diff --git a/notebooks/Gotthard2/Gotthard2_retrieve_constants_precorrection_NBC.ipynb b/notebooks/Gotthard2/Gotthard2_retrieve_constants_precorrection_NBC.ipynb
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+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# GOTTHARD2 Retrieving Constants Pre-correction #\n",
+ "\n",
+ "Author: European XFEL Detector Group, Version: 1.0\n",
+ "\n",
+ "Retrieving Required Constants for Offline Calibration of the Gotthard2 Detector"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "in_folder = \"/gpfs/exfel/exp/FXE/202221/p003225/raw\" # the folder to read data from, required\n",
+ "out_folder = \"/gpfs/exfel/data/scratch/ahmedk/test/gotthard2\" # the folder to output to, required\n",
+ "metadata_folder = \"\" # Directory containing calibration_metadata.yml when run by xfel-calibrate\n",
+ "run = 50 # run to process, required\n",
+ "\n",
+ "# Parameters used to access raw data.\n",
+ "karabo_id = \"FXE_XAD_G2XES\" # karabo prefix of Gotthard-II devices\n",
+ "karabo_da = [\"GH201\"] # data aggregators\n",
+ "receiver_template = \"RECEIVER\" # receiver template used to read INSTRUMENT keys.\n",
+ "control_template = \"CONTROL\" # control template used to read CONTROL keys.\n",
+ "instrument_source_template = \"{}/DET/{}:daqOutput\" # template for source name (filled with karabo_id & receiver_id). e.g. 'SPB_IRDA_JF4M/DET/JNGFR01:daqOutput'\n",
+ "ctrl_source_template = \"{}/DET/{}\" # template for control source name (filled with karabo_id_control)\n",
+ "karabo_id_control = \"\" # Control karabo ID. Set to empty string to use the karabo-id\n",
+ "\n",
+ "# Parameters for calibration database.\n",
+ "use_dir_creation_date = True # use the creation data of the input dir for database queries.\n",
+ "cal_db_interface = \"tcp://max-exfl017:8017#8025\" # the database interface to use.\n",
+ "cal_db_timeout = 180000 # timeout on caldb requests.\n",
+ "overwrite_creation_time = \"2022-06-28 13:00:00.00\" # To overwrite the measured creation_time. Required Format: YYYY-MM-DD HR:MN:SC.00 e.g. \"2022-06-28 13:00:00.00\"\n",
+ "\n",
+ "# Parameters affecting corrected data.\n",
+ "constants_file = \"\"#/gpfs/exfel/data/scratch/ahmedk/dont_remove/gotthard2/constants/calibration_constants_GH2.h5\" # Retrieve constants from local.\n",
+ "offset_correction = True # apply offset correction. This can be disabled to only apply LUT or apply LUT and gain correction for non-linear differential results.\n",
+ "gain_correction = True # apply gain correction.\n",
+ "\n",
+ "# Parameter conditions.\n",
+ "bias_voltage = -1 # Detector bias voltage, set to -1 to use value in raw file.\n",
+ "exposure_time = -1. # Detector exposure time, set to -1 to use value in raw file.\n",
+ "exposure_period = -1. # Detector exposure period, set to -1 to use value in raw file.\n",
+ "acquisition_rate = 1.1 # Detector acquisition rate (1.1/4.5), set to -1 to use value in raw file.\n",
+ "single_photon = 0 # Detector single photon mode (High/Low CDS), set to -1 to use value in raw file.\n",
+ "\n",
+ "if constants_file:\n",
+ " print(\"Skipping constant retrieval. Specified constants_file is used.\")\n",
+ " import sys\n",
+ "\n",
+ " sys.exit(0)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import datetime\n",
+ "from functools import partial\n",
+ "\n",
+ "import multiprocessing\n",
+ "from extra_data import RunDirectory\n",
+ "from pathlib import Path\n",
+ "\n",
+ "from cal_tools.gotthard2 import gotthard2lib\n",
+ "from cal_tools.tools import (\n",
+ " get_dir_creation_date,\n",
+ " get_from_db,\n",
+ " CalibrationMetadata,\n",
+ ")\n",
+ "from iCalibrationDB import Conditions, Constants"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "in_folder = Path(in_folder)\n",
+ "run_folder = in_folder / f\"r{run:04d}\"\n",
+ "out_folder = Path(out_folder)\n",
+ "out_folder.mkdir(parents=True, exist_ok=True)\n",
+ "metadata = CalibrationMetadata(metadata_folder or out_folder)\n",
+ "\n",
+ "if not karabo_id_control:\n",
+ " karabo_id_control = karabo_id\n",
+ "\n",
+ "instrument_src = instrument_source_template.format(karabo_id, receiver_template)\n",
+ "ctrl_src = ctrl_source_template.format(karabo_id_control, control_template)\n",
+ "\n",
+ "print(f\"Retrieve constants for modules: {karabo_da} for run {run}\")\n",
+ "\n",
+ "creation_time = None\n",
+ "if overwrite_creation_time:\n",
+ " creation_time = datetime.datetime.strptime(\n",
+ " overwrite_creation_time, \"%Y-%m-%d %H:%M:%S.%f\"\n",
+ " )\n",
+ "elif use_dir_creation_date:\n",
+ " creation_time = get_dir_creation_date(in_folder, run)\n",
+ " print(f\"Using {creation_time} as creation time\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Read slow data\n",
