mx-bluesky 1.2.0__py3-none-any.whl → 1.4.1__py3-none-any.whl

mx_bluesky/beamlines/i24/serial/fixed_target/i24ssx_Chip_StartUp_py3v1.py

@@ -2,34 +2,20 @@
 Startup utilities for chip
 """
 
-import logging
-import os
 import string
-import time
 from pathlib import Path
 
-import numpy as np
-
-from mx_bluesky.beamlines.i24.serial import log
 from mx_bluesky.beamlines.i24.serial.fixed_target.ft_utils import ChipType
+from mx_bluesky.beamlines.i24.serial.log import SSX_LOGGER, log_on_entry
 from mx_bluesky.beamlines.i24.serial.parameters import (
     FixedTargetParameters,
     get_chip_format,
 )
 from mx_bluesky.beamlines.i24.serial.parameters.constants import (
-    HEADER_FILES_PATH,
     PARAM_FILE_NAME,
     PARAM_FILE_PATH_FT,
 )
 
-logger = logging.getLogger("I24ssx.chip_startup")
-
-
-def setup_logging():
-    # Log should now change name daily.
-    logfile = time.strftime("i24fixedtarget_%d%B%y.log").lower()
-    log.config(logfile)
-
 
 def read_parameter_file(
     param_path: Path | str = PARAM_FILE_PATH_FT,
@@ -41,44 +27,19 @@ def read_parameter_file(
     return params
 
 
-@log.log_on_entry
+@log_on_entry
 def fiducials(chip_type: int):
     fiducial_list: list | None = None
     if chip_type in [ChipType.Oxford, ChipType.OxfordInner, ChipType.Minichip]:
         fiducial_list = []
     elif chip_type == ChipType.Custom:
         # No fiducial for custom
-        logger.warning("No fiducials for custom chip")
+        SSX_LOGGER.warning("No fiducials for custom chip")
     else:
-        logger.warning(f"Unknown chip_type, {chip_type}, in fiducials")
+        SSX_LOGGER.warning(f"Unknown chip_type, {chip_type}, in fiducials")
     return fiducial_list
 
 
-def get_xy(addr: str, chip_type: ChipType):
-    entry = addr.split("_")[-2:]
-    R, C = entry[0][0], entry[0][1]
-    r2, c2 = entry[1][0], entry[1][1]
-    blockR = string.ascii_uppercase.index(R)
-    blockC = int(C) - 1
-    lowercase_list = list(string.ascii_lowercase + string.ascii_uppercase + "0")
-    windowR = lowercase_list.index(r2)
-    windowC = lowercase_list.index(c2)
-
-    chip_params = get_chip_format(chip_type)
-
-    x = (
-        (blockC * chip_params.b2b_horz)
-        + (blockC * (chip_params.x_num_steps - 1) * chip_params.x_step_size)
-        + (windowC * chip_params.x_step_size)
-    )
-    y = (
-        (blockR * chip_params.b2b_vert)
-        + (blockR * (chip_params.y_num_steps - 1) * chip_params.y_step_size)
-        + (windowR * chip_params.y_step_size)
-    )
-    return x, y
-
-
 def pathli(l_in=None, way="typewriter", reverse=False):
     if l_in is None:
         l_in = []
@@ -118,9 +79,9 @@ def pathli(l_in=None, way="typewriter", reverse=False):
                 for _ in range(25):
                     long_list.append(entry)
         else:
-            logger.warning(f"No known path, way =  {way}")
+            SSX_LOGGER.warning(f"No known path, way =  {way}")
     else:
-        logger.warning("No list written")
+        SSX_LOGGER.warning("No list written")
     return long_list
 
