2,684
edits
(move Xcode sentences to Dependencies section) |
(→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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(35 intermediate revisions by 3 users not shown) | |||
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== The script == | == The script == | ||
<pre> | |||
#!/bin/bash | #!/bin/bash | ||
# purpose: generate XDS.INP | # purpose: generate XDS.INP | ||
Line 99: | Line 99: | ||
# revision 0.81 . KD 21/02/2018 when encountering CBF files from Eiger (ESRF), treat as Pilatus detector | # revision 0.81 . KD 21/02/2018 when encountering CBF files from Eiger (ESRF), treat as Pilatus detector | ||
# 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. | # 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 0.85 . 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 0.92 . KD 27/02/2020 read *_master.h5 from Diamond Light Source | |||
# 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)" | |||
# | # | ||
Line 109: | Line 122: | ||
# - 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 | # - on Mac OS X, the Xcode command line tools (from https://developer.apple.com/download/more/) are needed. | ||
# | # | ||
# notes for debugging of the script: | # notes for debugging of the script: | ||
# - add the - | # - 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 125: | Line 138: | ||
# | # | ||
# defaults: | # defaults: | ||
# | # | ||
# conversion radian / degrees: | |||
DEGTOR=57.2957795 | |||
DETECTOR="XXX MINIMUM_VALID_PIXEL_VALUE=XXX OVERLOAD=XXX" | DETECTOR="XXX MINIMUM_VALID_PIXEL_VALUE=XXX OVERLOAD=XXX" | ||
REVERSE_PHI="no" | REVERSE_PHI="no" | ||
Line 146: | Line 162: | ||
pol_frac=0.98 | pol_frac=0.98 | ||
STARTING_ANGLE=0 | STARTING_ANGLE=0 | ||
dtrek_det="" | |||
SEPMIN=7.0 | |||
CLUSTER_RADIUS=3.5 | |||
dname=`echo "$1" | xargs dirname` | dname=`echo "$1" | xargs dirname` | ||
Line 156: | Line 175: | ||
# cope with blanks in directory / file name | # cope with blanks in directory / file name | ||
IFS=$'\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 | ||
Line 219: | Line 238: | ||
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" $FIRSTFRAME | grep -i Eiger > /dev/null && DET=eiger | ||
Line 235: | Line 255: | ||
elif [ "$DET" == "mccd" ]; then | elif [ "$DET" == "mccd" ]; then | ||
echo Data from a MarCCD detector | echo Data from a MarCCD detector | ||
# http://www.sb.fsu.edu/~xray/Manuals/marCCD165header.html has header information | |||
DETECTOR="CCDCHESS MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65500" | DETECTOR="CCDCHESS MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65500" | ||
Line 242: | Line 263: | ||
# Check detector serial number and recognize beamline for reversed-phi setting. | # Check detector serial number and recognize beamline for reversed-phi setting. | ||
# Known detectors for reversed-phi in SPring-8: 24: BL26B2 Mar225, 31: BL32XU MX225HE, 38: BL44XU MX225HE, 42: BL44XU MX300HE, 40: BL41XU MX225HE, 106: BL32XU MX225HS | # Known detectors for reversed-phi in SPring-8: 24: BL26B2 Mar225, 31: BL32XU MX225HE, 38: BL44XU MX225HE, 42: BL44XU MX300HE, 40: BL41XU MX225HE, 106: BL32XU MX225HS | ||
# same for SSRF: BL17B1 rayonix MX300. As on 2019-10-13, this also needs doubling of ORGX and ORGY. But the beamline staff (Wenming) wants to fix the header. | |||
REVERSEPHI_SNs=" | REVERSEPHI_SNs=" | ||
24 | 24 | ||
Line 248: | Line 270: | ||
40 | 40 | ||
42 | 42 | ||
