cgse 2024.7.0__py3-none-any.whl → 2025.0.1__py3-none-any.whl

egse/reprocess.py

@@ -1,693 +0,0 @@
-import glob
-import logging
-import os.path
-from pathlib import Path
-from typing import Union
-
-import numpy as np
-import pandas as pd
-from pandas._libs.parsers import EmptyDataError
-from pandas.errors import ParserError
-
-from egse import h5
-from egse.config import find_file
-from egse.dpu.fitsgen import add_synoptics
-from egse.dpu.fitsgen import create_fits_from_hdf5
-from egse.dpu.fitsgen import get_hdf5_filenames_for_obsid
-from egse.dpu.fitsgen import get_od
-from egse.fee.n_fee_hk import ORIGIN as N_FEE_ORIGIN
-from egse.fee.n_fee_hk import ORIGIN as ORIGIN_NFEE_HK
-from egse.fee.n_fee_hk import get_calibrated_supply_voltages
-from egse.fee.n_fee_hk import get_calibrated_temperatures
-from egse.fee.nfee import HousekeepingData
-from egse.fov import ORIGIN as FOV_ORIGIN
-from egse.hk import read_conversion_dict
-from egse.obsid import ObservationIdentifier
-from egse.obsid import obsid_from_storage
-from egse.settings import Settings
-from egse.setup import NavigableDict
-from egse.setup import Setup
-from egse.spw import SpaceWirePacket
-from egse.storage import HDF5
-from egse.storage.persistence import CSV
-from egse.synoptics import ORIGIN as SYN_ORIGIN
-from egse.synoptics import read_hk_info as read_syn_info
-from egse.tcs.tcs import ORIGIN as TCS_ORIGIN
-
-LOGGER = logging.getLogger(__name__)
-
-# sensor_cal_filename = "/Users/sara/work/Instrumentation/Plato/softwareDevelopment/plato-cgse-conf/data/nfee_sensor_calibration_em_v3.yaml"
-# sensor_cal = NavigableDict(Settings.load(filename=sensor_cal_filename))#, add_local_settings=False))
-# data_dir = "/STER/platodata/SRON/plato-data"
-# site = "SRON"
-
-
-# def reprocess_campaign(od_start: str, od_end: str, sensor_cal: NavigableDict, archive_dir: str, fixed_archive_dir: str,
-#                        reprocessed_archive_dir: str):
-#     """ Re-process the daily data in the given timespan.
-#
-#     Args:
-#         - od_start:
-#         - od_end
-#         - archive_dir: Folder (with sub-folders /daily and /obs) in which the HK files are stored.
-#         - fixed_archive_dir: Folder (with sub-folders /daily and /obs) in which the fixed HK files are stored.
-#         - reprocessed_archive_dir: Folder (with sub-folders /daily and /obs) in which the re-processed files will be
-#                                    stored.
-#     """
-#
-#     delta = timedelta(days=1)
-#     date_end = datetime.strptime(od_end, "%Y%m%d")  # The last OD to re-process [YYYYMMDD]
-#     date = datetime.strptime(od_start, "%Y%m%d")    # The first OD to re-process [YYYYMMDD]
-#
-#     # Re-process the daily N-FEE HK (from the HDF5 files) + synoptics
-#
-#     while date <= date_end:
-#
-#         od = date.strftime("%Y%m%d")    # Current OD [YYYYMMDD]
-#         # day_dir = Path(f"{archive_dir}/daily/{od}")  # Sub-folder with the data for the given OD
-#
-#         reprocess_od(od, sensor_cal, archive_dir, fixed_archive_dir, reprocessed_archive_dir)
-#
-#         date += delta
-
-
-def reprocess_od(od: str, site: str, setup: Setup, archive_dir: str, fixed_archive_dir: str,
-                 reprocessed_archive_dir: str):
-    """ Re-processing for the given OD.
-
-    This re-processing consists of the following steps:
-        - Re-processing the N-FEE HK from the HDF5 files;
-        - Re-processing the synoptics from the contributing (and potentially fixed) HK files.
-
-    Args:
-        - od: Observation day in the format YYYYMMDD.
-        - site: Site ID (CSL/CSL1/CSL2/SRON/IAS/INTA).
-        - setup: Setup from which to read all calibration information.
-        - archive_dir: Folder (with sub-folders /daily and /obs) in which the HK files are stored.
