diff --git a/notebooks/Jungfrau/Jungfrau_dark_analysis_all_gains_burst_mode_NBC.ipynb b/notebooks/Jungfrau/Jungfrau_dark_analysis_all_gains_burst_mode_NBC.ipynb
index 7b96761764d81e77d20171fcb61942c69b4f321d..4369e67e30389710349e9d28f4b3e54e7d5b571d 100644
--- a/notebooks/Jungfrau/Jungfrau_dark_analysis_all_gains_burst_mode_NBC.ipynb
+++ b/notebooks/Jungfrau/Jungfrau_dark_analysis_all_gains_burst_mode_NBC.ipynb
@@ -63,8 +63,10 @@
},
"outputs": [],
"source": [
+ "import os\n",
"import warnings\n",
"warnings.filterwarnings('ignore')\n",
+ "import textwrap\n",
"\n",
"import matplotlib\n",
"matplotlib.use('agg')\n",
@@ -91,7 +93,7 @@
"from XFELDetAna.plotting.histogram import histPlot\n",
"from XFELDetAna.plotting.heatmap import heatmapPlot\n",
"\n",
- "import os\n",
+ "\n",
"os.makedirs(out_folder, exist_ok=True)"
]
},
@@ -477,8 +479,15 @@
" \n",
" metadata.calibration_constant_version.raw_data_location = file_loc\n",
" if db_output:\n",
- " metadata.send(cal_db_interface, timeout=cal_db_timeout)\n",
- " print('Constants {} is sent to the data base'.format(key))\n",
+ " try:\n",
+ " metadata.send(cal_db_interface, timeout=cal_db_timeout)\n",
+ " print(f'Constants {key} is sent to the data base\\n')\n",
+ " except Exception as e: \n",
+ " if \"has already been take\" in str(e):\n",
+ " print(f\"{key} has already been injected with the same parameter conditions\\n\")\n",
+ " else:\n",
+ " # To prevent having big error message in the pdf report.\n",
+ " print(\"\\n\".join(textwrap.wrap(str(e),100)))\n",
" \n",
" # save everything to file.\n",
" # one file - one entrt in the DB\n",
@@ -499,8 +508,19 @@
" data_to_store['file_loc'] = file_loc\n",
" \n",
" ofile = \"{}/const_{}_{}.h5\".format(out_folder, key, db_module)\n",
- " save_dict_to_hdf5(data_to_store, ofile)\n"
+ " save_dict_to_hdf5(data_to_store, ofile)\n",
+ " print(f\"Calibration constant {key} is stored locally at {out_folder}.\\n\")\n",
+ "print(f\"Operating conditions are:\\n• Bias voltage: {bias_voltage}\\n• Memory cells: {memoryCells}\\n\"\n",
+ " f\"• Integration time: {integration_time}\\n\"\n",
+ " f\"• Creation time: {metadata.calibration_constant_version.begin_at}\\n\")"
]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
}
],
"metadata": {
diff --git a/notebooks/ePix100/Characterize_Darks_ePix100_NBC.ipynb b/notebooks/ePix100/Characterize_Darks_ePix100_NBC.ipynb
index a8726ffb0bac06f2ea25a28b642b4fab4a860078..d829869675b67d244a4b44f0fd3a2f6634b59eab 100644
--- a/notebooks/ePix100/Characterize_Darks_ePix100_NBC.ipynb
+++ b/notebooks/ePix100/Characterize_Darks_ePix100_NBC.ipynb
@@ -20,13 +20,13 @@
"outputs": [],
"source": [
"cluster_profile = \"noDB\" # ipcluster profile to use\n",
- "in_folder = '/gpfs/exfel/exp/MID/201930/p900071/raw' # input folder, required\n",
- "out_folder = '/gpfs/exfel/exp/MID/201930/p900070/usr/dark/runs_4' # output folder, required\n",
+ "in_folder = '/gpfs/exfel/exp/HED/202030/p900136/raw' # input folder, required\n",
+ "out_folder = '/gpfs/exfel/data/scratch/ahmedk/test/HED_dark/' # output folder, required\n",
"sequence = 0 # sequence file to use\n",
- "run = 466 # which run to read data from, required\n",
+ "run = 182 # which run to read data from, required\n",
"\n",
- "karabo_id = \"MID_EXP_EPIX-1\" # karabo karabo_id\n",
- "karabo_da = [\"DA01\"] # data aggregators\n",
+ "karabo_id = \"HED_IA1_EPX100-2\" # karabo karabo_id\n",
+ "karabo_da = [\"EPIX02\"] # data aggregators\n",
"receiver_id = \"RECEIVER\" # inset for receiver devices\n",
