mx-bluesky 1.4.0__py3-none-any.whl → 1.4.1a0__py3-none-any.whl

mx_bluesky/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '1.4.0'
-__version_tuple__ = version_tuple = (1, 4, 0)
+__version__ = version = '1.4.1a0'
+__version_tuple__ = version_tuple = (1, 4, 1)

mx_bluesky/beamlines/i04/thawing_plan.py

@@ -3,7 +3,7 @@ from collections.abc import Callable
 import bluesky.plan_stubs as bps
 import bluesky.preprocessors as bpp
 from bluesky.preprocessors import run_decorator, subs_decorator
-from dls_bluesky_core.core import MsgGenerator
+from bluesky.utils import MsgGenerator
 from dodal.beamlines.i04 import MURKO_REDIS_DB, REDIS_HOST, REDIS_PASSWORD
 from dodal.common import inject
 from dodal.devices.oav.oav_detector import OAV

mx_bluesky/beamlines/i24/serial/dcid.py

@@ -1,6 +1,5 @@
 import datetime
 import json
-import logging
 import math
 import os
 import re
@@ -10,6 +9,7 @@ from functools import lru_cache
 
 import requests
 
+from mx_bluesky.beamlines.i24.serial.log import SSX_LOGGER
 from mx_bluesky.beamlines.i24.serial.parameters import SSXType
 from mx_bluesky.beamlines.i24.serial.setup_beamline import (
     Detector,
@@ -25,8 +25,6 @@ try:
 except ImportError:
     pass
 
-logger = logging.getLogger("I24ssx.DCID")
-
 
 # Collection start/end script to kick off analysis
 COLLECTION_START_SCRIPT = "/dls_sw/i24/scripts/RunAtStartOfCollect-i24-ssx.sh"
@@ -41,7 +39,7 @@ CREDENTIALS_LOCATION = "/scratch/ssx_dcserver.key"
 def get_auth_header() -> dict:
     """Read the credentials file and build the Authorisation header"""
     if not os.path.isfile(CREDENTIALS_LOCATION):
-        logger.warning(
+        SSX_LOGGER.warning(
             "Could not read %s; attempting to proceed without credentials",
             CREDENTIALS_LOCATION,
         )
@@ -205,12 +203,12 @@ class DCID:
 
             # Log what we are doing here
             try:
-                logger.info(
+                SSX_LOGGER.info(
                     "BRIDGE: POST /dc --data %s",
                     repr(json.dumps(data)),
                 )
             except Exception:
-                logger.info(
+                SSX_LOGGER.info(
                     "Caught exception converting data to JSON. Data:\n%s\nVERBOSE:\n%s",
                     str({k: type(v) for k, v in data.items()}),
                 )
@@ -224,20 +222,20 @@ class DCID:
             )
             resp.raise_for_status()
             self.dcid = resp.json()["dataCollectionId"]
-            logger.info("Generated DCID %s", self.dcid)
+            SSX_LOGGER.info("Generated DCID %s", self.dcid)
         except requests.HTTPError as e:
             self.error = True
-            logger.error(
+            SSX_LOGGER.error(
                 "DCID generation Failed; Reason from server: %s", e.response.text
             )
             if self.emit_errors:
                 raise
-            logger.exception("Error generating DCID: %s", e)
+            SSX_LOGGER.exception("Error generating DCID: %s", e)
         except Exception as e:
             self.error = True
             if self.emit_errors:
                 raise
-            logger.exception("Error generating DCID: %s", e)
+            SSX_LOGGER.exception("Error generating DCID: %s", e)
 
     def __int__(self):
         return self.dcid
@@ -248,13 +246,13 @@ class DCID:
             return None
         try:
             command = [COLLECTION_START_SCRIPT, str(self.dcid)]
-            logger.info("Running %s", " ".join(command))
+            SSX_LOGGER.info("Running %s", " ".join(command))
             subprocess.Popen(command)
         except Exception as e:
             self.error = True
             if self.emit_errors:
                 raise
-            logger.warning("Error starting start of collect script: %s", e)
+            SSX_LOGGER.warning("Error starting start of collect script: %s", e)
 
     def notify_end(self):
         """Send notifications that the collection has now ended"""
@@ -262,13 +260,13 @@ class DCID:
             return
         try:
             command = [COLLECTION_END_SCRIPT, str(self.dcid)]
-            logger.info("Running %s", " ".join(command))
+            SSX_LOGGER.info("Running %s", " ".join(command))
             subprocess.Popen(command)
         except Exception as e:
             self.error = True
             if self.emit_errors:
                 raise
-            logger.warning("Error running end of collect notification: %s", e)
+            SSX_LOGGER.warning("Error running end of collect notification: %s", e)
 
