import pytest
 from bec_lib.messages import FileMessage, ScanStatusMessage
 from jfjoch_client.models.broker_status import BrokerStatus
@@ -78,7 +79,7 @@ def detector_list(request) -> Generator[DetectorList, None, None]:
             ),
             DetectorListElement(
                 id=2,
-                description="EIGER 8.5M (tmp)",
+                description="EIGER 9M",
                 serial_number="123456",
                 base_ipv4_addr="192.168.0.1",
                 udp_interface_count=1,
@@ -103,7 +104,11 @@ def eiger_1_5m(mock_scan_info) -> Generator[Eiger1_5M, None, None]:
     name = "eiger_1_5m"
     dev = Eiger1_5M(name=name, beam_center=(256, 256), detector_distance=100.0)
     dev.scan_info.msg = mock_scan_info
-    yield dev
+    try:
+        yield dev
+    finally:
+        if dev._destroyed is False:
+            dev.destroy()
 
 
 @pytest.fixture(scope="function")
@@ -113,7 +118,19 @@ def eiger_9m(mock_scan_info) -> Generator[Eiger9M, None, None]:
     name = "eiger_9m"
     dev = Eiger9M(name=name)
     dev.scan_info.msg = mock_scan_info
-    yield dev
+    try:
+        yield dev
+    finally:
+        if dev._destroyed is False:
+            dev.destroy()
+
+
+def test_eiger_wait_for_connection(eiger_1_5m, eiger_9m):
+    """Test the wait_for_connection metho is calling status_get on the JFJ API client."""
+    for eiger in (eiger_1_5m, eiger_9m):
+        with mock.patch.object(eiger.jfj_client.api, "status_get") as mock_status_get:
+            eiger.wait_for_connection(timeout=1)
+            mock_status_get.assert_called_once_with(_request_timeout=1)
 
 
 @pytest.mark.parametrize("detector_state", ["Idle", "Inactive"])
@@ -141,7 +158,7 @@ def test_eiger_1_5m_on_connected(eiger_1_5m, detector_list, detector_state):
         else:
             eiger.on_connected()
             assert mock_set_det.call_args == mock.call(
-                DetectorSettings(frame_time_us=500, timing=DetectorTiming.TRIGGER), timeout=10
+                DetectorSettings(frame_time_us=500, timing=DetectorTiming.TRIGGER), timeout=5
             )
             assert mock_file_writer.call_args == mock.call(
                 file_writer_settings=FileWriterSettings(
@@ -179,7 +196,7 @@ def test_eiger_9m_on_connected(eiger_9m, detector_list, detector_state):
         else:
             eiger.on_connected()
             assert mock_set_det.call_args == mock.call(
-                DetectorSettings(frame_time_us=500, timing=DetectorTiming.TRIGGER), timeout=10
+                DetectorSettings(frame_time_us=500, timing=DetectorTiming.TRIGGER), timeout=5
             )
             assert mock_file_writer.call_args == mock.call(
                 file_writer_settings=FileWriterSettings(
@@ -216,11 +233,39 @@ def test_eiger_on_stop(eiger_1_5m):
         stop_event.wait(timeout=5)  # Thread should be killed from task_handler
 
 
+def test_eiger_on_destroy(eiger_1_5m):
+    """Test the on_destroy logic of the Eiger detector. This is equivalent for 9M and 1_5M."""
+    eiger = eiger_1_5m
+    start_event = threading.Event()
+    stop_event = threading.Event()
+
+    def tmp_task():
+        start_event.set()
+        try:
+            while True:
+                time.sleep(0.1)
+        finally:
+            stop_event.set()
+
+    eiger.task_handler.submit_task(tmp_task)
+    start_event.wait(timeout=5)
+
+    with (
+        mock.patch.object(eiger.jfj_preview_client, "stop") as mock_jfj_preview_client_stop,
+        mock.patch.object(eiger.jfj_client, "stop") as mock_jfj_client_stop,
+    ):
+        eiger.on_destroy()
+        mock_jfj_preview_client_stop.assert_called_once()
+        mock_jfj_client_stop.assert_called_once()
+        stop_event.wait(timeout=5)
+
+
 @pytest.mark.timeout(25)
 @pytest.mark.parametrize("raise_timeout", [True, False])
 def test_eiger_on_complete(eiger_1_5m, raise_timeout):
     """Test the on_complete logic of the Eiger detector. This is equivalent for 9M and 1_5M."""
     eiger = eiger_1_5m
+    eiger._wait_for_on_complete = 1  # reduce wait time for testing
 
     callback_completed_event = threading.Event()
 