-        - fixed_archive_dir: Folder (with sub-folders /daily and /obs) in which the fixed HK files are stored.
-        - reprocessed_archive_dir: Folder (with sub-folders /daily and /obs) in which the re-processed synoptics file
-                                   will be stored.
-    """
-
-    fee_calibration = setup.camera.fee.calibration
-
-    # Order is important here: Synoptics builds further on N-FEE HK
-    reprocess_daily_n_fee_hk(od, site, fee_calibration, archive_dir, reprocessed_archive_dir, setup)  # N-FEE HK
-    reprocess_daily_synoptics(od, site, archive_dir, fixed_archive_dir, reprocessed_archive_dir, setup)    # Synoptics
-    
-
-
-def reprocess_obsid(obsid: Union[str, int, ObservationIdentifier], site: str, setup: Setup, archive_dir: str,
-                    fixed_archive_dir: str, reprocessed_archive_dir: str):
-    """ Re-processing for the given obsid.
-
-    This re-processing consists of the following steps:
-        - Re-processing the N-FEE HK from the HDF5 files;
-        - Re-processing the synoptics from the contributing (and potentially fixed HK files);
-        - Re-processing the FITS files from the HDF5 files and (re-processed) synoptics.
-
-    Args:
-        - obsid: Observation identifier.
-        - site: Site ID (CSL/CSL1/CSL2/SRON/IAS/INTA).
-        - setup: Setup from which to read all calibration information.
-        - archive_dir: Folder (with sub-folders /daily and /obs) in which the HK files are stored.
-        - fixed_archive_dir: Folder (with sub-folders /daily and /obs) in which the fixed HK files are stored.
-        - reprocessed_archive_dir: Folder (with sub-folders /daily and /obs) in which the re-processed synoptics file
-                                   will be stored.
-    """
-
-    fee_calibration = setup.camera.fee.calibration
-
-    # Order is important here: Synoptics builds further on N-FEE HK
-    reprocess_obs_n_fee_hk(obsid, fee_calibration, archive_dir, reprocessed_archive_dir, setup)  # N-FEE HK
-    reprocess_obs_synoptics(obsid, site, archive_dir, fixed_archive_dir, reprocessed_archive_dir, setup)   # Synoptics
-
-    reprocess_ccd_data(obsid, archive_dir, reprocessed_archive_dir, setup)                          # FITS files
-
-
-def reprocess_daily_n_fee_hk(od: str, site: str, fee_calibration: NavigableDict, archive_dir: str,
-                             reprocessed_archive_dir: str, setup: Setup):
-    """ Re-processing the N-FEE HK for the given OD.
-
-    The procedure is as follows:
-        - Read the N-FEE HK information from the TM dictionary.  This comprises the name conversion from the original
-          name (used by the N-FEE itself and in the HDF5 files) to the conventional name starting with "NFEE", and the
-          calibration information for the supply voltages and temperatures.
-        - Determine the filename for the N-FEE HK for the given OD.
-        - Determine the list of HDF5 filenames acquired during the given OD.
-        - Determine the column names to use in the new N-FEE HK file and create a new N-FEE HK file with these.
-        - Loop over all these HDF5 files.  For each of them, read the uncalibrated values and apply the calibration,
-          according to the given calibration information.  Then append the raw and calibrated values to the N-FEE HK
-          file.
-
-    Args:
-        - od: Observation day in the format YYYYMMDD.
-        - site: Site ID (CSL/CSL1/CSL2/SRON/IAS/INTA).
-        - fee_calibration: Calibration data for the N-FEE HK.
-        - archive_dir: Folder (with sub-folders /daily and /obs) in which the HDF5 files are stored.
-        - reprocessed_archive_dir: Folder (with sub-folders /daily and /obs) in which the re-processed N-FEE HK files
-                                   will be stored.
-        - setup: Setup.