     def collection_complete(
         self, end_time: str | datetime.datetime | None = None, aborted: bool = False
@@ -285,7 +283,7 @@ class DCID:
             # end_time might be a string from time.ctime
             if isinstance(end_time, str):
                 end_time = datetime.datetime.strptime(end_time, "%a %b %d %H:%M:%S %Y")
-                logger.debug("Parsed end time: %s", end_time)
+                SSX_LOGGER.debug("Parsed end time: %s", end_time)
 
             if not end_time:
                 end_time = datetime.datetime.now().astimezone()
@@ -302,13 +300,13 @@ class DCID:
             if self.dcid is None:
                 # Print what we would have sent. This means that if something is failing,
                 # we still have the data to upload in the log files.
-                logger.info(
+                SSX_LOGGER.info(
                     'BRIDGE: No DCID but Would PATCH "/dc/XXXX" --data=%s',
                     repr(json.dumps(data)),
                 )
                 return
 
-            logger.info(
+            SSX_LOGGER.info(
                 'BRIDGE: PATCH "/dc/%s" --data=%s', self.dcid, repr(json.dumps(data))
             )
             response = requests.patch(
@@ -318,7 +316,7 @@ class DCID:
                 headers=get_auth_header(),
             )
             response.raise_for_status()
-            logger.info("Successfully updated end time for DCID %d", self.dcid)
+            SSX_LOGGER.info("Successfully updated end time for DCID %d", self.dcid)
         except Exception as e:
             resp_obj = getattr(e, "response", None)
             try:
@@ -333,7 +331,7 @@ class DCID:
             self.error = True
             if self.emit_errors:
                 raise
-            logger.warning("Error completing DCID: %s (%s)", e, resp_str)
+            SSX_LOGGER.warning("Error completing DCID: %s (%s)", e, resp_str)
 
 
 def get_pilatus_filename_template_from_pvs() -> str:
@@ -385,9 +383,9 @@ def get_beamsize() -> tuple[float | None, float | None]:
     h_mode = caget("BL24I-OP-MFM-01:G1:TARGETAPPLY")
     # Validate these and note an error otherwise
     if not v_mode.startswith("VMFM") or v_mode[4:] not in focus_modes:
-        logger.error("Unrecognised vertical beam mode %s", v_mode)
+        SSX_LOGGER.error("Unrecognised vertical beam mode %s", v_mode)
     if not h_mode.startswith("HMFM") or h_mode[4:] not in focus_modes:
-        logger.error("Unrecognised horizontal beam mode %s", h_mode)
+        SSX_LOGGER.error("Unrecognised horizontal beam mode %s", h_mode)
     _, h, _ = focus_modes.get(h_mode[4:], (None, None, None))
     _, _, v = focus_modes.get(v_mode[4:], (None, None, None))
 

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

@@ -16,7 +16,7 @@ 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.hutch_shutter import HutchShutter, ShutterDemand
 from dodal.devices.i24.aperture import Aperture
@@ -262,7 +262,7 @@ def main_extruder_plan(
         SSX_LOGGER.info("Using Eiger detector")
 
         SSX_LOGGER.debug(f"Creating the directory for the collection in {filepath}.")
-        Path(filepath).mkdir(parents=True)
+        Path(filepath).mkdir(parents=True, exist_ok=True)
 
         caput(pv.eiger_seqID, int(caget(pv.eiger_seqID)) + 1)
         SSX_LOGGER.info(f"Eiger quickshot setup: filepath {filepath}")

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

@@ -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
 

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."""

mx_bluesky/beamlines/i24/serial/fixed_target/i24ssx_Chip_Collect_py3v1.py

@@ -10,7 +10,7 @@ from time import sleep
 import bluesky.plan_stubs as bps
 import bluesky.preprocessors as bpp
 import numpy as np
-from blueapi.core import MsgGenerator
+from bluesky.utils import MsgGenerator
 from dodal.common import inject
 from dodal.devices.hutch_shutter import HutchShutter, ShutterDemand
 from dodal.devices.i24.aperture import Aperture
@@ -77,7 +77,7 @@ def calculate_collection_timeout(parameters: FixedTargetParameters) -> float:
     Returns:
         The estimated collection time, in s.
     """
-    buffer = PMAC_MOVE_TIME * parameters.total_num_images + 2
+    buffer = PMAC_MOVE_TIME * parameters.total_num_images + 600
     pump_setting = parameters.pump_repeat
     collection_time = parameters.total_num_images * parameters.exposure_time_s
     if pump_setting in [
@@ -97,7 +97,7 @@ def calculate_collection_timeout(parameters: FixedTargetParameters) -> float:
         )
         if pump_setting == PumpProbeSetting.Medium1:
             # Long delay between pump and probe, with fast shutter opening and closing.
-            timeout = timeout + SHUTTER_OPEN_TIME
+            timeout = timeout + SHUTTER_OPEN_TIME * parameters.total_num_images
     return timeout
 
