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Generate XDS.INP: Difference between revisions
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revision 1.00 . Gleb Bourenkov 10/11/2020 add ROTATION_AXIS=0 -1 0 for beamline P14 (EMBL Hamburg) detectors Eiger 16M S/N E-32-0107; previously Eiger 4M S/N E-08-0107 and PILATUS 6M-F, S/N 60-0115-F
(v0.97 add Eiger2 UNTRUSTED_RECTANGLEs from Andreas Förster) |
(revision 1.00 . Gleb Bourenkov 10/11/2020 add ROTATION_AXIS=0 -1 0 for beamline P14 (EMBL Hamburg) detectors Eiger 16M S/N E-32-0107; previously Eiger 4M S/N E-08-0107 and PILATUS 6M-F, S/N 60-0115-F) |
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# revision 0.96 . KD 03/10/2020 make script echo detector serial number if inverted ROTATION_AXIS is detected. | # revision 0.96 . KD 03/10/2020 make script echo detector serial number if inverted ROTATION_AXIS is detected. | ||
# revision 0.97 . KD 19/10/2020 add UNTRUSTED_RECTANGLEs for Eiger2 (which has a few pixels less than Eiger (thanks to Andreas Förster) | # revision 0.97 . KD 19/10/2020 add UNTRUSTED_RECTANGLEs for Eiger2 (which has a few pixels less than Eiger (thanks to Andreas Förster) | ||
REVISION=" | # revision 0.98 . Thomas Hauß (HZB) 06/11/2020 switch Python print syntax to Python3 | ||
# revision 0.99 . Aaron Finke (CHESS) 07/11/2020 add ROTATION_AXIS=-1 0 0 for EIGER2 16M detector at MX beamline ID7B2 (CHESS) | |||
# revision 1.00 . Gleb Bourenkov 10/11/2020 add ROTATION_AXIS=0 -1 0 for beamline P14 (EMBL Hamburg) detectors Eiger 16M S/N E-32-0107; previously Eiger 4M S/N E-08-0107 and PILATUS 6M-F, S/N 60-0115-F | |||
REVISION="1.00 (10-Nov-2020)" | |||
# | # | ||
| Line 529: | Line 532: | ||
fi | fi | ||
fi | fi | ||
# | # PETRA P14: raw data from Eiger are stored as CBF files so this is treated as Pilatus | ||
if [ "$DET_SN" == "Dectris Eiger 16M, E-32-0107" -o "$DET_SN" == "Dectris Eiger 4M, E-08-0107" -o "$DET_SN" == "PILATUS 6M-F, S/N 60-0115-F" ] ; then | |||
rotation_axis="0 -1 0" | |||
echo ROTATION_AXIS="0 -1 0" at PETRA P14 | |||
fi | |||
elif [ "$DET" == "eiger" ]; then | elif [ "$DET" == "eiger" ]; then | ||
| Line 537: | Line 544: | ||
if [ "$DLS" == 1 ]; then | if [ "$DLS" == 1 ]; then | ||
echo Eiger HDF5 from Diamond | echo Eiger HDF5 from Diamond | ||
# unfortunately h5dump 1.10 is required to get this right for the DLS .h5 files. This version is available at DLS but | # unfortunately h5dump 1.10 is required to get this right for the DLS .h5 files. This version is available at DLS but maybe not elsewhere | ||
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}'` | ||
# v0.95: fix the next 2 lines by taking care of negative values with the \- , and stop after first "(0)" | # v0.95: fix the next 2 lines by taking care of negative values with the \- , and stop after first "(0)" | ||
| Line 553: | Line 560: | ||
# If rotation vector set (NeXus) | # If rotation vector 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"` | ||
# Eiger 16M SSRF BL17U1 | # Eiger 16M SSRF BL17U1 has S/N E-32-0111; EIGER2 16M CHESS ID7B2 has S/N E-32-0123 (A. Finke 2020-11-07) v0.99 | ||
SN=`h5dump -d "/entry/instrument/detector/detector_number" $FIRSTFRAME | awk '/\(0\): /{print $2}' | sed s/\"//g` | SN=`h5dump -d "/entry/instrument/detector/detector_number" $FIRSTFRAME | awk '/\(0\): /{print $2}' | sed s/\"//g` | ||
if [ "$SN" == "E-32-0111" ]; then | if [ "$SN" == "E-32-0111" ] || [ "$SN" == "E-32-0123" ]; then | ||
rotation_axis="-1 0 0" | rotation_axis="-1 0 0" | ||
echo SSRF BL17U1 with inverted rotation axis | echo SSRF BL17U1 or CHESS ID7B2 with inverted rotation axis | ||
