diff --git a/notebooks/pnCCD/Characterize_pnCCD_Dark_NBC.ipynb b/notebooks/pnCCD/Characterize_pnCCD_Dark_NBC.ipynb
index a0063669d74c3ae384fcaf8f9827024502f97a99..d0130889643859dc904448f39d0346ae71636ff7 100644
--- a/notebooks/pnCCD/Characterize_pnCCD_Dark_NBC.ipynb
+++ b/notebooks/pnCCD/Characterize_pnCCD_Dark_NBC.ipynb
@@ -34,9 +34,9 @@
"in_folder = \"/gpfs/exfel/exp/SQS/202031/p900166/raw\" # input folder, required\n",
"out_folder = '/gpfs/exfel/data/scratch/ahmedk/test/pnccd' # output folder, required\n",
"sequence = 0 # sequence file to use\n",
- "run = 34 # which run to read data from, required\n",
+ "run = 39 # which run to read data from, required\n",
"\n",
- "db_module = \"PnCCD1\"\n",
+ "db_module = \"pnCCD_M205_M206\"\n",
"karabo_da = ['PNCCD01'] # data aggregators\n",
"karabo_da_control = \"PNCCD02\" # file inset for control data\n",
"karabo_id = \"SQS_NQS_PNCCD1MP\" # karabo prefix of PNCCD devices\n",
@@ -56,7 +56,7 @@
"number_dark_frames = 0 # number of images to be used, if set to 0 all available images are used\n",
"chunkSize = 100 # number of images to read per chunk\n",
"fix_temperature = 0. # fix temperature in K, set to 0. to use value from slow data\n",
- "gain = 1 # the detector's gain setting, It is later read from file and this value is overwritten\n",
+ "gain = 0. # the detector's gain setting, It is later read from file and this value is overwritten\n",
"bias_voltage = 0. # the detector's bias voltage. set to 0. to use value from slow data.\n",
"integration_time = 70 # detector's integration time\n",
"commonModeAxis = 0 # axis along which common mode will be calculated (0: along rows, 1: along columns)\n",
@@ -203,12 +203,20 @@
" ctrl_fname = os.path.join(ped_dir, path_template.format(run, karabo_da_control)).format(sequence)\n",
" ctrl_path = h5path_ctrl.format(karabo_id)\n",
" mdl_ctrl_path = f\"/CONTROL/{karabo_id}/MDL/\"\n",
- " with h5py.File(ctrl_fname, \"r\") as f:\n",
- " if bias_voltage == 0.:\n",
- " bias_voltage = abs(f[os.path.join(mdl_ctrl_path, \"DAQ_MPOD/u0voltage/value\")][0])\n",
- " gain = f[os.path.join(mdl_ctrl_path, \"DAQ_GAIN/spNCCDGain/value\")][0]\n",
- " if fix_temperature == 0.:\n",
- " fix_temperature = f[os.path.join(ctrl_path, \"inputA/krdg/value\")][0]"
+ " try:\n",
+ " with h5py.File(ctrl_fname, \"r\") as f:\n",
+ " if bias_voltage == 0.:\n",
+ " print(\"bias voltage control h5path:\", os.path.join(mdl_ctrl_path, \"DAQ_MPOD/u0voltage/value\"))\n",
+ " bias_voltage = abs(f[os.path.join(mdl_ctrl_path, \"DAQ_MPOD/u0voltage/value\")][0])\n",
+ " gain = f[os.path.join(mdl_ctrl_path, \"DAQ_GAIN/pNCCDGain/value\")][0]\n",
+ " if fix_temperature == 0.:\n",
+ " fix_temperature = f[os.path.join(ctrl_path, \"inputA/krdg/value\")][0]\n",
+ " except KeyError:\n",
+ " print(\"Error !!! during extracting slow data\")\n",
+ " traceback.print_exc(limit=1)\n",
+ " print(\"bias voltage control h5path:\", os.path.join(mdl_ctrl_path, \"DAQ_MPOD/u0voltage/value\"))\n",
+ " print(\"gain control h5path:\", os.path.join(mdl_ctrl_path, \"DAQ_GAIN/pNCCDGain/value\"))\n",
+ " print(\"fix_temperature control h5path:\", os.path.join(ctrl_path, \"inputA/krdg/value\"))"
]
},
{
@@ -1003,7 +1011,7 @@
" condition = Conditions.Dark.CCD(bias_voltage=bias_voltage,\n",
" integration_time=integration_time,\n",
" gain_setting=gain,\n",
- " temperature=temperature_k,\n",
+ " temperature=fix_temperature,\n",
" pixels_x=pixels_x,\n",
" pixels_y=pixels_y)\n",
"\n",
@@ -1026,10 +1034,14 @@
"\n",
" if db_output:\n",
" try:\n",
