mx-bluesky 0.0.2__py3-none-any.whl → 0.3.1__py3-none-any.whl

mx_bluesky/I24/serial/fixed_target/i24ssx_Chip_StartUp_py3v1.py

@@ -1,463 +0,0 @@
-"""
-Startup utilities for chip
-
-This version changed to python3 March2020 by RLO
-"""
-from __future__ import annotations
-
-import logging
-import os
-import string
-import time
-from pathlib import Path
-from typing import Dict, List
-
-import numpy as np
-
-from mx_bluesky.I24.serial import log
-from mx_bluesky.I24.serial.fixed_target.ft_utils import ChipType
-from mx_bluesky.I24.serial.parameters.constants import (
-    HEADER_FILES_PATH,
-    PARAM_FILE_PATH_FT,
-)
-
-logger = logging.getLogger("I24ssx.chip_startup")
-
-
-def setup_logging():
-    # Log should now change name daily.
-    logfile = time.strftime("i24fixedtarget_%d%B%y.log").lower()
-    log.config(logfile)
-
-
-def scrape_parameter_file(param_path: Path | str = PARAM_FILE_PATH_FT):
-    if not isinstance(param_path, Path):
-        param_path = Path(param_path)
-
-    with open(param_path / "parameters.txt", "r") as filein:
-        f = filein.readlines()
-    for line in f:
-        entry = line.rstrip().split()
-        if "chip_name" in entry[0].lower():
-            chip_name = entry[1]
-        elif line.startswith("visit"):
-            visit = entry[1]
-        elif line.startswith("sub_dir"):
-            sub_dir = entry[1]
-        elif line.startswith("protein_name"):
-            sub_dir = entry[1]
-        elif "n_exposures" in entry[0].lower():
-            n_exposures = int(entry[1])
-        elif "chip_type" in entry[0].lower():
-            chip_type = int(entry[1])
-        elif "map_type" in entry[0].lower():
-            map_type = int(entry[1])
-        elif "pump_repeat" in entry[0].lower():
-            pump_repeat = int(entry[1])
-
-    for line in f:
-        entry = line.rstrip().split()
-        if "pumpexptime" == entry[0].lower().strip():
-            pumpexptime = float(entry[1])
-        if "exptime" in entry[0].lower():
-            exptime = float(entry[1])
-        if "dcdetdist" in entry[0].lower():
-            dcdetdist = float(entry[1])
-        if "prepumpexptime" in entry[0].lower():
-            prepumpexptime = float(entry[1])
-        if "pumpdelay" in entry[0].lower():
-            pumpdelay = float(entry[1])
-        if "det_type" in entry[0].lower():
-            det_type = entry[1]
-    return (
-        chip_name,
-        visit,
-        sub_dir,
-        n_exposures,
-        chip_type,
-        map_type,
-        pump_repeat,
-        pumpexptime,
-        pumpdelay,
-        exptime,
-        dcdetdist,
-        prepumpexptime,
-        det_type,
-    )
-
-
-def read_parameters(
-    param_path: Path | str = PARAM_FILE_PATH_FT, filename: str | None = None
-) -> Dict[str, str]:
-    """
-    Read the parameter file into a lookup dictionary.
-
-    Does the same thing as scrape_parameter_file except doesn't rely on you
-    getting the order of arguments right every time (or having to load every one
-    if you don't need them all).
-
-    Args:
-        filename: The file to read. If None, will load from default location.
-
-    Returns:
-        A dictionary with a string entry for every key in the file.
-    """
-    if not isinstance(param_path, Path):
-        param_path = Path(param_path)
-    if filename is None:
-        filename = "parameters.txt"
-    datafile = param_path / filename
-    data = datafile.read_text()
-    args = {}
-    for line in data.splitlines():
-        key, value = line.split(maxsplit=1)
-        args[key.lower()] = value
-    return args
-
-
-@log.log_on_entry
-def fiducials(chip_type: int):
-    if chip_type in [ChipType.Oxford, ChipType.OxfordInner, ChipType.Minichip]:
-        fiducial_list: list = []
-        # No fiducial for custom
-    elif chip_type == ChipType.Custom:
-        logger.warning("No fiducials for custom chip")
-    else:
-        logger.warning("Unknown chip_type, %s, in fiducials" % chip_type)
-    return fiducial_list
-
-
-@log.log_on_entry
-def get_format(chip_type: int):
-    if chip_type == ChipType.Oxford:
-        w2w = 0.125
-        b2b_horz = 0.800
-        b2b_vert = 0.800
-        chip_format = [8, 8, 20, 20]
-    elif chip_type == ChipType.OxfordInner:
-        w2w = 0.600
-        b2b_horz = 0.0
-        b2b_vert = 0.0
-        chip_format = [1, 1, 25, 25]
-    elif chip_type == ChipType.Minichip:
-        w2w = 0.125
-        b2b_horz = 0
-        b2b_vert = 0
-        chip_format = [1, 1, 20, 20]
-    else:
-        msg = "Unknown chip_type, %s" % chip_type
-        logger.error(msg)
-        raise ValueError(msg)
-    cell_format = chip_format + [w2w, b2b_horz, b2b_vert]
-    logger.info("Cell format for chip type %s: %s" % (chip_type, cell_format))
-    return cell_format
-
-
-def get_xy(addr: str, chip_type: int):
-    entry = addr.split("_")[-2:]
-    R, C = entry[0][0], entry[0][1]
-    r2, c2 = entry[1][0], entry[1][1]
-    blockR = string.ascii_uppercase.index(R)
