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Commit af2f19eb authored by Philipp Schmidt's avatar Philipp Schmidt
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(fixup) Minor fixes to correction notebook

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notebooks/DynamicFF/Correct_DynamicFF_NBC.ipynb
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%% Cell type:markdown id: tags:
# Dynamic Flat-field Offline Correction
Author: Egor Sobolev
Offline dynamic flat-field correction
%% Cell type:code id: tags:
``` python
in_folder = "/gpfs/exfel/exp/SPB/202430/p900425/raw" # input folder, required
out_folder ="/gpfs/exfel/exp/SPB/202430/p900425/scratch/proc/r0003" # output folder, required
metadata_folder = "" # Directory containing calibration_metadata.yml when run by xfel-calibrate
run = 3 # which run to read data from, required
# Data files parameters.
karabo_da = ['-1'] # data aggregators
karabo_id = "SPB_MIC_HPVX2" # karabo prefix of Shimadzu HPV-X2 devices
# Database access parameters.
cal_db_interface = "tcp://max-exfl-cal001:8021" # calibration DB interface to use
cal_db_interface = "tcp://max-exfl-cal001:8021" # Unused, calibration DB interface to use
# Correction parameters
n_components = 20 # number of principal components of flat-field to use in correction
downsample_factors = [1, 1] # list of downsample factors for each image dimention (y, x)
num_proc = 32 # number of processes running correction in parallel
```
%% Cell type:code id: tags:
``` python
import os
import h5py
import warnings
from logging import warning
warnings.filterwarnings('ignore')
import numpy as np
import matplotlib.pyplot as plt
from IPython.display import display, Markdown
from datetime import datetime
from extra_data import RunDirectory, by_id
%matplotlib inline
from cal_tools.step_timing import StepTimer
from cal_tools.files import sequence_trains, DataFile
from cal_tools.tools import get_dir_creation_date
from cal_tools.restful_config import calibration_client, restful_config
from cal_tools.calcat_interface2 import CalibrationData, setup_client
from cal_tools.shimadzu import ShimadzuHPVX2
from dynflatfield import (
DynamicFlatFieldCorrectionCython as DynamicFlatFieldCorrection,
FlatFieldCorrectionFileProcessor
)
from dynflatfield.draw import plot_images, plot_camera_image
```
%% Cell type:code id: tags:
``` python
creation_time = get_dir_creation_date(in_folder, run)
print(f"Creation time is {creation_time}")
cc = calibration_client()
pdus = cc.get_all_phy_det_units_from_detector(
{"detector_identifier": karabo_id})
if not pdus["success"]:
raise ValueException("Failed to retrieve PDUs")
detector_info = pdus['data'][0]['detector']
detector = ShimadzuHPVX2(detector_info["source_name_pattern"])
index_group = detector.image_index_group
image_key = detector.image_key
print(f"Instrument {detector.instrument}")
print(f"Detector in use is {karabo_id}")
modules = {}
for pdu in pdus["data"]:
db_module = pdu["physical_name"]
module = pdu["module_number"]
da = pdu["karabo_da"]
if karabo_da[0] != "-1" and da not in karabo_da:
continue
instrument_source_name = detector.instrument_source(module)
corrected_source_name = detector.corrected_source(module)
print('-', da, db_module, module, instrument_source_name)
modules[da] = dict(
db_module=db_module,
module=module,
raw_source_name=instrument_source_name,
corrected_source_name=corrected_source_name,
)
step_timer = StepTimer()
```
%% Cell type:markdown id: tags:
# Calibration constants
%% Cell type:code id: tags:
``` python
# !!! REMOVE IT for production
# ---------------------------------------------------
from cal_tools.restful_config import restful_config
from cal_tools.calcat_interface2 import setup_client
calcat_config = restful_config.get('calcat')
setup_client( # won't be needed in production
#base_url=calcat_config['base-api-url'].rpartition('/')[0],
base_url='https://in.xfel.eu/test_calibration',
client_id=calcat_config['user-id'],
client_secret=calcat_config['user-secret'],
user_email=calcat_config['user-email'],
)
caldb_root = "/gpfs/exfel/d/cal_tst/caldb_store"
creation_time = datetime.now()
# ===================================================
step_timer.start()
dc = RunDirectory(f"{in_folder}/r{run:04d}")
conditions = detector.conditions(dc)
caldata = CalibrationData.from_condition(
conditions, 'SPB_MIC_HPVX2', event_at=creation_time)
aggregators = {}
corrections = {}
for da in modules:
try:
# !!! REMOVE caldb_root for production
dark = caldata["Offset", da].ndarray(caldb_root=caldb_root)
