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These commands can be executed in psana (1) environment.

Panel constants repository and file naming conventions

Currently per-panel calibration constants resides under directory called as "repository"

/reg/g/psdm/detector/gains/epix10k/panels/

/reg/g/psdm/detector/gains/epix10k/panels/logs/

/reg/g/psdm/detector/gains/epix10k/panels/<panel-id>/<calibration-type>/<file-name.dat/txt>

The panel constants file name consists of fields to provide unique self-describing content

<panel-type>_<panel-id-short-number>-<timestamp-as-YYYYmmDDHHMMSS>_<experiment>_r<run-number>_<calibration-type>_<gain-range>.dat

for example 

epix10ka_0110_20210727105515_detdaq19_r0082_pedestals_FH.dat

See more in EPIX10KA Per-panel calibration constants

Example of commands

Examples assume that processing is done on 2020-07-14 on detdaq18 run 80 or 92. These parameters needs to substututed for real be substituted in actual processing.

Offset and gain calibration

Regular offset and gain calibration

Script epix10ka_offset_calibration works on special runs containing 103 calib-cycles =  5 dark + 2 x (7x7) charge injection.

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List of commands to process all panels in batch:

bsub -o 2020-07-14-r92-offset-log00 -q psanaq epix10ka_offset_calibration -e detdaq18 -d DetLab.0:Epix10ka2M.0 -r92 -i0  -p
bsub -o 2020-07-14-r92-offset-log01 -q psanaq epix10ka_offset_calibration -e detdaq18 -d DetLab.0:Epix10ka2M.0 -r92 -i1  -p
bsub -o 2020-07-14-r92-offset-log02 -q psanaq epix10ka_offset_calibration -e detdaq18 -d DetLab.0:Epix10ka2M.0 -r92 -i2  -p
bsub -o 2020-07-14-r92-offset-log03 -q psanaq epix10ka_offset_calibration -e detdaq18 -d DetLab.0:Epix10ka2M.0 -r92 -i3  -p
bsub -o 2020-07-14-r92-offset-log04 -q psanaq ...
epix10ka_offset_calibration -e detdaq18 -d DetLab.0:Epix10ka2M.0 -r92 -i4 i15 -p

bsub#in -o 2020-07-14-r92-offset-log05 -q psanaq epix10ka_offset_calibration -e detdaq18 -d DetLab.0:Epix10ka2M.0 -r92 -i5  -pbatch (should be in slurm now)
bsub -o 2020-07-14-detdaq18-r92-offset-log06log15 -q psanaq epix10ka_offset_calibration -e detdaq18 -d DetLab.0:Epix10ka2M.0 -r92 -i6 i15 -p
bsub -o 2020-07-14-r92-offset-log07 -q psanaq epix10ka_offset_calibration -e detdaq18 -d DetLab.0:Epix10ka2M.0 -r92 -i7  -p
bsub -o 2020-07-14-r92-offset-log08 -q psanaq epix10ka_offset_calibration -e detdaq18 -d DetLab.0:Epix10ka2M.0 -r92 -i8  -p
bsub -o 2020-07-14-r92-offset-log09 -q psanaq epix10ka_offset_calibration -e detdaq18 -d DetLab.0:Epix10ka2M.0 -r92 -i9  -p
bsub -o 2020-07-14-r92-offset-log10 -q psanaq epix10ka_offset_calibration -e detdaq18 -d DetLab.0:Epix10ka2M.0 -r92 -i10 -p
bsub -o 2020-07-14-r92-offset-log11 -q psanaq epix10ka_offset_calibration -e detdaq18 -d DetLab.0:Epix10ka2M.0 -r92 -i11 -p
bsub -o 2020-07-14-r92-offset-log12 -q psanaq epix10ka_offset_calibration -e detdaq18 -d DetLab.0:Epix10ka2M.0 -r92 -i12 -p
bsub -o 2020-07-14-r92-offset-log13 -q psanaq epix10ka_offset_calibration -e detdaq18 -d DetLab.0:Epix10ka2M.0 -r92 -i13 -p
bsub -o 2020-07-14-r92-offset-log14 -q psanaq epix10ka_offset_calibration -e detdaq18 -d DetLab.0:Epix10ka2M.0 -r92 -i14 -p
bsub -o 2020-07-14-r92-offset-log15 -q psanaq epix10ka_offset_calibration -e detdaq18 -d DetLab.0:Epix10ka2M.0 -r92 -i15 -p

To save batch log files for references in future please move them by command:

mv 2020-07-14-r92-offset-log* /reg/g/psdm/detector/gains/epix10k/panels/logs/

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Log files can be found in:

/reg/g/psdm/detector/gains/epix10k/panels/logs/

If everything in log files looks fine, they have the same size, then per-panel-per-gain-range constants needs to be merged and deployed.

Alternative offset calibration

Regular offset calibration procedure is complicated and may not be available for new detectors.

If the offset files are missing in the directory /reg/g/psdm/detector/gains/epix10k/panels/<panel-id>/offset/

pedestals for gain switching modes created by command epix10ka_deploy_constants will be zeros.

