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General remarks

Command geometry_convert with parameters executed in psana environment converts geometry constants between psana and CrystFEL formats forth and back depending on input file name extension. Converter works for a few major composite detectors cspad, pnccd, epix10ka, jungfrau. 

Forward conversion by default changes coordinate frame from psana (the same as in optical metrology) to CrystFEL (LAB frame: z-along photon beam, y-up, x=[y×z]). The LAB frame is widely used in crystallography data processing. Backward conversion does not change coordinate frame and generates panels' positions and tilts as is. Pixel coordinates reconstructed in psana from this file will also be defined in the LAB frame.

Conversion commands

Conversion from psana to CrystFEL

Command for "forward" conversion of the detector geometry constants from psana to CrystFEL needs in a couple of parameters for detector type (-d) and input psana geometry file name (-f). It is also convenient to specify unique output CrystFEL geometry file name (-o), for example

      geometry_convert -d cspad -f geo-cspad-psana.data -o geo-cspad-crystfel.geom

By default converter changes coordinate frame from psana (similar to one in optical metrology) to LAB (usually used in CrystFEL). Parameter --cframe 0 allows to keep the coordinate frame unchanged.

For now, forward converter recognizes detector types epix10ka, epix10kav2, jungfrau, cspad, pnccd, pnccdv2, associated with segment types EPIX10KA:V1, EPIX10KA:V2, JUNGFRAU:V1, SENS2X1:V1, PNCCD:V1, MTRX:V2:512:512:75:75, respectively, used in the input geometry file.

Conversion from CrystFEL to psana

Command for "backward" conversion of the detector geometry constants from CrystFEL to psana needs in a couple of parameters for detector type (-d) and input CrystFEL geometry file name (-f). Optional output file name (-o) for psana geometry is also useful, for example

   geometry_convert -d epix10ka -f geo-epix10ka2m-crystfel.geom -o geo-epix10ka2m-psana.txt

The file name extension *.geom in option -f launches conversion from CrystFEL to psana.

For now, backward converter recognizes detector types epix10ka, jungfrau, cspad, cspadv2, pnccd.

Special case of CSPAD detector

ASIC naming convention in CrystFEL are slightly different for cspad with and without moving quads. For now, appropriate detector type (-d) should be selected explicitly as cspad or cspadv2, respectively, for exampe

  geometry_convert -d cspad -f geo-cspad-cxi-crystfel.geom -o geo-cspad-cxi-psana.data

  geometry_convert -d cspadv2 -f geo-cspad-xpp-crystfel.geom -o geo-cspad-xpp-psana.data

Command help

More information about command and parameters can be obtained with help option (-h),

  geometry_convert -h

Current result for command geometry_convert -h 
Converts geometry constants from psana to CrystFEL format and backward (see
--fname).

optional arguments:
  -h, --help            show this help message and exit
  -d DETTYPE, --dettype DETTYPE
                        detector type, one of epix10ka, jungfrau, cspad,
                        pnccd, def=epix10ka
  -f FNAME, --fname FNAME
                        input geometry file name. File name extention *.geom
                        launches converter from CrystFEL to psana,
                        def=/reg/g/psdm/detector/data_test/geometry/geo-
                        epix10ka2m-16-segment.data
  -o OFNAME, --ofname OFNAME
                        output file name, def=geo-crystfel.txt
  -l LOGLEV, --loglev LOGLEV
                        logging level name, one of NOTSET, DEBUG, INFO,
                        WARNING, ERROR, CRITICAL, def=INFO
  --cframe CFRAME       coordinate frame 0/1 for psana/LAB, def=1. Works for
                        PSANA->CRYSTFEL conversion ONLY where it selects frame
                        for pixel coordinates. Backward conversion
                        CRYSTFEL->PSANA does not change frame. For test
                        perpose it is assumed that forth and back conversion
                        PSANA->CRYSTFEL->PSANA should not change constants in
                        the geometry file (up to precision lose at conversion)
                        if they are defined for the same coordinate frame. For
                        this type of test parameter should be set to 0 to keep
                        psana frame unchanged.

Test of converter

CSPAD

Panel type SENS2X1:V1 describes cspad 2x1 panel geometry in psana. There are two types of cspad detectors, xpp- and cxi-like, w/o and with quads, which has different configuration both in psana and CrystFEL.

  cp /reg/g/psdm/detector/data_test/geometry/geo-cspad-test.data .
  geometry_convert -d cspad -f geo-cspad-test.data -o geo-cspad-test-cframe-psana.geom --cframe 0
  geometry_convert -d cspadv2 -f geo-cspad-test-cframe-psana.geom -o geo-cspad-test-back.data
  geometry_image -g geo-cspad-test.data -a /reg/g/psdm/detector/data_test/npy/nda-mfx11116-r0624-e005365-MfxEndstation-0-Cspad-0-max.txt -R10 -i0

epix10ka2m

Panel types

  cp /reg/g/psdm/detector/data_test/geometry/geo-epix10ka2m-test.txt .
  geometry_convert -d epix10ka -f geo-epix10ka2m-test.txt -o geo-epix10ka2m-test-cframe-psana.geom --cframe 0
  geometry_convert -d epix10ka -f geo-epix10ka2m-test-cframe-psana.geom -o geo-epix10ka2m-test-back.txt
  then see the minor difference between geo-epix10ka2m-test.txt and geo-epix10ka2m-test-back.txt
  or check image with each of geometry files:
  geometry_image -g geo-epix10ka2m-test-back.txt -a /reg/g/psdm/detector/data_test/npy/nda-mfxc00118-r0184-epix10ka2m-silver-behenate-max.txt -R10 -i0

jungfrau

There may be two segment types Jungfrau:V1 and Jungfrau:V2 which represent the same panel from two sides. Forward test works for both types, backward returns panels of the Jungfrau:V2 type.

  cp /reg/g/psdm/detector/data_test/geometry/geo-jungfrau-8-test.data .
  geometry_convert -d jungfrau -f geo-jungfrau-8-test.data -o geo-jungfrau-8-test-cframe-psana.geom --cframe 0
  geometry_convert -d jungfrau -f geo-jungfrau-8-test-cframe-psana.geom -o geo-jungfrau-8-test-back.data
  geometry_image -g geo-jungfrau-8-test.data -a /reg/g/psdm/detector/data_test/npy/nda-cxilv9518-r0008-jungfrau-lysozyme-max.npy -R10 -i0

pnccd

A waste majority of pnccd geometry files in psana use old-style segment description as PNCCD:V1 with matrix coordinate reference frame. Forward conversion from psana-to-CrystFEL naturally supports this format. However, this format is not convenient for uniform backward conversion from CrystFEL-to-psana the arbitrary Cartesian frame. Backward conversion use segment description as MTRX:V2 in output file. The same segment type can be used in the conversion from psana-to-CrystFEL, but all geometry constants for panel position and orientation needs to be changed.  This issue creates a mess in direct comparison between original   and forth-and-back converted geometry file. For now this type of test is unavailable.

Conversion from psana-to-CrystFEL was tested long time ago and presumably works.

Reference


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