Difference between revisions of "Generate XDS.INP"

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(bugfix)
Line 1: Line 1:
 
This script should be in your $PATH as "generate_XDS.INP" . As the name suggests, it generates XDS.INP based on a list of frame names supplied on the commandline.
 
This script should be in your $PATH as "generate_XDS.INP" . As the name suggests, it generates XDS.INP based on a list of frame names supplied on the commandline.
Currently works for MarCCD, ADSC and Pilatus 6M detectors.
+
Currently works for MarCCD, ADSC and Pilatus 6M detectors. Also supports bzip2-ed frames (leave out the .bz2 extension, as [http://strucbio.biologie.uni-konstanz.de/~dikay/XDS_html_doc/html_doc/xds_parameters.html#NAME_TEMPLATE_OF_DATA_FRAMES= documented] for XDS!).
  
 
<pre>
 
<pre>
Line 23: Line 23:
 
# 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=0.16
+
# revision 0.17 . KD 3/2011 - make it work for .bz2 frames; improve screen output
 +
REVISION=0.17
 
#
 
#
 
# usage: e.g. generate_XDS.INP "frms/mydata_1_???.img"
 
# usage: e.g. generate_XDS.INP "frms/mydata_1_???.img"
Line 41: Line 42:
 
#
 
#
 
# ====== Start of script ======
 
# ====== Start of script ======
echo generate_XDS.INP version $REVISION . Latest version at http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP
+
echo generate_XDS.INP version $REVISION . Obtain the latest version from
 +
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!
 
   exit
 
   exit
 
fi
 
fi
Line 66: Line 69:
 
# 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 $1 | head -1)
+
     TMP_PATH=$(/bin/ls -C1 $1 $1.bz2 | head -1)
 
     TMP_FILENAME=$(basename ${TMP_PATH})
 
     TMP_FILENAME=$(basename ${TMP_PATH})
 
     if [ ${#TMP_FILENAME} -gt 65 ]; then
 
     if [ ${#TMP_FILENAME} -gt 65 ]; then
Line 85: Line 88:
 
    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 previous line changed to:
 +
      NAME_TEMPLATE_OF_DATA_FRAMES="images/${TMP_FILENAME}"  
 
echo "              Using template filename \"${NAME_TEMPLATE_OF_DATA_FRAMES}\""
 
echo "              Using template filename \"${NAME_TEMPLATE_OF_DATA_FRAMES}\""
 
     fi
 
     fi
Line 92: Line 97:
 
# 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 | egrep -v "_00000.cbf|_000.img" > tmp1 || exit 1
+
/bin/ls -C1 $1 $1.bz2 | egrep -v "_00000.cbf|_000.img" > tmp1 || exit 1
  
 
# we can continue - the frames are found
 
# we can continue - the frames are found
echo Full documentation, including complete detector templates and XDS binaries, can be found at
 
echo http://www.mpimf-heidelberg.mpg.de/~kabsch/xds . More documentation: see XDSwiki
 
  
 
# 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)
Line 109: Line 112:
 
# find out detector type
 
# find out detector type
 
DET=XXX
 
DET=XXX
strings `head -1 tmp1` | egrep -q 'marccd|Corrected' && DET=mccd
+
FIRSTFRAME=`head -1 tmp1`
strings `head -1 tmp1` | grep -q PILATUS            && DET=pilatus
+
echo $FIRSTFRAME | grep -q bz2 && bzcat $FIRSTFRAME > tmp1 && FIRSTFRAME=tmp1
strings `head -1 tmp1` | grep -q BEAM_CENTER_X      && DET=adsc
+
strings $FIRSTFRAME | egrep -q 'marccd|Corrected' && DET=mccd
 +
strings $FIRSTFRAME | grep -q PILATUS            && DET=pilatus
 +
strings $FIRSTFRAME | grep -q BEAM_CENTER_X      && 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 122: Line 127:
 