43 | |||
106 | 106 | ||
" | " | ||
Line 268: | Line 291: | ||
DETECTOR_DISTANCE=$(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 | ||
Line 332: | Line 361: | ||
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=//` | ||
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 | ! 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 ` | ||
Line 363: | Line 392: | ||
# 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 $DET_SN | ||
# For convention 1; Known PF detectors = 449: NW12A Q210, 472: NE3A Q270, 474: BL17A Q270, 912: BL5A Q315, 923: ALS BL5.0.2 Q315, 933: AichiSR BL2S1 Q315, 916: APS 24 IDE, 928: AS MX2 | |||
ORG1_SNs=" | ORG1_SNs=" | ||
449 | 449 | ||
Line 374: | Line 404: | ||
446 | 446 | ||
916 | 916 | ||
905 | |||
928 | |||
" | " | ||
ORG4_SNs=" | ORG4_SNs=" | ||
Line 381: | Line 413: | ||
ORGX=$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=$ORGY3 | ||
echo the following default was chosen because the detector serial number was not special-cased: | |||
fi | fi | ||
# Check detector serial number and recognize beamline for reversed-phi setting. | # Check detector serial number and recognize beamline for reversed-phi setting. | ||
# Known detectors for reversed-phi in SPring-8: 915: BL38B1 Q315; APS 19-ID: 458; BM30A: 924 | # Known detectors for reversed-phi in SPring-8: 915: BL38B1 Q315; APS 19-ID: 458; BM30A: 924 | ||
# 928 is at Australian Beamline MX2 | |||
# revision 0.83 of this script removes 458 from the list! | |||
REVERSEPHI_SNs=" | REVERSEPHI_SNs=" | ||
915 | 915 | ||
924 | 924 | ||
928 | |||
" | " | ||
if echo "${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 | ||
Line 427: | Line 464: | ||
mv tmp1 tmp2 | mv tmp1 tmp2 | ||
OVERLOAD=1048574 | OVERLOAD=1048574 | ||
SEPMIN=4 | |||
CLUSTER_RADIUS=2 | |||
grep -q Count_cutoff tmp2 && OVERLOAD=`awk '/Count_cutoff/{print $2}' tmp2` | grep -q Count_cutoff tmp2 && OVERLOAD=`awk '/Count_cutoff/{print $2}' tmp2` | ||
DETECTOR="PILATUS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD= $OVERLOAD !PILATUS" | DETECTOR="PILATUS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD= $OVERLOAD !PILATUS" | ||
Line 461: | Line 500: | ||
# Known detectors for reversed-phi at MX2 beamline (Brazilian Synchrotron National Laboratory - LNLS) | # Known detectors for reversed-phi at MX2 beamline (Brazilian Synchrotron National Laboratory - LNLS) | ||
# Known detectors for reversed-phi at CHESS F1 PILATUS3 6M, S/N 60-0127 | # Known detectors for reversed-phi at CHESS F1 PILATUS3 6M, S/N 60-0127 | ||
# Known detectors for reversed-phi at SSRF BL18U1 (S/N 60-0123) and BL19U1 (S/N XX-XXX) (!; 2019-10-19: staff will fix this) | |||
DET_SN=`grep "Detector:" tmp2 | sed "s/^.*Detector: *//"` | DET_SN=`grep "Detector:" tmp2 | sed "s/^.*Detector: *//"` | ||
REVERSEPHI_SNs=" | REVERSEPHI_SNs=" | ||
Line 467: | Line 507: | ||
PILATUS 2M, S/N 24-0109 | PILATUS 2M, S/N 24-0109 | ||
PILATUS3 6M, S/N 60-0127 | PILATUS3 6M, S/N 60-0127 | ||
PILATUS3 6M, S/N 60-0123 | |||
" | " | ||
if echo "${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 479: | Line 524: | ||
fi | fi | ||
# insert similar code for Petra P14 here | # insert similar code for Petra P14 here | ||
elif [ "$DET" == "eiger" ]; then | elif [ "$DET" == "eiger" ]; then | ||
OVERLOAD=`h5dump -d "/entry/instrument/detector/detectorSpecific/countrate_correction_count_cutoff" $FIRSTFRAME | awk '/\(0\):/{print $2}' ` | # find out if HDF5 from Diamond (DLS=1) or Dectris (DLS=0) | ||
