diff --git a/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb b/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb
index 497bb4d1bd6f2944a738a88ca5e63a0c6cfa60e8..761119c47bb08571eb3afe97a467dc326abf1610 100644
--- a/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb
+++ b/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb
@@ -33,9 +33,9 @@
"karabo_id_control = \"\" # if control is on a different ID, set to empty string if it is the same a 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-exfl016:8017#8025\" # the database interface to use\n",
"cal_db_timeout = 180000 # timeout on caldb requests\n",
+ "creation_time = \"\" # To overwrite the measured creation_time. Required Format: YYYY-MM-DD HR:MN:SC e.g. \"2022-06-28 13:00:00\"\n",
"\n",
"# Parameters affecting corrected data.\n",
"relative_gain = True # do relative gain correction.\n",
@@ -96,7 +96,7 @@
"from cal_tools.files import DataFile\n",
"from cal_tools.step_timing import StepTimer\n",
"from cal_tools.tools import (\n",
- " get_dir_creation_date,\n",
+ " calcat_creation_time,\n",
" map_seq_files,\n",
" CalibrationMetadata,\n",
")\n",
@@ -129,10 +129,9 @@
"print(f\"Instrument H5File source: {instrument_src}\")\n",
"print(f\"Process modules: {karabo_da}\")\n",
"\n",
- "creation_time = None\n",
- "if use_dir_creation_date:\n",
- " creation_time = get_dir_creation_date(in_folder, run)\n",
- " print(f\"Using {creation_time} as creation time\")\n",
+ "# Run's creation time:\n",
+ "creation_time = calcat_creation_time(in_folder, run, creation_time)\n",
+ "print(f\"Creation time: {creation_time}\")\n",
"\n",
"if karabo_id_control == \"\":\n",
" karabo_id_control = karabo_id\n",
@@ -203,10 +202,6 @@
" gain_setting = ctrl_data.get_gain_setting()\n",
" gain_mode = ctrl_data.get_gain_mode()\n",
"\n",
- "# A workound for correcting runs of forceswitchg1 and forceswitchg2\n",
- "# of single cell mode.\n",
- "memory_cells = 1 if memory_cells == 2 and \"forceswitch\" in ctrl_data.run_settings else 16\n",
- "\n",
"print(f\"Integration time is {integration_time} us\")\n",
"print(f\"Gain setting is {gain_setting} (run settings: {ctrl_data.run_settings})\")\n",
"print(f\"Gain mode is {gain_mode} ({ctrl_data.run_mode})\")\n",
@@ -256,7 +251,8 @@
" detector_name=karabo_id,\n",
" sensor_bias_voltage=bias_voltage,\n",
" event_at=creation_time,\n",
- " modules=[int(x[-2:]) for x in karabo_da],\n",
+ " snapshot_at=creation_time,\n",
+ " modules=karabo_da,\n",
" memory_cells=memory_cells,\n",
" integration_time=integration_time,\n",
" gain_setting=gain_setting,\n",
@@ -269,7 +265,21 @@
" const_data = jf_cal.ndarray_map(calibrations=constant_names)\n",
" \n",
" for mod_info in jf_cal.physical_detector_units.values():\n",
- " da_to_pdu[mod_info[\"karabo_da\"]] = mod_info[\"physical_name\"]"
+ " da_to_pdu[mod_info[\"karabo_da\"]] = mod_info[\"physical_name\"]\n",
+ "\n",
+ "# Validate the constants availability and raise/warn correspondingly. \n",
+ "for mod, calibrations in const_data.items():\n",
+ " missing_dark_constants = set(\n",
+ " c for c in [\"Offset10Hz\", \"BadPixelsDark10Hz\"] if c not in calibrations.keys())\n",
+ " missing_gain_constants = set(\n",
