fix(tests): x_ray_eye_align correct imports fixed after refactor of LamNI

csaxs_bec/bec_ipython_client/plugins/LamNI/__init__.py

@@ -1,2 +1,6 @@
-from .load_additional_correction import lamni_read_additional_correction
-from .x_ray_eye_align import DataDrivenLamNI, LamNI, MagLamNI, XrayEyeAlign
+from .alignment import XrayEyeAlign
+from .lamni import LamNI
+from .lamni_optics_mixin import LamNIInitError, LaMNIInitStages, LamNIOpticsMixin
+__all__ = [
+    "LamNI", "XrayEyeAlign", "LamNIInitError", "LaMNIInitStages", "LamNIOpticsMixin"
+]

csaxs_bec/bec_ipython_client/plugins/LamNI/alignment.py

@@ -0,0 +1,461 @@
+import builtins
+import time
+from collections import defaultdict
+
+import numpy as np
+from bec_lib import bec_logger
+from typeguard import typechecked
+
+from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_get, epics_put, fshopen
+
+logger = bec_logger.logger
+
+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
+    PIXEL_CALIBRATION = 0.2 / 218  # .2 with binning
+
+    def __init__(self, client, lamni) -> None:
+        self.client = client
+        self.lamni = lamni
+        self.device_manager = client.device_manager
+        self.scans = client.scans
+        self.alignment_values = defaultdict(list)
+        self._reset_init_values()
+        self.corr_pos_x = []
+        self.corr_pos_y = []
+        self.corr_angle = []
+        self.corr_pos_x_2 = []
+        self.corr_pos_y_2 = []
+        self.corr_angle_2 = []
+
+    # ------------------------------------------------------------------
+    # Correction reset
+    # ------------------------------------------------------------------
+
+    def reset_correction(self):
+        self.corr_pos_x = []
+        self.corr_pos_y = []
+        self.corr_angle = []
+
+    def reset_correction_2(self):
+        self.corr_pos_x_2 = []
+        self.corr_pos_y_2 = []
+        self.corr_angle_2 = []
+
+    def reset_xray_eye_correction(self):
+        self.client.delete_global_var("tomo_fit_xray_eye")
+
+    # ------------------------------------------------------------------
+    # FOV offset properties
+    # ------------------------------------------------------------------
+
+    @property
+    def tomo_fovx_offset(self):
+        val = self.client.get_global_var("tomo_fov_offset")
+        if val is None:
+            return 0.0
+        return val[0] / 1000
+
+    @tomo_fovx_offset.setter
+    @typechecked
+    def tomo_fovx_offset(self, val: float):
+        val_old = self.client.get_global_var("tomo_fov_offset")
+        if val_old is None:
+            val_old = [0.0, 0.0]
+        self.client.set_global_var("tomo_fov_offset", [val * 1000, val_old[1]])
+
+    @property
+    def tomo_fovy_offset(self):
+        val = self.client.get_global_var("tomo_fov_offset")
+        if val is None:
+            return 0.0
+        return val[1] / 1000
+
+    @tomo_fovy_offset.setter
+    @typechecked
+    def tomo_fovy_offset(self, val: float):
+        val_old = self.client.get_global_var("tomo_fov_offset")
+        if val_old is None:
+            val_old = [0.0, 0.0]
+        self.client.set_global_var("tomo_fov_offset", [val_old[0], val * 1000])
+
+    # ------------------------------------------------------------------
+    # Internal helpers
+    # ------------------------------------------------------------------
+
+    def _reset_init_values(self):
+        self.shift_xy = [0, 0]
+        self._xray_fov_xy = [0, 0]
+
+    def _disable_rt_feedback(self):
+        self.device_manager.devices.rtx.controller.feedback_disable()
+
+    def _enable_rt_feedback(self):
+        self.device_manager.devices.rtx.controller.feedback_enable_with_reset()
+
+    def tomo_rotate(self, val: float):
+        # pylint: disable=undefined-variable
+        umv(self.device_manager.devices.lsamrot, val)
+
+    def get_tomo_angle(self):
+        return self.device_manager.devices.lsamrot.readback.read()["lsamrot"]["value"]
+
+    # ------------------------------------------------------------------
+    # X-ray eye camera control
+    # ------------------------------------------------------------------
+
+    def save_frame(self):
+        epics_put("XOMNYI-XEYE-SAVFRAME:0", 1)
+
+    def update_frame(self):
+        epics_put("XOMNYI-XEYE-ACQDONE:0", 0)
+        # start live
+        epics_put("XOMNYI-XEYE-ACQ:0", 1)
+        # wait for start live
+        while epics_get("XOMNYI-XEYE-ACQDONE:0") == 0:
+            time.sleep(0.5)
+            print("waiting for live view to start...")
+        fshopen()
+
+        epics_put("XOMNYI-XEYE-ACQDONE:0", 0)
+
+        while epics_get("XOMNYI-XEYE-ACQDONE:0") == 0:
+            print("waiting for new frame...")
+            time.sleep(0.5)
+
+        time.sleep(0.5)
+        # stop live view
+        epics_put("XOMNYI-XEYE-ACQ:0", 0)
+        time.sleep(1)
+        print("got new frame")
+
+    def update_fov(self, k: int):
+        self._xray_fov_xy[0] = max(epics_get(f"XOMNYI-XEYE-XWIDTH_X:{k}"), self._xray_fov_xy[0])
+        self._xray_fov_xy[1] = max(0, self._xray_fov_xy[0])
+
+    @property
+    def movement_buttons_enabled(self):
+        return [epics_get("XOMNYI-XEYE-ENAMVX:0"), epics_get("XOMNYI-XEYE-ENAMVY:0")]
+
+    @movement_buttons_enabled.setter
+    def movement_buttons_enabled(self, enabled: bool):
+        enabled = int(enabled)
+        epics_put("XOMNYI-XEYE-ENAMVX:0", enabled)
+        epics_put("XOMNYI-XEYE-ENAMVY:0", enabled)
+
+    def send_message(self, msg: str):
+        epics_put("XOMNYI-XEYE-MESSAGE:0.DESC", msg)
+
+    # ------------------------------------------------------------------
+    # Alignment procedure
+    # ------------------------------------------------------------------
+
+    def align(self):
+        self._reset_init_values()
+        self.reset_correction()
+        self.reset_correction_2()
+
+        self._disable_rt_feedback()
+        epics_put("XOMNYI-XEYE-PIXELSIZE:0", self.PIXEL_CALIBRATION)
+        self._enable_rt_feedback()
+
+        self.movement_buttons_enabled = False
+        epics_put("XOMNYI-XEYE-ACQ:0", 0)
+        self.send_message("please wait...")
+        epics_put("XOMNYI-XEYE-SAMPLENAME:0.DESC", "Let us LAMNI...")
+
+        self._disable_rt_feedback()
+        k = 0
+
+        self.lamni.lfzp_in()
+        self.update_frame()
+
+        self.movement_buttons_enabled = False
+        epics_put("XOMNYI-XEYE-SUBMIT:0", 0)
+        epics_put("XOMNYI-XEYE-STEP:0", 0)
+        self.send_message("Submit center value of FZP.")
+
+        while True:
+            if epics_get("XOMNYI-XEYE-SUBMIT:0") == 1:
+                val_x = epics_get(f"XOMNYI-XEYE-XVAL_X:{k}") * self.PIXEL_CALIBRATION  # in mm
+                val_y = epics_get(f"XOMNYI-XEYE-YVAL_Y:{k}") * self.PIXEL_CALIBRATION  # in mm
+                self.alignment_values[k] = [val_x, val_y]
+                print(
+                    f"Clicked position {k}: x {self.alignment_values[k][0]}, y"
+                    f" {self.alignment_values[k][1]}"
+                )
+
+                if k == 0:  # received center value of FZP
+                    self.send_message("please wait ...")
+                    self.lamni.loptics_out()
+                    epics_put("XOMNYI-XEYE-SUBMIT:0", -1)
+                    self.movement_buttons_enabled = False
+                    print("Moving sample in, FZP out")
+
+                    self._disable_rt_feedback()
+                    time.sleep(0.3)
+                    self._enable_rt_feedback()
+                    time.sleep(0.3)
+
+                    self.update_frame()
+                    self.send_message("Go and find the sample")
+                    epics_put("XOMNYI-XEYE-SUBMIT:0", 0)
+                    self.movement_buttons_enabled = True
+
+                elif k == 1:  # received sample center value at samrot 0
+                    msg = (
+                        f"Base shift values from movement are x {self.shift_xy[0]}, y"
+                        f" {self.shift_xy[1]}"
+                    )
+                    print(msg)
+                    logger.info(msg)
+                    self.shift_xy[0] += (
+                        self.alignment_values[0][0] - self.alignment_values[1][0]
+                    ) * 1000
+                    self.shift_xy[1] += (
+                        self.alignment_values[1][1] - self.alignment_values[0][1]
+                    ) * 1000
+                    print(
+                        "Base shift values from movement and clicked position are x"
+                        f" {self.shift_xy[0]}, y {self.shift_xy[1]}"
+                    )
+
+                    self.scans.lamni_move_to_scan_center(
+                        self.shift_xy[0] / 1000, self.shift_xy[1] / 1000, self.get_tomo_angle()
+                    ).wait()
+
+                    self.send_message("please wait ...")
+                    epics_put("XOMNYI-XEYE-SUBMIT:0", -1)
+                    self.movement_buttons_enabled = False
+                    time.sleep(1)
+
+                    self.scans.lamni_move_to_scan_center(
+                        self.shift_xy[0] / 1000, self.shift_xy[1] / 1000, self.get_tomo_angle()
+                    ).wait()
+
+                    epics_put("XOMNYI-XEYE-ANGLE:0", self.get_tomo_angle())
+                    self.update_frame()
+                    self.send_message("Submit sample center and FOV (0 deg)")
+                    epics_put("XOMNYI-XEYE-SUBMIT:0", 0)
+                    self.update_fov(k)
+
+                elif 1 < k < 10:  # received sample center value at samrot 0 ... 315
+                    self.send_message("please wait ...")
+                    epics_put("XOMNYI-XEYE-SUBMIT:0", -1)
+
+                    self._disable_rt_feedback()
+                    self.tomo_rotate((k - 1) * 45 - 45 / 2)
+                    self.scans.lamni_move_to_scan_center(
+                        self.shift_xy[0] / 1000, self.shift_xy[1] / 1000, self.get_tomo_angle()
+                    ).wait()
+                    self._disable_rt_feedback()
+                    self.tomo_rotate((k - 1) * 45)
+                    self.scans.lamni_move_to_scan_center(
+                        self.shift_xy[0] / 1000, self.shift_xy[1] / 1000, self.get_tomo_angle()
+                    ).wait()
+
+                    epics_put("XOMNYI-XEYE-ANGLE:0", self.get_tomo_angle())
+                    self.update_frame()
+                    self.send_message("Submit sample center")
+                    epics_put("XOMNYI-XEYE-SUBMIT:0", 0)
+                    epics_put("XOMNYI-XEYE-ENAMVX:0", 1)
+                    self.update_fov(k)
+
+                elif k == 10:  # received sample center value at samrot 270, done
+                    self.send_message("done...")
+                    epics_put("XOMNYI-XEYE-SUBMIT:0", -1)
+                    self.movement_buttons_enabled = False
+                    self.update_fov(k)
+                    break
+
+                k += 1
+                epics_put("XOMNYI-XEYE-STEP:0", k)
+
+            if k < 2:
+                _xrayeyalignmvx = epics_get("XOMNYI-XEYE-MVX:0")
+                _xrayeyalignmvy = epics_get("XOMNYI-XEYE-MVY:0")
+                if _xrayeyalignmvx != 0 or _xrayeyalignmvy != 0:
+                    self.shift_xy[0] = self.shift_xy[0] + _xrayeyalignmvx
+                    self.shift_xy[1] = self.shift_xy[1] + _xrayeyalignmvy
+                    self.scans.lamni_move_to_scan_center(
+                        self.shift_xy[0] / 1000, self.shift_xy[1] / 1000, self.get_tomo_angle()
+                    ).wait()
+                    print(
+                        f"Current center horizontal {self.shift_xy[0]} vertical {self.shift_xy[1]}"
+                    )
+                    epics_put("XOMNYI-XEYE-MVY:0", 0)
+                    epics_put("XOMNYI-XEYE-MVX:0", 0)
+                    self.update_frame()
+
+            time.sleep(0.2)
+
+        self.write_output()
+        fovx = self._xray_fov_xy[0] * self.PIXEL_CALIBRATION * 1000 / 2
+        fovy = self._xray_fov_xy[1] * self.PIXEL_CALIBRATION * 1000 / 2
+        print(
+            f"The largest field of view from the xrayeyealign was \nfovx = {fovx:.0f} microns,"
+            f" fovy = {fovy:.0f} microns"
+        )
+        print("Use matlab routine to fit the current alignment...")
+        print(
+            "This additional shift is applied to the base shift values\n which are x"
+            f" {self.shift_xy[0]}, y {self.shift_xy[1]}"
+        )
+
+        self._disable_rt_feedback()
+        self.tomo_rotate(0)
+
+        print(
+            "\n\nNEXT LOAD ALIGNMENT PARAMETERS\nby running"
+            " lamni.align.read_xray_eye_correction()\n"
+        )
+
+        self.client.set_global_var("tomo_fov_offset", self.shift_xy)
+
+    # ------------------------------------------------------------------
+    # Alignment output
+    # ------------------------------------------------------------------
+
+    def write_output(self):
+        import os
+        with open(
+            os.path.expanduser("~/Data10/specES1/internal/xrayeye_alignmentvalues"), "w"
+        ) as alignment_values_file:
+            alignment_values_file.write("angle\thorizontal\tvertical\n")
+            for k in range(2, 11):
+                fovx_offset = (self.alignment_values[0][0] - self.alignment_values[k][0]) * 1000
+                fovy_offset = (self.alignment_values[k][1] - self.alignment_values[0][1]) * 1000
+                print(
+                    f"Writing to file new alignment: number {k}, value x {fovx_offset}, y"
+                    f" {fovy_offset}"
+                )
+                alignment_values_file.write(f"{(k-2)*45}\t{fovx_offset}\t{fovy_offset}\n")
+
+    # ------------------------------------------------------------------
+    # X-ray eye sinusoidal correction (loaded from MATLAB fit files)
+    # ------------------------------------------------------------------
+
+    def read_xray_eye_correction(self, dir_path=None):
+        import os
+        if dir_path is None:
+            dir_path = os.path.expanduser("~/Data10/specES1/internal/")
+        tomo_fit_xray_eye = np.zeros((2, 3))
+        for i, axis in enumerate(["x", "y"]):
+            for j, coeff in enumerate(["A", "B", "C"]):
+                with open(os.path.join(dir_path, f"ptychotomoalign_{coeff}{axis}.txt"), "r") as f:
+                    tomo_fit_xray_eye[i][j] = f.readline()
+
+        self.client.set_global_var("tomo_fit_xray_eye", tomo_fit_xray_eye.tolist())
+        # x amp, phase, offset, y amp, phase, offset
+        #  0 0    0 1    0 2     1 0    1 1    1 2
+        print("New alignment parameters loaded from X-ray eye")
+        print(
+            f"X Amplitude {tomo_fit_xray_eye[0][0]}, "
+            f"X Phase {tomo_fit_xray_eye[0][1]}, "
+            f"X Offset {tomo_fit_xray_eye[0][2]}, "
+            f"Y Amplitude {tomo_fit_xray_eye[1][0]}, "
+            f"Y Phase {tomo_fit_xray_eye[1][1]}, "
+            f"Y Offset {tomo_fit_xray_eye[1][2]}"
+        )
+
+    def lamni_compute_additional_correction_xeye_mu(self, angle):
+        """Compute sinusoidal correction from the X-ray eye fit for the given angle."""
+        tomo_fit_xray_eye = self.client.get_global_var("tomo_fit_xray_eye")
+        if tomo_fit_xray_eye is None:
+            print("Not applying any additional correction. No x-ray eye data available.\n")
+            return (0, 0)
+
+        # x amp, phase, offset, y amp, phase, offset
+        #  0 0    0 1    0 2     1 0    1 1    1 2
+        correction_x = (
+            tomo_fit_xray_eye[0][0] * np.sin(np.radians(angle) + tomo_fit_xray_eye[0][1])
+            + tomo_fit_xray_eye[0][2]
+        ) / 1000
+        correction_y = (
+            tomo_fit_xray_eye[1][0] * np.sin(np.radians(angle) + tomo_fit_xray_eye[1][1])
+            + tomo_fit_xray_eye[1][2]
+        ) / 1000
+
+        print(f"Xeye correction x {correction_x}, y {correction_y} for angle {angle}\n")
+        return (correction_x, correction_y)
+
+    # ------------------------------------------------------------------
+    # Additional lookup-table corrections (iteration 1 and 2)
+    # ------------------------------------------------------------------
+
+    def read_additional_correction(self, correction_file: str):
+        self.corr_pos_x, self.corr_pos_y, self.corr_angle = self._read_correction_file_xy(
+            correction_file
+        )
+
+    def read_additional_correction_2(self, correction_file: str):
+        self.corr_pos_x_2, self.corr_pos_y_2, self.corr_angle_2 = self._read_correction_file_xy(
+            correction_file
+        )
+
+    def _read_correction_file_xy(self, correction_file: str):
+        """Parse a correction file that contains corr_pos_x, corr_pos_y and corr_angle entries."""
+        with open(correction_file, "r") as f:
+            num_elements = f.readline()
+            int_num_elements = int(num_elements.split(" ")[2])
+            print(int_num_elements)
+            corr_pos_x = []
+            corr_pos_y = []
+            corr_angle = []
+            for j in range(0, int_num_elements * 3):
+                line = f.readline()
+                value = line.split(" ")[2]
+                name = line.split(" ")[0].split("[")[0]
+                if name == "corr_pos_x":
+                    corr_pos_x.append(float(value) / 1000)
+                elif name == "corr_pos_y":
+                    corr_pos_y.append(float(value) / 1000)
+                elif name == "corr_angle":
+                    corr_angle.append(float(value))
+        return corr_pos_x, corr_pos_y, corr_angle
+
+    def compute_additional_correction(self, angle):
+        return self._compute_correction_xy(
+            angle, self.corr_pos_x, self.corr_pos_y, self.corr_angle, label="1"
+        )
+
+    def compute_additional_correction_2(self, angle):
+        return self._compute_correction_xy(
+            angle, self.corr_pos_x_2, self.corr_pos_y_2, self.corr_angle_2, label="2"
+        )
+
+    def _compute_correction_xy(self, angle, corr_pos_x, corr_pos_y, corr_angle, label=""):
+        """Find the correction for the closest angle in the lookup table."""
+        if not corr_pos_x:
+            print(f"Not applying additional correction {label}. No data available.\n")
+            return (0, 0)
+
+        shift_x = corr_pos_x[0]
+        shift_y = corr_pos_y[0]
+        angledelta = np.fabs(corr_angle[0] - angle)
+
+        for j in range(1, len(corr_pos_x)):
+            newangledelta = np.fabs(corr_angle[j] - angle)
+            if newangledelta < angledelta:
+                shift_x = corr_pos_x[j]
+                shift_y = corr_pos_y[j]
+                angledelta = newangledelta
+
+        if shift_x == 0 and angle < corr_angle[0]:
+            shift_x = corr_pos_x[0]
+            shift_y = corr_pos_y[0]
+
+        if shift_x == 0 and angle > corr_angle[-1]:
+            shift_x = corr_pos_x[-1]
+            shift_y = corr_pos_y[-1]
+
+        print(f"Additional correction shifts {label}: {shift_x} {shift_y}")
+        return (shift_x, shift_y)

