diff --git a/notebooks/AGIPD/Chracterize_AGIPD_Gain_PC_NBC.ipynb b/notebooks/AGIPD/Chracterize_AGIPD_Gain_PC_NBC.ipynb
index af08e704474fc49dfb65baf0cd8c63fa020ce6af..fa42a7ac209591b2a4f1adceab87f92e58c35ddc 100644
--- a/notebooks/AGIPD/Chracterize_AGIPD_Gain_PC_NBC.ipynb
+++ b/notebooks/AGIPD/Chracterize_AGIPD_Gain_PC_NBC.ipynb
@@ -38,10 +38,10 @@
"source": [
"in_folder = '/gpfs/exfel/exp/MID/201931/p900091/raw' # path to input data, required\n",
"modules = [1,] # modules to work on, required, range allowed\n",
- "out_folder = \"/gpfs/exfel/exp/SPB/201931/p900091/usr/PC/\" # path to output to, required\n",
+ "out_folder = \"/gpfs/exfel/exp/MID/201931/p900091/usr/PC/4.5_250/\" # path to output to, required\n",
"runs = [30, 23, 24, 25, 26, 27, 28, 29] # runs to use, required, range allowed\n",
"n_sequences = 3 # number of sequence files, starting for 0 to evaluate\n",
- "cluster_profile = \"noDB44\" # The ipcluster profile to use\n",
+ "cluster_profile = \"noDB\" # The ipcluster profile to use\n",
"local_output = True # output constants locally\n",
"db_output = False # output constants to database\n",
"bias_voltage = 300 # detector bias voltage\n",
@@ -53,7 +53,10 @@
"instrument = \"MID\"\n",
"high_res_badpix_3d = False # set this to True if you need high-resolution 3d bad pixel plots. Runtime: ~ 1h\n",
"acq_rate = 0. # the detector acquisition rate, use 0 to try to auto-determine\n",
- "dont_use_dir_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"
]
},
{
@@ -68,14 +71,17 @@
"outputs": [],
"source": [
"# imports, usually no need to change anything here\n",
- "import os\n",
+ "from datetime import datetime\n",
+ "import dateutil.parser\n",
"import h5py\n",
+ "import os\n",
+ "\n",
+ "\n",
"import numpy as np\n",
"import matplotlib\n",
"matplotlib.use(\"Qt4Agg\")\n",
"import matplotlib.pyplot as plt\n",
"%matplotlib inline\n",
- "\n",
"# make sure a cluster is running with ipcluster start --n=32, give it a while to start\n",
"from ipyparallel import Client\n",
"\n",
@@ -88,13 +94,13 @@
"warnings.filterwarnings('ignore')\n",
"\n",
"from iCalibrationDB import ConstantMetaData, Constants, Conditions, Detectors, Versions\n",
- "\n",
"from cal_tools.tools import gain_map_files, parse_runs, run_prop_seq_from_path, get_notebook_name, get_dir_creation_date\n",
"from cal_tools.influx import InfluxLogger\n",
"from cal_tools.enums import BadPixels\n",
"from cal_tools.plotting import show_overview, plot_badpix_3d\n",
- "from cal_tools.agipdlib import get_acq_rate, get_num_cells\n",
- "from datetime import datetime\n",
+ "from cal_tools.agipdlib import get_acq_rate, get_num_cells, get_gain_setting\n",
+ "\n",
+ "\n",
"\n",
"IL_MODE = interlaced \n",
"maxcells = mem_cells if not interlaced else mem_cells*2\n",
@@ -121,8 +127,7 @@
"else:\n",
" loc = \"MID_DET_AGIPD1M-1\"\n",
" dinstance = \"AGIPD1M2\"\n",
- "print(\"Detector in use is {}\".format(loc))\n",
- "\n"
+ "print(\"Detector in use is {}\".format(loc))"
]
},
{
@@ -148,7 +153,7 @@
"run = runs[0]\n",
"bursts_per_file = []\n",
"channel = 0\n",
- "creation_time=None\n",
+ "\n",
"for seq in range(seqs):\n",
" fname = os.path.join(path_temp.format(run),\n",
" image_name_temp.format(run, channel, seq))\n",
@@ -158,7 +163,19 @@
" acq_rate = get_acq_rate(fname, loc, channel)\n",
" print(\"Acquisition rate set from file: {} MHz\".format(acq_rate))\n",
" \n",
- " if not dont_use_dir_date:\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",
" creation_time = get_dir_creation_date(in_folder, run)\n",
" \n",
" if mem_cells == 0:\n",
@@ -181,6 +198,30 @@
" print(\"Using {} as creation time\".format(creation_time.isoformat()))"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "control_fname = f'{in_folder}/r{runs[0]:04d}/RAW-R{runs[0]:04d}-{karabo_da_control}-S00000.h5'\n",
