Generate XDS.INP: Difference between revisions

Generate XDS.INP (view source)

Revision as of 12:01, 15 September 2016

2,702 bytes added , 15 September 2016

rev 0.65 add Bruker Photonics II

Kay

Bureaucrats

2,652

edits

@@ Line 1: / Line 1: @@
-This script generates XDS.INP based on a list of frame names supplied on the commandline. It currently works for MarCCD, ADSC, Pilatus and a few Rigaku detectors; since this is just a bash script, extension to other detectors is very easy.
+This script generates XDS.INP based on a list of frame names supplied on the commandline. It currently works for MarCCD, ADSC, Pilatus, Eiger some Rigaku and one Bruker detector(s); since this is just a bash script, extension to other detectors is very easy.
-The [[Eiger]] detector is not yet implemented in the script, but this will eventually come.
 == Usage ==
@@ Line 83: / Line 81: @@
 # revision 0.64 . KD 16/06/2016 reverse phi @APS 19ID (reported by Wolfram Tempel)
 # revision 0.65 . Keitaro 07/09/2016 Fix for "too many arguments" problem in ls
-REVISION="0.65 (07-Sep-2016)"
+# revision 0.65 . KD 15/09/2016 Add Bruker Photonics II with .cbf frames
+REVISION="0.66 (15-Sep-2016)"
 #
 # usage: e.g. generate_XDS.INP "/file/system/frms/mydata_1_???.img"
@@ Line 122: / Line 121: @@
 SENSOR_THICKNESS=0
 TRUSTED_REGION="0.0 1.2 ! partially use corners of detector (0 1.4143: use all pixels)"
+# default MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT
+MNOPIAS=3
+# default DIRECTION_OF_DETECTOR_X-AXIS
+DIRECTION_OF_DETECTOR_X_AXIS="1 0 0"
+# default FRACTION_OF_POLARIZATION
+pol_frac=0.98
 dname=`echo "$1" | xargs dirname`
@@ Line 191: / Line 196: @@
   grep -q "^SOURCE_WAVELENGTH= *1" tmp2 && DET=dtrek
   grep -q BEAM_CENTER_X tmp2       && DET=adsc
   grep -q mar345 tmp2		 && DET=MAR345
+ grep -q BRUKER tmp2 && grep -q CBF tmp2  && DET=Bruker-cbf
 else
   h5dump -d "/entry/instrument/detector/description" $FIRSTFRAME | grep -i Eiger > /dev/null && DET=eiger
@@ Line 535: / Line 541: @@
   OSCILLATION_RANGE=`grep 'PHI' tmp2 | awk '{print $5-$3}'`
   TRUSTED_REGION="0 0.99"
+elif [ "$DET" == "Bruker-cbf" ]; then
+ echo  "Data from a Bruker-cbf detector"
+# conversion radian / degrees:
+ DEGTOR=57.2957795
+# MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT:
+ MNOPIAS=6
+# use complete detector including corners:
+ TRUSTED_REGION="0 1.42"
+# polarization
+ pol_frac=`awk '/polarizn_source_ratio/{print $2}' tmp2`
+ pol_frac=`echo "${pol_frac}+0.5" | bc -l`
+ OVERLOAD=`awk '/_array_intensities.overload/{print $2}' tmp2`
+ DETECTOR="BRUKER MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=${OVERLOAD}"
+ NX=`awk '/X-Binary-Size-Fastest-Dimension/{print $2}' tmp2`
+ NY=`awk '/X-Binary-Size-Second-Dimension/{print $2}' tmp2`
+ QX=`awk '/ELEMENT_X ELEMENT_X/{print $4}' tmp2`
