mx-bluesky 0.0.1__py3-none-any.whl → 0.3.1__py3-none-any.whl

mx_bluesky/__main__.py

@@ -9,9 +9,8 @@ __all__ = ["main"]
 
 def main(args=None):
     parser = ArgumentParser()
-    parser.add_argument("--version", action="version", version=__version__)
+    parser.add_argument("-v", "--version", action="version", version=__version__)
     args = parser.parse_args(args)
-
     run_plan()
 
 

mx_bluesky/_version.py

@@ -1,4 +1,16 @@
 # file generated by setuptools_scm
 # don't change, don't track in version control
-__version__ = version = '0.0.1'
-__version_tuple__ = version_tuple = (0, 0, 1)
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple, Union
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '0.3.1'
+__version_tuple__ = version_tuple = (0, 3, 1)

mx_bluesky/example.py

@@ -1,13 +1,13 @@
-from bluesky import RunEngine
 from bluesky.plan_stubs import rd
+from bluesky.run_engine import RunEngine
 from ophyd import Component, Device, EpicsSignal
 
 
 class Synchrotron(Device):
-    ring_current: EpicsSignal = Component(EpicsSignal, "SR-DI-DCCT-01:SIGNAL")
+    ring_current = Component(EpicsSignal, "SR-DI-DCCT-01:SIGNAL")
 
 
-def test_plan(synch: Synchrotron):
+def example_plan(synch: Synchrotron):
     current = yield from rd(synch.ring_current)
     print(current)
 
@@ -16,4 +16,4 @@ def run_plan():
     RE = RunEngine()
     my_synch = Synchrotron(name="Synchrotron")
     my_synch.wait_for_connection()
-    RE(test_plan(my_synch))
+    RE(example_plan(my_synch))

mx_bluesky/i04/__init__.py

@@ -0,0 +1,3 @@
+from mx_bluesky.i04.thawing_plan import thaw, thaw_and_center
+
+__all__ = ["thaw", "thaw_and_center"]

mx_bluesky/i04/callbacks/murko_callback.py

@@ -0,0 +1,45 @@
+import copy
+import json
+
+from bluesky.callbacks import CallbackBase
+from dodal.log import LOGGER
+from event_model.documents import Event, RunStart
+from redis import StrictRedis
+
+
+class MurkoCallback(CallbackBase):
+    def __init__(self, redis_host: str, redis_password: str, redis_db: int = 0):
+        self.redis_client = StrictRedis(
+            host=redis_host, password=redis_password, db=redis_db
+        )
+        self.last_uuid = None
+
+    def start(self, doc: RunStart) -> RunStart | None:
+        self.murko_metadata = {
+            "zoom_percentage": doc.get("zoom_percentage"),
+            "microns_per_x_pixel": doc.get("microns_per_x_pixel"),
+            "microns_per_y_pixel": doc.get("microns_per_y_pixel"),
+            "beam_centre_i": doc.get("beam_centre_i"),
+            "beam_centre_j": doc.get("beam_centre_j"),
+            "sample_id": doc.get("sample_id"),
+        }
+        self.last_uuid = None
+        return doc
+
+    def event(self, doc: Event) -> Event:
+        if latest_omega := doc["data"].get("smargon-omega"):
+            if self.last_uuid is not None:
+                self.call_murko(self.last_uuid, latest_omega)
+        elif (uuid := doc["data"].get("oav_to_redis_forwarder-uuid")) is not None:
+            self.last_uuid = uuid
+        return doc
+
+    def call_murko(self, uuid: str, omega: float):
+        metadata = copy.deepcopy(self.murko_metadata)
+        metadata["omega_angle"] = omega
+        metadata["uuid"] = uuid
+
+        # Send metadata to REDIS and trigger murko
+        self.redis_client.hset("test-metadata", uuid, json.dumps(metadata))
+        self.redis_client.publish("murko", json.dumps(metadata))
+        LOGGER.info("Metadata sent to redis")

