diff --git a/notebooks/Gotthard2/Correction_Gotthard2_NBC.ipynb b/notebooks/Gotthard2/Correction_Gotthard2_NBC.ipynb
index 9aa7bab8c50a44d7cdb511e5f501d3c3415fc838..621025e921ae29eb57967758c5fbe8a89672c5ce 100644
--- a/notebooks/Gotthard2/Correction_Gotthard2_NBC.ipynb
+++ b/notebooks/Gotthard2/Correction_Gotthard2_NBC.ipynb
@@ -35,23 +35,26 @@
"karabo_id_control = \"\" # Control karabo ID. Set to empty string to use the karabo-id\n",
"\n",
"# Parameters for calibration database.\n",
- "use_dir_creation_date = True # use the creation data of the input dir for database queries\n",
- "cal_db_interface = \"tcp://max-exfl017:8017#8025\" # the database interface to use\n",
- "cal_db_timeout = 180000 # timeout on caldb requests\n",
+ "use_dir_creation_date = True # use the creation data of the input dir for database queries.\n",
+ "cal_db_interface = \"tcp://max-exfl017:8017#8025\" # the database interface to use.\n",
+ "cal_db_timeout = 180000 # timeout on caldb requests.\n",
+ "overwrite_creation_time = \"\" # To overwrite the measured creation_time. Required Format: YYYY-MM-DD HR:MN:SC.00 e.g. \"2022-06-28 13:00:00.00\"\n",
"\n",
"# Parameters affecting corrected data.\n",
- "gain_correction = True # do relative gain correction\n",
+ "constants_file = \"/gpfs/exfel/data/scratch/ahmedk/dont_remove/gotthard2/constants/calibration_constants_GH2.h5\" # Retrieve constants from local.\n",
+ "offset_correction = True # apply offset correction. This can be disabled to only apply LUT or apply LUT and gain correction for non-linear differential results.\n",
+ "gain_correction = True # apply gain correction.\n",
"\n",
"# Parameter conditions.\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",
+ "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",
+ "acquisition_rate = -1. # Detector acquisition rate (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",
- "pulse_idx_preview = 3 # pulse index to preview. The following even/odd pulse index is used for preview. # TODO: update to pulseId preview.\n",
+ "pulse_idx_preview = 3 # pulse index to preview. The following even/odd pulse index is used for preview. # TODO: update to pulseId preview.\n",
"\n",
"\n",
"def balance_sequences(in_folder, run, sequences, sequences_per_node, karabo_da):\n",
@@ -66,7 +69,7 @@
"metadata": {},
"outputs": [],
"source": [
- "import warnings\n",
+ "import datetime\n",
"from functools import partial\n",
"\n",
"import h5py\n",
@@ -85,9 +88,6 @@
" get_dir_creation_date,\n",
")\n",
"from iCalibrationDB import Conditions, Constants\n",
- "warnings.filterwarnings('ignore')\n",
- "\n",
- "prettyPlotting = True\n",
"\n",
"%matplotlib inline"
]
@@ -107,22 +107,19 @@
"if not karabo_id_control:\n",
" karabo_id_control = karabo_id\n",
"\n",
- "instrument_src = instrument_source_template.format(\n",
- " karabo_id, receiver_template)\n",
+ "instrument_src = instrument_source_template.format(karabo_id, receiver_template)\n",
"ctrl_src = ctrl_source_template.format(karabo_id_control, control_template)\n",
"\n",
"print(f\"Process modules: {karabo_da} for run {run}\")\n",
"\n",
"creation_time = None\n",
- "if use_dir_creation_date:\n",
+ "if overwrite_creation_time:\n",
+ " creation_time = datetime.datetime.strptime(\n",
