mx-bluesky 1.4.6__py3-none-any.whl → 1.4.8__py3-none-any.whl

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

@@ -4,7 +4,7 @@ Fixed target data collection
 
 from datetime import datetime
 from pathlib import Path
-from time import sleep
+from traceback import format_exception
 
 import bluesky.plan_stubs as bps
 import bluesky.preprocessors as bpp
@@ -52,52 +52,6 @@ from mx_bluesky.beamlines.i24.serial.setup_beamline.setup_zebra_plans import (
 )
 from mx_bluesky.beamlines.i24.serial.write_nexus import call_nexgen
 
-# Move this in common place as part of
-# https://github.com/DiamondLightSource/mx-bluesky/pull/603
-PMAC_MOVE_TIME = 0.008  # Move time between positions on chip ~ 7-8 ms
-
-
-def calculate_collection_timeout(parameters: FixedTargetParameters) -> float:
-    """Give an estimation of the time the plan should wait for the data collection \
-        to be finished.
-
-    For non-pump probe collections and collection with short delays, it should be \
-    enough to use the collection time plus a genereous 30s buffer.
-    For EAVA (Excite and visit again) collections instead, the laser dwell and laser \
-    delay times should be included in the calculation. For long dalays between pump \
-    and probe, the shutter opening time will also need to be taken into account.
-    For more details on the dynamics see
-    https://confluence.diamond.ac.uk/display/MXTech/Dynamics+and+fixed+targets.
-
-    Args:
-        parameters (FixedTargerParameters): The collection parameters.
-
-    Returns:
-        The estimated collection time, in s.
-    """
-    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 [
-        PumpProbeSetting.NoPP,
-        PumpProbeSetting.Short1,
-        PumpProbeSetting.Short2,
-    ]:
-        timeout = collection_time + buffer
-    else:
-        # EAVA: Excite and visit again
-        num_windows = parameters.total_num_images / parameters.num_exposures
-        timeout = (
-            collection_time
-            + parameters.laser_dwell_s * num_windows  # type: ignore
-            + parameters.laser_delay_s
-            + buffer
-        )
-        if pump_setting == PumpProbeSetting.Medium1:
-            # Long delay between pump and probe, with fast shutter opening and closing.
-            timeout = timeout + SHUTTER_OPEN_TIME * parameters.total_num_images
-    return timeout
-
 
 def write_userlog(
     parameters: FixedTargetParameters,
@@ -362,7 +316,7 @@ def start_i24(
             f"Fastchip Pilatus setup: exposure time {parameters.exposure_time_s}"
         )
 
-        sup.pilatus(
+        yield from sup.pilatus(
             "fastchip",
             [
                 filepath,
@@ -407,7 +361,7 @@ def start_i24(
         caput(pv.pilat_acquire, "1")  # Arm pilatus
         yield from arm_zebra(zebra)
         caput(pv.pilat_filename, filename)
-        sleep(1.5)
+        yield from bps.sleep(1.5)
 
     elif parameters.detector_name == "eiger":
         SSX_LOGGER.info("Using Eiger detector")
@@ -423,7 +377,7 @@ def start_i24(
             f"Triggered Eiger setup: exposure time {parameters.exposure_time_s}"
         )
 
-        sup.eiger(
+        yield from sup.eiger(
             "triggered",
             [
                 filepath,
@@ -431,6 +385,7 @@ def start_i24(
                 parameters.total_num_images,
                 parameters.exposure_time_s,
             ],
+            dcm,
         )
 
         # DCID process depends on detector PVs being set up already
@@ -468,7 +423,7 @@ def start_i24(
             )
         yield from arm_zebra(zebra)
 
