mx-bluesky 1.5.9__py3-none-any.whl → 1.5.11__py3-none-any.whl

mx_bluesky/beamlines/i24/serial/extruder/{i24ssx_Extruder_Collect_py3v2.py → i24ssx_extruder_collect_py3v2.py}

@@ -46,7 +46,7 @@ from mx_bluesky.beamlines.i24.serial.setup_beamline import (
 )
 from mx_bluesky.beamlines.i24.serial.setup_beamline import setup_beamline as sup
 from mx_bluesky.beamlines.i24.serial.setup_beamline.setup_detector import (
-    UnknownDetectorType,
+    UnknownDetectorTypeError,
     get_detector_type,
 )
 from mx_bluesky.beamlines.i24.serial.setup_beamline.setup_zebra_plans import (
@@ -113,17 +113,17 @@ def laser_check(
     """
     SSX_LOGGER.debug(f"Laser check: {mode}")
 
-    LASER_TTL = zebra.mapping.outputs.TTL_PILATUS  # Update with dodal changes
+    laser_ttl = zebra.mapping.outputs.TTL_PILATUS  # Update with dodal changes
 
     if mode == "laseron":
         yield from bps.abs_set(
-            zebra.output.out_pvs[LASER_TTL], zebra.mapping.sources.SOFT_IN3
+            zebra.output.out_pvs[laser_ttl], zebra.mapping.sources.SOFT_IN3
         )
         yield from set_shutter_mode(zebra, "auto")
 
     if mode == "laseroff":
         yield from bps.abs_set(
-            zebra.output.out_pvs[LASER_TTL], zebra.mapping.sources.DISCONNECT
+            zebra.output.out_pvs[laser_ttl], zebra.mapping.sources.DISCONNECT
         )
         yield from set_shutter_mode(zebra, "manual")
 
@@ -230,7 +230,7 @@ def main_extruder_plan(
 
         SSX_LOGGER.debug(f"Creating the directory for the collection in {filepath}.")
 
-        caput(pv.eiger_seqID, int(caget(pv.eiger_seqID)) + 1)
+        caput(pv.eiger_seq_id, int(caget(pv.eiger_seq_id)) + 1)
         SSX_LOGGER.info(f"Eiger quickshot setup: filepath {filepath}")
         SSX_LOGGER.info(f"Eiger quickshot setup: filepath {parameters.filename}")
         SSX_LOGGER.info(
@@ -282,7 +282,7 @@ def main_extruder_plan(
     else:
         err = f"Unknown Detector Type, det_type = {parameters.detector_name}"
         SSX_LOGGER.error(err)
-        raise UnknownDetectorType(err)
+        raise UnknownDetectorTypeError(err)
 
     beam_settings = yield from read_beam_info_from_hardware(
         dcm, mirrors, beam_center_device, parameters.detector_name
@@ -291,7 +291,7 @@ def main_extruder_plan(
     # Do DCID creation BEFORE arming the detector
     filetemplate = f"{parameters.filename}.nxs"
     if parameters.detector_name == "eiger":
-        complete_filename = cagetstring(pv.eiger_ODfilenameRBV)
+        complete_filename = cagetstring(pv.eiger_od_filename_rbv)
         filetemplate = f"{complete_filename}.nxs"
     dcid.generate_dcid(
         beam_settings=beam_settings,
@@ -387,7 +387,7 @@ def tidy_up_at_collection_end_plan(
     # Clean Up
     if parameters.detector_name == "eiger":
         yield from sup.eiger("return-to-normal", None, dcm)
-        SSX_LOGGER.debug(f"{parameters.filename}_{caget(pv.eiger_seqID)}")
+        SSX_LOGGER.debug(f"{parameters.filename}_{caget(pv.eiger_seq_id)}")
     SSX_LOGGER.debug("End of Run")
     SSX_LOGGER.info("Close hutch shutter")
     yield from bps.abs_set(shutter, ShutterDemand.CLOSE, wait=True)
@@ -402,7 +402,7 @@ def collection_complete_plan(
     if detector_name == "eiger":
         SSX_LOGGER.info("Eiger Acquire STOP")
         caput(pv.eiger_acquire, 0)
-        caput(pv.eiger_ODcapture, "Done")
+        caput(pv.eiger_od_capture, "Done")
 
     yield from bps.sleep(0.5)
 
