Generate XDS.INP: Difference between revisions

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Generate XDS.INP (view source)

Revision as of 17:13, 16 January 2020

2,839 bytes added ,  16 January 2020
→‎The script: version 0.91 (allow negative STARTING_ANGLE for Eiger)
(→‎The script: version 0.91 (allow negative STARTING_ANGLE for Eiger))
(21 intermediate revisions by 3 users not shown)
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== The script ==
== The script ==
<pre>


<pre>
#!/bin/bash                                                                   
#!/bin/bash                                                                   
# purpose: generate XDS.INP                                                   
# purpose: generate XDS.INP                                                   
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# revision 0.82 . KD 01/03/2018 STARTING_ANGLE for MarCCD/Pilatus/PHOTON, enabling to use dials.rs_mapper with spot2pdb.
# revision 0.82 . KD 01/03/2018 STARTING_ANGLE for MarCCD/Pilatus/PHOTON, enabling to use dials.rs_mapper with spot2pdb.
# revision 0.83 . KD 25/06/2018 for ADSC detector #458 at APS BM19, revert the definition of ROTATION_AXIS=-1 0 0. See "Beamline notes" in this wiki.
# revision 0.83 . KD 25/06/2018 for ADSC detector #458 at APS BM19, revert the definition of ROTATION_AXIS=-1 0 0. See "Beamline notes" in this wiki.
# revision 0.84 . KD 10/10/2018 implement Pilatus detector with d*TREK header -
# revision 0.84 . KD 10/10/2018 implement Pilatus detector with d*TREK header  
REVISION="0.84 (10-Oct-2018)"
# revision 0.85 . Jie Nan 09/01/2019 STARTING_ANGLE for Eiger
# revision 0.86 . Keitaro 03/05/2019 Add PILATUS3 6M, S/N 60-0123 at SSRF BL18U-1 with ROTATION_AXIS=-1 0 0
# revision 0.87 . KD 12/10/2019 Add PILATUS XXX, S/N XX-XXX at SSRF BL19U1 and MarCCD detector #43 at BL17B1 with ROTATION_AXIS=-1 0 0
# revision 0.88 . KD 16/10/2019 fixes for SSRF, add "-maxdepth 1" to "find -H ..."
# revision 0.89 . KD 21/10/2019 add ADSC S/N 905 at ALS 8.2.1, S/N 928 at Australian Synchrotron MX2 beamline; final SSRF fixes
# revision 0.90 . KD 25/10/2019 add OLDMAR detector type. Tested w/ SBGrid data set 6. Anomalous signal may have wrong hand!
# revision 0.91 . KD 16/01/2020 Allow negative starting angle for Eiger (found -33 at SLS !).
REVISION="0.91 (16-Jan-2020)"


#                                                                                                             
#                                                                                                             
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#                                                                                                                 
#                                                                                                                 
# notes for debugging of the script:                                                                             
# notes for debugging of the script:                                                                             
# - add the -v option to the first line, to see where an error occurs                                             
# - add the -x option to the first line, to see where an error occurs                                             
# - comment out the removal of tmp1 and tmp2 in the last line                                                     
# - comment out the removal of tmp1 and tmp2 in the last line                                                     
#                                                                                                                 
#                                                                                                                 
Line 164: Line 171:
# cope with blanks in directory / file name
# cope with blanks in directory / file name
IFS=$'\n'
IFS=$'\n'
find -H $dname -name "$bname" -or -name "${bname}.bz2" -or -name "${bname}.gz" -or -name "${bname}.xz" | egrep -v "_00000.cbf|_000.img" | sort > tmp1
find -H $dname -maxdepth 1 -name "$bname" -or -name "${bname}.bz2" -or -name "${bname}.gz" -or -name "${bname}.xz" | egrep -v "_00000.cbf|_000.img" | sort > tmp1
if [ ! -s tmp1 ]
if [ ! -s tmp1 ]
then
then
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  grep -q mar345 tmp2 && DET=MAR345     
  grep -q mar345 tmp2 && DET=MAR345     
  grep -q BRUKER tmp2 && grep -q CBF tmp2  && DET=Bruker-cbf   
  grep -q BRUKER tmp2 && grep -q CBF tmp2  && DET=Bruker-cbf   
  grep -q CMOS1 tmp2 && DET=adsc-CMOS1                  
  grep -q CMOS1 tmp2 && DET=adsc-CMOS1  
grep -q MARCONTROL tmp2 && DET=OLDMAR                   
else
else
  h5dump -d "/entry/instrument/detector/description" $FIRSTFRAME | grep -i Eiger > /dev/null && DET=eiger
  h5dump -d "/entry/instrument/detector/description" $FIRSTFRAME | grep -i Eiger > /dev/null && DET=eiger
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   # Check detector serial number and recognize beamline for reversed-phi setting.
   # Check detector serial number and recognize beamline for reversed-phi setting.
   # Known detectors for reversed-phi in SPring-8: 24: BL26B2 Mar225, 31: BL32XU MX225HE, 38: BL44XU MX225HE, 42: BL44XU MX300HE, 40: BL41XU MX225HE, 106: BL32XU MX225HS
   # Known detectors for reversed-phi in SPring-8: 24: BL26B2 Mar225, 31: BL32XU MX225HE, 38: BL44XU MX225HE, 42: BL44XU MX300HE, 40: BL41XU MX225HE, 106: BL32XU MX225HS
  # same for SSRF: BL17B1 rayonix MX300. As on 2019-10-13, this also needs doubling of ORGX and ORGY. But the beamline staff (Wenming) wants to fix the header.
   REVERSEPHI_SNs="
   REVERSEPHI_SNs="
24
24
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40
40
42
42
43
106
106
"
"
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       BEAM_CENTER_X=`grep BEAM_CENTER_X tmp2 | sed s/BEAM_CENTER_X=//`
       BEAM_CENTER_X=`grep BEAM_CENTER_X tmp2 | sed s/BEAM_CENTER_X=//`
       BEAM_CENTER_Y=`grep BEAM_CENTER_Y tmp2 | sed s/BEAM_CENTER_Y=//`
       BEAM_CENTER_Y=`grep BEAM_CENTER_Y tmp2 | sed s/BEAM_CENTER_Y=//`
# fix 2010-04-26 - tell user about possible ORGX, ORGY alternatives -  
   