 
@@ -234,8 +234,6 @@ def load_motion_program_data(
             SSX_LOGGER.info(f"Map type is None, setting program prefix to {prefix}")
         elif map_type == MappingType.Lite:
             prefix = 12
-        elif map_type == MappingType.Full:
-            prefix = 13
         else:
             SSX_LOGGER.warning(f"Unknown Map Type, map_type = {map_type}")
             return
@@ -301,14 +299,6 @@ def get_prog_num(
         SSX_LOGGER.info(f"Map type: {str(map_type)}")
         SSX_LOGGER.info("Program number: 12")
         return 12
-    if map_type == MappingType.Full:
-        # TODO See https://github.com/DiamondLightSource/mx-bluesky/issues/515
-        SSX_LOGGER.info(f"Map type: {str(map_type)}")
-        SSX_LOGGER.info("Program number: 13")
-        # TODO once reinstated return 13
-        msg = "Full mapping is broken and currently disabled."
-        SSX_LOGGER.error(msg)
-        raise ValueError(msg)
 
 
 @log_on_entry
@@ -352,14 +342,6 @@ def datasetsizei24(
         total_numb_imgs = int(np.prod(chip_format) * block_count * n_exposures)
         SSX_LOGGER.info(f"Calculated number of images: {total_numb_imgs}")
 
-    elif map_type == MappingType.Full:
-        SSX_LOGGER.error("Not Set Up For Full Mapping")
-        raise ValueError("The beamline is currently not set for Full Mapping.")
-
-    else:
-        SSX_LOGGER.warning(f"Unknown Map Type, map_type = {str(map_type)}")
-        raise ValueError("Unknown map type")
-
     SSX_LOGGER.info("Set PV to calculated number of images.")
     caput(pv.me14e_gp10, int(total_numb_imgs))
 
@@ -444,7 +426,11 @@ def start_i24(
         )
 
         SSX_LOGGER.debug("Arm Pilatus. Arm Zebra.")
-        shutter_time_offset = SHUTTER_OPEN_TIME if PumpProbeSetting.Medium1 else 0.0
+        shutter_time_offset = (
+            SHUTTER_OPEN_TIME
+            if parameters.pump_repeat is PumpProbeSetting.Medium1
+            else 0.0
+        )
         yield from setup_zebra_for_fastchip_plan(
             zebra,
             parameters.detector_name,
@@ -467,7 +453,7 @@ def start_i24(
         SSX_LOGGER.info("Using Eiger detector")
 
         SSX_LOGGER.debug(f"Creating the directory for the collection in {filepath}.")
-        Path(filepath).mkdir(parents=True)
+        Path(filepath).mkdir(parents=True, exist_ok=True)
 
         SSX_LOGGER.info(f"Triggered Eiger setup: filepath {filepath}")
         SSX_LOGGER.info(f"Triggered Eiger setup: filename {filename}")
@@ -503,7 +489,11 @@ def start_i24(
         )
 
         SSX_LOGGER.debug("Arm Zebra.")
-        shutter_time_offset = SHUTTER_OPEN_TIME if PumpProbeSetting.Medium1 else 0.0
+        shutter_time_offset = (
+            SHUTTER_OPEN_TIME
+            if parameters.pump_repeat is PumpProbeSetting.Medium1
+            else 0.0
+        )
         yield from setup_zebra_for_fastchip_plan(
             zebra,
             parameters.detector_name,

mx_bluesky/beamlines/i24/serial/fixed_target/i24ssx_Chip_Manager_py3v1.py

@@ -5,7 +5,6 @@ This version changed to python3 March2020 by RLO
 
 import json
 import re
-import shutil
 import sys
 import time
 from pathlib import Path
@@ -14,25 +13,14 @@ from time import sleep
 
 import bluesky.plan_stubs as bps
 import numpy as np
-from blueapi.core import MsgGenerator
-from dodal.beamlines import i24
+from bluesky.utils import MsgGenerator
 from dodal.common import inject
 from dodal.devices.i24.beamstop import Beamstop, BeamstopPositions
 from dodal.devices.i24.dual_backlight import BacklightPositions, DualBacklight
 from dodal.devices.i24.i24_detector_motion import DetectorMotion
 from dodal.devices.i24.pmac import PMAC, EncReset, LaserSettings
 