# find parameters of first frame
 
# find parameters of first frame
 
elif [ "$DET" == "mccd" ]; then
 
elif [ "$DET" == "mccd" ]; then
 
+
  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
  MARFRAME=`head -1 tmp1`
 
  
 
   # 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 $MARFRAME | 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 $MARFRAME | 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 $MARFRAME | 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 $MARFRAME | 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 $MARFRAME | 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 $MARFRAME | 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 $MARFRAME | 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 $MARFRAME | 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 $MARFRAME | 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 $MARFRAME | 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`
  
Line 176: Line 181:
  
 
   DETECTOR="ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000"
 
   DETECTOR="ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000"
   echo this is an ADSC detector. Obtaining ORGX, ORGY from the header depends on beamline setup.
+
   echo Data from ADSC detector. Obtaining ORGX, ORGY depends on beamline setup:
 
   SENSOR_THICKNESS=0.01
 
   SENSOR_THICKNESS=0.01
   strings `head -1 tmp1` | sed s/\;// > tmp2
+
   strings $FIRSTFRAME | sed s/\;// > tmp2
  
 
       # find X_RAY_WAVELENGTH:
 
       # find X_RAY_WAVELENGTH:
Line 195: Line 200:
 
       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 ATTENTION: 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 ATTENTION: 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/$QX" | bc -l `
       echo ATTENTION: at e.g. ALS 8.2.2 use: ORGX=$ORGX ORGY=$ORGY - this is now written to XDS.INP
+
       echo - at e.g. ALS 8.2.2 use: ORGX=$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:
Line 213: Line 218:
 
   SENSOR_THICKNESS=0.32
 
   SENSOR_THICKNESS=0.32
 
   NX=2463 NY=2527 QX=0.172 QY=0.172
 
   NX=2463 NY=2527 QX=0.172 QY=0.172
   echo this is a Pilatus detector
+
   echo Data from a Pilatus detector
   head -50 `head -1 tmp1` | sed s/#//> tmp2
+
   head -50 $FIRSTFRAME | sed s/#//> tmp2
  
 
       # find X_RAY_WAVELENGTH:
 
       # find X_RAY_WAVELENGTH:
Line 256: Line 261:
 
UNIT_CELL_CONSTANTS= 70 80 90 90 90 90 ! put correct values if known
 
UNIT_CELL_CONSTANTS= 70 80 90 90 90 90 ! put correct values if known
 
INCLUDE_RESOLUTION_RANGE=50 0  ! after CORRECT, insert high resol limit; re-run CORRECT
 
INCLUDE_RESOLUTION_RANGE=50 0  ! after CORRECT, insert high resol limit; re-run CORRECT
 
  
 
FRIEDEL'S_LAW=FALSE    ! This acts only on the CORRECT step
 
FRIEDEL'S_LAW=FALSE    ! This acts only on the CORRECT step
Line 293: Line 297:
 
eof
 
eof
 
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 After running xds, inspect at least BKGPIX.cbf and FRAME.cbf with XDS-Viewer!
+
echo Full documentation, including complete detector templates, is at
 +
echo http://www.mpimf-heidelberg.mpg.de/~kabsch/xds . More documentation in XDSwiki
 +
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!
 
rm -f tmp1 tmp2  
 
rm -f tmp1 tmp2  
 
 
</pre>
 
</pre>

Revision as of 18:06, 30 March 2011

This script should be in your $PATH as "generate_XDS.INP" . As the name suggests, it generates XDS.INP based on a list of frame names supplied on the commandline. Currently works for MarCCD, ADSC and Pilatus 6M detectors. Also supports bzip2-ed frames (leave out the .bz2 extension, as documented for XDS!).