@@ -230,7 +275,7 @@ def test_eiger_on_complete(eiger_1_5m, raise_timeout):
 
     unblock_wait_for_idle = threading.Event()
 
-    def mock_wait_for_idle(timeout: int, request_timeout: float):
+    def mock_wait_for_idle(timeout: float, raise_on_timeout: bool) -> bool:
         if unblock_wait_for_idle.wait(timeout):
             if raise_timeout:
                 return False
@@ -238,11 +283,18 @@ def test_eiger_on_complete(eiger_1_5m, raise_timeout):
         return False
 
     with (
+        mock.patch.object(
+            eiger.jfj_client.api, "status_get", return_value=BrokerStatus(state="Idle")
+        ),
         mock.patch.object(eiger.jfj_client, "wait_for_idle", side_effect=mock_wait_for_idle),
         mock.patch.object(
             eiger.jfj_client.api,
             "statistics_data_collection_get",
-            return_value=MeasurementStatistics(run_number=1),
+            return_value=MeasurementStatistics(
+                run_number=1,
+                images_collected=eiger.scan_info.msg.num_points
+                * eiger.scan_info.msg.scan_parameters["frames_per_trigger"],
+            ),
         ),
     ):
         status = eiger.complete()
@@ -284,7 +336,7 @@ def test_eiger_file_event_callback(eiger_1_5m, tmp_path):
     assert file_msg.hinted_h5_entries == {"data": "entry/data/data"}
 
 
-def test_eiger_on_sage(eiger_1_5m):
+def test_eiger_on_stage(eiger_1_5m):
     """Test the on_stage and on_unstage logic of the Eiger detector. This is equivalent for 9M and 1_5M."""
     eiger = eiger_1_5m
     scan_msg = eiger.scan_info.msg
@@ -316,3 +368,35 @@ def test_eiger_on_sage(eiger_1_5m):
         )
         assert mock_start.call_args == mock.call(settings=data_settings)
         assert eiger.staged is Staged.yes
+
+
+def test_eiger_set_det_distance_test_beam_center(eiger_1_5m):
+    """Test the set_detector_distance and set_beam_center methods. Equivalent for 9M and 1_5M."""
+    eiger = eiger_1_5m
+    old_distance = eiger.detector_distance
+    new_distance = old_distance + 100
+    old_beam_center = eiger.beam_center
+    new_beam_center = (old_beam_center[0] + 20, old_beam_center[1] + 50)
+    eiger.set_detector_distance(new_distance)
+    assert eiger.detector_distance == new_distance
+    eiger.set_beam_center(x=new_beam_center[0], y=new_beam_center[1])
+    assert eiger.beam_center == new_beam_center
+    with pytest.raises(ValueError):
+        eiger.set_beam_center(x=-10, y=100)  # Cannot set negative beam center
+    with pytest.raises(ValueError):
+        eiger.detector_distance = -50  # Cannot set negative detector distance
+
+
+def test_eiger_preview_callback(eiger_1_5m):
+    """Preview callback test for the Eiger detector. This is equivalent for 9M and 1_5M."""
+    eiger = eiger_1_5m
+    # NOTE: I don't find models for the CBOR messages used by JFJ, currently using a dummay dict.
+    # Please adjust once the proper model is found.
+    for msg_type in ["start", "end", "image", "calibration", "metadata"]:
+        msg = {"type": msg_type, "data": {"default": np.array([[1, 2], [3, 4]])}}
+        with mock.patch.object(eiger.preview_image, "put") as mock_preview_put:
+            eiger._preview_callback(msg)
+            if msg_type == "image":
+                mock_preview_put.assert_called_once_with(msg["data"]["default"])
+            else:
+                mock_preview_put.assert_not_called()

tests/tests_devices/test_fupr_ophyd.py

@@ -2,6 +2,7 @@ from unittest import mock
 
 import pytest
 from ophyd_devices.tests.utils import SocketMock
+from ophyd_devices.utils.socket import SocketSignal
 
 from csaxs_bec.devices.omny.galil.fupr_ophyd import FuprGalilController, FuprGalilMotor
 