@@ -413,32 +413,20 @@ def collection_complete_plan(
     yield from bps.null()
 
 
-def run_extruder_plan(
-    zebra: Zebra = inject("zebra"),
-    aperture: Aperture = inject("aperture"),
-    backlight: DualBacklight = inject("backlight"),
-    beamstop: Beamstop = inject("beamstop"),
-    detector_stage: YZStage = inject("detector_motion"),
-    shutter: HutchShutter = inject("shutter"),
-    dcm: DCM = inject("dcm"),
-    mirrors: FocusMirrorsMode = inject("focus_mirrors"),
-    attenuator: ReadOnlyAttenuator = inject("attenuator"),
-    beam_center_eiger: DetectorBeamCenter = inject("eiger_bc"),
+def run_plan_in_wrapper(
+    zebra: Zebra,
+    aperture: Aperture,
+    backlight: DualBacklight,
+    beamstop: Beamstop,
+    detector_stage: YZStage,
+    shutter: HutchShutter,
+    dcm: DCM,
+    mirrors: FocusMirrorsMode,
+    beam_center_eiger: DetectorBeamCenter,
+    parameters: ExtruderParameters,
+    dcid: DCID,
+    start_time: datetime,
 ) -> MsgGenerator:
-    start_time = datetime.now()
-    SSX_LOGGER.info(f"Collection start time: {start_time.ctime()}")
-
-    parameters: ExtruderParameters = yield from read_parameters(
-        detector_stage, attenuator
-    )
-    # Create collection directory
-    parameters.collection_directory.mkdir(parents=True, exist_ok=True)
-
-    beam_center_device = beam_center_eiger
-
-    # DCID - not generated yet
-    dcid = DCID(emit_errors=False, expt_params=parameters)
-
     yield from bpp.contingency_wrapper(
         main_extruder_plan(
             zebra=zebra,
@@ -449,7 +437,7 @@ def run_extruder_plan(
             shutter=shutter,
             dcm=dcm,
             mirrors=mirrors,
-            beam_center_device=beam_center_device,
+            beam_center_device=beam_center_eiger,
             parameters=parameters,
             dcid=dcid,
             start_time=start_time,
@@ -469,3 +457,45 @@ def run_extruder_plan(
         ),
         auto_raise=False,
     )
+
+
+def run_extruder_plan(
+    zebra: Zebra = inject("zebra"),
+    aperture: Aperture = inject("aperture"),
+    backlight: DualBacklight = inject("backlight"),
+    beamstop: Beamstop = inject("beamstop"),
+    detector_stage: YZStage = inject("detector_motion"),
+    shutter: HutchShutter = inject("shutter"),
+    dcm: DCM = inject("dcm"),
+    mirrors: FocusMirrorsMode = inject("focus_mirrors"),
+    attenuator: ReadOnlyAttenuator = inject("attenuator"),
+    beam_center_eiger: DetectorBeamCenter = inject("eiger_bc"),
+) -> MsgGenerator:
+    start_time = datetime.now()
+    SSX_LOGGER.info(f"Collection start time: {start_time.ctime()}")
+
+    parameters: ExtruderParameters = yield from read_parameters(
+        detector_stage, attenuator
+    )
+    # Create collection directory
+    parameters.collection_directory.mkdir(parents=True, exist_ok=True)
+
+    beam_center_device = beam_center_eiger
+
+    # DCID - not generated yet
+    dcid = DCID(emit_errors=False, expt_params=parameters)
+
+    yield from run_plan_in_wrapper(
+        zebra,
+        aperture,
+        backlight,
+        beamstop,
+        detector_stage,
+        shutter,
+        dcm,
+        mirrors,
+        beam_center_device,
+        parameters,
+        dcid,
+        start_time,
+    )

mx_bluesky/beamlines/i24/serial/fixed_target/{i24ssx_Chip_Collect_py3v1.py → i24ssx_chip_collect_py3v1.py}

@@ -31,7 +31,7 @@ from mx_bluesky.beamlines.i24.serial.fixed_target.ft_utils import (
     MappingType,
     PumpProbeSetting,
 )
-from mx_bluesky.beamlines.i24.serial.fixed_target.i24ssx_Chip_Manager_py3v1 import (
+from mx_bluesky.beamlines.i24.serial.fixed_target.i24ssx_chip_manager_py3v1 import (
     read_parameters,
     upload_chip_map_to_geobrick,
 )
@@ -335,7 +335,7 @@ def start_i24(
 