+ " c for c in [\"BadPixelsFF10Hz\", \"RelativeGain10Hz\"] if relative_gain and c not in calibrations.keys()) # noqa\n",
+ " if missing_dark_constants:\n",
+ " raise KeyError(\n",
+ " f\"Dark constants {missing_dark_constants} are not available for correction. Module: {mod}\") # noqa\n",
+ " if missing_gain_constants:\n",
+ " warning(\n",
+ " f\"Gain constants {missing_gain_constants} were not retrieved. Module: {mod}\")\n",
+ " relative_gain = False"
]
},
{
@@ -295,9 +305,9 @@
" except KeyError as e:\n",
" # Fail processing if dark constants are not available.\n",
" raise KeyError(f\"Dark constant is not available for correction for {module}. {e}\")\n",
- "\n",
- " gain_map = constant_arrays[\"RelativeGain10Hz\"]\n",
- " mask_ff = constant_arrays[\"BadPixelsFF10Hz\"]\n",
+ " \n",
+ " gain_map = constant_arrays.get(\"RelativeGain10Hz\")\n",
+ " mask_ff = constant_arrays.get(\"BadPixelsFF10Hz\")\n",
"\n",
" # Combine masks\n",
" if mask_ff is not None:\n",
@@ -333,10 +343,6 @@
"constants = {}\n",
"for offset_map, mask, gain_map, k_da in r:\n",
"\n",
- " if gain_map is None:\n",
- " warning(\"No gain map found. Relative gain correction is disabled.\")\n",
- " relative_gain = False\n",
- "\n",
" constants[k_da] = (offset_map, mask, gain_map)\n",
"\n",
"const_data.clear()\n",
@@ -881,7 +887,7 @@
"metadata": {},
"outputs": [],
"source": [
- "for i, (pdu, mod) in enumerate(zip(db_modules, karabo_da)):\n",
+ "for i, (pdu, mod) in enumerate(da_to_pdu.items()): \n",
" h, ex, ey = np.histogram2d(\n",
" raw[i].flatten(),\n",
" gain[i].flatten(),\n",
@@ -910,7 +916,7 @@
"metadata": {},
"outputs": [],
"source": [
- "for i, (pdu, mod) in enumerate(zip(db_modules, karabo_da)): \n",
+ "for i, (pdu, mod) in enumerate(da_to_pdu.items()): \n",
" fig, axs = plt.subplots(nrows=2, ncols=1, figsize=(18, 10))\n",
" corrected_flatten = corrected[i].flatten()\n",
" for ax, hist_range in zip(axs, [(-100, 1000), (-1000, 10000)]):\n",
diff --git a/notebooks/Jungfrau/Jungfrau_retrieve_constants_precorrection_NBC.ipynb b/notebooks/Jungfrau/Jungfrau_retrieve_constants_precorrection_NBC.ipynb
index 808ff32290aeeac2a4897d599fd05ae326a535aa..7a56e49a6b02794821509dac1e41f0435afe5a18 100644
--- a/notebooks/Jungfrau/Jungfrau_retrieve_constants_precorrection_NBC.ipynb
+++ b/notebooks/Jungfrau/Jungfrau_retrieve_constants_precorrection_NBC.ipynb
@@ -33,9 +33,9 @@
"karabo_id_control = \"\" # if control is on a different ID, set to empty string if it is the same a 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-exfl016:8017#8025\" # the database interface to use\n",
"cal_db_timeout = 180000 # timeout on cal db requests\n",
+ "creation_time = \"\" # To overwrite the measured creation_time. Required Format: YYYY-MM-DD HR:MN:SC e.g. \"2022-06-28 13:00:00\"\n",
"\n",
"# Parameters affecting corrected data.\n",
"relative_gain = True # do relative gain correction\n",
@@ -55,6 +55,8 @@
"metadata": {},
"outputs": [],
"source": [
+ "from logging import warning\n",
+ "\n",
"from extra_data import RunDirectory\n",
"from pathlib import Path\n",
"\n",
@@ -62,7 +64,7 @@
"from cal_tools.jungfraulib import JungfrauCtrl\n",
"from cal_tools.step_timing import StepTimer\n",
"from cal_tools.tools import (\n",
