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# revision 0.23 . KD 1/2012 - add UNTRUSTED_QUADRILATERAL, remove MINIMUM_ZETA (0.05 is default now)
# revision 0.23 . KD 1/2012 - add UNTRUSTED_QUADRILATERAL, remove MINIMUM_ZETA (0.05 is default now)
# revision 0.24 . KD 3/2012 - remove revision 0.10 since XDS now takes much longer paths
# revision 0.24 . KD 3/2012 - remove revision 0.10 since XDS now takes much longer paths
# revision 0.25 . KD 3/2012 - remove revision 0.22 for PSI Pilatus 2M; see http://www.globalphasing.com/autoproc/wiki/index.cgi?TroubleShootingKnownIssues
# revision 0.25 . KD 3/2012 - remove revision 0.22 for PSI Pilatus 2M; see http://www.globalphasing.com/autoproc/wiki/index.cgi?
REVISION="0.25 (30-Mar-2012)"
# revision 0.26 . KD 7/2012 - Mac-compatibility: replace od flags --skip-bytes= and --read-bytes= with -j and -N (thanks to Oliver Clarke for working this out!)
TroubleShootingKnownIssues
REVISION="0.26 (02-Jul-2012)"
#
#
# usage: e.g. generate_XDS.INP "frms/mydata_1_???.img"
# usage: e.g. generate_XDS.INP "frms/mydata_1_???.img"
# known problems:
# known problems:
# - 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)
# - on Mac OS X, Xcode (from http://developer.apple.com/tools/xcode) might be needed - not sure about this
#
#
# notes for debugging of the script:
# notes for debugging of the script:
# use first frame of dataset to obtain parameters
# use first frame of dataset to obtain parameters
# offsets are documented; values can be find in mccd_xdsparams.pl script
# offsets are documented; values can be found in mccd_xdsparams.pl script
let SKIP=1024+80
let SKIP=1024+80
NX=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
NX=$(od -t dI -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}')
let SKIP=$SKIP+4
let SKIP=$SKIP+4
NY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
NY=$(od -t dI -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}')
let SKIP=1720
let SKIP=1720
DETECTOR_DISTANCE=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
DETECTOR_DISTANCE=$(od -t dI -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}')
DETECTOR_DISTANCE=`echo "scale=3; $DETECTOR_DISTANCE/1000" | bc -l`
DETECTOR_DISTANCE=`echo "scale=3; $DETECTOR_DISTANCE/1000" | bc -l`
let SKIP=1024+256+128+256+4
let SKIP=1024+256+128+256+4
ORGX=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
ORGX=$(od -t dI -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}')
ORGX=`echo "scale=2; $ORGX/1000" | bc -l `
ORGX=`echo "scale=2; $ORGX/1000" | bc -l `
let SKIP=$SKIP+4
let SKIP=$SKIP+4
ORGY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
ORGY=$(od -t dI -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}')
ORGY=`echo "scale=2; $ORGY/1000" | bc -l `
ORGY=`echo "scale=2; $ORGY/1000" | bc -l `
let SKIP=1024+256+128+256+44
let SKIP=1024+256+128+256+44
PHISTART=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
PHISTART=$(od -t dI -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}')
let SKIP=1024+256+128+256+76
let SKIP=1024+256+128+256+76
PHIEND=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
PHIEND=$(od -t dI -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}')
OSCILLATION_RANGE=`echo "scale=3; ($PHIEND-($PHISTART))/1000" | bc -l`
OSCILLATION_RANGE=`echo "scale=3; ($PHIEND-($PHISTART))/1000" | bc -l`
let SKIP=1024+256+128+256+128+4
let SKIP=1024+256+128+256+128+4
QX=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
QX=$(od -t dI -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}')
QX=`echo "scale=10; $QX/1000000" |bc -l `
QX=`echo "scale=10; $QX/1000000" |bc -l `
let SKIP=$SKIP+4
let SKIP=$SKIP+4
QY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
QY=$(od -t dI -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}')
QY=`echo "scale=10; $QY/1000000" |bc -l `
QY=`echo "scale=10; $QY/1000000" |bc -l `
let SKIP=1024+256+128+256+128+128+12
let SKIP=1024+256+128+256+128+128+12
X_RAY_WAVELENGTH=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
X_RAY_WAVELENGTH=$(od -t dI -j $SKIP -N 4 $FIRSTFRAME | head -1 | awk '{print $2}')
X_RAY_WAVELENGTH=`echo "scale=5; $X_RAY_WAVELENGTH/100000" | bc -l`
X_RAY_WAVELENGTH=`echo "scale=5; $X_RAY_WAVELENGTH/100000" | bc -l`
