diff --git a/notebooks/pnCCD/Characterize_pnCCD_Dark_NBC.ipynb b/notebooks/pnCCD/Characterize_pnCCD_Dark_NBC.ipynb
index cb1e13f64cfc762a9080a2c63c551e93b582d8ea..f3e8d5cf8d7bdb397b27b50d376eedab3058c9ff 100644
--- a/notebooks/pnCCD/Characterize_pnCCD_Dark_NBC.ipynb
+++ b/notebooks/pnCCD/Characterize_pnCCD_Dark_NBC.ipynb
@@ -45,7 +45,6 @@
"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",
"# Parameters used for injecting calibration constants.\n",
- "set_parameters_manually = False # Boolean for setting parameter values manually instead of reading control values.\n",
"fix_temperature_top = 0. # fix temperature of top pnCCD sensor in K. Set to 0, to use the value from slow data\n",
"fix_temperature_bot = 0. # fix temperature of bottom pnCCD sensor in K. Set to 0, to use the value from slow data\n",
"temp_limits = 5 # temperature limits in which calibration parameters are considered equal\n",
@@ -59,7 +58,7 @@
"sigmaNoise = 10. # pixels whose signal value exceeds sigmaNoise*noise will be considered as cosmics and are masked\n",
"bad_pixel_offset_sigma = 4. # any pixel whose offset beyond this standard deviations is a bad pixel\n",
"bad_pixel_noise_sigma = 4. # any pixel whose noise beyond this standard deviations is a bad pixel\n",
- "max_trains = 500 # Maximum number of trains to use for dark processing.\n",
+ "max_trains = 500 # Maximum number of trains to use for dark processing. Set to 0 to process all trains.\n",
"min_trains = 1 # Minimum number of trains to proceed with dark processing.\n",
"\n",
"# Don't delete. myMDC sends this parameter by default.\n",
@@ -185,18 +184,16 @@
"run_dc = RunDirectory(f\"{in_folder}/r{run:04d}\")\n",
"\n",
"# extract control data\n",
- "if not set_parameters_manually:\n",
- " ctrl_data = pnccdlib.PnccdCtrl(run_dc, karabo_id)\n",
- " \n",
- " if bias_voltage == 0:\n",
- " bias_voltage = ctrl_data.get_bias_voltage()\n",
- " if gain == -1:\n",
- " gain = ctrl_data.get_gain()\n",
- " if fix_temperature_top == 0:\n",
- " fix_temperature_top = ctrl_data.get_fix_temperature_top()\n",
- " if fix_temperature_bot == 0:\n",
- " fix_temperature_bot = ctrl_data.get_fix_temperature_bot()\n",
+ "ctrl_data = pnccdlib.PnccdCtrl(run_dc, karabo_id)\n",
"\n",
+ "if bias_voltage == 0:\n",
+ " bias_voltage = ctrl_data.get_bias_voltage()\n",
+ "if gain == -1:\n",
+ " gain = ctrl_data.get_gain()\n",
+ "if fix_temperature_top == 0:\n",
+ " fix_temperature_top = ctrl_data.get_fix_temperature_top()\n",
+ "if fix_temperature_bot == 0:\n",
+ " fix_temperature_bot = ctrl_data.get_fix_temperature_bot()\n",
"\n",
"# Printing the Parameters Read from the Data File:\n",
"display(Markdown('### Detector Parameters'))\n",
@@ -253,7 +250,7 @@
"data = data.astype(np.float32)\n",
"\n",
"noiseMap = np.std(data, axis=0, dtype=np.float64)\n",
- "offsetMap = np.mean(data, axis=0)\n",
+ "offsetMap = np.mean(data, axis=0, dtype=np.float64)\n",
"step_timer.done_step(f'Initial maps are created from {n_trains} trains.')"
]
},
diff --git a/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb b/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb
index ed111a76d780b7dafb59f0391c1a33afd047824f..f7bc8a91781e608289f94dd99dd377f4bff0bd23 100644
--- a/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb
+++ b/notebooks/pnCCD/Correct_pnCCD_NBC.ipynb
@@ -37,7 +37,6 @@
"saturated_threshold = 32000. # full well capacity in ADU\n",
"\n",
"# Conditions for retrieving calibration constants\n",
- "set_parameters_manually = False # Boolean for setting parameter values manually instead of reading control values.\n",
"fix_temperature_top = 0. # fix temperature for top sensor in K, set to 0. to use value from slow data.\n",
"fix_temperature_bot = 0. # fix temperature for bottom senspr in K, set to 0. to use value from slow data.\n",
"gain = -1 # the detector's gain setting. Set to -1 to use the value from the slow data.\n",
@@ -186,23 +185,19 @@
"run_dc = RunDirectory(Path(in_folder) / f\"r{run:04d}\")\n",
"ctrl_data = pnccdlib.PnccdCtrl(run_dc, karabo_id)\n",
"\n",
- "proposal = run_dc.run_metadata()[\"proposalNumber\"]\n",
- "print(f'Proposal: {proposal}, Run: {run}')\n",
- "\n",
"# extract control data\n",
- "if not set_parameters_manually:\n",
- " step_timer.start()\n",
+ "step_timer.start()\n",
"\n",
- " if bias_voltage == 0.:\n",
- " bias_voltage = ctrl_data.get_bias_voltage()\n",
- " if gain == -1:\n",
- " gain = ctrl_data.get_gain()\n",
- " if fix_temperature_top == 0:\n",
- " fix_temperature_top = ctrl_data.get_fix_temperature_top()\n",
- " if fix_temperature_bot == 0:\n",
- " fix_temperature_bot = ctrl_data.get_fix_temperature_bot()\n",
+ "if bias_voltage == 0.:\n",
+ " bias_voltage = ctrl_data.get_bias_voltage()\n",
+ "if gain == -1:\n",
+ " gain = ctrl_data.get_gain()\n",
+ "if fix_temperature_top == 0:\n",
+ " fix_temperature_top = ctrl_data.get_fix_temperature_top()\n",
+ "if fix_temperature_bot == 0:\n",
+ " fix_temperature_bot = ctrl_data.get_fix_temperature_bot()\n",
"\n",
- " step_timer.done_step(\"Reading control parameters.\")\n",
+ "step_timer.done_step(\"Reading control parameters.\")\n",
"\n",
"# Printing the Parameters Read from the Data File:\n",
"display(Markdown('### Detector Parameters'))\n",
@@ -791,8 +786,7 @@
" # Copy RAW non-calibrated sources.\n",
" with h5py.File(seq_f, 'r') as sfile:\n",
" h5_copy_except.h5_copy_except_paths(\n",
- " sfile, ofile,\n",
- " [\"INSTRUMENT/\"+instrument_src+\"/data/image\"],\n",
+ " sfile, ofile, [],\n",
" )\n",
" # TODO: to clear this up: why save corrected data in data/pixels rather than data/image.\n",
" write_datasets(corr_arrays, ofile)\n",