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Generate XDS.INP: Difference between revisions
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→The script: rev 0.22
(formulas for SEPMIN and CLUSTER_RADIUS) |
(→The script: rev 0.22) |
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| Line 10: | Line 10: | ||
<pre> | <pre> | ||
#!/bin/bash | #!/bin/bash | ||
# purpose: generate XDS.INP | # purpose: generate XDS.INP | ||
# | # | ||
# tested with some datasets from ALS, SSRL, SLS, ESRF and BESSY; only MARCCD, ADSC/SMV, PILATUS detectors; | # tested with some datasets from ALS, SSRL, SLS, ESRF and BESSY; only MARCCD, ADSC/SMV, PILATUS detectors; | ||
# for other detectors, values marked with XXX must be manually filled in. | # for other detectors, values marked with XXX must be manually filled in. | ||
# | # | ||
# revision 0.03 . Kay Diederichs 2/2010 | # revision 0.03 . Kay Diederichs 2/2010 | ||
# revision 0.04 . Kay Diederichs 4/2010 - include alternative ORGX, ORGY calculations for ADSC | # revision 0.04 . Kay Diederichs 4/2010 - include alternative ORGX, ORGY calculations for ADSC | ||
# revision 0.05 . Kay Diederichs 5/2010 - grep for "Corrected" in addition to "marccd"; needed for BESSY | # revision 0.05 . Kay Diederichs 5/2010 - grep for "Corrected" in addition to "marccd"; needed for BESSY | ||
# revision 0.06 . KD 6/2010 - add UNTRUSTED_RECTANGLE and UNTRUSTED_ELLIPSE; use `whereis catmar` and so on | # revision 0.06 . KD 6/2010 - add UNTRUSTED_RECTANGLE and UNTRUSTED_ELLIPSE; use `whereis catmar` and so on | ||
# revision 0.07 . KD 6/2010 - decide about ORGX/Y info in MAR header being pixels or mm; other fixes | # revision 0.07 . KD 6/2010 - decide about ORGX/Y info in MAR header being pixels or mm; other fixes | ||
# revision 0.08 . KD 6/2010 - fixes for Pilatus 6M | # revision 0.08 . KD 6/2010 - fixes for Pilatus 6M | ||
# revision 0.09 . KD 6/2010 - get rid of requirement for mccd_xdsparams.pl and/or catmar; rather use "od" | # revision 0.09 . KD 6/2010 - get rid of requirement for mccd_xdsparams.pl and/or catmar; rather use "od" | ||
# revision 0.10 . Tim Gruene 7/2010 - set link 'images' to image directory if path exceeds 72 characters | # revision 0.10 . Tim Gruene 7/2010 - set link 'images' to image directory if path exceeds 72 characters | ||
# revision 0.11 . KD 7/2010 - for MarCCD: look for distance info at different byte position | # revision 0.11 . KD 7/2010 - for MarCCD: look for distance info at different byte position | ||
# revision 0.12 . KD 7/2010 - fix for negative PHISTART | # revision 0.12 . KD 7/2010 - fix for negative PHISTART | ||
# revision 0.13 . KD 8/2010 - store correct NX NY QX QY in XDS.INP | # revision 0.13 . KD 8/2010 - store correct NX NY QX QY in XDS.INP | ||
# revision 0.14 . KD 1/2011 - SENSOR_THICKNESS for Pilatus; MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=3 | # revision 0.14 . KD 1/2011 - SENSOR_THICKNESS for Pilatus; MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=3 | ||
# revision 0.15 . KD 2/2011 - add comment for -ive sign of APS 19-ID and Australian Synchrotron rotation axis | # revision 0.15 . KD 2/2011 - add comment for -ive sign of APS 19-ID and Australian Synchrotron rotation axis | ||
# revision 0.16 . KD 3/2011 - SENSOR_THICKNESS=0.01 for ADSC and MarCCD. Add comment about SILICON= | # revision 0.16 . KD 3/2011 - SENSOR_THICKNESS=0.01 for ADSC and MarCCD. Add comment about SILICON= | ||
# revision 0.17 . KD 3/2011 - make it work for .bz2 frames; improve screen output | # revision 0.17 . KD 3/2011 - make it work for .bz2 frames; improve screen output | ||
# revision 0.18 . KD 4/2011 - faster by doing "strings" only once; revert "images/${1##/*/}" "correction" | # revision 0.18 . KD 4/2011 - faster by doing "strings" only once; revert "images/${1##/*/}" "correction" | ||
# revision 0.19 . KD 6/2011 - bugfix for 0.18 | # revision 0.19 . KD 6/2011 - bugfix for 0.18 | ||
# revision 0.20 . KD 7/2011 - redirect stderr of /bin/ls to /dev/null | # revision 0.20 . KD 7/2011 - redirect stderr of /bin/ls to /dev/null | ||
# revision 0.21 . KD 11/2011 - SEPMIN, CLUSTER_RADIUS hints; read NX NY from header (for Pilatus 2M) | # revision 0.21 . KD 11/2011 - SEPMIN, CLUSTER_RADIUS hints; read NX NY from header (for Pilatus 2M) | ||
REVISION="0. | # revision 0.22 . KD 12/2011 - Pilatus 2M UNTRUSTED_RECTANGLE lines, SENSOR_THICKNESS from header | ||
# | REVISION="0.22 (02-Dec-2011)" | ||
# usage: e.g. generate_XDS.INP "frms/mydata_1_???.img" | # | ||
# make sure to have the two quotation marks ! | # usage: e.g. generate_XDS.INP "frms/mydata_1_???.img" | ||
# the ? are wildcards for the frame numbers. | # make sure to have the two quotation marks ! | ||
# | # the ? are wildcards for the frame numbers. | ||
# limitations: | # | ||
# - frame numbers are assumed to start with 1 and run consecutively | # limitations: | ||
# | # - frame numbers are assumed to start with 1 and run consecutively | ||
# known problems: | # | ||
# known problems: | |||
# - 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) | ||
# | # | ||
# 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 -v 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 | ||
# | # | ||
# ====== Start of script ====== | # ====== Start of script ====== | ||
echo generate_XDS.INP version $REVISION . Obtain the latest version from | echo generate_XDS.INP version $REVISION . Obtain the latest version from | ||
echo http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP | echo http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP | ||
if [ "$1" == "help" ] || [ "$1" == "-help" ] || [ "$1" == "-h" ]; then | if [ "$1" == "help" ] || [ "$1" == "-help" ] || [ "$1" == "-h" ]; then | ||
echo usage: generate_XDS.INP \"frms/mydata_1_???.img\" \(_with_ the quotation marks!\) | echo usage: generate_XDS.INP \"frms/mydata_1_???.img\" \(_with_ the quotation marks!\) | ||
echo if the frames are compressed with bzip2, leave out the .bz2 extension! | echo if the frames are compressed with bzip2, leave out the .bz2 extension! | ||