-        sleep(1.5)
+        yield from bps.sleep(1.5)
 
     else:
         msg = f"Unknown Detector Type, det_type = {parameters.detector_name}"
@@ -501,12 +456,12 @@ def finish_i24(
         SSX_LOGGER.debug("Finish I24 Pilatus")
         complete_filename = f"{parameters.filename}_{caget(pv.pilat_filenum)}"
         yield from reset_zebra_when_collection_done_plan(zebra)
-        sup.pilatus("return-to-normal", None)
-        sleep(0.2)
+        yield from sup.pilatus("return-to-normal", None)
+        yield from bps.sleep(0.2)
     elif parameters.detector_name == "eiger":
         SSX_LOGGER.debug("Finish I24 Eiger")
         yield from reset_zebra_when_collection_done_plan(zebra)
-        sup.eiger("return-to-normal", None)
+        yield from sup.eiger("return-to-normal", None, dcm)
         complete_filename = cagetstring(pv.eiger_ODfilenameRBV)  # type: ignore
     else:
         raise ValueError(f"{parameters.detector_name=} unrecognised")
@@ -521,12 +476,12 @@ def finish_i24(
     write_userlog(parameters, complete_filename, transmission, wavelength)
 
 
-def run_aborted_plan(pmac: PMAC, dcid: DCID):
+def run_aborted_plan(pmac: PMAC, dcid: DCID, exception: Exception):
     """Plan to send pmac_strings to tell the PMAC when a collection has been aborted, \
         either by pressing the Abort button or because of a timeout, and to reset the \
         P variable.
     """
-    SSX_LOGGER.warning("Data Collection Aborted")
+    SSX_LOGGER.warning(f"Data Collection Aborted: {format_exception(exception)}")
     yield from bps.trigger(pmac.abort_program, wait=True)
 
     end_time = datetime.now()
@@ -595,7 +550,7 @@ def main_fixed_target_plan(
 
     SSX_LOGGER.info("Moving to Start")
     yield from bps.trigger(pmac.to_xyz_zero)
-    sleep(2.0)
+    yield from bps.sleep(2.0)
 
     # Now ready for data collection. Open fast shutter (zebra gate)
     SSX_LOGGER.info("Opening fast shutter.")
@@ -622,12 +577,6 @@ def kickoff_and_complete_collection(pmac: PMAC, parameters: FixedTargetParameter
         parameters.chip.chip_type, parameters.map_type, parameters.pump_repeat
     )
     yield from bps.abs_set(pmac.program_number, prog_num, group="setup_pmac")
-    # Calculate approx collection time
-    total_collection_time = calculate_collection_timeout(parameters)
-    SSX_LOGGER.info(f"Estimated collection time: {total_collection_time}s.")
-    yield from bps.abs_set(
-        pmac.collection_time, total_collection_time, group="setup_pmac"
-    )
     yield from bps.wait(group="setup_pmac")  # Make sure the soft signals are set
 
     @bpp.run_decorator(md={"subplan_name": "run_ft_collection"})
@@ -666,7 +615,7 @@ def tidy_up_after_collection_plan(
     """
     SSX_LOGGER.info("Closing fast shutter")
     yield from close_fast_shutter(zebra)
-    sleep(2.0)
+    yield from bps.sleep(2.0)
 
     # This probably should go in main then
     if parameters.detector_name == "pilatus":
@@ -676,7 +625,7 @@ def tidy_up_after_collection_plan(
         SSX_LOGGER.debug("Eiger Acquire STOP")
         caput(pv.eiger_acquire, 0)
         caput(pv.eiger_ODcapture, "Done")
-    sleep(0.5)
+    yield from bps.sleep(0.5)
 
     yield from finish_i24(zebra, pmac, shutter, dcm, parameters)
 
@@ -732,7 +681,7 @@ def run_fixed_target_plan(
             parameters,
             dcid,
         ),
-        except_plan=lambda e: (yield from run_aborted_plan(pmac, dcid)),
+        except_plan=lambda e: (yield from run_aborted_plan(pmac, dcid, e)),
         final_plan=lambda: (
             yield from tidy_up_after_collection_plan(
                 zebra, pmac, shutter, dcm, parameters, dcid

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

@@ -6,10 +6,8 @@ This version changed to python3 March2020 by RLO
 import json
 import re
 import sys
-import time
 from pathlib import Path
 from pprint import pformat
-from time import sleep
 
 import bluesky.plan_stubs as bps
 import numpy as np
@@ -100,7 +98,7 @@ def initialise_stages(
 
     caput(pv.pilat_cbftemplate, 0)
 
