diff --git a/notebooks/LPD/LPD_Correct_Fast.ipynb b/notebooks/LPD/LPD_Correct_Fast.ipynb
index 184d6ce8689670217f7ca7e831804c14bceeea92..4fd91a297b48fe4f592193f0f5912462ae85d602 100644
--- a/notebooks/LPD/LPD_Correct_Fast.ipynb
+++ b/notebooks/LPD/LPD_Correct_Fast.ipynb
@@ -40,7 +40,7 @@
"creation_time = \"\" # The timestamp to use with Calibration DB. Required Format: \"YYYY-MM-DD hh:mm:ss\" e.g. 2019-07-04 11:02:41\n",
"cal_db_interface = '' # Not needed, compatibility with current webservice.\n",
"cal_db_timeout = 0 # Not needed, compatbility with current webservice.\n",
- "cal_db_root = '/gpfs/exfel/d/cal/caldb_store'\n",
+ "cal_db_root = '/gpfs/exfel/d/cal/caldb_store' # The calibration database root path to access constant files. For example accessing constants from the test database.\n",
"\n",
"# Operating conditions\n",
"mem_cells = 512 # Memory cells, LPD constants are always taken with 512 cells.\n",
@@ -85,7 +85,6 @@
},
"outputs": [],
"source": [
- "from collections import OrderedDict\n",
"from logging import warning\n",
"from pathlib import Path\n",
"from time import perf_counter\n",
@@ -100,19 +99,17 @@
"import matplotlib.pyplot as plt\n",
"%matplotlib inline\n",
"\n",
- "from calibration_client import CalibrationClient\n",
- "from calibration_client.modules import CalibrationConstantVersion\n",
"import extra_data as xd\n",
"import extra_geom as xg\n",
"import pasha as psh\n",
- "\n",
"from extra_data.components import LPD1M\n",
"\n",
+ "import cal_tools.restful_config as rest_cfg\n",
+ "from cal_tools.calcat_interface import CalCatError, LPD_CalibrationData\n",
"from cal_tools.lpdalgs import correct_lpd_frames\n",
"from cal_tools.lpdlib import get_mem_cell_pattern, make_cell_order_condition\n",
"from cal_tools.tools import CalibrationMetadata, calcat_creation_time\n",
- "from cal_tools.files import DataFile\n",
- "from cal_tools.restful_config import restful_config"
+ "from cal_tools.files import DataFile"
]
},
{
@@ -136,19 +133,16 @@
"\n",
"output_source = output_source or input_source\n",
"\n",
- "cal_db_root = Path(cal_db_root)\n",
- "\n",
- "metadata = CalibrationMetadata(metadata_folder or out_folder)\n",
- "\n",
"creation_time = calcat_creation_time(in_folder, run, creation_time)\n",
"print(f'Using {creation_time.isoformat()} as creation time')\n",
"\n",
"# Pick all modules/aggregators or those selected.\n",
- "if not karabo_da or karabo_da == ['']:\n",
- " if not modules or modules == [-1]:\n",
+ "if karabo_da == ['']:\n",
+ " if modules == [-1]:\n",
" modules = list(range(16))\n",
- "\n",
" karabo_da = [f'LPD{i:02d}' for i in modules]\n",
+ "else:\n",
+ " modules = [int(x[-2:]) for x in karabo_da]\n",
" \n",
"# Pick all sequences or those selected.\n",
"if not sequences or sequences == [-1]:\n",
@@ -236,26 +230,6 @@
"# Obtain and prepare calibration constants"
]
},
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "# Connect to CalCat.\n",
- "calcat_config = restful_config['calcat']\n",
- "client = CalibrationClient(\n",
- " base_api_url=calcat_config['base-api-url'],\n",
- " use_oauth2=calcat_config['use-oauth2'],\n",
- " client_id=calcat_config['user-id'],\n",
- " client_secret=calcat_config['user-secret'],\n",
- " user_email=calcat_config['user-email'],\n",
- " token_url=calcat_config['token-url'],\n",