+ QY=`awk '/ELEMENT_Y ELEMENT_Y/{print $4}' tmp2`
+# ORGX/Y-offsets relative to center of detector:
+ ORGX=`grep " 0 0 ? ? ?" tmp2 | awk '/ H /{print $2}'`
+ ORGY=`grep " 0 0 ? ? ?" tmp2 | awk '/ V /{print $2}'`
+# total ORGX/Y
+ ORGX=`echo "scale=2; ${NX}/2+($ORGX/$QX)" | bc -l`
+ ORGY=`echo "scale=2; ${NY}/2-($ORGY/$QY)" | bc -l`
+ DETECTOR_DISTANCE=`grep "0 0 ? ? ?" tmp2 | awk '/DX /{print $2}'`
+ X_RAY_WAVELENGTH=`awk '/diffrn_radiation_wavelength.wavelength/{print $2}' tmp2`
+ OMEGA=`awk '/OMEGA \? \? \?/{print $5}' tmp2`
+ DELTAOMEGA=`awk '/OMEGA \? \? \?/{print $6}' tmp2`
+ PHI=`awk '/PHI \? \? \?/{print $5}' tmp2`
+ DELTAPHI=`awk '/PHI \? \? \?/{print $6}' tmp2`
+ KAPPA=`awk '/CHI \? \? \?/{print $5}' tmp2`
+ echo OMEGA DELTAOMEGA PHI DELTAPHI KAPPA= $OMEGA $DELTAOMEGA $PHI $DELTAPHI $KAPPA
+# test whether the absolute value of deltaphi is > absolute value of deltaomega
+ if (( $(echo "${DELTAPHI}^2 > ${DELTAOMEGA}^2"|bc -l) )); then
+    echo PHI scan
+    R3=`echo "scale=7; s($KAPPA/$DEGTOR)*s($OMEGA/$DEGTOR)" | bc -l`
+    R1=`echo "scale=7; s($KAPPA/$DEGTOR)*c($OMEGA/$DEGTOR)" | bc -l`
+    R2=`echo "scale=7; c($KAPPA/$DEGTOR)         	  " | bc -l`
+    rotation_axis="$R1 $R2 $R3"
+    OSCILLATION_RANGE=${DELTAPHI}
+# here we could check if DELTAPHI is <0, and if so, negate it and rotation_axis
+ else
+    echo OMEGA scan
+    rotation_axis="0 -1 0"
+    OSCILLATION_RANGE=${DELTAOMEGA}
+# here we could check if DELTAOMEGA is <0, and if so, negate it and rotation_axis
+ fi
+# 2theta
+  TWOTHETA=`awk '/TWOTHETA \? \? \?/{print $5}' tmp2`
+  echo TWOTHETA=$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 $R3"
+# end of Bruker-cbf section
 else
    echo should never come here
@@ Line 584: / Line 648: @@
 VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS=6000. 30000. ! often 7000 or 8000 is ok
 STRONG_PIXEL=4           ! COLSPOT: only use strong reflections (default is 3)
-MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=3 ! default of 6 is sometimes too high
+MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=$MNOPIAS ! default of 6 is sometimes too high
 ! close spots/long cell axis: reduce SEPMIN and CLUSTER_RADIUS from their defaults of 6 and 3
 ! SEPMIN=4  CLUSTER_RADIUS=2 ! should be default for Pilatus and other detectors with low PSF
@@ Line 626: / Line 690: @@
   else
   cat >> XDS.INP << eof
-DIRECTION_OF_DETECTOR_X-AXIS=1 0 0
+DIRECTION_OF_DETECTOR_X-AXIS=$DIRECTION_OF_DETECTOR_X_AXIS
 DIRECTION_OF_DETECTOR_Y-AXIS=0 1 0
 eof
@@ Line 632: / Line 696: @@
   cat >> XDS.INP << eof
 INCIDENT_BEAM_DIRECTION=0 0 1
-FRACTION_OF_POLARIZATION=0.98   ! better value is provided by beamline staff!
+FRACTION_OF_POLARIZATION=${pol_frac}   ! better value is provided by beamline staff!
 POLARIZATION_PLANE_NORMAL=0 1 0
 eof