#!/bin/bash
# purpose: generate XDS.INP
#
# tested with some datasets from ALS, SSRL, SLS, ESRF and BESSY; only MARCCD, ADSC/SMV, PILATUS 6M detectors; 
# for other detectors, values marked with XXX must be manually filled in.
#
# revision 0.03 . Kay Diederichs 2/2010 
# 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 0.06 . 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 0.08 . 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 0.10 . 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 0.12 . KD 7/2010 - fix for negative PHISTART
# revision 0.13 . KD 8/2010 - store correct NX NY QX QY in XDS.INP
# revision 0.14 . 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 0.16 . 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
#
# usage: e.g. generate_XDS.INP "frms/mydata_1_???.img"
# 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
# 
# known problems:
# - 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)
#
# notes for debugging of the script:
# - 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
#
# ====== Start of script ======
echo generate_XDS.INP version $REVISION . Obtain the latest version from
echo http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP
if [ "$1" == "help" ] || [ "$1" == "-help" ] || [ "$1" == "-h" ]; then
  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!
  exit
fi
#
# defaults:
#
DETECTOR="XXX MINIMUM_VALID_PIXEL_VALUE=XXX OVERLOAD=XXX"
ORGX=XXX
ORGY=XXX
DETECTOR_DISTANCE=XXX
OSCILLATION_RANGE=XXX
X_RAY_WAVELENGTH=XXX
QX=XXX
QY=XXX
NX=XXX
NY=XXX
SENSOR_THICKNESS=0
# see how we are called:
NAME_TEMPLATE_OF_DATA_FRAMES="$1"

# check that the image template name does not exceed 72 characters
# and set a link if necessary
if [ ${#1} -gt 72 ]; then
    TMP_PATH=$(/bin/ls -C1 $1 $1.bz2 | head -1)
    TMP_FILENAME=$(basename ${TMP_PATH})
    if [ ${#TMP_FILENAME} -gt 65 ]; then
	echo "---> Unable to proceed: image filename "
	echo "--->  \"${TMP_FILENAME}\""
        echo "---> exceeds 72 characters."
        echo "---> Please rename files or set links."	
	exit
    else
	echo "---> Warning: Template name exceeds 72 characters. Setting link \"images\""
        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 previous line changed to:
      NAME_TEMPLATE_OF_DATA_FRAMES="images/${TMP_FILENAME}" 
	echo "              Using template filename \"${NAME_TEMPLATE_OF_DATA_FRAMES}\""
    fi
fi

# 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
/bin/ls -C1 $1 $1.bz2 | egrep -v "_00000.cbf|_000.img" > tmp1 || exit 1

# we can continue - the frames are found

# set upper limit of DATA_RANGE to number of frames (see "limitations" above)
DATA_RANGE=`wc -l tmp1 | awk '{print $1}'`

# set upper limit of SPOT_RANGE to half of DATA_RANGE, but not less than 1
SPOT_RANGE=`echo "scale=0; $DATA_RANGE/2" | bc -l`
SPOT_RANGE=`echo "if ($SPOT_RANGE<1) 1;if ($SPOT_RANGE>1) $SPOT_RANGE" | bc -l`

echo DATA_RANGE=1 $DATA_RANGE

# find out detector type
DET=XXX
FIRSTFRAME=`head -1 tmp1`
echo $FIRSTFRAME | grep -q bz2 && bzcat $FIRSTFRAME > tmp1 && FIRSTFRAME=tmp1
strings $FIRSTFRAME | egrep -q 'marccd|Corrected' && DET=mccd
strings $FIRSTFRAME | grep -q PILATUS             && DET=pilatus
strings $FIRSTFRAME | grep -q BEAM_CENTER_X       && DET=adsc
# identify other detector types in the same way (MAR IP would be straightforward)

# parse ASCII header of first frame

if [ "$DET" == "XXX" ]; then
  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"

# find parameters of first frame
elif [ "$DET" == "mccd" ]; then
  echo Data from a MarCCD detector
  
  DETECTOR="CCDCHESS MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65500"
  SENSOR_THICKNESS=0.01
  # use first frame of dataset to obtain parameters