- " refresh_url=calcat_config['refresh-url'],\n",
- " auth_url=calcat_config['auth-url'],\n",
- " scope='')"
- ]
- },
{
"cell_type": "code",
"execution_count": null,
@@ -270,41 +244,30 @@
{
"cell_type": "code",
"execution_count": null,
- "metadata": {},
+ "metadata": {
+ "tags": []
+ },
"outputs": [],
"source": [
- "const_data = {}\n",
- "const_load_mp = psh.ProcessContext(num_workers=24)\n",
- "\n",
- "if const_yaml: # Read constants from YAML file.\n",
- " start = perf_counter()\n",
- " for da, ccvs in const_yaml.items():\n",
- "\n",
- " for calibration_name, ccv in ccvs['constants'].items():\n",
- " if ccv['file-path'] is None:\n",
- " warning(f\"Missing {calibration_name} for {da}\")\n",
- " continue\n",
- "\n",
- " dtype = np.uint32 if calibration_name.startswith('BadPixels') else np.float32\n",
- "\n",
- " const_data[(da, calibration_name)] = dict(\n",
- " path=Path(ccv['file-path']),\n",
- " dataset=ccv['dataset-name'],\n",
- " data=const_load_mp.alloc(shape=(256, 256, mem_cells, 3), dtype=dtype)\n",
+ "const_data = dict() # {\"ModuleName\": {\"ConstantName\": ndarray}}\n",
+ "start = perf_counter()\n",
+ "if const_yaml:\n",
+ " const_load_mp = psh.ProcessContext(num_workers=24)\n",
+ "\n",
+ " for mod, constants in const_yaml.items():\n",
+ " const_data[mod] = {} # An empty dictionary stays for a module with no constants.\n",
+ " for cname, cmdata in constants[\"constants\"].items():\n",
+ " const_data[mod][cname] = const_load_mp.alloc(\n",
+ " shape=(256, 256, mem_cells, 3), # All LPD constants have the same shape.\n",
+ " dtype=np.uint32 if cname.startswith('BadPixels') else np.float32\n",
" )\n",
- "else: # Retrieve constants from CALCAT.\n",
- " dark_calibrations = {\n",
- " 1: 'Offset', # np.float32\n",
- " 14: 'BadPixelsDark' # should be np.uint32, but is np.float64\n",
- " }\n",
- "\n",
- " base_condition = [\n",
- " dict(parameter_name='Sensor Bias Voltage', value=bias_voltage),\n",
- " dict(parameter_name='Memory cells', value=mem_cells),\n",
- " dict(parameter_name='Feedback capacitor', value=capacitor),\n",
- " dict(parameter_name='Pixels X', value=256),\n",
- " dict(parameter_name='Pixels Y', value=256),\n",
- " ]\n",
+ " def load_constant_dataset(wid, index, mod):\n",
+ " for cname, mdata in const_yaml[mod][\"constants\"].items():\n",
+ " with h5py.File(mdata[\"path\"], \"r\") as cf:\n",
+ " cf[f\"{mdata['dataset']}/data\"].read_direct(const_data[mod][cname])\n",
+ "\n",
+ " const_load_mp.map(load_constant_dataset, karabo_da)\n",
+ "else:\n",
" cell_ids_pattern_s = None\n",
" if use_cell_order != 'never':\n",
" # Read the order of memory cells used\n",
@@ -313,57 +276,28 @@
" use_cell_order, get_mem_cell_pattern(raw_data, det_inp_sources)\n",
" )\n",
" print(\"Memory cells order:\", cell_ids_pattern_s)\n",
- "\n",
- " if cell_ids_pattern_s is not None:\n",
- " dark_condition = base_condition + [\n",
- " dict(parameter_name='Memory cell order', value=cell_ids_pattern_s),\n",
- " ]\n",
- " else:\n",
- " dark_condition = base_condition.copy()\n",
- "\n",
- " illuminated_calibrations = {\n",
- " 20: 'BadPixelsFF', # np.uint32\n",
- " 42: 'GainAmpMap', # np.float32\n",
- " 43: 'FFMap', # np.float32\n",
- " 44: 'RelativeGain' # np.float32\n",
- " }\n",
- "\n",
- " illuminated_condition = base_condition + [\n",
