Multi-panel composite detector needs in geometry constants 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
To get current information about geometry constants deployment script and examples, 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.
Default geometry modification
Command parameters allow to make a few modifications to the default geometry file before deployment. These modifications include detector position and orientation and Rayonix segment binning.
Position and orientation
Camera position and orientation parameters (--posx/y/z, and --rotx/y/z) are included in the geometry file line beginning with "IP" (which by default set in by parameter --parent IP). It is assumed that all files in repository should have the line beginning with "IP". Otherwise, parameter --parent can be changed.
Rayonix binning
Default geometry file for Rayonix /reg/g/psdm/detector/calib/geometry/rayonix/rayonix_default.data has pre-defined segment description like MTRX:V2:3840:3840:44.5:44.5, that can be changed by experiment dependent binning. For detector of type rayonix this string parameters are compared with parameters from configuration object for specified experiment (-e EXP, --exp EXP) and run number (-r RUN, --run RUN). Segment binning values from configuration are substituted, e.g. for xpptut15 run 240 this line is replaced with MTRX:V2:1920:1920:88:88. For backward compatibility of already deployed geometry files similar check and substitution is done on flight at geometry loading in the Detector.geoaccess, check_rayonix_geo methods (requested by Chuck).
Troubleshooting
From log-file or dump on terminal
(ana-4.0.37) [dubrovin@psanagpu106:~/LCLS/con-py2]$ geometry_deploy_constants -e xpptut15 -r 460 -d MecTargetChamber.0:Cspad2x2.3 -D -c ./calib --posz -100000 --posx 10 --posy -20 --rotz 90
Arguments: Namespace(deploy=True, det='MecTargetChamber.0:Cspad2x2.3', dircalib='./calib', dirmode=511, dirrepo='/reg/g/psdm/detector/calib/geometry/', dsname=None, dssuffix=None, exp='xpptut15', filemode=438, loglev='INFO', parent='IP', posx=10.0, posy=-20.0, posz=-100000.0, rotx=0, roty=0, rotz=90.0, run='460', runrange='0-end', tstamp=None)
[I] geometry_deploy_constants L0131 log file: /reg/g/psdm/detector/calib/geometry/logs/2022/2022-03-25T104317_log_geometry_deploy_constants_dubrovin.txt
[I] UtilsCalib.py L0305 record at start:
2022-03-25T10:43:17 user:dubrovin@psanagpu106 cwd:/cds/home/d/dubrovin/LCLS/con-py2 rel:ana-4.0.37 dirrepo:/reg/g/psdm/detector/calib/geometry command:/cds/home/d/dubrovin/LCLS/con-py2/arch/x86_64-rhel7-gcc48-opt/bin/geometry_deploy_constants -e xpptut15 -r 460 -d MecTargetChamber.0:Cspad2x2.3 -D -c ./calib --posz -100000 --posx 10 --posy -20 --rotz 90
saved in: /reg/g/psdm/logs/atstart/2022/2022_lcls1_geometry_deploy_constants.txt
[I] UtilsGeometryDeploy.py L0032 input parameters
roty : 0
rotx : 0
dirrepo : /reg/g/psdm/detector/calib/geometry/
rotz : 90.0
run : 460
exp : xpptut15
parent : IP
deploy : True
det : MecTargetChamber.0:Cspad2x2.3
posy : -20.0
dsname : None
dircalib : ./calib
tstamp : None
loglev : INFO
dssuffix : None
dirmode : 511
posx : 10.0
filemode : 438
posz : -100000.0
runrange : 0-end
repoman : <Detector.UtilsCalib.RepoManager object at 0x7f9443b06350>
[I] UtilsGeometryDeploy.py L0054 open dataset exp=xpptut15:run=460
[I] UtilsGeometryDeploy.py L0065 directory for dettype: /reg/g/psdm/detector/calib/geometry/cspad2x2
[I] UtilsGeometryDeploy.py L0070 list of found in repository geometry files for dettype_detname: cspad2x2_MecTargetChamber-0-Cspad2x2-3
cspad2x2_MecTargetChamber-0-Cspad2x2-3_20130213.data
cspad2x2_MecTargetChamber-0-Cspad2x2-3_20150402.data
cspad2x2_MecTargetChamber-0-Cspad2x2-3_20140425.data
[I] UtilsGeometryDeploy.py L0076 file_for_timestamp(tsrun=20130428): /reg/g/psdm/detector/calib/geometry/cspad2x2/cspad2x2_MecTargetChamber-0-Cspad2x2-3_20130213.data
[I] UtilsGeometryDeploy.py L0086 geo_det: parent: IP 0 geo: CSPAD2X2:V1 0 x0: 0 y0: 0 z0:-1000000 rot_z: 0.000 rot_y: 0.000 rot_x: 0.000 tilt_z: 0.00000 tilt_y: 0.00000 tilt_x: 0.00000
[I] UtilsGeometryDeploy.py L0095 geo_det updated: parent: IP 0 geo: CSPAD2X2:V1 0 x0: 10 y0: -20 z0: -100000 rot_z: 90.000 rot_y: 0.000 rot_x: 0.000 tilt_z: 0.00000 tilt_y: 0.00000 tilt_x: 0.00000
[I] GeometryAccess.py L0263 Save file: /reg/g/psdm/detector/calib/geometry/cspad2x2/cspad2x2_tmp.data
[I] UtilsGeometryDeploy.py L0104 standard calib dir: /reg/d/psdm/XPP/xpptut15/calib
[I] UtilsGeometryDeploy.py L0105 non-default calib dir: ./calib
[I] UtilsGeometryDeploy.py L0114 deploy calib file /reg/g/psdm/detector/calib/geometry/cspad2x2/cspad2x2_tmp.data under ./calib/CsPad2x2::CalibV1/MecTargetChamber.0:Cspad2x2.3/geometry
create_path: ./calib/CsPad2x2::CalibV1/MecTargetChamber.0:Cspad2x2.3/geometry/0-end.data
Directory exists: .
Directory exists: ./calib
Directory exists: ./calib/CsPad2x2::CalibV1
Directory exists: ./calib/CsPad2x2::CalibV1/MecTargetChamber.0:Cspad2x2.3
Directory exists: ./calib/CsPad2x2::CalibV1/MecTargetChamber.0:Cspad2x2.3/geometry
cmd: cat /reg/g/psdm/detector/calib/geometry/cspad2x2/cspad2x2_tmp.data > ./calib/CsPad2x2::CalibV1/MecTargetChamber.0:Cspad2x2.3/geometry/0-end.data
cmd: echo "file:0-end.data copy_of:/reg/g/psdm/detector/calib/geometry/cspad2x2/cspad2x2_tmp.data ctype:geometry user:dubrovin host:psanagpu106 cptime:2022-03-25T10:43:18 cwd:/cds/home/d/dubrovin/LCLS/con-py2 cmt:" >> ./calib/CsPad2x2::CalibV1/MecTargetChamber.0:Cspad2x2.3/geometry/HISTORY
(ana-4.0.37) [dubrovin@psanagpu106:~/LCLS/con-py2]$
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