Merge branch 'main' into fixes_for_ophyd_async_0.9.0a1

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

@@ -18,9 +18,6 @@
     moveto,
     moveto_preset,
     pumpprobe_calc,
-    save_screen_map,
-    upload_parameters,
-    write_parameter_file,
 )
 from .log import clean_up_log_config_at_end, setup_collection_logs
 from .setup_beamline.setup_detector import setup_detector_stage
@@ -44,9 +41,6 @@
     "load_lite_map",
     "load_stock_map",
     "pumpprobe_calc",
-    "save_screen_map",
-    "upload_parameters",
-    "write_parameter_file",
     "setup_collection_logs",
     "clean_up_log_config_at_end",
 ]

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

@@ -4,9 +4,7 @@
     - March 21 added logging and Eiger functionality
 """
 
-import json
 import re
-import shutil
 import sys
 import time
 from datetime import datetime
@@ -40,10 +38,6 @@
     log_on_entry,
 )
 from mx_bluesky.beamlines.i24.serial.parameters import ExtruderParameters
-from mx_bluesky.beamlines.i24.serial.parameters.constants import (
-    PARAM_FILE_NAME,
-    PARAM_FILE_PATH,
-)
 from mx_bluesky.beamlines.i24.serial.setup_beamline import Pilatus, caget, caput, pv
 from mx_bluesky.beamlines.i24.serial.setup_beamline import setup_beamline as sup
 from mx_bluesky.beamlines.i24.serial.setup_beamline.setup_detector import (
@@ -141,12 +135,20 @@ def enter_hutch(
 
 
 @log_on_entry
-def write_parameter_file(
-    detector_stage: DetectorMotion, attenuator: ReadOnlyAttenuator
-):
-    """Writes a json parameter file that can later be parsed by the model."""
-    param_file: Path = PARAM_FILE_PATH / PARAM_FILE_NAME
-    SSX_LOGGER.debug(f"Writing Parameter File to: {param_file}\n")
+def read_parameters(detector_stage: DetectorMotion, attenuator: ReadOnlyAttenuator):
+    """ Read the parameters from user input and create the parameter model for an \
+        extruder collection.
+
+    Args:
+        detector_stage (DetectorMotion): The detector stage device.
+        attenuator (ReadOnlyAttenuator): A read-only attenuator device to get the \
+            transmission value.
+
+    Returns:
+        ExtruderParameters: Parameter model for extruder collections
+
+    """
+    SSX_LOGGER.info("Creating parameter model from input.")
 
     det_type = yield from get_detector_type(detector_stage)
     SSX_LOGGER.warning(f"DETECTOR TYPE: {det_type}")
@@ -182,12 +184,11 @@ def write_parameter_file(
         "laser_dwell_s": pump_exp,
         "laser_delay_s": pump_delay,
     }
-    with open(param_file, "w") as f:
-        json.dump(params_dict, f, indent=4)
 
     SSX_LOGGER.info("Parameters \n")
     SSX_LOGGER.info(pformat(params_dict))
     yield from bps.null()
+    return ExtruderParameters(**params_dict)
 
 
 @log_on_entry
@@ -467,11 +468,6 @@ def collection_complete_plan(
     dcid.collection_complete(end_time, aborted=False)
     SSX_LOGGER.info(f"End Time = {end_time.ctime()}")
 
-    # Copy parameter file
-    shutil.copy2(
-        PARAM_FILE_PATH / PARAM_FILE_NAME,
-        collection_directory / PARAM_FILE_NAME,
-    )
     yield from bps.null()
 
 
@@ -489,8 +485,9 @@ def run_extruder_plan(
     start_time = datetime.now()
     SSX_LOGGER.info(f"Collection start time: {start_time.ctime()}")
 
-    yield from write_parameter_file(detector_stage, attenuator)
-    parameters = ExtruderParameters.from_file(PARAM_FILE_PATH / PARAM_FILE_NAME)
+    parameters: ExtruderParameters = yield from read_parameters(
+        detector_stage, attenuator
+    )
 
     beam_center_device = sup.get_beam_center_device(parameters.detector_name)
 

src/mx_bluesky/beamlines/i24/serial/fixed_target/FT-gui-edm/MappingLite-oxford_py3v1.edl