       COMMENT_ORGXY="
       COMMENT_ORGXY="
! Following are possible beam center interpretations for ADSC detectors"
! Following are possible beam center interpretations for ADSC detectors"
# at ESRF, PF, ALS 5.0.2 and ... (pls fill in!) the following should be used:         
# at ESRF, PF, ALS 5.0.2, AS MX2 and ... (pls fill in!) the following should be used:         
       ORGX1=`echo "scale=1; $BEAM_CENTER_Y/$QX" | bc -l`
       ORGX1=`echo "scale=1; $BEAM_CENTER_Y/$QX" | bc -l`
       ORGY1=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l`
       ORGY1=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l`
       echo - at ESRF, PF, APS Argonne BLs use: ORGX=$ORGX1 ORGY=$ORGY1                     
       echo - at ESRF, PF, ALS 8.2.1, APS Argonne BLs use: ORGX=$ORGX1 ORGY=$ORGY1                     
       COMMENT_ORGXY="${COMMENT_ORGXY}
       COMMENT_ORGXY="${COMMENT_ORGXY}
! ORGX= $ORGX1 ORGY= $ORGY1 ! For ESRF, PF, APS Argonne ..."
! ORGX= $ORGX1 ORGY= $ORGY1 ! For ESRF, PF, APS, AS MX2 ..."
# this 2nd alternative convention should be used at the following beamlines (pls complete the list): ALS 5.0.3, ...
# this 2nd alternative convention should be used at the following beamlines (pls complete the list): ALS 5.0.3, ...
       ORGX2=`echo "scale=1; $NX-$BEAM_CENTER_X/$QX" | bc -l `
       ORGX2=`echo "scale=1; $NX-$BEAM_CENTER_X/$QX" | bc -l `
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       # Decision of beam center convention based on detector serial numbers.
       # Decision of beam center convention based on detector serial numbers.
       DET_SN=`grep DETECTOR_SN tmp2 | sed -e "s/DETECTOR_SN=//"`
       DET_SN=`grep DETECTOR_SN tmp2 | sed -e "s/DETECTOR_SN=//"`
       # For convention 1; Known PF detectors = 449: NW12A Q210, 472: NE3A Q270, 474: BL17A Q270, 912: BL5A Q315, 923: ALS BL5.0.2 Q315, 933: AichiSR BL2S1 Q315, 916: APS 24 IDE
      echo Detector serial number is $DET_SN
       # For convention 1; Known PF detectors = 449: NW12A Q210, 472: NE3A Q270, 474: BL17A Q270, 912: BL5A Q315, 923: ALS BL5.0.2 Q315, 933: AichiSR BL2S1 Q315, 916: APS 24 IDE, 928: AS MX2
       ORG1_SNs="
       ORG1_SNs="
449
449
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446
446
916
916
905
928
"
"
       ORG4_SNs="
       ORG4_SNs="
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       ORGX=$ORGX1
       ORGX=$ORGX1
       ORGY=$ORGY1
       ORGY=$ORGY1
      echo the following was chosen based on detector serial number:
       elif echo "${DET_SN}${ORG4_SNs}" | sort | uniq -d | grep [0-9] > /dev/null; then
       elif echo "${DET_SN}${ORG4_SNs}" | sort | uniq -d | grep [0-9] > /dev/null; then
       ORGX=$ORGX4
       ORGX=$ORGX4
       ORGY=$ORGY4
       ORGY=$ORGY4
      echo the following was chosen based on detector serial number:
       else
       else
       ORGX=$ORGX3
       ORGX=$ORGX3
       ORGY=$ORGY3
       ORGY=$ORGY3
      echo the following default was chosen because the detector serial number was not special-cased:
       fi
       fi


