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

@@ -6,8 +6,8 @@ from rich.console import Console
 from rich.table import Table
 
 from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_put, fshclose
+from csaxs_bec.bec_ipython_client.plugins.omny.omny_general_tools import OMNYTools
 
-# import builtins to avoid linter errors
 dev = builtins.__dict__.get("dev")
 umv = builtins.__dict__.get("umv")
 bec = builtins.__dict__.get("bec")
@@ -17,26 +17,31 @@ 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
@@ -47,10 +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
@@ -75,14 +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
@@ -92,15 +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)
@@ -108,15 +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()
 
@@ -134,8 +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.")
@@ -174,6 +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
@@ -188,13 +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:
@@ -211,15 +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()
 
@@ -229,18 +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")
@@ -251,28 +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")
@@ -281,11 +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."
                 )
@@ -320,10 +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/flomni/flomni.py

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

csaxs_bec/devices/omny/galil/galil_ophyd.py

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

csaxs_bec/devices/omny/galil/galil_rio.py

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

csaxs_bec/devices/omny/galil/lgalil_ophyd.py

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

csaxs_bec/devices/omny/rt/rt_lamni_ophyd.py

@@ -11,6 +11,7 @@ from ophyd.status import wait as status_wait
 from ophyd.utils import LimitError, ReadOnlyError
 from ophyd_devices.utils.controller import Controller, threadlocked
 from ophyd_devices.utils.socket import SocketIO, SocketSignal, raise_if_disconnected
+from prettytable import PrettyTable
 
 from csaxs_bec.devices.omny.rt.rt_ophyd import RtCommunicationError, RtError
 
@@ -51,6 +52,7 @@ class RtLamniController(Controller):
     _axes_per_controller = 3
     USER_ACCESS = [
         "socket_put_and_receive",
+        "socket_put",
         "set_rotation_angle",
         "feedback_disable",
         "feedback_enable_without_reset",
@@ -62,6 +64,9 @@ 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()

tests/conftest.py

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

tests/tests_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",

tests/tests_devices/test_fupr_ophyd.py

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

tests/tests_devices/test_galil.py

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