csaxs_bec/bec_ipython_client/plugins/LamNI/extra_tomo.py

@@ -0,0 +1,211 @@
+"""
+extra_tomo.py
+=============
+Specialist LamNI subclasses for specific experimental configurations.
+Import explicitly when needed, e.g.:
+
+    from csaxs_bec...extra_tomo import MagLamNI
+    from csaxs_bec...extra_tomo import DataDrivenLamNI
+"""
+
+import builtins
+import datetime
+import os
+import time
+
+import h5py
+import numpy as np
+from bec_lib import bec_logger
+from bec_lib.alarm_handler import AlarmBase
+
+from .lamni import LamNI
+
+logger = bec_logger.logger
+
+if builtins.__dict__.get("bec") is not None:
+    bec = builtins.__dict__.get("bec")
+    dev = builtins.__dict__.get("dev")
+    umv = builtins.__dict__.get("umv")
+    scans = builtins.__dict__.get("scans")
+
+
+class MagLamNI(LamNI):
+    """LamNI subclass for magnetic experiments (XMCD).
+
+    Adds a slow rotation helper and allows injection of a custom
+    per-angle callback via the ``lamni_at_each_angle`` builtin.
+    """
+
+    def sub_tomo_scan(self, subtomo_number, start_angle=None):
+        super().sub_tomo_scan(subtomo_number, start_angle)
+        # self.rotate_slowly(0)
+
+    def rotate_slowly(self, angle, step_size=20):
+        """Rotate to target angle in small steps to avoid mechanical stress."""
+        current_angle = dev.lsamrot.read(cached=True)["value"]
+        steps = int(np.ceil(np.abs(current_angle - angle) / step_size)) + 1
+        for target_angle in np.linspace(current_angle, angle, steps, endpoint=True):
+            umv(dev.lsamrot, target_angle)
+            scans.lamni_move_to_scan_center(
+                self.align.tomo_fovx_offset, self.align.tomo_fovy_offset, target_angle
+            )
+
+    def _at_each_angle(self, angle: float) -> None:
+        if "lamni_at_each_angle" in builtins.__dict__:
+            # pylint: disable=undefined-variable
+            lamni_at_each_angle(self, angle)
+            return
+
+        self.tomo_scan_projection(angle)
+        self.tomo_reconstruct()
+
+
+class DataDrivenLamNI(LamNI):
+    """LamNI subclass that reads per-projection scan parameters from an HDF5 file.
+
+    Instead of a fixed FOV and step size for the whole tomogram, each
+    projection can have individual values for step size, loptz position
+    and lateral shifts, as specified in a datadriven_params.h5 file.
+    """
+
+    def __init__(self, client):
+        super().__init__(client)
+        self.tomo_data = {}
+
+    def tomo_scan(
+        self,
+        subtomo_start=1,
+        start_index=None,
+        fname="~/Data10/data_driven_config/datadriven_params.h5",
+    ):
+        """Start a data-driven tomo scan.
+
+        Args:
+            subtomo_start (int): Unused; kept for API compatibility. Use start_index to resume.
+            start_index (int, optional): Skip projections before this index. Defaults to None.
+            fname (str): Path to the HDF5 parameter file. Defaults to the standard location.
+        """
+        bec = builtins.__dict__.get("bec")
+        scans = builtins.__dict__.get("scans")
+
+        fname = os.path.expanduser(fname)
+        if not os.path.exists(fname):
+            raise FileNotFoundError(f"Could not find datadriven params file in {fname}.")
+
+        content = f"Loading tomo parameters from {fname}."
+        logger.warning(content)
+        msg = bec.logbook.LogbookMessage()
+        msg.add_text(content).add_tag(["Data_driven_file", "BEC"])
+        self.client.logbook.send_logbook_message(msg)
+
+        self._update_tomo_data_from_file(fname)
+        self._current_special_angles = self.special_angles.copy()
+
+        if subtomo_start == 1 and start_index is None:
+            self.tomo_id = self.add_sample_database(
+                self.sample_name,
+                str(datetime.date.today()),
+                bec.active_account.decode(),
+                bec.queue.next_scan_number,
+                "lamni",
+                "test additional info",
+                "BEC",
+            )
+            self.write_pdf_report()
+
+        with scans.dataset_id_on_hold:
+            self.sub_tomo_data_driven(start_index)
+
+    def sub_tomo_scan(self, subtomo_number=None, start_angle=None):
+        raise NotImplementedError(
+            "Cannot run sub_tomo_scan with DataDrivenLamNI. "
+            "Use lamni.tomo_scan(start_index=<N>) to resume instead."
+        )
+
+    def _at_each_angle(
+        self, angle=None, stepsize=None, loptz_pos=None, manual_shift_x=0, manual_shift_y=0
+    ):
+        self.manual_shift_x = manual_shift_x
+        self.manual_shift_y = manual_shift_y
+        self.tomo_shellstep = stepsize
+        if loptz_pos is not None:
+            dev.rtx.controller.feedback_disable()
+            umv(dev.loptz, loptz_pos)
+        super()._at_each_angle(angle=angle)
+
+    def sub_tomo_data_driven(self, start_index=None):
+        """Iterate over all projections defined in the loaded HDF5 parameter file."""
+        for scan_index, scan_data in enumerate(zip(*self.tomo_data.values())):
+            if start_index and scan_index < start_index:
+                continue
+            (
+                angle,
+                stepsize,
+                loptz_pos,
+                propagation_distance,
+                manual_shift_x,
+                manual_shift_y,
+                subtomo_number,
+            ) = scan_data
+            bec.metadata.update(
+                {key: float(val) for key, val in zip(self.tomo_data.keys(), scan_data)}
+            )
+            successful = False
+            error_caught = False
+            if 0 <= angle < 360.05:
+                print(f"Starting LamNI scan for angle {angle}")
+                while not successful:
+                    self._start_beam_check()
+                    if not self.special_angles:
+                        self._current_special_angles = []
+                    if self._current_special_angles:
+                        next_special_angle = self._current_special_angles[0]
+                        if np.isclose(angle, next_special_angle, atol=0.5):
+                            self._current_special_angles.pop(0)
+                            num_repeats = self.special_angle_repeats
+                    else:
+                        num_repeats = 1
+                    try:
+                        start_scan_number = bec.queue.next_scan_number
+                        for i in range(num_repeats):
+                            self._at_each_angle(
+                                float(angle),
+                                stepsize=float(stepsize),
+                                loptz_pos=float(loptz_pos),
+                                manual_shift_x=float(manual_shift_x),
+                                manual_shift_y=float(manual_shift_y),
+                            )
+                        error_caught = False
+                    except AlarmBase as exc:
+                        if exc.alarm_type == "TimeoutError":
+                            bec.queue.request_queue_reset()
+                            time.sleep(2)
+                            error_caught = True
+                        else:
+                            raise exc
+
+                    if self._was_beam_okay() and not error_caught:
+                        successful = True
+                    else:
+                        self._wait_for_beamline_checks()
+
+                end_scan_number = bec.queue.next_scan_number
+                for scan_nr in range(start_scan_number, end_scan_number):
+                    self._write_tomo_scan_number(scan_nr, angle, subtomo_number)
+
+    def _update_tomo_data_from_file(self, fname: str) -> None:
+        """Load projection parameters from the HDF5 file into self.tomo_data."""
+        with h5py.File(fname, "r") as file:
+            self.tomo_data["theta"] = np.array([*file["theta"]]).flatten()
+            self.tomo_data["stepsize"] = np.array([*file["stepsize"]]).flatten()
+            self.tomo_data["loptz"] = np.array([*file["loptz"]]).flatten()
+            self.tomo_data["propagation_distance"] = np.array(
+                [*file["relative_propagation_distance"]]
+            ).flatten()
+            self.tomo_data["manual_shift_x"] = np.array([*file["manual_shift_x"]]).flatten()
+            self.tomo_data["manual_shift_y"] = np.array([*file["manual_shift_y"]]).flatten()
+            self.tomo_data["subtomo_id"] = np.array([*file["subtomo_id"]]).flatten()
+
+        shapes = [data.shape for data in self.tomo_data.values()]
+        if len(set(shapes)) > 1:
+            raise ValueError(f"Tomo data file has entries of inconsistent lengths: {shapes}.")

csaxs_bec/bec_ipython_client/plugins/LamNI/lamni_optics_mixin.py

@@ -6,39 +6,42 @@ 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")
+umv = builtins.__dict__.get("umv")
 bec = builtins.__dict__.get("bec")
-scans = builtins.__dict__.get("scans")
 
-def umv(*args):
-    return scans.umv(*args, relative=False)
 
 class LamNIInitError(Exception):
     pass
 
 
-class LaMNIInitStagesMixin:
+class LaMNIInitStages:
+    """Handles hardware initialization and referencing of LamNI stages."""
+
+    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":
-            print("staring...")
+
+        if self.OMNYTools.yesno("Start initialization of LamNI stages. OK?"):
+            print("starting...")
             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
@@ -49,10 +52,9 @@ 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
@@ -77,14 +79,14 @@ class LaMNIInitStagesMixin:
         self.drive_axis_to_limit(dev.lsamy, "reverse")
         self.find_reference_mark(dev.lsamy)
 
-        # the dual encoder requires the reference mark to pass on both encoders
         print("Referencing lsamrot")
         self.drive_axis_to_limit(dev.lsamrot, "reverse")
         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
@@ -94,15 +96,6 @@ class LaMNIInitStagesMixin:
         print("Referencing leyey")
         self.drive_axis_to_limit(dev.leyey, "forward")
 
-        # set_lm lsamx 6 14
-        # set_lm lsamy 6 14
-        # set_lm lsamrot -3 362
-        # set_lm loptx -1 -0.2
-        # set_lm lopty 3.0 3.6
-        # set_lm loptz 82 87
-        # set_lm leyex 0 25
-        # set_lm leyey 0.5 50
-
         print("Init of Smaract stages")
         dev.losax.controller.find_reference_mark(2, 0, 1000, 1)
         time.sleep(1)
@@ -110,15 +103,6 @@ class LaMNIInitStagesMixin:
         time.sleep(1)
         dev.losax.controller.find_reference_mark(1, 0, 1000, 1)
         time.sleep(1)
-        # dev.losax.controller.find_reference_mark(3, 1, 1000, 1)
-        # time.sleep(1)
-        # dev.losax.controller.find_reference_mark(4, 1, 1000, 1)
-        # time.sleep(1)
-
-        # set_lm losax -1.5 0.25
-        # set_lm losay -2.5 4.1
-        # set_lm losaz -4.1 -0.5
-        # set_lm lcsy -1.5 5
 
         self._align_setup()
 
@@ -136,8 +120,7 @@ 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.")
@@ -176,6 +159,8 @@ class LaMNIInitStagesMixin:
 
 
 class LamNIOpticsMixin:
+    """Optics movement methods: FZP, OSA, central stop and X-ray eye."""
+
     @staticmethod
     def _get_user_param_safe(device, var):
         param = dev[device].user_parameter
@@ -190,13 +175,11 @@ class LamNIOpticsMixin:
         umv(dev.leyey, leyey_out)
 
         epics_put("XOMNYI-XEYE-ACQ:0", 2)
-        # move rotation stage to zero to avoid problems with wires
         umv(dev.lsamrot, 0)
         umv(dev.dttrz, 5854, dev.fttrz, 2395)
 
     def leye_in(self):
         bec.queue.next_dataset_number += 1
-        # move rotation stage to zero to avoid problems with wires
         umv(dev.lsamrot, 0)
         umv(dev.dttrz, 6419.677, dev.fttrz, 2959.979)
         while True:
@@ -213,15 +196,10 @@ class LamNIOpticsMixin:
     def _lfzp_in(self):
         loptx_in = self._get_user_param_safe("loptx", "in")
         lopty_in = self._get_user_param_safe("lopty", "in")
-        umv(
-            dev.loptx, loptx_in, dev.lopty, lopty_in
-        )  # for 7.2567 keV and 150 mu, 60 nm fzp, loptz 83.6000 for propagation 1.4 mm
+        umv(dev.loptx, loptx_in, dev.lopty, lopty_in)
 
     def lfzp_in(self):
-        """
-        move in the lamni zone plate.
-        This will disable rt feedback, move the FZP and re-enabled the feedback.
-        """
+        """Move in the LamNI zone plate, disabling/re-enabling RT feedback around the move."""
         if "rtx" in dev and dev.rtx.enabled:
             dev.rtx.controller.feedback_disable()
 
@@ -231,18 +209,15 @@ class LamNIOpticsMixin:
             dev.rtx.controller.feedback_enable_with_reset()
 
     def loptics_in(self):
-        """
-        Move in the lamni optics, including the FZP and the OSA.
-        """
+        """Move in the LamNI optics (FZP + OSA)."""
         self.lfzp_in()
         self.losa_in()
 
     def loptics_out(self):
-        """Move out the lamni optics"""
+        """Move out the LamNI optics."""
         if "rtx" in dev and dev.rtx.enabled:
             dev.rtx.controller.feedback_disable()
 