       # Check detector serial number and recognize beamline for reversed-phi setting.
       # Check detector serial number and recognize beamline for reversed-phi setting.
       # Known detectors for reversed-phi in SPring-8: 915: BL38B1 Q315; APS 19-ID: 458; BM30A: 924
       # Known detectors for reversed-phi in SPring-8: 915: BL38B1 Q315; APS 19-ID: 458; BM30A: 924
      # 928 is at Australian Beamline MX2
       # revision 0.83 of this script removes 458 from the list!
       # revision 0.83 of this script removes 458 from the list!
       REVERSEPHI_SNs="
       REVERSEPHI_SNs="
915
915
924
924
928
"
"
       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
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       # Known detectors for reversed-phi at MX2 beamline (Brazilian Synchrotron National Laboratory - LNLS)
       # Known detectors for reversed-phi at MX2 beamline (Brazilian Synchrotron National Laboratory - LNLS)
       # Known detectors for reversed-phi at CHESS F1 PILATUS3 6M, S/N 60-0127
       # Known detectors for reversed-phi at CHESS F1 PILATUS3 6M, S/N 60-0127
      # Known detectors for reversed-phi at SSRF BL18U1 (S/N 60-0123) and BL19U1 (S/N XX-XXX) (!; 2019-10-19: staff will fix this)
       DET_SN=`grep "Detector:" tmp2 | sed "s/^.*Detector: *//"`
       DET_SN=`grep "Detector:" tmp2 | sed "s/^.*Detector: *//"`
       REVERSEPHI_SNs="
       REVERSEPHI_SNs="
Line 477: Line 496:
PILATUS 2M, S/N 24-0109
PILATUS 2M, S/N 24-0109
PILATUS3 6M, S/N 60-0127
PILATUS3 6M, S/N 60-0127
PILATUS3 6M, S/N 60-0123
"
"
       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"
      fi
      if [ "$DET_SN" == "PILATUS XXX, S/N XX-XXX" ] ; then
        REVERSE_PHI="yes"
        echo inverted rotation axis at SSRF BL19U1
       fi
       fi
        
        
Line 509: Line 533:
   DETECTOR_DISTANCE=`h5dump -d "/entry/instrument/detector/detector_distance" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2*1000}'`
   DETECTOR_DISTANCE=`h5dump -d "/entry/instrument/detector/detector_distance" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2*1000}'`
   OSCILLATION_RANGE=`h5dump -d "/entry/sample/goniometer/omega_range_average" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2}'`
   OSCILLATION_RANGE=`h5dump -d "/entry/sample/goniometer/omega_range_average" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2}'`
 
  #STARTING_ANGLE:
  # the \- was introduced in version 0.91 :
  STARTING_ANGLE=`h5dump -d "/entry/sample/goniometer/omega_start" $FIRSTFRAME | awk '/\(0\): [\-0-9]/{print $2}'`


   # 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
  SN=`h5dump -d "/entry/instrument/detector/detector_number" $FIRSTFRAME | awk '/\(0\): /{print $2}' | sed s/\"//g`
  if [ "$SN" == "E-32-0111" ]; then
    rotation_axis="-1 0 0"
    echo SSRF BL17U1 with inverted rotation axis
  fi
   SEPMIN=4
   SEPMIN=4
   CLUSTER_RADIUS=2
   CLUSTER_RADIUS=2
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     DETECTOR="PILATUS MINIMUM_VALID_PIXEL_VALUE=0"
     DETECTOR="PILATUS MINIMUM_VALID_PIXEL_VALUE=0"
     dtrek_det="pilatus"
     dtrek_det="pilatus"
     SEPMIN=4
     SEPMIN=3
     CLUSTER_RADIUS=2
     CLUSTER_RADIUS=1.5
     rotation_axis="0 1 0"  # TODO: read from header
     rotation_axis="0 1 0"  # TODO: read from header
     flip=-1
     flip=-1
Line 644: Line 679:
  X_RAY_WAVELENGTH=`grep 'WAVELENGTH' tmp2 | awk '{print $2}'`  
  X_RAY_WAVELENGTH=`grep 'WAVELENGTH' tmp2 | awk '{print $2}'`  
  OSCILLATION_RANGE=`grep 'PHI' tmp2 | awk '{print $5-$3}'`     
  OSCILLATION_RANGE=`grep 'PHI' tmp2 | awk '{print $5-$3}'`     
  TRUSTED_REGION="0 0.99"         
  TRUSTED_REGION="0 0.99"  
 