exit | exit | ||
fi | fi | ||
# | # | ||
# defaults: | # defaults: | ||
# | # | ||
DETECTOR="XXX MINIMUM_VALID_PIXEL_VALUE=XXX OVERLOAD=XXX" | DETECTOR="XXX MINIMUM_VALID_PIXEL_VALUE=XXX OVERLOAD=XXX" | ||
ORGX=XXX | ORGX=XXX | ||
ORGY=XXX | ORGY=XXX | ||
DETECTOR_DISTANCE=XXX | DETECTOR_DISTANCE=XXX | ||
OSCILLATION_RANGE=XXX | OSCILLATION_RANGE=XXX | ||
X_RAY_WAVELENGTH=XXX | X_RAY_WAVELENGTH=XXX | ||
QX=XXX | QX=XXX | ||
QY=XXX | QY=XXX | ||
NX=XXX | NX=XXX | ||
NY=XXX | NY=XXX | ||
SENSOR_THICKNESS=0 | SENSOR_THICKNESS=0 | ||
# see how we are called: | # see how we are called: | ||
NAME_TEMPLATE_OF_DATA_FRAMES="$1" | NAME_TEMPLATE_OF_DATA_FRAMES="$1" | ||
# check that the image template name does not exceed 72 characters | # check that the image template name does not exceed 72 characters | ||
# and set a link if necessary | # and set a link if necessary | ||
if [ ${#1} -gt 72 ]; then | if [ ${#1} -gt 72 ]; then | ||
TMP_PATH=$(/bin/ls -C1 $1 $1.bz2 2>/dev/null | head -1) | TMP_PATH=$(/bin/ls -C1 $1 $1.bz2 2>/dev/null | head -1) | ||
TMP_FILENAME=$(basename ${TMP_PATH}) | TMP_FILENAME=$(basename ${TMP_PATH}) | ||
if [ ${#TMP_FILENAME} -gt 65 ]; then | if [ ${#TMP_FILENAME} -gt 65 ]; then | ||
echo "---> Unable to proceed: image filename " | |||
echo "---> \"${TMP_FILENAME}\"" | |||
echo "---> exceeds 72 characters." | echo "---> exceeds 72 characters." | ||
echo "---> Please rename files or set links." | echo "---> Please rename files or set links." | ||
exit | |||
else | else | ||
echo "---> Warning: Template name exceeds 72 characters. Setting link \"images\"" | |||
echo " to image directory" | echo " to image directory" | ||
TMP_DIRNAME=$(dirname ${TMP_PATH}) | |||
if [ -e "images" ]; then | |||
echo "*** Error: The file or directory \"images\" already exists. Please remove" | |||
echo " and re-run." | |||
exit | |||
else | |||
ln -s ${TMP_DIRNAME} images | |||
fi | |||
NAME_TEMPLATE_OF_DATA_FRAMES="images/${1##/*/}" | |||
# KD 30.3.11 I believe the previous line should be changed to: | # KD 30.3.11 I believe the previous line should be changed to: | ||
# NAME_TEMPLATE_OF_DATA_FRAMES="images/${TMP_FILENAME}" | # NAME_TEMPLATE_OF_DATA_FRAMES="images/${TMP_FILENAME}" | ||
# but I have not had the time to properly test this | # but I have not had the time to properly test this | ||
echo " Using template filename \"${NAME_TEMPLATE_OF_DATA_FRAMES}\"" | |||
fi | fi | ||
fi | fi | ||
# list frames matching the wildcards in NAME_TEMPLATE_OF_DATA_FRAMES | # list frames matching the wildcards in NAME_TEMPLATE_OF_DATA_FRAMES | ||
# don't accept the "direct beam" shot at SLS/Pilatus PX-I and PX-II | # don't accept the "direct beam" shot at SLS/Pilatus PX-I and PX-II | ||
/bin/ls -C1 $1 $1.bz2 2>/dev/null | egrep -v "_00000.cbf|_000.img" > tmp1 || exit 1 | /bin/ls -C1 $1 $1.bz2 2>/dev/null | egrep -v "_00000.cbf|_000.img" > tmp1 || exit 1 | ||
| Line 114: | Line 115: | ||
