Evolution of calibration system of LCLS creates new opportunities and increase complexity. Large number of detectors and scripts for calibration processing makes it hard to track down what is going on. This note is intended to collect in one spot references to location of all intermediate repositories and log files.

Environment variables

psana/psdm

lcls1

source /cds/sw/ds/ana/conda1/manage/bin/psconda.sh, setup_testrel

export SIT_ROOT=/reg/g/psdm/
export SIT_DATA=/cds/group/psdm/data/
export SIT_PSDM_DATA=/cds/data/psdm/

in Detector/src/dir_root.py

DIR_ROOT = os.getenv('SIT_ROOT') # /reg/g/psdm/

DIR_LOG_AT_START = /cds/group/psdm/detector/logs/atstart/

DIR_REPO = /cds/group/psdm/detector/calib/constants/

lclc2

source /cds/sw/ds/ana/conda2/manage/bin/psconda.sh

export DIR_PSDM=/cds/group/psdm # or /sdf/group/psdm # s3df

in lcls2/psana/psana/detector/dir_root.py

DIR_ROOT = os.getenv('DIR_PSDM')

DIR_LOG_AT_START = /cds/group/psdm/detector/logs/atstart/

DIR_REPO = /cds/group/psdm/detector/calib2/constants/

s3df

lcls1

source /sdf/group/lcls/ds/ana/sw/conda1/manage/bin/psconda.sh, setup_testrel

export SIT_ROOT=/sdf/group/lcls/ds/ana/
export SIT_DATA=/sdf/group/lcls/ds/ana/data/
export SIT_PSDM_DATA=/sdf/data/lcls/ds/

lclc2

source /sdf/group/lcls/ds/ana/sw/conda2/manage/bin/psconda.sh

Repositories

Structure

Log files at start, in the script level directory, and detector-type level directory:

<DIR_LOG_AT_START>/<year>/<year>_lcls<1-or-2>_<script-name>.txt

<DIR_REPO>/scripts/<script-name>/logs/<year>/<time-stamp-of-processing>_log_<script-name>_<uid>.txt@ <<< this is a reference if processing script is completed.

<DIR_REPO>/<dettype>/logs/<year>/<time-stamp-of-processing>_log_<script-name>_<uid>.txt

panel aliases and per-panel calibration files:

<DIR_REPO>/<dettype>/.aliases.txt

<DIR_REPO>/<dettype>/<panel-id>/<calib-type>/<dettype>_<det-id-alias>_<YYYYMMSS<6-digit-μs>>_<experiment-name>_r<run-number>_<calib-type>.dat

Examples

/cds/group/psdm/detector/logs/atstart/2023/2023_lcls1_det_raw_pixel_status.txt

/cds/group/psdm/detector/calib/constants/scripts/det_raw_pixel_status/logs/2023/2023-04-21T103547_log_det_raw_pixel_status_dubrovin.txt@ <<< reference to:

/cds/group/psdm/detector/calib/constants/epix100a/logs/2023/2023-04-21T103547_log_det_raw_pixel_status_dubrovin.txt

Code Block

title	/cds/group/psdm/detector/calib/constants/epix100a/.aliases.txt
collapse	true

0001 3925999620-0996513537-2080374794-1794135040-0940361739-2398406657-0419430424 2023-04-21T08:26:51  xpplw3319 r0287 XppGon.0:Epix100a.3 dubrovin
0002 3925999620-0996579585-0553648138-1232098304-1221641739-2650251521-3976200215 2023-04-21T11:10:23  xpplw3319 r0287 XppGon.0:Epix100a.2 dubrovin
0003 3925999620-0996432897-3590324234-1232100352-1154532875-2654088449-0033554455 2023-04-21T11:10:33  xpplw3319 r0287 XppGon.0:Epix100a.1 dubrovin
0004 3925999620-1000248321-4076863498-1794137088-0410306571-2402454273-0067108888 2023-04-21T11:10:46  xpplw3319 r0287 XppGon.0:Epix100a.4 dubrovin

/cds/group/psdm/detector/calib/constants/epix100a/3925999620-0996513537-2080374794-1794135040-0940361739-2398406657-0419430424/status_data/epix100a_0001_20210716061106_xpplw3319_r0287_status_data.dat