@@ -3,8 +3,8 @@ beginScreenProperties
 major 4
 minor 0
 release 1
-x 1062
-y 369
+x 308
+y 339
 w 650
 h 400
 font "arial-medium-r-18.0"
@@ -179,50 +179,6 @@ font "arial-medium-r-18.0"
 colorPv "ME14E-MO-IOC-01:GP67"
 endObjectProperties
 
-# (Shell Command)
-object shellCmdClass
-beginObjectProperties
-major 4
-minor 3
-release 0
-x 40
-y 290
-w 194
-h 40
-fgColor index 0
-bgColor index 23
-topShadowColor index 1
-botShadowColor index 11
-font "arial-medium-r-18.0"
-buttonLabel "Save Screen Map"
-numCmds 1
-command {
-  0 "blueapi -c CONFIG_LOCATION controller run save_screen_map"
-}
-endObjectProperties
-
-# (Shell Command)
-object shellCmdClass
-beginObjectProperties
-major 4
-minor 3
-release 0
-x 12
-y 337
-w 244
-h 53
-fgColor index 13
-bgColor index 49
-topShadowColor index 1
-botShadowColor index 11
-font "arial-medium-r-18.0"
-buttonLabel "Upload Parameters"
-numCmds 1
-command {
-  0 "blueapi -c CONFIG_LOCATION controller run upload_parameters '\{\"pmac\":\"pmac\"\}'"
-}
-endObjectProperties
-
 # (Message Button)
 object activeMessageButtonClass
 beginObjectProperties

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

@@ -2,14 +2,12 @@
 Fixed target data collection
 """
 
-import shutil
 from datetime import datetime
 from pathlib import Path
 from time import sleep
 
 import bluesky.plan_stubs as bps
 import bluesky.preprocessors as bpp
-import numpy as np
 from bluesky.utils import MsgGenerator
 from dodal.common import inject
 from dodal.devices.attenuator import ReadOnlyAttenuator
@@ -35,18 +33,11 @@
     PumpProbeSetting,
 )
 from mx_bluesky.beamlines.i24.serial.fixed_target.i24ssx_Chip_Manager_py3v1 import (
-    write_parameter_file,
+    read_parameters,
+    upload_chip_map_to_geobrick,
 )
 from mx_bluesky.beamlines.i24.serial.log import SSX_LOGGER, log_on_entry
-from mx_bluesky.beamlines.i24.serial.parameters import (
-    ChipDescription,
-    FixedTargetParameters,
-)
-from mx_bluesky.beamlines.i24.serial.parameters.constants import (
-    LITEMAP_PATH,
-    PARAM_FILE_NAME,
-    PARAM_FILE_PATH_FT,
-)
+from mx_bluesky.beamlines.i24.serial.parameters import FixedTargetParameters
 from mx_bluesky.beamlines.i24.serial.setup_beamline import caget, cagetstring, caput, pv
 from mx_bluesky.beamlines.i24.serial.setup_beamline import setup_beamline as sup
 from mx_bluesky.beamlines.i24.serial.setup_beamline.setup_zebra_plans import (
@@ -107,19 +98,6 @@ def calculate_collection_timeout(parameters: FixedTargetParameters) -> float:
     return timeout
 
 
-def copy_files_to_data_location(
-    dest_dir: Path | str,
-    param_path: Path = PARAM_FILE_PATH_FT,
-    map_file: Path = LITEMAP_PATH,
-    map_type: MappingType = MappingType.Lite,
-):
-    if not isinstance(dest_dir, Path):
-        dest_dir = Path(dest_dir)
-    shutil.copy2(param_path / "parameters.txt", dest_dir / "parameters.txt")
-    if map_type == MappingType.Lite:
-        shutil.copy2(map_file / "currentchip.map", dest_dir / "currentchip.map")
-
-
 def write_userlog(
     parameters: FixedTargetParameters,
     filename: str,
@@ -308,50 +286,18 @@ def get_prog_num(
 
