Set up i24 serial to run on procserv

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

@@ -269,23 +269,8 @@ 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")
+        logger.debug(f"Creating the directory for the collection in {filepath}.")
+        Path(filepath).mkdir(parents=True)
 
         caput(pv.eiger_seqID, int(caget(pv.eiger_seqID)) + 1)
         logger.info(f"Eiger quickshot setup: filepath {filepath}")

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

@@ -3862,7 +3862,7 @@ 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
 

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

@@ -56,10 +56,10 @@
 )
 from mx_bluesky.beamlines.i24.serial.write_nexus import call_nexgen
 
-ABORTED = False
-
 logger = logging.getLogger("I24ssx.fixed_target")
 
+PMAC_MOVE_TIME = 0.008  # Move time between positions on chip ~ 7-8 ms
+
 
 def setup_logging():
     # Log should now change name daily
@@ -85,7 +85,8 @@ def calculate_collection_timeout(parameters: FixedTargetParameters) -> float:
     Returns:
         The estimated collection time, in s.
     """
-    buffer = 30
+    buffer = PMAC_MOVE_TIME * parameters.total_num_images + 2
+    # buffer = 30
     pump_setting = parameters.pump_repeat
     collection_time = parameters.total_num_images * parameters.exposure_time_s
     if pump_setting in [
@@ -474,24 +475,8 @@ def start_i24(
     elif parameters.detector_name == "eiger":
         logger.info("Using Eiger detector")
 
-        logger.warning(
-            """TEMPORARY HACK!
-            Running a Single image pilatus data collection to create directory."""
-        )
-        num_imgs = 1
-        sup.pilatus(
-            "quickshot-internaltrig",
-            [filepath, filename, num_imgs, parameters.exposure_time_s],
-        )
-        logger.debug("Sleep 2s waiting for pilatus to arm")
-        sleep(2)
-        sleep(0.5)
-        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")
+        logger.debug(f"Creating the directory for the collection in {filepath}.")
+        Path(filepath).mkdir(parents=True)
 
         logger.info(f"Triggered Eiger setup: filepath {filepath}")
         logger.info(f"Triggered Eiger setup: filename {filename}")

src/mx_bluesky/beamlines/i24/serial/run_extruder.sh

@@ -1,19 +1,36 @@
 #!/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" )" )
+if [[ $NO_PROCESERV_TEST == true ]]; then
+    echo "Start the blueapi sever"
+
+    # Get the directory of this script
+    current=$( realpath "$( dirname "$0" )" )
 
-# Run script to start blueapi serve
-. $current/start_blueapi.sh
+    # Run script to start blueapi serve
+    . $current/start_blueapi.sh
+fi
 
 # 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!"
 
-pgrep blueapi | xargs kill
-echo "Blueapi process killed"
+if [[ $NO_PROCESERV_TEST == true ]]; then
+    # In this case blueapi server needs to be killed.
+    pgrep blueapi | xargs kill
+    echo "Blueapi process killed"
+fi

src/mx_bluesky/beamlines/i24/serial/run_fixed_target.sh

@@ -1,22 +1,38 @@
 #!/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
 
 # Export env variable for the stages edm to work properly
 export EDMDATAFILES="/dls_sw/prod/R3.14.12.3/support/motor/6-7-1dls14/motorApp/opi/edl"
 
-# Get the directory of this script
-current=$( realpath "$( dirname "$0" )" )
+if [[ $NO_PROCESERV_TEST == true ]]; then
+    echo "Start the blueapi sever"
+
+    # Get the directory of this script
+    current=$( realpath "$( dirname "$0" )" )
 
-# Run script to start blueapi serve
-. $current/start_blueapi.sh
+    # Run script to start blueapi serve
+    . $current/start_blueapi.sh
+fi
 
 # 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!"
 
-pgrep blueapi | xargs kill
-echo "Blueapi process killed"
+if [[ $NO_PROCESERV_TEST == true ]]; then
+    # In this case blueapi server needs to be killed.
+    pgrep blueapi | xargs kill
+    echo "Blueapi process killed"
+fi

src/mx_bluesky/beamlines/i24/serial/run_serial.py

@@ -1,3 +1,4 @@
+import argparse
 import logging
 import subprocess
 from os import environ
@@ -6,6 +7,13 @@
 logger = logging.getLogger("I24ssx.run")
 
 
+def _parse_input(expt: str):
+    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:
     return environ.get("BEAMLINE") or default
 
@@ -19,18 +27,26 @@
 
 
 def run_extruder():
+    args = _parse_input("extruder")
     loc = get_location()
     logger.debug(f"Running on {loc}.")
     edm_path = get_edm_path()
     filepath = _get_file_path()
+    test_mode = "--test" if args.test else ""
     logger.debug(f"Running {filepath}/run_extruder.sh")
-    subprocess.run(["sh", filepath / "run_extruder.sh", edm_path.as_posix()])
+    subprocess.run(
+        ["bash", filepath / "run_extruder.sh", edm_path.as_posix(), test_mode]
+    )
 
 
 def run_fixed_target():
+    args = _parse_input("fixed target")
     loc = get_location()
     logger.info(f"Running on {loc}.")
     edm_path = get_edm_path()
     filepath = _get_file_path()
+    test_mode = "--test" if args.test else ""
     logger.debug(f"Running {filepath}/run_fixed_target.sh")
-    subprocess.run(["sh", filepath / "run_fixed_target.sh", edm_path.as_posix()])
+    subprocess.run(
+        ["bash", filepath / "run_fixed_target.sh", edm_path.as_posix(), test_mode]
+    )

