diff --git a/notebooks/Gotthard2/Characterize_Darks_Gotthard2_NBC.ipynb b/notebooks/Gotthard2/Characterize_Darks_Gotthard2_NBC.ipynb
index 70e0450aea363aba8ab16e96bff6ff626a80bd15..6548a50025758c5ca7aa186c2db0f6fc54dc7e89 100644
--- a/notebooks/Gotthard2/Characterize_Darks_Gotthard2_NBC.ipynb
+++ b/notebooks/Gotthard2/Characterize_Darks_Gotthard2_NBC.ipynb
@@ -24,6 +24,7 @@
"source": [
"in_folder = \"/gpfs/exfel/exp/FXE/202231/p900298/raw\" # the folder to read data from, required\n",
"out_folder = \"/gpfs/exfel/data/scratch/ahmedk/test/gotthard2/darks\" # the folder to output to, required\n",
+ "metadata_folder = '' # Directory containing calibration_metadata.yml when run by xfel-calibrate\n",
"run_high = 7 # run number for G0 dark run, required\n",
"run_med = 8 # run number for G1 dark run, required\n",
"run_low = 9 # run number for G2 dark run, required\n",
@@ -73,6 +74,7 @@
"from extra_data import RunDirectory\n",
"from pathlib import Path\n",
"\n",
+ "import yaml\n",
"from cal_tools.calcat_interface import CalCatApi\n",
"from cal_tools.enums import BadPixels\n",
"from cal_tools.gotthard2 import gotthard2algs, gotthard2lib\n",
@@ -81,7 +83,6 @@
"from cal_tools.tools import (\n",
" calcat_creation_time,\n",
" get_constant_from_db_and_time,\n",
- " get_pdu_from_db,\n",
" get_report,\n",
" save_const_to_h5,\n",
" send_to_db,\n",
@@ -107,7 +108,7 @@
"ctrl_src = ctrl_source_template.format(karabo_id_control, control_template)\n",
"\n",
"# Read report path to associate it later with injected constants.\n",
- "report = get_report(out_folder)\n",
+ "report = get_report(metadata_folder)\n",
"\n",
"# Run's creation time:\n",
"creation_time = calcat_creation_time(in_folder, run_high, creation_time)\n",
@@ -546,6 +547,26 @@
")\n",
"step_timer.done_step(\"Injecting constants.\")"
]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "id": "98ca9486",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# TODO: store old constants for comparison.\n",
+ "for mod, pdu in da_to_pdu.items():\n",
+ " mod_file = mod.replace(\"/\", \"-\")\n",
+ " with open(f\"{metadata_folder or out_folder}/module_metadata_{mod_file}.yml\", \"w\") as fd:\n",
+ " yaml.safe_dump(\n",
+ " {\n",
+ " \"module\": mod,\n",
+ " \"pdu\": pdu,\n",
+ " },\n",
+ " fd,\n",
+ " )"
+ ]
}
],
"metadata": {
diff --git a/notebooks/Gotthard2/Summary_Darks_Gotthard2_NBC.ipynb b/notebooks/Gotthard2/Summary_Darks_Gotthard2_NBC.ipynb
new file mode 100644
index 0000000000000000000000000000000000000000..9bc054213abea01838eb5cf5f877d30b736a3a42
--- /dev/null
+++ b/notebooks/Gotthard2/Summary_Darks_Gotthard2_NBC.ipynb
@@ -0,0 +1,202 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Gotthard2 Dark Summary\n",
+ "\n",
+ "Author: European XFEL Detector Department, Version: 1.0\n",
+ "\n",
+ "Summary for process dark constants and a comparison with previously injected constants with the same conditions."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "in_folder = \"/gpfs/exfel/exp/DETLAB/202330/p900326/raw\" # the folder to read data from, required\n",
+ "out_folder = \"/gpfs/exfel/data/scratch/ahmedk/test/gotthard2\" # path to output to, required\n",
+ "metadata_folder = \"\" # Directory containing calibration_metadata.yml when run by xfel-calibrate.\n",
+ "run_high = 20 # run number for G0 dark run, required\n",
+ "run_med = 21 # run number for G1 dark run, required\n",
+ "run_low = 22 # run number for G2 dark run, required\n",
+ "\n",
+ "# Parameters used to access raw data.\n",
+ "karabo_id = \"DETLAB_25UM_GH2\" # detector identifier.\n",
+ "karabo_da = [\"DA01/1\", \"DA01/2\"] # list of data aggregators, which corresponds to different JF modules. This is only needed for the detectors of one module.\n",
+ "control_template = \"CONTROL\" # control template used to read CONTROL keys.\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 to be used for injecting dark calibration constants.\n",
+ "local_output = True # Boolean indicating that local constants were stored in the out_folder\n",
+ "\n",
+ "# Skip the whole notebook if local_output is false in the preceding notebooks.\n",
