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

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

@@ -1,14 +1,16 @@
 import json
+from abc import abstractmethod
 from pathlib import Path
 from typing import Literal
 
-from pydantic import BaseModel, field_validator
+from pydantic import BaseModel, ConfigDict, field_validator
 
 from mx_bluesky.beamlines.i24.serial.fixed_target.ft_utils import (
     ChipType,
     MappingType,
     PumpProbeSetting,
 )
+from mx_bluesky.beamlines.i24.serial.parameters.constants import SSXType
 
 
 class SerialExperiment(BaseModel):
@@ -20,6 +22,7 @@ class SerialExperiment(BaseModel):
     exposure_time_s: float
     detector_distance_mm: float
     detector_name: Literal["eiger", "pilatus"]
+    transmission: float
 
     @field_validator("visit", mode="before")
     @classmethod
@@ -36,23 +39,38 @@ class SerialExperiment(BaseModel):
 class LaserExperiment(BaseModel):
     """Laser settings for pump probe serial collections."""
 
-    laser_dwell_s: float | None = None  # pump exposure time
-    laser_delay_s: float | None = None  # pump delay
+    laser_dwell_s: float = 0.0  # pump exposure time
+    laser_delay_s: float = 0.0  # pump delay
     pre_pump_exposure_s: float | None = None  # Pre illumination, just for chip
 
 
-class ExtruderParameters(SerialExperiment, LaserExperiment):
-    """Extruder parameter model."""
-
-    num_images: int
-    pump_status: bool
-
+class SerialAndLaserExperiment(SerialExperiment, LaserExperiment):
     @classmethod
     def from_file(cls, filename: str | Path):
         with open(filename) as fh:
             raw_params = json.load(fh)
         return cls(**raw_params)
 
+    @property
+    @abstractmethod
+    def nexgen_experiment_type(self) -> str:
+        pass
+
+
+class ExtruderParameters(SerialAndLaserExperiment):
+    """Extruder parameter model."""
+
+    num_images: int
+    pump_status: bool
+
+    @property
+    def nexgen_experiment_type(self) -> str:
+        return "extruder"
+
+    @property
+    def ispyb_experiment_type(self) -> SSXType:
+        return SSXType.EXTRUDER
+
 
 class ChipDescription(BaseModel):
     """Parameters defining the chip in use for FT collection."""
@@ -86,7 +104,7 @@ class ChipDescription(BaseModel):
             return ((self.y_num_steps - 1) * self.y_step_size) + self.b2b_vert
 
 
-class FixedTargetParameters(SerialExperiment, LaserExperiment):
+class FixedTargetParameters(SerialAndLaserExperiment):
     """Fixed target parameter model."""
 
     num_exposures: int
@@ -96,8 +114,17 @@ class FixedTargetParameters(SerialExperiment, LaserExperiment):
     checker_pattern: bool = False
     total_num_images: int = 0  # Calculated in the code for now
 
-    @classmethod
-    def from_file(cls, filename: str | Path):
-        with open(filename) as fh:
-            raw_params = json.load(fh)
-        return cls(**raw_params)
+    @property
+    def nexgen_experiment_type(self) -> str:
+        return "fixed-target"
+
+    @property
+    def ispyb_experiment_type(self) -> SSXType:
+        return SSXType.FIXED
+
+
+class BeamSettings(BaseModel):
+    model_config = ConfigDict(frozen=True)
+    wavelength_in_a: float
+    beam_size_in_um: tuple[float, float]
+    beam_center_in_mm: tuple[float, float]

mx_bluesky/beamlines/i24/serial/parameters/fixed_target/cs/cs_maker.json

@@ -1,8 +1,8 @@
 {
-    "scalex": 10004.0,
-    "scaley": 10005.2,
+    "scalex": 10004.7,
+    "scaley": 10004.4,
     "scalez": 10000.0,
-    "skew": -0.01,
+    "skew": 0.120,
     "Sx_dir": 1,
     "Sy_dir": 1,
     "Sz_dir": 1

mx_bluesky/beamlines/i24/serial/run_extruder.sh

@@ -1,19 +1,44 @@
 #!/bin/bash
 
+NO_PROCESERV_TEST=false
+
+case "$2" in
+    -t | --test)
+        echo "Will run serial in test mode without procserv."
+        NO_PROCESERV_TEST=true
+        ;;
+esac
+
+
 # Get edm path from input
 edm_path=$1
 
 # Get the directory of this script
 current=$( realpath "$( dirname "$0" )" )
 
-# Run script to start blueapi serve
-. $current/start_blueapi.sh
+if [[ $NO_PROCESERV_TEST == true ]]; then
+    echo "Start the blueapi sever"
+
+    # Run script to start blueapi serve
+    . $current/start_blueapi.sh
+fi
+
+echo "Set up logging configuration"
+blueapi -c "${current}/blueapi_config.yaml" controller run setup_collection_logs '{"expt":"Serial Jet"}'
 
 # Open the edm screen for an extruder serial collection
 echo "Starting extruder edm screen."
 edm -x "${edm_path}/EX-gui/DiamondExtruder-I24-py3v1.edl"
 