 
@@ -154,175 +115,5 @@ def get_alphanumeric(chip_type: ChipType):
     for block in block_list:
         for window in window_list:
             alphanumeric_list.append(block + "_" + window)
-    logger.info(f"Length of alphanumeric list = {len(alphanumeric_list)}")
+    SSX_LOGGER.info(f"Length of alphanumeric list = {len(alphanumeric_list)}")
     return alphanumeric_list
-
-
-@log.log_on_entry
-def get_shot_order(chip_type: ChipType):
-    cell_format = get_chip_format(chip_type)
-    blk_num = cell_format.x_blocks
-    wnd_num = cell_format.x_num_steps
-    uppercase_list = list(string.ascii_uppercase)[:blk_num]
-    number_list = [str(x) for x in range(1, blk_num + 1)]
-    lowercase_list = list(string.ascii_lowercase + string.ascii_uppercase + "0")[
-        :wnd_num
-    ]
-
-    block_list = zippum([uppercase_list, "snake", 0], [number_list, "expand", 0])
-    window_dn = zippum([lowercase_list, "expand", 0], [lowercase_list, "snake", 0])
-    window_up = zippum([lowercase_list, "expand", 1], [lowercase_list, "snake", 0])
-
-    switch = 0
-    count = 0
-    collect_list = []
-    for block in block_list:
-        if switch == 0:
-            for window in window_dn:
-                collect_list.append(block + "_" + window)
-            count += 1
-            if count == blk_num:
-                count = 0
-                switch = 1
-        else:
-            for window in window_up:
-                collect_list.append(block + "_" + window)
-            count += 1
-            if count == blk_num:
-                count = 0
-                switch = 0
-
-    logger.info(f"Length of collect list = {len(collect_list)}")
-    return collect_list
-
-
-@log.log_on_entry
-def write_file(
-    location: str = "i24",
-    suffix: str = ".addr",
-    order: str = "alphanumeric",
-    param_file_path: Path = PARAM_FILE_PATH_FT,
-    save_path: Path = HEADER_FILES_PATH,
-):
-    if location == "i24":
-        params = read_parameter_file(param_file_path)
-    else:
-        msg = f"Unknown location, {location}"
-        logger.error(msg)
-        raise ValueError(msg)
-    chip_file_path = save_path / f"chips/{params.directory}/{params.filename}{suffix}"
-
-    fiducial_list = fiducials(params.chip.chip_type.value)
-
-    if order == "alphanumeric":
-        addr_list = get_alphanumeric(params.chip.chip_type)
-    elif order == "shot":
-        addr_list = get_shot_order(params.chip.chip_type)
-    else:
-        raise ValueError(f"{order=} unrecognised")
-
-    with open(chip_file_path, "a") as g:
-        for addr in addr_list:
-            xtal_name = "_".join([params.filename, addr])
-            (x, y) = get_xy(xtal_name, params.chip.chip_type)
-            if addr in fiducial_list:
-                pres = "0"
-            else:
-                if "rand" in suffix:
-                    pres = str(np.random.randint(2))
-                else:
-                    pres = "-1"
-            line = "\t".join([xtal_name, str(x), str(y), "0.0", pres]) + "\n"
-            g.write(line)
-
-    logger.info(f"Write {chip_file_path} completed")
-
-
-@log.log_on_entry
-def check_files(
-    location: str,
-    suffix_list: list[str],
-    param_file_path: Path | str = PARAM_FILE_PATH_FT,
-    save_path: Path = HEADER_FILES_PATH,
-):