-        # self.lcs_out()
         self.losa_out()
         loptx_out = self._get_user_param_safe("loptx", "out")
         lopty_out = self._get_user_param_safe("lopty", "out")
@@ -253,28 +228,17 @@ class LamNIOpticsMixin:
             dev.rtx.controller.feedback_enable_with_reset()
 
     def lcs_in(self):
-        # umv lcsx -1.852 lcsy -0.095
         pass
 
     def lcs_out(self):
         umv(dev.lcsy, 3)
 
     def losa_in(self):
-        # 6.2 keV, 170 um FZP
-        # umv(dev.losax, -1.4450000, dev.losay, -0.1800)
-        # umv(dev.losaz, -1)
-        # 6.7, 170
-        # umv(dev.losax, -1.4850, dev.losay, -0.1930)
-        # umv(dev.losaz, 1.0000)
-        # 7.2, 150
         losax_in = self._get_user_param_safe("losax", "in")
         losay_in = self._get_user_param_safe("losay", "in")
         losaz_in = self._get_user_param_safe("losaz", "in")
         umv(dev.losax, losax_in, dev.losay, losay_in)
         umv(dev.losaz, losaz_in)
-        # 11 kev
-        # umv(dev.losax, -1.161000, dev.losay, -0.196)
-        # umv(dev.losaz, 1.0000)
 
     def losa_out(self):
         losay_out = self._get_user_param_safe("losay", "out")
@@ -283,11 +247,10 @@ class LamNIOpticsMixin:
         umv(dev.losay, losay_out)
 
     def lfzp_info(self, mokev_val=-1):
-
         if mokev_val == -1:
             try:
                 mokev_val = dev.mokev.readback.get()
-            except:
+            except Exception:
                 print(
                     "Device mokev does not exist. You can specify the energy in keV as an argument instead."
                 )
@@ -322,10 +285,6 @@ class LamNIOpticsMixin:
             )
 
         console.print(table)
-
-        print("OSA Information:")
-        # print(f"Current losaz %.1f\n", A[losaz])
-        # print("The OSA will collide with the sample plane at %.1f\n\n", 89.3-A[loptz])
         print(
             "The numbers presented here are for a sample in the plane of the lamni sample holder.\n"
         )

csaxs_bec/bec_ipython_client/plugins/LamNI/load_additional_correction.py

@@ -1,22 +0,0 @@
-def lamni_read_additional_correction():
-    # "additional_correction_shift"
-    # [0][] x , [1][] y, [2][] angle, [3][0] number of elements
-
-    with open("correction_lamni_um_S01405_.txt", "r") as f:
-        num_elements = f.readline()
-        int_num_elements = int(num_elements.split(" ")[2])
-        print(int_num_elements)
-        corr_pos_x = []
-        corr_pos_y = []
-        corr_angle = []
-        for j in range(0, int_num_elements * 3):
-            line = f.readline()
-            value = line.split(" ")[2]
-            name = line.split(" ")[0].split("[")[0]
-            if name == "corr_pos_x":
-                corr_pos_x.append(value)
-            elif name == "corr_pos_y":
-                corr_pos_y.append(value)
-            elif name == "corr_angle":
-                corr_angle.append(value)
-    return (corr_pos_x, corr_pos_y, corr_angle, num_elements)

