diff --git a/notebooks/DynamicFF/Characterize_DynamicFF_NBC.ipynb b/notebooks/DynamicFF/Characterize_DynamicFF_NBC.ipynb
index 40897d331b0b8f0389d0df0251711f607ea147a3..54c4412b7a4d324f101027ce3bde451dc25d0114 100644
--- a/notebooks/DynamicFF/Characterize_DynamicFF_NBC.ipynb
+++ b/notebooks/DynamicFF/Characterize_DynamicFF_NBC.ipynb
@@ -20,29 +20,21 @@
"in_folder = \"/gpfs/exfel/exp/SPB/202430/p900425/raw\" # input folder, required\n",
"out_folder = '/gpfs/exfel/data/scratch/esobolev/test/shimadzu' # output folder, required\n",
"metadata_folder = \"\" # Directory containing calibration_metadata.yml when run by xfel-calibrate\n",
- "runs = [1, 2] # list of two run numbers: dark field and flat field\n",
+ "run_high = 1 # run number in which dark data was recorded, required\n",
+ "run_low = 2 # run number in which flat-field data was recorded, required\n",
+ "operation_mode = \"TI_DynamicFF\" # Detector operation mode, optional (defaults to \"TI_DynamicFF\")\n",
"\n",
"# Data files parameters.\n",
"karabo_da = ['-1'] # data aggregators\n",
"karabo_id = \"SPB_MIC_HPVX2\" # karabo prefix of Shimadzu HPV-X2 devices\n",
"\n",
- "#receiver_id = \"PNCCD_FMT-0\" # inset for receiver devices\n",
- "#path_template = 'RAW-R{:04d}-{}-S{{:05d}}.h5' # the template to use to access data\n",
- "#instrument_source_template = 'SPB_EHD_MIC/CAM/HPVX2_{module}:daqOutput' # data source path in h5file.\n",
- "#instrument_source_template = 'SPB_EHD_HPVX2_{module}/CAM/CAMERA:daqOutput'\n",
- "#image_key = \"data.image.pixels\" # image data key in Karabo or exdf notation\n",
- "\n",
- "#db_module_template = \"Shimadzu_HPVX2_{}\"\n",
- "\n",
"# Database access parameters.\n",
- "use_dir_creation_date = True # use dir creation date as data production reference date\n",
"cal_db_interface = \"tcp://max-exfl-cal001:8021\" # calibration DB interface to use\n",
- "cal_db_timeout = 300000 # timeout on caldb requests\n",
"db_output = True # if True, the notebook sends dark constants to the calibration database\n",
"local_output = True # if True, the notebook saves dark constants locally\n",
- "creation_time = \"\" # To overwrite the measured creation_time. Required Format: YYYY-MM-DD HR:MN:SC.00 e.g. 2019-07-04 11:02:41.00\n",
"\n",
- "n_components = 50 # Number of principal components to compute"
+ "# Calibration constants parameters\n",
+ "n_components = 50 # Number of principal components of flat-field to compute (default: 50)"
]
},
{
@@ -68,12 +60,9 @@
"from cal_tools.step_timing import StepTimer\n",
"from cal_tools.tools import (\n",
" get_dir_creation_date,\n",
- "# get_pdu_from_db,\n",
" get_random_db_interface,\n",
" get_report,\n",
- "# save_const_to_h5,\n",
" save_dict_to_hdf5,\n",
- "# send_to_db,\n",
" run_prop_seq_from_path,\n",
")\n",
"from cal_tools.restful_config import calibration_client\n",
@@ -89,19 +78,6 @@
"metadata": {},
"outputs": [],
"source": [
- "creation_time=None\n",
- "if use_dir_creation_date:\n",
- " creation_time = get_dir_creation_date(in_folder, max(runs))\n",
- "\n",
- "print(f\"Using {creation_time} as creation time of constant.\")\n",
- "\n",
- "run, proposal, seq = run_prop_seq_from_path(in_folder)\n",
- "#file_loc = f'proposal: {prop}, runs: {dark_run} {flat_run}'\n",
- "\n",
- "# Read report path and create file location tuple to add with the injection\n",