- " dict(parameter_name='Source Energy', value=photon_energy),\n",
- " dict(parameter_name='category', value=category)\n",
- " ]\n",
- "\n",
- " print('Querying calibration database', end='', flush=True)\n",
- " start = perf_counter()\n",
- " for calibrations, condition in [\n",
- " (dark_calibrations, dark_condition),\n",
- " (illuminated_calibrations, illuminated_condition)\n",
- " ]:\n",
- " resp = CalibrationConstantVersion.get_closest_by_time_by_detector_conditions(\n",
- " client, karabo_id, list(calibrations.keys()),\n",
- " {'parameters_conditions_attributes': condition},\n",
- " karabo_da='', event_at=creation_time.isoformat()\n",
- " )\n",
- "\n",
- " if not resp['success']:\n",
- " raise RuntimeError(resp)\n",
- "\n",
- " for ccv in resp['data']:\n",
- " cc = ccv['calibration_constant']\n",
- " da = ccv['physical_detector_unit']['karabo_da']\n",
- " calibration_name = calibrations[cc['calibration_id']]\n",
- " \n",
- " dtype = np.uint32 if calibration_name.startswith('BadPixels') else np.float32\n",
- " \n",
- " const_data[(da, calibration_name)] = dict(\n",
- " path=Path(ccv['path_to_file']) / ccv['file_name'],\n",
- " dataset=ccv['data_set_name'],\n",
- " data=const_load_mp.alloc(shape=(256, 256, mem_cells, 3), dtype=dtype)\n",
- " )\n",
- " print('.', end='', flush=True)\n",
- " \n",
+ " lpd_cal = LPD_CalibrationData(\n",
+ " detector_name=karabo_id,\n",
+ " modules=karabo_da,\n",
+ " sensor_bias_voltage=bias_voltage,\n",
+ " memory_cells=mem_cells,\n",
+ " feedback_capacitor=capacitor,\n",
+ " source_energy=photon_energy,\n",
+ " memory_cell_order=cell_ids_pattern_s,\n",
+ " category=category,\n",
+ " event_at=creation_time,\n",
+ " client=rest_cfg.calibration_client(),\n",
+ " caldb_root=Path(cal_db_root),\n",
+ " )\n",
+ " const_data = lpd_cal.ndarray_map([\"Offset\", \"BadPixelsDark\"])\n",
+ " try:\n",
+ " illum_const_data = lpd_cal.ndarray_map(lpd_cal.illuminated_calibrations)\n",
+ " for key, value in illum_const_data.items():\n",
+ " const_data.setdefault(key, {}).update(value)\n",
+ " except CalCatError as e: # TODO: replace when API errors are improved.\n",
+ " warning(f\"CalCatError: {e}\")\n",
"total_time = perf_counter() - start\n",
- "print(f'{total_time:.1f}s')"
+ "print(f'Loading constants {total_time:.1f}s')"
]
},
{
@@ -372,20 +306,22 @@
"metadata": {},
"outputs": [],
"source": [
- "def load_constant_dataset(wid, index, const_descr):\n",
- " ccv_entry = const_data[const_descr]\n",
- " \n",
- " with h5py.File(cal_db_root / ccv_entry['path'], 'r') as fp:\n",
- " fp[ccv_entry['dataset'] + '/data'].read_direct(ccv_entry['data'])\n",
- " \n",
- " print('.', end='', flush=True)\n",
- "\n",
- "print('Loading calibration data', end='', flush=True)\n",
- "start = perf_counter()\n",
- "const_load_mp.map(load_constant_dataset, list(const_data.keys()))\n",
- "total_time = perf_counter() - start\n",
- "\n",
- "print(f'{total_time:.1f}s')"
+ "# Validate the constants availability and raise/warn accordingly.\n",
+ "for mod, calibrations in const_data.items():\n",
+ " missing_offset = {\"Offset\"} - set(calibrations)\n",
+ " warn_missing_constants = {\n",
+ " \"BadPixelsDark\", \"BadPixelsFF\", \"GainAmpMap\",\n",
+ " \"FFMap\", \"RelativeGain\"} - set(calibrations)\n",
+ " if missing_offset:\n",