         # DCID process depends on detector PVs being set up already
         SSX_LOGGER.debug("Start DCID process")
-        complete_filename = cagetstring(pv.eiger_ODfilenameRBV)
+        complete_filename = cagetstring(pv.eiger_od_filename_rbv)
         filetemplate = f"{complete_filename}.nxs"
         dcid.generate_dcid(
             beam_settings=beam_settings,
@@ -401,7 +401,7 @@ def finish_i24(
         SSX_LOGGER.debug("Finish I24 Eiger")
         yield from reset_zebra_when_collection_done_plan(zebra)
         yield from sup.eiger("return-to-normal", None, dcm)
-        complete_filename = cagetstring(pv.eiger_ODfilenameRBV)  # type: ignore
+        complete_filename = cagetstring(pv.eiger_od_filename_rbv)  # type: ignore
     else:
         raise ValueError(f"{parameters.detector_name} unrecognised")
 
@@ -538,7 +538,7 @@ def collection_complete_plan(
     SSX_LOGGER.debug(f"Collection end time {end_time}")
     dcid.collection_complete(end_time, aborted=False)
 
-    # NOTE no files to copy anymore but shoud write userlog here
+    # NOTE no files to copy anymore but should write userlog here
     yield from bps.null()
 
 
@@ -562,7 +562,7 @@ def tidy_up_after_collection_plan(
     if parameters.detector_name == "eiger":
         SSX_LOGGER.debug("Eiger Acquire STOP")
         caput(pv.eiger_acquire, 0)
-        caput(pv.eiger_ODcapture, "Done")
+        caput(pv.eiger_od_capture, "Done")
         yield from bps.sleep(0.5)
 
     yield from finish_i24(zebra, pmac, shutter, dcm, parameters)

mx_bluesky/beamlines/i24/serial/fixed_target/{i24ssx_Chip_Manager_py3v1.py → i24ssx_chip_manager_py3v1.py}

@@ -459,7 +459,7 @@ def load_lite_map() -> MsgGenerator:
     SSX_LOGGER.debug("Run load stock map with 'clear' setting.")
     yield from load_stock_map("clear")
     # fmt: off
-    # Oxford_block_dict is wrong (columns and rows need to flip) added in script below to generate it automatically however kept this for backwards compatiability/reference
+    # Oxford_block_dict is wrong (columns and rows need to flip) added in script below to generate it automatically however kept this for backwards compatibility/reference
     oxford_block_dict = {   # noqa: F841
         'A1': '01', 'A2': '02', 'A3': '03', 'A4': '04', 'A5': '05', 'A6': '06', 'A7': '07', 'A8': '08',
         'B1': '16', 'B2': '15', 'B3': '14', 'B4': '13', 'B5': '12', 'B6': '11', 'B7': '10', 'B8': '09',
@@ -523,7 +523,7 @@ def load_lite_map() -> MsgGenerator:
 def moveto(place: str = "origin", pmac: PMAC = inject("pmac")) -> MsgGenerator:
     SSX_LOGGER.info(f"Move to: {place}")
     if place == Fiducials.zero:
-        SSX_LOGGER.info("Chip aspecific move.")
+        SSX_LOGGER.info("Chip moving to zero")
         yield from bps.trigger(pmac.to_xyz_zero)
         return
 
@@ -705,7 +705,7 @@ def cs_maker(pmac: PMAC = inject("pmac")) -> MsgGenerator:
 