- "#file_loc = f\"proposal:{proposal} runs:\" + ' '.join(str(run) for run in runs)\n",
- "\n",
- "report = get_report(metadata_folder)\n",
"cal_db_interface = get_random_db_interface(cal_db_interface)\n",
"print(f'Calibration database interface: {cal_db_interface}')\n",
"print()\n",
@@ -154,7 +130,10 @@
"metadata": {},
"outputs": [],
"source": [
- "dark_run = runs[0]\n",
+ "dark_run = run_high\n",
+ "dark_creation_time = get_dir_creation_date(in_folder, dark_run)\n",
+ "print(f\"Using {dark_creation_time} as creation time of Offset constant.\")\n",
+ "\n",
"for da, meta in modules.items():\n",
" source_name = detector.instrument_source(meta[\"module\"])\n",
" image_key = detector.image_key\n",
@@ -184,7 +163,9 @@
" conditions = detector.conditions(dark_dc, meta[\"module\"])\n",
" module_constants = constants.setdefault(meta[\"db_module\"], {})\n",
" module_constants[\"Offset\"] = dict(\n",
- " conditions=conditions, data=dark, pdu_no=meta[\"pdu_no\"])\n",
+ " conditions=conditions, data=dark, pdu_no=meta[\"pdu_no\"],\n",
+ " creation_time=dark_creation_time\n",
+ " )\n",
" step_timer.done_step(\"Process dark images\")\n",
" display()\n",
"\n",
@@ -210,7 +191,10 @@
},
"outputs": [],
"source": [
- "flat_run = runs[1]\n",
+ "flat_run = run_low\n",
+ "flat_creation_time = get_dir_creation_date(in_folder, flat_run)\n",
+ "print(f\"Using {flat_creation_time} as creation time of DynamicFF constant.\")\n",
+ "\n",
"for da, meta in modules.items():\n",
" source_name = detector.instrument_source(meta[\"module\"])\n",
" image_key = detector.image_key\n",
@@ -242,7 +226,8 @@
" conditions = detector.conditions(flat_dc, meta[\"module\"])\n",
" module_constants = constants.setdefault(meta[\"db_module\"], {})\n",
" module_constants[\"DynamicFF\"] = dict(\n",
- " conditions=conditions, data=flat_data, pdu_no=meta[\"pdu_no\"]\n",
+ " conditions=conditions, data=flat_data, pdu_no=meta[\"pdu_no\"],\n",
+ " creation_time=flat_creation_time\n",
" )\n",
" step_timer.done_step(\"Process flat-field images\")\n",
"\n",
@@ -285,13 +270,13 @@
"# Output Folder Creation:\n",
"os.makedirs(out_folder, exist_ok=True)\n",
"\n",
- "def inject_ccv(metadata_folder, calibration, cond, pdu, proposal, runs, const_file, begin_at):\n",
- " print(\"* Send to db:\", const_file)\n",
- " print(\" -\", metadata_folder)\n",
+ "def inject_ccv(in_folder, metadata_folder, runs, calibration, cond, pdu, const_input, begin_at):\n",
+ " print(\"* Send to db:\", const_input)\n",
+ " print(\" - in folder:\", in_folder)\n",
+ " print(\" - metadata folder:\", metadata_folder)\n",
+ " print(\" - runs:\", runs)\n",
" print(\" -\", calibration)\n",
" print(\" -\", cond)\n",
- " print(\" - proposal\", proposal)\n",
- " print(\" - runs\", runs)\n",
" print(\" -\", begin_at)\n",
"\n",
"for db_module, module_constants in constants.items():\n",
@@ -312,9 +297,9 @@
" save_dict_to_hdf5(data_to_store, ofile)\n",
" if db_output:\n",
" inject_ccv(\n",
- " metadata_folder, constant_name, conditions,\n",
- " pdus[\"data\"][constant[\"pdu_no\"]],\n",
- " proposal, runs, ofile, creation_time\n",
+ " in_folder, metadata_folder, [dark_run, flat_run],\n",
+ " constant_name, conditions, pdus[\"data\"][constant[\"pdu_no\"]],\n",
+ " ofile, constant[\"creation_time\"]\n",
" )\n",
"\n",
" if not local_output:\n",