+ " overwrite_creation_time, \"%Y-%m-%d %H:%M:%S.%f\"\n",
+ " )\n",
+ "elif use_dir_creation_date:\n",
" creation_time = get_dir_creation_date(in_folder, run)\n",
- " print(f\"Using {creation_time} as creation time\")\n",
- "\n",
- "# TODO: Remove later\n",
- "import datetime\n",
- "creation_time=datetime.datetime.strptime(\n",
- " \"2022-06-28 13:00:00.00\",\n",
- " \"%Y-%m-%d %H:%M:%S.%f\")\n"
+ " print(f\"Using {creation_time} as creation time\")"
]
},
{
@@ -137,11 +134,13 @@
" possible_patterns = list(f\"*{mod}*.h5\" for mod in karabo_da)\n",
"else:\n",
" possible_patterns = list(\n",
- " f\"*{mod}-S{s:05d}.h5\" for mod in karabo_da for s in sequences)\n",
+ " f\"*{mod}-S{s:05d}.h5\" for mod in karabo_da for s in sequences\n",
+ " )\n",
"\n",
"run_folder = Path(in_folder / f\"r{run:04d}\")\n",
- "seq_files = [f for f in run_folder.glob(\"*.h5\") if any(\n",
- " f.match(p) for p in possible_patterns)]\n",
+ "seq_files = [\n",
+ " f for f in run_folder.glob(\"*.h5\") if any(f.match(p) for p in possible_patterns)\n",
+ "]\n",
"\n",
"seq_files = sorted(seq_files)\n",
"\n",
@@ -170,13 +169,18 @@
"source": [
"# Read slow data\n",
"run_dc = RunDirectory(run_folder)\n",
- "g2ctrl = gotthard2lib.Gotthard2Ctrl(\n",
- " run_dc=run_dc, ctrl_src=ctrl_src)\n",
- "bias_voltage = g2ctrl.get_bias_voltage()\n",
- "exposure_time = g2ctrl.get_exposure_time()\n",
- "exposure_period = g2ctrl.get_exposure_period()\n",
- "operation_mode = g2ctrl.get_operation_mode()\n",
- "single_photon = g2ctrl.get_single_photon()"
+ "g2ctrl = gotthard2lib.Gotthard2Ctrl(run_dc=run_dc, ctrl_src=ctrl_src)\n",
+ "\n",
+ "if bias_voltage == -1:\n",
+ " bias_voltage = g2ctrl.get_bias_voltage()\n",
+ "if exposure_time == -1:\n",
+ " exposure_time = g2ctrl.get_exposure_time()\n",
+ "if exposure_period == -1:\n",
+ " exposure_period = g2ctrl.get_exposure_period()\n",
+ "if acquisition_rate == -1:\n",
+ " acquisition_rate = g2ctrl.get_acquisition_rate()\n",
+ "if single_photon == -1:\n",
+ " single_photon = g2ctrl.get_single_photon()"
]
},
{
@@ -190,86 +194,108 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "1cdbe818",
+ "id": "5717d722",
"metadata": {},
"outputs": [],
"source": [
- "condition = Conditions.Dark.Gotthard2(\n",
- " bias_voltage=bias_voltage,\n",
- " exposure_time=exposure_time,\n",
- " exposure_period=exposure_period,\n",
- " # TODO: put back with new data.\n",
- " # And decide what to do with old data missing these parameters.\n",
- "# single_photon=single_photon,\n",
- "# operation_mode=operation_mode,\n",
- ")\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(\n",
- " get_constant_from_db_and_time,\n",
- " karabo_id=karabo_id,\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",
- "\n",
- " constants = {\n",
- " \"LUT\": ((1280, 2, 4096), np.uint16), # TODO: what to do if LUT was not retrieved.\n",
- " \"Offset\": ((1280, 2, 3), np.float32),\n",
- " \"Noise\": ((1280, 2, 3), np.float32),\n",
- " \"BadPixelsDark\": ((1280, 2, 3), np.uint32),\n",
- " }\n",
- " cons_data = {}\n",
- " for cname, cempty in constants.items():\n",
- " cons_data[cname], when[cname] = retrieval_function(\n",
- " condition=condition,\n",
- " constant=getattr(Constants.Gotthard2, cname)(),\n",