     Skew:
     Skew is the difference between the Sz1 and Sz2 after rotation is taken out.
-    This should be measured in situ prior to expriment, ie. measure by hand using
+    This should be measured in situ prior to experiment, ie. measure by hand using
     opposite and adjacent RBV after calibration of scale factors.
     """
     chip_type = int(caget(CHIPTYPE_PV))
@@ -738,10 +738,10 @@ def cs_maker(pmac: PMAC = inject("pmac")) -> MsgGenerator:
             float(cs_info["scalez"]),
         )
         skew = float(cs_info["skew"])
-        Sx_dir, Sy_dir, Sz_dir = (
-            int(cs_info["Sx_dir"]),
-            int(cs_info["Sy_dir"]),
-            int(cs_info["Sz_dir"]),
+        sx_dir, sy_dir, sz_dir = (
+            int(cs_info["sx_dir"]),
+            int(cs_info["sy_dir"]),
+            int(cs_info["sz_dir"]),
         )
     except KeyError:
         SSX_LOGGER.error("Wrong or missing key in the cs json file.")
@@ -751,60 +751,60 @@ def cs_maker(pmac: PMAC = inject("pmac")) -> MsgGenerator:
         if val not in [1, -1]:
             raise ValueError("Wrong value for direction. Please set to either -1 or 1.")
 
-    check_dir(Sx_dir)
-    check_dir(Sy_dir)
-    check_dir(Sz_dir)
+    check_dir(sx_dir)
+    check_dir(sy_dir)
+    check_dir(sz_dir)
 
     # Rotation Around Z
-    # If stages upsidedown (I24) change sign of Sz
-    Sz1 = -1 * f1_y / fiducial_dict[chip_type][0]
-    Sz2 = f2_x / fiducial_dict[chip_type][1]
-    Sz = Sz_dir * ((Sz1 + Sz2) / 2)
-    Cz = np.sqrt(1 - Sz**2)
-    SSX_LOGGER.info(f"Sz1 , {Sz1:1.4f}, {np.degrees(np.arcsin(Sz1)):1.4f}")
-    SSX_LOGGER.info(f"Sz2 , {Sz2:1.4f}, {np.degrees(np.arcsin(Sz2)):1.4f}")
-    SSX_LOGGER.info(f"Sz , {Sz:1.4f}, {np.degrees(np.arcsin(Sz)):1.4f}")
-    SSX_LOGGER.info(f"Cz , {Cz:1.4f}, {np.degrees(np.arcsin(Cz)):1.4f}")
+    # If stages upsidedown (I24) change sign of sz
+    sz1 = -1 * f1_y / fiducial_dict[chip_type][0]
+    sz2 = f2_x / fiducial_dict[chip_type][1]
+    sz = sz_dir * ((sz1 + sz2) / 2)
+    cz = np.sqrt(1 - sz**2)
+    SSX_LOGGER.info(f"sz1 , {sz1:1.4f}, {np.degrees(np.arcsin(sz1)):1.4f}")
+    SSX_LOGGER.info(f"sz2 , {sz2:1.4f}, {np.degrees(np.arcsin(sz2)):1.4f}")
+    SSX_LOGGER.info(f"sz , {sz:1.4f}, {np.degrees(np.arcsin(sz)):1.4f}")
+    SSX_LOGGER.info(f"cz , {cz:1.4f}, {np.degrees(np.arcsin(cz)):1.4f}")
     # Rotation Around Y
-    Sy = Sy_dir * f1_z / fiducial_dict[chip_type][0]
-    Cy = np.sqrt(1 - Sy**2)
-    SSX_LOGGER.info(f"Sy , {Sy:1.4f}, {np.degrees(np.arcsin(Sy)):1.4f}")
-    SSX_LOGGER.info(f"Cy , {Cy:1.4f}, {np.degrees(np.arcsin(Cy)):1.4f}")
+    sy = sy_dir * f1_z / fiducial_dict[chip_type][0]
+    cy = np.sqrt(1 - sy**2)
+    SSX_LOGGER.info(f"sy , {sy:1.4f}, {np.degrees(np.arcsin(sy)):1.4f}")
+    SSX_LOGGER.info(f"cy , {cy:1.4f}, {np.degrees(np.arcsin(cy)):1.4f}")
     # Rotation Around X
-    # If stages upsidedown (I24) change sign of Sx
-    Sx = Sx_dir * f2_z / fiducial_dict[chip_type][1]
-    Cx = np.sqrt(1 - Sx**2)
-    SSX_LOGGER.info(f"Sx , {Sx:1.4f}, {np.degrees(np.arcsin(Sx)):1.4f}")
-    SSX_LOGGER.info(f"Cx , {Cx:1.4f}, {np.degrees(np.arcsin(Cx)):1.4f}")
+    # If stages upsidedown (I24) change sign of sx
+    sx = sx_dir * f2_z / fiducial_dict[chip_type][1]
+    cx = np.sqrt(1 - sx**2)
+    SSX_LOGGER.info(f"sx , {sx:1.4f}, {np.degrees(np.arcsin(sx)):1.4f}")
+    SSX_LOGGER.info(f"cx , {cx:1.4f}, {np.degrees(np.arcsin(cx)):1.4f}")
 