LCLS scripts

in repository

logs/<Year>_epix10ka_pedestals_calibration.txt - log record on start

logs/<Year>reg/g/psdm/detector/gains/epix10k/panels/

in repository

logs/<Year> - log record on startlogs/<Year>

script	record at start	repository	logs	control parameters	comments	Generic area detectors
area detectors
calibrun	>ana-4.0.46-py3: $SIT_ROOT/detector/logs/atstart/2022/2022_lcls1_calibrun.txt	>ana-4.0.46-py3: $SIT_ROOT/detector/calib/constants/calibrun/calibrun	/reg/g/psdm/logs/calibman /<Year>/<Month> /<year>/<month>/<repository>/logs/2022/2022-10-12T103606_log_calibrun_dubrovin.txt >ana-4.0.46-py3: <repository>/logs/<year>/<time-stamp> - _log -<login>-<job-id> _calibrun_<login>.txt <repository>/logs/2022/2022-10-12T103606_log_calibrun_dubrovin.txt	N/A	CLI dark processing for generic detector
calibfile	/reg/g/psdm/logs/calibman /<Year>/<Month>/calibfile.txt - log record on copy file /<year>/<month>/calibfile.txt >ana-4.0.46-py3: $SIT_ROOT/detector/logs/atstart/2022/2022_lcls1_calibfile.txt	>ana-4.0.46-py3: $SIT_ROOT/detector/calib/constants/calibfile/	>ana-4.0.46-py3: <repository>/logs/<year>/<time-stamp>_log_calibfile_<login>.txt <repository>/logs/2022/2022-10-13T170608_log_calibfile_dubrovin.txt	-l, --lfname	CLI for calib file deployment under .../<experiment>/calib/...	DEPRECATED calibman_deprecated
geometry_deploy_constants	/reg/g/psdm/logs/atstart/<year>/<year>_lcls1_geometry_deploy_constants.txt >ana-4.0.46-py3: $SIT_ROOT/detector/logs/atstart/2022/2022_lcls1_geometry_deploy_constants.txt ./work	/reg/g/psdm /logs/calibman/<Year>/<Month>/<time-stamp>-log-<login>-<job-id>.txt	N/A	GUI for generic detector - dark processing, file manager, image browser etc. Why it is deprecated? Beside dark processing it has many other useful maintenance and browsing options.
epix10ka
/detector/calib/geometry/ >ana-4.0.46-py3: $SIT_ROOT/detector/calib/geometry	<repository>/<dettype>/<dettype>_<full-lcls1-detector-name>_<time-stamp>.data >ana-4.0.46-py3: <repository>/logs/<year>/<time-stamp>_log_geometry_deploy_constants_<login>.txt <repository>/logs/2022/2022-10-14T094805_log_geometry_deploy_constants_dubrovin.txt	-o, --dirrepo	Geometry calibration constants deployment CLI
dcs	/reg/g/psdm/logs/atstart/<year>/<year>_lcls1_dcs.txt >ana-4.0.46-py3: $SIT_ROOT/detector/logs/atstart/<year>/<year>_lcls1_dcs.txt	/reg/g/psdm/<INS>/<experiment>/calib/<dettype> # default experiment-detector repo or parameter -c <path to local calib> e.g.: -c /reg/d/psdm/detector/calib # detector-dependent repo >ana-4.0.46-py3: $SIT_PSDM_DATA/XPP/xpptut15/calib/epix100a $SIT_PSDM_DATA/detector/calib/epix100a	run-time only		Interaction with dcs-store - hdf5 file calibration constants.
deploy_constants for releases > ana-4.0.42	/reg/g/psdm/logs/atstart/<year>/<year>_lcls1_deploy_constants.txt >ana-4.0.46-py3: $SIT_ROOT/detector/logs/atstart/2022/2022_lcls1_deploy_constants.txt epix10ka_offset_calibration	/reg/g/psdm/detector/calib/constants/ >ana-4.0.46-py3: $SIT_ROOT/detector /gains/epix10k/panels/ /calib/constants/	<repository>/logs/<year>/<time-stamp>_log_deploy_constants_<uid>.txt <repository>/logs/2022/2022-10-14T105634_log_deploy_constants_dubrovin.txt	-o , --dirrepo	Deployment of default constants for all generic (one gain range) detectors. Special case of deployment with merging at `-t status_extra`
det_pixel_status	$SIT_ROOT/detector/logs/atstart/<year>/<year>_lcls1_det_pixel_status.txt /sdf/group/lcls/ds/ana/detector/logs/atstart/2023/2023_lcls1_det_pixel_status.txt	$SIT_ROOT/detector/calib/constants/	begins with: /sdf/group/lcls/ds/ana/detector/calib/constants/scripts/det_pixel_status/logs/<year>/<time-stamp>_log_det_pixel_status_<uid>.txt move at the end to: /sdf/group/lcls/ds/ana/detector/calib/constants/epix100a/logs/<year>/<time-stamp>_log_det_pixel_status_<uid>.txt	-o, --dirrepo	Light data processing for bad pixel status. See: Bad pixel mask ...