- " empty_constant=np.zeros(cempty[0], dtype=cempty[1])\n",
- " )\n",
+ "# Used for old FXE runs before adding Gotthard2 to CALCAT\n",
"\n",
- " bpix = cons_data[\"BadPixelsDark\"]\n",
- " if gain_correction:\n",
- " for cname in [\"BadPixelsFF\", \"RelativeGain\"]:\n",
- " cons_data[cname], when[cname] = retrieval_function(\n",
- " condition=condition,\n",
- " constant=getattr(Constants.Gotthard2, cname)(),\n",
- " empty_constant=None\n",
- " )\n",
- " # combine masks\n",
- " if cons_data.get(\"BadPixelsFF\", None) is not None:\n",
- " bpix |= cons_data[\"BadPixelsFF\"]\n",
- " return (\n",
- " cons_data[\"LUT\"], cons_data[\"Offset\"],\n",
- " bpix, cons_data[\"RelativeGain\"], mod, when,\n",
- " )\n",
- "\n",
- "with multiprocessing.Pool() as pool:\n",
- " r = pool.map(get_constants_for_module, karabo_da)"
+ "constants = {}\n",
+ "if constants_file:\n",
+ " for mod in karabo_da:\n",
+ " constants[mod] = {}\n",
+ " # load constants temporarily using defined local paths.\n",
+ " with h5py.File(constants_file, \"r\") as cfile:\n",
+ " constants[mod][\"lut\"] = cfile[\"LUT\"][()]\n",
+ " constants[mod][\"offset\"] = cfile[\"offset_map\"][()].astype(np.float32)\n",
+ " constants[mod][\"gain\"] = cfile[\"gain_map\"][()].astype(np.float32)\n",
+ " constants[mod][\"badpixels\"] = cfile[\"bpix_ff\"][()].astype(np.uint32)"
]
},
{
"cell_type": "code",
"execution_count": null,
- "id": "8ddbc1ba",
+ "id": "1cdbe818",
"metadata": {},
"outputs": [],
"source": [
- "# Print timestamps for the retrieved constants.\n",
- "constants = {}\n",
- "for lut_map, offset_map, bpix, gain_map, mod, when in r:\n",
- " print(f'Constants for module {mod}:')\n",
- " for const in when:\n",
- " print(f' {const} injected at {when[const]}')\n",
- "\n",
- " if gain_map is None:\n",
- " print(\"No gain map found\")\n",
- " gain_correction = False\n",
- " constants[mod] = (lut_map, offset_map, bpix, gain_map)"
+ "if not constants_file:\n",
+ " condition = Conditions.Dark.Gotthard2(\n",
+ " bias_voltage=bias_voltage,\n",
+ " exposure_time=exposure_time,\n",
+ " exposure_period=exposure_period,\n",
+ " single_photon=single_photon,\n",
+ " acquisition_rate=acquisition_rate,\n",
+ " )\n",
+ "\n",
+ " def get_constants_for_module(mod: str):\n",
+ " \"\"\"Get calibration constants for given module for Gotthard2.\"\"\"\n",
+ " when = {}\n",
+ " retrieval_function = partial(\n",
+ " get_constant_from_db_and_time,\n",
+ " karabo_id=karabo_id,\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",
+ " empty_lut = (np.arange(2 ** 12).astype(np.float64) * 2 ** 10 / 2 ** 12).astype(\n",
+ " np.uint16\n",
+ " )\n",
+ " empty_lut = np.stack(1280 * [np.stack([empty_lut] * 2)], axis=0)\n",
+ " constants = {\n",
+ " \"LUT\": empty_lut,\n",
+ " \"Offset\": np.zeros((1280, 2, 3), dtype=np.float32),\n",
+ " \"Noise\": np.zeros((1280, 2, 3), dtype=np.float32),\n",
+ " \"BadPixelsDark\": np.zeros((1280, 2, 3), dtype=np.uint32),\n",
+ " }\n",
+ " cons_data = {}\n",
+ " for cname, cempty in constants.items():\n",
+ " cons_data[cname], when[cname] = retrieval_function(\n",
+ " condition=condition,\n",
+ " constant=getattr(Constants.Gotthard2, cname)(),\n",
+ " empty_constant=cempty,\n",
+ " )\n",
+ "\n",
+ " bpix = cons_data[\"BadPixelsDark\"]\n",
