diff --git a/notebooks/pnCCD/Characterize_pnCCD_Dark_NBC.ipynb b/notebooks/pnCCD/Characterize_pnCCD_Dark_NBC.ipynb
index 759a6a3c5eef2ff199736eff43b9c27451312328..4e9ae9715e8640678ab9f0719b46d9f426391f2d 100644
--- a/notebooks/pnCCD/Characterize_pnCCD_Dark_NBC.ipynb
+++ b/notebooks/pnCCD/Characterize_pnCCD_Dark_NBC.ipynb
@@ -35,9 +35,8 @@
"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}-{}-S{{:05d}}.h5' # the template to use to access data\n",
- "instrument_source_template = '{}/CAL/{}:output' # path in the HDF5 file the data is at\n",
- "ctrl_source_template = '{}/CTRL/TCTRL'\n",
- "mld_source_template = \"{}/MDL/{}\"\n",
+ "instrument_source_template = '{}/CAL/{}:output' # data source path in h5file. Template filled with karabo_id and receiver_id\n",
+ "ctrl_source_template = '{}/CTRL/TCTRL' # Control h5 source template. Filled with karabo_id\n",
"\n",
"# Database access parameters.\n",
"use_dir_creation_date = True # use dir creation date as data production reference date\n",
@@ -195,10 +194,9 @@
"\n",
"# extract control data\n",
"if karabo_da_control:\n",
- " mdl_src = mld_source_template.format(karabo_id, \"{}\")\n",
" ctrl_src = ctrl_source_template.format(karabo_id)\n",
"\n",
- " ctrl_data = pnccdlib.PnccdCtrl(run_dc, ctrl_src, mdl_src)\n",
+ " ctrl_data = pnccdlib.PnccdCtrl(run_dc, ctrl_src, karabo_id)\n",
" \n",
" if bias_voltage == 0:\n",
" bias_voltage = ctrl_data.get_bias_voltage()\n",
diff --git a/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb b/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb
index 0215548d2180477d9bf1fceac16ae1a8d44c97e4..28edae959cecd442bc6a2d3c26c78e40797f6ae8 100644
--- a/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb
+++ b/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb
@@ -27,11 +27,9 @@
"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}-{}-S{:05d}.h5' # the template to use to access data\n",
- "path_template_seqs = \"{}/r{:04d}/*PNCCD01-S*.h5\"\n",
- "instrument_source_template = '{}/CAL/{}:output' # path to data in the HDF5 file \n",
+ "path_template = 'RAW-R{:04d}-{}-S{:05d}.h5' # the template to use to access data\n",
+ "instrument_source_template = '{}/CAL/{}:output' # path to data in the HDF5 file \n",
"control_source_template = '{}/CTRL/TCTRL' # control source template\n",
- "mdl_source_template = \"{}/MDL/{}\" # middlelayer source template\n",
"\n",
"overwrite = True # keep this as True to not overwrite the output \n",
"\n",
@@ -40,7 +38,7 @@
"commonModeAxis = 0 # axis along which common mode will be calculated, 0 = row, and 1 = column \n",
"split_evt_primary_threshold = 4. # primary threshold for split event classification in terms of n sigma noise\n",
"split_evt_secondary_threshold = 3. # secondary threshold for split event classification in terms of n sigma noise\n",
- "saturated_threshold = 32000. # full well capacity in ADU\n",
+ "saturated_threshold = 32000. # full well capacity in ADU\n",
"chunk_size_idim = 1 # H5 chunking size of output data\n",
"# ONLY FOR TESTING\n",
"limit_images = 0 # this parameter is used for limiting number of images to correct from a sequence file. ONLY FOR TESTING.\n",
@@ -128,7 +126,7 @@
")\n",
"from cal_tools.step_timing import StepTimer\n",
"from cal_tools import h5_copy_except\n",
- "from iCalibrationDB import Conditions, ConstantMetaData, Constants, Detectors, Versions\n",
+ "from iCalibrationDB import Conditions, ConstantMetaData, Constants\n",
"from iCalibrationDB.detectors import DetectorTypes\n",
"\n",
"profiler = xprof.Profiler()\n",
@@ -192,10 +190,9 @@
"# extract control data\n",
"if karabo_da_control:\n",
" step_timer.start()\n",
- " mdl_src = mdl_source_template.format(karabo_id, \"{}\")\n",
" ctrl_src = control_source_template.format(karabo_id)\n",
" run_dc = RunDirectory(Path(in_folder) / f\"r{run:04d}\")\n",
- " ctrl_data = pnccdlib.PnccdCtrl(run_dc, ctrl_src, mdl_src)\n",
+ " ctrl_data = pnccdlib.PnccdCtrl(run_dc, ctrl_src, karabo_id)\n",
"\n",
" if bias_voltage == 0.:\n",
" bias_voltage = ctrl_data.get_bias_voltage()\n",
@@ -539,63 +536,50 @@
"source": [
"#***************** Histogram Calculators ******************#\n",
"# Will contain uncorrected data:\n",
- "histCalRaw = xcal.HistogramCalculator(\n",
- " sensorSize, \n",
