diff --git a/notebooks/ePix100/ePix100_retrieve_constants_precorrection.ipynb b/notebooks/ePix100/ePix100_retrieve_constants_precorrection.ipynb
deleted file mode 100644
index cf506f0e4a1bf79d355cf7e241871730f01bc4b4..0000000000000000000000000000000000000000
--- a/notebooks/ePix100/ePix100_retrieve_constants_precorrection.ipynb
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@@ -1,214 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "markdown",
- "metadata": {},
- "source": [
- "# ePix100 retrieve constants precorrection\n",
- "\n",
- "Author: European XFEL Detector Group, Version: 1.0\n",
- "\n",
- "The following notebook provides constants for the selected ePix100 modules before executing correction on the selected sequence files."
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "in_folder = \"/gpfs/exfel/exp/CALLAB/202031/p900113/raw\" # input folder, required\n",
- "out_folder = \"/gpfs/exfel/data/scratch/ahmedk/test/remove/epix_correct\" # output folder, required\n",
- "metadata_folder = \"\" # Directory containing calibration_metadata.yml when run by xfel-calibrate\n",
- "sequences = [-1] # sequences to correct, set to -1 for all, range allowed\n",
- "run = 9988 # which run to read data from, required\n",
- "\n",
- "# Parameters for accessing the raw data.\n",
- "karabo_id = \"MID_EXP_EPIX-1\" # Detector Karabo_ID\n",
- "karabo_da = \"EPIX01\" # data aggregators\n",
- "receiver_template = \"RECEIVER\" # detector receiver template for accessing raw data files\n",
- "instrument_source_template = '{}/DET/{}:daqOutput' # instrument detector data source in h5files\n",
- "\n",
- "# Parameters for the calibration database.\n",
- "creation_time = \"\" # The timestamp to use with Calibration DB. Required Format: \"YYYY-MM-DD hh:mm:ss\" e.g. 2019-07-04 11:02:41\n",
- "cal_db_interface = \"tcp://max-exfl016:8015#8025\" # calibration DB interface to use\n",
- "cal_db_timeout = 300000 # timeout on CalibrationDB requests\n",
- "\n",
- "# Conditions for retrieving calibration constants.\n",
- "bias_voltage = 200 # bias voltage\n",
- "in_vacuum = False # detector operated in vacuum\n",
- "fix_temperature = 290 # fixed temperature value in Kelvin. Default value -1 to use the value from files.\n",
- "integration_time = -1 # Detector integration time, Default value -1 to use the value from the slow data.\n",
- "gain_photon_energy = 9.0 # Photon energy used for gain calibration\n",
- "\n",
- "# Flags to select type of applied corrections.\n",
- "relative_gain = True # Apply relative gain correction."
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "from logging import warning\n",
- "\n",
- "import numpy as np\n",
- "from extra_data import RunDirectory\n",
- "from pathlib import Path\n",
- "\n",
- "import cal_tools.restful_config as rest_cfg\n",
- "from cal_tools.calcat_interface import EPIX100_CalibrationData\n",
- "from cal_tools.epix100 import epix100lib\n",
- "from cal_tools.tools import (\n",
- " calcat_creation_time,\n",
- " CalibrationMetadata,\n",
- ")"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "in_folder = Path(in_folder)\n",
- "out_folder = Path(out_folder)\n",
- "\n",
- "out_folder.mkdir(parents=True, exist_ok=True)\n",
- "\n",
- "metadata = CalibrationMetadata(metadata_folder or out_folder)\n",
- "# NOTE: this notebook will not overwrite calibration metadata file,\n",
- "# if it already contains details about which constants to use.\n",
- "retrieved_constants = metadata.setdefault(\"retrieved-constants\", {})"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "creation_time = calcat_creation_time(in_folder, run, creation_time)\n",
- "print(f\"Using {creation_time.isoformat()} as creation time\")"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "# Read control data.\n",