# set upper limit of DATA_RANGE to number of frames (see "limitations" above) | # set upper limit of DATA_RANGE to number of frames (see "limitations" above) | ||
DATA_RANGE=`wc -l tmp1 | awk '{print $1}'` | DATA_RANGE=`wc -l tmp1 | awk '{print $1}'` | ||
# set upper limit of SPOT_RANGE to half of DATA_RANGE, but not less than 1 | # set upper limit of SPOT_RANGE to half of DATA_RANGE, but not less than 1 | ||
SPOT_RANGE=`echo "scale=0; $DATA_RANGE/2" | bc -l` | SPOT_RANGE=`echo "scale=0; $DATA_RANGE/2" | bc -l` | ||
SPOT_RANGE=`echo "if ($SPOT_RANGE<1) 1;if ($SPOT_RANGE>1) $SPOT_RANGE" | bc -l` | SPOT_RANGE=`echo "if ($SPOT_RANGE<1) 1;if ($SPOT_RANGE>1) $SPOT_RANGE" | bc -l` | ||
| Line 123: | Line 124: | ||
# find out detector type | # find out detector type | ||
DET=XXX | DET=XXX | ||
FIRSTFRAME=`head -1 tmp1` | FIRSTFRAME=`head -1 tmp1` | ||
echo $FIRSTFRAME | grep -q bz2 && bzcat $FIRSTFRAME > tmp1 && FIRSTFRAME=tmp1 | echo $FIRSTFRAME | grep -q bz2 && bzcat $FIRSTFRAME > tmp1 && FIRSTFRAME=tmp1 | ||
strings $FIRSTFRAME > tmp2 | strings $FIRSTFRAME > tmp2 | ||
egrep -q 'marccd|Corrected' tmp2 && DET=mccd | egrep -q 'marccd|Corrected' tmp2 && DET=mccd | ||
grep -q PILATUS tmp2 && DET=pilatus | grep -q PILATUS tmp2 && DET=pilatus | ||
grep -q BEAM_CENTER_X tmp2 && DET=adsc | grep -q BEAM_CENTER_X tmp2 && DET=adsc | ||
# identify other detector types in the same way (MAR IP would be straightforward) | # identify other detector types in the same way (MAR IP would be straightforward) | ||
| Line 136: | Line 137: | ||
if [ "$DET" == "XXX" ]; then | if [ "$DET" == "XXX" ]; then | ||
echo "this is not a MAR, ADSC/SMV or PILATUS detector - fill in XXX values manually!" | echo "this is not a MAR, ADSC/SMV or PILATUS detector - fill in XXX values manually!" | ||
DETECTOR="XXX MINIMUM_VALID_PIXEL_VALUE=XXX OVERLOAD=XXX" | DETECTOR="XXX MINIMUM_VALID_PIXEL_VALUE=XXX OVERLOAD=XXX" | ||
# find parameters of first frame | # find parameters of first frame | ||
elif [ "$DET" == "mccd" ]; then | elif [ "$DET" == "mccd" ]; then | ||
echo Data from a MarCCD detector | echo Data from a MarCCD detector | ||
DETECTOR="CCDCHESS MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65500" | DETECTOR="CCDCHESS MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65500" | ||
SENSOR_THICKNESS=0.01 | SENSOR_THICKNESS=0.01 | ||
# use first frame of dataset to obtain parameters | # use first frame of dataset to obtain parameters | ||
# offsets are documented; values can be find in mccd_xdsparams.pl script | # offsets are documented; values can be find in mccd_xdsparams.pl script | ||
let SKIP=1024+80 | let SKIP=1024+80 | ||
NX=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | NX=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | ||
let SKIP=$SKIP+4 | let SKIP=$SKIP+4 | ||
NY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | NY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | ||
let SKIP=1720 | let SKIP=1720 | ||
DETECTOR_DISTANCE=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | DETECTOR_DISTANCE=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | ||
