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Commit b5a84d76 authored by Thomas Kluyver's avatar Thomas Kluyver
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Remove unused ePix100 pre notebook

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1 merge request!821[ePix100] [Correct] Remove pre notebook
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notebooks/ePix100/ePix100_retrieve_constants_precorrection.ipynb deleted 100644 → 0
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%% Cell type:markdown id: tags:
# ePix100 retrieve constants precorrection
Author: European XFEL Detector Group, Version: 1.0
The following notebook provides constants for the selected ePix100 modules before executing correction on the selected sequence files.
%% Cell type:code id: tags:
``` python
in_folder = "/gpfs/exfel/exp/CALLAB/202031/p900113/raw" # input folder, required
out_folder = "/gpfs/exfel/data/scratch/ahmedk/test/remove/epix_correct" # output folder, required
metadata_folder = "" # Directory containing calibration_metadata.yml when run by xfel-calibrate
sequences = [-1] # sequences to correct, set to -1 for all, range allowed
run = 9988 # which run to read data from, required
# Parameters for accessing the raw data.
karabo_id = "MID_EXP_EPIX-1" # Detector Karabo_ID
karabo_da = "EPIX01" # data aggregators
receiver_template = "RECEIVER" # detector receiver template for accessing raw data files
instrument_source_template = '{}/DET/{}:daqOutput' # instrument detector data source in h5files
# Parameters for the calibration database.
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
cal_db_interface = "tcp://max-exfl016:8015#8025" # calibration DB interface to use
cal_db_timeout = 300000 # timeout on CalibrationDB requests
# Conditions for retrieving calibration constants.
bias_voltage = 200 # bias voltage
in_vacuum = False # detector operated in vacuum
fix_temperature = 290 # fixed temperature value in Kelvin. Default value -1 to use the value from files.
integration_time = -1 # Detector integration time, Default value -1 to use the value from the slow data.
gain_photon_energy = 9.0 # Photon energy used for gain calibration
# Flags to select type of applied corrections.
relative_gain = True # Apply relative gain correction.
```
%% Cell type:code id: tags:
``` python
from logging import warning
import numpy as np
from extra_data import RunDirectory
from pathlib import Path
import cal_tools.restful_config as rest_cfg
from cal_tools.calcat_interface import EPIX100_CalibrationData
from cal_tools.epix100 import epix100lib
from cal_tools.tools import (
calcat_creation_time,
CalibrationMetadata,
)
```
%% Cell type:code id: tags:
``` python
in_folder = Path(in_folder)
out_folder = Path(out_folder)
out_folder.mkdir(parents=True, exist_ok=True)
metadata = CalibrationMetadata(metadata_folder or out_folder)
# NOTE: this notebook will not overwrite calibration metadata file,
# if it already contains details about which constants to use.
retrieved_constants = metadata.setdefault("retrieved-constants", {})
```
%% Cell type:code id: tags:
``` python
creation_time = calcat_creation_time(in_folder, run, creation_time)
print(f"Using {creation_time.isoformat()} as creation time")
```
%% Cell type:code id: tags:
``` python
# Read control data.
run_dc = RunDirectory(in_folder / f"r{run:04d}")
ctrl_data = epix100lib.epix100Ctrl(
run_dc=run_dc,
instrument_src=f"{karabo_id}/DET/{receiver_template}:daqOutput",
ctrl_src=f"{karabo_id}/DET/CONTROL",
)
if integration_time < 0:
integration_time = ctrl_data.get_integration_time()
integration_time_str_add = ""
else:
integration_time_str_add = "(manual input)"
if fix_temperature < 0:
temperature = ctrl_data.get_temprature()
temperature_k = temperature + 273.15
temp_str_add = ""
else:
temperature_k = fix_temperature
temperature = fix_temperature - 273.15
temp_str_add = "(manual input)"
print(f"Bias voltage is {bias_voltage} V")
print(f"Detector integration time is set to {integration_time} \u03BCs {integration_time_str_add}")
print(f"Mean temperature: {temperature:0.2f}°C / {temperature_k:0.2f} K {temp_str_add}")
print(f"Operated in vacuum: {in_vacuum}")
```
%% Cell type:code id: tags:
``` python
epix_cal = EPIX100_CalibrationData(
detector_name=karabo_id,
sensor_bias_voltage=bias_voltage,
integration_time=integration_time,
sensor_temperature=temperature_k,
in_vacuum=in_vacuum,
source_energy=gain_photon_energy,
event_at=creation_time,
client=rest_cfg.calibration_client(),
)
mdata_dict = {"constants": dict()}
constant_names = ["OffsetEPix100", "NoiseEPix100"]
if relative_gain:
constant_names += ["RelativeGainEPix100"]
# Retrieve metadata for all epix100 constants.
epix_metadata = epix_cal.metadata(constant_names)[karabo_da]
# Validate the constants availability and raise/warn correspondingly.
missing_dark_constants = {"OffsetEPix100", "NoiseEPix100"} - set(epix_metadata)
if missing_dark_constants:
raise ValueError(
f"Dark constants {missing_dark_constants} are not available to correct {karabo_da}.")
if relative_gain and "RelativeGainEPix100" not in epix_metadata.keys():
warning("RelativeGainEPix100 is not found in CALCAT.")
for cname, ccv_metadata in epix_metadata.items():
mdata_dict["constants"][cname] = {
"path": str(epix_cal.caldb_root / ccv_metadata["path"]),
"dataset": ccv_metadata["dataset"],
"creation-time": ccv_metadata["begin_validity_at"],
"ccv_id": ccv_metadata["ccv_id"],
}
print(f"Retrieved {cname} with creation-time: {ccv_metadata['begin_validity_at']}")
mdata_dict["physical-name"] = ccv_metadata["physical_name"]
retrieved_constants[karabo_da] = mdata_dict
metadata.save()
print(f"Stored retrieved constants in {metadata.filename}")
```
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