fi | fi | ||
fi | fi | ||
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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("'$FIRSTFRAME'","rb");f.seek(772);print "%.4d"%struct.unpack(">i",f.read(4))') | ||
NX=$(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("'$FIRSTFRAME'","rb");f.seek(344);print "-%.4f"%struct.unpack(">f",f.read(4))') | ! DETECTOR_DISTANCE=$(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("'$FIRSTFRAME'","rb");f.seek(544);print "%.4f"%struct.unpack(">f",f.read(4))') | ||
ORGX=$(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("'$FIRSTFRAME'","rb");f.seek(524);phis,phie=struct.unpack(">ff",f.read(8));print "%.4f"%(phie-phis)') | ! OSCILLATION_RANGE=$(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("'$FIRSTFRAME'","rb");f.seek(780);print "%.6f"%struct.unpack(">f",f.read(4))') | ||
QX=$(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("'$FIRSTFRAME'","rb");f.seek(292);print "%.6f"%struct.unpack(">f",f.read(4))') | ! X_RAY_WAVELENGTH=$(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" == "dtrek" ]; then | elif [ "$DET" == "dtrek" ]; then | ||
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See also [[Generate_XDS.INP#Dependencies]] below, and the [[Installation]] article. | See also [[Generate_XDS.INP#Dependencies]] below, and the [[Installation]] article. | ||
== Copying generate_XDS.INP from XDSwiki webserver == | |||
On Linux: | |||
wget https://strucbio.biologie.uni-konstanz.de/pub/linux_bin/generate_XDS.INP | |||
chmod a+x generate_XDS.INP | |||
On Mac: | |||
curl -o generate_XDS.INP https://strucbio.biologie.uni-konstanz.de/pub/linux_bin/generate_XDS.INP | |||
chmod a+x generate_XDS.INP | |||
See also [[Installation]]. | |||
== Obtaining generate_XDS.INP from this webpage == | == Obtaining generate_XDS.INP from this webpage == | ||
| Line 1,124: | Line 1,149: | ||
The script makes use of many GNU commands, like <code>ls, grep, egrep, awk, cut, cat, echo, wc, bc, head, sed, tail, cp, od, python</code>. Some of them (like <code>od</code> and <code>python</code>) are only used in case of specific detectors (MarCCD and RAXIS, respectively). | The script makes use of many GNU commands, like <code>ls, grep, egrep, awk, cut, cat, echo, wc, bc, head, sed, tail, cp, od, python</code>. Some of them (like <code>od</code> and <code>python</code>) are only used in case of specific detectors (MarCCD and RAXIS, respectively). | ||
The script will only work if all the required commands are available. They reside in either the <code>coreutils</code> RPM, or specific RPMs (<code>gawk, sed, bc, grep, python</code> ...). Please note that to get the <code>strings</code> command on some Linux distributions (e.g. FC23) you need to install the <code>binutils</code> RPM package. | The script will only work if all the required commands are available. They reside in either the <code>coreutils</code> RPM, or specific RPMs (<code>gawk, sed, bc, grep, python</code> ...). Please note that to get the <code>strings</code> command on some Linux distributions (e.g. FC23) you need to install the <code>binutils</code> RPM package. | ||
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). The .h5 files collected at Diamond Light Source require a very new version of h5dump (namely h5dump 1.10) to extract the OVERLOAD parameter from the .h5 file; this version is available by default in Ubuntu 20.04 and RHEL/CentOS 8. | ||
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. | 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. | ||