-from mx_bluesky.beamlines.i24.serial.fixed_target import (
-    i24ssx_Chip_Mapping_py3v1 as mapping,
-)
-from mx_bluesky.beamlines.i24.serial.fixed_target import (
-    i24ssx_Chip_StartUp_py3v1 as startup,
-)
-from mx_bluesky.beamlines.i24.serial.fixed_target.ft_utils import (
-    ChipType,
-    Fiducials,
-    MappingType,
-)
+from mx_bluesky.beamlines.i24.serial.fixed_target.ft_utils import ChipType, Fiducials
 from mx_bluesky.beamlines.i24.serial.log import (
     SSX_LOGGER,
     _read_visit_directory_from_file,
@@ -41,7 +29,6 @@ from mx_bluesky.beamlines.i24.serial.log import (
 from mx_bluesky.beamlines.i24.serial.parameters import get_chip_format
 from mx_bluesky.beamlines.i24.serial.parameters.constants import (
     CS_FILES_PATH,
-    FULLMAP_PATH,
     LITEMAP_PATH,
     PARAM_FILE_NAME,
     PARAM_FILE_PATH_FT,
@@ -106,6 +93,9 @@ def initialise_stages(
     sleep(0.1)
     SSX_LOGGER.info("Clearing General Purpose PVs 1-120")
     for i in range(4, 120):
+        if i == 100:
+            # Do not clear visit PV
+            continue
         pvar = "ME14E-MO-IOC-01:GP" + str(i)
         caput(pvar, 0)
         sys.stdout.write(".")
@@ -171,11 +161,6 @@ def write_parameter_file(
     SSX_LOGGER.info("Information written to file \n")
     SSX_LOGGER.info(pformat(params_dict))
 
-    if map_type == MappingType.Full:
-        # This step creates some header files (.addr, .spec), containing the parameters,
-        # that are only needed when full mapping is in use.
-        SSX_LOGGER.info("Full mapping in use. Running start up now.")
-        startup.run()
     yield from bps.null()
 
 
@@ -239,11 +224,11 @@ def save_screen_map() -> MsgGenerator:
     with open(litemap_path / "currentchip.map", "w") as f:
         SSX_LOGGER.debug("Printing only blocks with block_val == 1")
         for x in range(1, 82):
-            block_str = "ME14E-MO-IOC-01:GP%i" % (x + 10)
+            block_str = f"ME14E-MO-IOC-01:GP{x + 10:d}"
             block_val = int(caget(block_str))
             if block_val == 1:
-                SSX_LOGGER.info("%s %d" % (block_str, block_val))
-            line = "%02dstatus    P3%02d1 \t%s\n" % (x, x, block_val)
+                SSX_LOGGER.info(f"{block_str} {block_val:d}")
+            line = f"{x:02d}status    P3{x:02d}1 \t{block_val}\n"
             f.write(line)
     yield from bps.null()
 
@@ -286,29 +271,6 @@ def upload_parameters(pmac: PMAC = inject("pmac")) -> MsgGenerator:
     yield from bps.null()
 
 
-@log_on_entry
-def upload_full(pmac: PMAC | None = None) -> MsgGenerator:
-    if not pmac:
-        pmac = i24.pmac()
-
-    map_file: Path = FULLMAP_PATH / "currentchip.full"
-    if not map_file.exists():
-        raise FileNotFoundError(f"The file {map_file} has not yet been created")
-    with open(map_file) as fh:
-        f = fh.readlines()
-
-    for _i in range(len(f) // 2):
-        pmac_list = []
-        for _j in range(2):
-            pmac_list.append(f.pop(0).rstrip("\n"))
-        writeline = " ".join(pmac_list)
-        SSX_LOGGER.info(f"{writeline}")
-        yield from bps.abs_set(pmac.pmac_string, writeline, wait=True)
-        yield from bps.sleep(0.02)
-    SSX_LOGGER.debug("Upload fullmap done")
-    yield from bps.null()
-
-
 @log_on_entry
 def load_stock_map(map_choice: str = "clear") -> MsgGenerator:
     # TODO See https://github.com/DiamondLightSource/mx_bluesky/issues/122
@@ -553,7 +515,7 @@ def load_lite_map() -> MsgGenerator:
                     break
                 button_name = str(row) + str(column)
                 lab_num = x * 8 + z
-                label = "%02.d" % (lab_num + 1)
+                label = f"{lab_num + 1:02d}"
                 btn_names[button_name] = label
         block_dict = btn_names
     else:
@@ -576,26 +538,6 @@ def load_lite_map() -> MsgGenerator:
     yield from bps.null()
 
