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

mx_bluesky/beamlines/i24/serial/extruder/i24ssx_Extruder_Collect_py3v2.py

@@ -5,7 +5,6 @@ This version in python3 new Feb2021 by RLO
 """
 
 import json
-import logging
 import re
 import shutil
 import sys
@@ -17,19 +16,30 @@ from time import sleep
 
 import bluesky.plan_stubs as bps
 import bluesky.preprocessors as bpp
-from blueapi.core import MsgGenerator
+from bluesky.utils import MsgGenerator
 from dodal.common import inject
+from dodal.devices.attenuator import ReadOnlyAttenuator
 from dodal.devices.hutch_shutter import HutchShutter, ShutterDemand
 from dodal.devices.i24.aperture import Aperture
+from dodal.devices.i24.beam_center import DetectorBeamCenter
 from dodal.devices.i24.beamstop import Beamstop
 from dodal.devices.i24.dcm import DCM
 from dodal.devices.i24.dual_backlight import DualBacklight
+from dodal.devices.i24.focus_mirrors import FocusMirrorsMode
 from dodal.devices.i24.i24_detector_motion import DetectorMotion
 from dodal.devices.zebra import DISCONNECT, SOFT_IN3, Zebra
 
-from mx_bluesky.beamlines.i24.serial import log
-from mx_bluesky.beamlines.i24.serial.dcid import DCID
-from mx_bluesky.beamlines.i24.serial.parameters import ExtruderParameters, SSXType
+from mx_bluesky.beamlines.i24.serial.dcid import (
+    DCID,
+    get_pilatus_filename_template_from_device,
+    read_beam_info_from_hardware,
+)
+from mx_bluesky.beamlines.i24.serial.log import (
+    SSX_LOGGER,
+    _read_visit_directory_from_file,
+    log_on_entry,
+)
+from mx_bluesky.beamlines.i24.serial.parameters import ExtruderParameters
 from mx_bluesky.beamlines.i24.serial.parameters.constants import (
     PARAM_FILE_NAME,
     PARAM_FILE_PATH,
@@ -54,31 +64,22 @@ from mx_bluesky.beamlines.i24.serial.setup_beamline.setup_zebra_plans import (
 )
 from mx_bluesky.beamlines.i24.serial.write_nexus import call_nexgen
 
-usage = "%(prog)s command [options]"
-logger = logging.getLogger("I24ssx.extruder")
-
 SAFE_DET_Z = 1480
 
 
-def setup_logging():
-    logfile = time.strftime("i24extruder_%d%B%y.log").lower()
-    log.config(logfile)
-
-
 def flush_print(text):
     sys.stdout.write(str(text))
     sys.stdout.flush()
 
 
-@log.log_on_entry
+@log_on_entry
 def initialise_extruder(
     detector_stage: DetectorMotion = inject("detector_motion"),
 ) -> MsgGenerator:
-    setup_logging()
-    logger.info("Initialise Parameters for extruder data collection on I24.")
+    SSX_LOGGER.info("Initialise Parameters for extruder data collection on I24.")
 
     visit = caget(pv.ioc12_gp1)
-    logger.info(f"Visit defined {visit}")
+    SSX_LOGGER.info(f"Visit defined {visit}")
 
     # Define detector in use
     det_type = yield from get_detector_type(detector_stage)
@@ -93,11 +94,11 @@ def initialise_extruder(
     caput(pv.ioc12_gp10, 0)
     caput(pv.ioc12_gp15, det_type.name)
     caput(pv.pilat_cbftemplate, 0)
-    logger.info("Initialisation complete.")
+    SSX_LOGGER.info("Initialisation complete.")
     yield from bps.null()
 
 
-@log.log_on_entry
+@log_on_entry
 def laser_check(
     mode: str,
     zebra: Zebra = inject("zebra"),
@@ -116,8 +117,7 @@ def laser_check(
     detector in use is the Eiger, the Pilatus cable is repurposed to trigger the light \
     source, and viceversa.
     """
-    setup_logging()
-    logger.debug(f"Laser check: {mode}")
+    SSX_LOGGER.debug(f"Laser check: {mode}")
 
     det_type = yield from get_detector_type(detector_stage)
 