csaxs_bec/bec_ipython_client/plugins/cSAXS/cSAXSDLPCA200.py

@@ -1,443 +0,0 @@
-"""
-csaxs_dlpca200.py
-=================
-BEC control script for FEMTO DLPCA-200 Variable Gain Low Noise Current Amplifiers
-connected to Galil RIO digital outputs.
-
-DLPCA-200 Remote Control (datasheet page 4)
--------------------------------------------
-Sub-D pin → function:
-  Pin 10  →  gain LSB   (digital out channel, index 0 in bit-tuple)
-  Pin 11  →  gain MID   (digital out channel, index 1 in bit-tuple)
-  Pin 12  →  gain MSB   (digital out channel, index 2 in bit-tuple)
-  Pin 13  →  coupling   LOW = AC,  HIGH = DC
-  Pin 14  →  speed mode HIGH = low noise (Pin14=1), LOW = high speed (Pin14=0)
-
-Gain truth table (MSB, MID, LSB):
-  0,0,0  →  low-noise: 1e3   high-speed: 1e5
-  0,0,1  →  low-noise: 1e4   high-speed: 1e6
-  0,1,0  →  low-noise: 1e5   high-speed: 1e7
-  0,1,1  →  low-noise: 1e6   high-speed: 1e8
-  1,0,0  →  low-noise: 1e7   high-speed: 1e9
-  1,0,1  →  low-noise: 1e8   high-speed: 1e10
-  1,1,0  →  low-noise: 1e9   high-speed: 1e11
-
-Strategy: prefer low-noise mode (1e3–1e9). For 1e10 and 1e11,
-automatically fall back to high-speed mode.
-
-Device wiring example (galilrioesxbox):
-  bpm4:  Pin10→ch0, Pin11→ch1, Pin12→ch2, Pin13→ch3, Pin14→ch4
-  bim:   Pin10→ch6, Pin11→ch7, Pin12→ch8, Pin13→ch9, Pin14→ch10
-
-Usage examples
---------------
-  csaxs_amp = cSAXSDLPCA200(client)
-
-  csaxs_amp.set_gain("bpm4", 1e7)          # low-noise if possible
-  csaxs_amp.set_gain("bim",  1e10)         # auto high-speed
-  csaxs_amp.set_coupling("bpm4", "DC")
-  csaxs_amp.set_coupling("bim",  "AC")
-  csaxs_amp.info("bpm4")                   # print current settings
-  csaxs_amp.info_all()                     # print all configured amplifiers
-"""
-
-import builtins
-
-from bec_lib import bec_logger
-
-logger = bec_logger.logger
-
-bec = builtins.__dict__.get("bec")
-dev = builtins.__dict__.get("dev")
-
-
-# ---------------------------------------------------------------------------
-# Amplifier registry
-# ---------------------------------------------------------------------------
-# Each entry describes one DLPCA-200 amplifier connected to a Galil RIO.
-#
-# Keys inside "channels":
-#   gain_lsb   → digital output channel number wired to DLPCA-200 Pin 10
-#   gain_mid   → digital output channel number wired to DLPCA-200 Pin 11
-#   gain_msb   → digital output channel number wired to DLPCA-200 Pin 12
-#   coupling   → digital output channel number wired to DLPCA-200 Pin 13
-#   speed_mode → digital output channel number wired to DLPCA-200 Pin 14
-#
-# To add a new amplifier, simply extend this dict.
-# ---------------------------------------------------------------------------
-DLPCA200_AMPLIFIER_CONFIG: dict[str, dict] = {
-    "bpm4": {
-        "rio_device": "galilrioesxbox",
-        "description": "Beam Position Monitor 4 current amplifier",
-        "channels": {
-            "gain_lsb":   0,   # Pin 10 → Galil ch0
-            "gain_mid":   1,   # Pin 11 → Galil ch1
-            "gain_msb":   2,   # Pin 12 → Galil ch2
-            "coupling":   3,   # Pin 13 → Galil ch3
-            "speed_mode": 4,   # Pin 14 → Galil ch4
-        },
-    },
-    "bim": {
-        "rio_device": "galilrioesxbox",
-        "description": "Beam Intensity Monitor current amplifier",
-        "channels": {
-            "gain_lsb":   6,   # Pin 10 → Galil ch6
-            "gain_mid":   7,   # Pin 11 → Galil ch7
-            "gain_msb":   8,   # Pin 12 → Galil ch8
-            "coupling":   9,   # Pin 13 → Galil ch9
-            "speed_mode": 10,  # Pin 14 → Galil ch10
-        },
-    },
-}
-
-# ---------------------------------------------------------------------------
-# DLPCA-200 gain encoding tables
-# ---------------------------------------------------------------------------
-# (msb, mid, lsb) → gain in V/A
-_GAIN_BITS_LOW_NOISE: dict[tuple, int] = {
-    (0, 0, 0): int(1e3),
-    (0, 0, 1): int(1e4),
-    (0, 1, 0): int(1e5),
-    (0, 1, 1): int(1e6),
-    (1, 0, 0): int(1e7),
-    (1, 0, 1): int(1e8),
-    (1, 1, 0): int(1e9),
-}
-
-_GAIN_BITS_HIGH_SPEED: dict[tuple, int] = {
-    (0, 0, 0): int(1e5),
-    (0, 0, 1): int(1e6),
-    (0, 1, 0): int(1e7),
-    (0, 1, 1): int(1e8),
-    (1, 0, 0): int(1e9),
-    (1, 0, 1): int(1e10),
-    (1, 1, 0): int(1e11),
-}
-
-# Inverse maps: gain → (msb, mid, lsb, low_noise_flag)
-# low_noise_flag: True = Pin14 HIGH, False = Pin14 LOW
-_GAIN_TO_BITS: dict[int, tuple] = {}
-for _bits, _gain in _GAIN_BITS_LOW_NOISE.items():
-    _GAIN_TO_BITS[_gain] = (*_bits, True)
-for _bits, _gain in _GAIN_BITS_HIGH_SPEED.items():
-    if _gain not in _GAIN_TO_BITS:          # low-noise takes priority
-        _GAIN_TO_BITS[_gain] = (*_bits, False)
-
-VALID_GAINS = sorted(_GAIN_TO_BITS.keys())
-
-
-class cSAXSDLPCA200Error(Exception):
-    pass
-
-
-class cSAXSDLPCA200:
-    """
-    Control class for FEMTO DLPCA-200 current amplifiers connected via Galil RIO
-    digital outputs in a BEC environment.
-
-    Supports:
-    - Forward control: set_gain(), set_coupling()
-    - Readback reporting: info(), info_all(), read_settings()
-    - Robust error handling and logging following cSAXS conventions.
-    """
-
-    TAG = "[DLPCA200]"
-
-    def __init__(self, client, config: dict | None = None) -> None:
-        """
-        Parameters
-        ----------
-        client : BEC client object (passed through for future use)
-        config : optional override for DLPCA200_AMPLIFIER_CONFIG.
-                 Falls back to the module-level dict if not provided.
-        """
-        self.client = client
-        self._config: dict[str, dict] = config if config is not None else DLPCA200_AMPLIFIER_CONFIG
-
-    # ------------------------------------------------------------------
-    # Internal helpers
-    # ------------------------------------------------------------------
-
-    def _require_dev(self) -> None:
-        if dev is None:
-            raise cSAXSDLPCA200Error(
-                f"{self.TAG} BEC 'dev' namespace is not available in this session."
-            )
-
-    def _get_cfg(self, amp_name: str) -> dict:
-        """Return config dict for a named amplifier, raising on unknown names."""
-        if amp_name not in self._config:
-            known = ", ".join(sorted(self._config.keys()))
-            raise cSAXSDLPCA200Error(
-                f"{self.TAG} Unknown amplifier '{amp_name}'. Known: [{known}]"
-            )
-        return self._config[amp_name]
-
-    def _get_rio(self, amp_name: str):
-        """Return the live RIO device object for a given amplifier."""
-        self._require_dev()
-        cfg = self._get_cfg(amp_name)
-        rio_name = cfg["rio_device"]
-        try:
-            rio = getattr(dev, rio_name)
-        except AttributeError:
-            raise cSAXSDLPCA200Error(
-                f"{self.TAG} RIO device '{rio_name}' not found in BEC 'dev'."
-            )
-        return rio
-
-    def _dout_get(self, rio, ch: int) -> int:
-        """Read one digital output channel (returns 0 or 1)."""
-        attr = getattr(rio.digital_out, f"ch{ch}")
-        val = attr.get()
-        return int(val)
-
-    def _dout_set(self, rio, ch: int, value: bool) -> None:
-        """Write one digital output channel (True=HIGH=1, False=LOW=0)."""
-        attr = getattr(rio.digital_out, f"ch{ch}")
-        attr.set(value)
-
-    def _read_gain_bits(self, amp_name: str) -> tuple[int, int, int, int]:
-        """
-        Read current gain bit-state from hardware.
-
-        Returns
-        -------
-        (msb, mid, lsb, speed_mode)
-            speed_mode: 1 = low-noise (Pin14=HIGH), 0 = high-speed (Pin14=LOW)
-        """
-        rio = self._get_rio(amp_name)
-        ch = self._get_cfg(amp_name)["channels"]
-        msb        = self._dout_get(rio, ch["gain_msb"])
-        mid        = self._dout_get(rio, ch["gain_mid"])
-        lsb        = self._dout_get(rio, ch["gain_lsb"])
-        speed_mode = self._dout_get(rio, ch["speed_mode"])
-        return msb, mid, lsb, speed_mode
-
-    def _decode_gain(self, msb: int, mid: int, lsb: int, speed_mode: int) -> int | None:
-        """
-        Decode hardware bit-state into gain value (V/A).
-
-        speed_mode=1 → low-noise table, speed_mode=0 → high-speed table.
-        Returns None if the bit combination is not in the table.
-        """
-        bits = (msb, mid, lsb)
-        if speed_mode:
-            return _GAIN_BITS_LOW_NOISE.get(bits)
-        else:
-            return _GAIN_BITS_HIGH_SPEED.get(bits)
-
-    # ------------------------------------------------------------------
-    # Public API – control
-    # ------------------------------------------------------------------
-
-    def set_gain(self, amp_name: str, gain: float, force_high_speed: bool = False) -> None:
-        """
-        Set the transimpedance gain of a DLPCA-200 amplifier.
-
-        The method automatically selects low-noise mode (Pin14=HIGH) whenever
