Generate XDS.INP: Difference between revisions

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(formulas for SEPMIN and CLUSTER_RADIUS)
(→‎The script: rev 0.22)
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<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="0.21 (15-Jul-2011)"
# 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 [ ${#TMP_FILENAME} -gt 65 ]; then                        
echo "---> Unable to proceed: image filename "
        echo "---> Unable to proceed: image filename "          
echo "--->  \"${TMP_FILENAME}\""
        echo "--->  \"${TMP_FILENAME}\""                        
         echo "---> exceeds 72 characters."
         echo "---> exceeds 72 characters."                      
         echo "---> Please rename files or set links."
         echo "---> Please rename files or set links."            
exit
        exit                                                    
     else
     else                                                        
echo "---> Warning: Template name exceeds 72 characters. Setting link \"images\""
        echo "---> Warning: Template name exceeds 72 characters. Setting link \"images\""
         echo "              to image directory"
         echo "              to image directory"                                        
TMP_DIRNAME=$(dirname ${TMP_PATH})
        TMP_DIRNAME=$(dirname ${TMP_PATH})                                              
if [ -e "images" ]; then
        if [ -e "images" ]; then                                                        
    echo "***  Error:  The file or directory \"images\" already exists. Please remove"
            echo "***  Error:  The file or directory \"images\" already exists. Please remove"
    echo "              and re-run."
            echo "              and re-run."                                                  
    exit
            exit                                                                              
else
        else                                                                                  
    ln -s ${TMP_DIRNAME} images
            ln -s ${TMP_DIRNAME} images                                                      
fi
        fi                                                                                    
NAME_TEMPLATE_OF_DATA_FRAMES="images/${1##/*/}"
        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}\""
        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"
  SENSOR_THICKNESS=0.32
   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
! longest cell axis is DETECTOR_DISTANCE*X-RAY_WAVELENGTH/(SEPMIN*QX) ; CLUSTER_RADIUS=SEPMIN/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>


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