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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 frame 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.
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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. |
Reference
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.
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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
- EPIX10KA:V1 - 250um (wrong) wide pixel size
- EPIX10KA:V2 - 225um (correct) wide pixel size
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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.
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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.
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