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edits
Generate XDS.INP: Difference between revisions
→The script: revision 1.10 : NeXus header
(→See also: Known bugs: ROTATION_AXIS at X06SA) |
(→The script: revision 1.10 : NeXus header) |
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<pre> | <pre> | ||
</pre> | |||
#!/bin/bash | #!/bin/bash | ||
# purpose: generate XDS.INP | # purpose: generate XDS.INP | ||
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# revision 1.08 . KD, Thomas Hauß, Feng Yu 7/11/2021 fix TZ in timestamps for SSRF detectors | # revision 1.08 . KD, Thomas Hauß, Feng Yu 7/11/2021 fix TZ in timestamps for SSRF detectors | ||
# revision 1.09 . KD, Feng Yu 7/11/2021 fix detector number BNL E-18-0121 to be E-18-0104 | # revision 1.09 . KD, Feng Yu 7/11/2021 fix detector number BNL E-18-0121 to be E-18-0104 | ||
REVISION="1. | # revision 1.10 . KD NeXus header for Eiger | ||
REVISION="1.10 (7-MAR-2022)" | |||
# | # | ||
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# | # | ||
# known problems: | # known problems: | ||
# revision 1.10 . KD implement NeXus for Eiger | |||
# - for ADSC detectors, there are at least three ways to obtain ORGX and ORGY values from the header (see below); | # - for ADSC detectors, there are at least three ways to obtain ORGX and ORGY values from the header (see below); | ||
# - the same might be a problem for MAR headers, too (not sure about this) | # - the same might be a problem for MAR headers, too (not sure about this) | ||
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# default DIRECTION_OF_DETECTOR_X-AXIS | # default DIRECTION_OF_DETECTOR_X-AXIS | ||
DIRECTION_OF_DETECTOR_X_AXIS="1 0 0" | DIRECTION_OF_DETECTOR_X_AXIS="1 0 0" | ||
# default DIRECTION_OF_DETECTOR_Y-AXIS | |||
DIRECTION_OF_DETECTOR_Y_AXIS="0 1 0" | |||
# default FRACTION_OF_POLARIZATION | # default FRACTION_OF_POLARIZATION | ||
pol_frac=0.98 | pol_frac=0.98 | ||
| Line 472: | Line 478: | ||
DETECTOR_DISTANCE=`grep ^DISTANCE tmp2 | sed s/DISTANCE=/-/` | DETECTOR_DISTANCE=`grep ^DISTANCE tmp2 | sed s/DISTANCE=/-/` | ||
OSCILLATION_RANGE=`grep OMEGA_DELTA tmp2 | sed s/OMEGA_DELTA=//` | OSCILLATION_RANGE=`grep OMEGA_DELTA tmp2 | sed s/OMEGA_DELTA=//` | ||
g_DETECTOR_X_AXIS="-1 0 0" | |||
elif [ "$DET" == "experimental-ED" ]; then | elif [ "$DET" == "experimental-ED" ]; then | ||
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# rotation_axis=`h5dump -a "/entry/sample/transformations/omega/vector" $FIRSTFRAME 2>/dev/null | grep "(0):" | sed -e "s/^.*://; s/,//g"` | # rotation_axis=`h5dump -a "/entry/sample/transformations/omega/vector" $FIRSTFRAME 2>/dev/null | grep "(0):" | sed -e "s/^.*://; s/,//g"` | ||
# the above gives -1 0 0 for DLS data instead of the correct 1 0 0, so commented out for now | # the above gives -1 0 0 for DLS data instead of the correct 1 0 0, so commented out for now | ||
# comment while implementing rev 1.10: this is because the DLS headers are NeXus, so DIRECTION_OF_DETECTOR_X/Y_AXIS must be adjusted. | |||
else | else | ||
echo Eiger HDF5 from Dectris | echo Eiger HDF5 from Dectris | ||
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fi | fi | ||
echo "STARTING_ANGLE=$STARTING_ANGLE" | echo "STARTING_ANGLE=$STARTING_ANGLE" | ||
# If rotation | # If rotation axis set (NeXus) | ||
rotation_axis=`h5dump -a "/entry/sample/transformations/omega/vector" $FIRSTFRAME 2>/dev/null | grep "(0):" | sed -e "s/^.*://; s/,//g"` | rotation_axis=`h5dump -a "/entry/sample/transformations/omega/vector" $FIRSTFRAME 2>/dev/null | grep "(0):" | sed -e "s/^.*://; s/,//g"` | ||
# EIGER2 16M CHESS ID7B2 has S/N E-32-0123 (A. Finke 2020-11-07) v0.99 | # EIGER2 16M CHESS ID7B2 has S/N E-32-0123 (A. Finke 2020-11-07) v0.99 | ||
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SPOT_RANGE="1 `echo "scale=0; if (${nframes}<2) 1; if (${nframes}>1) ${nframes}/2"|bc -l`" | SPOT_RANGE="1 `echo "scale=0; if (${nframes}<2) 1; if (${nframes}>1) ${nframes}/2"|bc -l`" | ||
fi | fi | ||
fi | |||