DLS=0 | |||
OVERLOAD=`h5dump -d "/entry/instrument/detector/detectorSpecific/countrate_correction_count_cutoff" $FIRSTFRAME 2>/dev/null` || DLS=1 | |||
if [ "$DLS" == 1 ]; then | |||
echo Eiger HDF5 from Diamond | |||
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)" | |||
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 | |||
# rotation_axis=`h5dump -a "/entry/sample/transformations/omega/vector" $FIRSTFRAME 2>/dev/null | grep "(0):" | sed -e "s/^.*://; s/,//g"` | |||
# the above gives -1 0 0 for DLS data instead of the correct 1 0 0, so commented out for now | |||
else | |||
echo Eiger HDF5 from Dectris | |||
OVERLOAD=`h5dump -d "/entry/instrument/detector/detectorSpecific/countrate_correction_count_cutoff" $FIRSTFRAME | awk '/\(0\):/{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 to allow negative values : | |||
STARTING_ANGLE=`h5dump -d "/entry/sample/goniometer/omega_start" $FIRSTFRAME | awk '/\(0\): [\-0-9]/{print $2}'` | |||
# 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"` | |||
# 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 | |||
fi | |||
DETECTOR="EIGER MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD= $OVERLOAD" | DETECTOR="EIGER MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD= $OVERLOAD" | ||
QX=`h5dump -d "/entry/instrument/detector/x_pixel_size" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2*1000}'` | QX=`h5dump -d "/entry/instrument/detector/x_pixel_size" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2*1000}'` | ||
QY=`h5dump -d "/entry/instrument/detector/y_pixel_size" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2*1000}'` | QY=`h5dump -d "/entry/instrument/detector/y_pixel_size" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2*1000}'` | ||
echo | echo OVERLOAD=$OVERLOAD | ||
SENSOR_THICKNESS=`h5dump -d "/entry/instrument/detector/sensor_thickness" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2*1000}'` | SENSOR_THICKNESS=`h5dump -d "/entry/instrument/detector/sensor_thickness" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2*1000}'` | ||
X_RAY_WAVELENGTH=`h5dump -d "/entry/instrument/beam/incident_wavelength" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2}'` | X_RAY_WAVELENGTH=`h5dump -d "/entry/instrument/beam/incident_wavelength" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2}'` | ||
Line 496: | Line 568: | ||
ORGY=`h5dump -d "/entry/instrument/detector/beam_center_y" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2}'` | ORGY=`h5dump -d "/entry/instrument/detector/beam_center_y" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2}'` | ||
# find DETECTOR_DISTANCE | # find DETECTOR_DISTANCE : | ||
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 $2*1000}'` | ||
SEPMIN=4 | |||
CLUSTER_RADIUS=2 | |||
elif [ "$DET" == "raxis" ]; then | elif [ "$DET" == "raxis" ]; then | ||
echo Data from a RAXIS detector | echo Data from a RAXIS detector | ||
Line 525: | Line 596: | ||
elif [ "$DET" == "dtrek" ]; then | elif [ "$DET" == "dtrek" ]; then | ||
echo "Data from a RAXIS or Saturn detector with dTREK format" | echo "Data from a RAXIS or Saturn or Pilatus detector with dTREK format" | ||
sed s/\;// tmp2 > tmp1 | sed s/\;// tmp2 > tmp1 | ||
Line 531: | Line 602: | ||
dname=`grep "DETECTOR_NAMES=" tmp2 | sed -e "s/.*=//"` | dname=`grep "DETECTOR_NAMES=" tmp2 | sed -e "s/.*=//"` | ||
flip=1 | |||
if [ "$dname" == "CCD_" ]; then | if [ "$dname" == "CCD_" ]; then | ||