DETECTOR_DISTANCE=`echo "scale=3; $DETECTOR_DISTANCE/1000" | bc -l` | DETECTOR_DISTANCE=`echo "scale=3; $DETECTOR_DISTANCE/1000" | bc -l` | ||
let SKIP=1024+256+128+256+4 | let SKIP=1024+256+128+256+4 | ||
ORGX=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | ORGX=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | ||
ORGX=`echo "scale=2; $ORGX/1000" | bc -l ` | ORGX=`echo "scale=2; $ORGX/1000" | bc -l ` | ||
let SKIP=$SKIP+4 | let SKIP=$SKIP+4 | ||
ORGY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | ORGY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | ||
ORGY=`echo "scale=2; $ORGY/1000" | bc -l ` | ORGY=`echo "scale=2; $ORGY/1000" | bc -l ` | ||
let SKIP=1024+256+128+256+44 | let SKIP=1024+256+128+256+44 | ||
PHISTART=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | PHISTART=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | ||
let SKIP=1024+256+128+256+76 | let SKIP=1024+256+128+256+76 | ||
PHIEND=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | PHIEND=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | ||
OSCILLATION_RANGE=`echo "scale=3; ($PHIEND-($PHISTART))/1000" | bc -l` | OSCILLATION_RANGE=`echo "scale=3; ($PHIEND-($PHISTART))/1000" | bc -l` | ||
let SKIP=1024+256+128+256+128+4 | let SKIP=1024+256+128+256+128+4 | ||
QX=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | QX=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | ||
QX=`echo "scale=10; $QX/1000000" |bc -l ` | QX=`echo "scale=10; $QX/1000000" |bc -l ` | ||
let SKIP=$SKIP+4 | let SKIP=$SKIP+4 | ||
QY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | QY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | ||
QY=`echo "scale=10; $QY/1000000" |bc -l ` | QY=`echo "scale=10; $QY/1000000" |bc -l ` | ||
let SKIP=1024+256+128+256+128+128+12 | let SKIP=1024+256+128+256+128+128+12 | ||
X_RAY_WAVELENGTH=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | X_RAY_WAVELENGTH=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}') | ||
X_RAY_WAVELENGTH=`echo "scale=5; $X_RAY_WAVELENGTH/100000" | bc -l` | X_RAY_WAVELENGTH=`echo "scale=5; $X_RAY_WAVELENGTH/100000" | bc -l` | ||
# at most BLs, ORGX and ORGY are in pixels, but sometimes in mm ... guess: | # at most BLs, ORGX and ORGY are in pixels, but sometimes in mm ... guess: | ||
NXBYFOUR=`echo "scale=0; $NX/4" | bc -l ` | NXBYFOUR=`echo "scale=0; $NX/4" | bc -l ` | ||
ORGXINT=`echo "scale=0; $ORGX/1" | bc -l ` | ORGXINT=`echo "scale=0; $ORGX/1" | bc -l ` | ||
if [ $ORGXINT -lt $NXBYFOUR ]; then | if [ $ORGXINT -lt $NXBYFOUR ]; then | ||
ORGX=`echo "scale=1; $ORGX/$QX" | bc -l` | ORGX=`echo "scale=1; $ORGX/$QX" | bc -l` | ||
ORGY=`echo "scale=1; $ORGY/$QY" | bc -l` | ORGY=`echo "scale=1; $ORGY/$QY" | bc -l` | ||
echo MARCCD detector: header ORGX, ORGY seem to be in mm ... converting to pixels | echo MARCCD detector: header ORGX, ORGY seem to be in mm ... converting to pixels | ||
else | else | ||
echo MARCCD detector: header ORGX, ORGY seem to be in pixel units | echo MARCCD detector: header ORGX, ORGY seem to be in pixel units | ||
fi | fi | ||