+ " if gain_correction:\n",
+ " for cname in [\"BadPixelsFF\", \"RelativeGain\"]:\n",
+ " cons_data[cname], when[cname] = retrieval_function(\n",
+ " condition=condition,\n",
+ " constant=getattr(Constants.Gotthard2, cname)(),\n",
+ " empty_constant=None,\n",
+ " )\n",
+ " # combine masks\n",
+ " if cons_data.get(\"BadPixelsFF\", None) is not None:\n",
+ " bpix |= cons_data[\"BadPixelsFF\"]\n",
+ " return (\n",
+ " cons_data[\"LUT\"],\n",
+ " cons_data[\"Offset\"],\n",
+ " bpix,\n",
+ " cons_data.get(\"RelativeGain\", None),\n",
+ " mod,\n",
+ " when,\n",
+ " )\n",
+ "\n",
+ " with multiprocessing.Pool() as pool:\n",
+ " r = pool.map(get_constants_for_module, karabo_da)\n",
+ "\n",
+ " # Print timestamps for the retrieved constants.\n",
+ " constants = {}\n",
+ " for lut_map, offset_map, bpix, gain_map, mod, when in r:\n",
+ " constants[mod] = {}\n",
+ " print(f\"Constants for module {mod}:\")\n",
+ " for const in when:\n",
+ " print(f\" {const} injected at {when[const]}\")\n",
+ "\n",
+ " if gain_map is None:\n",
+ " print(\"No gain map found\")\n",
+ " gain_correction = False\n",
+ " constants[mod][\"lut\"] = lut_map\n",
+ " constants[mod][\"offset\"] = offset_map\n",
+ " constants[mod][\"gain\"] = gain_map\n",
+ " constants[mod][\"badpixels\"] = bpix"
]
},
{
@@ -291,12 +317,15 @@
"source": [
"def correct_train(wid, index, d):\n",
" g = gain[index]\n",
- " gotthard2algs.convert_to_10bit(d, lut, data_corr[index, ...])\n",
+ " gotthard2algs.convert_to_10bit(d, constants[mod][\"lut\"], data_corr[index, ...])\n",
" gotthard2algs.correct_train(\n",
- " data_corr[index, ...], mask[index, ...], g,\n",
- " offset_map,\n",
- " gain_map,\n",
- " bpix,\n",
+ " data_corr[index, ...],\n",
+ " mask[index, ...],\n",
+ " g,\n",
+ " constants[mod][\"offset\"],\n",
+ " constants[mod][\"gain\"],\n",
+ " constants[mod][\"badpixels\"],\n",
+ " apply_offset=offset_correction,\n",
" apply_gain=gain_correction,\n",
" )"
]
@@ -312,7 +341,7 @@
" # This is used in case receiver template consists of\n",
" # karabo data aggregator index. e.g. detector at DETLAB\n",
" instr_mod_src = instrument_src.format(mod[-2:])\n",
- " data_path = \"INSTRUMENT/\"+instr_mod_src+\"/data\"\n",
+ " data_path = \"INSTRUMENT/\" + instr_mod_src + \"/data\"\n",
" for raw_file in seq_files:\n",
" step_timer.start()\n",
"\n",
@@ -324,24 +353,24 @@
" data = dc[instr_mod_src, \"data.adc\"].ndarray()\n",
" gain = dc[instr_mod_src, \"data.gain\"].ndarray()\n",
" step_timer.start()\n",
- " lut, offset_map, bpix, gain_map = constants[mod]\n",
"\n",
" # Allocate shared arrays.\n",
" data_corr = context.alloc(shape=dshape, dtype=np.float32)\n",
" mask = context.alloc(shape=dshape, dtype=np.uint32)\n",
" context.map(correct_train, data)\n",
" step_timer.done_step(\"Correcting one sequence file\")\n",
+ "\n",
" step_timer.start()\n",
"\n",
" # Provided PSI gain map has 0 values. Set inf values to nan.\n",
+ " # TODO: This can maybe be removed after creating XFEL gain maps.?\n",
" data_corr[np.isinf(data_corr)] = np.nan\n",
" # Create CORR files and add corrected data sources.\n",
" # Exclude raw data images (data/adc)\n",
- " with h5py.File(out_file, 'w') as ofile:\n",
+ " with h5py.File(out_file, \"w\") as ofile:\n",
" # Copy RAW non-calibrated sources.\n",