-    if location == "i24":
-        params = read_parameter_file(param_file_path)
-    else:
-        msg = f"Unknown location, {location}"
-        logger.error(msg)
-        raise ValueError(msg)
-    chip_file_path = save_path / f"chips/{params.directory}/{params.filename}"
-
-    try:
-        os.stat(chip_file_path)
-    except Exception:
-        os.makedirs(chip_file_path)
-    for suffix in suffix_list:
-        full_fid = chip_file_path.with_suffix(suffix)
-        if full_fid.is_file():
-            time_str = time.strftime("%Y%m%d_%H%M%S_")
-            timestamp_fid = (  # noqa: F841
-                full_fid.parent / f"{time_str}_{params.filename}{full_fid.suffix}"
-            )
-            # FIXME hack / fix. Actually move the file
-            logger.info(f"File {full_fid} Already Exists")
-    logger.debug("Check files done")
-    return 1
-
-
-@log.log_on_entry
-def write_headers(
-    location: str,
-    suffix_list: list[str],
-    param_file_path: Path = PARAM_FILE_PATH_FT,
-    save_path: Path = HEADER_FILES_PATH,
-):
-    if location == "i24":
-        params = read_parameter_file(param_file_path)
-        chip_file_path = save_path / f"chips/{params.directory}/{params.filename}"
-
-        for suffix in suffix_list:
-            full_fid = chip_file_path.with_suffix(suffix)
-            with open(full_fid, "w") as g:
-                g.write(
-                    "#23456789012345678901234567890123456789012345678901234567890123456789012345678901234567890\n#\n"
-                )
-                g.write(f"#&i24\tchip_name    = {params.filename}\n")
-                g.write(f"#&i24\tvisit        = {params.visit}\n")
-                g.write(f"#&i24\tsub_dir      = {params.directory}\n")
-                g.write(f"#&i24\tn_exposures  = {params.num_exposures}\n")
-                g.write(f"#&i24\tchip_type    = {params.chip.chip_type.value}\n")
-                g.write(f"#&i24\tmap_type     = {params.map_type.value}\n")
-                g.write(f"#&i24\tpump_repeat  = {params.pump_repeat.value}\n")
-                g.write(f"#&i24\tpumpexptime  = {params.laser_dwell_s}\n")
-                g.write(f"#&i24\texptime      = {params.laser_delay_s}\n")
-                g.write(f"#&i24\tdcdetdist    = {params.detector_distance_mm}\n")
-                g.write(f"#&i24\tprepumpexptime  = {params.pre_pump_exposure_s}\n")
-                g.write(f"#&i24\tdet_Type     = {params.detector_name}\n")
-                g.write("#\n")
-                g.write(
-                    "#XtalAddr      XCoord  YCoord  ZCoord  Present Shot  Spare04 Spare03 Spare02 Spare01\n"
-                )
-    else:
-        msg = f"Unknown location, {location}"
-        logger.error(msg)
-        raise ValueError(msg)
-    logger.debug("Write headers done")
-
-
-def run():
-    logger.debug("Run Startup")
-    check_files("i24", [".addr", ".shot"])
-    logger.info("Checked Files")
-    write_headers("i24", [".addr", ".shot"])
-    logger.info("Written Headers")
-    logger.info("Writing to Files has been disabled. Headers Only")
-    # Makes a file with random crystal positions
-    check_files("i24", ["rando.spec"])
-    write_headers("i24", ["rando.spec"])
-    logger.debug("StartUp Done")
-
-
-if __name__ == "__main__":
-    setup_logging()
-    run()

