From 5ed9ecf12ba8fd7fa6af59d52a7437b1af913c84 Mon Sep 17 00:00:00 2001
From: ahmedk <karim.ahmed@xfel.eu>
Date: Mon, 7 Nov 2022 16:12:00 +0100
Subject: [PATCH] retest epix100 and add warning
---
notebooks/LPD/LPD_Correct_Fast.ipynb | 2 ++
...LPD_retrieve_constants_precorrection.ipynb | 33 -------------------
.../ePix100/Correction_ePix100_NBC.ipynb | 15 +++++----
...100_retrieve_constants_precorrection.ipynb | 24 ++++++++++----
4 files changed, 28 insertions(+), 46 deletions(-)
diff --git a/notebooks/LPD/LPD_Correct_Fast.ipynb b/notebooks/LPD/LPD_Correct_Fast.ipynb
index 397d144a4..be56e6b66 100644
--- a/notebooks/LPD/LPD_Correct_Fast.ipynb
+++ b/notebooks/LPD/LPD_Correct_Fast.ipynb
@@ -135,6 +135,8 @@
"cal_db_root = Path(cal_db_root)\n",
"\n",
"metadata = CalibrationMetadata(metadata_folder or out_folder)\n",
+ "# Constant paths & timestamps are saved under retrieved-constants in calibration_metadata.yml\n",
+ "retrieved_constants = metadata.setdefault(\"retrieved-constants\", {})\n",
"\n",
"creation_time = calcat_creation_time(in_folder, run, creation_time)\n",
"print(f'Using {creation_time.isoformat()} as creation time')\n",
diff --git a/notebooks/LPD/LPD_retrieve_constants_precorrection.ipynb b/notebooks/LPD/LPD_retrieve_constants_precorrection.ipynb
index 9d6088af1..5362f87e3 100644
--- a/notebooks/LPD/LPD_retrieve_constants_precorrection.ipynb
+++ b/notebooks/LPD/LPD_retrieve_constants_precorrection.ipynb
@@ -90,39 +90,6 @@
"step_timer = StepTimer()"
]
},
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "dark_calibrations = {\n",
- " 1: 'Offset',\n",
- " 14: 'BadPixelsDark',\n",
- "}\n",
- "\n",
- "dark_condition = [\n",
- " dict(parameter_id=1, value=bias_voltage), # Sensor bias voltage\n",
- " dict(parameter_id=7, value=mem_cells), # Memory cells\n",
- " dict(parameter_id=15, value=capacitor), # Feedback capacitor\n",
- " dict(parameter_id=13, value=256), # Pixels X\n",
- " dict(parameter_id=14, value=256), # Pixels Y\n",
- "]\n",
- "\n",
- "illuminated_calibrations = {\n",
- " 20: 'BadPixelsFF',\n",
- " 42: 'GainAmpMap',\n",
- " 43: 'FFMap',\n",
- " 44: 'RelativeGain',\n",
- "}\n",
- "\n",
- "illuminated_condition = dark_condition.copy()\n",
- "illuminated_condition += [\n",
- " dict(parameter_id=3, value=photon_energy), # Source energy\n",
- " dict(parameter_id=25, value=category) # category\n",
- "]"
- ]
- },
{
"cell_type": "code",
"execution_count": null,
diff --git a/notebooks/ePix100/Correction_ePix100_NBC.ipynb b/notebooks/ePix100/Correction_ePix100_NBC.ipynb
index 9a38ee093..ca19f1bdb 100644
--- a/notebooks/ePix100/Correction_ePix100_NBC.ipynb
+++ b/notebooks/ePix100/Correction_ePix100_NBC.ipynb
@@ -85,6 +85,7 @@
"source": [
"import tabulate\n",
"import warnings\n",
+ "from logging import warning\n",
"\n",
"import h5py\n",
"import pasha as psh\n",
@@ -292,12 +293,14 @@
" try:\n",
" const_data[cname] = epix_cal.ndarray(module=1, calibration=cname) # TODO: what is this module number?\n",
" except CalCatError as e:\n",
- " if cname == \"RelativeGainEPix100\":\n",
- " print(\"RelativeGainEPix100 is not found. No gain correction will be applied.\")\n",
- " relative_gain = False\n",
- " absolute_gain = False\n",
- " else:\n",
- " raise CalCatError(f\"{cname}: {e}\")"
+ " if cname != \"RelativeGainEPix100\":\n",
+ " raise\n",
+ "\n",
+ "# Set gain bools to False if constant is not available.\n",
+ "if relative_gain and \"RelativeGainEPix100\" not in const_data.values():\n",
+ " warning(\"RelativeGainEPix100 is not found in CALCAT. Gain correction wont be applied.\")\n",
+ " relative_gain = False\n",
+ " absolute_gain = False"
]
},
{
diff --git a/notebooks/ePix100/ePix100_retrieve_constants_precorrection.ipynb b/notebooks/ePix100/ePix100_retrieve_constants_precorrection.ipynb
index a8a56f47d..4c118dc56 100644
--- a/notebooks/ePix100/ePix100_retrieve_constants_precorrection.ipynb
+++ b/notebooks/ePix100/ePix100_retrieve_constants_precorrection.ipynb
@@ -51,11 +51,13 @@
"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",
- "from cal_tools.calcat_interface import EPIX100_CalibrationData\n",
+ "from cal_tools.calcat_interface import CalCatError, EPIX100_CalibrationData\n",
"from cal_tools.epix100 import epix100lib\n",
"from cal_tools.tools import (\n",
" calcat_creation_time,\n",
@@ -162,12 +164,20 @@
"\n",
"for cname in constant_names:\n",
" # Retrieve metadata for all epix100 constants.\n",
- " for cname, ccv_metadata in list(epix_cal.metadata([cname]).values())[0].items():\n",
- " mdata_dict[\"constants\"][cname] = dict()\n",
- " mdata_dict[\"constants\"][cname][\"path\"] = str(epix_cal.caldb_root / ccv_metadata[\"path\"])\n",
- " mdata_dict[\"constants\"][cname][\"dataset\"] = ccv_metadata[\"dataset\"]\n",
- " mdata_dict[\"constants\"][cname][\"creation-time\"] = ccv_metadata[\"begin_validity_at\"]\n",
- " print(f\"Retrieved {cname} with creation-time: {ccv_metadata['begin_validity_at']}\")\n",
+ " try:\n",
+ " epix_metadata = epix_cal.metadata([cname])\n",
+ " for cname, ccv_metadata in list(epix_metadata.values())[0].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",
+ " }\n",
+ " print(f\"Retrieved {cname} with creation-time: {ccv_metadata['begin_validity_at']}\")\n",
+ " except CalCatError:\n",
+ " if cname == \"RelativeGainEPix100\":\n",
+ " warning(\"RelativeGainEPix100 is not found in CALCAT.\")\n",
+ " else:\n",
+ " raise\n",
"mdata_dict[\"physical-detector-unit\"] = ccv_metadata[\"physical_name\"]\n",
"retrieved_constants[karabo_da] = mdata_dict\n",
"metadata.save()\n",
--
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