-    x1factor = mtr1_dir * scalex * (Cy * Cz)
-    y1factor = mtr2_dir * scaley * (-1.0 * Cx * Sz)
-    z1factor = mtr3_dir * scalez * Sy
+    x1factor = mtr1_dir * scalex * (cy * cz)
+    y1factor = mtr2_dir * scaley * (-1.0 * cx * sz)
+    z1factor = mtr3_dir * scalez * sy
 
-    x2factor = mtr1_dir * scalex * ((Sx * Sy * Cz) + (Cx * Sz))
-    y2factor = mtr2_dir * scaley * ((Cx * Cz) - (Sx * Sy * Sz))
-    z2factor = mtr3_dir * scalez * (-1.0 * Sx * Cy)
+    x2factor = mtr1_dir * scalex * ((sx * sy * cz) + (cx * sz))
+    y2factor = mtr2_dir * scaley * ((cx * cz) - (sx * sy * sz))
+    z2factor = mtr3_dir * scalez * (-1.0 * sx * cy)
 
-    x3factor = mtr1_dir * scalex * ((Sx * Sz) - (Cx * Sy * Cz))
-    y3factor = mtr2_dir * scaley * ((Cx * Sy * Sz) + (Sx * Cz))
-    z3factor = mtr3_dir * scalez * (Cx * Cy)
+    x3factor = mtr1_dir * scalex * ((sx * sz) - (cx * sy * cz))
+    y3factor = mtr2_dir * scaley * ((cx * sy * sz) + (sx * cz))
+    z3factor = mtr3_dir * scalez * (cx * cy)
 
     SSX_LOGGER.info(f"Skew being used is: {skew:1.4f}")
-    s1 = np.degrees(np.arcsin(Sz1))
-    s2 = np.degrees(np.arcsin(Sz2))
-    rot = np.degrees(np.arcsin((Sz1 + Sz2) / 2))
+    s1 = np.degrees(np.arcsin(sz1))
+    s2 = np.degrees(np.arcsin(sz2))
+    rot = np.degrees(np.arcsin((sz1 + sz2) / 2))
     calc_skew = (s1 - rot) - (s2 - rot)
     SSX_LOGGER.info(f"s1:{s1:1.4f} s2:{s2:1.4f} rot:{rot:1.4f}")
     SSX_LOGGER.info(f"Calculated rotation from current fiducials is: {rot:1.4f}")
     SSX_LOGGER.info(f"Calculated Skew from current fiducials is: {calc_skew:1.4f}")
     SSX_LOGGER.info("Calculated Skew has been known to have the wrong sign")
 
-    sinD = np.sin((skew / 2) * (np.pi / 180))
-    cosD = np.cos((skew / 2) * (np.pi / 180))
-    new_x1factor = (x1factor * cosD) + (y1factor * sinD)
-    new_y1factor = (x1factor * sinD) + (y1factor * cosD)
-    new_x2factor = (x2factor * cosD) + (y2factor * sinD)
-    new_y2factor = (x2factor * sinD) + (y2factor * cosD)
+    sin_d = np.sin((skew / 2) * (np.pi / 180))
+    cod_d = np.cos((skew / 2) * (np.pi / 180))
+    new_x1factor = (x1factor * cod_d) + (y1factor * sin_d)
+    new_y1factor = (x1factor * sin_d) + (y1factor * cod_d)
+    new_x2factor = (x2factor * cod_d) + (y2factor * sin_d)
+    new_y2factor = (x2factor * sin_d) + (y2factor * cod_d)
 
     cs1 = f"#1->{new_x1factor:+1.3f}X{new_y1factor:+1.3f}Y{z1factor:+1.3f}Z"
     cs2 = f"#2->{new_x2factor:+1.3f}X{new_y2factor:+1.3f}Y{z2factor:+1.3f}Z"

mx_bluesky/beamlines/i24/serial/fixed_target/{i24ssx_Chip_StartUp_py3v1.py → i24ssx_chip_startup_py3v1.py}

