From 1d5456126ca0e15efcf4f52da7196681195a8d2d Mon Sep 17 00:00:00 2001
From: Karim Ahmed <karim.ahmed@xfel.eu>
Date: Tue, 5 May 2020 16:06:21 +0200
Subject: [PATCH] gain_setting and expse creation_time
---
...aracterize_AGIPD_Gain_FlatFields_NBC.ipynb | 78 +++++++++++++++----
1 file changed, 62 insertions(+), 16 deletions(-)
diff --git a/notebooks/AGIPD/Characterize_AGIPD_Gain_FlatFields_NBC.ipynb b/notebooks/AGIPD/Characterize_AGIPD_Gain_FlatFields_NBC.ipynb
index e4eebca38..89bb40836 100644
--- a/notebooks/AGIPD/Characterize_AGIPD_Gain_FlatFields_NBC.ipynb
+++ b/notebooks/AGIPD/Characterize_AGIPD_Gain_FlatFields_NBC.ipynb
@@ -52,7 +52,10 @@
"db_input = True # retreive data from calibration database, setting offset-store will overwrite this\n",
"deviation_threshold = 0.75 # peaks with an absolute location deviation larger than the medium are are considere bad\n",
"acqrate = 2.2 # acquisition rate\n",
- "dont_use_dir_creation_date = False"
+ "use_dir_creation_date = True\n",
+ "creation_time = \"\" # To overwrite the measured creation_time. Required Format: YYYY-MM-DD HR:MN:SC.ms e.g. 2019-07-04 11:02:41.00\n",
+ "gain_setting = 0.1 # gain setting can have value 0 or 1, Default=0.1 for no (None) gain-setting\n",
+ "karabo_da_control = \"AGIPD1MCTRL00\" # karabo DA for control infromation"
]
},
{
@@ -66,13 +69,15 @@
},
"outputs": [],
"source": [
- "import warnings\n",
- "warnings.filterwarnings('ignore')\n",
"# std library imports\n",
+ "from datetime import datetime\n",
+ "import dateutil\n",
"from functools import partial\n",
- "import h5py\n",
+ "import warnings\n",
+ "warnings.filterwarnings('ignore')\n",
"import os\n",
"\n",
+ "import h5py\n",
"# numpy and matplot lib specific\n",
"import numpy as np\n",
"import matplotlib\n",
@@ -96,11 +101,12 @@
"profile = cluster_profile\n",
"\n",
"from iCalibrationDB import ConstantMetaData, Constants, Conditions, Detectors, Versions\n",
- "from cal_tools.tools import gain_map_files, parse_runs, run_prop_seq_from_path, get_notebook_name, get_dir_creation_date, get_random_db_interface\n",
- "from cal_tools.influx import InfluxLogger\n",
+ "from cal_tools.agipdlib import get_gain_setting\n",
"from cal_tools.enums import BadPixels\n",
+ "from cal_tools.influx import InfluxLogger\n",
"from cal_tools.plotting import show_overview, plot_badpix_3d\n",
- "from datetime import datetime\n",
+ "from cal_tools.tools import gain_map_files, parse_runs, run_prop_seq_from_path, get_notebook_name, get_dir_creation_date, get_random_db_interface\n",
+ "\n",
"\n",
"# usually no need to change these lines\n",
"sensor_size = [128, 512]\n",
@@ -114,7 +120,21 @@
"memory_cells = mem_cells\n",
"\n",
"\n",
- "if not dont_use_dir_creation_date:\n",
+ "\n",
+ "\n",
+ "# Define constant creation time.\n",
+ "if creation_time:\n",
+ " try:\n",
+ " creation_time = datetime.strptime(creation_time, '%Y-%m-%d %H:%M:%S.%f')\n",
+ " except Exception as e:\n",
+ " print(f\"creation_time value error: {e}.\" \n",
+ " \"Use same format as YYYY-MM-DD HR:MN:SC.ms e.g. 2019-07-04 11:02:41.00/n\")\n",
+ " creation_time = None\n",
+ " print(\"Given creation time wont be used.\")\n",
+ "else:\n",
+ " creation_time = None\n",
+ "\n",
+ "if not creation_time and use_dir_creation_date:\n",
" ntries = 100\n",
" while ntries > 0:\n",
" try:\n",
@@ -123,9 +143,8 @@
" except OSError:\n",
" pass\n",
" ntries -= 1\n",
- " \n",
" \n",
- " print(\"Using {} as creation time\".format(creation_time))\n",
+ "print(\"Using {} as creation time\".format(creation_time))\n",
" \n",
"runs = parse_runs(runs)\n",
"\n",