+ "if not local_output:\n",
+ " print('No local constants saved. Skipping summary plots')\n",
+ " import sys\n",
+ " sys.exit(0)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import warnings\n",
+ "from pathlib import Path\n",
+ "\n",
+ "warnings.filterwarnings('ignore')\n",
+ "\n",
+ "import h5py\n",
+ "import matplotlib\n",
+ "import matplotlib.pyplot as plt\n",
+ "import numpy as np\n",
+ "import yaml\n",
+ "from extra_data import RunDirectory\n",
+ "from IPython.display import Markdown, display\n",
+ "\n",
+ "from cal_tools.gotthard2 import gotthard2lib\n",
+ "\n",
+ "matplotlib.use(\"agg\")\n",
+ "%matplotlib inline\n",
+ "\n",
+ "from cal_tools.tools import CalibrationMetadata"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "out_folder = Path(out_folder)\n",
+ "metadata = CalibrationMetadata(metadata_folder or out_folder)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "if not karabo_id_control:\n",
+ " karabo_id_control = karabo_id\n",
+ "g2ctrl = gotthard2lib.Gotthard2Ctrl(\n",
+ " run_dc=RunDirectory(Path(in_folder) / f\"r{run_high:04d}\"),\n",
+ " ctrl_src=ctrl_source_template.format(karabo_id_control, control_template))\n",
+ "gh2_detector = g2ctrl.get_det_type()\n",
+ "print(f\"Processing {gh2_detector} Gotthard2.\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "mod_mapping = dict()\n",
+ "for fn in Path(metadata_folder or out_folder).glob(\"module_metadata_*.yml\"):\n",
+ " with fn.open(\"r\") as fd:\n",
+ " fdict = yaml.safe_load(fd)\n",
+ " mod_mapping[fdict[\"module\"].replace(\"-\", \"/\")] = fdict[\"pdu\"]\n",
+ "\n",
+ "mod_mapping = dict(sorted(mod_mapping.items(), key=lambda item: item[0]))"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "plt_map = dict()\n",
+ "dark_constants = [\"BadPixelsDark\", \"Offset\", \"Noise\"]\n",
+ "if gh2_detector == \"25um\":\n",
+ " for cname in dark_constants:\n",
+ " plt_map[cname] = np.zeros(\n",
+ " (1280 * 2, 2, 3),\n",
+ " dtype=np.uint32 if cname == \"BadPixelsDark\" else np.float32\n",
+ " )"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "for cname in dark_constants:\n",
+ "\n",
+ " for i, (mod, pdu) in enumerate(mod_mapping.items()):\n",
+ " module = mod.replace(\"-\", \"/\")\n",
+ "\n",
+ " with h5py.File(out_folder / f\"const_{cname}_{pdu}.h5\", 'r') as f:\n",
+ " if gh2_detector == \"25um\":\n",
+ " plt_map[cname][i::2] = f[\"data\"][()]\n",
+ " else:\n",
+ " plt_map[cname] = f[\"data\"][()]"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "if gh2_detector == \"50um\":\n",
+ " title = (\n",
+ " f\"{{}} data for \"\n",
+ " f\"{[f'{mod}({pdu})' for mod, pdu in mod_mapping.items()]}\"\n",
+ " )\n",
+ "else:\n",
+ " title = (\n",
+ " f\"Interleaved {{}} data for \"\n",
+ " f\"{[f'{mod}({pdu})' for mod, pdu in mod_mapping.items()]}\"\n",
+ " )\n",
+ "\n",
+ "for cname in dark_constants:\n",
+ " display(Markdown(f\"### {cname}\"))\n",
+ "\n",
+ " for cell in [0, 1]:\n",
+ " fig, ax = plt.subplots(figsize=(10, 5))\n",
+ " for g_idx in [0, 1, 2]:\n",
+ " ax.plot(plt_map[cname][:, cell, g_idx], label=f\"G{g_idx} {cname} map\")\n",
+ " ax.set_xticks(\n",
+ " np.arange(0, plt_map[cname].shape[0]+1, plt_map[cname].shape[0]//16)\n",
+ " )\n",
+ " ax.set_xlabel(\"Stripes #\")\n",
+ " ax.set_xlabel(cname)\n",
+ " ax.set_title(title.format(f\"{cname} map - Cell {cell}\"))\n",
+ " ax.legend()\n",
+ " plt.show()"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": ".cal3_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
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/src/xfel_calibrate/notebooks.py b/src/xfel_calibrate/notebooks.py
index 3d241b27e7f1d41050ce49b28be9823611d9040d..63231b4dff9c60cf7a62a808ef06b270da51e7a3 100644
--- a/src/xfel_calibrate/notebooks.py
+++ b/src/xfel_calibrate/notebooks.py
@@ -214,6 +214,8 @@ notebooks = {
"DARK": {
"notebook":
"notebooks/Gotthard2/Characterize_Darks_Gotthard2_NBC.ipynb",
+ "dep_notebooks": [
+ "notebooks/Gotthard2/Summary_Darks_Gotthard2_NBC.ipynb"],
"concurrency": {"parameter": "karabo_da",
"default concurrency": list(range(2)),
"cluster cores": 4},