 
-@log_on_entry
-def load_full_map() -> MsgGenerator:
-    from matplotlib import pyplot as plt
-
-    params = startup.read_parameter_file()
-
-    fullmap_fid = FULLMAP_PATH / f"{caget(MAP_FILEPATH_PV)}.spec"
-    SSX_LOGGER.info(f"Opening {fullmap_fid}")
-    mapping.plot_file(plt, fullmap_fid, params.chip.chip_type.value)
-    mapping.convert_chip_to_hex(fullmap_fid, params.chip.chip_type.value)
-    shutil.copy2(fullmap_fid.with_suffix(".full"), FULLMAP_PATH / "currentchip.full")
-    SSX_LOGGER.info(
-        "Copying {} to {}".format(
-            fullmap_fid.with_suffix(".full"), FULLMAP_PATH / "currentchip.full"
-        )
-    )
-    SSX_LOGGER.debug("Load full map done")
-    yield from bps.null()
-
-
 @log_on_entry
 def moveto(place: str = "origin", pmac: PMAC = inject("pmac")) -> MsgGenerator:
     SSX_LOGGER.info(f"Move to: {place}")
@@ -731,15 +673,15 @@ def fiducial(point: int = 1, pmac: PMAC = inject("pmac")) -> MsgGenerator:
     output_param_path.mkdir(parents=True, exist_ok=True)
     SSX_LOGGER.info(f"Writing Fiducial File {output_param_path}/fiducial_{point}.txt")
     SSX_LOGGER.info("MTR\tRBV\tRAW\tCorr\tf_value")
-    SSX_LOGGER.info("MTR1\t%1.4f\t%i" % (rbv_1, mtr1_dir))
-    SSX_LOGGER.info("MTR2\t%1.4f\t%i" % (rbv_2, mtr2_dir))
-    SSX_LOGGER.info("MTR3\t%1.4f\t%i" % (rbv_3, mtr3_dir))
+    SSX_LOGGER.info(f"MTR1\t{rbv_1:1.4f}\t{mtr1_dir:d}")
+    SSX_LOGGER.info(f"MTR2\t{rbv_2:1.4f}\t{mtr2_dir:d}")
+    SSX_LOGGER.info(f"MTR3\t{rbv_3:1.4f}\t{mtr3_dir:d}")
 
     with open(output_param_path / f"fiducial_{point}.txt", "w") as f:
         f.write("MTR\tRBV\tCorr\n")
-        f.write("MTR1\t%1.4f\t%i\n" % (rbv_1, mtr1_dir))
-        f.write("MTR2\t%1.4f\t%i\n" % (rbv_2, mtr2_dir))
-        f.write("MTR3\t%1.4f\t%i" % (rbv_3, mtr3_dir))
+        f.write(f"MTR1\t{rbv_1:1.4f}\t{mtr1_dir:d}\n")
+        f.write(f"MTR2\t{rbv_2:1.4f}\t{mtr2_dir:d}\n")
+        f.write(f"MTR3\t{rbv_3:1.4f}\t{mtr3_dir:d}")
     SSX_LOGGER.info(f"Fiducial {point} set.")
     yield from bps.null()
 
@@ -901,13 +843,13 @@ def cs_maker(pmac: PMAC = inject("pmac")) -> MsgGenerator:
     sleep(2.5)
     yield from set_pmac_strings_for_cs(pmac, {"cs1": cs1, "cs2": cs2, "cs3": cs3})
     yield from bps.trigger(pmac.to_xyz_zero)
-    sleep(0.1)
+    sleep(2.5)
     yield from bps.trigger(pmac.home, wait=True)
-    sleep(0.1)
+    sleep(2.5)
     SSX_LOGGER.debug(f"Chip_type is {chip_type}")
     if chip_type == 0:
         yield from bps.abs_set(pmac.pmac_string, "!x0.4y0.4", wait=True)
-        sleep(0.1)
+        sleep(2.5)
         yield from bps.trigger(pmac.home, wait=True)
     else:
         yield from bps.trigger(pmac.home, wait=True)