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Generate XDS.INP: Difference between revisions
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rev 0.6.1 (tentative Eiger hdf5 support using h5dump)
(rev 0.6.1 (tentative Eiger hdf5 support using h5dump)) |
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| Line 78: | Line 78: | ||
# revision 0.59 . KD 04/04/2016 check for ADSC detector _after_ checking for dtrek detector, to correct wrong choice for https://zenodo.org/record/45756 | # revision 0.59 . KD 04/04/2016 check for ADSC detector _after_ checking for dtrek detector, to correct wrong choice for https://zenodo.org/record/45756 | ||
# revision 0.60 . KD 04/04/2016 ADSC detector SN=458 at APS 19-ID has reverse phi (https://zenodo.org/record/45756) | # revision 0.60 . KD 04/04/2016 ADSC detector SN=458 at APS 19-ID has reverse phi (https://zenodo.org/record/45756) | ||
REVISION="0. | # revision 0.61 . Keitaro 10/04/2016 Add Eiger hdf5 support (may be incomplete; UNTRUSTED_RECTANGLE=s not set) NEED h5dump. | ||
REVISION="0.61 (10-Apr-2016)" | |||
# | # | ||
# usage: e.g. generate_XDS.INP "/file/system/frms/mydata_1_???.img" | # usage: e.g. generate_XDS.INP "/file/system/frms/mydata_1_???.img" | ||
| Line 146: | Line 147: | ||
spot_last=`echo "scale=0; $data_first+$data_half-1" | bc -l` | spot_last=`echo "scale=0; $data_first+$data_half-1" | bc -l` | ||
SPOT_RANGE="$data_first $spot_last" | SPOT_RANGE="$data_first $spot_last" | ||
FIRSTFRAME=`head -1 tmp1` | |||
echo $FIRSTFRAME | grep "\.h5$" && is_h5=1 || is_h5=0 | |||
if [ "$is_h5" == 1 ]; then | |||
nframes=`h5dump -A -g "/entry/data" $FIRSTFRAME | grep "DATASPACE SIMPLE" | sed -e "s/,.*//" | awk '{a+=$5}END{print a}'` | |||
DATA_RANGE="1 $nframes" | |||
SPOT_RANGE="1 `echo "scale=0; ${nframes}/2"|bc -l`" | |||
fi | |||
echo DATA_RANGE=$DATA_RANGE | echo DATA_RANGE=$DATA_RANGE | ||
| Line 152: | Line 162: | ||
DET=XXX | DET=XXX | ||
IFS=$'\n' | IFS=$'\n' | ||
echo $FIRSTFRAME | grep -q '\.bz2$' && bzcat $FIRSTFRAME > tmp1 && FIRSTFRAME=tmp1 | echo $FIRSTFRAME | grep -q '\.bz2$' && bzcat $FIRSTFRAME > tmp1 && FIRSTFRAME=tmp1 | ||
# for mac/linux compatibility. zcat foo.gz doesn't work on mac. | # for mac/linux compatibility. zcat foo.gz doesn't work on mac. | ||
| Line 158: | Line 167: | ||
echo $FIRSTFRAME | grep -q '\.xz$' && xzcat $FIRSTFRAME > tmp1 && FIRSTFRAME=tmp1 | echo $FIRSTFRAME | grep -q '\.xz$' && xzcat $FIRSTFRAME > tmp1 && FIRSTFRAME=tmp1 | ||
unset IFS | unset IFS | ||
# TODO: whenever FIRSTFRAME is used below, it should be copied to tmp2 (using IFS as above), and tmp2 should be used instead | if [ "$is_h5" == 0 ]; then | ||
# this was done for "mccd", but still has to be done for the "raxis" detector types | strings $FIRSTFRAME > tmp2 | ||
# the reason is that FIRSTFRAME may contain a blank, which makes some commands fail | # TODO: whenever FIRSTFRAME is used below, it should be copied to tmp2 (using IFS as above), and tmp2 should be used instead | ||
egrep -qi 'marccd|Corrected' tmp2 && DET=mccd | # this was done for "mccd", but still has to be done for the "raxis" detector types | ||
grep -q PILATUS tmp2 && DET=pilatus | # the reason is that FIRSTFRAME may contain a blank, which makes some commands fail | ||
head -n1 tmp2 | grep -q "^RAXIS" && DET=raxis | egrep -qi 'marccd|Corrected' tmp2 && DET=mccd | ||
head -n1 tmp2 | grep -q "^R-AXIS" && DET=raxis | grep -q PILATUS tmp2 && DET=pilatus | ||
grep -q "^SOURCE_WAVELENGTH= *1" tmp2 && DET=dtrek | head -n1 tmp2 | grep -q "^RAXIS" && DET=raxis | ||
grep -q BEAM_CENTER_X tmp2 && DET=adsc | head -n1 tmp2 | grep -q "^R-AXIS" && DET=raxis | ||
grep -q mar345 tmp2 && DET=MAR345 | grep -q "^SOURCE_WAVELENGTH= *1" tmp2 && DET=dtrek | ||
grep -q BEAM_CENTER_X tmp2 && DET=adsc | |||
grep -q mar345 tmp2 && DET=MAR345 | |||
else | |||