+ " warning(f\"Offset constant is not available to correct {mod}.\")\n",
+ " karabo_da.remove(mod)\n",
+ " if warn_missing_constants:\n",
+ " warning(f\"Constants {warn_missing_constants} were not retrieved for {mod}.\")\n",
+ "if not karabo_da: # Offsets are missing for all modules.\n",
+ " raise Exception(\"Could not find offset constants for any modules, will not correct data.\")\n",
+ "\n",
+ "# Remove skipped correction modules from data_to_process\n",
+ "data_to_process = [(mod, in_f, out_f) for mod, in_f, out_f in data_to_process if mod in karabo_da]"
]
},
{
@@ -411,11 +347,7 @@
"}\n",
"\n",
"def prepare_constants(wid, index, aggregator):\n",
- " consts = {calibration_name: entry['data']\n",
- " for (aggregator_, calibration_name), entry\n",
- " in const_data.items()\n",
- " if aggregator == aggregator_}\n",
- " \n",
+ " consts = const_data.get(aggregator, {})\n",
" def _prepare_data(calibration_name, dtype):\n",
" return consts[calibration_name] \\\n",
" .transpose(constant_order[calibration_name]) \\\n",
diff --git a/notebooks/LPD/LPD_retrieve_constants_precorrection.ipynb b/notebooks/LPD/LPD_retrieve_constants_precorrection.ipynb
index 419a9a43f18cfbb5c1ded27e4adcba718cce0e39..27b78bc715629114466f4dd7e6e845c494cc3381 100644
--- a/notebooks/LPD/LPD_retrieve_constants_precorrection.ipynb
+++ b/notebooks/LPD/LPD_retrieve_constants_precorrection.ipynb
@@ -47,8 +47,8 @@
"metadata": {},
"outputs": [],
"source": [
+ "from logging import warning\n",
"from pathlib import Path\n",
- "from time import perf_counter\n",
"\n",
"import numpy as np\n",
"\n",
@@ -57,12 +57,13 @@
"import extra_data as xd\n",
"\n",
"from cal_tools.lpdlib import get_mem_cell_pattern, make_cell_order_condition\n",
+ "import cal_tools.restful_config as rest_cfg\n",
+ "from cal_tools.calcat_interface import CalCatError, LPD_CalibrationData\n",
"from cal_tools.tools import (\n",
" CalibrationMetadata,\n",
" calcat_creation_time,\n",
- " save_constant_metadata,\n",
")\n",
- "from cal_tools.restful_config import restful_config"
+ "from cal_tools.step_timing import StepTimer"
]
},
{
@@ -87,6 +88,8 @@
" modules = list(range(16))\n",
"\n",
" karabo_da = [f'LPD{i:02d}' for i in modules]\n",
+ "else:\n",
+ " modules = [int(x[-2:]) for x in karabo_da]\n",
"\n",
"# List of detector sources.\n",
"det_inp_sources = [input_source.format(karabo_id=karabo_id, module_index=int(da[-2:])) for da in karabo_da]"
@@ -98,18 +101,7 @@
"metadata": {},
"outputs": [],
"source": [
- "# Connect to CalCat.\n",
- "calcat_config = restful_config['calcat']\n",
- "client = CalibrationClient(\n",
- " base_api_url=calcat_config['base-api-url'],\n",
- " use_oauth2=calcat_config['use-oauth2'],\n",
- " client_id=calcat_config['user-id'],\n",
- " client_secret=calcat_config['user-secret'],\n",
- " user_email=calcat_config['user-email'],\n",
- " token_url=calcat_config['token-url'],\n",
- " refresh_url=calcat_config['refresh-url'],\n",
- " auth_url=calcat_config['auth-url'],\n",
- " scope='')"
+ "step_timer = StepTimer()"
]
},
{
@@ -118,18 +110,8 @@
"metadata": {},
"outputs": [],
"source": [
- "dark_calibrations = {\n",
- " 1: 'Offset',\n",
- " 14: 'BadPixelsDark',\n",
- "}\n",
- "\n",
- "base_condition = [\n",
- " dict(parameter_name='Sensor Bias Voltage', value=bias_voltage),\n",