+ "\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": "code",
"execution_count": null,
@@ -524,7 +565,8 @@
" Constants.AGIPD.Offset(),\n",
" Conditions.Dark.AGIPD(\n",
" memory_cells=mem_cells,\n",
- " bias_voltage=bias_voltage, acquisition_rate=acq_rate),\n",
+ " bias_voltage=bias_voltage, acquisition_rate=acq_rate,\n",
+ " gain_setting=gain_setting),\n",
" np.zeros((128, 512, mem_cells, 3)),\n",
" cal_db_interface, creation_time=creation_time)\n",
" print(\"Offset for {} was injected on {}\".format(qm, when))\n",
@@ -534,7 +576,8 @@
" Constants.AGIPD.Noise(),\n",
" Conditions.Dark.AGIPD(\n",
" memory_cells=mem_cells,\n",
- " bias_voltage=bias_voltage, acquisition_rate=acq_rate),\n",
+ " bias_voltage=bias_voltage, acquisition_rate=acq_rate,\n",
+ " gain_setting=gain_setting),\n",
" np.zeros((128, 512, mem_cells, 3)),\n",
" cal_db_interface, creation_time=creation_time)\n",
" print(\"Noise for {} was injected on {}\".format(qm, when))\n",
@@ -544,7 +587,8 @@
" Constants.AGIPD.ThresholdsDark(),\n",
" Conditions.Dark.AGIPD(\n",
" memory_cells=mem_cells,\n",
- " bias_voltage=bias_voltage, acquisition_rate=acq_rate),\n",
+ " bias_voltage=bias_voltage, acquisition_rate=acq_rate,\n",
+ " gain_setting=gain_setting),\n",
" np.zeros((128, 512, mem_cells, 3)),\n",
" cal_db_interface, creation_time=creation_time)\n",
" print(\"Threshold for {} was injected on {}\".format(qm, when))\n",
@@ -1344,6 +1388,16 @@
" store_file.close()"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "proposal = list(filter(None, in_folder.strip('/').split('/')))[-2]\n",
+ "file_loc = proposal + ' ' + ' '.join(list(map(str,runs)))"
+ ]
+ },
{
"cell_type": "code",
"execution_count": null,
@@ -1355,8 +1409,6 @@
},
"outputs": [],
"source": [
- "#if instrument == \"MID\":\n",
- "# acq_rate = None\n",
"if db_output:\n",
" for qm, r in fres.items():\n",
" metadata = ConstantMetaData()\n",
@@ -1366,11 +1418,18 @@
"\n",
" # set the operating condition\n",
" condition = Conditions.Dark.AGIPD(memory_cells=maxcells, bias_voltage=bias_voltage,\n",
- " acquisition_rate=acq_rate)\n",
+ " acquisition_rate=acq_rate, gain_setting=gain_setting)\n",
" metadata.detector_condition = condition\n",
"\n",
" # specify the a version for this constant\n",
- " metadata.calibration_constant_version = Versions.Now(device=getattr(getattr(Detectors, dinstance), qm))\n",
+ " \n",
+ " if creation_time is None:\n",
+ " metadata.calibration_constant_version = Versions.Now(device=getattr(Detectors.AGIPD1M1, qm))\n",
+ " else:\n",
+ " metadata.calibration_constant_version = Versions.Timespan(device=getattr(Detectors.AGIPD1M1, qm),\n",
+ " start=creation_time)\n",
+ " \n",
+ " metadata.calibration_constant_version.raw_data_location = file_loc\n",
" metadata.send(cal_db_interface)\n",
" \n",
" # bad pixels\n",
@@ -1382,11 +1441,16 @@
" \n",
" # set the operating condition\n",
" condition = Conditions.Dark.AGIPD(memory_cells=maxcells, bias_voltage=bias_voltage,\n",
- " acquisition_rate=acq_rate)\n",
+ " acquisition_rate=acq_rate, gain_setting=gain_setting)\n",
" metadata.detector_condition = condition\n",
"\n",
" # specify the a version for this constant\n",
- " metadata.calibration_constant_version = Versions.Now(device=getattr(Detectors.AGIPD1M1, qm))\n",
+ " if creation_time is None:\n",
+ " metadata.calibration_constant_version = Versions.Now(device=getattr(Detectors.AGIPD1M1, qm))\n",
+ " else:\n",
+ " metadata.calibration_constant_version = Versions.Timespan(device=getattr(Detectors.AGIPD1M1, qm),\n",
+ " start=creation_time)\n",
+ " metadata.calibration_constant_version.raw_data_location = file_loc\n",
" metadata.send(cal_db_interface)"
]
},