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

@@ -3,7 +3,6 @@ Move on click gui for fixed targets at I24
 Robin Owen 12 Jan 2021
 """
 
-import logging
 from collections.abc import Sequence
 
 import bluesky.plan_stubs as bps
@@ -17,10 +16,9 @@ from mx_bluesky.beamlines.i24.serial.fixed_target import (
     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
 from mx_bluesky.beamlines.i24.serial.parameters.constants import OAV1_CAM
 
-logger = logging.getLogger("I24ssx.moveonclick")
-
 
 def _get_beam_centre(oav: OAV):
     """Extract the beam centre x/y positions from the display.configuration file.
@@ -28,28 +26,32 @@ def _get_beam_centre(oav: OAV):
     Args:
         oav (OAV): the OAV device.
     """
-    return oav.parameters.beam_centre_i, oav.parameters.beam_centre_j
+    beam_x = yield from bps.rd(oav.beam_centre_i)
+    beam_y = yield from bps.rd(oav.beam_centre_j)
+    return beam_x, beam_y
 
 
 def _calculate_zoom_calibrator(oav: OAV):
     """Set the scale for the zoom calibrator for the pmac moves."""
-    currentzoom = yield from bps.rd(oav.zoom_controller.percentage)
+    currentzoom = yield from bps.rd(oav.zoom_controller.percentage)  # type: ignore # See: https://github.com/bluesky/bluesky/issues/1809
     zoomcalibrator = 1.547 - (0.03 * currentzoom) + (0.0001634 * currentzoom**2)
     return zoomcalibrator
 
 
 def _move_on_mouse_click_plan(
-    oav: OAV, pmac: PMAC, beam_centre: Sequence[int], clicked_position: Sequence[int]
+    oav: OAV,
+    pmac: PMAC,
+    clicked_position: Sequence[int],
 ):
     """A plan that calculates the zoom calibrator and moves to the clicked \
         position coordinates.
     """
     zoomcalibrator = yield from _calculate_zoom_calibrator(oav)
-    beamX, beamY = beam_centre
+    beamX, beamY = yield from _get_beam_centre(oav)
     x, y = clicked_position
     xmove = -1 * (beamX - x) * zoomcalibrator
-    ymove = -1 * (beamY - y) * zoomcalibrator
-    logger.info(f"Moving X and Y {xmove} {ymove}")
+    ymove = 1 * (beamY - y) * zoomcalibrator
+    SSX_LOGGER.info(f"Moving X and Y {xmove} {ymove}")
     xmovepmacstring = "#1J:" + str(xmove)
     ymovepmacstring = "#2J:" + str(ymove)
     yield from bps.abs_set(pmac.pmac_string, xmovepmacstring, wait=True)
@@ -62,14 +64,13 @@ def onMouse(event, x, y, flags, param):
         RE = param[0]
         pmac = param[1]
         oav = param[2]
-        beamX, beamY = _get_beam_centre(oav)
-        logger.info(f"Clicked X and Y {x} {y}")
-        RE(_move_on_mouse_click_plan(oav, pmac, (beamX, beamY), (x, y)))
+        SSX_LOGGER.info(f"Clicked X and Y {x} {y}")
+        RE(_move_on_mouse_click_plan(oav, pmac, (x, y)))
 
 
-def update_ui(oav, frame):
+def update_ui(oav, frame, RE):
     # Get beam x and y values
-    beamX, beamY = _get_beam_centre(oav)
+    beamX, beamY = RE(_get_beam_centre(oav)).plan_result
 
     # Overlay text and beam centre
     cv.ellipse(
@@ -156,7 +157,7 @@ def start_viewer(oav: OAV, pmac: PMAC, RE: RunEngine, oav1: str = OAV1_CAM):
     cv.namedWindow("OAV1view")
     cv.setMouseCallback("OAV1view", onMouse, param=[RE, pmac, oav])  # type: ignore
 
-    logger.info("Showing camera feed. Press escape to close")
+    SSX_LOGGER.info("Showing camera feed. Press escape to close")
     # Read captured video and store them in success and frame
     success, frame = cap.read()
 
@@ -164,7 +165,7 @@ def start_viewer(oav: OAV, pmac: PMAC, RE: RunEngine, oav1: str = OAV1_CAM):
     while success:
         success, frame = cap.read()
 
-        update_ui(oav, frame)
+        update_ui(oav, frame, RE)
 
         k = cv.waitKey(1)
         if k == 113:  # Q
@@ -212,7 +213,7 @@ def start_viewer(oav: OAV, pmac: PMAC, RE: RunEngine, oav1: str = OAV1_CAM):
 
 
 if __name__ == "__main__":
-    RE = RunEngine()
+    RE = RunEngine(call_returns_result=True)
     # Get devices out of dodal
     oav: OAV = i24.oav()
     pmac: PMAC = i24.pmac()

mx_bluesky/beamlines/i24/serial/log.py

@@ -1,39 +1,30 @@
 import functools
 import logging
 import logging.config
+import time
 from os import environ
 from pathlib import Path
 