mx_bluesky/i04/thawing_plan.py

@@ -0,0 +1,84 @@
+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 dodal.beamlines.i04 import MURKO_REDIS_DB, REDIS_HOST, REDIS_PASSWORD
+from dodal.common import inject
+from dodal.devices.oav.oav_detector import OAV
+from dodal.devices.oav.oav_to_redis_forwarder import OAVToRedisForwarder
+from dodal.devices.robot import BartRobot
+from dodal.devices.smargon import Smargon
+from dodal.devices.thawer import Thawer, ThawerStates
+
+from mx_bluesky.i04.callbacks.murko_callback import MurkoCallback
+
+
+def thaw_and_center(
+    time_to_thaw: float,
+    rotation: float = 360,
+    robot: BartRobot = inject("robot"),
+    thawer: Thawer = inject("thawer"),
+    smargon: Smargon = inject("smargon"),
+    oav: OAV = inject("oav"),
+    oav_to_redis_forwarder: OAVToRedisForwarder = inject("oav_to_redis_forwarder"),
+) -> MsgGenerator:
+    zoom_percentage = yield from bps.rd(oav.zoom_controller.percentage)
+    sample_id = yield from bps.rd(robot.sample_id)
+
+    yield from bps.abs_set(oav.zoom_controller.level, "1.0x", wait=True)
+
+    @subs_decorator(MurkoCallback(REDIS_HOST, REDIS_PASSWORD, MURKO_REDIS_DB))
+    @run_decorator(
+        md={
+            "microns_per_x_pixel": oav.parameters.micronsPerXPixel,
+            "microns_per_y_pixel": oav.parameters.micronsPerYPixel,
+            "beam_centre_i": oav.parameters.beam_centre_i,
+            "beam_centre_j": oav.parameters.beam_centre_j,
+            "zoom_percentage": zoom_percentage,
+            "sample_id": sample_id,
+        }
+    )
+    def _thaw_and_center():
+        yield from bps.kickoff(oav_to_redis_forwarder, wait=True)
+        yield from bps.monitor(smargon.omega.user_readback, name="smargon")
+        yield from bps.monitor(oav_to_redis_forwarder.uuid, name="oav")
+        yield from thaw(time_to_thaw, rotation, thawer, smargon)
+        yield from bps.complete(oav_to_redis_forwarder)
+
+    yield from _thaw_and_center()
+
+
+def thaw(
+    time_to_thaw: float,
+    rotation: float = 360,
+    thawer: Thawer = inject("thawer"),
+    smargon: Smargon = inject("smargon"),
+) -> MsgGenerator:
+    """Rotates the sample and thaws it at the same time.
+
+    Args:
+        time_to_thaw (float): Time to thaw for, in seconds.
+        rotation (float, optional): How much to rotate by whilst thawing, in degrees.
+                                    Defaults to 360.
+        thawer (Thawer, optional): The thawing device. Defaults to inject("thawer").
+        smargon (Smargon, optional): The smargon used to rotate.
+                                     Defaults to inject("smargon")
+    """
+    inital_velocity = yield from bps.rd(smargon.omega.velocity)
+    new_velocity = abs(rotation / time_to_thaw) * 2.0
+
+    def do_thaw():
+        yield from bps.abs_set(smargon.omega.velocity, new_velocity, wait=True)
+        yield from bps.abs_set(thawer.control, ThawerStates.ON, wait=True)
+        yield from bps.rel_set(smargon.omega, rotation, wait=True)
+        yield from bps.rel_set(smargon.omega, -rotation, wait=True)
+
+    def cleanup():
+        yield from bps.abs_set(smargon.omega.velocity, inital_velocity, wait=True)
+        yield from bps.abs_set(thawer.control, ThawerStates.OFF, wait=True)
+
+    # Always cleanup even if there is a failure
+    yield from bpp.contingency_wrapper(
+        do_thaw(),
+        final_plan=cleanup,
+    )

mx_bluesky/i24/serial/__init__.py

@@ -0,0 +1,49 @@
+from .extruder.i24ssx_Extruder_Collect_py3v2 import (
+    enter_hutch,
+    initialise_extruder,
+    laser_check,
+    run_extruder_plan,
+)
+from .fixed_target.i24ssx_Chip_Collect_py3v1 import run_fixed_target_plan
+from .fixed_target.i24ssx_Chip_Manager_py3v1 import (
+    block_check,
+    cs_maker,
+    cs_reset,
+    define_current_chip,
+    fiducial,
+    initialise_stages,
+    laser_control,
+    load_lite_map,
+    load_stock_map,
+    moveto,
+    moveto_preset,
+    pumpprobe_calc,
+    save_screen_map,
+    upload_parameters,
+    write_parameter_file,
+)
+from .setup_beamline.setup_detector import setup_detector_stage
+
+__all__ = [
+    "setup_detector_stage",
+    "run_extruder_plan",
+    "initialise_extruder",
+    "enter_hutch",
+    "laser_check",
+    "run_fixed_target_plan",
+    "moveto",
+    "moveto_preset",
+    "block_check",
+    "cs_maker",
+    "cs_reset",
+    "define_current_chip",
+    "fiducial",
+    "initialise_stages",
+    "laser_control",
+    "load_lite_map",
+    "load_stock_map",
+    "pumpprobe_calc",
+    "save_screen_map",
+    "upload_parameters",
+    "write_parameter_file",
+]