elif [ "$DET" == "adsc" ]; then | elif [ "$DET" == "adsc" ]; then | ||
| Line 195: | Line 196: | ||
DETECTOR="ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000" | DETECTOR="ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000" | ||
echo Data from ADSC detector. Obtaining ORGX, ORGY depends on beamline setup: | echo Data from ADSC detector. Obtaining ORGX, ORGY depends on beamline setup: | ||
SENSOR_THICKNESS=0.01 | SENSOR_THICKNESS=0.01 | ||
sed s/\;// tmp2 > tmp1 | sed s/\;// tmp2 > tmp1 | ||
mv tmp1 tmp2 | mv tmp1 tmp2 | ||
# find X_RAY_WAVELENGTH: | # find X_RAY_WAVELENGTH: | ||
| Line 206: | Line 207: | ||
QX=`grep PIXEL_SIZE tmp2 | sed s/PIXEL_SIZE=//` | QX=`grep PIXEL_SIZE tmp2 | sed s/PIXEL_SIZE=//` | ||
# FIXME - next 2 lines should be done properly, from header | # FIXME - next 2 lines should be done properly, from header | ||
NY=$NX | NY=$NX | ||
QY=$QX | QY=$QX | ||
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 - | # fix 2010-04-26 - tell user about possible ORGX, ORGY alternatives - | ||
# at ESRF and ... (pls fill in!) the following should be used: | # at ESRF and ... (pls fill in!) the following should be used: | ||
ORGX=`echo "scale=1; $BEAM_CENTER_Y/$QX" | bc -l ` | ORGX=`echo "scale=1; $BEAM_CENTER_Y/$QX" | bc -l ` | ||
ORGY=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l ` | ORGY=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l ` | ||
echo - at ESRF BLs use: ORGX=$ORGX ORGY=$ORGY | echo - at ESRF BLs use: ORGX=$ORGX ORGY=$ORGY | ||
# 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, ... | ||
ORGX=`echo "scale=1; $NX-$BEAM_CENTER_X/$QX" | bc -l ` | ORGX=`echo "scale=1; $NX-$BEAM_CENTER_X/$QX" | bc -l ` | ||
ORGY=`echo "scale=1; $BEAM_CENTER_Y/$QX" | bc -l ` | ORGY=`echo "scale=1; $BEAM_CENTER_Y/$QX" | bc -l ` | ||
echo - at e.g. ALS 5.0.3 use: ORGX=$ORGX ORGY=$ORGY | echo - at e.g. ALS 5.0.3 use: ORGX=$ORGX ORGY=$ORGY | ||
# this 3rd alternative convention should be used at the following beamlines (pls complete the list): ALS 8.2.2, ... | # this 3rd alternative convention should be used at the following beamlines (pls complete the list): ALS 8.2.2, ... | ||
ORGX=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l ` | ORGX=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l ` | ||
ORGY=`echo "scale=1; $NX-$BEAM_CENTER_Y/$QX" | bc -l ` | ORGY=`echo "scale=1; $NX-$BEAM_CENTER_Y/$QX" | bc -l ` | ||
echo - at e.g. ALS 8.2.2 use: ORGX=$ORGX ORGY=$ORGY - this is written to XDS.INP | echo - at e.g. ALS 8.2.2 use: ORGX=$ORGX ORGY=$ORGY - this is written to XDS.INP | ||
# the latter alternative is written into the generated XDS.INP ! You have to correct this manually in XDS.INP, or adjust this script. | # the latter alternative is written into the generated XDS.INP ! You have to correct this manually in XDS.INP, or adjust this script. | ||
# find DETECTOR_DISTANCE and OSCILLATION_RANGE: | # find DETECTOR_DISTANCE and OSCILLATION_RANGE: | ||
DETECTOR_DISTANCE=`grep DISTANCE tmp2 | sed s/DISTANCE=//` | DETECTOR_DISTANCE=`grep DISTANCE tmp2 | sed s/DISTANCE=//` | ||