-    """
-
-    archive_od_dir = f"{archive_dir}/daily/{od}"
-    reprocessed_archive_od_dir = f"{reprocessed_archive_dir}/daily/{od}"
-
-    # Compose the list of HDF5 filenames for the given OD
-    # If there are no HDF5 files, exit with a proper log message
-
-    hdf5_filenames = glob.glob(f"{archive_od_dir}/*.{HDF5.extension}")
-    if len(hdf5_filenames) == 0:
-        LOGGER.info(f"No HDF5 files found in {archive_od_dir}")
-        return
-
-    # Use the same filename for the N-FEE HK as before, but store it in the re-processed archive now
-    # (don't touch the old N-FEE HK file)
-
-    n_fee_hk_filename = f"{reprocessed_archive_od_dir}/{od}_{site}_{N_FEE_ORIGIN}.{CSV.extension}"
-
-    _reprocess_n_fee_hk(hdf5_filenames, n_fee_hk_filename, fee_calibration, setup)
-
-
-def reprocess_obs_n_fee_hk(obsid: Union[str, int, ObservationIdentifier], fee_calibration: NavigableDict,
-                           archive_dir: str, reprocessed_archive_dir: str, setup: Setup):
-    """ Re-processing the synoptics for the given obsid.
-
-    The procedure is as follows:
-        - Read the N-FEE HK information from the TM dictionary.  This comprises the name conversion from the original
-          name (used by the N-FEE itself and in the HDF5 files) to the conventional name starting with "NFEE", and the
-          calibration information for the supply voltages and temperatures.
-        - Determine the filename for the N-FEE HK for the given obsid.
-        - Determine the list of HDF5 filenames acquired during the given obsid.
-        - Determine the column names to use in the new N-FEE HK file and create a new N-FEE HK file with these.
-        - Loop over all these HDF5 files.  For each of them, read the uncalibrated values and apply the calibration,
-          according to the given calibration information.  Then append the raw and calibrated values to the N-FEE HK
-          file.
-
-    Args:
-        - obsid: Observation identifier.
-        - site: Site ID (CSL/CSL1/CSL2/SRON/IAS/INTA).
-        - fee_calibration: Calibration data for the N-FEE HK.
-        - archive_dir: Folder (with sub-folders /daily and /obs) in which the HDF5 files are stored.
-        - reprocessed_archive_dir: Folder (with sub-folders /daily and /obs) in which the re-processed N-FEE HK files
-                                   will be stored.
-        - setup: Setup.
-    """
-
-    obsid = obsid_from_storage(obsid, archive_dir)
-
-    archive_obsid_dir = f"{archive_dir}/obs/{obsid}"
-    reprocessed_archive_obsid_dir = f"{reprocessed_archive_dir}/obs/{obsid}"
-
-    # Compose the list of HDF5 filenames for the given obsid
-    # If there are no HDF5 files, exit with a proper log message
-
-    hdf5_filenames = get_hdf5_filenames_for_obsid(obsid, data_dir=archive_dir)
-    if len(hdf5_filenames) == 0:
-        LOGGER.info(f"No HDF5 files found for obsid {obsid}")
-        return
-
-    # Use the same filename for the N-FEE HK as before, but store it in the re-processed archive now
-    # (don't touch the old N-FEE HK file)
-
-    pattern = f"{obsid}_{N_FEE_ORIGIN}_*_*.csv"
-    n_fee_hk_filename = find_file(pattern, root=archive_obsid_dir)
-    if n_fee_hk_filename is None:
-        od = get_od(obsid, archive_dir)[0]
-        n_fee_hk_filename = f"{reprocessed_archive_obsid_dir}/{obsid}_{N_FEE_ORIGIN}_{od}.{CSV.extension}"
-    else:
-        n_fee_hk_filename = f"{reprocessed_archive_obsid_dir}/{n_fee_hk_filename.stem}.{CSV.extension}"
-
-    _reprocess_n_fee_hk(hdf5_filenames, n_fee_hk_filename, fee_calibration, setup)
-
-
-def _reprocess_n_fee_hk(hdf5_filenames, n_fee_hk_filename: str, fee_calibration: NavigableDict, setup: Setup):
-    """ Re-processing the N-FEE HK.
-
-    The procedure is as follows for the "hk" dataset in all groups of the given list of HDF5 files:
-        - Extract the raw values from the SpW packets;
-        - Re-name the extracted parameters to the corresponding synoptical name;
-        - Apply the calibration for the supply voltages and temperatures;
-        - Append a row to the N-FEE HK file with the raw and calibrated values.
-
-    Args:
-        - hdf5_filenames: Filenames of the HDF5 files containing the raw N-FEE HK.
-        - n_fee_hk_filename: Filename for the re-processed N-FEE HK file.
