Generate XDS.INP: Difference between revisions

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# tested with some datasets from ALS, SSRL, SLS, ESRF and BESSY; only MARCCD, ADSC/SMV, PILATUS detectors;  

# revision 0.06 . KD 6/2010 - add UNTRUSTED_RECTANGLE and UNTRUSTED_ELLIPSE; use `whereis catmar` and so on  

# revision 0.15 . KD 2/2011 - add comment for -ive sign of APS 19-ID and Australian Synchrotron rotation axis

# revision 0.21 . KD 11/2011 - SEPMIN, CLUSTER_RADIUS hints; read NX NY from header (for Pilatus 2M)

# - for ADSC detectors, there are at least three ways to obtain ORGX and ORGY values from the header (see below);

# check that the image template name does not exceed 72 characters

# list frames matching the wildcards in NAME_TEMPLATE_OF_DATA_FRAMES

/bin/ls -C1 $1 $1.bz2 2>/dev/null | egrep -v "_00000.cbf|_000.img" > tmp1 || exit 1

# set upper limit of DATA_RANGE to number of frames (see "limitations" above)

# set upper limit of SPOT_RANGE to half of DATA_RANGE, but not less than 1

SPOT_RANGE=`echo "if ($SPOT_RANGE<1) 1;if ($SPOT_RANGE>1) $SPOT_RANGE" | bc -l`

# find out detector type

FIRSTFRAME=`head -1 tmp1`

echo $FIRSTFRAME | grep -q bz2 && bzcat $FIRSTFRAME > tmp1 && FIRSTFRAME=tmp1

# identify other detector types in the same way (MAR IP would be straightforward)

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

   echo "this is not a MAR, ADSC/SMV or PILATUS detector - fill in XXX values manually!"

# find parameters of first frame

   echo Data from a MarCCD detector

   DETECTOR="CCDCHESS MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65500"

   # offsets are documented; values can be find in mccd_xdsparams.pl script

   NX=$(od -t dI --skip-bytes=$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

   DETECTOR_DISTANCE=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')

   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+128+128+12

   X_RAY_WAVELENGTH=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')

# at most BLs, ORGX and ORGY are in pixels, but sometimes in mm ... guess:

     echo MARCCD detector: header ORGX, ORGY seem to be in mm ... converting to pixels

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:

       # find X_RAY_WAVELENGTH:

       QX=`grep PIXEL_SIZE tmp2 | sed s/PIXEL_SIZE=//`

# FIXME - next 2 lines should be done properly, from header

       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 -   

# this 2nd alternative convention should be used at the following beamlines (pls complete the list): ALS 5.0.3, ...

# this 3rd alternative convention should be used at the following beamlines (pls complete the list): ALS 8.2.2, ...  

# the latter alternative is written into the generated XDS.INP ! You have to correct this manually in XDS.INP, or adjust this script.

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

   DETECTOR="PILATUS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD= 1048576  !PILATUS"

       # find NX and NY; 2463/2527 is 6M, 1475/1679 is 2M

       NX=`grep X-Binary-Size-Fastest-Dimension tmp2 | awk '{print $2}'`

       # find ORGX and ORGY:

else

   echo should never come here

echo ORGX= $ORGX ORGY= $ORGY - check these values with adxv !

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

JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT

ORGX= $ORGX ORGY= $ORGY  ! check these values with adxv !

NAME_TEMPLATE_OF_DATA_FRAMES=$NAME_TEMPLATE_OF_DATA_FRAMES

! REFERENCE_DATA_SET=xxx/XDS_ASCII.HKL ! e.g. to ensure consistent indexing   

SPACE_GROUP_NUMBER=0                  ! 0 if unknown

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

! parameters specifically for this detector and beamline:

DETECTOR= $DETECTOR

! 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

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 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!

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