epix10ka
epix10ka_offset_calibration	<repository>/logs/<year> in repository logs/<Year>_epix10ka_offset_calibration.txt - log record on start >ana-4.0.37: /cds/group/psdm/logs/atstart/<year>/<year>_lcls1_epix10ka_offset_calibration.txt	/reg/g/psdm/detector/gains/epix10k/panels/	<repository>/logs/<year>logs/<Year>/<time-stamp>_log_epix10ka_offset_calibration_<login>.txt ????	-o, --dirrepo	Processing of the charge injection runs with 103 steps/calib-cycles
epix10ka_pedestals_calibration	<repository>/logs/<year>_epix10ka_pedestals_calibration.txt >ana-4.0.37: /cds/group/psdm/logs/atstart/<year>/<year>_lcls1_epix10ka_offset_calibration.txt	/reg/g/psdm/detector/gains/epix10k/panels/	<repository>/logs/<year>/<time-stamp>_log_epix10ka_pedestals_calibration_<login>.txt	-o, --dirrepo	Dark processing of runs with 5 steps/calib-cycles
epix10ka_deploy_constants	<repository>/	logs/<year>_epix10ka_deploy_constants.txt >ana-4.0.37: /cds/group/psdm/logs/atstart/<year>/<year>_lcls1_epix10ka_deploy_constants.txt		/reg/g/psdm/detector/gains/epix10k/panels/	<repository>/logs/<year>	/<time-stamp>_log_epix10ka_deploy_constants_<login>.txt	-o, --dirrepo	Merging and deployment ofper-panel constants.

Jungfrau
jungfrau_dark_proc	<repository>/logs/<year>_log_jungfrau_dark_proc.txt >ana-4.0.37: /cds/group/psdm/logs/atstart/<year>/<year>_lcls1_jungfrau_dark_proc.txt	/reg/g/psdm/detector/gains/jungfrau/panels/ contains per-panel constants	in repository logs/<Year>_log_jungfrau_dark_proc.txt - log record on start logs/<Year><repository>/logs/<year>/<time-stamp>_jungfrau_dark_proc_<login>.txt	-o, --dirrepo	replacement for jungfrau_ndarr_dark_proc intended for per-panel calibration constants. Dark processing of runs with 3 steps/calib-cycles
jungfrau_deploy_constants	<repository>/ reg/g/psdm/detector/gains/jungfrau/panels/ logs/<year>_log_jungfrau_deploy_constants.txt >ana-4.0.37: /cds/group/psdm/logs/atstart/<year>/<year>_lcls1 in repository logs/<Year>_log_jungfrau_deploy_constants.txt - log record on start	/reg/g/psdm/detector/gains/jungfrau/panels/	<repository>/logs/<year>logs/<Year>/<time-stamp>_jungfrau_deploy_constants_<login>.txt	-o, --dirrepo	works after jungfrau_dark_proc to merge and deploy constants under .../<experiment>/calib/...
jungfrau_gain_constants	>ana-4.0.44 /cds/group/psdm/logs/atstart/<year>/<year>_lcls1_jungfrau_gain_constants.txt	/reg/g/psdm/detector/gains/jungfrau/ - reference to dirs with gain constants for panel-ids	/reg/g/psdm/detectorlogs/calibcalibman/jungfrau_gain/<year>/jungfrau-<panel-id>.h5<time-stamp>-<experiment>-<run>-<login>.txt for >ana-4.0.44: /reg/g/psdm/ logs detector/ calibman gains/jungfrau _gain /logs/ <Year> <year>/<time-stamp> - _log_jungfrau_gain_constants_<experiment>- <run>- r<run>_<login>.txt	-R, --repdir
DEPRECATED jungfrau_ndarr_dark_proc			/reg/g/psdm/logs/calibman/<Year><year>/<Month><month>/jungfrau_ndarr_dark_proc.txt - log record on record at start		Dark processing and deployment of calibration constants for etire detector. It was DEPRECATED due to new per-panel approach to calibration constants. Replaced by jungfrau_dark_proc and jungfrau_deploy_constants