+ "run_dc = RunDirectory(run_folder)\n",
+ "g2ctrl = gotthard2lib.Gotthard2Ctrl(run_dc=run_dc, ctrl_src=ctrl_src)\n",
+ "\n",
+ "if bias_voltage == -1:\n",
+ " bias_voltage = g2ctrl.get_bias_voltage()\n",
+ "if exposure_time == -1:\n",
+ " exposure_time = g2ctrl.get_exposure_time()\n",
+ "if exposure_period == -1:\n",
+ " exposure_period = g2ctrl.get_exposure_period()\n",
+ "if acquisition_rate == -1:\n",
+ " acquisition_rate = g2ctrl.get_acquisition_rate()\n",
+ "if single_photon == -1:\n",
+ " single_photon = g2ctrl.get_single_photon()\n",
+ "\n",
+ "print(\"Bias Voltage:\", bias_voltage)\n",
+ "print(\"Exposure Time:\", exposure_time)\n",
+ "print(\"Exposure Period:\", exposure_period)\n",
+ "print(\"Acquisition Rate:\", acquisition_rate)\n",
+ "print(\"Single Photon:\", single_photon)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "condition = Conditions.Dark.Gotthard2(\n",
+ " bias_voltage=bias_voltage,\n",
+ " exposure_time=exposure_time,\n",
+ " exposure_period=exposure_period,\n",
+ " single_photon=single_photon,\n",
+ " acquisition_rate=acquisition_rate,\n",
+ ")\n",
+ "\n",
+ "def get_constants_for_module(mod: str):\n",
+ " \"\"\"Get calibration constants for given module for Gotthard2.\"\"\"\n",
+ " retrieval_function = partial(\n",
+ " get_from_db,\n",
+ " karabo_id=karabo_id,\n",
+ " karabo_da=mod,\n",
+ " cal_db_interface=cal_db_interface,\n",
+ " creation_time=creation_time,\n",
+ " timeout=cal_db_timeout,\n",
+ " verbosity=1,\n",
+ " meta_only=True,\n",
+ " load_data=False,\n",
+ " empty_constant=None\n",
+ " )\n",
+ "\n",
+ " mdata_dict = dict()\n",
+ " mdata_dict[\"constants\"] = dict()\n",
+ " constants = [\n",
+ " \"LUT\", \"Offset\", \"BadPixelsDark\",\n",
+ " \"RelativeGain\", \"BadPixelsFF\",\n",
+ " ]\n",
+ " for cname in constants:\n",
+ " mdata_dict[\"constants\"][cname] = dict()\n",
+ " if not gain_correction and cname in [\"BadPixelsFF\", \"RelativeGain\"]:\n",
+ " continue\n",
+ " _, mdata = retrieval_function(\n",
+ " condition=condition,\n",
+ " constant=getattr(Constants.Gotthard2, cname)(),\n",
+ " )\n",
+ " mdata_const = mdata.calibration_constant_version\n",
+ " const_mdata = mdata_dict[\"constants\"][cname]\n",
+ " # check if constant was successfully retrieved.\n",
+ " if mdata.comm_db_success:\n",
+ " const_mdata[\"file-path\"] = (\n",
+ " f\"{mdata_const.hdf5path}\" f\"{mdata_const.filename}\"\n",
+ " )\n",
+ " const_mdata[\"dataset-name\"] = mdata_const.h5path\n",
+ " const_mdata[\"creation-time\"] = f\"{mdata_const.begin_at}\"\n",
+ " mdata_dict[\"physical-detector-unit\"] = mdata_const.device_name\n",
+ " else:\n",
+ " const_mdata[\"file-path\"] = None\n",
+ " const_mdata[\"creation-time\"] = None\n",
+ " return mdata_dict, mod\n",
+ "\n",
+ "with multiprocessing.Pool() as pool:\n",
+ " results = pool.map(get_constants_for_module, karabo_da)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Constant paths are saved under retrieved-constants in calibration_metadata.yml\n",
+ "retrieved_constants = metadata.setdefault(\"retrieved-constants\", {})\n",
+ "timestamps = dict()\n",
+ "\n",
+ "for md_dict, mod in results:\n",
+ " if mod in retrieved_constants:\n",
+ " print(f\"Constant for {mod} already in calibration_metadata.yml, won't query again.\") # noqa\n",
+ " continue\n",
+ " retrieved_constants[mod] = md_dict\n",
+ " module_timestamps = timestamps[mod] = dict()\n",
+ "\n",
+ " print(f\"Module: {mod}:\")\n",
+ " for cname, mdata in md_dict[\"constants\"].items():\n",
+ " if hasattr(mdata[\"creation-time\"], 'strftime'):\n",
+ " mdata[\"creation-time\"] = mdata[\"creation-time\"].strftime('%y-%m-%d %H:%M')\n",
+ " print(f'{cname:.<12s}', mdata[\"creation-time\"])\n",
+ "\n",
+ " for cname in [\"Offset\", \"BadPixelsDark\", \"RelativeGain\", \"BadPixelsFF\"]:\n",
+ " if cname in md_dict[\"constants\"]:\n",
+ " module_timestamps[cname] = md_dict[\"constants\"][cname][\"creation-time\"]\n",
+ " else:\n",
+ " module_timestamps[cname] = \"NA\"\n",
+ "\n",
+ "time_summary = retrieved_constants.setdefault(\"time-summary\", {})\n",
+ "time_summary[\"SAll\"] = timestamps\n",
+ "\n",
+ "metadata.save()"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3.8.11 ('.cal4_venv')",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
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+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
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+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
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+ "orig_nbformat": 4,
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+}