@@ -17,6 +18,11 @@ def fsamroy(dm_with_devices):
         socket_cls=SocketMock,
         device_manager=dm_with_devices,
     )
+    for walk in fsamroy_motor.walk_signals():
+        if isinstance(walk.item, SocketSignal):
+            walk.item._readback_timeout = (
+                0.0  # Set the readback timeout to 0 to avoid waiting during tests
+            )
     fsamroy_motor.controller.on()
     assert isinstance(fsamroy_motor.controller, FuprGalilController)
     yield fsamroy_motor

tests/tests_devices/test_galil.py

@@ -9,7 +9,11 @@ from ophyd_devices.tests.utils import SocketMock
 from csaxs_bec.devices.npoint.npoint import NPointAxis, NPointController
 from csaxs_bec.devices.omny.galil.fgalil_ophyd import FlomniGalilController, FlomniGalilMotor
 from csaxs_bec.devices.omny.galil.fupr_ophyd import FuprGalilController, FuprGalilMotor
-from csaxs_bec.devices.omny.galil.galil_rio import GalilRIO, GalilRIOController, GalilRIOSignalRO
+from csaxs_bec.devices.omny.galil.galil_rio import (
+    GalilRIO,
+    GalilRIOAnalogSignalRO,
+    GalilRIOController,
+)
 from csaxs_bec.devices.omny.galil.lgalil_ophyd import LamniGalilController, LamniGalilMotor
 from csaxs_bec.devices.omny.galil.ogalil_ophyd import OMNYGalilController, OMNYGalilMotor
 from csaxs_bec.devices.omny.galil.sgalil_ophyd import GalilController, SGalilMotor
@@ -272,26 +276,27 @@ def test_galil_rio_signal_read(galil_rio):
     ## Test read of all channels
     ###########
 
-    assert galil_rio.an_ch0._READ_TIMEOUT == 0.1  # Default read timeout of 100ms
+    assert galil_rio.analog_in.ch0._readback_timeout == 0.1  # Default read timeout of 100ms
     # Mock the socket to return specific values
-    galil_rio.controller.sock.buffer_recv = [b" 1.234 2.345 3.456 4.567 5.678 6.789 7.890 8.901"]
-    galil_rio._last_readback = 0  # Force read from controller
-
+    analog_bufffer = b" 1.234 2.345 3.456 4.567 5.678 6.789 7.890 8.901\r\n"
+    galil_rio.controller.sock.buffer_recv = []  # Clear any existing buffer
+    galil_rio.controller.sock.buffer_recv.append(analog_bufffer)
     read_values = galil_rio.read()
     assert len(read_values) == 8  # 8 channels
+
     expected_values = {
-        galil_rio.an_ch0.name: {"value": 1.234},
-        galil_rio.an_ch1.name: {"value": 2.345},
-        galil_rio.an_ch2.name: {"value": 3.456},
-        galil_rio.an_ch3.name: {"value": 4.567},
-        galil_rio.an_ch4.name: {"value": 5.678},
-        galil_rio.an_ch5.name: {"value": 6.789},
-        galil_rio.an_ch6.name: {"value": 7.890},
-        galil_rio.an_ch7.name: {"value": 8.901},
+        galil_rio.analog_in.ch0.name: {"value": 1.234},
+        galil_rio.analog_in.ch1.name: {"value": 2.345},
+        galil_rio.analog_in.ch2.name: {"value": 3.456},
+        galil_rio.analog_in.ch3.name: {"value": 4.567},
+        galil_rio.analog_in.ch4.name: {"value": 5.678},
+        galil_rio.analog_in.ch5.name: {"value": 6.789},
+        galil_rio.analog_in.ch6.name: {"value": 7.890},
+        galil_rio.analog_in.ch7.name: {"value": 8.901},
     }
     # All timestamps should be the same
     assert all(
-        ret["timestamp"] == read_values[galil_rio.an_ch0.name]["timestamp"]
+        ret["timestamp"] == read_values[galil_rio.analog_in.ch0.name]["timestamp"]
         for signal_name, ret in read_values.items()
     )
     # Check values
@@ -301,7 +306,7 @@ def test_galil_rio_signal_read(galil_rio):
 
     # Check communication command to socker
     assert galil_rio.controller.sock.buffer_put == [
-        b"MG@AN[0],@AN[1],@AN[2],@AN[3],@AN[4],@AN[5],@AN[6],@AN[7]\r"
+        b"MG@AN[0], @AN[1], @AN[2], @AN[3], @AN[4], @AN[5], @AN[6], @AN[7]\r"
     ]
 
     ###########
@@ -313,11 +318,11 @@ def test_galil_rio_signal_read(galil_rio):
 
     def value_callback(value, old_value, **kwargs):
         obj = kwargs.get("obj")
-        galil = obj.parent
+        galil = obj.parent.parent
         readback = galil.read()
         value_callback_buffer.append(readback)
 