mx_bluesky/i24/serial/blueapi_config.yaml

@@ -0,0 +1,12 @@
+env:
+  sources:
+    - kind: dodal
+      module: dodal.beamlines.i24
+    - kind: planFunctions
+      module: mx_bluesky.i24.serial
+  events:
+    broadcast_status_events: False
+api:
+  port: 25565
+stomp:
+  host: i24-control.diamond.ac.uk

mx_bluesky/{I24 → i24}/serial/dcid.py

@@ -1,5 +1,3 @@
-from __future__ import annotations
-
 import datetime
 import json
 import logging
@@ -12,8 +10,8 @@ from functools import lru_cache
 
 import requests
 
-from mx_bluesky.I24.serial.parameters import SSXType
-from mx_bluesky.I24.serial.setup_beamline import (
+from mx_bluesky.i24.serial.parameters import SSXType
+from mx_bluesky.i24.serial.setup_beamline import (
     Detector,
     Eiger,
     Pilatus,
@@ -65,9 +63,7 @@ class DCID:
             stop collection if you can't get a DCID
         timeout: Length of time to wait for the DB server before giving up
         ssx_type: The type of SSX experiment this is for
-        visit: The name of the visit e.g. "mx12345-4"
-        image_dir: The location the images will be written
-
+        detector: The detector in use for current collection.
 
 
     Attributes:
@@ -78,31 +74,24 @@ class DCID:
     def __init__(
         self,
         *,
-        server: str = None,
+        server: str | None = None,
         emit_errors: bool = True,
         timeout: float = 10,
         ssx_type: SSXType = SSXType.FIXED,
-        visit: str,
-        image_dir: str,
-        start_time: datetime.datetime,
-        num_images: int,
-        exposure_time: float,
-        shots_per_position: int = 1,
         detector: Detector | Literal["eiger", "pilatus"] | None = None,
-        pump_exposure_time: float | None = None,
-        pump_delay: float | None = None,
-        pump_status: int = 0,
     ):
+        self.detector: Detector
         # Handle case of string literal
         if detector == "eiger":
-            detector = Eiger()
+            self.detector = Eiger()
         elif detector == "pilatus":
-            detector = Pilatus()
+            self.detector = Pilatus()
         elif detector is None:
-            detector = Pilatus()
+            self.detector = Pilatus()
             warnings.warn(
                 "Please pass detector= to DCID. Pilatus assumed, this will be removed in the future.",
                 UserWarning,
+                stacklevel=5,
             )
 
         self.server = server or DEFAULT_ISPYB_SERVER
@@ -111,6 +100,25 @@ class DCID:
         self.timeout = timeout
         self.ssx_type = SSXType(ssx_type)
         self.dcid = None
+
+    def generate_dcid(
+        self,
+        visit: str,
+        image_dir: str,
+        num_images: int,
+        exposure_time: float,
+        start_time: datetime.datetime | None = None,
+        shots_per_position: int = 1,
+        pump_exposure_time: float | None = None,
+        pump_delay: float = 0,
+        pump_status: int = 0,
+    ):
+        """Generate an ispyb DCID.
+
+        Args:
+            visit: The name of the visit e.g. "mx12345-4"
+            image_dir: The location the images will be written
+        """
         try:
             if not start_time:
                 start_time = datetime.datetime.now().astimezone()
@@ -118,24 +126,24 @@ class DCID:
                 start_time = start_time.astimezone()
 
