From b3c7ae92c7b9350a8fcb89cd96f1f66b6917c74c Mon Sep 17 00:00:00 2001
From: ahmedk <karim.ahmed@xfel.eu>
Date: Mon, 16 Oct 2023 11:08:53 +0200
Subject: [PATCH] fix manual edit for JUNGFRAU operating conditions
---
...Jungfrau_Gain_Correct_and_Verify_NBC.ipynb | 14 ++++----
...rk_analysis_all_gains_burst_mode_NBC.ipynb | 34 ++++++++++++-------
2 files changed, 29 insertions(+), 19 deletions(-)
diff --git a/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb b/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb
index 8caea9b49..eae5935ca 100644
--- a/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb
+++ b/notebooks/Jungfrau/Jungfrau_Gain_Correct_and_Verify_NBC.ipynb
@@ -46,12 +46,11 @@
"chunks_data = 1 # HDF chunk size for pixel data in number of frames.\n",
"\n",
"# Parameters for retrieving calibration constants\n",
- "manual_slow_data = False # if true, use manually entered bias_voltage, integration_time, gain_setting, and gain_mode values\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",
- "gain_mode = 0 # 0 for runs with dynamic gain setting, 1 for fixgain. It will be overwritten by value in file, if manual_slow_data is set to True.\n",
+ "integration_time = -1 # integration time in us. set to -1 to overwrite by value in file.\n",
+ "gain_setting = -1 # 0 for dynamic gain, 1 for dynamic HG0. set to -1 to overwrite by value in file.\n",
+ "gain_mode = -1 # 0 for runs with dynamic gain setting, 1 for fixed gain. Set to -1 to overwrite by value in file.\n",
"mem_cells = -1 # Set mem_cells to -1 to automatically use the value stored in RAW data.\n",
- "bias_voltage = 180 # will be overwritten by value in file\n",
+ "bias_voltage = -1 # Bias Voltage. Set to -1 to overwrite by value in file.\n",
"\n",
"# Parameters for plotting\n",
"skip_plots = False # exit after writing corrected files\n",
@@ -160,10 +159,13 @@
" mem_cells_name = \"single cell\" if memory_cells == 1 else \"burst\"\n",
" print(f\"Run is in manually set to {mem_cells_name} mode. With {memory_cells} memory cells\")\n",
"\n",
- "if not manual_slow_data:\n",
+ "if integration_time < 0:\n",
" integration_time = ctrl_data.get_integration_time()\n",
+ "if bias_voltage < 0:\n",
" bias_voltage = ctrl_data.get_bias_voltage()\n",
+ "if gain_setting < 0:\n",
" gain_setting = ctrl_data.get_gain_setting()\n",
+ "if gain_mode < 0:\n",
" gain_mode = ctrl_data.get_gain_mode()\n",
"\n",
"print(f\"Integration time is {integration_time} us\")\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 a630399b4..b95ad890d 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
@@ -49,11 +49,11 @@
"time_limits = 0.025 # to find calibration constants later on, the integration time is allowed to vary by 0.5 us\n",
"\n",
"# Parameters to be used for injecting dark calibration constants.\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, fixgain1, fixgain2. Will be overwritten by value in file\n",
- "gain_mode = 0 # 1 if medium and low runs are fixgain1 and fixgain2, otherwise 0. It will be overwritten by value in file, if manual_slow_data\n",
- "bias_voltage = 90 # sensor bias voltage in V, will be overwritten by value in file\n",
- "memory_cells = 16 # number of memory cells\n",
+ "integration_time = -1 # Integration time in us. Set to -1 to overwrite by value in file.\n",
+ "gain_setting = -1 # 0 for dynamic, forceswitchg1, forceswitchg2, 1 for dynamichg0, fixgain1, fixgain2. Set to overwrite by value in file.\n",
+ "gain_mode = -1 # 1 if medium and low runs are fixgain1 and fixgain2, otherwise 0. Set to -1 to overwrite by value in file.\n",
+ "bias_voltage = -1 # sensor bias voltage in V, will be overwritten by value in file\n",
+ "memory_cells = -1 # Number of memory cells.\n",
"\n",
"# Parameters used for plotting\n",
"detailed_report = False\n",
@@ -172,7 +172,7 @@
" runs=run_nums,\n",
" ctrl_src=ctrl_src,\n",
" )\n",
- "\n",
+ "_gain_mode = None\n",
"for gain, run_n in enumerate(run_nums):\n",
" run_dc = RunDirectory(f\"{in_folder}/r{run_n:04d}/\")\n",
" gain_runs[run_n] = [gain, run_dc]\n",
@@ -182,13 +182,15 @@
"\n",
" run_mcells, sc_start = ctrl_data.get_memory_cells()\n",
"\n",
- " if not manual_slow_data:\n",
+ " if integration_time < 0:\n",
" integration_time = ctrl_data.get_integration_time()\n",
+ " print(f\"Integration time is {integration_time} us\")\n",
+ " if bias_voltage < 0:\n",
" bias_voltage = ctrl_data.get_bias_voltage()\n",
+ " print(f\"Bias voltage is {bias_voltage} V\")\n",
+ " if gain_setting < 0:\n",
" gain_setting = ctrl_data.get_gain_setting()\n",
- " print(f\"Gain setting is {gain_setting} ({ctrl_data.run_settings})\")\n",
- " print(f\"Integration time is {integration_time} us\")\n",
- " print(f\"Bias voltage is {bias_voltage} V\")\n",
+ " print(f\"Gain setting is {gain_setting} ({ctrl_data.run_settings})\")\n",
" if run_mcells == 1:\n",
" memory_cells = 1\n",
" print('Dark runs in single cell mode, '\n",
@@ -197,11 +199,17 @@
" memory_cells = 16\n",
" print('Dark runs in burst mode, '\n",
" f'storage cell start: {sc_start:02d}')\n",
- " else:\n",
- " gain_mode = ctrl_data.get_gain_mode()\n",
+ " else: # medium and low gain\n",
+ " _gain_mode = ctrl_data.get_gain_mode()\n",
" med_low_settings.append(ctrl_data.run_mode)\n",
"\n",
- "print(f\"Gain mode is {gain_mode} ({med_low_settings})\")\n",
+ "# TODO: consider updating this cell into something similar to agipdlib.AgipdCtrlsRuns()\n",
+ "if gain_mode < 0:\n",
+ " gain_mode = _gain_mode\n",
+ " print(f\"Gain mode is {gain_mode} ({med_low_settings})\")\n",
+ "else:\n",
+ " print(f\"Gain mode is manually set to {gain_mode}.\")\n",
+ "\n",
"\n",
"step_timer.done_step(f'Reading control data.')"
]
--
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