-    blockC = int(C) - 1
-    lowercase_list = list(string.ascii_lowercase + string.ascii_uppercase + "0")
-    windowR = lowercase_list.index(r2)
-    windowC = lowercase_list.index(c2)
-
-    (
-        x_block_num,
-        y_block_num,
-        x_window_num,
-        y_window_num,
-        w2w,
-        b2b_horz,
-        b2b_vert,
-    ) = get_format(chip_type)
-
-    x = (blockC * b2b_horz) + (blockC * (x_window_num - 1) * w2w) + (windowC * w2w)
-    y = (blockR * b2b_vert) + (blockR * (y_window_num - 1) * w2w) + (windowR * w2w)
-    return x, y
-
-
-def pathli(l_in=[], way="typewriter", reverse=False):
-    if reverse is True:
-        li = list(reversed(l_in))
-    else:
-        li = list(l_in)
-    long_list = []
-    if li:
-        if way == "typewriter":
-            for i in range(len(li) ** 2):
-                long_list.append(li[i % len(li)])
-        elif way == "snake":
-            lr = list(reversed(li))
-            for rep in range(len(li)):
-                if rep % 2 == 0:
-                    long_list += li
-                else:
-                    long_list += lr
-        elif way == "snake53":
-            lr = list(reversed(li))
-            for rep in range(53):
-                if rep % 2 == 0:
-                    long_list += li
-                else:
-                    long_list += lr
-        elif way == "expand":
-            for entry in li:
-                for rep in range(len(li)):
-                    long_list.append(entry)
-        elif way == "expand28":
-            for entry in li:
-                for rep in range(28):
-                    long_list.append(entry)
-        elif way == "expand25":
-            for entry in li:
-                for rep in range(25):
-                    long_list.append(entry)
-        else:
-            logger.warning("No known path, way =  %s" % way)
-    else:
-        logger.warning("No list written")
-    return long_list
-
-
-def zippum(list_1_args, list_2_args):
-    list_1, type_1, reverse_1 = list_1_args
-    list_2, type_2, reverse_2 = list_2_args
-    A_path = pathli(list_1, type_1, reverse_1)
-    B_path = pathli(list_2, type_2, reverse_2)
-    zipped_list = []
-    for a, b in zip(A_path, B_path):
-        zipped_list.append(a + b)
-    return zipped_list
-
-
-def get_alphanumeric(chip_type):
-    cell_format = get_format(chip_type)
-    blk_num = cell_format[0]
-    wnd_num = cell_format[2]
-    uppercase_list = list(string.ascii_uppercase)[:blk_num]
-    lowercase_list = list(string.ascii_lowercase + string.ascii_uppercase + "0")[
-        :wnd_num
-    ]
-    number_list = [str(x) for x in range(1, blk_num + 1)]
-
-    block_list = zippum([uppercase_list, "expand", 0], [number_list, "typewriter", 0])
-    window_list = zippum(
-        [lowercase_list, "expand", 0], [lowercase_list, "typewriter", 0]
-    )
-
-    alphanumeric_list = []
-    for block in block_list:
-        for window in window_list:
-            alphanumeric_list.append(block + "_" + window)
-    logger.info("Length of alphanumeric list = %s" % len(alphanumeric_list))
-    return alphanumeric_list
-
-
-@log.log_on_entry
-def get_shot_order(chip_type):
-    cell_format = get_format(chip_type)
-    blk_num = cell_format[0]
-    wnd_num = cell_format[2]
-    uppercase_list = list(string.ascii_uppercase)[:blk_num]
-    number_list = [str(x) for x in range(1, blk_num + 1)]
-    lowercase_list = list(string.ascii_lowercase + string.ascii_uppercase + "0")[
-        :wnd_num
-    ]
-
-    block_list = zippum([uppercase_list, "snake", 0], [number_list, "expand", 0])
-    window_dn = zippum([lowercase_list, "expand", 0], [lowercase_list, "snake", 0])
-    window_up = zippum([lowercase_list, "expand", 1], [lowercase_list, "snake", 0])
-
-    switch = 0
-    count = 0
-    collect_list = []
-    for block in block_list:
-        if switch == 0:
-            for window in window_dn:
-                collect_list.append(block + "_" + window)
-            count += 1
-            if count == blk_num:
-                count = 0
-                switch = 1
-        else:
-            for window in window_up:
-                collect_list.append(block + "_" + window)
-            count += 1
-            if count == blk_num:
-                count = 0
-                switch = 0
-
-    logger.info("Length of collect list = %s" % len(collect_list))
-    return collect_list
-
-
-@log.log_on_entry
-def write_file(
-    location: str = "i24",
-    suffix: str = ".addr",
-    order: str = "alphanumeric",
-    param_file_path: Path = PARAM_FILE_PATH_FT,
-    save_path: Path = HEADER_FILES_PATH,
-):
-    if location == "i24":
-        (
-            chip_name,
-            visit,
-            sub_dir,
-            n_exposures,
-            chip_type,
-            map_type,
-            pump_repeat,
-            pumpexptime,
-            exptime,
-            dcdetdist,
-            prepumpexptime,
-        ) = scrape_parameter_file(param_file_path)