flat = caldata["DynamicFF", da].ndarray(caldb_root=caldb_root)
components = flat[1:][:n_components]
flat = flat[0]
dffc = DynamicFlatFieldCorrection.from_constants(
dark, flat, components, downsample_factors)
corrections[da] = dffc
file_da, _, _ = da.partition('/')
aggregators.setdefault(file_da, []).append(da)
except (KeyError, FileNotFoundError):
warning(f"Constants are not found for module {da}. "
"The module will not calibrated")
step_timer.done_step("Load calibration constants")
```
%% Cell type:markdown id: tags:
# Correction
%% Cell type:code id: tags:
``` python
# Output Folder Creation:
os.makedirs(out_folder, exist_ok=True)
report = []
for file_da, file_modules in aggregators.items():
dc = RunDirectory(f"{in_folder}/r{run:04d}", f"RAW-R{run:04d}-{file_da}-S*.h5")
# build train IDs
train_ids = set()
process_modules = []
for da in file_modules:
instrument_source = modules[da]["raw_source_name"]
if instrument_source in dc.all_sources:
keydata = dc[instrument_source][image_key].drop_empty_trains()
train_ids.update(keydata.train_ids)
process_modules.append(da)
else:
print(f"Source {instrument_source} for module {da} is missed")
train_ids = np.array(sorted(train_ids))
ts = dc.select_trains(by_id[train_ids]).train_timestamps().astype(np.uint64)
# correct and write sequence files
for seq_id, train_mask in sequence_trains(train_ids, 200):
step_timer.start()
print('* sequience', seq_id)
print('* sequence', seq_id)
seq_train_ids = train_ids[train_mask]
seq_timestamps = ts[train_mask]
dc_seq = dc.select_trains(by_id[seq_train_ids])
ntrains = len(seq_train_ids)
# create output file
channels = [f"{modules[da]['corrected_source_name']}/{index_group}"
for da in process_modules]
f = DataFile.from_details(out_folder, file_da, run, seq_id)
f.create_metadata(like=dc, instrument_channels=channels)
f.create_index(seq_train_ids, timestamps=seq_timestamps)
# create file structure
seq_report = {}
file_datasets = {}
for da in process_modules:
instrument_source = modules[da]["raw_source_name"]
keydata = dc_seq[instrument_source][image_key].drop_empty_trains()
count = keydata.data_counts()
i = np.flatnonzero(count.values)
count = keydata.data_counts(labelled=False)
i = np.flatnonzero(count)
raw_images = keydata.select_trains(np.s_[i]).ndarray()
# not pulse resolved
shape = keydata.shape
count = np.in1d(seq_train_ids, keydata.train_ids).astype(int)
corrected_source = modules[da]["corrected_source_name"]
src = f.create_instrument_source(corrected_source)
src.create_index(index_group=count)
# create key for images
ds_data = src.create_key(image_key, shape=shape, dtype=np.float32)
module_datasets = {image_key: ds_data}
# create keys for image parameters
for key in detector.copy_keys:
keydata = dc_seq[instrument_source][key].drop_empty_trains()
module_datasets[key] = (keydata, src.create_key(
key, shape=keydata.shape, dtype=keydata.dtype))
file_datasets[da] = module_datasets
step_timer.done_step("Create output file")
# correct and write data to file
for da in process_modules:
step_timer.start()
dc_seq = dc.select_trains(by_id[seq_train_ids])
dffc = corrections[da]
instrument_source = modules[da]["raw_source_name"]
proc = FlatFieldCorrectionFileProcessor(dffc, num_proc, instrument_source, image_key)
proc.start_workers()
proc.run(dc_seq)
proc.join_workers()
# not pulse resolved
corrected_images = np.stack(proc.rdr.results, 0)
file_datasets[da][image_key][:] = corrected_images
# copy image parameters
for key in detector.copy_keys:
keydata, ds = file_datasets[da][key]
ds[:] = keydata.ndarray()
seq_report[da] = (raw_images[0, 0], corrected_images[:20, 0])
step_timer.done_step("Correct flat-field")
f.close()
report.append(seq_report)
```
%% Cell type:code id: tags:
``` python
step_timer.start()
if report:
for da, (raw_image, corrected_images) in report[0].items():
source = modules[da]["raw_source_name"]
display(Markdown(f"## {source}"))
display(Markdown("### The first raw image"))
plot_camera_image(raw_images[0, 0])
plt.show()
display(Markdown("### The first corrected image"))
plot_camera_image(corrected_images[0])
plt.show()
display(Markdown("### The first corrected images in the trains (up to 20)"))
plot_images(corrected_images, figsize=(13, 8))
plt.show()
step_timer.done_step("Draw images")
```
%% Cell type:code id: tags:
``` python
print(f"Total processing time {step_timer.timespan():.01f} s")
step_timer.print_summary()
```
......
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