-    sleep(0.1)
+    yield from bps.sleep(0.1)
     SSX_LOGGER.info("Clearing General Purpose PVs 1-120")
     for i in range(4, 120):
         if i == 100:
@@ -259,7 +257,7 @@ def upload_chip_map_to_geobrick(pmac: PMAC, chip_map: list[int]) -> MsgGenerator
         SSX_LOGGER.debug(f"Set {pvar_str} for block {block}")
         yield from bps.abs_set(pmac.pmac_string, pvar_str, wait=True)
         # Wait for PMAC to be done processing PVAR string
-        sleep(0.02)
+        yield from bps.sleep(0.02)
     SSX_LOGGER.debug("Upload parameters done.")
 
 
@@ -832,16 +830,16 @@ def cs_maker(pmac: PMAC = inject("pmac")) -> MsgGenerator:
     SSX_LOGGER.info(f"{sqfact1:1.4f} \n {sqfact2:1.4f} \n {sqfact3:1.4f}")
     SSX_LOGGER.debug("Long wait, please be patient")
     yield from bps.trigger(pmac.to_xyz_zero)
-    sleep(2.5)
+    yield from bps.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(2.5)
+    yield from bps.sleep(2.5)
     yield from bps.trigger(pmac.home, wait=True)
-    sleep(2.5)
+    yield from bps.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(2.5)
+        yield from bps.sleep(2.5)
         yield from bps.trigger(pmac.home, wait=True)
     else:
         yield from bps.trigger(pmac.home, wait=True)
@@ -932,12 +930,12 @@ def block_check(pmac: PMAC = inject("pmac")) -> MsgGenerator:
             for entry in block_start_list:
                 if int(caget(pv.me14e_gp9)) != 0:
                     SSX_LOGGER.warning("Block Check Aborted")
-                    sleep(1.0)
+                    yield from bps.sleep(1.0)
                     break
                 block, x, y = entry
                 SSX_LOGGER.debug(f"Block: {block} -> (x={x} y={y})")
                 yield from bps.abs_set(pmac.pmac_string, f"!x{x}y{y}", wait=True)
-                time.sleep(0.4)
+                yield from bps.sleep(0.4)
         else:
             SSX_LOGGER.warning("Block Check Aborted due to GP 9 not equalling 0")
             break

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

@@ -34,7 +34,12 @@ def _get_beam_centre(oav: OAV):
 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)
-    zoomcalibrator = 1.547 - (0.03 * currentzoom) + (0.0001634 * currentzoom**2)
+    zoomcalibrator = (
+        1.285
+        - (0.02866 * currentzoom)
+        + (0.00025 * currentzoom**2)
+        - (0.0000008151 * currentzoom**3)
+    )
     return zoomcalibrator
 
 
@@ -49,8 +54,10 @@ def _move_on_mouse_click_plan(
     zoomcalibrator = yield from _calculate_zoom_calibrator(oav)
     beamX, beamY = yield from _get_beam_centre(oav)
     x, y = clicked_position
-    xmove = -1 * (beamX - x) * zoomcalibrator
-    ymove = 1 * (beamY - y) * zoomcalibrator
+    xmove = -10 * (beamX - x) * zoomcalibrator
+    ymove = 10 * (beamY - y) * zoomcalibrator
+    SSX_LOGGER.info(f"Zoom calibrator {zoomcalibrator}")
+    SSX_LOGGER.info(f"Beam centre {beamX} {beamY}")
     SSX_LOGGER.info(f"Moving X and Y {xmove} {ymove}")
     xmovepmacstring = "#1J:" + str(xmove)
     ymovepmacstring = "#2J:" + str(ymove)

mx_bluesky/beamlines/i24/serial/log.py

@@ -99,15 +99,6 @@ def config(
         dev_mode (bool, optional): If true, will log to graylog on localhost instead \
             of production. Defaults to False.
     """
-    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
         fileFormatter = logging.Formatter(
@@ -118,6 +109,15 @@ def config(
         FH.setLevel(logging.DEBUG)
         FH.setFormatter(fileFormatter)
         SSX_LOGGER.addHandler(FH)
+    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)
 
 
 def log_on_entry(func):