-    else:
-        msg = "Unknown location, %s" % location
-        logger.error(msg)
-        raise ValueError(msg)
-    chip_file_path = save_path / f"chips/{sub_dir}/{chip_name}{suffix}"
-
-    fiducial_list = fiducials(chip_type)
-    if order == "alphanumeric":
-        addr_list = get_alphanumeric(chip_type)
-
-    elif order == "shot":
-        addr_list = get_shot_order(chip_type)
-
-    with open(chip_file_path, "a") as g:
-        for addr in addr_list:
-            xtal_name = "_".join([chip_name, addr])
-            (x, y) = get_xy(xtal_name, chip_type)
-            if addr in fiducial_list:
-                pres = "0"
-            else:
-                if "rand" in suffix:
-                    pres = str(np.random.randint(2))
-                else:
-                    pres = "-1"
-            line = "\t".join([xtal_name, str(x), str(y), "0.0", pres]) + "\n"
-            g.write(line)
-
-    logger.info("Write %s completed" % chip_file_path)
-
-
-@log.log_on_entry
-def check_files(
-    location: str,
-    suffix_list: List[str],
-    param_file_path: Path | str = PARAM_FILE_PATH_FT,
-    save_path: Path = HEADER_FILES_PATH,
-):
-    if location == "i24":
-        (
-            chip_name,
-            visit,
-            sub_dir,
-            n_exposures,
-            chip_type,
-            map_type,
-            exptime,
-            pump_repeat,
-            pumpdelay,
-            pumpexptime,
-            dcdetdist,
-            prepumpexptime,
-            det_type,
-        ) = scrape_parameter_file(param_path=param_file_path)
-    else:
-        msg = "Unknown location, %s" % location
-        logger.error(msg)
-        raise ValueError(msg)
-    chip_file_path = save_path / f"chips/{sub_dir}/{chip_name}"
-
-    try:
-        os.stat(chip_file_path)
-    except Exception:
-        os.makedirs(chip_file_path)
-    for suffix in suffix_list:
-        full_fid = chip_file_path.with_suffix(suffix)
-        if full_fid.is_file():
-            time_str = time.strftime("%Y%m%d_%H%M%S_")
-            timestamp_fid = (  # noqa: F841
-                full_fid.parent / f"{time_str}_{chip_name}{full_fid.suffix}"
-            )
-            # FIXME hack / fix. Actually move the file
-            logger.info("File %s Already Exists" % full_fid)
-    logger.debug("Check files done")
-    return 1
-
-
-@log.log_on_entry
-def write_headers(
-    location: str,
-    suffix_list: List[str],
-    param_file_path: Path = PARAM_FILE_PATH_FT,
-    save_path: Path = HEADER_FILES_PATH,
-):
-    if location == "i24":
-        (
-            chip_name,
-            visit,
-            sub_dir,
-            n_exposures,
-            chip_type,
-            map_type,
-            pump_repeat,
-            pumpexptime,
-            pumpdelay,
-            exptime,
-            dcdetdist,
-            prepumpexptime,
-            det_type,
-        ) = scrape_parameter_file(param_path=PARAM_FILE_PATH_FT)
-        chip_file_path = save_path / f"chips/{sub_dir}/{chip_name}"
-
-        for suffix in suffix_list:
-            full_fid = chip_file_path.with_suffix(suffix)
-            with open(full_fid, "w") as g:
-                g.write(
-                    "#23456789012345678901234567890123456789012345678901234567890123456789012345678901234567890\n#\n"
-                )
-                g.write("#&i24\tchip_name    = %s\n" % chip_name)
-                g.write("#&i24\tvisit        = %s\n" % visit)
-                g.write("#&i24\tsub_dir      = %s\n" % sub_dir)
-                g.write("#&i24\tn_exposures  = %s\n" % n_exposures)
-                g.write("#&i24\tchip_type    = %s\n" % chip_type)
-                g.write("#&i24\tmap_type     = %s\n" % map_type)
-                g.write("#&i24\tpump_repeat  = %s\n" % pump_repeat)
-                g.write("#&i24\tpumpexptime  = %s\n" % pumpexptime)
-                g.write("#&i24\texptime      = %s\n" % exptime)
-                g.write("#&i24\tdcdetdist    = %s\n" % dcdetdist)
-                g.write("#&i24\tprepumpexptime  = %s\n" % prepumpexptime)
-                g.write("#&i24\tdet_Type     = %s\n" % det_type)
-                g.write("#\n")
-                g.write(
-                    "#XtalAddr      XCoord  YCoord  ZCoord  Present Shot  Spare04 Spare03 Spare02 Spare01\n"
-                )
-    else:
-        msg = "Unknown location, %s" % location
-        logger.error(msg)
-        raise ValueError(msg)
-    logger.debug("Write headers done")
-
-
-def run():
-    logger.debug("Run Startup")
-    check_files("i24", [".addr", ".shot"])
-    logger.info("Checked Files")
-    write_headers("i24", [".addr", ".shot"])
-    logger.info("Written Headers")
-    logger.info("Writing to Files has been disabled. Headers Only")
-    # Makes a file with random crystal positions
-    check_files("i24", ["rando.spec"])
-    write_headers("i24", ["rando.spec"])
-    logger.debug("StartUp Done")
-
-
-if __name__ == "__main__":
-    setup_logging()
-    run()