- " metadata.send(cal_db_interface)\n",
- " print(f\"Inject {const_name} constants from {metadata.calibration_constant_version.begin_at}\")\n",
- " except Exception as e:\n",
- " print(e)\n",
+ " metadata.send(cal_db_interface, timeout=cal_db_timeout)\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\"WARN: {const_name} has already been injected with the same parameter conditions\\n\")\n",
+ " else:\n",
+ " # To prevent having big error message out of the pdf report's page.\n",
+ " print(\"\\n\".join(textwrap.wrap(str(e),100)))\n",
"\n",
" if local_output:\n",
" save_const_to_h5(metadata, out_folder)\n",
@@ -1037,10 +1049,17 @@
"\n",
"print(\"Generated constants with conditions:\\n\")\n",
"print(f\"• bias_voltage: {bias_voltage}\\n• integration_time: {integration_time}\\n\"\n",
- " f\"• gain_setting: {gain}\\n• temperature: {temperature_k}\\n\"\n",
+ " f\"• gain_setting: {gain}\\n• temperature: {fix_temperature}\\n\"\n",
" f\"• creation_time: {creation_time}\\n\")"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
{
"cell_type": "code",
"execution_count": null,
diff --git a/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb b/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb
index e592a7cf0f5a28c98ac1c88d0784c2048712768a..b1484e339ed14465b720bee8c84e7a500fd416a5 100644
--- a/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb
+++ b/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb
@@ -22,17 +22,17 @@
},
"outputs": [],
"source": [
- "in_folder = \"/gpfs/exfel/exp/SQS/201930/p900075/raw\" # input folder\n",
+ "in_folder = \"/gpfs/exfel/exp/SQS/202031/p900166/raw\" # input folder\n",
"out_folder = '/gpfs/exfel/data/scratch/ahmedk/test/pnccd' # output folder\n",
- "run = 365 # which run to read data from\n",
- "sequences = [-1] # sequences to correct, set to -1 for all, range allowed\n",
+ "run = 39 # which run to read data from\n",
+ "sequences = [0] # sequences to correct, set to -1 for all, range allowed\n",
"\n",
- "db_module = \"PnCCD1\"\n",
+ "db_module = \"pnCCD_M205_M206\"\n",
"karabo_da = 'PNCCD01' # data aggregators\n",
"karabo_da_control = \"PNCCD02\" # file inset for control data\n",
"karabo_id = \"SQS_NQS_PNCCD1MP\" # karabo prefix of PNCCD devices\n",
"receiver_id = \"PNCCD_FMT-0\" # inset for receiver devices\n",
- "path_template = 'RAW-R{:04d}-PNCCD01-S{{:05d}}.h5' # the template to use to access data\n",
+ "path_template = 'RAW-R{:04d}-{}-S{{:05d}}.h5' # the template to use to access data\n",
"path_template_seqs = \"{}/r{:04d}/*PNCCD01-S*.h5\"\n",
"h5path = '/INSTRUMENT/{}/CAL/{}:output/data/' # path to data in the HDF5 file \n",
"h5path_ctrl = '/CONTROL/{}/CTRL/TCTRL'\n",
@@ -55,7 +55,7 @@
"\n",
"# pnCCD parameters:\n",
"fix_temperature = 0. # fix temperature in K, set to 0. to use value from slow data.\n",
- "gain = 1 # the detector's gain setting, It is later read from file and this value is overwritten\n",
+ "gain = 0. # the detector's gain setting, It is later read from file and this value is overwritten\n",
"bias_voltage = 0. # the detector's bias voltage. set to 0. to use value from slow data.\n",
"integration_time = 70\n",
"photon_energy = 1.6 # Al fluorescence in keV\n",
@@ -107,6 +107,7 @@
"import time\n",
"import copy\n",
"import os\n",
+ "import traceback\n",
"import glob\n",
"import datetime\n",
"from datetime import timedelta\n",
@@ -216,17 +217,23 @@
"source": [
"# extract slow data\n",
"if karabo_da_control:\n",
- "\n",
- " ctrl_fname = os.path.join(ped_dir, path_template.format(run, karabo_da_control)).format(sequence)\n",