-from dodal.log import (
-    ERROR_LOG_BUFFER_LINES,
-    integrate_bluesky_and_ophyd_logging,
-    set_up_all_logging_handlers,
-)
+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
 
-VISIT_PATH = Path("/dls_sw/i24/etc/ssx_current_visit.txt")
-
-
-class OphydDebugFilter(logging.Filter):  # NOTE yet to be fully tested
-    """Do not send ophyd debug log messages to stream handler."""
+from mx_bluesky.common.utils.log import do_default_logging_setup
 
-    def filter(self, record):
-        return "ophyd" not in record.getMessage().lower()
+VISIT_PATH = Path("/dls_sw/i24/etc/ssx_current_visit.txt")
 
 
 # Logging set up
-logger = logging.getLogger("I24ssx")
-logger.addHandler(logging.NullHandler())
-logger.parent = dodal_logger
+SSX_LOGGER = logging.getLogger("I24serial")
+SSX_LOGGER.addHandler(logging.NullHandler())
+SSX_LOGGER.parent = dodal_logger
+
 
 logging_config = {
     "version": 1,
     "disable_existing_loggers": False,
-    "filters": {
-        "ophyd_filter": {
-            "()": OphydDebugFilter,
-        }
-    },
     "formatters": {
         "default": {
             "class": "logging.Formatter",
@@ -42,18 +33,17 @@ logging_config = {
     },
     "handlers": {
         "console": {
-            "level": "DEBUG",
+            "level": "INFO",
             "class": "logging.StreamHandler",
             "formatter": "default",
-            "filters": ["ophyd_filter"],
             "stream": "ext://sys.stdout",
         }
     },
     "loggers": {
-        "I24ssx": {
+        "I24serial": {
             "handlers": ["console"],
             "level": "DEBUG",
-            "propagate": True,
+            "propagate": False,
         }
     },
 }
@@ -68,10 +58,8 @@ def _read_visit_directory_from_file() -> Path:
 
 
 def _get_logging_file_path() -> Path:
-    """Get the path to write the artemis log files to.
-    If on a beamline, this will be written to the according area depending on the
-    BEAMLINE envrionment variable. If no envrionment variable is found it will default
-    it to the tmp/dev directory.
+    """Get the path to write the serial experiment specific log file to.
+    If on a beamline, this will be written to the tmp folder in the current visit.
     Returns:
         logging_path (Path): Path to the log file for the file handler to write to.
     """
@@ -87,24 +75,11 @@ def _get_logging_file_path() -> Path:
     return logging_path
 
 
-def default_logging_setup(dev_mode: bool = False):
-    """ Default log setup for i24 serial.
-
-    - Set up handlers for parent logger (from dodal)
-    - integrate bluesky and ophyd loggers
-    - Remove dodal stream handler to avoid double messages (for now, use only the \
-        i24ssx default stream to keep the output expected by the scientists.)
-    """
-    handlers = set_up_all_logging_handlers(  # noqa: F841
-        dodal_logger,
-        _get_logging_file_path(),
-        "dodal.log",
-        dev_mode,
-        ERROR_LOG_BUFFER_LINES,
-    )
-    integrate_bluesky_and_ophyd_logging(dodal_logger)
-    # Remove dodal StreamHandler to avoid duplication of messages above debug
-    dodal_logger.removeHandler(dodal_logger.handlers[0])
+def _integrate_bluesky_logs(parent_logger: logging.Logger):
+    # Integrate only bluesky and ophyd_async logger
+    for log in [bluesky_logger, ophyd_async_logger]:
+        log.parent = parent_logger
+        log.setLevel(logging.DEBUG)
 