@@ -131,24 +131,25 @@ def laser_check(
         yield from set_shutter_mode(zebra, "manual")
 
 
-@log.log_on_entry
+@log_on_entry
 def enter_hutch(
     detector_stage: DetectorMotion = inject("detector_motion"),
 ) -> MsgGenerator:
     """Move the detector stage before entering hutch."""
-    setup_logging()
-    yield from bps.mv(detector_stage.z, SAFE_DET_Z)
-    logger.debug("Detector moved.")
+    yield from bps.mv(detector_stage.z, SAFE_DET_Z)  # type: ignore # See: https://github.com/bluesky/bluesky/issues/1809
+    SSX_LOGGER.debug("Detector moved.")
 
 
-@log.log_on_entry
-def write_parameter_file(detector_stage: DetectorMotion):
+@log_on_entry
+def write_parameter_file(
+    detector_stage: DetectorMotion, attenuator: ReadOnlyAttenuator
+):
     """Writes a json parameter file that can later be parsed by the model."""
     param_file: Path = PARAM_FILE_PATH / PARAM_FILE_NAME
-    logger.debug(f"Writing Parameter File to: {param_file}\n")
+    SSX_LOGGER.debug(f"Writing Parameter File to: {param_file}\n")
 
     det_type = yield from get_detector_type(detector_stage)
-    logger.warning(f"DETECTOR TYPE: {det_type}")
+    SSX_LOGGER.warning(f"DETECTOR TYPE: {det_type}")
     filename = caget(pv.ioc12_gp3)
     # If file name ends in a digit this causes processing/pilatus pain.
     # Append an underscore
@@ -158,21 +159,24 @@ def write_parameter_file(detector_stage: DetectorMotion):
             # Note for future reference. Appending underscore causes more hassle and
             # high probability of users accidentally overwriting data. Use a dash
             filename = filename + "-"
-            logger.info(
+            SSX_LOGGER.info(
                 f"Requested filename ends in a number. Appended dash: {filename}"
             )
 
-    pump_status = bool(caget(pv.ioc12_gp6))
-    pump_exp = float(caget(pv.ioc12_gp9)) if pump_status else None
-    pump_delay = float(caget(pv.ioc12_gp10)) if pump_status else None
+    transmission = yield from bps.rd(attenuator.actual_transmission)
+
+    pump_status = bool(int(caget(pv.ioc12_gp6)))
+    pump_exp = float(caget(pv.ioc12_gp9)) if pump_status else 0.0
+    pump_delay = float(caget(pv.ioc12_gp10)) if pump_status else 0.0
 
     params_dict = {
-        "visit": log._read_visit_directory_from_file().as_posix(),  # noqa
+        "visit": _read_visit_directory_from_file().as_posix(),  # noqa
         "directory": caget(pv.ioc12_gp2),
         "filename": filename,
         "exposure_time_s": float(caget(pv.ioc12_gp5)),
         "detector_distance_mm": float(caget(pv.ioc12_gp7)),
         "detector_name": str(det_type),
+        "transmission": transmission,
         "num_images": int(caget(pv.ioc12_gp4)),
         "pump_status": pump_status,
         "laser_dwell_s": pump_exp,
@@ -181,12 +185,12 @@ def write_parameter_file(detector_stage: DetectorMotion):
     with open(param_file, "w") as f:
         json.dump(params_dict, f, indent=4)
 
-    logger.info("Parameters \n")
-    logger.info(pformat(params_dict))
+    SSX_LOGGER.info("Parameters \n")
+    SSX_LOGGER.info(pformat(params_dict))
     yield from bps.null()
 