- " with h5py.File(raw_file, 'r') as sfile:\n",
- " h5_copy_except.h5_copy_except_paths(\n",
- " sfile, ofile, [f\"{data_path}/adc\"])\n",
+ " with h5py.File(raw_file, \"r\") as sfile:\n",
+ " h5_copy_except.h5_copy_except_paths(sfile, ofile, [f\"{data_path}/adc\"])\n",
" # Create datasets with the available corrected data\n",
" ddset = ofile.create_dataset(\n",
" f\"{data_path}/adc\",\n",
@@ -381,8 +410,9 @@
"outputs": [],
"source": [
"if skip_plots:\n",
- " print('Skipping plots')\n",
+ " print(\"Skipping plots\")\n",
" import sys\n",
+ "\n",
" sys.exit(0)"
]
},
@@ -398,7 +428,8 @@
" mod_dcs[mod] = {}\n",
" with RunDirectory(out_folder) as out_dc:\n",
" tid, mod_dcs[mod][\"train_corr_data\"] = next(\n",
- " out_dc[instr_mod_src, \"data.adc\"].trains())\n",
+ " out_dc[instr_mod_src, \"data.adc\"].trains()\n",
+ " )\n",
" with RunDirectory(run_folder) as in_dc:\n",
" train_dict = in_dc.train_from_id(tid)[1][instr_mod_src]\n",
" mod_dcs[mod][\"train_raw_data\"] = train_dict[\"data.adc\"]\n",
@@ -420,16 +451,17 @@
" raw_data = mod_dcs[mod][\"train_raw_data\"]\n",
" fig, ax = plt.subplots(figsize=(20, 10))\n",
" im = ax.plot(np.mean(raw_data, axis=0))\n",
- " ax.set_title(f'Module {mod}')\n",
+ " ax.set_title(f\"Module {mod}\")\n",
" ax.set_xlabel(\"Strip #\", size=15)\n",
" ax.set_ylabel(\"12-bit ADC output\", size=15)\n",
+ " plt.show()\n",
"step_timer.done_step(\"Plotting raw data\")"
]
},
{
"cell_type": "code",
"execution_count": null,
- "id": "512b48a6-9e2d-4fcc-b075-3698297177bf",
+ "id": "11337d95",
"metadata": {},
"outputs": [],
"source": [
@@ -441,9 +473,12 @@
" corr_data = mod_dcs[mod][\"train_corr_data\"]\n",
" fig, ax = plt.subplots(figsize=(20, 10))\n",
" im = ax.plot(np.mean(corr_data, axis=0))\n",
- " ax.set_title(f'Module {mod}')\n",
- " ax.set_xlabel(\"Strip #\", size=15)\n",
- " ax.set_ylabel(\"10-bit KeV. output\", size=15)\n",
+ " ax.set_title(f\"Module {mod}\")\n",
+ " ax.set_xlabel(\"Strip #\", size=20)\n",
+ " ax.set_ylabel(\"10-bit KeV. output\", size=20)\n",
+ " plt.xticks(fontsize=15)\n",
+ " plt.yticks(fontsize=15)\n",
+ " plt.show()\n",
"step_timer.done_step(\"Plotting corrected data\")"
]
},
@@ -457,8 +492,10 @@
"# Validate given \"pulse_idx_preview\"\n",
"\n",
"if pulse_idx_preview + 1 > data.shape[1]:\n",
- " print(f\"WARNING: selected pulse_idx_preview {pulse_idx_preview} is not available in data.\"\n",
- " \" Previewing 1st pulse.\")\n",
+ " print(\n",
+ " f\"WARNING: selected pulse_idx_preview {pulse_idx_preview} is not available in data.\"\n",
+ " \" Previewing 1st pulse.\"\n",
+ " )\n",
" pulse_idx_preview = 1\n",
"\n",
"if data.shape[1] == 1:\n",
@@ -466,7 +503,9 @@
" even_pulse = None\n",
"else:\n",
" odd_pulse = pulse_idx_preview if pulse_idx_preview % 2 else pulse_idx_preview + 1\n",
- " even_pulse = pulse_idx_preview if not (pulse_idx_preview % 2) else pulse_idx_preview + 1\n",
+ " even_pulse = (\n",
+ " pulse_idx_preview if not (pulse_idx_preview % 2) else pulse_idx_preview + 1\n",
+ " )\n",
"\n",
"if pulse_idx_preview + 1 > data.shape[1]:\n",
" pulse_idx_preview = 1\n",
@@ -489,23 +528,16 @@
" ax.plot(raw_data[odd_pulse], label=f\"Odd Pulse {odd_pulse}\")\n",
" if even_pulse:\n",
" ax.plot(raw_data[even_pulse], label=f\"Even Pulse {even_pulse}\")\n",