- "run_dc = RunDirectory(in_folder / f\"r{run:04d}\")\n",
- "\n",
- "ctrl_data = epix100lib.epix100Ctrl(\n",
- " run_dc=run_dc,\n",
- " instrument_src=f\"{karabo_id}/DET/{receiver_template}:daqOutput\",\n",
- " ctrl_src=f\"{karabo_id}/DET/CONTROL\",\n",
- " )\n",
- "\n",
- "if integration_time < 0:\n",
- " integration_time = ctrl_data.get_integration_time()\n",
- " integration_time_str_add = \"\"\n",
- "else:\n",
- " integration_time_str_add = \"(manual input)\"\n",
- "\n",
- "if fix_temperature < 0:\n",
- " temperature = ctrl_data.get_temprature()\n",
- " temperature_k = temperature + 273.15\n",
- " temp_str_add = \"\"\n",
- "else:\n",
- " temperature_k = fix_temperature\n",
- " temperature = fix_temperature - 273.15\n",
- " temp_str_add = \"(manual input)\"\n",
- "\n",
- "\n",
- "print(f\"Bias voltage is {bias_voltage} V\")\n",
- "print(f\"Detector integration time is set to {integration_time} \\u03BCs {integration_time_str_add}\")\n",
- "print(f\"Mean temperature: {temperature:0.2f}°C / {temperature_k:0.2f} K {temp_str_add}\")\n",
- "print(f\"Operated in vacuum: {in_vacuum}\")"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {
- "tags": []
- },
- "outputs": [],
- "source": [
- "epix_cal = EPIX100_CalibrationData(\n",
- " detector_name=karabo_id,\n",
- " sensor_bias_voltage=bias_voltage,\n",
- " integration_time=integration_time,\n",
- " sensor_temperature=temperature_k,\n",
- " in_vacuum=in_vacuum,\n",
- " source_energy=gain_photon_energy,\n",
- " event_at=creation_time,\n",
- " client=rest_cfg.calibration_client(),\n",
- " )\n",
- "\n",
- "mdata_dict = {\"constants\": dict()}\n",
- "\n",
- "constant_names = [\"OffsetEPix100\", \"NoiseEPix100\"]\n",
- "if relative_gain:\n",
- " constant_names += [\"RelativeGainEPix100\"]\n",
- "\n",
- "# Retrieve metadata for all epix100 constants.\n",
- "\n",
- "epix_metadata = epix_cal.metadata(constant_names)[karabo_da]\n",
- "\n",
- "# Validate the constants availability and raise/warn correspondingly.\n",
- "missing_dark_constants = {\"OffsetEPix100\", \"NoiseEPix100\"} - set(epix_metadata)\n",
- "if missing_dark_constants:\n",
- " raise ValueError(\n",
- " f\"Dark constants {missing_dark_constants} are not available to correct {karabo_da}.\")\n",
- "\n",
- "if relative_gain and \"RelativeGainEPix100\" not in epix_metadata.keys():\n",
- " warning(\"RelativeGainEPix100 is not found in CALCAT.\")\n",
- "\n",
- "for cname, ccv_metadata in epix_metadata.items():\n",
- " mdata_dict[\"constants\"][cname] = {\n",
- " \"path\": str(epix_cal.caldb_root / ccv_metadata[\"path\"]),\n",
- " \"dataset\": ccv_metadata[\"dataset\"],\n",
- " \"creation-time\": ccv_metadata[\"begin_validity_at\"],\n",
- " \"ccv_id\": ccv_metadata[\"ccv_id\"],\n",
- " }\n",
- " print(f\"Retrieved {cname} with creation-time: {ccv_metadata['begin_validity_at']}\")\n",
- "\n",
- "mdata_dict[\"physical-name\"] = ccv_metadata[\"physical_name\"]\n",
- "retrieved_constants[karabo_da] = mdata_dict\n",
- "metadata.save()\n",
- "print(f\"Stored retrieved constants in {metadata.filename}\")"
- ]
- }
- ],
- "metadata": {
- "kernelspec": {
- "display_name": "Python 3.8.11 ('.cal4_venv')",
- "language": "python",
- "name": "python3"
- },
- "language_info": {
- "codemirror_mode": {
- "name": "ipython",
- "version": 3
- },
- "file_extension": ".py",
- "mimetype": "text/x-python",
- "name": "python",
- "nbconvert_exporter": "python",
- "pygments_lexer": "ipython3",
- "version": "3.8.11"
- },
- "orig_nbformat": 4,
- "vscode": {
- "interpreter": {
- "hash": "ccde353e8822f411c1c49844e1cbe3edf63293a69efd975d1b44f5e852832668"
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- "nbformat": 4,
- "nbformat_minor": 2
-}