-echo "Edm screen closed, bye!"
+echo "Edm screen closed"
+
+echo "Clean up log configuration"
+blueapi -c "${current}/blueapi_config.yaml" controller run clean_up_log_config_at_end
+
+if [[ $NO_PROCESERV_TEST == true ]]; then
+    # In this case blueapi server needs to be killed.
+    pgrep blueapi | xargs kill
+    echo "Blueapi process killed"
+fi
 
-pgrep blueapi | xargs kill
-echo "Blueapi process killed"
+echo "All done, bye!"

mx_bluesky/beamlines/i24/serial/run_fixed_target.sh

@@ -1,5 +1,14 @@
 #!/bin/bash
 
+NO_PROCESERV_TEST=false
+
+case "$2" in
+    -t | --test)
+        echo "Will run serial in test mode without procserv."
+        NO_PROCESERV_TEST=true
+        ;;
+esac
+
 # Get edm path from input
 edm_path=$1
 
@@ -9,14 +18,30 @@ export EDMDATAFILES="/dls_sw/prod/R3.14.12.3/support/motor/6-7-1dls14/motorApp/o
 # Get the directory of this script
 current=$( realpath "$( dirname "$0" )" )
 
-# Run script to start blueapi serve
-. $current/start_blueapi.sh
+
+if [[ $NO_PROCESERV_TEST == true ]]; then
+    echo "Start the blueapi sever"
+
+    # Run script to start blueapi serve
+    . $current/start_blueapi.sh
+fi
+
+echo "Set up logging configuration"
+blueapi -c "${current}/blueapi_config.yaml" controller run setup_collection_logs '{"expt":"Serial Fixed"}'
 
 # Open the edm screen for a fixed target serial collection
 echo "Starting fixed target edm screen."
 edm -x "${edm_path}/FT-gui/DiamondChipI24-py3v1.edl"
 
-echo "Edm screen closed, bye!"
+echo "Edm screen closed"
+
+echo "Clean up log configuration"
+blueapi -c "${current}/blueapi_config.yaml" controller run clean_up_log_config_at_end
+
+if [[ $NO_PROCESERV_TEST == true ]]; then
+    # In this case blueapi server needs to be killed.
+    pgrep blueapi | xargs kill
+    echo "Blueapi process killed"
+fi
 
-pgrep blueapi | xargs kill
-echo "Blueapi process killed"
+echo "All done, bye!"

mx_bluesky/beamlines/i24/serial/run_serial.py

@@ -1,9 +1,17 @@
-import logging
+import argparse
 import subprocess
 from os import environ
 from pathlib import Path
 
-logger = logging.getLogger("I24ssx.run")
+from mx_bluesky.beamlines.i24.serial.log import SSX_LOGGER
+from mx_bluesky.beamlines.i24.serial.parameters import SSXType
+
+
+def _parse_input(expt: SSXType):
+    parser = argparse.ArgumentParser(description=f"Run a {expt} collection.")
+    parser.add_argument("-t", "--test", action="store_true", help="Run in test mode.")
+    args = parser.parse_args()
+    return args
 
 
 def get_location(default: str = "dev") -> str:
@@ -19,18 +27,26 @@ def _get_file_path() -> Path:
 
 
 def run_extruder():
+    args = _parse_input(SSXType.EXTRUDER)
     loc = get_location()
-    logger.debug(f"Running on {loc}.")
+    SSX_LOGGER.info(f"Running on {loc}.")
     edm_path = get_edm_path()
     filepath = _get_file_path()
-    logger.debug(f"Running {filepath}/run_extruder.sh")
-    subprocess.run(["sh", filepath / "run_extruder.sh", edm_path.as_posix()])
+    test_mode = "--test" if args.test else ""
+    SSX_LOGGER.debug(f"Running {filepath}/run_extruder.sh")
+    subprocess.run(
+        ["bash", filepath / "run_extruder.sh", edm_path.as_posix(), test_mode]
+    )
 
 
 def run_fixed_target():
+    args = _parse_input(SSXType.FIXED)
     loc = get_location()
-    logger.info(f"Running on {loc}.")
+    SSX_LOGGER.info(f"Running on {loc}.")
     edm_path = get_edm_path()
     filepath = _get_file_path()
-    logger.debug(f"Running {filepath}/run_fixed_target.sh")
-    subprocess.run(["sh", filepath / "run_fixed_target.sh", edm_path.as_posix()])
+    test_mode = "--test" if args.test else ""
+    SSX_LOGGER.debug(f"Running {filepath}/run_fixed_target.sh")
+    subprocess.run(
+        ["bash", filepath / "run_fixed_target.sh", edm_path.as_posix(), test_mode]
+    )

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

@@ -22,8 +22,6 @@ def caget(pv):
             a = Popen(["caget", pv], stdout=PIPE, stderr=PIPE)
             a_stdout, a_stderr = a.communicate()
             val = a_stdout.split()[1].decode("ascii")
-            # val = evaluate(val)
-            # val = val.decode('ascii')
         except Exception:
             print("Exception in ca_py3.py caget, maybe this PV doesnt exist:", pv)
             pass

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

@@ -23,6 +23,8 @@ def __which__():
     print("path to pv.py: ")
 
 
+requested_transmission = "BL24I-OP-ATTN-01:T2A:SETVAL1"
+
 # PILATUS
 pilat_filepath = "BL24I-EA-PILAT-01:cam1:FilePath"
 pilat_filename = "BL24I-EA-PILAT-01:cam1:FileName"