-    galil_rio.an_ch0.subscribe(value_callback, run=False)
+    galil_rio.analog_in.ch0.subscribe(value_callback, run=False)
     galil_rio.controller.sock.buffer_recv = [b" 2.5 2.6 2.7 2.8 2.9 3.0 3.1 3.2"]
     expected_values = [2.5, 2.6, 2.7, 2.8, 2.9, 3.0, 3.1, 3.2]
 
@@ -327,13 +332,15 @@ def test_galil_rio_signal_read(galil_rio):
 
     # Should have used the cached value
     for walk in galil_rio.walk_signals():
-        walk.item._READ_TIMEOUT = 10  # Make sure cached read is used
-    ret = galil_rio.an_ch0.read()
+        walk.item._readback_timeout = 10  # Make sure cached read is used
+    ret = galil_rio.analog_in.ch0.read()
 
     # Should not trigger callback since value did not change
-    assert np.isclose(ret[galil_rio.an_ch0.name]["value"], 1.234)
+    assert np.isclose(ret[galil_rio.analog_in.ch0.name]["value"], 1.234)
     # Same timestamp as for another channel as this is cached read
-    assert np.isclose(ret[galil_rio.an_ch0.name]["timestamp"], galil_rio.an_ch7.timestamp)
+    assert np.isclose(
+        ret[galil_rio.analog_in.ch0.name]["timestamp"], galil_rio.analog_in.ch7.timestamp
+    )
     assert len(value_callback_buffer) == 0
 
     ##################
@@ -341,10 +348,10 @@ def test_galil_rio_signal_read(galil_rio):
     ##################
 
     # Now force a read from the controller
-    galil_rio._last_readback = 0  # Force read from controller
-    ret = galil_rio.an_ch0.read()
+    galil_rio.analog_in.ch0._last_readback = 0  # Force read from controller
+    ret = galil_rio.analog_in.ch0.read()
 
-    assert np.isclose(ret[galil_rio.an_ch0.name]["value"], 2.5)
+    assert np.isclose(ret[galil_rio.analog_in.ch0.name]["value"], 2.5)
 
     # Check callback invocation, but only 1 callback even with galil_rio.read() call in callback
     assert len(value_callback_buffer) == 1
@@ -352,7 +359,45 @@ def test_galil_rio_signal_read(galil_rio):
     assert np.isclose(values, expected_values).all()
     assert all(
         [
-            value["timestamp"] == value_callback_buffer[0][galil_rio.an_ch0.name]["timestamp"]
+            value["timestamp"]
+            == value_callback_buffer[0][galil_rio.analog_in.ch0.name]["timestamp"]
             for value in value_callback_buffer[0].values()
         ]
     )
+
+
+def test_galil_rio_digital_out_signal(galil_rio):
+    """
+    Test that the Galil RIO digital output signal can be set correctly.
+    """
+    ## Test Read from digital output channels
+    buffer_receive = []
+    excepted_put_buffer = []
+    for ii in range(galil_rio.digital_out.ch0._NUM_DIGITAL_OUTPUT_CHANNELS):
+        cmd = f"MG@OUT[{ii}]\r".encode()
+        excepted_put_buffer.append(cmd)
+        recv = " 1.000".encode()
+        buffer_receive.append(recv)
+
+    galil_rio.controller.sock.buffer_recv = buffer_receive  # Mock response for readback
+
+    digital_read = galil_rio.read_configuration()  # Read to populate readback values
+
+    for walk in galil_rio.digital_out.walk_signals():
+        assert np.isclose(digital_read[walk.item.name]["value"], 1.0)
+
+    assert galil_rio.controller.sock.buffer_put == excepted_put_buffer
+
+    # Test writing to digital output channels
+    galil_rio.controller.sock.buffer_put = []  # Clear buffer put
+    galil_rio.controller.sock.buffer_recv = [b":"]  # Mock response for readback
+
+    # Set digital output channel 0 to high
+    galil_rio.digital_out.ch0.put(1)
+    assert galil_rio.controller.sock.buffer_put == [b"SB0\r"]
+
+    # Set digital output channel 0 to low
+    galil_rio.controller.sock.buffer_put = []  # Clear buffer put
+    galil_rio.controller.sock.buffer_recv = [b":"]  # Mock response for readback
+    galil_rio.digital_out.ch0.put(0)
+    assert galil_rio.controller.sock.buffer_put == [b"CB0\r"]