From bdee6c3f1340b5ca41f7c61e745da7603bb56edf Mon Sep 17 00:00:00 2001
From: ahmedk <karim.ahmed@xfel.eu>
Date: Thu, 16 Jun 2022 16:32:18 +0200
Subject: [PATCH] add operation mode and single photon
---
.../Gotthard2/Correction_Gotthard2_NBC.ipynb | 87 ++++++++++---------
setup.py | 5 +-
src/cal_tools/gotthard2/gotthard2lib.py | 16 ++--
3 files changed, 59 insertions(+), 49 deletions(-)
diff --git a/notebooks/Gotthard2/Correction_Gotthard2_NBC.ipynb b/notebooks/Gotthard2/Correction_Gotthard2_NBC.ipynb
index 07b5a6673..9d46e8a02 100644
--- a/notebooks/Gotthard2/Correction_Gotthard2_NBC.ipynb
+++ b/notebooks/Gotthard2/Correction_Gotthard2_NBC.ipynb
@@ -26,10 +26,17 @@
"sequences_per_node = 1 # number of sequence files per node if notebook executed through xfel-calibrate, set to 0 to not run SLURM parallel\n",
"\n",
"# Parameters used to access raw data.\n",
+<<<<<<< HEAD
"karabo_id = \"DET_LAB_G2\" # karabo prefix of Jungfrau devices\n",
"karabo_da = [\"DA01\"] # data aggregators\n",
"receiver_template = \"GOT{}\" # receiver template used to read INSTRUMENT keys.\n",
"control_template = \"CTRL{}\" # control template used to read CONTROL keys.\n",
+=======
+ "karabo_id = \"FXE_XAD_G2XES\" # karabo prefix of Gotthard-II devices\n",
+ "karabo_da = [\"GH201\"] # data aggregators\n",
+ "receiver_template = \"RECEIVER\" # receiver template used to read INSTRUMENT keys.\n",
+ "control_template = \"CONTROL\" # control template used to read CONTROL keys.\n",
+>>>>>>> add operation mode and single photon
"instrument_source_template = \"{}/DET/{}:daqOutput\" # template for source name (filled with karabo_id & receiver_id). e.g. 'SPB_IRDA_JF4M/DET/JNGFR01:daqOutput'\n",
"ctrl_source_template = \"{}/DET/{}\" # template for control source name (filled with karabo_id_control)\n",
"karabo_id_control = \"\" # Control karabo ID. Set to empty string to use the karabo-id\n",
@@ -44,11 +51,11 @@
"constants_file = \"/gpfs/exfel/data/scratch/ahmedk/dont_remove/gotthard2/constants/calibration_constants_GH2.h5\"\n",
"\n",
"# Parameter conditions.\n",
- "pulses = -1 # Number of detector pulses, -1 to use value in raw file.\n",
- "bias_voltage = -1 # Detector bias voltage, -1 to use value in raw file.\n",
- "integration_time = -1 # Detector integration time, -1 to use value in raw file.\n",
- "acquisition_rate = -1 # Detector acquisition rate, -1 to use value in raw file.\n",
- "gain_setting = -1 # Detector gain setting (High and Low CDS), -1 to use value in raw file.\n",
+ "bias_voltage = -1 # Detector bias voltage, set to -1 to use value in raw file.\n",
+ "exposure_time = -1 # Detector exposure time, set to -1 to use value in raw file.\n",
+ "exposure_period = -1 # Detector exposure period, set to -1 to use value in raw file.\n",
+ "operation_mode = -1 # Detector operation mode (1.1/4.5), set to -1 to use value in raw file.\n",
+ "single_photon = -1 # Detector single photon mode (High/Low CDS), set to -1 to use value in raw file.\n",
"\n",
"# Parameters for plotting\n",
"skip_plots = False # exit after writing corrected files\n",
@@ -175,60 +182,60 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "764f1295",
+ "id": "4a8c1b95",
"metadata": {},
"outputs": [],
"source": [
- "# condition = Conditions.Dark.jungfrau(\n",
- "# pulses=pulses,\n",
+ "# condition = Conditions.Dark.gotthard2(\n",
"# bias_voltage=bias_voltage,\n",
- "# integration_time=exposure_time,\n",
- "# acquisition_time=acquisition_time,\n",
- "# #gain_setting=gain_setting,\n",
+ "# exposure_time=exposure_time,\n",
+ "# exposure_period=exposure_period,\n",
+ "# single_photon=single_photon,\n",
+ "# operation_mode=operation_mode,\n",
"# )\n",
"\n",
- "# def get_constants_for_module(karabo_da: str):\n",
- "# \"\"\" Get calibration constants for given module for Gotthard2\"\"\"\n",
+ "# stripes = 1280\n",
+ "\n",
+ "\n",
+ "# def get_constants_for_module(mod: str):\n",
+ "# \"\"\"Get calibration constants for given module for Gotthard-II.\"\"\"\n",
"# when = {}\n",