+ " ctrl_fname = os.path.join(ped_dir, path_template.format(run, karabo_da_control)).format(sequences[0])\n",
" ctrl_path = h5path_ctrl.format(karabo_id)\n",
- " mdl_ctrl_path = \"/CONTROL/{}/MDL/\".format(karabo_id)\n",
- "\n",
- " with h5py.File(ctrl_fname, \"r\") as f:\n",
- " if bias_voltage == 0 :\n",
- " bias_voltage = abs(f[os.path.join(mdl_ctrl_path, \"DAQ_MPOD/u0voltage/value\")][0])\n",
- " gain = f[os.path.join(mdl_ctrl_path, \"DAQ_GAIN/spNCCDGain/value\")][0]\n",
- " if fix_temperature == 0.:\n",
- " fix_temperature = f[os.path.join(ctrl_path, \"inputA/krdg/value\")][0]"
+ " mdl_ctrl_path = f\"/CONTROL/{karabo_id}/MDL/\"\n",
+ " try:\n",
+ " with h5py.File(ctrl_fname, \"r\") as f:\n",
+ " if bias_voltage == 0.:\n",
+ " bias_voltage = abs(f[os.path.join(mdl_ctrl_path, \"DAQ_MPOD/u0voltage/value\")][0])\n",
+ " gain = f[os.path.join(mdl_ctrl_path, \"DAQ_GAIN/pNCCDGain/value\")][0]\n",
+ " if fix_temperature == 0.:\n",
+ " fix_temperature = f[os.path.join(ctrl_path, \"inputA/krdg/value\")][0]\n",
+ " except KeyError:\n",
+ " print(\"Error !!! during extracting slow data\")\n",
+ " traceback.print_exc(limit=1)\n",
+ " print(\"Control file name:\", ctrl_fname)\n",
+ " print(\"bias voltage control h5path:\", os.path.join(mdl_ctrl_path, \"DAQ_MPOD/u0voltage/value\"))\n",
+ " print(\"gain control h5path:\", os.path.join(mdl_ctrl_path, \"DAQ_GAIN/pNCCDGain/value\"))\n",
+ " print(\"fix_temperature control h5path:\", os.path.join(ctrl_path, \"inputA/krdg/value\"))"
]
},
{
@@ -241,7 +248,7 @@
"print(\"Bias voltage is {} V.\".format(bias_voltage))\n",
"print(\"Detector gain is set to {}.\".format(gain))\n",
"print(\"Detector integration time is set to {} ms\".format(integration_time))\n",
- "print(f\"Using a fixed temperature of {temperature_k} K\")"
+ "print(f\"Using a fixed temperature of {fix_temperature} K\")"
]
},
{
@@ -357,7 +364,7 @@
"metadata": {},
"outputs": [],
"source": [
- "def get_dark(db_parms, bias_voltage, integration_time, gain, temperature_k, creation_time, run):\n",
+ "def get_dark(db_parms, bias_voltage, integration_time, gain, fix_temperature, creation_time, run):\n",
"# This function is to retrieve the dark constants associated with the run of interest:\n",
"\n",
" cal_db_interface, cal_db_timeout = db_parms\n",
@@ -378,7 +385,7 @@
" condition = Conditions.Dark.CCD(bias_voltage=bias_voltage,\n",
" integration_time=integration_time,\n",
" gain_setting=gain,\n",
- " temperature=temperature_k,\n",
+ " temperature=fix_temperature,\n",
" pixels_x=pixels_x,\n",
" pixels_y=pixels_y)\n",
" \n",
@@ -414,7 +421,7 @@
"\n",
"db_parms = cal_db_interface, cal_db_timeout\n",
"\n",
- "constants = get_dark(db_parms, bias_voltage, integration_time, gain, temperature_k, creation_time, run)\n",
+ "constants = get_dark(db_parms, bias_voltage, integration_time, gain, fix_temperature, creation_time, run)\n",
"\n",
"fig = xana.heatmapPlot(constants[\"Offset\"][:,:,0], x_label='Columns', y_label='Rows', lut_label='Pedestal (ADU)', aspect=1, \n",
" x_range=(0, pixels_y), y_range=(0, pixels_x), vmax=16000, \n",
@@ -449,7 +456,7 @@
" condition = Conditions.Illuminated.CCD(bias_voltage=bias_voltage,\n",
" integration_time=integration_time,\n",
" gain_setting=gain,\n",
- " temperature=temperature_k,\n",
+ " temperature=fix_temperature,\n",
" pixels_x=pixels_x,\n",
" pixels_y=pixels_y, \n",
" photon_energy=photon_energy)\n",
@@ -1319,6 +1326,13 @@
" l = ax.legend()"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ },
{
"cell_type": "code",
"execution_count": null,