elif [ "$DET" == "OLDMAR" ]; then
 
echo  "Data from old type MAR image plate detector"
DETECTOR="MAR  MINIMUM_VALID_PIXEL_VALUE=0  OVERLOAD=130000"
NX=`awk 'NR==2 {print $2}' tmp2`
NY=$NX
QX=`awk 'NR==2 {print $15}' tmp2`
QY=$QX
ORGX=`awk 'NR==2 {print $19}' tmp2`
ORGY=`awk 'NR==2 {print $20}' tmp2`
DETECTOR_DISTANCE=`awk 'NR==2 {print $22}' tmp2`             
X_RAY_WAVELENGTH=`awk 'NR==2 {print $21}' tmp2`
OSCILLATION_RANGE=`awk 'NR==2 {print $24-$23}' tmp2`   
TRUSTED_REGION="0 0.99" 
rotation_axis="0 1 0" 
echo unsure if sign of anomalous signal is correct - please verify or try both hands!
        
elif [ "$DET" == "Bruker-cbf" ]; then
elif [ "$DET" == "Bruker-cbf" ]; then
    
    
Line 760: Line 813:
SEPMIN=$SEPMIN  CLUSTER_RADIUS=$CLUSTER_RADIUS ! 4 and 2 for Pixel Array Detectors
SEPMIN=$SEPMIN  CLUSTER_RADIUS=$CLUSTER_RADIUS ! 4 and 2 for Pixel Array Detectors
! since XDS 01-MAR-2015, POSITION supersedes DISTANCE.
! since XDS 01-MAR-2015, POSITION supersedes DISTANCE.
! nowadays headers are usually correct so refine POSITION in INTEGRATE but not IDXREF
! nowadays headers are usually correct so refine POSITION in INTEGRATE but not IDXREF if low to medium resolution
REFINE(IDXREF)=CELL BEAM ORIENTATION AXIS  ! refine POSITION only if known that header distance inaccurate
! however, if the spots from COLSPOT extend to 2A then POSITION could, and if 1.5A POSITION should be refined
REFINE(INTEGRATE)= POSITION BEAM ORIENTATION ! AXIS CELL
REFINE(IDXREF)=CELL BEAM ORIENTATION AXIS  ! add POSITION if high resolution, or DETECTOR_DISTANCE inaccurate
REFINE(INTEGRATE)= POSITION BEAM ORIENTATION ! AXIS CELL . If 1.5A or higher it is ok to refine CELL
! REFINE(CORRECT)=CELL BEAM ORIENTATION AXIS POSITION ! Default is: refine everything
! REFINE(CORRECT)=CELL BEAM ORIENTATION AXIS POSITION ! Default is: refine everything


Line 781: Line 835:
   else
   else
     echo !LIB=/usr/local/lib64/dectris-neggia.so >> XDS.INP
     echo !LIB=/usr/local/lib64/dectris-neggia.so >> XDS.INP
     echo /usr/local/lib64/dectris-neggia.so was not found!
     echo /usr/local/lib64/dectris-neggia.so was not found - specify location manually!
   fi
   fi
fi  
fi  
Line 798: Line 852:
   echo "ROTATION_AXIS= $rotation_axis  ! only read by IDXREF" >> XDS.INP
   echo "ROTATION_AXIS= $rotation_axis  ! only read by IDXREF" >> XDS.INP
  elif [ "$REVERSE_PHI" == "no" ]; then
  elif [ "$REVERSE_PHI" == "no" ]; then
   echo 'ROTATION_AXIS=1 0 0  ! Australian Synchrotron, SERCAT ID-22 (?), APS 19-ID (?), ESRF BM30A, SPring-8, SSRF BL17U need -1 0 0. Diamond ID24 needs 0 -1 0' >> XDS.INP
   echo 'ROTATION_AXIS=1 0 0  ! Australian Synchrotron, SERCAT ID-22 (?), APS 19-ID (?), ESRF BM30A, SPring-8, SSRF need -1 0 0. Diamond ID24 needs 0 -1 0' >> XDS.INP
  else
  else
   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
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