- " bins=bins, \n",
- " range=bin_range,\n",
- " nCells=memoryCells,\n",
- " blockSize=blockSize,\n",
- " parallel=run_parallel,\n",
- ")\n",
+ "histCalRaw = xcal.HistogramCalculator(sensorSize, \n",
+ " bins=bins, \n",
+ " range=bin_range,\n",
+ " nCells=memoryCells, \n",
+ " parallel=run_parallel,\n",
+ " blockSize=blockSize)\n",
"# Will contain offset corrected data:\n",
- "histCalOffsetCor = xcal.HistogramCalculator(\n",
- " sensorSize, \n",
- " bins=bins, \n",
- " range=bin_range,\n",
- " nCells=memoryCells, \n",
- " blockSize=blockSize,\n",
- " parallel=run_parallel,\n",
- ")\n",
+ "histCalOffsetCor = xcal.HistogramCalculator(sensorSize, \n",
+ " bins=bins, \n",
+ " range=bin_range,\n",
+ " nCells=memoryCells, \n",
+ " parallel=run_parallel,\n",
+ " blockSize=blockSize)\n",
"if corr_bools.get('common_mode'):\n",
" # Will contain common mode corrected data:\n",
- " histCalCommonModeCor = xcal.HistogramCalculator(\n",
- " sensorSize,\n",
- " bins=bins,\n",
- " range=bin_range,\n",
- " nCells=memoryCells,\n",
- " blockSize=blockSize,\n",
- " parallel=run_parallel,\n",
- " )\n",
- " \n",
+ " histCalCommonModeCor = xcal.HistogramCalculator(sensorSize,\n",
+ " bins=bins,\n",
+ " range=bin_range,\n",
+ " nCells=memoryCells, \n",
+ " parallel=run_parallel,\n",
+ " blockSize=blockSize)\n",
"if corr_bools.get('pattern_class'):\n",
" # Will contain split events pattern data:\n",
- " histCalPcorr = xcal.HistogramCalculator(\n",
- " sensorSize,\n",
- " bins=bins,\n",
- " range=bin_range,\n",
- " nCells=memoryCells, \n",
- " blockSize=blockSize,\n",
- " parallel=run_parallel,\n",
- " )\n",
+ " histCalPcorr = xcal.HistogramCalculator(sensorSize,\n",
+ " bins=bins,\n",
+ " range=bin_range,\n",
+ " nCells=memoryCells, \n",
+ " parallel=run_parallel,\n",
+ " blockSize=blockSize)\n",
" # Will contain singles events data:\n",
- " histCalPcorrS = xcal.HistogramCalculator(\n",
- " sensorSize,\n",
- " bins=bins,\n",
- " range=bin_range,\n",
- " nCells=memoryCells,\n",
- " blockSize=blockSize,\n",
- " parallel=run_parallel,\n",
- " )\n",
+ " histCalPcorrS = xcal.HistogramCalculator(sensorSize,\n",
+ " bins=bins,\n",
+ " range=bin_range,\n",
+ " nCells=memoryCells, \n",
+ " parallel=run_parallel,\n",
+ " blockSize=blockSize)\n",
"if corr_bools.get('relgain'):\n",
" # Will contain gain corrected data:\n",
- " histCalGainCor = xcal.HistogramCalculator(\n",
- " sensorSize,\n",
- " bins=bins,\n",
- " range=bin_range,\n",
- " nCells=memoryCells,\n",
- " blockSize=blockSize,\n",
- " parallel=run_parallel,\n",
- " )"
+ " histCalGainCor = xcal.HistogramCalculator(sensorSize,\n",
+ " bins=bins,\n",
+ " range=bin_range,\n",
+ " nCells=memoryCells, \n",
+ " parallel=run_parallel,\n",
+ " blockSize=blockSize)"
]
},
{
diff --git a/src/cal_tools/pnccdlib.py b/src/cal_tools/pnccdlib.py
index 81284fb173153293fa58340b2c5b1576d9391c6e..a3c46f36dcd7561f525021bbf3ad4d66605f1140 100644
--- a/src/cal_tools/pnccdlib.py
+++ b/src/cal_tools/pnccdlib.py
@@ -14,37 +14,31 @@ class PnccdCtrl():
self,
run_dc: "extra_data.DataCollection", # noqa
ctrl_src: str,
- mdl_src: str
+ karabo_id: str
):
""" Extract control data from given control paths.
:param run_dc: run Extra-data data collection.
:param ctrl_src: control source available in run_dc.
- :param mdl_src: middlelayer source available in run_dc.
+ :param karabo_id: Detector identifier name.
"""
self.run_dc = run_dc
self.ctrl_src = ctrl_src
- self.mdl_src = mdl_src
+ self.karabo_id = karabo_id
def get_bias_voltage(self):
return(
abs(self.run_dc[
- self.mdl_src.format("DAQ_MPOD"),
- "u0voltage.value"
- ][0].ndarray()[0])
+ f"{self.karabo_id}/MDL/DAQ_MPOD", "u0voltage.value"][0].ndarray()[0]) # noqa
)
def get_gain(self):
return(
- abs(self.run_dc[
- self.mdl_src.format("DAQ_GAIN"),
- "pNCCDGain.value"
- ][0].ndarray()[0])
+ self.run_dc[
+ f"{self.karabo_id}/MDL/DAQ_GAIN", "pNCCDGain.value"][0].ndarray()[0] # noqa
)
def get_fix_temperature_top(self):
- return(self.run_dc[
- self.ctrl_src, "inputA.krdg.value"][0].ndarray()[0])
+ return self.run_dc.get_run_value(self.ctrl_src, "inputA.krdg.value")
def get_fix_temperature_bot(self):
- return(self.run_dc[
- self.ctrl_src, "inputB.krdg.value"][0].ndarray()[0])
+ return self.run_dc.get_run_value(self.ctrl_src, "inputB.krdg.value")