- " get_dir_creation_date,\n",
+ " calcat_creation_time,\n",
" CalibrationMetadata,\n",
")"
]
@@ -85,10 +87,9 @@
"\n",
"out_folder.mkdir(parents=True, exist_ok=True)\n",
"\n",
- "creation_time = None\n",
- "if use_dir_creation_date:\n",
- " creation_time = get_dir_creation_date(in_folder, run)\n",
- " print(f\"Using {creation_time} as creation time\")\n",
+ "# Run's creation time:\n",
+ "creation_time = calcat_creation_time(in_folder, run, creation_time)\n",
+ "print(f\"Creation time: {creation_time}\")\n",
"\n",
"if karabo_id_control == \"\":\n",
" karabo_id_control = karabo_id"
@@ -145,37 +146,44 @@
" detector_name=karabo_id,\n",
" sensor_bias_voltage=bias_voltage,\n",
" event_at=creation_time,\n",
- " modules=None,\n",
+ " snapshot_at=creation_time,\n",
+ " modules=karabo_da,\n",
" memory_cells=memory_cells,\n",
" integration_time=integration_time,\n",
" gain_setting=gain_setting,\n",
" gain_mode=gain_mode,\n",
")\n",
- "constant_names = [\n",
- " \"Offset10Hz\", \"BadPixelsDark10Hz\",\n",
- " \"BadPixelsFF10Hz\", \"RelativeGain10Hz\",\n",
- "]\n",
+ "constant_names = [\"Offset10Hz\", \"BadPixelsDark10Hz\"]\n",
"\n",
- "mdata_dict = {\"constants\": dict()}\n",
+ "if relative_gain:\n",
+ " constant_names += [\"BadPixelsFF10Hz\", \"RelativeGain10Hz\"]\n",
"\n",
- "# Don't raise errors for now if relative_gain is on\n",
- "# and constant was not retrieved.\n",
- "raise_error = False if relative_gain else True\n",
- "jf_metadata = jf_cal.metadata(constant_names, raise_error=raise_error)\n",
+ "jf_metadata = jf_cal.metadata(constant_names)\n",
"\n",
+ "# Add constants metadata in retrieved_constants dict.\n",
"for mod, ccv_dict in jf_metadata.items():\n",
" mod_dict = retrieved_constants.setdefault(mod, dict())\n",
" const_dict = mod_dict.setdefault(\"constants\", dict())\n",
- " if [\"Offset10Hz\", \"BadPixelsDark10Hz\"] not in ccv_dict.keys():\n",
- " # Fail processing if dark constants are not available.\n",
- " raise KeyError(f\"Dark constant is not available for correction for {module}. {e}\")\n",
" for cname, ccv_metadata in ccv_dict.items():\n",
" const_dict[cname] = {\n",
" \"path\": str(jf_cal.caldb_root / ccv_metadata[\"path\"]),\n",
" \"dataset\": ccv_metadata[\"dataset\"],\n",
" \"creation-time\": ccv_metadata[\"begin_validity_at\"],\n",
" }\n",
- " mod_dict[\"physical-name\"] = ccv_metadata[\"physical_name\"]"
+ " mod_dict[\"physical-name\"] = ccv_metadata[\"physical_name\"]\n",
+ "\n",
+ "# Validate the constants availability and raise/warn correspondingly. \n",
+ "for mod, calibrations in jf_metadata.items():\n",
+ " missing_dark_constants = set(\n",
+ " c for c in [\"Offset10Hz\", \"BadPixelsDark10Hz\"] if c not in calibrations.keys())\n",
+ " missing_gain_constants = set(\n",
+ " c for c in [\"BadPixelsFF10Hz\", \"RelativeGain10Hz\"] if relative_gain and c not in calibrations.keys()) # noqa\n",
+ " if missing_dark_constants:\n",
+ " raise KeyError(\n",
+ " f\"Dark constants {missing_dark_constants} are not available for correction. Module: {mod}\") # noqa\n",
+ " if missing_gain_constants:\n",
+ " warning(\n",
+ " f\"Gain constants {missing_gain_constants} were not retrieved. Module: {mod}\")"
]
},
{