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Commit 01fa3065 authored by Karim Ahmed's avatar Karim Ahmed
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update correction notebook with func to get seq files and better karabo_da handline

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notebooks/Gotthard2/Correction_Gotthard2_NBC.ipynb
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{
"cells": [
{
"attachments": {},
"cell_type": "markdown",
"id": "bed7bd15-21d9-4735-82c1-c27c1a5e3346",
"metadata": {},
......@@ -30,12 +29,12 @@
"In case one of the gain constants were not retrieved `gain_correction` is switched to False and gain correction is disabled.\n",
"\n",
"The `data` datasets stored in the RECEIVER source along with the corrected image (`adc`) and `mask` are: \n",
" - gain\n",
" - bunchId\n",
" - memoryCell\n",
" - frameNumber\n",
" - timestamp\n",
" - trainId"
" - `gain`\n",
" - `bunchId`\n",
" - `memoryCell`\n",
" - `frameNumber`\n",
" - `timestamp`\n",
" - `trainId`"
]
},
{
......@@ -114,6 +113,7 @@
"from cal_tools.tools import (\n",
" calcat_creation_time,\n",
" write_constants_fragment,\n",
" map_seq_files,\n",
")\n",
"from XFELDetAna.plotting.heatmap import heatmapPlot\n",
"\n",
......@@ -146,34 +146,6 @@
"print(f\"Creation time: {creation_time}\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "b5eb816e-b5f2-44ce-9907-0273d82341b6",
"metadata": {},
"outputs": [],
"source": [
"# Select only sequence files to process for the selected detector.\n",
"if sequences == [-1]:\n",
" possible_patterns = list(f\"*{mod}*.h5\" for mod in karabo_da)\n",
"else:\n",
" possible_patterns = list(\n",
" f\"*{mod}-S{s:05d}.h5\" for mod in karabo_da for s in sequences\n",
" )\n",
"\n",
"run_folder = Path(in_folder / f\"r{run:04d}\")\n",
"seq_files = [\n",
" f for f in run_folder.glob(\"*.h5\") if any(f.match(p) for p in possible_patterns)\n",
"]\n",
"\n",
"seq_files = sorted(seq_files)\n",
"\n",
"if not seq_files:\n",
" raise ValueError(\"No sequence files available for the selected sequences.\")\n",
"\n",
"print(f\"Processing a total of {len(seq_files)} sequence files\")"
]
},
{
"cell_type": "code",
"execution_count": null,
......@@ -211,24 +183,65 @@
"print(\"Exposure Time:\", exposure_time)\n",
"print(\"Exposure Period:\", exposure_period)\n",
"print(\"Acquisition Rate:\", acquisition_rate)\n",
"print(\"Single Photon:\", single_photon)\n",
"print(\"Single Photon:\", single_photon)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "21a8953a-8c76-475e-8f4f-b201cc25c159",
"metadata": {},
"outputs": [],
"source": [
"g2_cal = GOTTHARD2_CalibrationData(\n",
" detector_name=karabo_id,\n",
" sensor_bias_voltage=bias_voltage,\n",
" exposure_time=exposure_time,\n",
" exposure_period=exposure_period,\n",
" acquisition_rate=acquisition_rate,\n",
" single_photon=single_photon,\n",
" event_at=creation_time,\n",
" client=rest_cfg.calibration_client(),\n",
")\n",
"\n",
"# Keep as long as it is essential to correct\n",
"# RAW data (FXE p003225) before the data mapping was added to CALCAT.\n",
"try: # in case local constants are used with old RAW data. This can be removed in the future.\n",
" da_to_pdu = g2_cal.mod_to_pdu\n",
"except CalCatError as e:\n",
" print(e)\n",
" db_modules = [None] * len(karabo_da)\n",
"\n",
"if karabo_da == [\"\"]:\n",
" karabo_da = sorted(da_to_pdu.keys())\n",
"else:\n",
" # Filter DA connected to detector in CALCAT\n",
" karabo_da = [da for da in karabo_da if da in da_to_pdu]\n",
" # Exclude non selected DA from processing.\n",