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

@@ -1,4 +1,5 @@
-from typing import Any
+from collections.abc import Sequence
+from typing import Any, Literal
 
 from mx_bluesky.beamlines.i24.serial.fixed_target.ft_utils import ChipType
 from mx_bluesky.beamlines.i24.serial.parameters.experiment_parameters import (
@@ -13,8 +14,27 @@ class EmptyMapError(Exception):
     pass
 
 
-def get_chip_format(chip_type: ChipType) -> ChipDescription:
-    """Default parameter values."""
+def get_chip_format(
+    chip_type: ChipType,
+    format: Sequence[int | float] | None = None,
+    origin: Literal["edm", "web"] = "edm",
+) -> ChipDescription:
+    """Get the default parameter values for the requested chip type.
+
+    For an Oxford-type chip, the default values are hard coded as the dimensions are
+    always the same. For a Custom chip instead, the number of steps and step size in
+    each direction must be entered through the GUI - web or edm. If the collection is
+    run through the edm, the values will be read from the general purpose PVs set on
+    there. If instead the plan is run from the web UI, the values will be passed in the
+    form of a list/tuple of 4 values.
+
+    Args:
+        chip_type (ChipType): Chip in use
+        custom_format (Sequence[int | float], optional): Number and size of steps input
+            from the web ui. Format should be: [int, int, float, float].
+            Defaults to None.
+        origin (str, optional): UI in use, can be either web or edm. Defaults to edm.
+    """
     defaults: dict[str, int | float] = {}
     match chip_type:
         case ChipType.Oxford:
@@ -33,10 +53,19 @@ def get_chip_format(chip_type: ChipType) -> ChipDescription:
             defaults["x_blocks"] = defaults["y_blocks"] = 1
             defaults["b2b_horz"] = defaults["b2b_vert"] = 0.0
         case ChipType.Custom:
-            defaults["x_num_steps"] = int(caget(pv.me14e_gp6))
-            defaults["y_num_steps"] = int(caget(pv.me14e_gp7))
-            defaults["x_step_size"] = float(caget(pv.me14e_gp8))
-            defaults["y_step_size"] = float(caget(pv.me14e_gp99))
+            if origin == "edm":
+                defaults["x_num_steps"] = int(caget(pv.me14e_gp6))
+                defaults["y_num_steps"] = int(caget(pv.me14e_gp7))
+                defaults["x_step_size"] = float(caget(pv.me14e_gp8))
+                defaults["y_step_size"] = float(caget(pv.me14e_gp99))
+            else:
+                # NOTE Test for WEB GUI
+                if not format:
+                    raise ValueError("Format for custom chip not passed")
+                defaults["x_num_steps"] = format[0]
+                defaults["y_num_steps"] = format[1]
+                defaults["x_step_size"] = format[2]
+                defaults["y_step_size"] = format[3]
             defaults["x_blocks"] = defaults["y_blocks"] = 1
             defaults["b2b_horz"] = defaults["b2b_vert"] = 0.0
         case ChipType.MISP:

mx_bluesky/beamlines/i24/serial/set_visit_directory.sh

@@ -35,7 +35,7 @@ if [[ "${visit: -1}" != "/" ]]; then
     visit="${visit}/"
 fi
 
-ex_pv=BL24I-EA-IOC-12:GP1
+ex_pv=BL24I-MO-IOC-13:GP1
 ft_pv=ME14E-MO-IOC-01:GP100
 
 shopt -s nocasematch

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

@@ -154,7 +154,6 @@ dcm_gap = "BL24I-MO-DCM-01:GAP"
 dcm_roll1 = "BL24I-MO-DCM-01:XTAL1:ROLL"
 dcm_roll2 = "BL24I-MO-DCM-01:XTAL2:ROLL"
 dcm_pitch2 = "BL24I-MO-DCM-01:XTAL2:PITCH"
-dcm_lambda = "BL24I-MO-DCM-01:LAMBDA"
 dcm_energy = "BL24I-MO-DCM-01:ENERGY"
 