@@ -70,10 +70,10 @@ def pathli(l_in=None, way="typewriter", reverse=False):
 def zippum(list_1_args, list_2_args):
     list_1, type_1, reverse_1 = list_1_args
     list_2, type_2, reverse_2 = list_2_args
-    A_path = pathli(list_1, type_1, reverse_1)
-    B_path = pathli(list_2, type_2, reverse_2)
+    a_path = pathli(list_1, type_1, reverse_1)
+    b_path = pathli(list_2, type_2, reverse_2)
     zipped_list = []
-    for a, b in zip(A_path, B_path, strict=False):
+    for a, b in zip(a_path, b_path, strict=False):
         zipped_list.append(a + b)
     return zipped_list
 

mx_bluesky/beamlines/i24/serial/fixed_target/i24ssx_moveonclick.py

@@ -13,7 +13,7 @@ from dodal.devices.i24.pmac import PMAC
 from dodal.devices.oav.oav_detector import OAV
 
 from mx_bluesky.beamlines.i24.serial.fixed_target import (
-    i24ssx_Chip_Manager_py3v1 as manager,
+    i24ssx_chip_manager_py3v1 as manager,
 )
 from mx_bluesky.beamlines.i24.serial.fixed_target.ft_utils import Fiducials
 from mx_bluesky.beamlines.i24.serial.log import SSX_LOGGER
@@ -52,12 +52,12 @@ def _move_on_mouse_click_plan(
         position coordinates.
     """
     zoomcalibrator = yield from _calculate_zoom_calibrator(oav)
-    beamX, beamY = yield from _get_beam_centre(oav)
+    beam_x, beam_y = yield from _get_beam_centre(oav)
     x, y = clicked_position
-    xmove = -10 * (beamX - x) * zoomcalibrator
-    ymove = 10 * (beamY - y) * zoomcalibrator
+    xmove = -10 * (beam_x - x) * zoomcalibrator
+    ymove = 10 * (beam_y - y) * zoomcalibrator
     SSX_LOGGER.info(f"Zoom calibrator {zoomcalibrator}")
-    SSX_LOGGER.info(f"Beam centre {beamX} {beamY}")
+    SSX_LOGGER.info(f"Beam centre {beam_x} {beam_y}")
     SSX_LOGGER.info(f"Moving X and Y {xmove} {ymove}")
     xmovepmacstring = "&2#5J:" + str(xmove)
     ymovepmacstring = "&2#6J:" + str(ymove)
@@ -66,22 +66,22 @@ def _move_on_mouse_click_plan(
 
 
 # Register clicks and move chip stages
-def onMouse(event, x, y, flags, param):
+def on_mouse(event, x, y, flags, param):
     if event == cv.EVENT_LBUTTONUP:
-        RE = param[0]
+        run_engine = param[0]
         pmac = param[1]
         oav = param[2]
         SSX_LOGGER.info(f"Clicked X and Y {x} {y}")
-        RE(_move_on_mouse_click_plan(oav, pmac, (x, y)))
+        run_engine(_move_on_mouse_click_plan(oav, pmac, (x, y)))
 
 
-def update_ui(oav, frame, RE):
+def update_ui(oav, frame, run_engine):
     # Get beam x and y values
-    beamX, beamY = RE(_get_beam_centre(oav)).plan_result
+    beam_x, beam_y = run_engine(_get_beam_centre(oav)).plan_result
 
     # Overlay text and beam centre
     cv.ellipse(
-        frame, (beamX, beamY), (12, 8), 0.0, 0.0, 360, (0, 255, 255), thickness=2
+        frame, (beam_x, beam_y), (12, 8), 0.0, 0.0, 360, (0, 255, 255), thickness=2
     )
     cv.putText(
         frame,
@@ -156,13 +156,13 @@ def update_ui(oav, frame, RE):
     cv.imshow("OAV1view", frame)
 
 
-def start_viewer(oav: OAV, pmac: PMAC, RE: RunEngine, oav1: str = OAV1_CAM):
-    # Create a video caputure from OAV1
+def start_viewer(oav: OAV, pmac: PMAC, run_engine: RunEngine, oav1: str = OAV1_CAM):
+    # Create a video capture from OAV1
     cap = cv.VideoCapture(oav1)
 
