From 0a995d3058e24ffbf90e8e4f30069f53138a06d4 Mon Sep 17 00:00:00 2001
From: Philipp Schmidt <philipp.schmidt@xfel.eu>
Date: Mon, 12 Jul 2021 10:54:19 +0200
Subject: [PATCH] Add notebook parameter for AGIPD integration time to override
detection
---
notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb | 4 +++-
.../AGIPD/AGIPD_Retrieve_Constants_Precorrection.ipynb | 4 +++-
notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb | 7 ++++---
.../AGIPD/Characterize_AGIPD_Gain_FlatFields_Summary.ipynb | 6 ++++--
notebooks/AGIPD/Chracterize_AGIPD_Gain_PC_NBC.ipynb | 4 +++-
5 files changed, 17 insertions(+), 8 deletions(-)
diff --git a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
index 5a257ef44..0d9de779b 100644
--- a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
+++ b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
@@ -49,6 +49,7 @@
"max_pulses = [0, 500, 1] # range list [st, end, step] of maximum pulse indices within a train. 3 allowed maximum list input elements.\n",
"mem_cells_db = 0 # set to a value different than 0 to use this value for DB queries\n",
"cell_id_preview = 1 # cell Id used for preview in single-shot plots\n",
+ "integration_time = -1 # integration time, negative values for auto-detection.\n",
"\n",
"# Correction parameters\n",
"blc_noise_threshold = 5000 # above this mean signal intensity now baseline correction via noise is attempted\n",
@@ -376,7 +377,8 @@
"gain_mode = get_gain_mode(control_fn, h5path_ctrl)\n",
"\n",
"# Evaluate integration time\n",
- "integration_time = get_integration_time(control_fn, h5path_ctrl)"
+ "if integration_time < 0:\n",
+ " integration_time = get_integration_time(control_fn, h5path_ctrl)"
]
},
{
diff --git a/notebooks/AGIPD/AGIPD_Retrieve_Constants_Precorrection.ipynb b/notebooks/AGIPD/AGIPD_Retrieve_Constants_Precorrection.ipynb
index f6b3b4751..e5dc04b60 100644
--- a/notebooks/AGIPD/AGIPD_Retrieve_Constants_Precorrection.ipynb
+++ b/notebooks/AGIPD/AGIPD_Retrieve_Constants_Precorrection.ipynb
@@ -44,6 +44,7 @@
"photon_energy = 9.2 # photon energy in keV\n",
"max_cells_db_dark = 0 # set to a value different than 0 to use this value for dark data DB queries\n",
"max_cells_db = 0 # set to a value different than 0 to use this value for DB queries\n",
+ "integration_time = -1 # integration time, negative values for auto-detection.\n",
"\n",
"# Correction Booleans\n",
"only_offset = False # Apply only Offset correction. if False, Offset is applied by Default. if True, Offset is only applied.\n",
@@ -163,7 +164,8 @@
"gain_mode = agipdlib.get_gain_mode(control_fn, h5path_ctrl)\n",
"\n",
"# Evaluate integration time\n",
- "integration_time = agipblib.get_integration_time(control_fn, h5path_ctrl)\n",
+ "if integration_time < 0:\n",
+ " integration_time = agipblib.get_integration_time(control_fn, h5path_ctrl)\n",
" \n",
"print(f\"Gain setting: {gain_setting}\")\n",
"print(f\"Gain mode: {gain_mode.name}\")\n",
diff --git a/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb b/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
index 565947c2d..35fddcd6a 100644
--- a/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
+++ b/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
@@ -186,9 +186,10 @@
"else:\n",
" print(f'Something is clearly wrong; slow data indicates gain modes {run_gain_modes}')\n",
"\n",
- "integration_times = [get_integration_time(fn, h5path_ctrl) for fn in control_names]\n",
- "if len(set(integration_times)) > 1:\n",
- " print(f'WARNING: integration time is not constant across the specified dark runs')\n",
+ "if integration_time < 0:\n",
+ " integration_times = [get_integration_time(fn, h5path_ctrl) for fn in control_names]\n",
+ " if len(set(integration_times)) > 1:\n",
+ " print(f'WARNING: integration time is not constant across the specified dark runs')\n",
"\n",
"integration_time = integration_times[0]\n",
"\n",
diff --git a/notebooks/AGIPD/Characterize_AGIPD_Gain_FlatFields_Summary.ipynb b/notebooks/AGIPD/Characterize_AGIPD_Gain_FlatFields_Summary.ipynb
index 51f0de6dc..7ab5a24ef 100644
--- a/notebooks/AGIPD/Characterize_AGIPD_Gain_FlatFields_Summary.ipynb
+++ b/notebooks/AGIPD/Characterize_AGIPD_Gain_FlatFields_Summary.ipynb
@@ -59,7 +59,8 @@
"bias_voltage = 300 # Bias voltage\n",
"acq_rate = 0. # the detector acquisition rate, use 0 to try to auto-determine\n",
"gain_setting = 0.1 # the gain setting, use 0.1 to try to auto-determine\n",
- "photon_energy = 8.05 # photon energy in keV"
+ "photon_energy = 8.05 # photon energy in keV\n",
+ "integration_time = -1 # integration time, negative values for auto-detection."
]
},
{
@@ -164,7 +165,8 @@
" gain_setting = 0\n",
"\n",
"# Evaluate integration time\n",
- "integration_time = get_integration_time(filename, h5path_ctrl)\n",
+ "if integration_time < 0:\n",
+ " integration_time = get_integration_time(filename, h5path_ctrl)\n",
" \n",
"# Evaluate detector instance for mapping\n",
"instrument = karabo_id.split(\"_\")[0]\n",
diff --git a/notebooks/AGIPD/Chracterize_AGIPD_Gain_PC_NBC.ipynb b/notebooks/AGIPD/Chracterize_AGIPD_Gain_PC_NBC.ipynb
index 14e5d5747..75c1a43da 100644
--- a/notebooks/AGIPD/Chracterize_AGIPD_Gain_PC_NBC.ipynb
+++ b/notebooks/AGIPD/Chracterize_AGIPD_Gain_PC_NBC.ipynb
@@ -58,6 +58,7 @@
"mem_cells = 0. # number of memory cells used, use 0 to auto-derive\n",
"acq_rate = 0. # the detector acquisition rate, use 0 to try to auto-determine\n",
"gain_setting = 0.1 # gain setting can have value 0 or 1, Default=0.1 for no (None) gain-setting\n",
+ "integration_time = -1 # integration time, negative values for auto-detection.\n",
"\n",
"interlaced = False # assume interlaced data format, for data prior to Dec. 2017\n",
"fit_hook = True # fit a hook function to medium gain slope\n",
@@ -243,7 +244,8 @@
" sequences = []\n",
"print(f\"Gain setting: {gain_setting}\")\n",
"\n",
- "integration_time = get_integration_time(control_fname, h5path_ctrl)\n",
+ "if integration_time < 0:\n",
+ " integration_time = get_integration_time(control_fname, h5path_ctrl)\n",
"print(f\"Integration time: {integration_time}\")"
]
},
--
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