 
-@log.log_on_entry
+@log_on_entry
 def main_extruder_plan(
     zebra: Zebra,
     aperture: Aperture,
@@ -195,12 +199,18 @@ def main_extruder_plan(
     detector_stage: DetectorMotion,
     shutter: HutchShutter,
     dcm: DCM,
+    mirrors: FocusMirrorsMode,
+    beam_center_device: DetectorBeamCenter,
     parameters: ExtruderParameters,
     dcid: DCID,
     start_time: datetime,
 ) -> MsgGenerator:
+    yield from sup.set_detector_beam_center_plan(
+        beam_center_device, parameters.detector_name
+    )
+
     # Setting up the beamline
-    logger.debug("Open hutch shutter")
+    SSX_LOGGER.info("Open hutch shutter")
     yield from bps.abs_set(shutter, ShutterDemand.OPEN, wait=True)
 
     yield from sup.setup_beamline_for_collection_plan(
@@ -213,25 +223,25 @@ def main_extruder_plan(
 
     # For pixel detector
     filepath = parameters.collection_directory.as_posix()
-    logger.debug(f"Filepath {filepath}")
-    logger.debug(f"Filename {parameters.filename}")
+    SSX_LOGGER.debug(f"Filepath {filepath}")
+    SSX_LOGGER.debug(f"Filename {parameters.filename}")
 
     if parameters.detector_name == "pilatus":
-        logger.info("Using pilatus mini cbf")
+        SSX_LOGGER.info("Using pilatus mini cbf")
         caput(pv.pilat_cbftemplate, 0)
-        logger.info(f"Pilatus quickshot setup: filepath {filepath}")
-        logger.info(f"Pilatus quickshot setup: filepath {parameters.filename}")
-        logger.info(
+        SSX_LOGGER.info(f"Pilatus quickshot setup: filepath {filepath}")
+        SSX_LOGGER.info(f"Pilatus quickshot setup: filepath {parameters.filename}")
+        SSX_LOGGER.info(
             f"Pilatus quickshot setup: number of images {parameters.num_images}"
         )
-        logger.info(
+        SSX_LOGGER.info(
             f"Pilatus quickshot setup: exposure time {parameters.exposure_time_s}"
         )
 
         if parameters.pump_status:
-            logger.info("Pump probe extruder data collection")
-            logger.info(f"Pump exposure time {parameters.laser_dwell_s}")
-            logger.info(f"Pump delay time {parameters.laser_delay_s}")
+            SSX_LOGGER.info("Pump probe extruder data collection")
+            SSX_LOGGER.info(f"Pump exposure time {parameters.laser_dwell_s}")
+            SSX_LOGGER.info(f"Pump delay time {parameters.laser_delay_s}")
             sup.pilatus(
                 "fastchip",
                 [
@@ -252,7 +262,7 @@ def main_extruder_plan(
                 wait=True,
             )
         else:
-            logger.info("Static experiment: no photoexcitation")
+            SSX_LOGGER.info("Static experiment: no photoexcitation")
             sup.pilatus(
                 "quickshot",
                 [
@@ -267,38 +277,25 @@ def main_extruder_plan(
             )
 
     elif parameters.detector_name == "eiger":
-        logger.info("Using Eiger detector")
-
-        logger.warning(
-            """TEMPORARY HACK!
-            Running a Single image pilatus data collection to create directory."""
-        )  # See https://github.com/DiamondLightSource/mx_bluesky/issues/45
-        num_shots = 1
-        sup.pilatus(
-            "quickshot-internaltrig",
-            [filepath, parameters.filename, num_shots, parameters.exposure_time_s],
-        )
-        logger.debug("Sleep 2s waiting for pilatus to arm")
-        sleep(2.5)
-        caput(pv.pilat_acquire, "0")  # Disarm pilatus
-        sleep(0.5)
-        caput(pv.pilat_acquire, "1")  # Arm pilatus
-        logger.debug("Pilatus data collection DONE")
-        sup.pilatus("return to normal", None)
-        logger.info("Pilatus back to normal. Single image pilatus data collection DONE")
+        SSX_LOGGER.info("Using Eiger detector")
+
+        SSX_LOGGER.debug(f"Creating the directory for the collection in {filepath}.")
+        Path(filepath).mkdir(parents=True, exist_ok=True)
 