DETECTOR="SATURN MINIMUM_VALID_PIXEL_VALUE=1" | DETECTOR="SATURN MINIMUM_VALID_PIXEL_VALUE=1" | ||
Line 548: | Line 619: | ||
echo "" | echo "" | ||
fi | fi | ||
elif [ "$dname" == "PILT_" ]; then | |||
DETECTOR="PILATUS MINIMUM_VALID_PIXEL_VALUE=0" | |||
dtrek_det="pilatus" | |||
SEPMIN=3 | |||
CLUSTER_RADIUS=1.5 | |||
rotation_axis="0 1 0" # TODO: read from header | |||
flip=-1 | |||
SENSOR_THICKNESS=0.45 # TODO: read from header | |||
# 2theta | |||
TWOTHETA=`awk '/PILT_GONIO_VALUES=/{print $2}' tmp2` | |||
echo TWOTHETA=$TWOTHETA | |||
R1=`echo "scale=7; c($TWOTHETA/$DEGTOR)" | bc -l` | |||
R3=`echo "scale=7; -s($TWOTHETA/$DEGTOR)" | bc -l` | |||
DIRECTION_OF_DETECTOR_X_AXIS="$R1 0 $R3" | |||
elif [ "$dname" == "RX_" ]; then | |||
DETECTOR="RAXIS MINIMUM_VALID_PIXEL_VALUE=0" | DETECTOR="RAXIS MINIMUM_VALID_PIXEL_VALUE=0" | ||
dtrek_det="raxis" | dtrek_det="raxis" | ||
else | |||
DETECTOR="XXX MINIMUM_VALID_PIXEL_VALUE=XXX" | |||
dtrek_det="unknown" | |||
fi | fi | ||
# find OVERLOAD | # find OVERLOAD | ||
SATURATED_VALUE=`grep SATURATED_VALUE tmp2 | head -1 | sed s/SATURATED_VALUE=//` | SATURATED_VALUE=`grep SATURATED_VALUE tmp2 | head -1 | sed s/SATURATED_VALUE=//` | ||
Line 582: | Line 669: | ||
idx=$((i-1)) | idx=$((i-1)) | ||
if [ "${GONIO_NAMES[$idx]}" == "Distance" ]; then | if [ "${GONIO_NAMES[$idx]}" == "Distance" ]; then | ||
DETECTOR_DISTANCE="${GONIO_VALUES[$idx]}" | |||
# TODO: Check unit!! - ${GONIO_UNITS[$idx]} | |||
fi | |||
if [ $flip -gt 0 ]; then | |||
DETECTOR_DISTANCE="-${GONIO_VALUES[$idx]}" | DETECTOR_DISTANCE="-${GONIO_VALUES[$idx]}" | ||
# TODO: Check unit!! - ${GONIO_UNITS[$idx]} | # TODO: Check unit!! - ${GONIO_UNITS[$idx]} | ||
echo "using distance <0" | |||
fi | fi | ||
done | done | ||
Line 611: | Line 703: | ||
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 | ||
echo "Data from a Bruker-cbf detector" | echo "Data from a Bruker-cbf detector" | ||
# MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT: | # MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT: | ||
MNOPIAS=6 | MNOPIAS=6 | ||
Line 642: | Line 750: | ||
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 $KAPPA | ||
Line 726: | Line 835: | ||
STRONG_PIXEL=4 ! COLSPOT: only use strong reflections (default is 3) | STRONG_PIXEL=4 ! COLSPOT: only use strong reflections (default is 3) | ||
MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=$MNOPIAS ! default of 6 is sometimes too high | MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=$MNOPIAS ! default of 6 is sometimes too high | ||
! close spots/long cell axis: reduce SEPMIN and CLUSTER_RADIUS from their defaults of | ! close spots/long cell axis: reduce SEPMIN and CLUSTER_RADIUS from their defaults of 7 and 3.5 | ||
SEPMIN=$SEPMIN CLUSTER_RADIUS=$CLUSTER_RADIUS ! 4 and 2 for Pixel Array Detectors | |||
! since XDS 01-MAR-2015, POSITION supersedes DISTANCE. | ! since XDS 01-MAR-2015, POSITION supersedes DISTANCE. | ||
! nowadays headers are usually correct so refine POSITION in INTEGRATE but not IDXREF | ! nowadays headers are usually correct so refine POSITION in INTEGRATE but not IDXREF if low to medium resolution | ||
REFINE(IDXREF)=CELL BEAM ORIENTATION AXIS ! | ! however, if the spots from COLSPOT extend to 2A then POSITION could, and if 1.5A POSITION should be refined | ||
REFINE(INTEGRATE)= POSITION BEAM ORIENTATION ! AXIS CELL | REFINE(IDXREF)=CELL BEAM ORIENTATION AXIS ! add POSITION if high resolution, or DETECTOR_DISTANCE inaccurate | ||