 
 def config(
@@ -124,7 +99,15 @@ def config(
         dev_mode (bool, optional): If true, will log to graylog on localhost instead \
             of production. Defaults to False.
     """
-    default_logging_setup(dev_mode=dev_mode)
+    do_default_logging_setup(
+        "mx-bluesky.log",
+        DEFAULT_GRAYLOG_PORT,
+        dev_mode=dev_mode,
+        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)
 
     if logfile:
         logs = _get_logging_file_path() / logfile
@@ -135,14 +118,40 @@ def config(
         FH = logging.FileHandler(logs, mode=write_mode, encoding="utf-8", delay=delayed)
         FH.setLevel(logging.DEBUG)
         FH.setFormatter(fileFormatter)
-        logger.addHandler(FH)
+        SSX_LOGGER.addHandler(FH)
 
 
 def log_on_entry(func):
     @functools.wraps(func)
     def decorator(*args, **kwargs):
         name = func.__name__
-        logger.debug(f"Running {name} ")
+        SSX_LOGGER.debug(f"Running {name} ")
         return func(*args, **kwargs)
 
     return decorator
+
+
+def setup_collection_logs(expt: str, dev_mode: bool = False) -> MsgGenerator:
+    """A small plan to set up the logging from blueapi on start up as we're running \
+        on procserv.
+        This setup will likely change once the beamline has a cluster.
+    """
+    if (
+        expt == "Serial Fixed"
+    ):  # SSXType.FIXED: See https://github.com/DiamondLightSource/mx-bluesky/issues/608
+        logfile = time.strftime("i24fixedtarget_%d%B%y.log").lower()
+    else:
+        logfile = time.strftime("i24extruder_%d%B%y.log").lower()
+
+    config(logfile, dev_mode=dev_mode)
+    yield from bps.null()
+
+
+def clean_up_log_config_at_end() -> MsgGenerator:
+    """A small plan for blueapi to tidy up logging configuration."""
+    # 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)
+    yield from bps.null()

mx_bluesky/beamlines/i24/serial/parameters/__init__.py

@@ -1,15 +1,19 @@
 from mx_bluesky.beamlines.i24.serial.parameters.constants import SSXType
 from mx_bluesky.beamlines.i24.serial.parameters.experiment_parameters import (
+    BeamSettings,
     ChipDescription,
     ExtruderParameters,
     FixedTargetParameters,
+    SerialAndLaserExperiment,
 )
 from mx_bluesky.beamlines.i24.serial.parameters.utils import get_chip_format
 
 __all__ = [
     "SSXType",
+    "BeamSettings",
     "ExtruderParameters",
     "ChipDescription",
     "FixedTargetParameters",
+    "SerialAndLaserExperiment",
     "get_chip_format",
 ]

mx_bluesky/beamlines/i24/serial/parameters/constants.py

@@ -10,6 +10,12 @@ class SSXType(Enum):
     EXTRUDER = "Serial Jet"
 
 
+BEAM_CENTER_POS: dict[str, list] = {
+    "eiger": [1600.0, 1697.4],
+    "pilatus": [1284.7, 1308.6],
+}
+
+
 OAV_CONFIG_FILES = {
     "zoom_params_file": "/dls_sw/i24/software/gda_versions/gda_9_34/config/xml/jCameraManZoomLevels.xml",
     "oav_config_json": "/dls_sw/i24/software/daq_configuration/json/OAVCentring.json",
@@ -41,7 +47,6 @@ PARAM_FILE_NAME = "parameters.json"
 PARAM_FILE_PATH = _params_file_location()
 PARAM_FILE_PATH_FT = PARAM_FILE_PATH / "fixed_target"
 LITEMAP_PATH = PARAM_FILE_PATH_FT / "litemaps"
-FULLMAP_PATH = PARAM_FILE_PATH_FT / "fullmaps"
 # Paths for r only
 PVAR_FILE_PATH = INTERNAL_FILES_PATH / "fixed_target/pvar_files"
 CS_FILES_PATH = INTERNAL_FILES_PATH / "fixed_target/cs"