"\n",
"db_modules = [da_to_pdu[da] for da in karabo_da]"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "9609a142-99a4-42e5-94f0-abe9cc99cc21",
"metadata": {},
"outputs": [],
"source": [
"# Decide if GH2 is 25um or 50um\n",
"gh2_hostname = run_dc.get_run_value(ctrl_src, \"rxHostname\")\n",
"# gh2_hostname is a vector of bytes objects.\n",
"# GH2 25um has two hostnames unlike 50um which has one.\n",
"gh2_detector = \"25um\" if gh2_hostname[1].decode(\"utf-8\") else \"50um\"\n",
"print(f\"Processing {gh2_detector} Gotthard2.\")\n",
"\n",
"# Decide if we are processing 2 25um or 1 50um Gotthard-II\n",
"\n",
"# Create the correction receiver name.\n",
"receivers = sorted(list(run_dc.select(f'{karabo_id}/DET/{receiver_template}*').all_sources))\n",
"\n",
"if gh2_detector == \"25um\": # For 25um use virtual karabo_das for CALCAT data mapping.\n",
" karabo_da = [f\"{karabo_da[0]}/1\", f\"{karabo_da[0]}/2\"]\n",
" print(\"Processing 25um Gotthard2.\")\n",
" corr_karabo_da = receivers[0].split(\"/\")[-1].split(\":\")[0][:-2]\n",
" corr_receiver = receivers[0].split(\"/\")[-1].split(\":\")[0][:-2]\n",
"else:\n",
" corr_karabo_da = receivers[0].split(\"/\")[-1].split(\":\")[0]"
" corr_receiver = receivers[0].split(\"/\")[-1].split(\":\")[0]"
]
},
{
......@@ -246,30 +259,9 @@
"metadata": {},
"outputs": [],
"source": [
"da_to_pdu = {}\n",
"# Used for old FXE (p003225) runs before adding Gotthard2 to CALCAT\n",
"const_data = dict()\n",
"\n",
"g2_cal = GOTTHARD2_CalibrationData(\n",
" detector_name=karabo_id,\n",
" sensor_bias_voltage=bias_voltage,\n",
" exposure_time=exposure_time,\n",
" exposure_period=exposure_period,\n",
" acquisition_rate=acquisition_rate,\n",
" single_photon=single_photon,\n",
" event_at=creation_time,\n",
" client=rest_cfg.calibration_client(),\n",
")\n",
"# Keep as long as it is essential to correct\n",
"# RAW data (FXE p003225) before the data mapping was added to CALCAT.\n",
"try: # in case local constants are used with old RAW data. This can be removed in the future.\n",
" for mod_info in g2_cal.physical_detector_units.values():\n",
" da_to_pdu[mod_info[\"karabo_da\"]] = mod_info[\"physical_name\"]\n",
" db_modules = [da_to_pdu[da] for da in karabo_da]\n",
"except CalCatError as e:\n",
" print(e)\n",
" db_modules = [None] * len(karabo_da)\n",
"\n",
"if constants_file:\n",
" for mod in karabo_da:\n",
" const_data[mod] = dict()\n",
......@@ -343,6 +335,22 @@
" (1280, 2, 3), dtype=np.float32)\n",
" const_data[mod][\"RelativeGainGotthard2\"] = const_data[mod][\"RelativeGainGotthard2\"].astype( # noqa\n",
" np.float32, copy=False) # Old gain constants are not float32."
"id": "b41f3720-2abd-43ed-b948-8d2f0815b6a3",
"metadata": {},
"outputs": [],
"source": [
"raw_da = karabo_da if gh2_detector == \"50um\" else [karabo_da[0].split(\"/\")[0]]\n",
"mapped_files, total_files = map_seq_files(\n",
" run_folder,\n",
" raw_da,\n",
" sequences,\n",
")\n",
"seq_files = mapped_files[raw_da[0]]\n",
"\n",
"if not len(seq_files):\n",
" raise IndexError(\n",
" \"No sequence files available to correct for the selected sequences and karabo_da.\")\n",
"print(f\"Processing a total of {total_files} sequence files\")"
]
},
{
......@@ -384,7 +392,7 @@
"metadata": {},
"outputs": [],
"source": [
"corr_data_source = f\"{karabo_id}/DET/{corr_karabo_da}:daqOutput\"\n",
"corr_data_source = f\"{karabo_id}/DET/{corr_receiver}:daqOutput\"\n",
"\n",
"for raw_file in seq_files:\n",
"\n",
......
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