         caput(pv.eiger_seqID, int(caget(pv.eiger_seqID)) + 1)
-        logger.info(f"Eiger quickshot setup: filepath {filepath}")
-        logger.info(f"Eiger quickshot setup: filepath {parameters.filename}")
-        logger.info(f"Eiger quickshot setup: number of images {parameters.num_images}")
-        logger.info(
+        SSX_LOGGER.info(f"Eiger quickshot setup: filepath {filepath}")
+        SSX_LOGGER.info(f"Eiger quickshot setup: filepath {parameters.filename}")
+        SSX_LOGGER.info(
+            f"Eiger quickshot setup: number of images {parameters.num_images}"
+        )
+        SSX_LOGGER.info(
             f"Eiger quickshot setup: exposure time {parameters.exposure_time_s}"
         )
 
         if parameters.pump_status:
-            logger.info("Pump probe extruder data collection")
-            logger.debug(f"Pump exposure time {parameters.laser_dwell_s}")
-            logger.debug(f"Pump delay time {parameters.laser_delay_s}")
+            SSX_LOGGER.info("Pump probe extruder data collection")
+            SSX_LOGGER.debug(f"Pump exposure time {parameters.laser_dwell_s}")
+            SSX_LOGGER.debug(f"Pump delay time {parameters.laser_delay_s}")
             sup.eiger(
                 "triggered",
                 [
@@ -319,7 +316,7 @@ def main_extruder_plan(
                 wait=True,
             )
         else:
-            logger.info("Static experiment: no photoexcitation")
+            SSX_LOGGER.info("Static experiment: no photoexcitation")
             sup.eiger(
                 "quickshot",
                 [
@@ -334,37 +331,50 @@ def main_extruder_plan(
             )
     else:
         err = f"Unknown Detector Type, det_type = {parameters.detector_name}"
-        logger.error(err)
+        SSX_LOGGER.error(err)
         raise UnknownDetectorType(err)
 
+    beam_settings = yield from read_beam_info_from_hardware(
+        dcm, mirrors, beam_center_device, parameters.detector_name
+    )
+
     # Do DCID creation BEFORE arming the detector
+    if parameters.detector_name == "eiger":
+        filetemplate = f"{parameters.filename}.nxs"
+    else:
+        filetemplate = yield from get_pilatus_filename_template_from_device()
     dcid.generate_dcid(
-        visit=parameters.visit.name,
+        beam_settings=beam_settings,
         image_dir=parameters.collection_directory.as_posix(),
-        start_time=start_time,
+        file_template=filetemplate,
         num_images=parameters.num_images,
-        exposure_time=parameters.exposure_time_s,
-        pump_exposure_time=parameters.laser_dwell_s,
-        pump_delay=parameters.laser_delay_s or 0,
-        pump_status=int(parameters.pump_status),
+        start_time=start_time,
+        pump_probe=parameters.pump_status,
     )
 
     # Collect
-    logger.info("Fast shutter opening")
+    SSX_LOGGER.info("Fast shutter opening")
     yield from open_fast_shutter(zebra)
     if parameters.detector_name == "pilatus":
-        logger.info("Pilatus acquire ON")
+        SSX_LOGGER.info("Pilatus acquire ON")
         caput(pv.pilat_acquire, 1)
     elif parameters.detector_name == "eiger":
-        logger.info("Triggering Eiger NOW")
+        SSX_LOGGER.info("Triggering Eiger NOW")
         caput(pv.eiger_trigger, 1)
 
     dcid.notify_start()
 
     if parameters.detector_name == "eiger":
-        wavelength = yield from bps.rd(dcm.wavelength_in_a)
-        logger.debug("Call nexgen server for nexus writing.")
-        call_nexgen(None, start_time, parameters, wavelength, "extruder")
+        SSX_LOGGER.debug("Call nexgen server for nexus writing.")
+        beam_x = yield from bps.rd(beam_center_device.beam_x)
+        beam_y = yield from bps.rd(beam_center_device.beam_y)
+        call_nexgen(
+            None,
+            parameters,
+            beam_settings.wavelength_in_a,
+            (beam_x, beam_y),
+            start_time,
+        )
 
     timeout_time = time.time() + parameters.num_images * parameters.exposure_time_s + 10
 