REFINE(INTEGRATE)= POSITION BEAM ORIENTATION ! AXIS CELL . If 1.5A or higher it is ok to refine CELL | |||
! REFINE(CORRECT)=CELL BEAM ORIENTATION AXIS POSITION ! Default is: refine everything | ! REFINE(CORRECT)=CELL BEAM ORIENTATION AXIS POSITION ! Default is: refine everything | ||
Line 745: | Line 855: | ||
if [ "$DET" == "eiger" ] && [ "$is_h5" == 1 ]; then | if [ "$DET" == "eiger" ] && [ "$is_h5" == 1 ]; then | ||
if [ -e /usr/local/lib64/dectris-neggia.so ]; then | if [ "$DLS" == 0 ] ; then | ||
if [ -e /usr/local/lib64/dectris-neggia.so ]; then | |||
echo LIB=/usr/local/lib64/dectris-neggia.so >> XDS.INP | |||
echo LIB= line was written to XDS.INP | |||
else | |||
echo !LIB=/usr/local/lib64/dectris-neggia.so >> XDS.INP | |||
echo /usr/local/lib64/dectris-neggia.so was not found - specify location manually! | |||
fi | |||
else | else | ||
echo !LIB=/usr/local/lib64/ | if [ -e /usr/local/lib64/durin-plugin.so ]; then | ||
echo LIB=/usr/local/lib64/durin-plugin.so >> XDS.INP | |||
fi | echo LIB= line was written to XDS.INP | ||
else | |||
echo !LIB=/usr/local/lib64/durin-plugin.so >> XDS.INP | |||
echo /usr/local/lib64/durin-plugin.so was not found - specify location manually! | |||
fi | |||
fi | |||
fi | fi | ||
Line 767: | Line 887: | ||
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 [ "$REVERSE_PHI" == "no" ]; then | ||
echo 'ROTATION_AXIS=1 0 0 ! Australian Synchrotron, SERCAT ID-22 (?), APS 19-ID (?), ESRF BM30A, SPring-8, SSRF | echo 'ROTATION_AXIS=1 0 0 ! Australian Synchrotron, SERCAT ID-22 (?), APS 19-ID (?), ESRF BM30A, SPring-8, SSRF need -1 0 0. Diamond ID24 needs 0 -1 0' >> XDS.INP | ||
else | else | ||
echo 'ROTATION_AXIS=-1 0 0 ! if this is wrong, please contact author.' >> XDS.INP | echo 'ROTATION_AXIS=-1 0 0 ! if this is wrong, please contact author.' >> XDS.INP | ||
Line 811: | Line 931: | ||
elif [ "$DET" == "pilatus" -o "$DET" == "eiger" ]; then | elif [ "$DET" == "pilatus" -o "$DET" == "eiger" ]; then | ||
cat >> XDS.INP << eof | cat >> XDS.INP << eof | ||
NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA=13 ! Default is 9 - Increasing may improve data | NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA=13 ! Default is 9 - Increasing may improve data | ||
NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA=13 ! accuracy, particularly if finely-sliced on phi, | NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA=13 ! accuracy, particularly if finely-sliced on phi, | ||
Line 906: | Line 1,025: | ||
echo BKGPIX.cbf, and the agreement of predicted and observed spots in FRAME.cbf! | echo BKGPIX.cbf, and the agreement of predicted and observed spots in FRAME.cbf! | ||
rm -f tmp1 tmp2 | rm -f tmp1 tmp2 | ||
</pre> | </pre> | ||
Line 957: | Line 1,075: | ||
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 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) | ||
Line 967: | Line 1,090: | ||
sudo apt-get install coreutils binutils gawk sed bc grep python hdf5-tools | sudo apt-get install coreutils binutils gawk sed bc grep python hdf5-tools | ||
See also [Installation]. | See also [[Installation]]. | ||
== Limitations == | == Limitations == | ||