LCLS2 scripts

in repository

logs/log_epix10ka_pedestals_calibration_<Year>.txt - log record on start

TODO: move year ahead, add saving entire log under logs/<Year>/...-o, --dirrepo

script	record at start	repository	logs	control parameters	comments
Generic calibration manager
calibman	/cds/group/psdm/detector/logs/atstart/2023/2023_lcls2_calibman.txt	/cds/group/psdm/detector/calib2/constants/ DEPRECATED: /lcls2/cds/group/psdm/logs/calibman/lcls2/<Year>	<repository>/{scripts/<script-name> OR <dettype>}/logs/<year>/<time-stamp>-<script-name>-<login>.txt	-L, --logdir	Interaction with MongoDB etc

epix10ka
epix10ka_pedestals_calibration	/cds/group/psdm/logs/atstart/<year>/<year>_logrec_epix10ka_pedestals_calibration.txt	/cds/group/psdm/detector/calib2/constants/ DEPRECATED: /cds/group/psdm/detector/gains2/epix10ka/panels/	<repository>/{scripts/<script-name> OR <dettype>}/logs/<year>/	<time-stamp>-<script-name>-<login>.txt	-o, --dirrepo
epix10ka_deploy_constants	/cds/group/psdm/logs/atstart/<year>/<year>_logrec_epix10ka_deploy_constants.txt	/cds/group/psdm/detector/calib2/constants/ DEPRECATED: /cds/group/psdm/detector/gains2/epix10ka/panels/	<repository>/{scripts/<script-name> OR <dettype>}/logs/<year>/<time-stamp>-<script-name>-<login>.txt	-o, --dirrepo
epix10ka_charge_injection	/cds/group/psdm/detector/logs/atstart/2023/2023_lcls2_epix10ka_charge_injection.txt	/cds/group/psdm/detector/calib2/constants/

epix100, opal
det_dark_proc deploy_constants	/cds/group/psdm/detector/ gains2 logs/atstart/ epix10ka/	in repository logs/log_epix10ka_deploy_constants_<Year>.txt - log record on start TODO: move year ahead, add saving entire log under logs/<Year>/...	2023/2023_lcls2_det_dark_proc.txt DEPRECATED: /cds/group/psdm/logs/atstart/<year>/<year>_log_det_dark_proc.txt	/cds/group/psdm/detector/calib2/constants/	<repository>/{scripts/<script-name> OR <dettype>}/logs/<year>/<time-stamp>-<script-name>-<login>.txt

Tentative logging for LCLS2

Q: is it ok to save logs in repo?

A: if repodir is changed path will be loss along with local location. It would be nice to have record at start in well known static directory. Each record points to the main log file etc.

Logging at start records

Is intended to keep all records at start for all scripts in a single place.

Root directory is intended to be hardwired, e.g.

/cds/group/psdm/logs/atstart/

Further path

/cds/group/psdm/logs/atstart/<year>/<year>-logrec-<script-name>.txt - single file per year per script.

Repository

Root directory

-o, --dirrepo

/cds/group/psdm/detector/gains2/<detector-type>/panels/

/cds/group/psdm/detector/gains2/<detector-type>/panels/<panel-id>,

where <detector-type> e.g. epix10ka

Logging files

/cds/group/psdm/detector/gains2/<detector-type>/panels/logs/<year>/<time-stamp>-<script-name>-<login>.txt

Beginning November 4, 2024, login to Confluence and Jira will change. Read more.

Versions Compared

Old Version 3

New Version Current

Key

Environment variables

psana/psdm

lcls1

lclc2

s3df

lcls1

lclc2

Repositories

Structure

Examples

LCLS scripts

LCLS2 scripts

Tentative logging for LCLS2

Logging at start records

Repository

Root directory

Logging files

References

Beginning November 4, 2024, login to Confluence and Jira will change. Read more.

Page History

Versions Compared

Old Version 3

New Version Current

Key

Environment variables

psana/psdm

lcls1

lclc2

s3df

lcls1

lclc2

Repositories

Structure

Examples

LCLS scripts

LCLS2 scripts

Tentative logging for LCLS2

Logging at start records

Repository

Root directory

Logging files

References