-        the requested gain is achievable in low-noise mode (1e3 – 1e9 V/A).
-        For gains of 1e10 and 1e11 V/A, high-speed mode is used automatically.
-
-        Parameters
-        ----------
-        amp_name : str
-            Amplifier name as defined in DLPCA200_AMPLIFIER_CONFIG (e.g. "bpm4").
-        gain : float or int
-            Target gain in V/A. Must be one of:
-            1e3, 1e4, 1e5, 1e6, 1e7, 1e8, 1e9, 1e10, 1e11.
-        force_high_speed : bool, optional
-            If True, force high-speed (low-noise=False) mode even for gains
-            below 1e10. Default: False (prefer low-noise).
-
-        Examples
-        --------
-        csaxs_amp.set_gain("bpm4", 1e7)          # low-noise mode (automatic)
-        csaxs_amp.set_gain("bim",  1e10)         # high-speed mode (automatic)
-        csaxs_amp.set_gain("bpm4", 1e7, force_high_speed=True)  # override to high-speed
-        """
-        gain_int = int(gain)
-        if gain_int not in _GAIN_TO_BITS:
-            valid_str = ", ".join(f"1e{int(round(__import__('math').log10(g)))}" for g in VALID_GAINS)
-            raise cSAXSDLPCA200Error(
-                f"{self.TAG} Invalid gain {gain:.2e} V/A for '{amp_name}'. "
-                f"Valid values: {valid_str}"
-            )
-
-        msb, mid, lsb, low_noise_preferred = _GAIN_TO_BITS[gain_int]
-
-        # Apply force_high_speed override
-        if force_high_speed and low_noise_preferred:
-            # Check if this gain is achievable in high-speed mode
-            hs_entry = next(
-                (bits for bits, g in _GAIN_BITS_HIGH_SPEED.items() if g == gain_int), None
-            )
-            if hs_entry is None:
-                raise cSAXSDLPCA200Error(
-                    f"{self.TAG} Gain {gain:.2e} V/A is not achievable in high-speed mode "
-                    f"for '{amp_name}'."
-                )
-            msb, mid, lsb = hs_entry
-            low_noise_preferred = False
-
-        use_low_noise = low_noise_preferred and not force_high_speed
-
-        try:
-            rio = self._get_rio(amp_name)
-            ch  = self._get_cfg(amp_name)["channels"]
-
-            self._dout_set(rio, ch["gain_msb"],   bool(msb))
-            self._dout_set(rio, ch["gain_mid"],   bool(mid))
-            self._dout_set(rio, ch["gain_lsb"],   bool(lsb))
-            self._dout_set(rio, ch["speed_mode"], use_low_noise)  # True=low-noise
-
-            mode_str = "low-noise" if use_low_noise else "high-speed"
-            logger.info(
-                f"{self.TAG} [{amp_name}] gain set to {gain_int:.2e} V/A "
-                f"({mode_str} mode, bits MSB={msb} MID={mid} LSB={lsb})"
-            )
-            print(
-                f"{amp_name}: gain → {gain_int:.2e} V/A  [{mode_str}]  "
-                f"(bits: MSB={msb} MID={mid} LSB={lsb})"
-            )
-
-        except cSAXSDLPCA200Error:
-            raise
-        except Exception as exc:
-            raise cSAXSDLPCA200Error(
-                f"{self.TAG} Failed to set gain on '{amp_name}': {exc}"
-            ) from exc
-
-    def set_coupling(self, amp_name: str, coupling: str) -> None:
-        """
-        Set AC or DC coupling on a DLPCA-200 amplifier.
-
-        Parameters
-        ----------
-        amp_name : str
-            Amplifier name (e.g. "bpm4", "bim").
-        coupling : str
-            "AC" or "DC" (case-insensitive).
-            DC → Pin13 HIGH,  AC → Pin13 LOW.
-
-        Examples
-        --------
-        csaxs_amp.set_coupling("bpm4", "DC")
-        csaxs_amp.set_coupling("bim",  "AC")
-        """
-        coupling_upper = coupling.strip().upper()
-        if coupling_upper not in ("AC", "DC"):
-            raise cSAXSDLPCA200Error(
-                f"{self.TAG} Invalid coupling '{coupling}' for '{amp_name}'. "
-                f"Use 'AC' or 'DC'."
-            )
-
-        pin13_high = coupling_upper == "DC"
-
-        try:
-            rio = self._get_rio(amp_name)
-            ch  = self._get_cfg(amp_name)["channels"]
-            self._dout_set(rio, ch["coupling"], pin13_high)
-
-            logger.info(f"{self.TAG} [{amp_name}] coupling set to {coupling_upper}")
-            print(f"{amp_name}: coupling → {coupling_upper}")
-
-        except cSAXSDLPCA200Error:
-            raise
-        except Exception as exc:
-            raise cSAXSDLPCA200Error(
-                f"{self.TAG} Failed to set coupling on '{amp_name}': {exc}"
-            ) from exc
-
-    # ------------------------------------------------------------------
-    # Public API – readback / reporting
-    # ------------------------------------------------------------------
-
-    def read_settings(self, amp_name: str) -> dict:
-        """
-        Read back the current settings from hardware digital outputs.
-
-        Returns
-        -------
-        dict with keys:
-            "amp_name"   : str
-            "gain"       : int or None    – gain in V/A (None if unknown bit pattern)
-            "mode"       : str            – "low-noise" or "high-speed"
-            "coupling"   : str            – "AC" or "DC"
-            "bits"       : dict           – raw bit values {msb, mid, lsb, speed_mode, coupling}
-        """
-        rio = self._get_rio(amp_name)
-        ch  = self._get_cfg(amp_name)["channels"]
-
-        msb        = self._dout_get(rio, ch["gain_msb"])
-        mid        = self._dout_get(rio, ch["gain_mid"])
-        lsb        = self._dout_get(rio, ch["gain_lsb"])
-        speed_mode = self._dout_get(rio, ch["speed_mode"])
-        coupling_bit = self._dout_get(rio, ch["coupling"])
-
-        gain = self._decode_gain(msb, mid, lsb, speed_mode)
-        mode = "low-noise" if speed_mode else "high-speed"
-        coupling = "DC" if coupling_bit else "AC"
-
-        return {
-            "amp_name": amp_name,
-            "gain":     gain,
-            "mode":     mode,
-            "coupling": coupling,
-            "bits": {
-                "msb":        msb,
-                "mid":        mid,
-                "lsb":        lsb,
-                "speed_mode": speed_mode,
-                "coupling":   coupling_bit,
-            },
-        }
-
-    def info(self, amp_name: str) -> None:
-        """
-        Print a plain summary of the current settings for one amplifier.
-
-        Example output
-        --------------
-        Amplifier   : bpm4
-        Description : Beam Position Monitor 4 current amplifier
-        RIO device  : galilrioesxbox
-        Gain        : 1.00e+07 V/A
-        Mode        : low-noise
-        Coupling    : DC
-        Raw bits    : MSB=1 MID=0 LSB=0  speed=1 coup=1
-        """
-        cfg = self._get_cfg(amp_name)
-
-        try:
-            s = self.read_settings(amp_name)
-        except Exception as exc:
-            print(f"{self.TAG} [{amp_name}] Could not read settings: {exc}")
-            return
-
-        gain_str = (
-            f"{s['gain']:.2e} V/A" if s["gain"] is not None else "UNKNOWN (invalid bit pattern)"
-        )
-        bits = s["bits"]
-
-        print(f"  {'Amplifier':<12}: {amp_name}")
-        print(f"  {'Description':<12}: {cfg.get('description', '')}")
-        print(f"  {'RIO device':<12}: {cfg['rio_device']}")
-        print(f"  {'Gain':<12}: {gain_str}")
-        print(f"  {'Mode':<12}: {s['mode']}")
-        print(f"  {'Coupling':<12}: {s['coupling']}")
-        print(f"  {'Raw bits':<12}: MSB={bits['msb']} MID={bits['mid']} LSB={bits['lsb']}  speed={bits['speed_mode']} coup={bits['coupling']}")
-
-    def info_all(self) -> None:
-        """
-        Print a plain summary for ALL configured amplifiers.
-        """
-        print("\nDLPCA-200 Amplifier Status Report")
-        print("-" * 40)
-        for amp_name in sorted(self._config.keys()):
-            self.info(amp_name)
-            print()
-
-    def list_amplifiers(self) -> list[str]:
-        """Return sorted list of configured amplifier names."""
-        return sorted(self._config.keys())

csaxs_bec/bec_ipython_client/plugins/cSAXS/filter_transmission.py

@@ -41,10 +41,8 @@ import builtins
 if builtins.__dict__.get("bec") is not None:
     bec = builtins.__dict__.get("bec")
     dev = builtins.__dict__.get("dev")
-    scans = builtins.__dict__.get("scans")
-
-def umv(*args):
-    return scans.umv(*args, relative=False)
+    umv = builtins.__dict__.get("umv")
+    umvr = builtins.__dict__.get("umvr")
 
 class cSAXSFilterTransmission:
     """

csaxs_bec/bec_ipython_client/plugins/cSAXS/smaract.py

@@ -8,14 +8,11 @@ from bec_lib import bec_logger
 logger = bec_logger.logger
 
 # Pull BEC globals if present
-if builtins.__dict__.get("bec") is not None:
-    bec = builtins.__dict__.get("bec")
-    dev = builtins.__dict__.get("dev")
-    scans = builtins.__dict__.get("scans")
+bec = builtins.__dict__.get("bec")
+dev = builtins.__dict__.get("dev")
+umv = builtins.__dict__.get("umv")
+umvr = builtins.__dict__.get("umvr")
 
