In multi-panel composite detectors detector geometry constants are required to get arrays of pixel 3-d coordinates and derived objects. Mapping of correct constants with specific detector is a big issue if it is done manually. This note is about script automating/simplifying this job.
Command line interface
To get current information about geometry constants deployment script, use command:
geometry_deploy_constants -h
(ana-4.0.37) [<username>@psanagpu106:~/LCLS/con-py2]$ geometry_deploy_constants -e xpptut15 -r 320 -d XppGon.0:Cspad.0 -D -c ./calib -h
usage:
geometry_deploy_constants -e <experiment> -d <detector> -r <run-number> [-D] [-L <logging-mode>] [...]
REGULAR COMMAND EXAMPLE:
geometry_deploy_constants -e cxilu9218 -d CxiDs1.0:Jungfrau.0 -r238 --posz -100000 --posx 0 --posy 0 --rotz 90 -D --runrange 10-20
TEST COMMANDS:
Ex.1 for Cspad CXI : geometry_deploy_constants -e xpptut15 -r 380 -d CxiDs1.0:Cspad.0 -D -c ./calib
Ex.2 for Cspad CXI : geometry_deploy_constants -e xpptut15 -r 380 -d CxiDs2.0:Cspad.0 -D -c ./calib
Ex.3 for Cspad XPP : geometry_deploy_constants -e xpptut15 -r 320 -d XppGon.0:Cspad.0 -D -c ./calib
Ex.4 for cspad2x2 : geometry_deploy_constants -e xpptut15 -r 460 -d MecTargetChamber.0:Cspad2x2.3 -D -c ./calib --posz -100000 --posx 10 --posy -20 --rotz 90
Ex.5 for jungfrau512k : geometry_deploy_constants -e xpptut15 -r 410 -d MfxEndstation.0:Jungfrau.1 -D -c ./calib
Ex.6 for jungfrau1M : geometry_deploy_constants -e xpptut15 -r 430 -d MfxEndstation.0:Jungfrau.0 -D -c ./calib
Ex.7 for jungfrau4M : geometry_deploy_constants -e xpptut15 -r 530 -d DetLab.0:Jungfrau.2 -D -c ./calib
Ex.8 for epix10ka2m : geometry_deploy_constants -e xpptut15 -r 570 -d MfxEndstation.0:Epix10ka2M.0 -D -c ./calib
Ex.9 for epix100a : geometry_deploy_constants -e xpptut15 -r 260 -d XcsEndstation.0:Epix100a.1 -D -c ./calib
Ex.10 for pnCCD : geometry_deploy_constants -e xpptut15 -r 450 -d Camp.0:pnCCD.1 -D -c ./calib
Ex.11 for epix10kaquad : geometry_deploy_constants -e xpptut15 -r 590 -d MecTargetChamber.0:Epix10kaQuad.0 -D -c ./calib
Ex.12 for epix10kaquad : geometry_deploy_constants -e xpptut15 -r 590 -d MecTargetChamber.0:Epix10kaQuad.1 -D -c ./calib
Ex.13 for epix10kaquad : geometry_deploy_constants -e xpptut15 -r 590 -d MecTargetChamber.0:Epix10kaQuad.2 -D -c ./calib
Ex.14 for epix10kaquad : geometry_deploy_constants -e xpptut15 -r 590 -d MecTargetChamber.0:Epix10kaQuad.3 -D -c ./calib
Help: geometry_deploy_constants -h
Deployment of geometry calibration parameters
optional arguments:
-h, --help show this help message and exit
-e EXP, --exp EXP experiment name, default = None
-d DET, --det DET detector name, default = None
-r RUN, --run RUN run number of the existing dataset to get run time-
stamp, detector full name etc., default = None
-t TSTAMP, --tstamp TSTAMP
non-default time stamp (<YYYYmmddHHMMSS) or run
number(<10000) for constants selection in repo. By
default run time is used, default = None
-s DSSUFFIX, --dssuffix DSSUFFIX
dataset name suffix beyond
exp=<expname>:run=<runnum><dssuffix>, for example
":smd:dir=<path>/xtc/", default = None
-x DSNAME, --dsname DSNAME
overrides exp=<expname>:run=<runnum><dssuffix> if
specified, e.g. path to *.xtc file, default = None
-o DIRREPO, --dirrepo DIRREPO
non-default repository of calibration results, default
= /reg/g/psdm/detector/calib/geometry/
-c DIRCALIB, --dircalib DIRCALIB
deployment calib directory if different from standard
one, default = None
-l LOGLEV, --loglev LOGLEV
logging mode, one of INFO, CRITICAL, WARN, WARNING,
ERROR, DEBUG, NOTSET, default = INFO
--dirmode DIRMODE mode for all mkdir, default = 511
--filemode FILEMODE mode for all saved files, default = 438
-D, --deploy deploy constants to the calib dir, default = False
-R RUNRANGE, --runrange RUNRANGE
validity run range for output calibration file,
default = 0-end
--parent PARENT parent frame name containing the detector geometry
object, default = IP
--posx POSX detector position x[um] relative IP, default =
0.000000
--posy POSY detector position y[um] relative IP, default =
0.000000
--posz POSZ detector position z[um] relative IP, default =
-100000.000000
--rotx ROTX detector rotation angle [degree] around axis x,
default = 0.000000
--roty ROTY detector position angle [degree] around axis y,
default = 0.000000
--rotz ROTZ detector position angle [degree] around axis z,
default = 0.000000
Algorithm
Command geometry_deploy_constants <parameters> checks experiment (-e, –-exp) run (-r, –-run) information for requested detector (-d, –-det), finds the run time stamp, finds appropriate file with geometry constants in the repository (-o, --dirrepo), changes detector orientation, apply translation relative IP (if parameters --parent, --pos*, --rot* specified) and deploys constants under <experiment>/calib directory, or directory specified by parameter (-c, --calibdir). Results of this command, depending on parameter (-l, --loglev), are dumped on terminal and preserved in the logfile
<dirrepo>/logs/<year>/<time-stamp>_log_geometry_deploy_constants_<user-login-name>.txt
Repository
Conventions about repository containing files with geometry calibration constants.