mx_bluesky/I24/serial/log.py

@@ -1,101 +0,0 @@
-from __future__ import annotations
-
-import functools
-import logging
-import logging.config
-from os import environ
-from pathlib import Path
-from typing import Optional
-
-# Logging set up
-logging.getLogger("I24ssx").addHandler(logging.NullHandler())
-
-logging_config = {
-    "version": 1,
-    "disable_existing_loggers": False,
-    "formatters": {
-        "default": {
-            "class": "logging.Formatter",
-            "format": "%(message)s",
-        }
-    },
-    "handlers": {
-        "console": {
-            "level": "DEBUG",
-            "class": "logging.StreamHandler",
-            "formatter": "default",
-            "stream": "ext://sys.stdout",
-        }
-    },
-    "loggers": {
-        "I24ssx": {
-            "handlers": ["console"],
-            "level": "DEBUG",
-            "propagate": True,
-        }
-    },
-}
-
-logging.config.dictConfig(logging_config)
-
-
-def _get_logging_file_path() -> Path:
-    """Get the path to write the artemis log files to.
-    If on a beamline, this will be written to the according area depending on the
-    BEAMLINE envrionment variable. If no envrionment variable is found it will default
-    it to the tmp/dev directory.
-    Returns:
-        logging_path (Path): Path to the log file for the file handler to write to.
-    """
-    beamline: Optional[str] = environ.get("BEAMLINE")
-    logging_path: Path
-
-    if beamline:
-        logging_path = Path("/dls_sw/" + beamline + "/logs/serial/")
-    else:
-        logging_path = Path("./tmp/logs/")
-
-    try:
-        Path(logging_path).mkdir(parents=True, exist_ok=True)
-    except OSError:
-        # Until https://github.com/DiamondLightSource/mx_bluesky/issues/45 is fixed
-        # Logs could also go to the current visit directory, but not always possible
-        # when testing
-        logging_path = Path("~/serial_logs/").expanduser().resolve()
-        Path(logging_path).mkdir(parents=True, exist_ok=True)
-    return logging_path
-
-
-def config(logfile: str | None = None, write_mode: str = "a", delayed: bool = False):
-    """
-    Configure the logging.
-
-    Args:
-        logfile (str, optional): Filename for logfile. If passed, create a file handler\
-            for the logger to write to file the log output. Defaults to None.
-        write_mode (str, optional): String indicating writing mode for the output \
-            .log file. Defaults to "a".
-    """
-    logger = logging.getLogger("I24ssx")
-    if logfile:
-        logs = _get_logging_file_path() / logfile
-        fileFormatter = logging.Formatter(
-            "%(asctime)s %(levelname)s: \t(%(name)s) %(message)s",
-            datefmt="%d-%m-%Y %I:%M:%S",
-        )
-        FH = logging.FileHandler(logs, mode=write_mode, encoding="utf-8", delay=delayed)
-        FH.setLevel(logging.DEBUG)
-        FH.setFormatter(fileFormatter)
-        logger.addHandler(FH)
-
-
-def log_on_entry(func):
-    logger = logging.getLogger("I24ssx")
-
-    @functools.wraps(func)
-    def decorator(*args, **kwargs):
-        name = func.__name__
-        logger.debug("Running %s " % name)
-        return func(*args, **kwargs)
-
-    return decorator