-        - fee_calibration: Calibration data for the N-FEE HK.
-        - setup: Setup.
-    """
-
-    hk_names_mapping = read_conversion_dict(ORIGIN_NFEE_HK, use_site=False, setup=setup)
-
-    supply_voltage_calibration = fee_calibration.supply_voltages
-    temperature_calibration = fee_calibration.temperatures
-
-    # name_conversion, n_fee_supply_voltage_cal = read_n_fee_hk_info()
-    column_names = ["timestamp", *list(hk_names_mapping.values())]
-
-    with CSV(filename=n_fee_hk_filename, prep={"column_names": column_names, "mode": 'w'}) as csv:
-
-        for hdf5_filename in hdf5_filenames:
-
-            with h5.get_file(hdf5_filename, mode="r") as hdf5_file:
-
-                try:
-
-                    for group in h5.groups(hdf5_file):
-
-                        # Read the HK from the HDF5 groups and rename them
-
-                        if "hk" in group:
-
-                            # Create a dictionary in which we will gather all the raw and calibrated data for the
-                            # timestamp in the current group of the current HDF5 file
-
-                            values = {"timestamp": group["timecode"].attrs["timestamp"]}
-
-                            hk_packet = SpaceWirePacket.create_packet(h5.get_data(group["hk"]))
-                            hk_data = HousekeepingData(hk_packet.data)
-
-                            for orig_name in hk_data:
-                                try:
-                                    new_name = hk_names_mapping[orig_name]
-                                    values[new_name] = hk_data[orig_name]
-                                except KeyError:
-                                    pass
-
-                            # Apply the correct calibration
-
-                            calibrated_supply_voltages = get_calibrated_supply_voltages(values,
-                                                                                        supply_voltage_calibration)
-                            values.update(calibrated_supply_voltages)
-                            calibrated_temperatures = get_calibrated_temperatures(values, temperature_calibration, setup)
-                            values.update(calibrated_temperatures)
-
-                            # Store the new N-FEE HK
-
-                            csv.create(values)
-                except RuntimeError as exc:
-                    LOGGER.warning(f"Problem occurred when reading HK from {hdf5_filename} ({exc}).  Skipping...")
-
-
-def reprocess_daily_synoptics(od: str, site: str, archive_dir: str, fixed_archive_dir: str,
-                              reprocessed_archive_dir: str, setup: Setup):
-    """ Re-processing the N-FEE HK for the given OD.
-
-    The procedure is as follows:
-        - Compose a list of HK files contributing to the synoptics.
-        - Read those files one by one and concatenate them.
-        - Sort the concatenated tables in order of ascending timestamp.
-        - Store only the relevant columns in the synoptics file.
-
-    Args:
-        - od: Observation day in the format YYYYMMDD.
-        - site: Site ID (CSL/CSL1/CSL2/SRON/IAS/INTA).
-        - archive_dir: Folder (with sub-folders /daily and /obs) in which the HDF5 files are stored.
-        - fixed_archive_dir: Folder (with sub-folders /daily and /obs) in which the fixed HK files are stored.
-        - reprocessed_archive_dir: Folder (with sub-folders /daily and /obs) in which the re-processed N-FEE HK files
-                                   will be stored.
-        - setup: Setup.
-    """
-
-    archive_day_dir = f"{archive_dir}/daily/{od}"
-    fixed_archive_day_dir = f"{fixed_archive_dir}/daily/{od}"
-    reprocessed_archive_day_dir = f"{reprocessed_archive_dir}/daily/{od}"
-
-    # Determine the filename for the HK that contribute to the synoptics
-    #       - At this point, the N-FEE HK is re-processed already
-    #       - Most of the other HK will be stored in the original archive, but some of it may be fixed (for some reason)
-
-    syn_input_filenames = get_syn_input_filenames_od(od, site, archive_day_dir, fixed_archive_day_dir,
-                                                     reprocessed_archive_day_dir)
-
-    if len(syn_input_filenames) == 0:
-        LOGGER.info(f"No HK files contributing the synoptics found in {archive_day_dir} nor {fixed_archive_day_dir}")
-        return
-
-    synoptics_filename = f"{reprocessed_archive_day_dir}/{od}_{site}_{SYN_ORIGIN}.{CSV.extension}"
-    _reprocess_synoptics(syn_input_filenames, synoptics_filename, setup)
-
-
-def reprocess_obs_synoptics(obsid: Union[str, int, ObservationIdentifier], site: str, archive_dir: str,
-                            fixed_archive_dir: str, reprocessed_archive_dir: str, setup: Setup):
-    """ Re-processing the N-FEE HK for the given obsid.