- " dict(parameter_name='Memory cells', value=mem_cells),\n",
- " dict(parameter_name='Feedback capacitor', value=capacitor),\n",
- " dict(parameter_name='Pixels X', value=256),\n",
- " dict(parameter_name='Pixels Y', value=256),\n",
- "]\n",
+ "step_timer.start()\n",
+ "\n",
"cell_ids_pattern_s = None\n",
"if use_cell_order != 'never':\n",
" # Read the order of memory cells used\n",
@@ -139,77 +121,57 @@
" )\n",
" print(\"Memory cells order:\", cell_ids_pattern_s)\n",
"\n",
- "if cell_ids_pattern_s is not None:\n",
- " dark_condition = base_condition + [\n",
- " dict(parameter_name='Memory cell order', value=cell_ids_pattern_s),\n",
- " ]\n",
- "else:\n",
- " dark_condition = base_condition.copy()\n",
- "\n",
- "illuminated_calibrations = {\n",
- " 20: 'BadPixelsFF',\n",
- " 42: 'GainAmpMap',\n",
- " 43: 'FFMap',\n",
- " 44: 'RelativeGain',\n",
- "}\n",
- "\n",
- "illuminated_condition = base_condition + [\n",
- " dict(parameter_name='Source Energy', value=photon_energy),\n",
- " dict(parameter_name='category', value=category)\n",
- "]"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": [
- "const_data = {}\n",
- "\n",
- "print('Querying calibration database', end='', flush=True)\n",
- "start = perf_counter()\n",
- "for k_da in karabo_da:\n",
- " pdu = None\n",
- " retrieved_constants[k_da] = dict()\n",
- " const_mdata = retrieved_constants[k_da][\"constants\"] = dict()\n",
- " for calibrations, condition in [\n",
- " (dark_calibrations, dark_condition),\n",
- " (illuminated_calibrations, illuminated_condition)\n",
- " ]:\n",
- " resp = CalibrationConstantVersion.get_closest_by_time_by_detector_conditions(\n",
- " client, karabo_id, list(calibrations.keys()),\n",
- " {'parameters_conditions_attributes': condition},\n",
- " karabo_da=k_da, event_at=creation_time.isoformat())\n",
- "\n",
- " if not resp[\"success\"]:\n",
- " print(f\"ERROR: Constants {list(calibrations.values())} \"\n",
- " f\"were not retrieved, {resp['app_info']}\")\n",
- " for cname in calibrations.values():\n",
- " if cname == 'Offset':\n",
- " raise Exception(\"Could not find offset constant, will not correct data\")\n",
- " const_mdata[cname] = dict()\n",
- " const_mdata[cname][\"file-path\"] = None\n",
- " const_mdata[cname][\"dataset-name\"] = None\n",
- " const_mdata[cname][\"creation-time\"] = None \n",
- " continue\n",
- "\n",
- " for ccv in resp[\"data\"]:\n",
- " cc = ccv['calibration_constant']\n",
- " cname = calibrations[cc['calibration_id']]\n",
- " const_mdata[cname] = dict()\n",
- " const_mdata[cname][\"file-path\"] = str(Path(ccv['path_to_file']) / ccv['file_name'])\n",
- " const_mdata[cname][\"dataset-name\"] = ccv['data_set_name']\n",
- " const_mdata[cname][\"creation-time\"] = ccv['begin_at']\n",
- " pdu = ccv['physical_detector_unit']['physical_name']\n",
- "\n",
- " print('.', end='', flush=True)\n",
- " retrieved_constants[k_da][\"physical-detector-unit\"] = pdu\n",
+ "lpd_cal = LPD_CalibrationData(\n",
+ " detector_name=karabo_id,\n",
+ " modules=karabo_da,\n",
+ " sensor_bias_voltage=bias_voltage,\n",
+ " memory_cells=mem_cells,\n",
+ " feedback_capacitor=capacitor,\n",
+ " source_energy=photon_energy,\n",
+ " memory_cell_order=cell_ids_pattern_s,\n",
+ " category=category,\n",
+ " event_at=creation_time,\n",
+ " client=rest_cfg.calibration_client(),\n",