OSCILLATION_RANGE=`grep OSC_RANGE tmp2 | sed s/OSC_RANGE=//` | OSCILLATION_RANGE=`grep OSC_RANGE tmp2 | sed s/OSC_RANGE=//` | ||
elif [ "$DET" == "pilatus" ]; then | elif [ "$DET" == "pilatus" ]; then | ||
DETECTOR="PILATUS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD= 1048576 !PILATUS" | DETECTOR="PILATUS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD= 1048576 !PILATUS" | ||
QX=0.172 QY=0.172 | |||
QX=0.172 QY=0.172 | echo Data from a Pilatus detector | ||
echo Data from a Pilatus detector | sed s/#// tmp2 > tmp1 | ||
sed s/#// tmp2 > tmp1 | mv tmp1 tmp2 | ||
mv tmp1 tmp2 | |||
# find X_RAY_WAVELENGTH: | # find SENSOR_THICKNESS: | ||
X_RAY_WAVELENGTH=`grep Wavelength tmp2 | sed -e s/Wavelength// -e s/A// | awk '{print $1}'` | SENSOR_THICKNESS=`grep thickness tmp2 | sed -e s/'Silicon sensor, thickness'// | awk '{print $1*1000}'` | ||
# find X_RAY_WAVELENGTH: | |||
X_RAY_WAVELENGTH=`grep Wavelength tmp2 | sed -e s/Wavelength// -e s/A// | awk '{print $1}'` | |||
# find NX and NY; 2463/2527 is 6M, 1475/1679 is 2M | # find NX and NY; 2463/2527 is 6M, 1475/1679 is 2M | ||
NX=`grep X-Binary-Size-Fastest-Dimension tmp2 | awk '{print $2}'` | NX=`grep X-Binary-Size-Fastest-Dimension tmp2 | awk '{print $2}'` | ||
NY=`grep X-Binary-Size-Second-Dimension tmp2 | awk '{print $2}'` | NY=`grep X-Binary-Size-Second-Dimension tmp2 | awk '{print $2}'` | ||
# find ORGX and ORGY: | # find ORGX and ORGY: | ||
| Line 255: | Line 257: | ||
else | else | ||
echo should never come here | echo should never come here | ||
exit 1 | exit 1 | ||
fi | fi | ||
echo ORGX= $ORGX ORGY= $ORGY - check these values with adxv ! | echo ORGX= $ORGX ORGY= $ORGY - check these values with adxv ! | ||
echo DETECTOR_DISTANCE= $DETECTOR_DISTANCE | echo DETECTOR_DISTANCE= $DETECTOR_DISTANCE | ||
echo OSCILLATION_RANGE= $OSCILLATION_RANGE | echo OSCILLATION_RANGE= $OSCILLATION_RANGE | ||
echo X-RAY_WAVELENGTH= $X_RAY_WAVELENGTH | echo X-RAY_WAVELENGTH= $X_RAY_WAVELENGTH | ||
# now we know everything that is required to generate XDS.INP | # now we know everything that is required to generate XDS.INP | ||
| Line 268: | Line 270: | ||
JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT | JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT | ||
ORGX= $ORGX ORGY= $ORGY ! check these values with adxv ! | ORGX= $ORGX ORGY= $ORGY ! check these values with adxv ! | ||
DETECTOR_DISTANCE= $DETECTOR_DISTANCE | DETECTOR_DISTANCE= $DETECTOR_DISTANCE | ||
OSCILLATION_RANGE= $OSCILLATION_RANGE | OSCILLATION_RANGE= $OSCILLATION_RANGE | ||
X-RAY_WAVELENGTH= $X_RAY_WAVELENGTH | X-RAY_WAVELENGTH= $X_RAY_WAVELENGTH | ||
NAME_TEMPLATE_OF_DATA_FRAMES=$NAME_TEMPLATE_OF_DATA_FRAMES | NAME_TEMPLATE_OF_DATA_FRAMES=$NAME_TEMPLATE_OF_DATA_FRAMES | ||
! REFERENCE_DATA_SET=xxx/XDS_ASCII.HKL ! e.g. to ensure consistent indexing | ! REFERENCE_DATA_SET=xxx/XDS_ASCII.HKL ! e.g. to ensure consistent indexing | ||
DATA_RANGE=1 $DATA_RANGE | DATA_RANGE=1 $DATA_RANGE | ||
SPOT_RANGE=1 $SPOT_RANGE | SPOT_RANGE=1 $SPOT_RANGE | ||
