Generate XDS.INP: Difference between revisions

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Generate XDS.INP (view source)

Revision as of 09:32, 22 October 2020

3,832 bytes added ,  22 October 2020
→‎Dependencies
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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="0.92 (27-Feb-2020)"
# 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 0.96 . 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 (19-Oct-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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   if echo "${DET_SN}${REVERSEPHI_SNs}" | sort | uniq -d | grep [0-9] > /dev/null; then
   if echo "${DET_SN}${REVERSEPHI_SNs}" | sort | uniq -d | grep [0-9] > /dev/null; then
     REVERSE_PHI="yes"
     REVERSE_PHI="yes"
    echo inverted ROTATION_AXIS since Detector Serial Number is "${DET_SN}"
   fi
   fi


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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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       if echo "${DET_SN}${REVERSEPHI_SNs}" | sort | uniq -d | grep [0-9] > /dev/null; then
       if echo "${DET_SN}${REVERSEPHI_SNs}" | sort | uniq -d | grep [0-9] > /dev/null; then
         REVERSE_PHI="yes"
         REVERSE_PHI="yes"
        echo inverted ROTATION_AXIS since detector serial number is ${DET_SN}
       fi
       fi


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       if echo "${DET_SN}${REVERSEPHI_SNs}" | sort | uniq -d | grep [0-9] > /dev/null; then
       if echo "${DET_SN}${REVERSEPHI_SNs}" | sort | uniq -d | grep [0-9] > /dev/null; then
         REVERSE_PHI="yes"
         REVERSE_PHI="yes"
        echo inverted ROTATION_AXIS since detector serial number is ${DET_SN}
       fi
       fi
       if [ "$DET_SN" == "PILATUS XXX, S/N XX-XXX" ] ; then
       if [ "$DET_SN" == "PILATUS XXX, S/N XX-XXX" ] ; then
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         if grep -q "Oscillation_axis X.CW +SLOW" tmp2 ; then
         if grep -q "Oscillation_axis X.CW +SLOW" tmp2 ; then
           rotation_axis="0 -1 0"
           rotation_axis="0 -1 0"
          echo ROTATION_AXIS="0 -1 0" at Diamond I24
         fi
         fi
       fi
       fi
# insert similar code for Petra P14 here
# FIXME: insert similar code for Petra P14 here


elif [ "$DET" == "eiger" ]; then
elif [ "$DET" == "eiger" ]; then
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   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 usually 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}'`
     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"`
Line 739: Line 757:


