From 23518b6a9ad3374b108facf55d69587a921ec124 Mon Sep 17 00:00:00 2001
From: Thomas Kluyver <thomas.kluyver@xfel.eu>
Date: Fri, 31 Mar 2023 14:54:29 +0200
Subject: [PATCH] Don't use pre notebook for ePix 100
---
.../ePix100/Correction_ePix100_NBC.ipynb | 74 +++++++++++--------
src/xfel_calibrate/notebooks.py | 1 -
2 files changed, 42 insertions(+), 33 deletions(-)
diff --git a/notebooks/ePix100/Correction_ePix100_NBC.ipynb b/notebooks/ePix100/Correction_ePix100_NBC.ipynb
index 499a0d2cf..f850adfdd 100644
--- a/notebooks/ePix100/Correction_ePix100_NBC.ipynb
+++ b/notebooks/ePix100/Correction_ePix100_NBC.ipynb
@@ -157,12 +157,7 @@
"outputs": [],
"source": [
"creation_time = calcat_creation_time(in_folder, run, creation_time)\n",
- "print(f\"Using {creation_time.isoformat()} as creation time\")\n",
- "\n",
- "metadata = CalibrationMetadata(metadata_folder or out_folder)\n",
- "# Constant paths are saved under retrieved-constants in calibration_metadata.yml.\n",
- "# NOTE: this notebook shouldn't overwrite calibration metadata file.\n",
- "const_yaml = metadata.get(\"retrieved-constants\", {})"
+ "print(f\"Using {creation_time.isoformat()} as creation time\")"
]
},
{
@@ -274,30 +269,20 @@
"if relative_gain:\n",
" constant_names += [\"RelativeGainEPix100\"]\n",
"\n",
- "const_data = dict()\n",
- "\n",
- "if const_yaml: # Used while reproducing corrected data.\n",
- " print(f\"Using stored constants in {metadata.filename}\")\n",
- " when = dict()\n",
- " for cname, mdata in const_yaml[karabo_da][\"constants\"].items():\n",
- " const_data[cname] = dict()\n",
- " when[cname] = mdata[\"creation-time\"]\n",
- " if when[cname]:\n",
- " with h5py.File(mdata[\"path\"], \"r\") as cf:\n",
- " const_data[cname] = np.copy(\n",
- " cf[f\"{mdata['dataset']}/data\"])\n",
- "else:\n",
- " 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",
- " const_data = epix_cal.ndarray_map(calibrations=constant_names)[karabo_da]\n",
+ "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",
+ "const_metadata = epix_cal.metadata(calibrations=constant_names)\n",
+ "\n",
+ "# Load the constant data from files\n",
+ "const_data = epix_cal.ndarray_map(metadata=const_metadata)[karabo_da]\n",
"\n",
"# Validate the constants availability and raise/warn correspondingly. \n",
"missing_dark_constants = {\"OffsetEPix100\", \"NoiseEPix100\"} - set(const_data)\n",
@@ -312,6 +297,31 @@
" absolute_gain = False"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Record constant details in YAML metadata\n",
+ "epix_metadata = const_metadata[karabo_da]\n",
+ "CalibrationMetadata(metadata_folder or out_folder).add_fragment({\n",
+ " \"retrieved-constants\": {\n",
+ " karabo_da: {\n",
+ " \"constants\": {\n",
+ " 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",
+ " } for cname, ccv_metadata in epix_metadata.items()\n",
+ " },\n",
+ " \"physical-name\": list(epix_metadata.values())[0][\"physical_name\"],\n",
+ " }\n",
+ " }\n",
+ "})"
+ ]
+ },
{
"cell_type": "code",
"execution_count": null,
@@ -892,7 +902,7 @@
],
"metadata": {
"kernelspec": {
- "display_name": "Python 3.8.11 ('.cal3_venv')",
+ "display_name": "Python 3",
"language": "python",
"name": "python3"
},
@@ -906,7 +916,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
- "version": "3.8.11"
+ "version": "3.8.12"
},
"latex_envs": {
"LaTeX_envs_menu_present": true,
diff --git a/src/xfel_calibrate/notebooks.py b/src/xfel_calibrate/notebooks.py
index 55f1113a4..9a5f29c2f 100644
--- a/src/xfel_calibrate/notebooks.py
+++ b/src/xfel_calibrate/notebooks.py
@@ -217,7 +217,6 @@ notebooks = {
},
"CORRECT": {
- "pre_notebooks": ["notebooks/ePix100/ePix100_retrieve_constants_precorrection.ipynb"],
"notebook": "notebooks/ePix100/Correction_ePix100_NBC.ipynb",
"concurrency": {"parameter": "sequences",
"default concurrency": [-1],
--
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