From bba83f55173a8f7c5cc99c2d78203d14b62b3297 Mon Sep 17 00:00:00 2001
From: ahmedk <karim.ahmed@xfel.eu>
Date: Fri, 15 Mar 2024 12:32:51 +0100
Subject: [PATCH] fix get_bias_voltage by passing channel value and add
comments to discuss in MR
---
.../AGIPD/AGIPD_Correct_and_Verify.ipynb | 21 ++++++++++++-------
.../Characterize_AGIPD_Gain_Darks_NBC.ipynb | 12 +++++------
src/cal_tools/agipdlib.py | 16 +++++++++-----
3 files changed, 31 insertions(+), 18 deletions(-)
diff --git a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
index cf85b3e52..b5a01841c 100644
--- a/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
+++ b/notebooks/AGIPD/AGIPD_Correct_and_Verify.ipynb
@@ -388,13 +388,12 @@
"outputs": [],
"source": [
"first_mod_channel = sorted(modules)[0]\n",
- "\n",
- "instrument_src_mod = [\n",
+ "instrument_src_first_mod = [\n",
" s for s in list(dc.all_sources) if f\"{first_mod_channel}CH\" in s][0]\n",
"\n",
"agipd_cond = AgipdCtrl(\n",
" run_dc=dc,\n",
- " image_src=instrument_src_mod,\n",
+ " image_src=instrument_src_first_mod,\n",
" ctrl_src=ctrl_src,\n",
" raise_error=False, # to be able to process very old data without gain_setting value\n",
")"
@@ -417,11 +416,22 @@
" acq_rate = agipd_cond.get_acq_rate()\n",
"if mem_cells == -1:\n",
" mem_cells = agipd_cond.get_num_cells()\n",
+ "if mem_cells is None:\n",
+ " # TODO FOR MR REVIEWERS:n This check is only useful in case we read mem_cells from fast data instead of slow data.\n",
+ " # I vote for moving this ValueError to the function instead or we better return None and handle it from the Nb like now?\n",
+ " raise ValueError(f\"No raw images found for {instrument_src_first_mod}\")\n",
"# TODO: look for alternative for passing creation_time\n",
"if gain_setting == -1:\n",
" gain_setting = agipd_cond.get_gain_setting(creation_time)\n",
"if bias_voltage == -1:\n",
- " bias_voltage = agipd_cond.get_bias_voltage(karabo_id_control)\n",
+ " # TODO FOR MR REVIEWERS: Shall I read all bias voltage modules and compare values\n",
+ " # or could this be adding complications?\n",
+ " # This comparison would work only in case there is an issue with the detector.\n",
+ " # Then there is a possibility that the dark constants were injected with\n",
+ " # different voltage values for each module. If this comparison is not done and this issue is in place\n",
+ " # We will reach the same detector issue conclusion after realizing constants were not retrieved for all modules.\n",
+ " bias_voltage = agipd_cond.get_bias_voltage(\n",
+ " karabo_id_control, module=first_mod_channel)\n",
"if integration_time == -1:\n",
" integration_time = agipd_cond.get_integration_time()\n",
"if gain_mode == -1:\n",
@@ -436,9 +446,6 @@
"metadata": {},
"outputs": [],
"source": [
- "if mem_cells is None:\n",
- " raise ValueError(f\"No raw images found for {instrument_src_mod}\")\n",
- "\n",
"mem_cells_db = mem_cells if mem_cells_db == -1 else mem_cells_db\n",
"\n",
"print(f\"Maximum memory cells to calibrate: {mem_cells}\")"
diff --git a/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb b/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
index bc519599e..48510efc7 100644
--- a/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
+++ b/notebooks/AGIPD/Characterize_AGIPD_Gain_Darks_NBC.ipynb
@@ -245,12 +245,11 @@
"source": [
"step_timer.start()\n",
"\n",
- "# Read slow data from 1st channel only.\n",
- "# Read all modules in one notebook and validate the conditions across detectors?\n",
- "# Currently slurm jobs run per one module.\n",
+ "# Read slow data from 1st channel of the selected module only.\n",
+ "# Currently dark slurm jobs run per one module.\n",
+ "first_mod_channel = sorted(modules)[0]\n",
"\n",
- "# TODO: what if first module is not available. Maybe only channel 2 available\n",
- "instrument_src_mod = instrument_src.format(modules[0])\n",
+ "instrument_src_mod = instrument_src.format(first_mod_channel)\n",
"\n",
"agipd_ctrl_dark = AgipdCtrlRuns(\n",
" raw_folder=in_folder,\n",
@@ -275,7 +274,8 @@
" acq_rate = agipd_ctrl_dark.get_acq_rate()\n",
"\n",
"if bias_voltage == 0:\n",
- " bias_voltage = agipd_ctrl_dark.get_bias_voltage(karabo_id_control)\n",
+ " bias_voltage = agipd_ctrl_dark.get_bias_voltage(\n",
+ " karabo_id_control, module=first_mod_channel)\n",
"\n",
"fixed_gain_mode = False\n",
"if gain_mode == -1:\n",
diff --git a/src/cal_tools/agipdlib.py b/src/cal_tools/agipdlib.py
index 74c3b852b..f72b0136b 100644
--- a/src/cal_tools/agipdlib.py
+++ b/src/cal_tools/agipdlib.py
@@ -233,9 +233,11 @@ class AgipdCtrl:
300 was the default bias_voltage value for
MID_DET_AGIPD1M-1 and SPB_DET_AGIPD1M-1.
- :param karabo_id_control: The karabo deviceId for the CONTROL device.
- :param module: defaults to module 0
- :return: bias voltage
+ Args:
+ karabo_id_control: The karabo deviceId for the CONTROL device.
+ module: defaults to module 0
+ Returns:
+ float: bias voltage value
"""
# TODO: Add a breaking fix by passing the source and key through
# get_bias_voltage arguments.
@@ -415,7 +417,11 @@ class AgipdCtrlRuns:
self._validate_same_value("Integration Time", integration_times)
return integration_times[0]
- def get_bias_voltage(self, karabo_id_control: str = None):
+ def get_bias_voltage(
+ self,
+ karabo_id_control: str = None,
+ module: Optional[int] = 0
+ ):
"""
Args:
karabo_id_control (str):
@@ -425,7 +431,7 @@ class AgipdCtrlRuns:
int: Bias voltage.
"""
bias_voltages = [
- c.get_bias_voltage(karabo_id_control) for c in self.run_ctrls]
+ c.get_bias_voltage(karabo_id_control, module) for c in self.run_ctrls]
self._validate_same_value("Bias Voltage", bias_voltages)
return bias_voltages[0]
--
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