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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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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 and optionally 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 Forward converter recognizes detector types detectors epix10ka, epix10kav2, jungfrau, cspad, pnccd , pnccdv2, associated with segment types from their segment names EPIX10KA:V1, EPIX10KA:V2, JUNGFRAU:V1, JUNGFRAU:V2, SENS2X1:V1, PNCCD:V1, MTRX:V2:512:512:75:75 , respectively, used in the input geometry file.loaded from the input geometry file.
Use dataset for z position correction
Since ana-4.0.47-py3 three optional parameters added to apply z-position correction from PV variables.
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--dsname DSNAME FOR Z CORRECTION FROM DATA - dataset (str) like
exp=<experiment>:run=<run-number>:smd:..., def=None
--zpvname ZPVNAME FOR Z CORRECTION FROM DATA - z-correction variable
name ex: CXI:DS1:MMS:06.RBV or alias ex: DscCsPad_z,
def=None
--f_um F_UM FOR Z CORRECTION FROM DATA - factor for conversion PV
value to um, def=1000.000000 |
To apply z position correction at least --dsname parameter should be specified. In this case PV names CXI:DS1:MMS:06.RBV, CXI:DS2:MMS:06.RBV, MFX:DET:MMS:04.RBV, XPP:ROB:POS:Z, AMO:LMP:MMS:10.RBV are tested for availability.
- if nothing found, the list of all available PV names is printed, correction is not applied,
- if more than one found, specification of one of them is requested in parameter --zpvname,
- if one is found - its value is used with factor --f_um to apply correction.
- if --zpvname is specified incorrectly and not found, the list of all available PV names is printed, correction is not applied.\
Example of the command with z position correction:
geometry_convert -f geo-jungfrau.data -o geo-jungfrau.geom --dsname exp=cxic00318:run=123:smd --zpvname CXI:DS1:MMS:06.RBV
Conversion 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
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For now, backward converter recognizes works for detector types epix10ka, jungfrau, cspad (with quads like in cxi), cspadv2 (without quads like in xpp), pnccd. Information about detector type is missing in the CrystFEL *.geom file, so parameted -d needs to be specified.
Special case of CSPAD detector
ASIC naming convention in CrystFEL are slightly different for cspad with and without moving quads. For now, appropriate Appropriate detector type (-d) should be selected specified explicitly as cspad or cspadv2, respectively, for exampe
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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. |
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.
DETTYPE, --dettype DETTYPE
USED FOR CRYSTFEL TO PSANA ONLY -
detector type, one of epix10ka, jungfrau, cspad, cspadv2,
pnccd, def=epix10ka
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