  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 \? \? \?/{print $5}' tmp2`
# fix 16.3.20: instead of print, use printf "%.5f", because bc does not accept e.g. 3.1e-005
  DELTAOMEGA=`awk '/OMEGA \? \? \?/{print $6}' tmp2`
  OMEGA=`awk '/OMEGA \? \? \?/{printf "%.5f",$5}' tmp2`
  PHI=`awk '/PHI \? \? \?/{print $5}' tmp2`
  DELTAOMEGA=`awk '/OMEGA \? \? \?/{printf "%.5f",$6}' tmp2`
  DELTAPHI=`awk '/PHI \? \? \?/{printf "%5.4f",$6}' tmp2`
  PHI=`awk '/PHI \? \? \?/{printf "%.5f",$5}' tmp2`
  KAPPA=`awk '/CHI \? \? \?/{print $5}' tmp2`
  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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!                                                  and does not seem to have any downsides.  
!                                                  and does not seem to have any downsides.  
eof
eof
   if [ $NX == "1475" ]; then
   if [ $NX == "1028"  -a $NY == "1062" ]; then
# Eiger2 1M ; v0.97 numbers from Andreas Förster
    cat >> XDS.INP << eof
UNTRUSTED_RECTANGLE=    0 1029    512  551
eof
  elif [ $NX == "1475" ]; then
     if ! grep -q Flat_field tmp2 ; then
     if ! grep -q Flat_field tmp2 ; then
     cat >> XDS.INP << eof
     cat >> XDS.INP << eof
Line 956: Line 980:
eof
eof
     fi
     fi
  elif [ $NX == "2068"  -a $NY == "2162" ]; then
# Eiger2 4M ; v0.97 numbers from Andreas Förster
    cat >> XDS.INP << eof
!EXCLUSION OF VERTICAL DEAD AREAS OF THE EIGER2 4M DETECTOR
UNTRUSTED_RECTANGLE= 1028 1041      0 2163
!EXCLUSION OF HORIZONTAL DEAD AREAS OF THE EIGER 4M DETECTOR
UNTRUSTED_RECTANGLE=    0 2069    512  551
UNTRUSTED_RECTANGLE=    0 2069  1062 1101
UNTRUSTED_RECTANGLE=    0 2069  1612 1651
eof
   elif [ $NX == "2463" ]; then
   elif [ $NX == "2463" ]; then
# Pilatus 6M
# Pilatus 6M
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UNTRUSTED_RECTANGLE= 0 3110 2717 2757
UNTRUSTED_RECTANGLE= 0 3110 2717 2757
eof
eof
   elif [ $NX == "4150" -a $NY == "4371" ]; then
  elif [ $NX == "3108"  -a $NY == "3262" ]; then
# Eiger2 9M ; v0.97 numbers from Andreas Förster
    cat >> XDS.INP << eof
!EXCLUSION OF VERTICAL DEAD AREAS OF THE EIGER2 9M DETECTOR
UNTRUSTED_RECTANGLE= 1028 1041      0 3262
UNTRUSTED_RECTANGLE= 2068 2081      0 3263
!EXCLUSION OF HORIZONTAL DEAD AREAS OF THE EIGER2 9M DETECTOR
UNTRUSTED_RECTANGLE=    0 3109    512  551
UNTRUSTED_RECTANGLE=    0 3109  1062 1101
UNTRUSTED_RECTANGLE=    0 3109  1612 1651
UNTRUSTED_RECTANGLE=    0 3109  2162 2201
UNTRUSTED_RECTANGLE=    0 3109  2712 2751
eof
   elif [ $NX == "4150" -a $NY == "4371" ]; then
# Eiger 16M
# Eiger 16M
     cat >> XDS.INP << eof
     cat >> XDS.INP << eof
Line 1,004: Line 1,051:
  UNTRUSTED_RECTANGLE= 2069 2082      0 4371  
  UNTRUSTED_RECTANGLE= 2069 2082      0 4371  
  UNTRUSTED_RECTANGLE= 3109 3122      0 4371
  UNTRUSTED_RECTANGLE= 3109 3122      0 4371
eof
  elif [ $NX == "4148" -a $NY == "4362" ]; then
# Eiger2 16M ; v0.97 numbers from Andreas Förster
    cat >> XDS.INP << eof
!EXCLUSION OF HORIZONTAL DEAD AREAS OF THE EIGER2 16M DETECTOR
UNTRUSTED_RECTANGLE= 1028 1041      0 4363
UNTRUSTED_RECTANGLE= 2068 2081      0 4363
UNTRUSTED_RECTANGLE= 3108 3121      0 4363
!EXCLUSION OF VERTICAL DEAD AREAS OF THE EIGER2 16M DETECTOR
UNTRUSTED_RECTANGLE=    0 4149    512  551
UNTRUSTED_RECTANGLE=    0 4149  1062 1101
UNTRUSTED_RECTANGLE=    0 4149  1612 1651
UNTRUSTED_RECTANGLE=    0 4149  2162 2201
UNTRUSTED_RECTANGLE=    0 4149  2712 2751
UNTRUSTED_RECTANGLE=    0 4149  3262 3301
UNTRUSTED_RECTANGLE=    0 4149  3812 3851
eof
eof
   fi
   fi
Line 1,061: Line 1,124:
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. 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.


An easy way to check for missing programs is
One way to check for missing programs is
  whereis ls grep egrep awk cut cat echo wc bc head sed tail cp od python strings h5dump
  #!/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)
Kay
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