mx_bluesky/I24/serial/parameters/__init__.py

@@ -1,5 +0,0 @@
-from __future__ import annotations
-
-from mx_bluesky.I24.serial.parameters.constants import SSXType
-
-__all__ = ["SSXType"]

mx_bluesky/I24/serial/parameters/constants.py

@@ -1,39 +0,0 @@
-from enum import Enum
-from pathlib import Path
-
-
-class SSXType(Enum):
-    FIXED = "Serial Fixed"
-    EXTRUDER = "Serial Jet"
-
-
-OAV_CONFIG_FILES = {
-    "zoom_params_file": "/dls_sw/i24/software/gda/config/xml/jCameraManZoomLevels.xml",
-    "oav_config_json": "/dls_sw/i24/software/daq_configuration/json/OAVCentring.json",
-    "display_config": "/dls_sw/i24/software/gda_versions/var/display.configuration",
-}
-OAV1_CAM = "http://bl24i-di-serv-01.diamond.ac.uk:8080/OAV1.mjpg.mjpg"
-
-PARAM_FILE_PATH = Path("src/mx_bluesky/I24/serial/parameters").expanduser().resolve()
-PARAM_FILE_PATH_FT = (
-    Path("src/mx_bluesky/I24/serial/parameters/fixed_target").expanduser().resolve()
-)
-LITEMAP_PATH = (
-    Path("src/mx_bluesky/I24/serial/parameters/fixed_target/litemaps")
-    .expanduser()
-    .resolve()
-)
-FULLMAP_PATH = (
-    Path("src/mx_bluesky/I24/serial/parameters/fixed_target/fullmaps")
-    .expanduser()
-    .resolve()
-)
-PVAR_FILE_PATH = (
-    Path("src/mx_bluesky/I24/serial/parameters/fixed_target/pvar_files")
-    .expanduser()
-    .resolve()
-)
-HEADER_FILES_PATH = Path("/dls_sw/i24/scripts/fastchips/").expanduser().resolve()
-CS_FILES_PATH = (
-    Path("src/mx_bluesky/I24/serial/parameters/fixed_target/cs").expanduser().resolve()
-)

mx_bluesky/I24/serial/parameters/fixed_target/cs/cs_maker.json

@@ -1,9 +0,0 @@
-{
-    "scalex": 10002.4,
-    "scaley": 9997.5,
-    "scalez": 10000.0,
-    "skew": -0.163,
-    "Sx_dir": -1,
-    "Sy_dir": 1,
-    "Sz_dir": -1
-}

mx_bluesky/I24/serial/parameters/fixed_target/cs/fiducial_1.txt

@@ -1,4 +0,0 @@
-MTR	RBV	RAW	Corr	f_value
-MTR1	25.3964	254025	1	25.3964
-MTR2	-0.5533	-5532	1	-0.5533
-MTR3	0.0000	0	-1	0.0000

mx_bluesky/I24/serial/parameters/fixed_target/cs/fiducial_2.txt

@@ -1,4 +0,0 @@
-MTR	RBV	RAW	Corr	f_value
-MTR1	0.4709	4710	1	0.4709
-MTR2	25.4079	254014	1	25.4079
-MTR3	0.0000	0	-1	0.0000