  # offsets are documented; values can be find in mccd_xdsparams.pl script
  let SKIP=1024+80
  NX=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
  let SKIP=$SKIP+4
  NY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')

  let SKIP=1720
  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`
    
  let SKIP=1024+256+128+256+4
  ORGX=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
  ORGX=`echo "scale=2; $ORGX/1000" | bc -l `
  let SKIP=$SKIP+4
  ORGY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
  ORGY=`echo "scale=2; $ORGY/1000" | bc -l `

  let SKIP=1024+256+128+256+44
  PHISTART=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
  let SKIP=1024+256+128+256+76
  PHIEND=$(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`
  
  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=`echo "scale=10; $QX/1000000" |bc -l `
  let SKIP=$SKIP+4
  QY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
  QY=`echo "scale=10; $QY/1000000" |bc -l `

  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=`echo "scale=5; $X_RAY_WAVELENGTH/100000" | bc -l`

# at most BLs, ORGX and ORGY are in pixels, but sometimes in mm ... guess:
  NXBYFOUR=`echo "scale=0; $NX/4" | bc -l `
  ORGXINT=`echo "scale=0; $ORGX/1" | bc -l `
  if [ $ORGXINT -lt $NXBYFOUR ]; then
     ORGX=`echo "scale=1; $ORGX/$QX" | bc -l`
     ORGY=`echo "scale=1; $ORGY/$QY" | bc -l`
     echo MARCCD detector: header ORGX, ORGY seem to be in mm ... converting to pixels
  else
     echo MARCCD detector: header ORGX, ORGY seem to be in pixel units
  fi

elif [ "$DET" == "adsc" ]; then

  DETECTOR="ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000"
  echo Data from ADSC detector. Obtaining ORGX, ORGY depends on beamline setup:
  SENSOR_THICKNESS=0.01
  strings $FIRSTFRAME | sed s/\;// > tmp2

      # find X_RAY_WAVELENGTH:
      X_RAY_WAVELENGTH=`grep WAVELENGTH tmp2 | head -1 | sed s/WAVELENGTH=//`

      # find NX, QX, ORGX and ORGY:
      NX=`grep SIZE1 tmp2 | tail -1 | sed s/SIZE1=//`
      QX=`grep PIXEL_SIZE tmp2 | sed s/PIXEL_SIZE=//`
# FIXME - next 2 lines should be done properly, from header
      NY=$NX      
      QY=$QX
      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=//`
# fix 2010-04-26 - tell user about possible ORGX, ORGY alternatives -  
# at ESRF and ... (pls fill in!) the following should be used:
      ORGX=`echo "scale=1; $BEAM_CENTER_Y/$QX" | bc -l `
      ORGY=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l `
      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, ...
      ORGX=`echo "scale=1; $NX-$BEAM_CENTER_X/$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 
# 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 `
      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
# 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:
      DETECTOR_DISTANCE=`grep DISTANCE tmp2 | sed s/DISTANCE=//`
      OSCILLATION_RANGE=`grep OSC_RANGE tmp2 | sed s/OSC_RANGE=//`

elif [ "$DET" == "pilatus" ]; then
  DETECTOR="PILATUS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD= 1048576  !PILATUS 6M"
  SENSOR_THICKNESS=0.32
  NX=2463 NY=2527 QX=0.172 QY=0.172
  echo Data from a Pilatus detector
  head -50 $FIRSTFRAME | sed s/#//> tmp2

      # find X_RAY_WAVELENGTH:
      X_RAY_WAVELENGTH=`grep Wavelength tmp2 | sed -e s/Wavelength// -e s/A// | awk '{print $1}'`

      # find ORGX and ORGY:
      ORGX=`grep Beam_xy tmp2 | sed -e s/\(// -e s/\)// -e s/\,// | awk '{print $2}'`
      ORGY=`grep Beam_xy tmp2 | sed -e s/\(// -e s/\)// -e s/\,// | awk '{print $3}'`

      # find DETECTOR_DISTANCE and OSCILLATION_RANGE:
      DETECTOR_DISTANCE=`awk '/distance/{print $2}' tmp2`
      DETECTOR_DISTANCE=`echo "$DETECTOR_DISTANCE*1000" | bc -l`