@@ -381,25 +391,25 @@ def main_extruder_plan(
         if zebra_arm_status == 0:  # not zebra.pc.is_armed():
             # As soon as zebra is disarmed, exit.
             # Epics updates this PV once the collection is done.
-            logger.info("Zebra disarmed - Collection done.")
+            SSX_LOGGER.info("Zebra disarmed - Collection done.")
             break
         if time.time() >= timeout_time:
-            logger.warning(
+            SSX_LOGGER.warning(
                 """
                 Something went wrong and data collection timed out. Aborting.
             """
             )
             raise TimeoutError("Data collection timed out.")
 
-    logger.debug("Collection completed without errors.")
+    SSX_LOGGER.info("Collection completed without errors.")
 
 
-@log.log_on_entry
+@log_on_entry
 def collection_aborted_plan(
     zebra: Zebra, detector_name: str, dcid: DCID
 ) -> MsgGenerator:
     """A plan to run in case the collection is aborted before the end."""
-    logger.warning("Data Collection Aborted")
+    SSX_LOGGER.warning("Data Collection Aborted")
     yield from disarm_zebra(zebra)  # If aborted/timed out zebra still armed
     if detector_name == "pilatus":
         caput(pv.pilat_acquire, 0)
@@ -410,7 +420,7 @@ def collection_aborted_plan(
     dcid.collection_complete(end_time, aborted=True)
 
 
-@log.log_on_entry
+@log_on_entry
 def tidy_up_at_collection_end_plan(
     zebra: Zebra,
     shutter: HutchShutter,
@@ -431,23 +441,23 @@ def tidy_up_at_collection_end_plan(
         sup.pilatus("return-to-normal", None)
     elif parameters.detector_name == "eiger":
         sup.eiger("return-to-normal", None)
-        logger.debug(f"{parameters.filename}_{caget(pv.eiger_seqID)}")
-    logger.debug("End of Run")
-    logger.debug("Close hutch shutter")
+        SSX_LOGGER.debug(f"{parameters.filename}_{caget(pv.eiger_seqID)}")
+    SSX_LOGGER.debug("End of Run")
+    SSX_LOGGER.info("Close hutch shutter")
     yield from bps.abs_set(shutter, ShutterDemand.CLOSE, wait=True)
 
     dcid.notify_end()
 
 
-@log.log_on_entry
+@log_on_entry
 def collection_complete_plan(
     collection_directory: Path, detector_name: str, dcid: DCID
 ) -> MsgGenerator:
     if detector_name == "pilatus":
-        logger.info("Pilatus Acquire STOP")
+        SSX_LOGGER.info("Pilatus Acquire STOP")
         caput(pv.pilat_acquire, 0)
     elif detector_name == "eiger":
-        logger.info("Eiger Acquire STOP")
+        SSX_LOGGER.info("Eiger Acquire STOP")
         caput(pv.eiger_acquire, 0)
         caput(pv.eiger_ODcapture, "Done")
 
@@ -455,7 +465,7 @@ def collection_complete_plan(
 
     end_time = datetime.now()
     dcid.collection_complete(end_time, aborted=False)
-    logger.info(f"End Time = {end_time.ctime()}")
+    SSX_LOGGER.info(f"End Time = {end_time.ctime()}")
 