* The script tries to interpret the header of the frames, so is currently limited to Dectris (Pilatus, Eiger), ADSC (Quantum), Rigaku (several types), MAR (CCD and image plate) detectors, and one Bruker detector. Other detectors need some values to be manually filled into XDS.INP - the relevant places are marked with XXX. These are detector properties (type, pixel size and number, min and max counts in a pixel), and experimental parameters like | * The script tries to interpret the header of the frames, so is currently limited to Dectris (Pilatus, Eiger), ADSC (Quantum), Rigaku (several types), MAR (CCD and image plate) detectors, and one Bruker detector. Other detectors need some values to be manually filled into XDS.INP - the relevant places are marked with XXX. These are detector properties (type, pixel size and number, min and max counts in a pixel), and experimental parameters like ROTATION_AXIS, OSCILLATION_RANGE, X-RAY_WAVELENGTH, DETECTOR_DISTANCE, and XORG, YORG. For fine-tuning of detector parameters, see the [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_prepare.html detector-specific templates]. | ||
* The authors have made a "best effort" to provide a XDS.INP that results in the correct sign of the anomalous signal. In the case of one detector type (internally called Rigaku SMV) this requires reversal of one detector axis, and a negative DETECTOR_DISTANCE, as is found in some of the [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_prepare.html detector-specific templates]. '''For an unusual or unknown detector setup, the correct sign of the anomalous signal needs to be established and verified e.g. with a good dataset from a test crystal that has | * The authors have made a "best effort" to provide a XDS.INP that results in the correct sign of the anomalous signal. In the case of one detector type (internally called Rigaku SMV) this requires reversal of one detector axis, and a negative DETECTOR_DISTANCE, as is found in some of the [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_prepare.html detector-specific templates]. '''For an unusual or unknown detector setup, the correct sign of the anomalous signal needs to be established and verified e.g. with a good dataset from a test crystal that has an anomalous signal.''' The authors do not take any responsibility for problems arising from incorrect sign of the anomalous signal, nor - obviously! - for any other mischief arising in or from data processing. | ||
* At some beamlines, the ROTATION_AXIS should be -1 0 0 ("backwards") instead of the usual 1 0 0 ("horizontal"), or even 0 1 0 ("vertical") like at one of the PETRA Hamburg BLs. We have only just started the article [[Beamline notes]], and the frame headers do not have this information, so the default chosen by [[generate_XDS.INP]] may be wrong and need manual correction. | * At some beamlines, the ROTATION_AXIS should be -1 0 0 ("backwards") instead of the usual 1 0 0 ("horizontal"), or even 0 1 0 ("vertical") like at one of the PETRA Hamburg BLs. We have only just started the article [[Beamline notes]], and the frame headers do not have this information, so the default chosen by [[generate_XDS.INP]] may be wrong and need manual correction. | ||
* Sometimes, the x- and y- values of the primary beam position recorded in the header should be used for ORGY and ORGX (i.e reversed) instead of as ORGX and ORGY. For ADSC, this has been implemented in the script for a number of beamlines. | * Sometimes, the x- and y- values of the primary beam position recorded in the header should be used for ORGY and ORGX (i.e reversed) instead of as ORGX and ORGY. For ADSC, this has been implemented in the script for a number of beamlines. |