Content

Introduction

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 storeThis note explains organization and content of the calibration store, tools for maintenance and use of calibration parameters, and useful references to othe confluence documents.

Calibration store use regular file system to accumulate calibration files with a few simple rules about organization of the calibration store.

...

Advantage or this approach: clean, simple structure of the calibration store structure and files' content with sufficient flexibility for analysis of data. Although, it is not recommended, regular OS tools can be used to browse, modify, re-locate files.

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:

/reg/d/psdm/<PATH>/<INSTRUMENT>/<experiment>/xtc
<PATH>/reg<INSTRUMENT>/d<experiment>/psdmhdf5
<PATH>/<INSTRUMENT>/<experiment>/hdf5
calib

where <PATH> depends on computer farm:

...

Full path to the calibration file consists of a few sub-directories under the calib directory, representing functional logical layers:

/reg/d/psdm/<PATH>/<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.

Example:

<PATH>/reg/d/psdm/CXI/cxi12315/calib/CsPad::CalibV1/CxiDs1.0:Cspad.0/pedestals/1-end.data

Tools

Calibration management tool

<PATH>/CXI/cxi12315/calib/CsPad2x2::CalibV1/CxiSc2.0:Cspad2x2.0/geometry/5-end.data
<PATH>/AMO/amo12313/calib/PNCCD::CalibV1/Camp.0:pnCCD.1/pixel_status/8-22.data

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

...

Apply calibration in psana

Intensity correction

...

• .

Geometry

Image reconstructed with geometry file can be obtained with module ImgAlgos::NDArrImageProducer.

Information about pixel coordinates, indexes in the image, areas, mask, etc. can be produced with ImgAlgos::PixCoordsProducer.

• 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

• class PSCalib::CalibParsStore - C++ interface to correction intensity parameters.class PSCalib::GeometryAccess - C++ interface to geometry parameters.class PSCalib.GeometryAccess - Python interface to geometry parameters.

References

• Calibration Management Tool
• Detector Geometry
• CSPAD Alignment
• CSPAD2x2 Alignment
• Calibration Management Tool - DEPREATED
• Detector Calibration Store - DEPREATED