 
 @log_on_entry
-def datasetsizei24(
-    n_exposures: int,
-    chip_params: ChipDescription,
-    map_type: MappingType,
-) -> int:
-    # Calculates how many images will be collected based on map type and N repeats
-    SSX_LOGGER.info("Calculate total number of images expected in data collection.")
-
-    if map_type == MappingType.NoMap:
-        if chip_params.chip_type == ChipType.Custom:
-            total_numb_imgs = chip_params.x_num_steps * chip_params.y_num_steps
-            SSX_LOGGER.info(
-                f"Map type: None \tCustom chip \tNumber of images {total_numb_imgs}"
-            )
-        else:
-            chip_format = chip_params.chip_format[:4]
-            total_numb_imgs = int(np.prod(chip_format))
-            SSX_LOGGER.info(
-                f"""Map type: None \tOxford chip {chip_params.chip_type} \t \
-                    Number of images {total_numb_imgs}"""
-            )
-
-    elif map_type == MappingType.Lite:
-        SSX_LOGGER.info(f"Using Mapping Lite on chip type {chip_params.chip_type}")
-        chip_format = chip_params.chip_format[2:4]
-        block_count = 0
-        with open(LITEMAP_PATH / "currentchip.map") as f:
-            for line in f.readlines():
-                entry = line.split()
-                if entry[2] == "1":
-                    block_count += 1
-
-        SSX_LOGGER.info(f"Block count={block_count}")
-        SSX_LOGGER.info(f"Chip format={chip_format}")
-
-        SSX_LOGGER.info(f"Number of exposures={n_exposures}")
-
-        total_numb_imgs = int(np.prod(chip_format) * block_count * n_exposures)
-        SSX_LOGGER.info(f"Calculated number of images: {total_numb_imgs}")
+def set_datasize(
+    parameters: FixedTargetParameters,
+):
+    SSX_LOGGER.info("Setting PV to calculated total number of images")
 
-    SSX_LOGGER.info("Set PV to calculated number of images.")
-    caput(pv.me14e_gp10, int(total_numb_imgs))
+    SSX_LOGGER.debug(f"Map type: {parameters.map_type}")
+    SSX_LOGGER.debug(f"Chip type: {parameters.chip.chip_type}")
+    if parameters.map_type == MappingType.Lite:
+        SSX_LOGGER.debug(f"Num exposures: {parameters.num_exposures}")
+        SSX_LOGGER.debug(f"Block count: {len(parameters.chip_map)}")
 
-    return int(total_numb_imgs)
+    caput(pv.me14e_gp10, parameters.total_num_images)
 
 
 @log_on_entry
@@ -622,9 +568,7 @@ def main_fixed_target_plan(
         parameters.checker_pattern,
     )
 
-    parameters.total_num_images = datasetsizei24(
-        parameters.num_exposures, parameters.chip, parameters.map_type
-    )
+    set_datasize(parameters)
 
     start_time = yield from start_i24(
         zebra,
@@ -695,8 +639,7 @@ def collection_complete_plan(
     SSX_LOGGER.debug(f"Collection end time {end_time}")
     dcid.collection_complete(end_time, aborted=False)
 
-    # Copy parameter file and eventual chip map to collection directory
-    copy_files_to_data_location(collection_directory, map_type=map_type)
+    # NOTE no files to copy anymore but shoud write userlog here
     yield from bps.null()
 
 
@@ -749,29 +692,13 @@ def run_fixed_target_plan(
     mirrors: FocusMirrorsMode = inject("focus_mirrors"),
     attenuator: ReadOnlyAttenuator = inject("attenuator"),
 ) -> MsgGenerator:
-    # in the first instance, write params here
-    yield from write_parameter_file(detector_stage, attenuator)
-
-    SSX_LOGGER.info("Getting parameters from file.")
-    parameters = FixedTargetParameters.from_file(PARAM_FILE_PATH_FT / PARAM_FILE_NAME)
-
-    log_msg = f"""
-            Parameters for I24 serial collection: \n
-                Chip name is {parameters.filename}
-                visit = {parameters.visit}
-                sub_dir = {parameters.directory}
-                n_exposures = {parameters.num_exposures}
-                chip_type = {str(parameters.chip.chip_type)}
-                map_type = {str(parameters.map_type)}
-                dcdetdist = {parameters.detector_distance_mm}
-                exptime = {parameters.exposure_time_s}
-                det_type = {parameters.detector_name}
-                pump_repeat = {str(parameters.pump_repeat)}
-                pumpexptime = {parameters.laser_dwell_s}
-                pumpdelay = {parameters.laser_delay_s}
-                prepumpexptime = {parameters.pre_pump_exposure_s}
-        """
-    SSX_LOGGER.info(log_msg)
+    # Read the parameters
+    parameters: FixedTargetParameters = yield from read_parameters(
+        detector_stage, attenuator
+    )
+
+    if parameters.chip_map:
+        upload_chip_map_to_geobrick(pmac, parameters.chip_map)
 
     beam_center_device = sup.get_beam_center_device(parameters.detector_name)