     # Copy parameter file
     shutil.copy2(
@@ -473,20 +483,19 @@ def run_extruder_plan(
     detector_stage: DetectorMotion = inject("detector_motion"),
     shutter: HutchShutter = inject("shutter"),
     dcm: DCM = inject("dcm"),
+    mirrors: FocusMirrorsMode = inject("focus_mirrors"),
+    attenuator: ReadOnlyAttenuator = inject("attenuator"),
 ) -> MsgGenerator:
-    setup_logging()
     start_time = datetime.now()
-    logger.info(f"Collection start time: {start_time.ctime()}")
+    SSX_LOGGER.info(f"Collection start time: {start_time.ctime()}")
 
-    yield from write_parameter_file(detector_stage)
+    yield from write_parameter_file(detector_stage, attenuator)
     parameters = ExtruderParameters.from_file(PARAM_FILE_PATH / PARAM_FILE_NAME)
 
+    beam_center_device = sup.get_beam_center_device(parameters.detector_name)
+
     # DCID - not generated yet
-    dcid = DCID(
-        emit_errors=False,
-        ssx_type=SSXType.EXTRUDER,
-        detector=parameters.detector_name,
-    )
+    dcid = DCID(emit_errors=False, expt_params=parameters)
 
     yield from bpp.contingency_wrapper(
         main_extruder_plan(
@@ -497,6 +506,8 @@ def run_extruder_plan(
             detector_stage=detector_stage,
             shutter=shutter,
             dcm=dcm,
+            mirrors=mirrors,
+            beam_center_device=beam_center_device,
             parameters=parameters,
             dcid=dcid,
             start_time=start_time,

mx_bluesky/beamlines/i24/serial/fixed_target/FT-gui-edm/DiamondChipI24-py3v1.edl

@@ -323,7 +323,7 @@ font "helvetica-bold-r-24.0"
 buttonLabel "Start"
 numCmds 1
 command {
-  0 "blueapi -c CONFIG_LOCATION controller run run_fixed_target_plan '\{\"zebra\":\"zebra\",\"pmac\":\"pmac\",\"aperture\":\"aperture\",\"backlight\":\"backlight\",\"beamstop\":\"beamstop\",\"detector_stage\":\"detector_motion\",\"shutter\":\"shutter\",\"dcm\":\"dcm\"\}'"
+  0 "blueapi -c CONFIG_LOCATION controller run run_fixed_target_plan '\{\"zebra\":\"zebra\",\"pmac\":\"pmac\",\"aperture\":\"aperture\",\"backlight\":\"backlight\",\"beamstop\":\"beamstop\",\"detector_stage\":\"detector_motion\",\"shutter\":\"shutter\",\"dcm\":\"dcm\",\"mirrors\":\"focus_mirrors\",\"attenuator\":\"attenuator\"\}'"
 }
 endObjectProperties
 
@@ -1270,21 +1270,18 @@ topShadowColor index 1
 botShadowColor index 8
 controlPv "ME14E-MO-IOC-01:GP2"
 font "arial-medium-r-18.0"
-numItems 3
+numItems 2
 symbolTag {
   0 "None"
   1 "Mapping Lite"
-  2 "Full Mapping"
 }
 symbol0 {
   0 "NN"
   1 "ML"
-  2 "FM"
 }
 value0 {
   0 "none"
   1 "mappinglite"
-  2 "fullmapping"
 }
 endObjectProperties
 
@@ -3862,7 +3859,7 @@ buttonLabel "Stages"
 numPvs 4
 numDsps 1
 displayFileName {
-  0 "/dls_sw/work/R3.14.12.3/ioc/ME14E/BL/data/ME14E-motors.edl"
+  0 "/dls_sw/work/R3.14.12.7/ioc/ME14E/BL/data/ME14E-motors.edl"
 }
 endObjectProperties
 

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

@@ -12,7 +12,6 @@ from enum import Enum, IntEnum
 class MappingType(IntEnum):
     NoMap = 0
     Lite = 1
-    Full = 2
 
     def __str__(self) -> str:
         """Returns the mapping."""