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Generate XDS.INP: Difference between revisions
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→The script: v0.95 fix DLS Eiger HDF5 variant OSCILLATION_RANGE, STARTING_ANGLE. Attention: DLS Eiger variant needs h5dump 1.10 for OVERLOAD!
(→The script: v0.95 fix DLS Eiger HDF5 variant OSCILLATION_RANGE, STARTING_ANGLE. Attention: DLS Eiger variant needs h5dump 1.10 for OVERLOAD!) |
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# revision 0.91 . KD 16/01/2020 Allow negative starting angle for Eiger (found -33 at SLS !). | # revision 0.91 . KD 16/01/2020 Allow negative starting angle for Eiger (found -33 at SLS !). | ||
# revision 0.92 . KD 27/02/2020 read *_master.h5 from Diamond Light Source | # revision 0.92 . KD 27/02/2020 read *_master.h5 from Diamond Light Source | ||
REVISION="0. | # revision 0.93 . KD 13/03/2020 print out 2theta for MarCCD (DETECTOR_*_AXIS can be derived from this) | ||
# revision 0.94 . KD 16/03/2020 bugfix for Bruker-cbf to make bc accept e.g. 3.1e-005 by using awk printf "%.5f" instead of awk print | |||
# revision 0.95 . KD 29/07/2020 fix DLS Eiger HDF5 variant OSCILLATION_RANGE, STARTING_ANGLE. Attention: DLS Eiger variant needs h5dump 1.10 for OVERLOAD! | |||
REVISION="0.95 (29-Jul-2020)" | |||
# | # | ||
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elif [ "$DET" == "mccd" ]; then | elif [ "$DET" == "mccd" ]; then | ||
echo Data from a MarCCD detector | echo Data from a MarCCD detector | ||
# http://www.sb.fsu.edu/~xray/Manuals/marCCD165header.html has header information | |||
DETECTOR="CCDCHESS MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65500" | DETECTOR="CCDCHESS MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65500" | ||
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DETECTOR_DISTANCE=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}') | DETECTOR_DISTANCE=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}') | ||
DETECTOR_DISTANCE=`echo "scale=3; $DETECTOR_DISTANCE/1000" | bc -l` | DETECTOR_DISTANCE=`echo "scale=3; $DETECTOR_DISTANCE/1000" | bc -l` | ||
# Mar 12, 2020 KD | |||
let SKIP=1724 | |||
TWOTHETA=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}') | |||
TWOTHETA=`echo "scale=3; $TWOTHETA/1000" | bc -l` | |||
echo 2THETA= $TWOTHETA | |||
let SKIP=1024+256+128+256+44 | let SKIP=1024+256+128+256+44 | ||
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echo Eiger HDF5 from Diamond | echo Eiger HDF5 from Diamond | ||
OVERLOAD=`h5dump -d "/entry/instrument/detector/saturation_value" $FIRSTFRAME | awk '/\(0\):/{print $2}'` | OVERLOAD=`h5dump -d "/entry/instrument/detector/saturation_value" $FIRSTFRAME | awk '/\(0\):/{print $2}'` | ||
OSCILLATION_RANGE=`h5dump -d "/entry/data/omega" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $3-$2}'` | # v0.95: fix the next 2 lines by taking care of negative values with the \- , and stop after first "(0)" | ||
STARTING_ANGLE=`h5dump -d "/entry/data/omega" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2}' | sed -e "s/,//"` | OSCILLATION_RANGE=`h5dump -d "/entry/data/omega" $FIRSTFRAME | awk '/\(0\): [\-0-9]/{print $3-$2;exit}'` | ||
STARTING_ANGLE=`h5dump -d "/entry/data/omega" $FIRSTFRAME | awk '/\(0\): [\-0-9]/{print $2;exit}' | sed -e "s/,//"` | |||
echo OSCILLATION_RANGE=$OSCILLATION_RANGE STARTING_ANGLE=$STARTING_ANGLE | echo OSCILLATION_RANGE=$OSCILLATION_RANGE STARTING_ANGLE=$STARTING_ANGLE | ||
# 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"` | ||
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X_RAY_WAVELENGTH=`awk '/diffrn_radiation_wavelength.wavelength/{print $2}' tmp2` | X_RAY_WAVELENGTH=`awk '/diffrn_radiation_wavelength.wavelength/{print $2}' tmp2` | ||
OMEGA=`awk '/OMEGA \? \? \?/{ | # fix 16.3.20: instead of print, use printf "%.5f", because bc does not accept e.g. 3.1e-005 | ||
DELTAOMEGA=`awk '/OMEGA \? \? \?/{ | OMEGA=`awk '/OMEGA \? \? \?/{printf "%.5f",$5}' tmp2` | ||
PHI=`awk '/PHI \? \? \?/{ | DELTAOMEGA=`awk '/OMEGA \? \? \?/{printf "%.5f",$6}' tmp2` | ||
DELTAPHI=`awk '/PHI \? \? \?/{printf "% | PHI=`awk '/PHI \? \? \?/{printf "%.5f",$5}' tmp2` | ||
KAPPA=`awk '/CHI \? \? \?/{ | DELTAPHI=`awk '/PHI \? \? \?/{printf "%.5f",$6}' tmp2` | ||
KAPPA=`awk '/CHI \? \? \?/{printf "%.5f",$5}' tmp2` | |||
# echo OMEGA DELTAOMEGA PHI DELTAPHI KAPPA= $OMEGA $DELTAOMEGA $PHI $DELTAPHI $KAPPA | # echo OMEGA DELTAOMEGA PHI DELTAPHI KAPPA= $OMEGA $DELTAOMEGA $PHI $DELTAPHI $KAPPA | ||
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For Eiger data processing, the <code>h5dump</code> program must be installed. This is part of <code>hdf5-tools</code> (Ubuntu) or <code>hdf5</code> (RHEL). | For Eiger data processing, the <code>h5dump</code> program must be installed. This is part of <code>hdf5-tools</code> (Ubuntu) or <code>hdf5</code> (RHEL). | ||
On Mac OS X, installation of the "Command Line Tools" (from http://developer.apple.com/downloads; requires Apple ID) is required. These are also part of the (larger, but also free) [http://developer.apple.com/tools/xcode Xcode] package. This package comes with a license that has to be accepted by the user when running a Command Line Tool (e.g. <code>strings</code>) for the first time. | On Mac OS X, installation of the "Command Line Tools" (from http://developer.apple.com/downloads; requires Apple ID) is required (open a terminal and type <code>xcode-select --install</code>). These are also part of the (larger, but also free) [http://developer.apple.com/tools/xcode Xcode] package. This package comes with a license that has to be accepted by the user when running a Command Line Tool (e.g. <code>strings</code>) for the first time. | ||
One way to check for missing programs is | |||
#!/bin/bash | |||
for i in ls grep egrep awk cut cat echo wc bc head sed tail cp od python strings h5dump ; do | |||
if [ ! -x /bin/$i ] && [ ! -x /usr/bin/$i ]; then | |||
echo $i not found | |||
fi | |||
done | |||
A command that should go a long way in providing all these tools for RedHat-derived distros is (as root) | A command that should go a long way in providing all these tools for RedHat-derived distros is (as root) | ||