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Commit b5ef7995 authored by Karim Ahmed's avatar Karim Ahmed
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New notebook for injecting constants from stored h5files

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notebooks/LPD/inject_calibration_constants_from_h5files.ipynb 0 → 100644
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View file @ b5ef7995
%% Cell type:markdown id: tags:
# Injecting calibration constant data to the database #
Author: European XFEL Detector Group, Version: 1.0
Reading h5files of calibration constants to inject them to the database. Used for LPD
%% Cell type:code id: tags:
``` python
# calibration constant parameters:
constant_names = ["GainMap", "GainAmpMap", "FFMap", "BadPixelsFF"] # calibration constant name, required.
in_folder = "/gpfs/exfel/data/scratch/yousefh/LPD_CalinConst_Provisional/" # calibration constant file, required.
proposal = "" # Add proposal number to be sent to the database as a part of Raw data location.
runs = [] # Add list of runs to be sent to the database as a part of Raw data location.
# detector parameters:
karabo_id = "FXE_DET_LPD1M-1" # detector identifier, required.
karabo_da = ["LPD00"] # karabo data aggregators, required.
# calibration database parameters:
cal_db_interface = "tcp://max-exfl017:8020"
# calibration constant conditions:
memory_cells = 512
bias_voltage = 250
capacitor = 5
creation_time = '2020-01-20T14:12:06' # creation time for the injected constants. required format '2019-01-20T14:12:06'
```
%% Cell type:code id: tags:
``` python
import datetime
import h5py
from pathlib import Path
from iCalibrationDB import (
Constants,
Conditions,
)
from cal_tools.tools import (
get_from_db,
get_pdu_from_db,
send_to_db,
)
```
%% Cell type:code id: tags:
``` python
pixels_x = pixels_y = 256
# if proposal or runs are given assign file_loc
# for calibration constant versions metadata.
file_loc = ""
if proposal:
file_loc += f"proposal:{proposal}"
if len(runs) > 0:
file_loc += f"runs: {runs}"
if file_loc == ""
print(
"No proposal or runs were given for constant source."
" No \"Raw data location\" will be injected with the constants"
)
```
%% Cell type:code id: tags:
``` python
def validate_input_paths(in_folder):
# Validate input parameters:
if not (in_folder):
raise ValueError(
"ERROR: \"in_folder\" is not given."
" Please provide the constants input folder."
)
c_folder = Path(in_folder)
if not c_folder.isdir():
raise ValueError(
f"ERROR: in_folder {in_folder} directory doesn't exist."
)
try:
creation_time = datetime.datetime.strptime(creation_time, '%Y-%m-%dT%H:%M:%S')
except ValueError:
raise ValueError("Incorrect data format, should be YYYY-MM-DDTHH:MM:SS i.e. 2019-01-20T14:12:06")
return c_folder, creation_time
```
%% Cell type:code id: tags:
``` python
c_folder, creation_time = validate_input_paths(in_folder)
# create a report path for calibration constant versions metadata.
report_path = get_report(
out_folder=in_folder,
default_path=f"No_report/LPD_{datetime.datetime.now().strftime('%Y-%m-%dT%H:%M:%S')}"
)
# Calibration constants condition object.
condition = Conditions.Dark.LPD(
memory_cells=memory_cells,
bias_voltage=bias_voltage,
pixels_x=pixels_x,
pixels_y=pixels_y,
capacitor=capacitor,
)
mod_mapping = {}
for const in constant_names:
# Calibration constant object.
constant = getattr(Constants.LPD, const)()
if len(mod_mapping.keys()) == 0
# Retrieve the detector modules if it is not known.
physical_units = get_pdu_from_db(
karabo_id=karabo_id,
karabo_da=karabo_da,
constant=constant,
condition=condition,
cal_db_interface=cal_db_interface,
snapshot_at=creation_time
)
mod_mapping = dict(zip(karabo_da, physical_units))
print("Physical detector units retrieved are: ", mod_mapping)
for pdu, k_da in zip(physical_units, karabo_da):
cfile = c_folder / f"{const}_{k_da}"
# load constant data.
with h5py.File(cfile, "r") as f:
cdata = f[const][()]
# Validate for only LPD at the moment.
if not cdata.shape == (pixels_x, pixels_y, memory_cells, 3):
raise ValueError(
f"ERROR: {const} constant data shape is not as expected."
f" {cdata.shape} != ({pixels_x}, {pixels_y}, {memory_cells}, 3)."
)
constant.data = cdata
md = send_to_db(
db_module=pdu,
karabo_id=karabo_id,
constant=constant,
condition=condition,
file_loc=file_loc,
report_path=report_path,
cal_db_interface=cal_db_interface,
creation_time=creation_time,
)
```
%% Output
No proposal or runs were given for constant source. No "Raw data location" will be injected with the constants
Physical detector units retrieved are: {'LPD00': 'LPD_SIV1_LPDV2_SM015'}
BadPixelsFF is injected with creation-time: 2020-01-20 14:12:06
src/cal_tools/tools.py
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− 2
View file @ b5ef7995
......@@ -373,13 +373,13 @@ def get_random_db_interface(cal_db_interface):
return cal_db_interface
def get_report(out_folder: str):
def get_report(out_folder: str, default_path: str = ""):
"""Get the report path from calibration_metadata.yml
stored in the out_folder.
"""
metadata = CalibrationMetadata(out_folder)
report_path = metadata.get("report-path", "")
report_path = metadata.get("report-path", default_path)
if not report_path:
print("WARNING: No report path will be injected "
"with the constants.\n")
......
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