 # S2
@@ -258,22 +257,22 @@ step09_pmac_response = "BL24I-MO-IOC-09:ASYN9.AINP"
 step10_pmac_response = "BL24I-MO-IOC-10:ASYN10.AINP"
 step11_pmac_response = "BL24I-MO-IOC-11:ASYN11.AINP"
 step12_pmac_response = "BL24I-MO-IOC-12:ASYN12.AINP"
-# General Purpose PV
-ioc12_gp1 = "BL24I-EA-IOC-12:GP1"
-ioc12_gp2 = "BL24I-EA-IOC-12:GP2"
-ioc12_gp3 = "BL24I-EA-IOC-12:GP3"
-ioc12_gp4 = "BL24I-EA-IOC-12:GP4"
-ioc12_gp5 = "BL24I-EA-IOC-12:GP5"
-ioc12_gp6 = "BL24I-EA-IOC-12:GP6"
-ioc12_gp7 = "BL24I-EA-IOC-12:GP7"
-ioc12_gp8 = "BL24I-EA-IOC-12:GP8"
-ioc12_gp9 = "BL24I-EA-IOC-12:GP9"
-ioc12_gp10 = "BL24I-EA-IOC-12:GP10"
-ioc12_gp11 = "BL24I-EA-IOC-12:GP11"
-ioc12_gp12 = "BL24I-EA-IOC-12:GP12"
-ioc12_gp13 = "BL24I-EA-IOC-12:GP13"
-ioc12_gp14 = "BL24I-EA-IOC-12:GP14"
-ioc12_gp15 = "BL24I-EA-IOC-12:GP15"
+# General Purpose PV. Now use STEP13
+ioc13_gp1 = "BL24I-MO-IOC-13:GP1"
+ioc13_gp2 = "BL24I-MO-IOC-13:GP2"
+ioc13_gp3 = "BL24I-MO-IOC-13:GP3"
+ioc13_gp4 = "BL24I-MO-IOC-13:GP4"
+ioc13_gp5 = "BL24I-MO-IOC-13:GP5"
+ioc13_gp6 = "BL24I-MO-IOC-13:GP6"
+ioc13_gp7 = "BL24I-MO-IOC-13:GP7"
+ioc13_gp8 = "BL24I-MO-IOC-13:GP8"
+ioc13_gp9 = "BL24I-MO-IOC-13:GP9"
+ioc13_gp10 = "BL24I-MO-IOC-13:GP10"
+ioc13_gp11 = "BL24I-MO-IOC-13:GP11"
+ioc13_gp12 = "BL24I-MO-IOC-13:GP12"
+ioc13_gp13 = "BL24I-MO-IOC-13:GP13"
+ioc13_gp14 = "BL24I-MO-IOC-13:GP14"
+ioc13_gp15 = "BL24I-MO-IOC-13:GP15"
 # ME14E
 me14e_pmac_str = "ME14E-MO-CHIP-01:PMAC_STRING"
 me14e_stage_x = "ME14E-MO-CHIP-01:X"

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

@@ -19,8 +19,8 @@ class Pilatus:
         round(a * b, 3) for a, b in zip(image_size_pixels, pixel_size_mm, strict=False)
     )
 
-    det_y_threshold = 560.0
-    det_y_target = 566.0
+    det_y_threshold = 640.0
+    det_y_target = 647.0
 
     class pv:
         detector_distance = pv.pilat_detdist
@@ -48,8 +48,8 @@ class Eiger:
         round(a * b, 3) for a, b in zip(image_size_pixels, pixel_size_mm, strict=False)
     )
 
-    det_y_threshold = -10.0
-    det_y_target = -22.0
+    det_y_threshold = 70.0
+    det_y_target = 59.0
 
     class pv:
         detector_distance = pv.eiger_detdist