             # Gather data from the beamline
-            detector_distance = float(caget(detector.pv.detector_distance))
-            wavelength = float(caget(detector.pv.wavelength))
-            resolution = get_resolution(detector, detector_distance, wavelength)
+            detector_distance = float(caget(self.detector.pv.detector_distance))
+            wavelength = float(caget(self.detector.pv.wavelength))
+            resolution = get_resolution(self.detector, detector_distance, wavelength)
             beamsize_x, beamsize_y = get_beamsize()
-            transmission = float(caget(detector.pv.transmission)) * 100
-            xbeam, ybeam = get_beam_center(detector)
+            transmission = float(caget(self.detector.pv.transmission)) * 100
+            xbeam, ybeam = get_beam_center(self.detector)
 
-            if isinstance(detector, Pilatus):
+            if isinstance(self.detector, Pilatus):
                 # Mirror the construction that the PPU does
                 fileTemplate = get_pilatus_filename_template_from_pvs()
                 startImageNumber = 0
-            elif isinstance(detector, Eiger):
+            elif isinstance(self.detector, Eiger):
                 # Eiger base filename is directly written to the PV
                 # Nexgen then uses this to write the .nxs file
-                fileTemplate = cagetstring(detector.pv.file_name) + ".nxs"
+                fileTemplate = str(cagetstring(self.detector.pv.file_name)) + ".nxs"
                 startImageNumber = 1
             else:
-                raise ValueError("Unknown detector:", detector)
+                raise ValueError("Unknown detector:", self.detector)
 
             events = [
                 {
@@ -154,7 +162,8 @@ class DCID:
                 # pump_status = 1: pump then probe
                 # pump_status = 2: pump within probe
                 # pump_status = 3-7: different EAVA modes (i.e. also pump then probe)
-                if pump_status != 2:
+                if pump_status != 2 and self.ssx_type is SSXType.FIXED:
+                    # Pump status could be 1 for extruder but not have this.
                     # pump then probe - pump_delay corresponds to time *before* first image
                     pump_delay = -pump_delay
                 events.append(
@@ -170,7 +179,7 @@ class DCID:
 
             data = {
                 "detectorDistance": float(detector_distance),
-                "detectorId": detector.id,
+                "detectorId": self.detector.id,
                 "exposureTime": float(exposure_time),
                 "fileTemplate": fileTemplate,
                 "imageDirectory": str(image_dir),
@@ -276,7 +285,7 @@ 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.info("Parsed end time: %s", end_time)
+                logger.debug("Parsed end time: %s", end_time)
 
             if not end_time:
                 end_time = datetime.datetime.now().astimezone()
@@ -311,8 +320,8 @@ class DCID:
             response.raise_for_status()
             logger.info("Successfully updated end time for DCID %d", self.dcid)
         except Exception as e:
+            resp_obj = getattr(e, "response", None)
             try:
-                resp_obj = getattr(e, "response", None)
                 if resp_obj is not None:
                     resp_str = resp_obj.text
                 # resp_str = repr(getattr(e, "Iresponse", "<no attribute>"))
@@ -338,17 +347,20 @@ def get_pilatus_filename_template_from_pvs() -> str:
     filename_template = cagetstring(pv.pilat_filetemplate)
     file_number = int(caget(pv.pilat_filenumber))
     # Exploit fact that passing negative numbers will put the - before the 0's
-    expected_filename = filename_template % (filename, f"{file_number:05d}_", -9)
+    expected_filename = str(filename_template % (filename, f"{file_number:05d}_", -9))
     # Now, find the -09 part of this
     numberpart = re.search(r"(-0+9)", expected_filename)
     # Make sure this was the only one
-    assert re.search(r"(-0+9)", expected_filename[numberpart.end() :]) is None
-    template_fill = "#" * len(numberpart.group(0))
-    return (
-        expected_filename[: numberpart.start()]
-        + template_fill
-        + expected_filename[numberpart.end() :]
-    )
+    if numberpart is not None:
+        assert re.search(r"(-0+9)", expected_filename[numberpart.end() :]) is None
+        template_fill = "#" * len(numberpart.group(0))
+        return (
+            expected_filename[: numberpart.start()]
+            + template_fill
+            + expected_filename[numberpart.end() :]
+        )
+    else:
+        raise ValueError(f"{filename=} did not contain the numbers for templating")
 
 
 def get_beamsize() -> tuple[float | None, float | None]:

mx_bluesky/{I24 → i24}/serial/extruder/EX-gui-edm/DetStage.edl

@@ -113,7 +113,7 @@ font "arial-medium-r-18.0"
 buttonLabel "Move Stage"
 numCmds 1
 command {
-  0 "python SCRIPTS_LOCATION/setup_beamline/setup_detector.py \"Serial Jet\""
+  0 "blueapi -c CONFIG_LOCATION controller run setup_detector_stage '\{\"expt_type\":\"Serial Jet\"\}'"
 }
 endObjectProperties
 