tests/unit_tests/beamlines/i24/serial/extruder/test_extruder_collect.py

@@ -139,7 +139,11 @@ async def test_laser_check(
     "mx_bluesky.beamlines.i24.serial.extruder.i24ssx_Extruder_Collect_py3v2.setup_logging"
 )
 @patch("mx_bluesky.beamlines.i24.serial.extruder.i24ssx_Extruder_Collect_py3v2.bps.rd")
+@patch(
+    "mx_bluesky.beamlines.i24.serial.extruder.i24ssx_Extruder_Collect_py3v2.Path.mkdir"
+)
 def test_run_extruder_quickshot_with_eiger(
+    fake_mkdir,
     fake_read,
     fake_log_setup,
     mock_quickshot_plan,
@@ -180,9 +184,9 @@ def test_run_extruder_quickshot_with_eiger(
     assert fake_dcid.generate_dcid.call_count == 1
     assert fake_dcid.notify_start.call_count == 1
     assert fake_sup.setup_beamline_for_collection_plan.call_count == 1
-    # Check temporary piilatus hack is in there
-    assert fake_sup.pilatus.call_count == 2
     mock_quickshot_plan.assert_called_once()
+    assert fake_mkdir.call_count == 1
+    fake_mkdir.assert_called_once()
 
 
 @patch("mx_bluesky.beamlines.i24.serial.extruder.i24ssx_Extruder_Collect_py3v2.sleep")

tests/unit_tests/beamlines/i24/serial/fixed_target/test_ft_collect.py

@@ -15,6 +15,8 @@
     PumpProbeSetting,
 )
 from mx_bluesky.beamlines.i24.serial.fixed_target.i24ssx_Chip_Collect_py3v1 import (
+    PMAC_MOVE_TIME,
+    calculate_collection_timeout,
     datasetsizei24,
     finish_i24,
     get_chip_prog_values,
@@ -37,6 +39,27 @@ def fake_generator(value):
     return value
 
 
+def test_calculate_collection_timeout(dummy_params_without_pp):
+    dummy_params_without_pp.total_num_images = 400
+    expected_collection_time = (
+        dummy_params_without_pp.total_num_images
+        * dummy_params_without_pp.exposure_time_s
+    )
+    buffer = dummy_params_without_pp.total_num_images * PMAC_MOVE_TIME + 2
+    timeout = calculate_collection_timeout(dummy_params_without_pp)
+
+    assert timeout == expected_collection_time + buffer
+
+
+def test_calculate_collection_timeout_for_eava(dummy_params_with_pp):
+    dummy_params_with_pp.total_num_images = 400
+    buffer = dummy_params_with_pp.total_num_images * PMAC_MOVE_TIME + 2
+    expected_pump_and_probe_time = 12.05
+    timeout = calculate_collection_timeout(dummy_params_with_pp)
+
+    assert timeout == expected_pump_and_probe_time + buffer
+
+
 @patch("mx_bluesky.beamlines.i24.serial.fixed_target.i24ssx_Chip_Collect_py3v1.caput")
 def test_datasetsizei24_for_one_block_and_two_exposures(
     fake_caput, dummy_params_without_pp
@@ -134,7 +157,11 @@ def test_load_motion_program_data(
 @patch("mx_bluesky.beamlines.i24.serial.fixed_target.i24ssx_Chip_Collect_py3v1.caget")
 @patch("mx_bluesky.beamlines.i24.serial.fixed_target.i24ssx_Chip_Collect_py3v1.sup")
 @patch("mx_bluesky.beamlines.i24.serial.fixed_target.i24ssx_Chip_Collect_py3v1.sleep")
+@patch(
+    "mx_bluesky.beamlines.i24.serial.fixed_target.i24ssx_Chip_Collect_py3v1.Path.mkdir"
+)
 def test_start_i24_with_eiger(
+    fake_mkdir,
     fake_sleep,
     fake_sup,
     fake_caget,
@@ -165,9 +192,9 @@ def test_start_i24_with_eiger(
     assert fake_sup.eiger.call_count == 1
     assert fake_sup.setup_beamline_for_collection_plan.call_count == 1
     assert fake_sup.move_detector_stage_to_position_plan.call_count == 1
-    # Pilatus gets called for hack to create directory
-    assert fake_sup.pilatus.call_count == 2
     assert fake_dcid.generate_dcid.call_count == 1
+    assert fake_mkdir.call_count == 1
+    fake_mkdir.assert_called_once()
 
     shutter_call_list = [
         call("Reset", wait=True, timeout=10.0),

utility_scripts/procserv_ioc_start.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+# Sources the python environment and starts a blueapi server
+# on a python IOC to run serial on I24 with procserv
+
+# Get the directory of this script
+current_directory=$( realpath "$( dirname "$0" )" )
+# Get the directory with the venv
+env_directory=$(dirname $current_directory)
+# And where the blueapi config lives
+config_directory="${env_directory}/src/mx_bluesky/beamlines/i24/serial"
+
+# Source modules environment
+source /dls_sw/etc/profile
+# Activate virtual environment
+source $env_directory/.venv/bin/activate
+
+# Start blueapi server
+blueapi -c "${config_directory}/blueapi_config.yaml" serve