+ ")\n",
+ "\n",
+ "# Initialize const_data in case no constants were retrieved.\n",
+ "lpd_cal_metadata = {mod: {\"no-constants-retrieved\": None} for mod in karabo_da}\n",
+ "\n",
+ "constant_data = lpd_cal.metadata([\"Offset\", \"BadPixelsDark\"])\n",
+ "try:\n",
+ " illum_const_data = lpd_cal.metadata(lpd_cal.illuminated_calibrations)\n",
+ " for key, value in illum_const_data.items():\n",
+ " const_data.setdefault(key, {}).update(value)\n",
+ "except CalCatError as e: # TODO: replace when API errors are improved.\n",
+ " warning(f\"CalCatError: {e}\")\n",
+ "\n",
+ "# Validate the constants availability and raise/warn correspondingly. \n",
+ "for mod, ccv_dict in lpd_cal_metadata.items():\n",
+ " missing_offset = {\"Offset\"} - set(ccv_dict)\n",
+ " warn_missing_constants = {\n",
+ " \"BadPixelsDark\", \"BadPixelsFF\", \"GainAmpMap\", \"FFMap\", \"RelativeGain\"} - set(ccv_dict)\n",
+ " if missing_offset:\n",
+ " warning(f\"Offset constant is not available to correct {mod}\")\n",
+ " karabo_da.remove(mod)\n",
+ " if warn_missing_constants:\n",
+ " warning(f\"Constants {warn_missing_constants} were not retrieved for {mod}.\")\n",
+ "if not karabo_da: # Offsets are missing for all modules.\n",
+ " raise Exception(\"Could not find offset constants for all modules, will not correct data.\")\n",
+ "\n",
+ "for mod, ccv_dict in lpd_cal_metadata.items():\n",
+ " mdata_dict = {\"constants\": dict()}\n",
+ " for cname, ccv_metadata in ccv_dict.items():\n",
+ " mdata_dict[\"constants\"][cname] = {\n",
+ " \"path\": str(lpd_cal.caldb_root / ccv_metadata[\"path\"]),\n",
+ " \"dataset\": ccv_metadata[\"dataset\"],\n",
+ " \"creation-time\": ccv_metadata[\"begin_validity_at\"],\n",
+ " \"ccv_id\": ccv_metadata[\"ccv_id\"],\n",
+ " }\n",
+ " mdata_dict[\"physical-name\"] = ccv_metadata[\"physical_name\"]\n",
+ " retrieved_constants[mod] = mdata_dict\n",
"metadata.save()\n",
"\n",
- "total_time = perf_counter() - start\n",
- "print(f'{total_time:.1f}s')\n",
- "print(f\"Stored retrieved constants in {metadata.filename}\")"
+ "step_timer.done_step(f\"Stored retrieved constants in {metadata.filename}.\")"
]
}
],
diff --git a/src/cal_tools/calcat_interface.py b/src/cal_tools/calcat_interface.py
index 1ad313f0a97f51ed2fc9f2b4e8eacb36a7d96598..bca8e5a3f08f75050537aac0d89c8e165bf373c4 100644
--- a/src/cal_tools/calcat_interface.py
+++ b/src/cal_tools/calcat_interface.py
@@ -1001,8 +1001,18 @@ class LPD_CalibrationData(SplitConditionCalibrationData):
"Pixels X",
"Pixels Y",
"Feedback capacitor",
+ "Memory cell order",
+ ]
+
+ illuminated_parameters = [
+ "Sensor Bias Voltage",
+ "Memory cells",
+ "Pixels X",
+ "Pixels Y",
+ "Feedback capacitor",
+ "Source Energy",
+ "category"
]
- illuminated_parameters = dark_parameters + ["Source Energy", "category"]
def __init__(
self,
@@ -1013,6 +1023,7 @@ class LPD_CalibrationData(SplitConditionCalibrationData):
pixels_x=256,
pixels_y=256,
source_energy=9.2,
+ memory_cell_order=None,
category=1,
modules=None,
client=None,
@@ -1034,6 +1045,7 @@ class LPD_CalibrationData(SplitConditionCalibrationData):
self.pixels_x = pixels_x
self.pixels_y = pixels_y
self.feedback_capacitor = feedback_capacitor
+ self.memory_cell_order = memory_cell_order
self.source_energy = source_energy
self.category = category