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Generate XDS.INP: Difference between revisions

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Generate XDS.INP (view source)

Revision as of 11:07, 8 July 2014

521 bytes added ,  8 July 2014
rev 0.47
(rev 0.47)
Line 62: Line 62:
# revision 0.45 . KD cope with blanks in filenames
# revision 0.45 . KD cope with blanks in filenames
# revision 0.46 . Keitaro 6/2014 automatically set ROTATION_AXIS=-1 0 0 for Mar225 at SPring-8 BL26B2.
# revision 0.46 . Keitaro 6/2014 automatically set ROTATION_AXIS=-1 0 0 for Mar225 at SPring-8 BL26B2.
REVISION="0.46 (17-Jun-2014)"
# revision 0.47 . Keitaro 7/2014 more generic dTREK format support (Saturn and RAXIS)
REVISION="0.47 (08-Jul-2014)"
#                                                                                                             
#                                                                                                             
# usage: e.g. generate_XDS.INP "/file/system/frms/mydata_1_???.img"                                                       
# usage: e.g. generate_XDS.INP "/file/system/frms/mydata_1_???.img"                                                       
Line 138: Line 139:
head -n1 tmp2 | grep -q "^RAXIS" && DET=raxis
head -n1 tmp2 | grep -q "^RAXIS" && DET=raxis
head -n1 tmp2 | grep -q "^R-AXIS" && DET=raxis
head -n1 tmp2 | grep -q "^R-AXIS" && DET=raxis
grep -q "^DETECTOR_TYPE=RAXIS" tmp2 && DET=raxis_smv
grep -q "^SOURCE_WAVELENGTH=1" tmp2 && DET=dtrek
grep -q mar345 tmp2 && DET=MAR345                         
grep -q mar345 tmp2 && DET=MAR345                         


Line 348: Line 349:
   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))')


elif [ "$DET" == "raxis_smv" ]; then
elif [ "$DET" == "dtrek" ]; then
   echo "Data from a RAXIS detector with SMV header (dTREK image)"
   echo "Data from a RAXIS or Saturn detector with dTREK format"
 
  DETECTOR="RAXIS MINIMUM_VALID_PIXEL_VALUE=0"


   sed s/\;// tmp2 > tmp1
   sed s/\;// tmp2 > tmp1
   mv tmp1 tmp2
   mv tmp1 tmp2
  dname=`grep "DETECTOR_NAMES=" tmp2 | sed -e "s/.*=//"`
  if [ "$dname" == "CCD_" ]; then
    DETECTOR="SATURN MINIMUM_VALID_PIXEL_VALUE=1"
    dtrek_det="saturn"
  else # should be RX_
    DETECTOR="RAXIS MINIMUM_VALID_PIXEL_VALUE=0"
    dtrek_det="raxis"
  fi
  # Saturn on SPring-8 BL26B1
  if grep "CCD_DETECTOR_IDENTIFICATION=MSC_REIT_A200_SN09250183" tmp2 > /dev/null; then
  REVERSE_PHI="yes"
  fi


   # find OVERLOAD
   # find OVERLOAD
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   # find NX,NY,QX,QY
   # find NX,NY,QX,QY
  # NOTE that "RX_" may be different. probably we should check DETECTOR_NAMES= in header (RX_ is expected currently).
   # NX,NY should be read from *_DETECTOR_DIMENSIONS?
   # NX,NY should be read from RX_DETECTOR_DIMENSIONS?
   NX=`grep SIZE1 tmp2 | tail -1 | sed s/SIZE1=//`
   NX=`grep SIZE1 tmp2 | tail -1 | sed s/SIZE1=//`
   NY=`grep SIZE2 tmp2 | tail -1 | sed s/SIZE2=//`
   NY=`grep SIZE2 tmp2 | tail -1 | sed s/SIZE2=//`
   DET_SIZE=(`grep RX_DETECTOR_SIZE tmp2 | tail -1 | sed s/RX_DETECTOR_SIZE=//`)
   DET_SIZE=(`grep ${dname}DETECTOR_SIZE tmp2 | tail -1 | sed s/.*_DETECTOR_SIZE=//`)
   QX=`echo "scale=1; ${DET_SIZE[0]} / $NX" | bc -l`
   QX=`echo "scale=6; ${DET_SIZE[0]} / $NX" | bc -l`
   QY=`echo "scale=1; ${DET_SIZE[1]} / $NY" | bc -l`
   QY=`echo "scale=6; ${DET_SIZE[1]} / $NY" | bc -l`