h5dump -d "/entry/instrument/detector/description" $FIRSTFRAME | grep -i Eiger > /dev/null && DET=eiger | |||
fi | |||
# identify other detector types in the same way | # identify other detector types in the same way | ||
| Line 375: | Line 388: | ||
fi | fi | ||
elif [ "$DET" == "eiger" ]; then | |||
OVERLOAD=`h5dump -d "/entry/instrument/detector/detectorSpecific/countrate_correction_count_cutoff" $FIRSTFRAME | awk '/\(0\):/{print $2}' ` | |||
DETECTOR="EIGER MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD= $OVERLOAD !EIGER" | |||
QX=`h5dump -d "/entry/instrument/detector/x_pixel_size" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2*1000}'` | |||
QY=`h5dump -d "/entry/instrument/detector/y_pixel_size" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2*1000}'` | |||
echo Data from a Eiger hdf5 | |||
SENSOR_THICKNESS=`h5dump -d "/entry/instrument/detector/sensor_thickness" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2*1000}'` | |||
X_RAY_WAVELENGTH=`h5dump -d "/entry/instrument/beam/incident_wavelength" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2}'` | |||
NX=`h5dump -d "/entry/instrument/detector/detectorSpecific/x_pixels_in_detector" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2}'` | |||
NY=`h5dump -d "/entry/instrument/detector/detectorSpecific/y_pixels_in_detector" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2}'` | |||
# find ORGX and ORGY: | |||
ORGX=`h5dump -d "/entry/instrument/detector/beam_center_x" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2}'` | |||
ORGY=`h5dump -d "/entry/instrument/detector/beam_center_y" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2}'` | |||
# find DETECTOR_DISTANCE and OSCILLATION_RANGE: | |||
DETECTOR_DISTANCE=`h5dump -d "/entry/instrument/detector/detector_distance" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2*1000}'` | |||
OSCILLATION_RANGE=`h5dump -d "/entry/sample/goniometer/omega_range_average" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2}'` | |||
# If rotation vector set (NeXus) | |||
rotation_axis=`h5dump -a "/entry/sample/transformations/omega/vector" $FIRSTFRAME | grep "(0):" | sed -e "s/^.*://; s/,//g"` | |||
elif [ "$DET" == "raxis" ]; then | elif [ "$DET" == "raxis" ]; then | ||
echo Data from a RAXIS detector | echo Data from a RAXIS detector | ||
| Line 413: | Line 450: | ||
rotx=`echo "scale=6; -1.0*${tmpmat[0]}" | bc -l` | rotx=`echo "scale=6; -1.0*${tmpmat[0]}" | bc -l` | ||
roty=`echo "scale=6; -1.0*${tmpmat[1]}" | bc -l` | roty=`echo "scale=6; -1.0*${tmpmat[1]}" | bc -l` | ||
rotation_axis="$rotx $roty 0" | |||
if [ `echo "(${tmpmat[0]}*${tmpmat[3]}-(${tmpmat[1]}*${tmpmat[2]}))/1"|bc` -lt 0 ]; then | if [ `echo "(${tmpmat[0]}*${tmpmat[3]}-(${tmpmat[1]}*${tmpmat[2]}))/1"|bc` -lt 0 ]; then | ||
echo "" | echo "" | ||
| Line 561: | Line 598: | ||
eof | eof | ||
else | else | ||
if [ "$ | if [ "$rotation_axis" != "" ]; then | ||
echo "ROTATION_AXIS= $ | echo "ROTATION_AXIS= $rotation_axis" >> XDS.INP | ||
elif [ "$REVERSE_PHI" == "no" ]; then | elif [ "$REVERSE_PHI" == "no" ]; then | ||
echo 'ROTATION_AXIS=1 0 0 ! Australian Synchrotron, SERCAT ID-22 (?), APS 19-ID (?), ESRF BM30A, SPring-8, SSRF BL17U need -1 0 0. Diamond ID24 needs 0 -1 0' >> XDS.INP | echo 'ROTATION_AXIS=1 0 0 ! Australian Synchrotron, SERCAT ID-22 (?), APS 19-ID (?), ESRF BM30A, SPring-8, SSRF BL17U need -1 0 0. Diamond ID24 needs 0 -1 0' >> XDS.INP | ||
| Line 598: | Line 635: | ||
!EXCLUDE_RESOLUTION_RANGE= 1.751 1.691 !ice-ring at 1.721 Angstrom - weak | !EXCLUDE_RESOLUTION_RANGE= 1.751 1.691 !ice-ring at 1.721 Angstrom - weak | ||
eof | eof | ||
if [ "$DET" == "pilatus" ]; then | if [ "$DET" == "pilatus" -o "$DET" == "eiger" ]; then | ||
cat >> XDS.INP << eof | cat >> XDS.INP << eof | ||
SEPMIN=4 CLUSTER_RADIUS=2 | SEPMIN=4 CLUSTER_RADIUS=2 | ||