-
-    The procedure is as follows:
-        - Compose a list of HK files contributing to the synoptics.
-        - Read those files one by one and concatenate them.
-        - Sort the concatenated tables in order of ascending timestamp.
-        - Store only the relevant columns in the synoptics file.
-
-    Args:
-        - obsid: Observation identifier.
-        - site: Site ID (CSL/CSL1/CSL2/SRON/IAS/INTA).
-        - archive_dir: Folder (with sub-folders /daily and /obs) in which the HDF5 files are stored.
-        - fixed_archive_dir: Folder (with sub-folders /daily and /obs) in which the fixed HK files are stored.
-        - reprocessed_archive_dir: Folder (with sub-folders /daily and /obs) in which the re-processed synoptics files
-                                   will be stored.
-        - setup: Setup.
-        """
-
-    obsid = obsid_from_storage(obsid, archive_dir)
-
-    archive_obs_dir = f"{archive_dir}/obs/{obsid}"
-    fixed_archive_obs_dir = f"{fixed_archive_dir}/obs/{obsid}"
-    reprocessed_archive_obs_dir = f"{reprocessed_archive_dir}/obs/{obsid}"
-
-    # Determine the filename for the HK that contribute to the synoptics
-    #       - At this point, the N-FEE HK is re-processed already
-    #       - Most of the other HK will be stored in the original archive, but some of it may be fixed (for some reason)
-
-    syn_input_filenames = get_syn_input_filename_obs(obsid, site, archive_obs_dir, fixed_archive_obs_dir,
-                                                     reprocessed_archive_obs_dir)
-
-    if len(syn_input_filenames) == 0:
-        LOGGER.info(f"No HK files contributing the synoptics found in {archive_obs_dir} nor {fixed_archive_obs_dir}")
-        return
-
-    pattern = f"{obsid}_{SYN_ORIGIN}_*_*.csv"
-    synoptics_filename = find_file(pattern, root=archive_obs_dir)
-
-    if not os.path.exists(f"{reprocessed_archive_obs_dir}"):
-        os.makedirs(f"{reprocessed_archive_obs_dir}/{obsid}")
-
-    if synoptics_filename is None:
-        od = get_od(obsid, archive_dir)[0]
-        synoptics_filename = f"{reprocessed_archive_obs_dir}/{obsid}_{SYN_ORIGIN}_{od}.{CSV.extension}"
-    else:
-        synoptics_filename = f"{reprocessed_archive_obs_dir}/{synoptics_filename.stem}.{CSV.extension}"
-
-    _reprocess_synoptics(syn_input_filenames, synoptics_filename, setup)
-
-
-def _reprocess_synoptics(syn_input_filenames, synoptics_filename: str, setup: Setup):
-    """ Re-processing the synoptics.
-
-    The procedure is as follows:
-        - Compose a list of HK files contributing to the synoptics.
-        - Read those files one by one and concatenate them.
-        - Sort the concatenated tables in order of ascending timestamp.
-        - Store only the relevant columns in the synoptics file.
-
-    Args:
-        - syn_input_filenames: Filenames of the HK files contributing to the synoptics.
-        - synoptics_filename: Filename for the re-processed synoptics file.
-        - setup: Setup.
-    """
-
-    syn_names, original_name_egse, original_name_th = read_syn_info(setup)
-
-    # Concatenate the content of all contributing HK files
-
-    concatenated_hk = pd.DataFrame()
-
-    for syn_input_filename in syn_input_filenames:
-        try:
-            syn_input_file = pd.read_csv(syn_input_filename)
-
-            concatenated_hk = concatenated_hk.append(syn_input_file)
-        except (ParserError, EmptyDataError) as exc:
-            LOGGER.warning(f"Problem with the content of {syn_input_file} ({exc}).  "
-                           f"The file is either empty or poorly formatted.  Skipping...")