@@ -169,6 +188,29 @@
"cal_db_interface = get_random_db_interface(cal_db_interface)"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "control_fname = f'{in_folder}/{runs[0]}/RAW-{runs[0].upper()}-{karabo_da_control}-S00000.h5'\n",
+ "if gain_setting == 0.1:\n",
+ " if creation_time.replace(tzinfo=None) < dateutil.parser.parse('2020-01-31'):\n",
+ " print(\"Set gain-setting to None for runs taken before 2020-01-31\")\n",
+ " gain_setting = None\n",
+ " else:\n",
+ " try:\n",
+ " gain_setting = get_gain_setting(control_fname, h5path_ctrl)\n",
+ " except Exception as e:\n",
+ " print(f'Error while reading gain setting from: \\n{control_fname}')\n",
+ " print(e)\n",
+ " print(\"Gain setting is not found in the control information\")\n",
+ " print(\"Data will not be processed\")\n",
+ " sequences = []\n",
+ "print(f\"Gain setting: {gain_setting}\")"
+ ]
+ },
{
"cell_type": "markdown",
"metadata": {},
@@ -212,7 +254,8 @@
" det = getattr(Detectors, dinstance)\n",
"\n",
" # set the operating condition\n",
- " condition = Conditions.Dark.AGIPD(memory_cells=max_cells, bias_voltage=bias_voltage, acquisition_rate=acqrate)\n",
+ " condition = Conditions.Dark.AGIPD(memory_cells=max_cells, bias_voltage=bias_voltage,\n",
+ " acquisition_rate=acqrate, gain_setting=gain_setting)\n",
" metadata.detector_condition = condition\n",
"\n",
" # specify the a version for this constant\n",
@@ -230,7 +273,8 @@
" metadata.calibration_constant = noise\n",
"\n",
" # set the operating condition\n",
- " condition = Conditions.Dark.AGIPD(memory_cells=max_cells, bias_voltage=bias_voltage, acquisition_rate=acqrate)\n",
+ " condition = Conditions.Dark.AGIPD(memory_cells=max_cells, bias_voltage=bias_voltage,\n",
+ " acquisition_rate=acqrate, gain_setting=gain_setting)\n",
" metadata.detector_condition = condition\n",
"\n",
" # specify the a version for this constant\n",
@@ -248,7 +292,8 @@
" metadata.calibration_constant = thresholds\n",
"\n",
" # set the operating condition\n",
- " condition = Conditions.Dark.AGIPD(memory_cells=max_cells, bias_voltage=bias_voltage, acquisition_rate=acqrate)\n",
+ " condition = Conditions.Dark.AGIPD(memory_cells=max_cells, bias_voltage=bias_voltage,\n",
+ " acquisition_rate=acqrate, gain_setting=gain_setting)\n",
" metadata.detector_condition = condition\n",
"\n",
" # specify the a version for this constant\n",
@@ -267,7 +312,8 @@
" metadata.calibration_constant = pc\n",
"\n",
" # set the operating condition\n",
- " condition = Conditions.Dark.AGIPD(memory_cells=max_cells, bias_voltage=bias_voltage, acquisition_rate=acqrate)\n",
+ " condition = Conditions.Dark.AGIPD(memory_cells=max_cells, bias_voltage=bias_voltage,\n",
+ " acquisition_rate=acqrate, gain_setting=gain_setting)\n",
" metadata.detector_condition = condition\n",
"\n",
" # specify the a version for this constant\n",
@@ -1093,7 +1139,7 @@
" # set the operating condition\n",
" condition = Conditions.Illuminated.AGIPD(memory_cells, bias_voltage, 9.2,\n",
" pixels_x=512, pixels_y=128, beam_energy=None,\n",
- " acquisition_rate=acqrate)\n",
+ " acquisition_rate=acqrate, gain_setting=gain_setting)\n",
" \n",
" metadata.detector_condition = condition\n",
"\n",
@@ -1116,7 +1162,7 @@
" # set the operating condition\n",
" condition = Conditions.Illuminated.AGIPD(memory_cells, bias_voltage, 9.2,\n",
" pixels_x=512, pixels_y=128, beam_energy=None,\n",
- " acquisition_rate=acqrate)\n",
+ " acquisition_rate=acqrate, gain_setting=gain_setting)\n",
" \n",
" metadata.detector_condition = condition\n",
"\n",
--
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