"# retrieval_function = partial(get_constant_from_db_and_time(\n",
"# karabo_id=karabo_id,\n",
- "# karabo_da=karabo_da,\n",
+ "# karabo_da=mod,\n",
"# cal_db_interface=cal_db_interface,\n",
"# creation_time=creation_time,\n",
"# timeout=cal_db_timeout,\n",
"# print_once=False,\n",
"# ))\n",
- "# lut, when[\"Offset\"] = retrieval_function(\n",
- "# condition=condition,\n",
- "# constant=Constants.jungfrau.LUT(),\n",
- "# empty_constant=np.zeros((stripes, 2, 3))\n",
- "# )\n",
- "# offset_map, when[\"Offset\"] = retrieval_function(\n",
- "# condition=condition,\n",
- "# constant=Constants.jungfrau.Offset(),\n",
- "# empty_constant=np.zeros((stripes, 2, 3))\n",
- "# )\n",
- "# bpix_map, when[\"BadPixelsDark\"] = retrieval_function(\n",
- "# condition=condition,\n",
- "# constant=Constants.jungfrau.BadPixelsDark(),\n",
- "# empty_constant=np.zeros((stripes, 2, 3), dtype=np.uint32),\n",
- "# )\n",
- "# if gain_correction:\n",
- "# mask_ff, when[\"BadPixelsFF\"] = retrieval_function(\n",
- "# condition=condition,\n",
- "# constant=Constants.jungfrau.BadPixelsFF(),\n",
- "# empty_constant=None\n",
- "# )\n",
- "# gain_map, when[\"Gain\"] = retrieval_function(\n",
+ "\n",
+ "# constants = {\n",
+ "# \"LUT\":np.uint32,\n",
+ "# \"Offset\":np.float32,\n",
+ "# \"Noise\":np.float32,\n",
+ "# \"BadPixelsDark\":np.float32\n",
+ "# }\n",
+ "# cons_data[mod] = {}\n",
+ "# for cname, ctype in constants.items():\n",
+ "# cons_data[mod][cname], when[cname] = retrieval_function(\n",
"# condition=condition,\n",
- "# constant=Constants.jungfrau.RelativeGain(),\n",
- "# empty_constant=None\n",
+ "# constant=getattr(Constants.gotthard2, cname)(),\n",
+ "# empty_constant=np.zeros((stripes, 2, 3), dtype=ctype)\n",
"# )\n",
+ "# if gain_correction:\n",
+ "# for cname in [\"BadPixelsFF\", \"RelativeGain\"]:\n",
+ "# cons_data[mod][cname], when[cname] = retrieval_function(\n",
+ "# condition=condition,\n",
+ "# constant=Constants.gotthard2.BadPixelsFF(),\n",
+ "# empty_constant=None\n",
+ "# )\n",
"\n",
"# # combine masks\n",
- "# if mask_ff is not None:\n",
- "# mask |= np.moveaxis(mask_ff, 0, 1)\n",
+ "# if cons_data[mod].get(\"BadPixelsFF\", None) is not None:\n",
+ "# mask |= np.moveaxis(cons_data[mod][\"BadPixelsFF\"], 0, 1)\n",
+ "\n",
"\n",
+ "# cons_data = {}\n",
"# with multiprocessing.Pool() as pool:\n",
"# r = pool.map(get_constants_for_module, karabo_da)"
]
diff --git a/setup.py b/setup.py
index 7331ed67c..d9e929fe0 100644
--- a/setup.py
+++ b/setup.py
@@ -24,10 +24,13 @@ ext_modules = [
extra_compile_args=['-O3', '-fopenmp', '-march=native',
'-ftree-vectorize', '-frename-registers'],
extra_link_args=['-fopenmp'],
- )
+ ),
+ Extension(
"cal_tools.gotthard2.gotthard2algs",
["src/cal_tools/gotthard2/gotthard2algs.pyx"],
include_dirs=[numpy.get_include()],
+ extra_compile_args=["-fopenmp", "-march=native"],
+ extra_link_args=["-fopenmp"],
),
]
diff --git a/src/cal_tools/gotthard2/gotthard2lib.py b/src/cal_tools/gotthard2/gotthard2lib.py
index 26a3798d6..50794ac36 100644
--- a/src/cal_tools/gotthard2/gotthard2lib.py
+++ b/src/cal_tools/gotthard2/gotthard2lib.py
@@ -14,19 +14,19 @@ class Gotthard2Ctrl():
self.run_dc = run_dc
self.ctrl_src = ctrl_src
- def get_pulses(self):
- return(self.run_dc[self.ctrl_src, "numberOfFrames"].as_single_value())
-
def get_bias_voltage(self):
return(self.run_dc[self.ctrl_src, "highVoltageMax"].as_single_value())
- def get_acquisition_time(self):
- return(
- float(self.run_dc.get_run_value(self.ctrl_src, "operationMode")))
-
def get_exposure_time(self):
return(self.run_dc[self.ctrl_src, "exposureTime"].as_single_value())
- def get_gain_setting(self):
+ def get_exposure_period(self):
+ return(self.run_dc[self.ctrl_src, "exposurePeriod"].as_single_value())
+
+ def get_operation_mode(self):
+ return(
+ float(self.run_dc.get_run_value(self.ctrl_src, "operationMode")))
+
+ def get_single_photon(self):
return(
bool(self.run_dc[self.ctrl_src, "singlePhoton"].as_single_value()))
--
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