Currently -o,--dirrepo is set to /reg/g/psdm/detector/calib/geometry/
(ana-4.0.37) [<username>@psanagpu106:/reg/g/psdm/detector/calib/geometry]$ ls -l
total 4
drwxr-xr-x 1 dubrovin br 0 Mar 22 14:13 andor
drwxr-xr-x 1 dubrovin br 0 Mar 22 14:08 andor3d
drwxrwxr-- 1 dubrovin br 0 Mar 24 11:30 cspad
drwxrwxr-- 1 dubrovin br 0 Mar 24 11:55 cspad2x2
drwxrwxr-- 1 dubrovin br 0 Mar 24 12:00 epix100a
drwxrwxr-- 1 dubrovin br 0 Mar 23 14:54 epix10ka
drwxr-xr-x 1 dubrovin br 0 Mar 24 12:14 epix10ka2m
drwxr-xr-x 1 dubrovin br 0 Mar 24 13:42 epix10kaquad
drwxrwxr-- 1 dubrovin br 0 Mar 23 10:14 jungfrau
drwxrwxrwx 1 dubrovin br 0 Mar 15 09:55 logs
drwxrwxr-- 1 dubrovin br 0 Mar 17 15:02 pnccd
drwxr-xr-x 1 dubrovin br 0 Mar 22 09:33 rayonix
and beside logfiles under subdirectory logs/ it contains directories for "all" detector types which need in geometry constants.
Currently repository is fully populated for cspad, cspad2x2, epix100a, epix10ka, epix10ka2m, epix10kaquad, jungfrau, pnccd. If other detector(s) required they need to be populated here.
/reg/g/psdm/detector/calib/geometry]$ ls -l1 epix10ka2m
total 68
-rw-r--r-- 1 dubrovin br 3662 Mar 22 13:16 2018-11-15-geometry-epix10ka2m.txt
-rw-r--r-- 1 dubrovin br 3720 Mar 22 13:15 2020-02-25-geometry-epix10ka2m.1-v0-z0.txt
-rw-r--r-- 1 dubrovin br 3350 Mar 22 13:15 2020-02-25-geometry-epix10ka2m.1-v1-mfxc00118-0044-z0.txt
-rw-r--r-- 1 dubrovin br 3355 Mar 22 13:14 2020-02-25-geometry-epix10ka2m.1-v1-mfxc00318-0013-z0.txt
-rw-r--r-- 1 dubrovin br 3268 Mar 22 13:15 2020-06-25-geometry-epix10ka2m.0-v1.txt
-rw-r--r-- 1 dubrovin br 3424 Mar 22 13:14 2020-09-10-geometry-epix10ka2m.1-v1-cortilt-center.txt
-rw-r--r-- 1 dubrovin br 3340 Mar 22 11:12 2021-02-02-geometry-epix10ks2m.1-recentred-for-psana.txt
-rw-r--r-- 1 dubrovin br 3267 Mar 22 11:12 2021-02-02-geometry-epix10ks2m.1.txt
-rw-r--r-- 1 dubrovin br 3355 Mar 22 13:21 epix10ka2m_default.data
lrwxrwxrwx 1 dubrovin br 42 Mar 22 10:50 epix10ka2m_MfxEndstation-0-Epix10ka2M-0_20200225.data -> 2020-02-25-geometry-epix10ka2m.1-v0-z0.txt
lrwxrwxrwx 1 dubrovin br 54 Mar 22 10:55 epix10ka2m_MfxEndstation-0-Epix10ka2M-0_20200910.data -> 2020-09-10-geometry-epix10ka2m.1-v1-cortilt-center.txt
lrwxrwxrwx 1 dubrovin br 56 Mar 22 13:09 epix10ka2m_MfxEndstation-0-Epix10ka2M-0_20210202.data -> 2021-02-02-geometry-epix10ks2m.1-recentred-for-psana.txt
lrwxrwxrwx 1 dubrovin br 34 Mar 22 10:43 epix10ka2m_XcsEndstation-0-Epix10ka2M-0_20181115.data -> 2018-11-15-geometry-epix10ka2m.txt
lrwxrwxrwx 1 dubrovin br 39 Mar 22 10:45 epix10ka2m_XppGon-0-Epix10ka2M-0_20200625.data -> 2020-06-25-geometry-epix10ka2m.0-v1.txt
Script finds path to the geometry file using its name conventions:
<dirrepo>/<det-type>/<dettype>_<full-lcls1-detector-name>_<time-stamp>.data
where the time-stamp is presented in format YYYYMMDD (it is assumed that optical metrology or variation of geometry constants do not need to be changed more often than once per day...).
If geometry file for specified detector and time-stamp is missing, constants from <dettype>_default.data will be loaded.
Tracking down possible issues
From log-file (or dump on terminal) it should be quite clear what script is doing and what problem might be. Please pay attention that
- script grabs expected file for requested detector and time-stamp
- check if the geometry file in its final destination under the calib/ directory is available and not empty
- please report about any issues
References