-def umv(*args):
-    return scans.umv(*args, relative=False)
-    
 
 class cSAXSInitSmaractStagesError(Exception):
     pass
@@ -386,6 +383,7 @@ class cSAXSInitSmaractStages:
         if not self._yesno("Proceed with the motions listed above?", "y"):
             logger.info("[cSAXS] Motion to initial position aborted by user.")
             return
+
         # --- Execution phase (SIMULTANEOUS MOTION) ---
         if umv is None:
             logger.error("[cSAXS] 'umv' is not available in this session.")

csaxs_bec/bec_ipython_client/plugins/flomni/flomni.py

@@ -22,10 +22,8 @@ logger = bec_logger.logger
 if builtins.__dict__.get("bec") is not None:
     bec = builtins.__dict__.get("bec")
     dev = builtins.__dict__.get("dev")
-    scans = builtins.__dict__.get("scans")
-
-def umv(*args):
-    return scans.umv(*args, relative=False)
+    umv = builtins.__dict__.get("umv")
+    umvr = builtins.__dict__.get("umvr")
 
 
 class FlomniToolsError(Exception):
@@ -37,32 +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/bec_ipython_client/plugins/flomni/gui_tools.py

@@ -7,10 +7,8 @@ from bec_widgets.cli.client import BECDockArea
 if builtins.__dict__.get("bec") is not None:
     bec = builtins.__dict__.get("bec")
     dev = builtins.__dict__.get("dev")
-    scans = builtins.__dict__.get("scans")
-
-def umv(*args):
-    return scans.umv(*args, relative=False)
+    umv = builtins.__dict__.get("umv")
+    umvr = builtins.__dict__.get("umvr")
 
 
 class flomniGuiToolsError(Exception):

csaxs_bec/bec_ipython_client/plugins/flomni/x_ray_eye_align.py

@@ -13,10 +13,8 @@ logger = bec_logger.logger
 # import builtins to avoid linter errors
 bec = builtins.__dict__.get("bec")
 dev = builtins.__dict__.get("dev")
-scans = builtins.__dict__.get("scans")
-
-def umv(*args):
-    return scans.umv(*args, relative=False)
+umv = builtins.__dict__.get("umv")
+umvr = builtins.__dict__.get("umvr")
 
 if TYPE_CHECKING:
     from bec_ipython_client.plugins.flomni import Flomni

csaxs_bec/bec_ipython_client/plugins/omny/gui_tools.py

@@ -7,10 +7,8 @@ from bec_widgets.cli.client import BECDockArea
 if builtins.__dict__.get("bec") is not None:
     bec = builtins.__dict__.get("bec")
     dev = builtins.__dict__.get("dev")
-    scans = builtins.__dict__.get("scans")
-
-def umv(*args):
-    return scans.umv(*args, relative=False)
+    umv = builtins.__dict__.get("umv")
+    umvr = builtins.__dict__.get("umvr")
 
 
 class OMNYGuiToolsError(Exception):

csaxs_bec/bec_ipython_client/plugins/omny/omny.py

@@ -27,10 +27,9 @@ logger = bec_logger.logger
 if builtins.__dict__.get("bec") is not None:
     bec = builtins.__dict__.get("bec")
     dev = builtins.__dict__.get("dev")
-    scans = builtins.__dict__.get("scans")
+    umv = builtins.__dict__.get("umv")
+    umvr = builtins.__dict__.get("umvr")
 
-def umv(*args):
-    return scans.umv(*args, relative=False)
 
 class OMNYInitError(Exception):
     pass

csaxs_bec/bec_ipython_client/plugins/omny/omny_general_tools.py

@@ -16,10 +16,8 @@ from rich.table import Table
 if builtins.__dict__.get("bec") is not None:
     bec = builtins.__dict__.get("bec")
     dev = builtins.__dict__.get("dev")
-    scans = builtins.__dict__.get("scans")
-
-def umv(*args):
-    return scans.umv(*args, relative=False)
+    umv = builtins.__dict__.get("umv")
+    umvr = builtins.__dict__.get("umvr")
 
 
 class OMNYToolsError(Exception):

csaxs_bec/bec_ipython_client/plugins/omny/omny_sample_transfer_mixin.py

@@ -16,10 +16,8 @@ from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_get, epics_put, fsh
 if builtins.__dict__.get("bec") is not None:
     bec = builtins.__dict__.get("bec")
     dev = builtins.__dict__.get("dev")
-    scans = builtins.__dict__.get("scans")
-
-def umv(*args):
-    return scans.umv(*args, relative=False)
+    umv = builtins.__dict__.get("umv")
+    umvr = builtins.__dict__.get("umvr")
 
 
 class OMNYTransferError(Exception):

csaxs_bec/bec_ipython_client/plugins/omny/x_ray_eye_align.py

@@ -13,10 +13,8 @@ logger = bec_logger.logger
 # import builtins to avoid linter errors
 bec = builtins.__dict__.get("bec")
 dev = builtins.__dict__.get("dev")
-scans = builtins.__dict__.get("scans")
-
-def umv(*args):
-    return scans.umv(*args, relative=False)
+umv = builtins.__dict__.get("umv")
+umvr = builtins.__dict__.get("umvr")
 
 if TYPE_CHECKING:
     from bec_ipython_client.plugins.omny import OMNY

csaxs_bec/bec_ipython_client/startup/post_startup.py

@@ -30,74 +30,29 @@ logger = bec_logger.logger
 
 logger.info("Using the cSAXS startup script.")
 
+# pylint: disable=import-error
+_args = _main_dict["args"]
+
+_session_name = "cSAXS"
+if _args.session.lower() == "lamni":
+    from csaxs_bec.bec_ipython_client.plugins.cSAXS import *
+    from csaxs_bec.bec_ipython_client.plugins.LamNI import *
+
+    _session_name = "LamNI"
+    lamni = LamNI(bec)
+    logger.success("LamNI session loaded.")
+
+elif _args.session.lower() == "csaxs":
+    print("Loading cSAXS session")
+    from csaxs_bec.bec_ipython_client.plugins.cSAXS import *
+
+    logger.success("cSAXS session loaded.")
 
 from csaxs_bec.bec_ipython_client.plugins.tool_box.debug_tools import DebugTools
 
 debug = DebugTools()
 logger.success("Debug tools loaded. Use 'debug' to access them.")
 
-# pylint: disable=import-error
-_args = _main_dict["args"]
-
-_session_name = "cSAXS"
-
-print("Loading cSAXS session")
-from csaxs_bec.bec_ipython_client.plugins.cSAXS.cSAXS import cSAXS
-csaxs = cSAXS(bec)
-logger.success("cSAXS session loaded.")
-
-
-if _args.session.lower() == "lamni":
-    from csaxs_bec.bec_ipython_client.plugins.LamNI import LamNI
-
-    _session_name = "LamNI"
-    lamni = LamNI(bec)
-    logger.success("LamNI session loaded.")
-    print(r"""
-    ██████╗ ███████╗ ██████╗     ██╗      █████╗ ███╗   ███╗███╗   ██╗██╗
-    ██╔══██╗██╔════╝██╔════╝     ██║     ██╔══██╗████╗ ████║████╗  ██║██║
-    ██████╔╝█████╗  ██║          ██║     ███████║██╔████╔██║██╔██╗ ██║██║
-    ██╔══██╗██╔══╝  ██║          ██║     ██╔══██║██║╚██╔╝██║██║╚██╗██║██║
-    ██████╔╝███████╗╚██████╗     ███████╗██║  ██║██║ ╚═╝ ██║██║ ╚████║██║
-    ╚═════╝ ╚══════╝ ╚═════╝     ╚══════╝╚═╝  ╚═╝╚═╝     ╚═╝╚═╝  ╚═══╝╚═╝
-                                                                            
-                                B E C   L a m N I
-    """)
-
-elif _args.session.lower() == "omny":
-    from csaxs_bec.bec_ipython_client.plugins.flomni import OMNY
-
-    _session_name = "OMNY"
-    omny = OMNY(bec)
-    logger.success("OMNY session loaded.")
-    print(r"""
-    ██████╗ ███████╗ ██████╗      ██████╗ ███╗   ███╗███╗   ██╗██╗   ██╗
-    ██╔══██╗██╔════╝██╔════╝     ██╔═══██╗████╗ ████║████╗  ██║╚██╗ ██╔╝
-    ██████╔╝█████╗  ██║          ██║   ██║██╔████╔██║██╔██╗ ██║ ╚████╔╝ 
-    ██╔══██╗██╔══╝  ██║          ██║   ██║██║╚██╔╝██║██║╚██╗██║  ╚██╔╝  
-    ██████╔╝███████╗╚██████╗     ╚██████╔╝██║ ╚═╝ ██║██║ ╚████║   ██║   
-    ╚═════╝ ╚══════╝ ╚═════╝      ╚═════╝ ╚═╝     ╚═╝╚═╝  ╚═══╝   ╚═╝   
-                                                                        
-                                B E C   O M N Y
-    """)
-
-elif _args.session.lower() == "flomni":
-    from csaxs_bec.bec_ipython_client.plugins.flomni import Flomni
-
-    _session_name = "flomni"
-    flomni = Flomni(bec)
-    logger.success("flomni session loaded.")
-    print(r"""
-    ██████╗ ███████╗ ██████╗     ███████╗██╗      ██████╗ ███╗   ███╗███╗   ██╗██╗
-    ██╔══██╗██╔════╝██╔════╝     ██╔════╝██║     ██╔═══██╗████╗ ████║████╗  ██║██║
-    ██████╔╝█████╗  ██║          █████╗  ██║     ██║   ██║██╔████╔██║██╔██╗ ██║██║
-    ██╔══██╗██╔══╝  ██║          ██╔══╝  ██║     ██║   ██║██║╚██╔╝██║██║╚██╗██║██║
-    ██████╔╝███████╗╚██████╗     ██║     ███████╗╚██████╔╝██║ ╚═╝ ██║██║ ╚████║██║
-    ╚═════╝ ╚══════╝ ╚═════╝     ╚═╝     ╚══════╝ ╚═════╝ ╚═╝     ╚═╝╚═╝  ╚═══╝╚═╝
-                                                                                    
-                                B E C   f l O M N I
-    """)
-
 