"path_template = 'RAW-R{:04d}-{}-S{{:05d}}.h5' # the template to use to access data\n",
"h5path = '/INSTRUMENT/{}/DET/{}:daqOutput/data/image/pixels' # path in the HDF5 file to images\n",
@@ -41,7 +41,7 @@
"\n",
"number_dark_frames = 0 # number of images to be used, if set to 0 all available images are used\n",
"temp_limits = 5 # limit for parameter Operational temperature\n",
- "db_module = 'ePix100_M15' # detector karabo_id\n",
+ "db_module = 'ePix100_M17' # detector karabo_id\n",
"bias_voltage = 200 # bias voltage\n",
"in_vacuum = False # detector operated in vacuum\n",
"fix_temperature = 290. # fix temperature to this value"
@@ -53,33 +53,32 @@
"metadata": {},
"outputs": [],
"source": [
- "import XFELDetAna.xfelprofiler as xprof\n",
+ "from IPython.display import display, Markdown, Latex\n",
+ "import os\n",
+ "import textwrap\n",
"\n",
+ "import numpy as np\n",
+ "import h5py\n",
+ "import matplotlib.pyplot as plt\n",
+ "%matplotlib inline\n",
+ "import warnings\n",
+ "warnings.filterwarnings('ignore')\n",
+ "\n",
+ "from cal_tools.tools import get_dir_creation_date, save_const_to_h5, get_random_db_interface\n",
+ "from iCalibrationDB import (ConstantMetaData, Constants, Conditions, Detectors,\n",
+ " Versions)\n",
+ "from iCalibrationDB.detectors import DetectorTypes\n",
+ "import XFELDetAna.xfelprofiler as xprof\n",
"profiler = xprof.Profiler()\n",
"profiler.disable()\n",
"from XFELDetAna.util import env\n",
"env.iprofile = cluster_profile\n",
- "\n",
- "import warnings\n",
- "warnings.filterwarnings('ignore')\n",
- "\n",
"from XFELDetAna import xfelpycaltools as xcal\n",
"from XFELDetAna import xfelpyanatools as xana\n",
"from XFELDetAna.plotting.util import prettyPlotting\n",
- "\n",
"prettyPlotting = True\n",
"from XFELDetAna.xfelreaders import ChunkReader\n",
"from XFELDetAna.detectors.fastccd import readerh5 as fastccdreaderh5\n",
- "from cal_tools.tools import get_dir_creation_date, save_const_to_h5, get_random_db_interface\n",
- "\n",
- "from iCalibrationDB import (ConstantMetaData, Constants, Conditions, Detectors,\n",
- " Versions)\n",
- "from iCalibrationDB.detectors import DetectorTypes\n",
- "\n",
- "import numpy as np\n",
- "import h5py\n",
- "import matplotlib.pyplot as plt\n",
- "%matplotlib inline\n",
"\n",
"h5path = h5path.format(karabo_id, receiver_id)\n",
"h5path_t = h5path_t.format(karabo_id, receiver_id)\n",
@@ -89,7 +88,7 @@
" if limit == 0:\n",
" return nImages\n",
" else:\n",
- " return min(nImages, limit)\n"
+ " return min(nImages, limit)"
]
},
{
@@ -99,21 +98,22 @@
"outputs": [],
"source": [
"proposal = list(filter(None, in_folder.strip('/').split('/')))[-2]\n",
- "file_loc = 'proposal:{} runs:{}'.format(proposal, run)\n",
+ "file_loc = f'proposal:{proposal} runs:{run}'\n",
"\n",
"x = 708 # rows of the xPix100\n",
"y = 768 # columns of the xPix100\n",
"\n",
- "ped_dir = \"{}/r{:04d}\".format(in_folder, run)\n",
+ "ped_dir = os.path.join(in_folder, f\"r{run:04d}\")\n",
"fp_name = path_template.format(run, karabo_da[0]).format(sequence)\n",
- "filename = '{}/{}'.format(ped_dir, fp_name)\n",
+ "filename = os.path.join(ped_dir, fp_name)\n",
"\n",
- "print(\"Reading data from: {}\\n\".format(filename))\n",
- "print(\"Run number: {}\".format(run))\n",
- "print(\"HDF5 path: {}\".format(h5path))\n",
+ "print(f\"Reading data from: {filename}\\n\")\n",
+ "print(f\"Run number: {run}\")\n",
+ "print(f\"HDF5 path: {h5path}\")\n",
"if use_dir_creation_date:\n",