Philip has developed a script to populate the panel offset directory with files of type offsetph like

epix10ka_0110_20210513000001_detdaq19_r0082_offsetph_AML.dat

Hart, Philip Adam <philiph@slac.stanford.edu> Wed 10/13/2021 12:48 PM
JFTR, under ~/philiph/psana/mfxc00118/mfxlx4219
I have run
python deployOfficial10kOffsetsV2.py MFX
source deploy_offsetph_constants.sh
with output
2021-10-13-r384-log-epix10ka-deploy-constants
and now we have what look like sensible AML-L pedestals.
Bhavna, we should officialize this during in a calm in the storm.
Thanks,
Philip

Example for population of the offset directory with correct names is in

https://github.com/lcls-psana/Detector/blob/master/examples/ex_epix10ka_save_ctype_in_repo.py

Formulae for pedestals of AML-L and AHL-L is changed by Philip's request,
AML_L pedestal = FL + offset, if offset is available, otherwise 0 (or can be changed to FL).

Pedestal calibration

Script epix10ka_pedestals_calibration works on special runs containing 5 dark calib-cycles.

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Interactive commands:

epix10ka_pedestals_calibration -e detdaq18 -d DetLab.0:Epix10ka2M.0 -r80 -c 0 &> 2020-07-14-r80-cc0-log-epix10ka-pedestals-calibration&
epix10ka_pedestals_calibration -e detdaq18 -d DetLab.0:Epix10ka2M.0 -r80 -c 1 &> 2020-07-14-r80-cc1-log-epix10ka-pedestals-calibration&
epix10ka_pedestals_calibration -e detdaq18 -d DetLab.0:Epix10ka2M.0 -r80 -c 2 &> 2020-07-14-r80-cc2-log-epix10ka-pedestals-calibration&
epix10ka_pedestals_calibration -e detdaq18 -d DetLab.0:Epix10ka2M.0 -r80 -c 3 &> 2020-07-14-r80-cc3-log-epix10ka-pedestals-calibration&
epix10ka_pedestals_calibration -e detdaq18 -d DetLab.0:Epix10ka2M.0 -r80 -c 4 &> 2020-07-14-r80-cc4-log-epix10ka-pedestals-calibration& 

Similar batch commands:

Log files:

/reg/g/psdm/detector/gains/epix10k/panels/logs/

If everything in log files looks fine, they have the same size, then per-panel-per-gain-range constants needs to be merged and deployed.

Merging and deployment

Script epix10ka_deploy_constants merges per-panel-per-gain-range constants in full scale calibration files of shape (7, <number-of-panels>, 352, 384) and deploys them under experiment calib directory.

Execution time is a few minutes, so everything can be done interactively.

Command:

epix10ka_deploy_constants

bsub -o 2020-07-14-r80-cc0-log-epix10ka-pedestals-calibration -q psanaq epix10ka_pedestals_calibration -e detdaq18 -d DetLab.0:Epix10ka2M.0 -r80 -c 0
bsub -o 2020-07-14-r80-cc1-log-epix10ka-pedestals-calibration -q psanaq epix10ka_pedestals_calibration -e detdaq18 -d DetLab.0:Epix10ka2M.0 -r80 -c 1
bsub -o 2020-07-14-r80-cc2-log-epix10ka-pedestals-calibration -q psanaq epix10ka_pedestals_calibration -e detdaq18 -d DetLab.0:Epix10ka2M.0 -r80r92 -c 2
bsubD -o 2020-07-14-r80-cc3-log-epix10ka-pedestals-calibration -q psanaq epix10ka_pedestals_calibration -e detdaq18 -d DetLab.0:Epix10ka2M.0 -r80 -c 3
bsub -o 2020-07-14-r80-cc4-log-epix10ka-pedestals-calibration -q psanaq epix10ka_pedestals_calibration -e detdaq18 -d DetLab.0:Epix10ka2M.0 -r80 -c 4p psrc

Parameter "-p psrc" specifies what constants need to be saved, where "c" stands for charge injection gains (see help).

By default "-p psrg" and constant gains are deployed as high/medium/low = 16.4/5.466/0.164 ADU/keV.

Log file in:

Then preserve log files:mv 2020-07-14-r80-cc*-log-epix10ka-pedestals-calibration /reg/g/psdm/detector/gains/epix10k/panels/logs/

Geometry

Geometry constants generated from optical metrology (see dates in directory names) and data tuning in psana format resides under

• /reg/g/psdm/detector/alignment/

...

• epix10ka/
• /reg/g/psdm/detector/alignment/epix10ka2m/
• /reg/g/psdm/detector/alignment/epix10kaquad/

The last line of the geometry file needs in adjustment of the detector position relative IP.

Constants needs to be deployed under <experiment>/calib/ directory using command in lcls environment set by source /cds/sw/ds/ana/conda1/manage/bin/psconda.sh like

• calibfile deploy -h

If everything in log files looks fine, they have the same size, then per-panel-per-gain-range constants needs to be merged and deployed.

Merging and deployment

References

• Jungfrau and Epix10ka Calibration - brief overview

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• EPIX10KA2M References
• EPIX10KA Per-panel calibration constants