 # SETUP BEAMLINE INFO
 from bec_ipython_client.plugins.SLS.sls_info import OperatorInfo, SLSInfo

csaxs_bec/device_configs/bl_detectors.yaml

@@ -9,27 +9,27 @@ 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
+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
-#   deviceConfig:
-#     camera_id: 201
-#     bits_per_pixel: 24
-#     m_n_colormode: 1
-#     live_mode: True
-#   onFailure: raise
-#   enabled: true
-#   readoutPriority: async
-#   softwareTrigger: True
+ids_cam:
+  description: IDS camera for live image acquisition
+  deviceClass: csaxs_bec.devices.ids_cameras.IDSCamera
+  deviceConfig:
+    camera_id: 201
+    bits_per_pixel: 24
+    m_n_colormode: 1
+    live_mode: True
+  onFailure: raise
+  enabled: true
+  readoutPriority: async
+  softwareTrigger: True
 

csaxs_bec/device_configs/bl_general.yaml

@@ -1,25 +0,0 @@
-############################################################
-##################### EPS ##################################
-############################################################
-x12saEPS:
-  description: X12SA EPS info and control
-  deviceClass: csaxs_bec.devices.epics.eps.EPS
-  deviceConfig: {}
-  enabled: true
-  onFailure: buffer
-  readOnly: false
-  readoutPriority: baseline
-############################################################
-##################### GalilRIO #############################
-############################################################
-
-galilrioesxbox:
-  description: Galil RIO for remote gain switching and slow reading ES XBox
-  deviceClass: csaxs_bec.devices.omny.galil.galil_rio.GalilRIO
-  deviceConfig:
-    host: galilrioesxbox.psi.ch
-  enabled: true
-  onFailure: raise
-  readOnly: false
-  readoutPriority: baseline
-  connectionTimeout: 20

csaxs_bec/device_configs/main.yaml

@@ -1,11 +1,11 @@
 # This is the main configuration file that is
 # commented or uncommented according to the type of experiment
 
-# optics:
-#   - !include ./bl_optics_hutch.yaml
+optics:
+  - !include ./bl_optics_hutch.yaml
 
-# frontend:
-#   - !include ./bl_frontend.yaml
+frontend:
+  - !include ./bl_frontend.yaml
 
 endstation:
   - !include ./bl_endstation.yaml
@@ -16,8 +16,8 @@ detectors:
 #sastt:
 #  - !include ./sastt.yaml
 
-flomni:
- - !include ./ptycho_flomni.yaml
+#flomni:
+#  - !include ./ptycho_flomni.yaml
 
 #omny:
 #  - !include ./ptycho_omny.yaml

csaxs_bec/device_configs/ptycho_flomni.yaml

@@ -471,7 +471,7 @@ omnyfsh:
 #################### GUI Signals ###########################
 ############################################################
 omny_xray_gui:
-  description: Gui signals
+  description: Gui Epics signals
   deviceClass: csaxs_bec.devices.omny.xray_epics_gui.OMNYXRayEpicsGUI
   deviceConfig: {}
   enabled: true
@@ -486,25 +486,4 @@ calculated_signal:
     compute_method: "def just_rand():\n return 42"
   enabled: true
   readOnly: false
-  readoutPriority: baseline
-
-############################################################
-#################### OMNY Pandabox #########################
-############################################################
-omny_panda:
-  readoutPriority: async
-  deviceClass: csaxs_bec.devices.panda_box.panda_box_omny.PandaBoxOMNY
-  deviceConfig:
-    host: omny-panda.psi.ch
-    signal_alias:
-      FMC_IN.VAL1.Min: cap_voltage_fzp_y_min
-      FMC_IN.VAL1.Max: cap_voltage_fzp_y_max
-      FMC_IN.VAL1.Mean: cap_voltage_fzp_y_mean
-      FMC_IN.VAL2.Min: cap_voltage_fzp_x_min
-      FMC_IN.VAL2.Max: cap_voltage_fzp_x_max
-      FMC_IN.VAL2.Mean: cap_voltage_fzp_x_mean
-  deviceTags:
-    - detector
-  enabled: true
-  readOnly: false
-  softwareTrigger: false
+  readoutPriority: baseline

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 +64,9 @@ class RtLamniController(Controller):
         "_set_axis_velocity_maximum_speed",
         "_position_sampling_single_read",
         "_position_sampling_single_reset_and_start_sampling",
+        "show_signal_strength_interferometer",
+        "show_analog_signals",
+        "show_feedback_status",
     ]
 
     def __init__(
@@ -208,8 +213,9 @@ 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 +276,44 @@ 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 +391,48 @@ 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()

csaxs_bec/devices/panda_box/panda_box.py

@@ -1,101 +0,0 @@
-"""Module to integrate the PandaBox for cSAXS measurements."""
-
-import time
-
-from bec_lib.logger import bec_logger
-from ophyd_devices import AsyncMultiSignal, StatusBase
-from ophyd_devices.devices.panda_box.panda_box import PandaBox, PandaState
-from pandablocks.responses import FrameData
-
-logger = bec_logger.logger
-
-
-class PandaBoxCSAXS(PandaBox):
-
-    def on_init(self):
-        super().on_init()
-        self._acquisition_group = "burst"
-        self._timeout_on_completed = 10
-
-    def on_stage(self):
-        # TODO, adjust as seen fit.
-        # Adjust the acquisition group based on scan parameters if needed
-        if self.scan_info.msg.scan_type == "fly":
-            self._acquisition_group = "fly"
-        elif self.scan_info.msg.scan_type == "step":
-            if self.scan_info.msg.scan_parameters["frames_per_trigger"] == 1:
-                self._acquisition_group = "monitored"
-            else:
-                self._acquisition_group = "burst"
-
-    def on_complete(self):
-        """On complete is called after the scan is complete. We need to wait for the capture to complete before we can disarm the PandaBox."""
-
-        def _check_capture_complete():
-            captured = 0
-            start_time = time.monotonic()
-            try:
-                expected_points = int(self.scan_info.msg.num_points * self.scan_info.msg.scan_parameters.get("frames_per_trigger",1))
-                while captured < expected_points:
-                    logger.info(
-                        f"Run with captured {captured} and expected points : {expected_points}."
-                    )
-                    ret = self.send_raw("*PCAP.CAPTURED?")
-                    captured = int(ret[0].split("=")[-1])
-                    time.sleep(0.01)
-                    if (time.monotonic() - start_time) > self._timeout_on_completed:
-                        raise TimeoutError(f"Pandabox {self.name} did not complete after {self._timeout_on_completed} with points captured {captured}/{expected_points}")
-            finally:
-                self._disarm()
-
-        _check_capture_complete()
-
-        # NOTE: This utility class allows to submit a blocking function to a thread and return a status object
-        # that can be awaited for. This allows for asynchronous waiting for the capture to complete without blocking
-        # the main duty cycle of the device server. The device server knows how to handle the status object (future)
-        # and will wait for it to complete.
-        # status = self.task_handler.submit_task(_check_capture_complete, run=True)
-
-        # status_panda_state = StatusBase(obj=self)
-        # self.add_status_callback(
-        #     status, success=[PandaState.END, PandaState.DISARMED], failure=[PandaState.READY]
-        # )
-        # ret_status = status & status_panda_state
-        # self.cancel_on_stop(ret_status)
-        # return ret_status
-
-
-if __name__ == "__main__":
-    import time
-
-    panda = PandaBoxCSAXS(
-        name="omny_panda",
-        host="omny-panda.psi.ch",
-        signal_alias={
-            "FMC_IN.VAL2.Value": "alias",
-            "FMC_IN.VAL1.Min": "alias2",
-            "FMC_IN.VAL1.Max": "alias3",
-            "FMC_IN.VAL1.Mean": "alias4",
-        },
-    )
-    panda.on_connected()
-    status = StatusBase(obj=panda)
-    panda.add_status_callback(
-        status=status, success=[PandaState.DISARMED], failure=[PandaState.READY]
-    )
-    panda.stop()
-    status.wait(timeout=2)
-    panda.unstage()
-    logger.info(f"Panda connected")
-    ret = panda.stage()
-    logger.info(f"Panda staged")
-    ret = panda.pre_scan()
-    ret.wait(timeout=5)
-    logger.info(f"Panda pre scan done")
-    time.sleep(5)
-    panda.stop()
-    st = panda.complete()
-    st.wait(timeout=5)
-    logger.info(f"Measurement completed")
-    panda.unstage()
-    logger.info(f"Panda Unstaged")

csaxs_bec/devices/panda_box/panda_box_omny.py

@@ -1,102 +0,0 @@
-"""Module to integrate the PandaBox for cSAXS measurements."""
-
-import time
-
-from bec_lib.logger import bec_logger
-from ophyd_devices import AsyncMultiSignal, StatusBase
-from ophyd_devices.devices.panda_box.panda_box import PandaBox, PandaState
-from pandablocks.responses import FrameData
-
-logger = bec_logger.logger
-
-
-class PandaBoxOMNY(PandaBox):
-
-    def on_init(self):
-        super().on_init()
-        self._acquisition_group = "burst"
-        self._timeout_on_completed = 10
-
-    def on_stage(self):
-        
-        # TODO, adjust as seen fit.
-        # Adjust the acquisition group based on scan parameters if needed
-        if self.scan_info.msg.scan_type == "fly":
-            self._acquisition_group = "fly"
-        elif self.scan_info.msg.scan_type == "step":
-            if self.scan_info.msg.scan_parameters["frames_per_trigger"] == 1:
-                self._acquisition_group = "monitored"
-            else:
-                self._acquisition_group = "burst"
-
-    def on_complete(self):
-        """On complete is called after the scan is complete. We need to wait for the capture to complete before we can disarm the PandaBox."""
-
-        def _check_capture_complete():
-            captured = 0
-            start_time = time.monotonic()
-            try:
-                expected_points = int(self.scan_info.msg.num_points * self.scan_info.msg.scan_parameters.get("frames_per_trigger",1))
-                while captured < expected_points:
-                    logger.info(
-                        f"Run with captured {captured} and expected points : {expected_points}."
-                    )
-                    ret = self.send_raw("*PCAP.CAPTURED?")
-                    captured = int(ret[0].split("=")[-1])
-                    time.sleep(0.01)
-                    if (time.monotonic() - start_time) > self._timeout_on_completed:
-                        raise TimeoutError(f"Pandabox {self.name} did not complete after {self._timeout_on_completed} with points captured {captured}/{expected_points}")
-            finally:
-                self._disarm()
-
-        _check_capture_complete()
-
-        # NOTE: This utility class allows to submit a blocking function to a thread and return a status object
-        # that can be awaited for. This allows for asynchronous waiting for the capture to complete without blocking
-        # the main duty cycle of the device server. The device server knows how to handle the status object (future)
-        # and will wait for it to complete.
-        # status = self.task_handler.submit_task(_check_capture_complete, run=True)
-
-        # status_panda_state = StatusBase(obj=self)
-        # self.add_status_callback(
-        #     status, success=[PandaState.END, PandaState.DISARMED], failure=[PandaState.READY]
-        # )
-        # ret_status = status & status_panda_state
-        # self.cancel_on_stop(ret_status)
-        # return ret_status
-
-
-if __name__ == "__main__":
-    import time
-
-    panda = PandaBoxCSAXS(
-        name="omny_panda",
-        host="omny-panda.psi.ch",
-        signal_alias={
-            "FMC_IN.VAL2.Value": "alias",
-            "FMC_IN.VAL1.Min": "alias2",
-            "FMC_IN.VAL1.Max": "alias3",
-            "FMC_IN.VAL1.Mean": "alias4",
-        },
-    )
-    panda.on_connected()
-    status = StatusBase(obj=panda)
-    panda.add_status_callback(
-        status=status, success=[PandaState.DISARMED], failure=[PandaState.READY]
-    )
-    panda.stop()
-    status.wait(timeout=2)
-    panda.unstage()
-    logger.info(f"Panda connected")
-    ret = panda.stage()
-    logger.info(f"Panda staged")
-    ret = panda.pre_scan()
-    ret.wait(timeout=5)
-    logger.info(f"Panda pre scan done")
-    time.sleep(5)
-    panda.stop()
-    st = panda.complete()
-    st.wait(timeout=5)
-    logger.info(f"Measurement completed")
-    panda.unstage()
-    logger.info(f"Panda Unstaged")