     # Create window named OAV1view and set onmouse to this
     cv.namedWindow("OAV1view")
-    cv.setMouseCallback("OAV1view", onMouse, param=[RE, pmac, oav])  # type: ignore
+    cv.setMouseCallback("OAV1view", on_mouse, param=[run_engine, pmac, oav])  # type: ignore
 
     SSX_LOGGER.info("Showing camera feed. Press escape to close")
     # Read captured video and store them in success and frame
@@ -172,44 +172,44 @@ def start_viewer(oav: OAV, pmac: PMAC, RE: RunEngine, oav1: str = OAV1_CAM):
     while success:
         success, frame = cap.read()
 
-        update_ui(oav, frame, RE)
+        update_ui(oav, frame, run_engine)
 
         k = cv.waitKey(1)
         if k == 113:  # Q
-            RE(manager.moveto(Fiducials.zero, pmac))
+            run_engine(manager.moveto(Fiducials.zero, pmac))
         if k == 119:  # W
-            RE(manager.moveto(Fiducials.fid1, pmac))
+            run_engine(manager.moveto(Fiducials.fid1, pmac))
         if k == 101:  # E
-            RE(manager.moveto(Fiducials.fid2, pmac))
+            run_engine(manager.moveto(Fiducials.fid2, pmac))
         if k == 97:  # A
-            RE(bps.trigger(pmac.home, wait=True))
+            run_engine(bps.trigger(pmac.home, wait=True))
             print("Current position set as origin")
         if k == 115:  # S
-            RE(manager.fiducial(1))
+            run_engine(manager.fiducial(1))
         if k == 100:  # D
-            RE(manager.fiducial(2))
+            run_engine(manager.fiducial(2))
         if k == 99:  # C
-            RE(manager.cs_maker(pmac))
+            run_engine(manager.cs_maker(pmac))
         if k == 98:  # B
-            RE(
+            run_engine(
                 manager.block_check()
             )  # doesn't work well for blockcheck as image doesn't update
         if k == 104:  # H
-            RE(bps.abs_set(pmac.pmac_string, "&2#6J:-10", wait=True))
+            run_engine(bps.abs_set(pmac.pmac_string, "&2#6J:-10", wait=True))
         if k == 110:  # N
-            RE(bps.abs_set(pmac.pmac_string, "&2#6J:10", wait=True))
+            run_engine(bps.abs_set(pmac.pmac_string, "&2#6J:10", wait=True))
         if k == 109:  # M
-            RE(bps.abs_set(pmac.pmac_string, "&2#5J:-10", wait=True))
+            run_engine(bps.abs_set(pmac.pmac_string, "&2#5J:-10", wait=True))
         if k == 98:  # B
-            RE(bps.abs_set(pmac.pmac_string, "&2#5J:10", wait=True))
+            run_engine(bps.abs_set(pmac.pmac_string, "&2#5J:10", wait=True))
         if k == 105:  # I
-            RE(bps.abs_set(pmac.pmac_string, "&2#7J:-150", wait=True))
+            run_engine(bps.abs_set(pmac.pmac_string, "&2#7J:-150", wait=True))
         if k == 111:  # O
-            RE(bps.abs_set(pmac.pmac_string, "&2#7J:150", wait=True))
+            run_engine(bps.abs_set(pmac.pmac_string, "&2#7J:150", wait=True))
         if k == 117:  # U
-            RE(bps.abs_set(pmac.pmac_string, "&2#7J:-1000", wait=True))
+            run_engine(bps.abs_set(pmac.pmac_string, "&2#7J:-1000", wait=True))
         if k == 112:  # P
-            RE(bps.abs_set(pmac.pmac_string, "&2#7J:1000", wait=True))
+            run_engine(bps.abs_set(pmac.pmac_string, "&2#7J:1000", wait=True))
         if k == 0x1B:  # esc
             cv.destroyWindow("OAV1view")
             print("Pressed escape. Closing window")
@@ -220,8 +220,8 @@ def start_viewer(oav: OAV, pmac: PMAC, RE: RunEngine, oav1: str = OAV1_CAM):
 