      OSCILLATION_RANGE=`awk '/Angle/{print $2}' tmp2`

else
  echo should never come here
  exit 1
fi

echo ORGX= $ORGX ORGY= $ORGY - check these values with adxv !
echo DETECTOR_DISTANCE= $DETECTOR_DISTANCE
echo OSCILLATION_RANGE= $OSCILLATION_RANGE
echo X-RAY_WAVELENGTH= $X_RAY_WAVELENGTH

# now we know everything that is required to generate XDS.INP

cat > XDS.INP << eof
JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT
ORGX= $ORGX ORGY= $ORGY  ! check these values with adxv !
DETECTOR_DISTANCE= $DETECTOR_DISTANCE
OSCILLATION_RANGE= $OSCILLATION_RANGE
X-RAY_WAVELENGTH= $X_RAY_WAVELENGTH
NAME_TEMPLATE_OF_DATA_FRAMES=$NAME_TEMPLATE_OF_DATA_FRAMES
! REFERENCE_DATA_SET=xxx/XDS_ASCII.HKL ! e.g. to ensure consistent indexing  
DATA_RANGE=1 $DATA_RANGE
SPOT_RANGE=1 $SPOT_RANGE
! BACKGROUND_RANGE=1 10 ! rather use defaults (first 5 degree of rotation)

SPACE_GROUP_NUMBER=0                   ! 0 if unknown
UNIT_CELL_CONSTANTS= 70 80 90 90 90 90 ! put correct values if known
INCLUDE_RESOLUTION_RANGE=50 0  ! after CORRECT, insert high resol limit; re-run CORRECT

FRIEDEL'S_LAW=FALSE     ! This acts only on the CORRECT step
! If the anom signal turns out to be, or is known to be, very low or absent,
! use FRIEDEL'S_LAW=TRUE instead (or comment out the line); re-run CORRECT

! remove the "!" in the following line:
! STRICT_ABSORPTION_CORRECTION=TRUE
! if the anomalous signal is strong: in that case, in CORRECT.LP the three
! "CHI^2-VALUE OF FIT OF CORRECTION FACTORS" values are significantly> 1, e.g. 1.5
!
! exclude (mask) untrusted areas of detector, e.g. beamstop shadow :
! UNTRUSTED_RECTANGLE= 1800 1950 2100 2150 ! x-min x-max y-min y-max ! repeat
! UNTRUSTED_ELLIPSE= 2034 2070 1850 2240 ! x-min x-max y-min y-max ! if needed
!
! parameters with changes wrt default values:
TRUSTED_REGION=0.00 1.2  ! partially use corners of detectors; 1.41421=full use
VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS=7000. 30000. ! often 8000 is ok
MINIMUM_ZETA=0.05        ! integrate close to the Lorentz zone; 0.15 is default
STRONG_PIXEL=6           ! COLSPOT: only use strong reflections (default is 3)
MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=3 ! default of 6 is sometimes too high
REFINE(INTEGRATE)=CELL BEAM ORIENTATION ! AXIS DISTANCE 

! parameters specifically for this detector and beamline:
DETECTOR= $DETECTOR
SENSOR_THICKNESS= $SENSOR_THICKNESS 
! 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)
NX= $NX NY= $NY  QX= $QX  QY= $QY ! to make CORRECT happy if frames are unavailable
DIRECTION_OF_DETECTOR_X-AXIS=1 0 0
DIRECTION_OF_DETECTOR_Y-AXIS=0 1 0
INCIDENT_BEAM_DIRECTION=0 0 1
ROTATION_AXIS=1 0 0    ! at e.g. SERCAT ID-22, APS 19-ID, Australian Synchrotron this needs to be -1 0 0
FRACTION_OF_POLARIZATION=0.98   ! better value is provided by beamline staff!
POLARIZATION_PLANE_NORMAL=0 1 0
eof
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 http://www.mpimf-heidelberg.mpg.de/~kabsch/xds . More documentation in XDSwiki
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!
rm -f tmp1 tmp2