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This page is about file system based repository for calibration files used in LCLS software.
Introduction
LCLS experiments use different type of detectors which produce raw data. Detectors are not perfect and in most cases these raw data can not directly be used in analysis. They need to be calibrated. Generic type of corrections for pixel geometry and intensity, such as dark rate (pedestals), common mode, mask, etc. need to be done in almost all experiments. These corrections use files with calibration parameters residing in calibration store.
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This note explains organization and content of the calibration store, tools for maintenance, application of corrections in psana, access in code to calibration parameters, and relevant references to other confluence documents.
Location
Directory containing calibration files is located at the same level as directories with data xtc
or hdf5
files:
Code Block |
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/reg/d/psdm/<PATH>/<INSTRUMENT>/<experiment>/xtc <PATH>/reg<INSTRUMENT>/d<experiment>/psdmhdf5 <PATH>/<INSTRUMENT>/<experiment>/hdf5 calib |
where <PATH> depends on computer farm:
Computer farm | PATH | Comments |
---|---|---|
pcds before s3df | /reg/d/psdm | deprecated |
pcds with s3df | /cds/data/psdm |
...
s3df | /sdf/data/lcls/ds |
Full path to the calibration file consists of a few sub-directories under the calib
directory, representing functional logical layers:
Code Block |
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<PATH>/reg/d/psdm/<INSTRUMENT>/<experiment>/calib/<calib-version>/<data-source>/<type>/<file> |
...
<calib-version>
- is a directory reserved for different versions of calibration software. For each detector type it is defined through the dictionary.<data-source>
- actual source of data. Each detector has an unique name in DAQ, which also includes its position. For example:CxiDs1.0:Cspad.0
,CxiDg1.0:Tm6740.0
,CxiEndstation.0:Opal2000.1
, etc.<type>
- type of calibration files:pedestals,
pixel_rms,
pixel_status,
pixel_mask,
pixel_gain,
pixel_bkgd,
common_mode,
filter,
geometry
, etc.- (
center, tilt, marg_gap_shift
, etc. are deprecated types).
<file>
- calibration file name consisting of the validity run range and extension .data. For example:3-15.data
,1-end.data
,7-end.data
, etc.
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Example:
Code Block |
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/reg/d/psdm/<PATH>/CXI/cxi12315/calib/CsPad::CalibV1/CxiDs1.0:Cspad.0/pedestals/1-end.data /reg/d/psdm/<PATH>/CXI/cxi12315/calib/CsPad2x2::CalibV1/CxiSc2.0:Cspad2x2.0/geometry/5-end.data /reg/d/psdm<PATH>/AMO/amo12313/calib/PNCCD::CalibV1/Camp.0:pnCCD.1/pixel_status/8-22.data |
Tools
Calibration management tool
Tools
General detector tools
- makepeds - tool supported by Silke and her team
- calibrun - dark processing script for regular detectors
- calibfile - constants deployment script
- det_ndarr_raw_proc - dark processing engine used in calibrun
- det_pixel_status - NEW - evaluates pixel statul on light data diles
- geometry_deploy_constants
- deploy_constants - used in calibfile
Tools for epix10ka and jungfrau detectors
- epix10ka_pedestals_calibration
- epix10ka_deploy_constants
- jungfrau_dark_proc
- jungfrau_deploy_constants
- jungfrau_gain_constants
Information scripts
- datinfo - retrieves major info about data in xtc file
- event_keys
- epix10ka_id
- jungfrau_id
- find_detector_names
- find_detector_runs
- find_runs_for_data_type
- dcs - DEPRECATED - script for population and deployment of hdf5 calibration files
- calibman - DEPRECATED - Calibration Management Tool - is a central tool for maintenance of calibration store. It allows to create,deploy, modify, and re-locate calibration files.
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Apply calibration in psana
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Image intensity correction can be done with psana module ImgAlgos::NDArrCalib.
Geometry
Image reconstructed with geometry file can be obtained with module ImgAlgos::NDArrImageProducer.
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Geometry
- optical_metrology_check
- optical_metrology_* - optical metrology processing for specific detectors, cspad_v1_cxi, cspad_v1_xpp, cspad2x2, epix10ka2m
Direct access to calibration parameters in code
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- class PSCalib.GeometryAccess - Python interface to geometry parameters.
References
- Detector Calibration Store
- DEPRECATED - IT WAS NEVER IMPLEMENTED: Calibration Store for LCLS2
- Calibration Management Tool
- Detector Geometry
- CSPAD Alignment
- CSPAD2x2 Alignment
- psana - Module Catalog
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- Calibration Management Tool - DEPREATED
- Detector Calibration Store - DEPREATED