-
-    # Sort according to ascending timestamp
-
-    concatenated_hk = concatenated_hk.sort_values(by=['timestamp'])
-
-    # Convert the HK names to synoptical names (starting with "GSYN_")
-
-    concatenated_hk = concatenated_hk.rename(columns=original_name_egse)
-    concatenated_hk = concatenated_hk.rename(columns=original_name_th)
-
-    # # Fill NaNs
-    #
-    # concatenated_hk = concatenated_hk.fillna(method="ffill")
-    # # concatenated_hk = concatenated_hk.fillna(method="bfill")    # This is only relevant for the first few seconds
-
-    available_syn_names = np.delete(syn_names, np.where(syn_names == "timestamp"))
-    missing_syn_names = np.array([])
-
-    for syn_name in available_syn_names:
-        if syn_name not in concatenated_hk:
-            available_syn_names = np.delete(available_syn_names, np.where(available_syn_names == syn_name))
-            missing_syn_names = np.append(missing_syn_names, syn_name)
-
-    # For numerical columns, use the mean; for boolean columns, use any (unless they are all NaN)
-
-    # agg_dict = {syn_name: np.mean for syn_name in available_syn_names}
-    #
-    # def any_func(arr):
-    #     if arr.isnull().values.all():
-    #         return float('nan')
-    #     return any(arr)
-    #
-    # def mean_func(arr):
-    #     if arr.isnull().values.all():
-    #         return float('nan')
-    #     return np.nanmean(arr)
-    #
-    # agg_dict = {syn_name: mean_func for syn_name in available_syn_names}
-    #
-    # agg_dict["GSYN_OGSE_LAMP_ON"] = any_func
-    # agg_dict["GSYN_OGSE_LASER_ON"] = any_func
-    # agg_dict["GSYN_OGSE_SHUTTER_OPEN"] = any_func
-    #
-    # concatenated_hk = concatenated_hk.groupby("timestamp").agg(agg_dict)
-
-    num_rows = len(concatenated_hk.index)
-    for missing_syn_name in missing_syn_names:
-        concatenated_hk[missing_syn_name] = [float('nan')] * num_rows
-
-    concatenated_hk.to_csv(synoptics_filename, columns=syn_names, index=False)
-
-
-def get_syn_input_filenames_od(od: str, site: str, archive_day_dir: str, fixed_archive_day_dir: str,
-                               reprocessed_archive_day_dir: str):
-    """ Return list of filenames for the HK files contributing to the synoptics of the given TH for the given OD.
-
-    Returns: List of filenames for the HK files contributing to the synoptics of the given TH.
-
-    Args:
-        - od: Observation day in the format YYYYMMDD.
-        - site: Site ID (CSL/CSL1/CSL2/SRON/IAS/INTA).
-        - archive_day_dir: Folder in which the HK files are stored for the given OD.
-        - fixed_archive_day_dir: Folder in which the fixed HK files are stored for the given OD.
-        - reprocessed_archive_day_dir: Folder in which the re-processed synoptics file will be stored for the given OD.
-    """
-
-    syn_input_origins = get_syn_input_origins(site)
-    return get_syn_input_filenames_from_origins_od(syn_input_origins, od, site, archive_day_dir, fixed_archive_day_dir,
-                                                   reprocessed_archive_day_dir)
-
-
-def get_syn_input_filename_obs(obsid: str, site: str, archive_obs_dir: str, fixed_archive_obs_dir: str,
-                               reprocessed_archive_obs_dir: str):
-    """ Return list of filenames for the HK files contributing to the synoptics of the given TH for the given obsid.
-
-    Returns: List of filenames for the HK files contributing to the synoptics of the given TH.
-
-    Args:
-        - obsid: Observation identifier.
-        - site: Site ID (CSL/CSL1/CSL2/SRON/IAS/INTA).
-        - archive_obs_dir: Folder in which the HK files are stored for the given obsid.
-        - fixed_archive_obs_dir: Folder in which the fixed HK files are stored for the given obsid.
-        - reprocessed_archive_obs_dir: Folder in which the re-processed synoptics file will be stored for the given
-                                       obsid.
-    """
-
-    syn_input_origins = get_syn_input_origins(site)
-    return get_syn_input_filenames_from_origins_obs(syn_input_origins, obsid, archive_obs_dir,
-                                                    fixed_archive_obs_dir, reprocessed_archive_obs_dir)
-
-
-def get_syn_input_origins(site: str):
-    """ Return list of storage mnemonics for the HK files contributing to the synoptics at the given TH.