# rev 1.10: check for NeXus header. If found, its geometry will overwrite any rotation_axis set until here. | |||
NeXus=0 | |||
h5dump -d "/entry/definition" $FIRSTFRAME | grep -q NXmx && NeXus=1 | |||
if [ "$NeXus" == "1" ]; then | |||
echo NeXus header found. This defines DIRECTION_OF_DETECTOR_X/Y-AXIS and ROTATION_AXIS. | |||
DIRECTION_OF_DETECTOR_X_AXIS=$(h5dump -d "/entry/instrument/detector/module/fast_pixel_direction" $FIRSTFRAME 2>/dev/null | grep "(0):" | tail -1 | sed -e "s/^.*://; s/,//g") | |||
DIRECTION_OF_DETECTOR_Y_AXIS=$(h5dump -d "/entry/instrument/detector/module/slow_pixel_direction" $FIRSTFRAME 2>/dev/null | grep "(0):" | tail -1 | sed -e "s/^.*://; s/,//g") | |||
rotation_axis=$(h5dump -a "/entry/sample/transformations/omega/vector" $FIRSTFRAME 2>/dev/null | grep "(0):" | sed -e "s/^.*://; s/,//g") | |||
else | |||
echo no NeXus header found. | |||
fi | fi | ||
echo DATA_RANGE=$DATA_RANGE | echo DATA_RANGE=$DATA_RANGE | ||
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#let SKIP=768 | #let SKIP=768 | ||
#NX=$(od -t x -j $SKIP -N 4 $FIRSTFRAME |awk 'NR==1{print toupper($2)}'|perl -nle '@array= $_ =~/.{2}/g; print "ibase=16;obase=A;".join("",reverse @array)'|bc) | #NX=$(od -t x -j $SKIP -N 4 $FIRSTFRAME |awk 'NR==1{print toupper($2)}'|perl -nle '@array= $_ =~/.{2}/g; print "ibase=16;obase=A;".join("",reverse @array)'|bc) | ||
NX=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(768);print("%.4d"%struct.unpack(">i",f.read(4)))') | NX=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(768);print("%.4d"%struct.unpack(">i",f.read(4)))') | ||
NY=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(772);print("%.4d"%struct.unpack(">i",f.read(4)))') | NY=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(772);print("%.4d"%struct.unpack(">i",f.read(4)))') | ||
DETECTOR_DISTANCE=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(344);print("-%.4f"%struct.unpack(">f",f.read(4)))') | DETECTOR_DISTANCE=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(344);print("-%.4f"%struct.unpack(">f",f.read(4)))') | ||
ORGX=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(540);print("%.4f"%struct.unpack(">f",f.read(4)))') | ORGX=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(540);print("%.4f"%struct.unpack(">f",f.read(4)))') | ||
ORGY=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(544);print("%.4f"%struct.unpack(">f",f.read(4)))') | ORGY=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(544);print("%.4f"%struct.unpack(">f",f.read(4)))') | ||
OSCILLATION_RANGE=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(524);phis,phie=struct.unpack(">ff",f.read(8));print("%.4f"%(phie-phis))') | OSCILLATION_RANGE=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(524);phis,phie=struct.unpack(">ff",f.read(8));print("%.4f"%(phie-phis))') | ||
QX=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(776);print("%.6f"%struct.unpack(">f",f.read(4)))') | QX=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(776);print("%.6f"%struct.unpack(">f",f.read(4)))') | ||
QY=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(780);print("%.6f"%struct.unpack(">f",f.read(4)))') | QY=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(780);print("%.6f"%struct.unpack(">f",f.read(4)))') | ||
X_RAY_WAVELENGTH=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(292);print("%.6f"%struct.unpack(">f",f.read(4)))') | X_RAY_WAVELENGTH=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(292);print("%.6f"%struct.unpack(">f",f.read(4)))') | ||
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cat >> XDS.INP << eof | cat >> XDS.INP << eof | ||
DIRECTION_OF_DETECTOR_X-AXIS=$DIRECTION_OF_DETECTOR_X_AXIS | DIRECTION_OF_DETECTOR_X-AXIS=$DIRECTION_OF_DETECTOR_X_AXIS | ||
DIRECTION_OF_DETECTOR_Y-AXIS= | DIRECTION_OF_DETECTOR_Y-AXIS=$DIRECTION_OF_DETECTOR_Y_AXIS | ||
eof | eof | ||
fi | fi | ||
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echo spots in FRAME.cbf! | echo spots in FRAME.cbf! | ||
rm -f tmp1 tmp2 | rm -f tmp1 tmp2 | ||
== System-wide or personal installation == | == System-wide or personal installation == | ||