From 5c85745474f7dfd2654d28a606a482566714f29f Mon Sep 17 00:00:00 2001
From: Cyril Danilevski <cyril.danilevski@xfel.eu>
Date: Thu, 16 Sep 2021 11:46:46 +0200
Subject: [PATCH] Add Gain setting to Jungfrau notebooks
---
.../Jungfrau_Gain_Correct_and_Verify_NBC.ipynb | 10 +++++++---
..._dark_analysis_all_gains_burst_mode_NBC.ipynb | 16 ++++++++++++----
2 files changed, 19 insertions(+), 7 deletions(-)
diff --git a/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb b/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb
index cd968ed1f..f12b51ac3 100644
--- a/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb
+++ b/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb
@@ -44,6 +44,7 @@
"photon_energy = 9.2 # photon energy in keV\n",
"chunk_size_idim = 1 # chunking size of imaging dimension, adjust if user software is sensitive to this.\n",
"integration_time = 4.96 # integration time in us, will be overwritten by value in file\n",
+ "gain_setting = 0 # 0 for dynamic gain, 1 for dynamic HG0, will be overwritten by value in file\n",
"mem_cells = 0 # leave memory cells equal 0, as it is saved in control information starting 2019.\n",
"db_module = [\"Jungfrau_M275\"] # ID of module in calibration database\n",
"manual_slow_data = False # if true, use manually entered bias_voltage and integration_time values\n",
@@ -184,7 +185,9 @@
" run_path = h5path_run.format(karabo_id_control, receiver_control_id)\n",
" integration_time = float(f[f'{run_path}/exposureTime/value'][()]*1e6)\n",
" bias_voltage = int(np.squeeze(f[f'{run_path}/vHighVoltage/value'])[0])\n",
- "\n",
+ " \n",
+ " gain_s = f[f'/RUN/{karabo_id_control}/DET/CONTROL/settings/value'][0].decode()\n",
+ " gain_setting = 1 if gain_s == 'dynamichg0' else 0 # gain_s == 'dynamicgain'\n",
"\n",
"control_path = h5path_cntrl.format(karabo_id_control, receiver_control_id)\n",
"try:\n",
@@ -206,6 +209,7 @@
" print(f\"Error trying to access memory cell from contol information: {e}\")\n",
"\n",
"print(f\"Integration time is {integration_time} us\")\n",
+ "print(f\"Gain setting is {gain_setting}\")\n",
"print(f\"Bias voltage is {bias_voltage} V\")\n",
"print(f\"Number of memory cells is {memory_cells}\")"
]
@@ -220,6 +224,7 @@
" memory_cells=memory_cells,\n",
" bias_voltage=bias_voltage,\n",
" integration_time=integration_time,\n",
+ " gain_setting=gain_setting,\n",
")\n",
"\n",
"def get_constants_for_module(karabo_da: str):\n",
@@ -304,8 +309,7 @@
"outputs": [],
"source": [
"def copy_and_sanitize_non_cal_data(infile, outfile, h5base):\n",
- " \"\"\" Copy and sanitize data in `infile` that is not touched by `correctLPD`\n",
- " \"\"\"\n",
+ " \"\"\"Copy and sanitize data from `infile` that is not calibrated.\"\"\"\n",
"\n",
" h5base = h5base.lstrip(\"/\")\n",
" dont_copy = [\"adc\", ]\n",
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 9c2c7086b..71d405404 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
@@ -42,6 +42,7 @@
"db_output = False # output constants to database\n",
"\n",
"integration_time = 1000 # integration time in us, will be overwritten by value in file\n",
+ "gain_setting = 0 # 0 for dynamic, forceswitchg1, forceswitchg2, 1 for dynamichg0, fixedgain1, fixgain2. Will be overwritten by value in file\n",
"bias_voltage = 90 # sensor bias voltage in V, will be overwritten by value in file\n",
"badpixel_threshold_sigma = 5. # bad pixels defined by values outside n times this std from median\n",
"offset_abs_threshold_low = [1000, 10000, 10000] # absolute bad pixel threshold in terms of offset, lower values\n",
@@ -217,6 +218,13 @@
" run_path = h5path_run.format(karabo_id_control, receiver_control_id)\n",
" integration_time = float(f[f'{run_path}/exposureTime/value'][()]*1e6)\n",
" bias_voltage = int(np.squeeze(f[f'{run_path}/vHighVoltage/value'])[0])\n",
+ " \n",
+ " if r_n == run_high:\n",
+ " gain_s = f[f'/RUN/{karabo_id_control}/DET/CONTROL/settings/value'][0].decode()\n",
+ " gain_setting = 1 if gain_s == \"dynamichg0\" else 0\n",
+ " print(f\"Constants Gain setting is {gain_setting} ({gain_s})\")\n",
+ "\n",
+ "\n",
" print(\"Integration time is {} us\".format(integration_time))\n",
" print(\"Bias voltage is {} V\".format(bias_voltage))\n",
" if this_run_mcells == 1:\n",
@@ -381,9 +389,7 @@
" ax_n0.set_xlabel(f'RMS noise {g_name[g_idx]} ' + unit, fontsize=15)\n",
" #ax_n0.set_yscale('log')\n",
" \n",
- " plt.show()\n",
- " \n",
- " "
+ " plt.show() "
]
},
{
@@ -474,7 +480,8 @@
"\n",
" # set the operating condition\n",
" condition = Conditions.Dark.jungfrau(memory_cells=memoryCells, bias_voltage=bias_voltage,\n",
- " integration_time=integration_time)\n",
+ " integration_time=integration_time,\n",
+ " gain_setting=gain_setting)\n",
" \n",
" for parm in condition.parameters:\n",
" if parm.name == \"Integration Time\":\n",
@@ -504,6 +511,7 @@
"print(\"Constants parameter conditions are:\\n\")\n",
"print(f\"• Bias voltage: {bias_voltage}\\n• Memory cells: {memoryCells}\\n\"\n",
" f\"• Integration time: {integration_time}\\n\"\n",
+ " f\"• Gain setting: {gain_setting}\\n\"\n",
" f\"• Creation time: {md.calibration_constant_version.begin_at if md is not None else creation_time}\\n\")"
]
},
--
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