-
-    Returns: List of storage mnemonics for the HK files contributing to the synoptics at the given TH.
-    """
-
-    # Non-TH-specific HK files:
-    #   - N-FEE HK (potentially re-processed)
-    #   - FOV HK
-
-    common_syn_input_origins = [N_FEE_ORIGIN, FOV_ORIGIN]
-
-    # TH-specific HK files
-
-    sitehash = {
-        "CSL": csl_get_syn_input_origins,
-        "CSL1": csl_get_syn_input_origins,
-        "CSL2": csl_get_syn_input_origins,
-        "IAS": ias_get_syn_input_origins,
-        "INTA": inta_get_syn_input_origins,
-        "SRON": sron_get_syn_input_origins,
-    }
-
-    th_syn_input_origins = sitehash[site]()
-
-    return [*common_syn_input_origins, *th_syn_input_origins]
-
-
-def csl_get_syn_input_origins():
-    """ Return list of storage mnemonics for the HK files contributing to the synoptics specifically for CSL.
-
-    Returns: List of storage mnemonics for the HK files contributing to the synoptics specifically for CSL.
-    """
-
-    return ["OGSE"]
-        #[Settings.load("OGSE Control Server").STORAGE_MNEMONIC]
-
-
-def sron_get_syn_input_origins():
-    """ Return list of storage mnemonics for the HK files contributing to the synoptics specifically for SRON.
-
-    Returns: List of storage mnemonics for the HK files contributing to the synoptics specifically for SRON.
-    """
-
-    return [TCS_ORIGIN,
-            Settings.load("BeagleBone Lamp Control Server").STORAGE_MNEMONIC,
-            Settings.load("Thorlabs PM100 Control Server").STORAGE_MNEMONIC,
-            Settings.load("Standa 8SMC5 Control Server").STORAGE_MNEMONIC,
-            Settings.load("Thorlabs SC10 Control Server").STORAGE_MNEMONIC,
-            Settings.load("Agilent 34970 Control Server").DAQ0["STORAGE_MNEMONIC"],
-            Settings.load("Agilent 34970 Control Server").DAQ1["STORAGE_MNEMONIC"],
-            Settings.load("Agilent 34972 Control Server").DAQ0["STORAGE_MNEMONIC"],
-            Settings.load("Agilent 34972 Control Server").DAQ1["STORAGE_MNEMONIC"]]
-
-
-def ias_get_syn_input_origins():
-    """ Return list of storage mnemonics for the HK files contributing to the synoptics specifically for IAS.
-
-    Returns: List of storage mnemonics for the HK files contributing to the synoptics specifically for IAS.
-    """
-
-    return [TCS_ORIGIN,
-            f"DAS-{Settings.load('Keithley Control Server').STORAGE_MNEMONIC}",
-            f"DAS-{Settings.load('SRS PTC10 Control Server').STORAGE_MNEMONIC}",
-            Settings.load("Lamp EQ99 Control Server").STORAGE_MNEMONIC,
-            Settings.load("Thorlabs PM100 Control Server").STORAGE_MNEMONIC,
-            "KSC101"]
-
-
-def inta_get_syn_input_origins():
-    """ Return list of storage mnemonics for the HK files contributing to the synoptics specifically for INTA.
-
-    Returns: List of storage mnemonics for the HK files contributing to the synoptics specifically for INTA.
-    """
-
-    # return [TCS_ORIGIN,
-    #         ]
-    raise NotImplementedError
-
-
-def get_syn_input_filenames_from_origins_od(origins: list, od: str, site: str, archive_day_dir: str,
-                                            fixed_archive_day_dir: str, reprocessed_archive_day_dir: str):
-    """
-    Return list of filenames for the given OD for the given list of origins.
-
-    Returns: List of filenames for the given OD for the given list of origins.
-
-    Args:
-        - origins: List of storage mnemonics for the HK files contributing to the synoptics at the given TH.
-        - od: Observation day in the format YYYYMMDD.
-        - site: Site ID (CSL/CSL1/CSL2/SRON/IAS/INTA).
-        - archive_day_dir: Folder in which the HK files are stored for the given OD.
-        - fixed_archive_day_dir: Folder in which the fixed HK files are stored for the given OD.
-        - reprocessed_archive_day_dir: Folder in which the re-processed synoptics file will be stored for the given OD.