- " ax.set_title(f'Module {mod}')\n",
- " ax.set_xlabel(\"Strip #\", size=15)\n",
- " ax.set_ylabel(\"12-bit ADC output\", size=15)\n",
+ " ax.set_title(f\"Module {mod}\")\n",
+ " ax.set_xlabel(\"Strip #\", size=20)\n",
+ " ax.set_ylabel(\"12-bit ADC RAW\", size=20)\n",
+ " plt.xticks(fontsize=15)\n",
+ " plt.yticks(fontsize=15)\n",
" ax.legend()\n",
+ " plt.show()\n",
"step_timer.done_step(\"Plotting RAW odd/even pulses.\")"
]
},
- {
- "cell_type": "markdown",
- "id": "f1ddac79-5590-4bdb-9cfa-147d73f5dd5f",
- "metadata": {},
- "source": [
- "### Single RAW Train Preview\n",
- "\n",
- "A single image from the first RAW train"
- ]
- },
{
"cell_type": "code",
"execution_count": null,
@@ -521,10 +553,11 @@
" ax.plot(corr_data[odd_pulse], label=f\"Odd Pulse {odd_pulse}\")\n",
" if even_pulse:\n",
" ax.plot(corr_data[even_pulse], label=f\"Even Pulse {even_pulse}\")\n",
- " ax.set_title(f'Module {mod}')\n",
+ " ax.set_title(f\"Module {mod}\")\n",
" ax.set_xlabel(\"Strip #\", size=15)\n",
- " ax.set_ylabel(\"10-bit KeV. output\", size=15)\n",
+ " ax.set_ylabel(\"10-bit KeV CORRECTED\", size=15)\n",
" ax.legend()\n",
+ " plt.show()\n",
"step_timer.done_step(\"Plotting CORRECTED odd/even pulses.\")"
]
}
@@ -546,6 +579,11 @@
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.11"
+ },
+ "vscode": {
+ "interpreter": {
+ "hash": "916dbcbb3f70747c44a77c7bcd40155683ae19c65e1c03b4aa3499c5328201f1"
+ }
}
},
"nbformat": 4,
diff --git a/src/cal_tools/gotthard2/gotthard2lib.py b/src/cal_tools/gotthard2/gotthard2lib.py
index c7f29721b6dd7a28d9ff4cbe9aa84bfc79e9b86b..8a0a32b5d974f11c510abf5165440eb89333faed 100644
--- a/src/cal_tools/gotthard2/gotthard2lib.py
+++ b/src/cal_tools/gotthard2/gotthard2lib.py
@@ -25,15 +25,13 @@ class Gotthard2Ctrl():
return(round(
self.run_dc[self.ctrl_src, "exposurePeriod"].as_single_value(), 4)) # noqa
- def get_operation_mode(self):
- if "operationMode.value" in self.run_dc.keys_for_source(
- self.ctrl_src):
+ def get_acquisition_rate(self):
+ if "acquisitionRate.value" in self.run_dc.keys_for_source(self.ctrl_src): # noqa
return(
float(self.run_dc.get_run_value(
- self.ctrl_src, "operationMode")))
+ self.ctrl_src, "acquisitionRate")))
def get_single_photon(self):
- if "singlePhoton.value" in self.run_dc.keys_for_source(
- self.ctrl_src):
+ if "singlePhoton.value" in self.run_dc.keys_for_source(self.ctrl_src): # noqa
return(
bool(self.run_dc[self.ctrl_src, "singlePhoton"].as_single_value())) # noqa
diff --git a/src/cal_tools/gotthard2algs.pyx b/src/cal_tools/gotthard2algs.pyx
index f588d47b46c74eb538c061e4a90da9b4a1469f34..606de03f484234f38075414cade4ef23e79bcde6 100644
--- a/src/cal_tools/gotthard2algs.pyx
+++ b/src/cal_tools/gotthard2algs.pyx
@@ -31,6 +31,7 @@ def correct_train(
float[:, :, :] offset_map,
float[:, :, :] gain_map,
unsigned int[:, :, :] bpix_map,
+ unsigned short short apply_offset = 1,
unsigned short short apply_gain = 1,
):
"""Correct Gotthard2 raw data.
@@ -50,7 +51,8 @@ def correct_train(
if g == 3:
g = 2
raw_val = data[pulse, x]
- raw_val -= offset_map[x, cell, g]
+ if apply_offset == 1:
+ raw_val -= offset_map[x, cell, g]
if apply_gain == 1:
raw_val /= gain_map[x, cell, g]
mask[pulse, x] = bpix_map[x, cell, g]