csaxs_bec/scans/LamNIFermatScan.py

@@ -210,7 +210,7 @@ class LamNIFermatScan(ScanBase, LamNIMixin):
     arg_input = {}
     arg_bundle_size = {"bundle": len(arg_input), "min": None, "max": None}
 
-    def __init__(self, *args, parameter: dict = None, frames_per_trigger:int=1, exp_time:float=0,**kwargs):
+    def __init__(self, *args, parameter: dict = None, **kwargs):
         """
         A LamNI scan following Fermat's spiral.
 
@@ -230,10 +230,10 @@ class LamNIFermatScan(ScanBase, LamNIMixin):
 
         Examples:
             >>> scans.lamni_fermat_scan(fov_size=[20], step=0.5, exp_time=0.1)
-            >>> scans.lamni_fermat_scan(fov_size=[20, 25], center_x=0.02, center_y=0, shift_x=0, shift_y=0, angle=0, step=0.5, fov_circular=0, exp_time=0.1, frames_per_trigger=1)
+            >>> scans.lamni_fermat_scan(fov_size=[20, 25], center_x=0.02, center_y=0, shift_x=0, shift_y=0, angle=0, step=0.5, fov_circular=0, exp_time=0.1)
         """
 
-        super().__init__(parameter=parameter, frames_per_trigger=frames_per_trigger, exp_time=exp_time,**kwargs)
+        super().__init__(parameter=parameter, **kwargs)
         self.axis = []
         scan_kwargs = parameter.get("kwargs", {})
         self.fov_size = scan_kwargs.get("fov_size")
@@ -482,7 +482,6 @@ class LamNIFermatScan(ScanBase, LamNIMixin):
         yield from self.open_scan()
         yield from self.stage()
         yield from self.run_baseline_reading()
-        yield from self.pre_scan()
         yield from self.scan_core()
         yield from self.finalize()
         yield from self.unstage()

csaxs_bec/scans/flomni_fermat_scan.py

@@ -52,7 +52,6 @@ class FlomniFermatScan(SyncFlyScanBase):
         angle: float = None,
         corridor_size: float = 3,
         parameter: dict = None,
-        frames_per_trigger:int=1,
         **kwargs,
     ):
         """
@@ -63,8 +62,7 @@ class FlomniFermatScan(SyncFlyScanBase):
             fovy(float) [um]: Fov in the piezo plane (i.e. piezo range). Max 100 um
             cenx(float) [um]: center position in x.
             ceny(float) [um]: center position in y.
-            exp_time(float) [s]: exposure time per burst frame
-            frames_per_trigger(int) : Number of burst frames per point
+            exp_time(float) [s]: exposure time
             step(float) [um]: stepsize
             zshift(float) [um]: shift in z
             angle(float) [deg]: rotation angle (will rotate first)
@@ -73,10 +71,10 @@ class FlomniFermatScan(SyncFlyScanBase):
         Returns:
 
         Examples:
-            >>> scans.flomni_fermat_scan(fovx=20, fovy=25, cenx=0.02, ceny=0, zshift=0, angle=0, step=0.5, exp_time=0.01, frames_per_trigger=1)
+            >>> scans.flomni_fermat_scan(fovx=20, fovy=25, cenx=0.02, ceny=0, zshift=0, angle=0, step=0.5, exp_time=0.01)
         """
 
-        super().__init__(parameter=parameter, exp_time=exp_time, frames_per_trigger=frames_per_trigger, **kwargs)
+        super().__init__(parameter=parameter, exp_time=exp_time, **kwargs)
         self.show_live_table = False
         self.axis = []
         self.fovx = fovx
@@ -325,7 +323,6 @@ class FlomniFermatScan(SyncFlyScanBase):
         yield from self.stage()
         yield from self.run_baseline_reading()
         yield from self._prepare_setup_part2()
-        yield from self.pre_scan()
         yield from self.scan_core()
         yield from self.finalize()
         yield from self.unstage()

csaxs_bec/scans/omny_fermat_scan.py

@@ -51,7 +51,6 @@ class OMNYFermatScan(SyncFlyScanBase):
         angle: float = None,
         corridor_size: float = 3,
         parameter: dict = None,
-        frames_per_trigger:int=1,
         **kwargs,
     ):
         """
@@ -63,7 +62,6 @@ class OMNYFermatScan(SyncFlyScanBase):
             cenx(float) [um]: center position in x.
             ceny(float) [um]: center position in y.
             exp_time(float) [s]: exposure time
-            frames_per_trigger:int: Number of burst frames per trigger, defaults to 1.
             step(float) [um]: stepsize
             zshift(float) [um]: shift in z
             angle(float) [deg]: rotation angle (will rotate first)
@@ -75,7 +73,7 @@ class OMNYFermatScan(SyncFlyScanBase):
             >>> scans.omny_fermat_scan(fovx=20, fovy=25, cenx=10, ceny=0, zshift=0, angle=0, step=2, exp_time=0.01)
         """
 
-        super().__init__(parameter=parameter, exp_time=exp_time, frames_per_trigger=frames_per_trigger, **kwargs)
+        super().__init__(parameter=parameter, **kwargs)
         self.axis = []
         self.fovx = fovx
         self.fovy = fovy
@@ -301,7 +299,6 @@ class OMNYFermatScan(SyncFlyScanBase):
         yield from self.stage()
         yield from self.run_baseline_reading()
         yield from self._prepare_setup_part2()
-        yield from self.pre_scan()
         yield from self.scan_core()
         yield from self.finalize()
         yield from self.unstage()

docs/user/ptychography/flomni.md

@@ -193,15 +193,14 @@ The basic scan function can be called by `scans.flomni_fermat_scan()` and offers
 | fovy (float) | Fov in the piezo plane (i.e. piezo range). Max 100 um |
 | cenx (float) | center position in x |
 | ceny (float) | center position in y |
-| exp_time (float) | exposure time per frame |
-| frames_per_trigger(int) | Number of burst frames per position |
+| exp_time (float) | exposure time |
 | step (float) | stepsize |
 | zshift (float) | shift in z |
 | angle (float) | rotation angle (will rotate first) |
 | corridor_size (float) | corridor size for the corridor optimization. Default 3 um |
 
 Example:  
-`scans.flomni_fermat_scan(fovx=20, fovy=25, cenx=0.02, ceny=0, zshift=0, angle=0, step=0.5, exp_time=0.01, frames_per_trigger=1)`
+`scans.flomni_fermat_scan(fovx=20, fovy=25, cenx=0.02, ceny=0, zshift=0, angle=0, step=0.5, exp_time=0.01)`
 
 #### Overview of the alignment steps
 

docs/user/ptychography/omny.md

@@ -327,15 +327,14 @@ The basic scan function can be called by `scans.omny_fermat_scan()` and offers a
 | fovy (float) | Fov in the piezo plane (i.e. piezo range). Max 100 um |
 | cenx (float) | center position in x |
 | ceny (float) | center position in y |
-| exp_time (float) | exposure time per frame |
-| frames_per_trigger(int) | Number of burst frames per position |
+| exp_time (float) | exposure time |
 | step (float) | stepsize |
 | zshift (float) | shift in z |
 | angle (float) | rotation angle (will rotate first) |
 | corridor_size (float) | corridor size for the corridor optimization. Default 3 um |
 
 Example:  
-`scans.omny_fermat_scan(fovx=20, fovy=25, cenx=0.02, ceny=0, zshift=0, angle=0, step=0.5, exp_time=0.01, frames_per_trigger=1)`
+`scans.omny_fermat_scan(fovx=20, fovy=25, cenx=0.02, ceny=0, zshift=0, angle=0, step=0.5, exp_time=0.01)`
 
 #### Overview of the alignment steps
 

tests/tests_bec_ipython_client/test_x_ray_eye_align.py

@@ -35,16 +35,16 @@ def test_save_frame(bec_client_mock):
     lamni = LamNI(client)
     align = XrayEyeAlign(client, lamni)
     with mock.patch(
-        "csaxs_bec.bec_ipython_client.plugins.LamNI.x_ray_eye_align.epics_put"
+        "csaxs_bec.bec_ipython_client.plugins.LamNI.alignment.epics_put"
     ) as epics_put_mock:
         align.save_frame()
         epics_put_mock.assert_called_once_with("XOMNYI-XEYE-SAVFRAME:0", 1)
 
 
 def test_update_frame(bec_client_mock):
-    epics_put = "csaxs_bec.bec_ipython_client.plugins.LamNI.x_ray_eye_align.epics_put"
-    epics_get = "csaxs_bec.bec_ipython_client.plugins.LamNI.x_ray_eye_align.epics_get"
-    fshopen = "csaxs_bec.bec_ipython_client.plugins.LamNI.x_ray_eye_align.fshopen"
+    epics_put = "csaxs_bec.bec_ipython_client.plugins.LamNI.alignment.epics_put"
+    epics_get = "csaxs_bec.bec_ipython_client.plugins.LamNI.alignment.epics_get"
+    fshopen = "csaxs_bec.bec_ipython_client.plugins.LamNI.alignment.fshopen"
     client = bec_client_mock
     client.device_manager.devices.xeye = DeviceBase(
         name="xeye",