@@ -136,4 +136,3 @@ value {
 }
 autoSize
 endObjectProperties
-

mx_bluesky/{I24 → i24}/serial/extruder/EX-gui-edm/DiamondExtruder-I24-py3v1.edl

@@ -3,8 +3,8 @@ beginScreenProperties
 major 4
 minor 0
 release 1
-x 3046
-y 314
+x 1018
+y 277
 w 700
 h 900
 font "arial-medium-r-18.0"
@@ -370,7 +370,7 @@ font "arial-medium-r-24.0"
 buttonLabel "Start"
 numCmds 1
 command {
-  0 "python SCRIPTS_LOCATION/extruder/i24ssx_Extruder_Collect_py3v2.py run"
+  0 "blueapi -c CONFIG_LOCATION controller run run_extruder_plan"
 }
 endObjectProperties
 
@@ -832,7 +832,7 @@ botShadowColor index 11
 font "arial-medium-r-18.0"
 numCmds 1
 command {
-  0 "python SCRIPTS_LOCATION/extruder/i24ssx_Extruder_Collect_py3v2.py initialise"
+  0 "blueapi -c CONFIG_LOCATION controller run initialise_extruder"
 }
 endObjectProperties
 
@@ -856,31 +856,6 @@ value {
 autoSize
 endObjectProperties
 
-# (Message Button)
-object activeMessageButtonClass
-beginObjectProperties
-major 4
-minor 1
-release 0
-x 561
-y 400
-w 100
-h 40
-fgColor index 0
-onColor index 21
-offColor index 21
-topShadowColor index 1
-botShadowColor index 11
-controlPv "BL24I-EA-IOC-12:GP8"
-pressValue "1"
-releaseValue "1"
-onLabel "Abort"
-offLabel "Abort"
-toggle
-3d
-font "arial-medium-r-24.0"
-endObjectProperties
-
 # (Message Button)
 object activeMessageButtonClass
 beginObjectProperties
@@ -2204,7 +2179,7 @@ font "arial-medium-r-20.0"
 buttonLabel "Laser On"
 numCmds 1
 command {
-  0 "python SCRIPTS_LOCATION/extruder/i24ssx_Extruder_Collect_py3v2.py moveto laseron"
+  0 "blueapi -c CONFIG_LOCATION controller run laser_check '\{\"mode\":\"laseron\"\}'"
 }
 endObjectProperties
 
@@ -2226,7 +2201,7 @@ font "arial-medium-r-20.0"
 buttonLabel "Laser Off"
 numCmds 1
 command {
-  0 "python SCRIPTS_LOCATION/extruder/i24ssx_Extruder_Collect_py3v2.py moveto laseroff"
+  0 "blueapi -c CONFIG_LOCATION controller run laser_check '\{\"mode\":\"laseroff\"\}'"
 }
 endObjectProperties
 
@@ -2248,7 +2223,7 @@ font "arial-medium-r-18.0"
 buttonLabel "Enter hutch"
 numCmds 1
 command {
-  0 "python SCRIPTS_LOCATION/extruder/i24ssx_Extruder_Collect_py3v2.py moveto enterhutch"
+  0 "blueapi -c CONFIG_LOCATION controller run enter_hutch"
 }
 endObjectProperties
 
@@ -2275,3 +2250,24 @@ displayFileName {
 }
 endObjectProperties
 
+# (Shell Command)
+object shellCmdClass
+beginObjectProperties
+major 4
+minor 3
+release 0
+x 559
+y 399
+w 100
+h 40
+fgColor index 0
+bgColor index 21
+topShadowColor index 0
+botShadowColor index 11
+font "arial-medium-r-24.0"
+buttonLabel "Abort"
+numCmds 1
+command {
+  0 "blueapi -c CONFIG_LOCATION controller abort"
+}
+endObjectProperties

mx_bluesky/{I24 → i24}/serial/extruder/EX-gui-edm/microdrop_alignment.edl

@@ -1081,4 +1081,3 @@ value {
 }
 autoSize
 endObjectProperties
-