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Generate XDS.INP: Difference between revisions
→The script
(→The script: revision 0.31) |
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# revision 0.30 . Keitaro 3/2013 - for ADSC: write all possible beam center conventions in XDS.INP as comments | # revision 0.30 . Keitaro 3/2013 - for ADSC: write all possible beam center conventions in XDS.INP as comments | ||
# revision 0.31 . Keitaro 3/2013 - add comment for reversed phi for SPring-8 | # revision 0.31 . Keitaro 3/2013 - add comment for reversed phi for SPring-8 | ||
REVISION="0. | # revision 0.32 . Keitaro 3/2013 - add RAXIS support. only tested with RAXIS IV++ and VII. | ||
REVISION="0.32 (15-Mar-2013)" | |||
# | # | ||
# usage: e.g. generate_XDS.INP "frms/mydata_1_???.img" | # usage: e.g. generate_XDS.INP "frms/mydata_1_???.img" | ||
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grep -q PILATUS tmp2 && DET=pilatus | grep -q PILATUS tmp2 && DET=pilatus | ||
grep -q BEAM_CENTER_X tmp2 && DET=adsc | grep -q BEAM_CENTER_X tmp2 && DET=adsc | ||
head -n1 tmp2 | grep -q "^RAXIS" && DET=raxis | |||
# identify other detector types in the same way (MAR IP would be straightforward) | # identify other detector types in the same way (MAR IP would be straightforward) | ||
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OSCILLATION_RANGE=`awk '/Angle/{print $2}' tmp2` | OSCILLATION_RANGE=`awk '/Angle/{print $2}' tmp2` | ||
elif [ "$DET" == "raxis" ]; then | |||
echo Data from a RAXIS detector | |||
DETECTOR="RAXIS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=2000000" | |||
#let SKIP=768 | |||
#NX=$(od -t x -j $SKIP -N 4 $FIRSTFRAME |awk 'NR==1{print toupper($2)}'|perl -nle '@array= $_ =~/.{2}/g; print "ibase=16;obase=A;".join("",reverse @array)'|bc) | |||
NX=$(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("'$FIRSTFRAME'","rb");f.seek(772);print "%.4d"%struct.unpack(">i",f.read(4))') | |||
DETECTOR_DISTANCE=$(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("'$FIRSTFRAME'","rb");f.seek(540);print "%.4f"%struct.unpack(">f",f.read(4))') | |||
ORGY=$(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("'$FIRSTFRAME'","rb");f.seek(524);phis,phie=struct.unpack(">ff",f.read(8));print "%.4f"%(phie-phis)') | |||
QX=$(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("'$FIRSTFRAME'","rb");f.seek(780);print "%.6f"%struct.unpack(">f",f.read(4))') | |||
X_RAY_WAVELENGTH=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(292);print "%.6f"%struct.unpack(">f",f.read(4))') | |||
else | else | ||
echo should never come here | echo should never come here | ||
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! as about 32* what CORRECT.LP suggests (absorption of phosphor is much higher than that of silicon) | ! as about 32* what CORRECT.LP suggests (absorption of phosphor is much higher than that of silicon) | ||
NX= $NX NY= $NY QX= $QX QY= $QY ! to make CORRECT happy if frames are unavailable | NX= $NX NY= $NY QX= $QX QY= $QY ! to make CORRECT happy if frames are unavailable | ||
eof | |||
if [ "$DET" == "raxis" ]; then | |||
cat >> XDS.INP << eof | |||
DIRECTION_OF_DETECTOR_X-AXIS=1 0 0 | |||
DIRECTION_OF_DETECTOR_Y-AXIS=0 -1 0 | |||
INCIDENT_BEAM_DIRECTION=0 0 1 | |||
ROTATION_AXIS=0 1 0 | |||
!FRACTION_OF_POLARIZATION=0.98 ! uncomment if synchrotron | |||
POLARIZATION_PLANE_NORMAL=1 0 0 | |||
eof | |||
else | |||
cat >> XDS.INP << eof | |||
DIRECTION_OF_DETECTOR_X-AXIS=1 0 0 | DIRECTION_OF_DETECTOR_X-AXIS=1 0 0 | ||
DIRECTION_OF_DETECTOR_Y-AXIS=0 1 0 | DIRECTION_OF_DETECTOR_Y-AXIS=0 1 0 | ||
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FRACTION_OF_POLARIZATION=0.98 ! better value is provided by beamline staff! | FRACTION_OF_POLARIZATION=0.98 ! better value is provided by beamline staff! | ||
POLARIZATION_PLANE_NORMAL=0 1 0 | POLARIZATION_PLANE_NORMAL=0 1 0 | ||
eof | |||
fi | |||
cat >> XDS.INP << eof | |||
!used by DEFPIX and CORRECT to exclude ice-reflections / ice rings - uncomment if necessary | !used by DEFPIX and CORRECT to exclude ice-reflections / ice rings - uncomment if necessary | ||
!EXCLUDE_RESOLUTION_RANGE= 3.93 3.87 !ice-ring at 3.897 Angstrom | !EXCLUDE_RESOLUTION_RANGE= 3.93 3.87 !ice-ring at 3.897 Angstrom | ||