! BACKGROUND_RANGE=1 10 ! rather use defaults (first 5 degree of rotation) | ! BACKGROUND_RANGE=1 10 ! rather use defaults (first 5 degree of rotation) | ||
SPACE_GROUP_NUMBER=0 ! 0 if unknown | SPACE_GROUP_NUMBER=0 ! 0 if unknown | ||
| Line 301: | Line 303: | ||
MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=3 ! default of 6 is sometimes too high | MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=3 ! default of 6 is sometimes too high | ||
! close spots: reduce SEPMIN and CLUSTER_RADIUS from their defaults of 6 and 3, e.g. to 4 and 2 | ! close spots: reduce SEPMIN and CLUSTER_RADIUS from their defaults of 6 and 3, e.g. to 4 and 2 | ||
REFINE(INTEGRATE)=CELL BEAM ORIENTATION ! AXIS DISTANCE | |||
REFINE(INTEGRATE)=CELL BEAM ORIENTATION ! AXIS DISTANCE | |||
! parameters specifically for this detector and beamline: | ! parameters specifically for this detector and beamline: | ||
DETECTOR= $DETECTOR | DETECTOR= $DETECTOR | ||
SENSOR_THICKNESS= $SENSOR_THICKNESS | SENSOR_THICKNESS= $SENSOR_THICKNESS | ||
! attention CCD detectors: for very high resolution (better than 1A) make sure to specify SILICON | ! attention CCD detectors: for very high resolution (better than 1A) make sure to specify SILICON | ||
! as about 32* what CORRECT.LP suggests (absorption of phosphor is much higher than that of silicon) | ! as about 32* what CORRECT.LP suggests (absorption of phosphor is much higher than that of silicon) | ||
NX= $NX NY= $NY QX= $QX QY= $QY ! to make CORRECT happy if frames are unavailable | NX= $NX NY= $NY QX= $QX QY= $QY ! to make CORRECT happy if frames are unavailable | ||
| Line 317: | Line 318: | ||
POLARIZATION_PLANE_NORMAL=0 1 0 | POLARIZATION_PLANE_NORMAL=0 1 0 | ||
eof | eof | ||
if [ "$DET" == "pilatus" ]; then | |||
if [ $NX == "1475" ]; then | |||
cat >> XDS.INP << eof | |||
!EXCLUSION OF VERTICAL DEAD AREAS OF THE PILATUS 2M DETECTOR | |||
UNTRUSTED_RECTANGLE= 486 496 0 1680 | |||
UNTRUSTED_RECTANGLE= 980 990 0 1680 | |||
!EXCLUSION OF HORIZONTAL DEAD AREAS OF THE PILATUS 2M DETECTOR | |||
UNTRUSTED_RECTANGLE= 0 1476 194 214 | |||
UNTRUSTED_RECTANGLE= 0 1476 406 426 | |||
UNTRUSTED_RECTANGLE= 0 1476 618 638 | |||
UNTRUSTED_RECTANGLE= 0 1476 830 850 | |||
UNTRUSTED_RECTANGLE= 0 1476 1042 1062 | |||
UNTRUSTED_RECTANGLE= 0 1476 1254 1274 | |||
UNTRUSTED_RECTANGLE= 0 1476 1466 1486 | |||
eof | |||
# elif [ $NX == "2463" ]; then | |||
# cat >> XDS.INP << eof | |||
#eof | |||
fi | |||
fi | |||
echo XDS.INP is ready for use. The file has only the most important keywords. | echo XDS.INP is ready for use. The file has only the most important keywords. | ||
echo Full documentation, including complete detector templates, is at | echo Full documentation, including complete detector templates, is at | ||
| Line 322: | Line 343: | ||
echo After running xds, inspect, using XDS-Viewer, at least the beamstop mask in | echo After running xds, inspect, using XDS-Viewer, at least the beamstop mask in | ||
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> | ||