-    """
-
-    filenames = []
-
-    for origin in origins:
-
-        filename = f"{od}_{site}_{origin}.{CSV.extension}"
-
-        # The N-FEE HK must be re-processed already
-
-        if origin == N_FEE_ORIGIN:
-            if Path(f"{reprocessed_archive_day_dir}/{filename}").is_file():
-                filenames.append(f"{reprocessed_archive_day_dir}/{filename}")
-            else:
-                LOGGER.debug(f"No re-processed N-FEE HK available in {reprocessed_archive_day_dir}")
-
-        # For all other HK: first check whether there is a fixed version.  If there is one, use that; otherwise, use
-        # the original version from the archive (if that is available).
-
-        else:
-
-            if Path(f"{fixed_archive_day_dir}/{filename}").is_file():
-                filenames.append(f"{fixed_archive_day_dir}/{filename}")
-                LOGGER.debug(f"Using the fixed HK for {origin}")
-            elif Path(f"{archive_day_dir}/{filename}").is_file():
-                filenames.append(f"{archive_day_dir}/{filename}")
-                LOGGER.debug(f"Using the originally archived HK for {origin}")
-            else:
-                LOGGER.debug(f"No HK file available for {origin}, neither in {fixed_archive_day_dir} nor "
-                             f"{archive_day_dir}")
-
-    return filenames
-
-
-def get_syn_input_filenames_from_origins_obs(origins: list, obsid: str, archive_obs_dir: str,
-                                             fixed_archive_obs_dir: str, reprocessed_archive_obs_dir: str):
-    """ Return list of filenames for the given obsid for the given list of origins.
-
-    Returns: List of filenames for the given obsid for the given list of origins.
-
-    Args:
-        - origins: List of storage mnemonics for the HK files contributing to the synoptics at the given TH.
-        - obsid: Observation identifier.
-        - archive_obs_dir: Folder in which the HK files are stored for the given obsid.
-        - fixed_archive_obs_dir: Folder in which the fixed HK files are stored for the given obsid.
-        - reprocessed_archive_obs_dir: Folder in which the re-processed synoptics file will be stored for the given
-                                       obsid.
-    """
-
-    filenames = []
-
-    for origin in origins:
-
-        pattern = f"{obsid}_{origin}_*_*.{CSV.extension}"
-        filename = find_file(pattern, root=reprocessed_archive_obs_dir)
-
-        if filename is None:
-
-            filename = find_file(pattern, root=fixed_archive_obs_dir)
-
-            if filename is None:
-                filename = find_file(pattern, root=archive_obs_dir)
-
-                if filename is None:
-                    LOGGER.debug(f"No HK file available for {origin}, neither in {fixed_archive_obs_dir} nor "
-                                 f"{archive_obs_dir}")
-                else:
-                    filenames.append(f"{archive_obs_dir}/{filename}")
-                    LOGGER.debug(f"Using the originally archived HK for {origin}")
-            else:
-                filenames.append(f"{fixed_archive_obs_dir}/{filename.stem}.{CSV.extension}")
-                LOGGER.debug(f"Using the fixed HK for {origin}")
-
-        else:
-            filenames.append(f"{fixed_archive_obs_dir}/{filename.stem}.{CSV.extension}")
-            LOGGER.debug(f"Using the re-processed HK for {origin}")
-
-    return filenames
-
-
-def reprocess_ccd_data(obsid: str, archive_dir: str, reprocessed_archive_dir: str, setup: Setup):
-    """ Re-processing of the CCD data for the given obsid.
-
-    Args:
-        - obsid: Observation identifier.
-        - archive_dir: Folder (with sub-folders /daily and /obs) in which the HDF5 and HK files are stored.
-        - fixed_archive_dir: Folder (with sub-folders /daily and /obs) in which the fixed HK files are stored.
-        - reprocessed_archive_dir: Folder (with sub-folders /daily and /obs) in which the re-processed files will be
-                                   stored.
-    """
-
-    hdf5_filenames = get_hdf5_filenames_for_obsid(obsid, data_dir=archive_dir)
-    create_fits_from_hdf5(hdf5_filenames, location=reprocessed_archive_dir, setup=setup)
-
-    fee_side = setup.camera.fee.ccd_sides.enum
-
-    add_synoptics(obsid, data_dir=reprocessed_archive_dir, fee_side=fee_side)