   # find ORGX, ORGY
   # find ORGX, ORGY
   SPATIAL_DISTORTION_INFO=(`grep RX_SPATIAL_DISTORTION_INFO tmp2 | tail -1 | sed s/RX_SPATIAL_DISTORTION_INFO=//`)
   SPATIAL_DISTORTION_INFO=(`grep ${dname}SPATIAL_DISTORTION_INFO tmp2 | tail -1 | sed s/.*_SPATIAL_DISTORTION_INFO=//`)
   ORGX=${SPATIAL_DISTORTION_INFO[0]}
   ORGX=${SPATIAL_DISTORTION_INFO[0]}
   ORGY=${SPATIAL_DISTORTION_INFO[1]}
   ORGY=${SPATIAL_DISTORTION_INFO[1]}


   # find DETECTOR_DISTANCE  
   # find DETECTOR_DISTANCE  
   GONIO_NAMES=(`grep RX_GONIO_NAMES tmp2 | tail -1 | sed s/RX_GONIO_NAMES=//`)
   GONIO_NAMES=(`grep ${dname}GONIO_NAMES tmp2 | tail -1 | sed s/.*_GONIO_NAMES=//`)
   GONIO_VALUES=(`grep RX_GONIO_VALUES tmp2 | tail -1 | sed s/RX_GONIO_VALUES=//`)
   GONIO_VALUES=(`grep ${dname}GONIO_VALUES tmp2 | tail -1 | sed s/.*_GONIO_VALUES=//`)
   GONIO_UNITS=(`grep RX_GONIO_UNITS tmp2 | tail -1 | sed s/RX_GONIO_UNITS=//`)
   GONIO_UNITS=(`grep ${dname}GONIO_UNITS tmp2 | tail -1 | sed s/.*_GONIO_UNITS=//`)
   for i in `seq 1 ${#GONIO_NAMES[*]}`
   for i in `seq 1 ${#GONIO_NAMES[*]}`
   do
   do
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eof
eof
if [ "$DET" == "raxis" -o "$DET" == "raxis_smv" ]; then
if [ "$DET" == "raxis" -o "$dtrek_det" == "raxis" ]; then
  cat >> XDS.INP << eof
  cat >> XDS.INP << eof
DIRECTION_OF_DETECTOR_X-AXIS=1 0 0
DIRECTION_OF_DETECTOR_X-AXIS=1 0 0
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   echo 'ROTATION_AXIS=-1 0 0  ! if this is wrong, please contact author.' >> XDS.INP
   echo 'ROTATION_AXIS=-1 0 0  ! if this is wrong, please contact author.' >> XDS.INP
  fi
  fi
if [ "$dtrek_det" == "saturn" ]; then
cat >> XDS.INP << eof
DIRECTION_OF_DETECTOR_X-AXIS=-1 0 0
DIRECTION_OF_DETECTOR_Y-AXIS= 0 1 0
eof
else
  cat >> XDS.INP << eof
  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
eof
fi
cat >> XDS.INP << eof
INCIDENT_BEAM_DIRECTION=0 0 1
INCIDENT_BEAM_DIRECTION=0 0 1
FRACTION_OF_POLARIZATION=0.98  ! better value is provided by beamline staff!
FRACTION_OF_POLARIZATION=0.98  ! better value is provided by beamline staff!
Keitaro
33

edits

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