 
 if __name__ == "__main__":
-    RE = RunEngine(call_returns_result=True)
+    run_engine = RunEngine(call_returns_result=True)
     # Get devices out of dodal
     oav: OAV = i24.oav(connect_immediately=True)
     pmac: PMAC = i24.pmac(connect_immediately=True)
-    start_viewer(oav, pmac, RE)
+    start_viewer(oav, pmac, run_engine)

mx_bluesky/beamlines/i24/serial/log.py

@@ -9,7 +9,7 @@ import bluesky.plan_stubs as bps
 from bluesky.log import logger as bluesky_logger
 from bluesky.utils import MsgGenerator
 from dodal.log import DEFAULT_GRAYLOG_PORT, ophyd_async_logger
-from dodal.log import LOGGER as dodal_logger
+from dodal.log import LOGGER as DODAL_LOGGER
 
 from mx_bluesky.common.utils.log import do_default_logging_setup
 
@@ -19,7 +19,7 @@ VISIT_PATH = Path("/dls_sw/i24/etc/ssx_current_visit.txt")
 # Logging set up
 SSX_LOGGER = logging.getLogger("I24serial")
 SSX_LOGGER.addHandler(logging.NullHandler())
-SSX_LOGGER.parent = dodal_logger
+SSX_LOGGER.parent = DODAL_LOGGER
 
 
 logging_config = {
@@ -101,14 +101,14 @@ def config(
     """
     if logfile:
         logs = _get_logging_file_path() / logfile
-        fileFormatter = logging.Formatter(
+        file_formatter = logging.Formatter(
             "%(asctime)s %(levelname)s: \t(%(name)s) %(message)s",
             datefmt="%d-%m-%Y %I:%M:%S",
         )
-        FH = logging.FileHandler(logs, mode=write_mode, encoding="utf-8", delay=delayed)
-        FH.setLevel(logging.DEBUG)
-        FH.setFormatter(fileFormatter)
-        SSX_LOGGER.addHandler(FH)
+        fh = logging.FileHandler(logs, mode=write_mode, encoding="utf-8", delay=delayed)
+        fh.setLevel(logging.DEBUG)
+        fh.setFormatter(file_formatter)
+        SSX_LOGGER.addHandler(fh)
     do_default_logging_setup(
         "mx-bluesky.log",
         DEFAULT_GRAYLOG_PORT,
@@ -116,8 +116,8 @@ def config(
         integrate_all_logs=False,
     )
     # Remove dodal StreamHandler to avoid duplication of messages above debug
-    dodal_logger.removeHandler(dodal_logger.handlers[0])
-    _integrate_bluesky_logs(dodal_logger)
+    DODAL_LOGGER.removeHandler(DODAL_LOGGER.handlers[0])
+    _integrate_bluesky_logs(DODAL_LOGGER)
 
 
 def log_on_entry(func):
@@ -151,6 +151,6 @@ def clean_up_log_config_at_end() -> MsgGenerator:
     # See https://github.com/DiamondLightSource/mx-bluesky/issues/609
     for handler in SSX_LOGGER.handlers:
         SSX_LOGGER.removeHandler(handler)
-    for handler in dodal_logger.handlers:
-        dodal_logger.removeHandler(handler)
+    for handler in DODAL_LOGGER.handlers:
+        DODAL_LOGGER.removeHandler(handler)
     yield from bps.null()

mx_bluesky/beamlines/i24/serial/parameters/fixed_target/cs/cs_maker.json

@@ -3,7 +3,7 @@
     "scaley": 10011.9,
     "scalez": 10000.0,
     "skew": 0.025,
-    "Sx_dir": 1,
-    "Sy_dir": 1,
-    "Sz_dir": 1
+    "sx_dir": 1,
+    "sy_dir": 1,
+    "sz_dir": 1
 }

mx_bluesky/beamlines/i24/serial/setup_beamline/ca.py

@@ -38,15 +38,3 @@ def caput(pv, new_val):
     else:
         a = Popen(["caput", pv, str(new_val)], stdout=PIPE, stderr=PIPE)
         a_stdout, a_stderr = a.communicate()
-
-
-def evaluate(val):
-    try:
-        int(val)
-        return int(val)
-    except Exception:
-        try:
-            float(val)
-            return float(val)
-        except ValueError:
-            return val