" creation_time = get_dir_creation_date(in_folder, run)\n",
- " print(\"Using {} as creation time\".format(creation_time.isoformat()))\n"
+ " print(f\"Using {creation_time.isoformat()} as creation time\")\n",
+ "os.makedirs(out_folder, exist_ok=True)"
]
},
{
@@ -138,18 +138,16 @@
"run_parallel = False\n",
"\n",
"with h5py.File(filename, 'r') as f:\n",
- " integration_time = int(f['{}/CONTROL/expTime/value'.format(h5path_cntrl)][0])\n",
+ " integration_time = int(f[os.path.join(h5path_cntrl, \"CONTROL\",\"expTime\", \"value\")][0])\n",
" temperature = np.mean(f[h5path_t])/100.\n",
" temperature_k = temperature + 273.15\n",
" if fix_temperature != 0:\n",
" temperature_k = fix_temperature\n",
" print(\"Temperature is fixed!\")\n",
- " print(\"Bias voltage is {} V\".format(bias_voltage))\n",
- " print(\"Detector integration time is set to {}\".format(integration_time))\n",
- " print(\"Mean temperature was {:0.2f} °C / {:0.2f} K\".format(temperature,\n",
- " temperature_k))\n",
- " \n",
- " print(\"Operated in vacuum: {} \".format(in_vacuum))"
+ " print(f\"Bias voltage is {bias_voltage} V\")\n",
+ " print(f\"Detector integration time is set to {integration_time}\")\n",
+ " print(f\"Mean temperature was {temperature:0.2f} °C / {temperature_k:0.2f} K\")\n",
+ " print(f\"Operated in vacuum: {in_vacuum} \")"
]
},
{
@@ -292,18 +290,25 @@
" start=creation_time)\n",
" \n",
" metadata.calibration_constant_version.raw_data_location = file_loc\n",
- " \n",
+ "\n",
" if db_output:\n",
" try:\n",
" metadata.send(cal_db_interface, timeout=cal_db_timeout)\n",
- " print(\"Inject {} constants from {}\".format(const_name, \n",
- " metadata.calibration_constant_version.begin_at))\n",
- " except Exception as e:\n",
- " print(e)\n",
- " \n",
+ " print(f\"Inject {const_name} constants from {metadata.calibration_constant_version.begin_at}\\n\")\n",
+ " except Exception as e: \n",
+ " if \"has already been take\" in str(e):\n",
+ " print(f\"{const_name} has already been injected with the same parameter conditions\\n\")\n",
+ " else:\n",
+ " # To prevent having big error message in the pdf report.\n",
+ " print(\"\\n\".join(textwrap.wrap(str(e),100)))\n",
+ "\n",
" if local_output:\n",
" save_const_to_h5(metadata, out_folder)\n",
- " print(\"Calibration constant {} is stored locally.\".format(const))"
+ " print(f\"Calibration constant {const_name} is stored locally at {out_folder}.\")\n",
+ "\n",
+ "print(f\"Operating conditions are:\\n• Bias voltage: {bias_voltage}\\n• Integration time: {integration_time}\\n\"\n",
+ " f\"• Temperature: {temperature_k}\\n• In Vacuum: {in_vacuum}\\n\"\n",
+ " f\"• Creation time: {metadata.calibration_constant_version.begin_at}\\n\")"
]
}
],
diff --git a/xfel_calibrate/notebooks.py b/xfel_calibrate/notebooks.py
index 494d3686fdc36fe2bbe7c02912d42e00a1ceac66..0f13d654da6d6b0a0cb59a3f51c46a71229dd2cd 100644
--- a/xfel_calibrate/notebooks.py
+++ b/xfel_calibrate/notebooks.py
@@ -175,22 +175,6 @@ notebooks = {
"cluster cores": 14},
},
},
- "EPIX": {
- "DARK": {
- "notebook": "notebooks/ePix100/Characterize_Darks_ePix_NBC.ipynb",
- "concurrency": {"parameter": None,
- "default concurrency": None,
- "cluster cores": 4},
- },
-
- "CORRECT": {
- "notebook": "notebooks/ePix100/Correction_ePix_NBC.ipynb",
- "concurrency": {"parameter": "sequences",
- "default concurrency": [-1],
- "use function": "balance_sequences",
- "cluster cores": 4},
- },
- },
"EPIX100": {
"DARK": {
"notebook": "notebooks/ePix100/Characterize_Darks_ePix100_NBC.ipynb",