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Generate XDS.INP: Difference between revisions
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rev 0.51
(→The script: for REFINE() keywords, add POSITION to DISTANCE because XDS 01-MAR-2015 changes this) |
(rev 0.51) |
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# revision 0.49 . Nobuhisa 2/2015 add detector serial number for AichiSR BL2S1 to beam center convention 1 | # revision 0.49 . Nobuhisa 2/2015 add detector serial number for AichiSR BL2S1 to beam center convention 1 | ||
# revision 0.50 . KD 03/2015 workaround for Mar-1 change of parameter name "DISTANCE" to "POSITION" in REFINE(*) keywords | # revision 0.50 . KD 03/2015 workaround for Mar-1 change of parameter name "DISTANCE" to "POSITION" in REFINE(*) keywords | ||
REVISION="0. | # revision 0.51 . Keitaro 03/2015 add .gz and .xz support and remove limitation - frame numbers can start with any. | ||
REVISION="0.51 (20-Mar-2015)" | |||
# | # | ||
# usage: e.g. generate_XDS.INP "/file/system/frms/mydata_1_???.img" | # usage: e.g. generate_XDS.INP "/file/system/frms/mydata_1_???.img" | ||
# make sure to have the two quotation marks ! | # make sure to have the two quotation marks ! | ||
# the ? are wildcards for the frame numbers. | # the ? are wildcards for the frame numbers. | ||
# | # | ||
# known problems: | # known problems: | ||
| Line 114: | Line 112: | ||
# cope with blanks in directory / file name | # cope with blanks in directory / file name | ||
IFS=$'\n' | IFS=$'\n' | ||
/bin/ls -C1 $1 $1.bz2 2>/dev/null | egrep -v "_00000.cbf|_000.img" > tmp1 || exit 1 | /bin/ls -C1 $1 $1.bz2 $1.gz $1.xz 2>/dev/null | egrep -v "_00000.cbf|_000.img" > tmp1 || exit 1 | ||
unset IFS | unset IFS | ||
# we can continue - the frames are found | # we can continue - the frames are found | ||
# | # Find the first '?' position and the number of '?' to determine DATA_RANGE=. | ||
pos1=`echo "$1" | awk '{print index($0, "?")}'` | |||
pos2=`echo "$1" | sed -e "s/[^\?]//g" | awk '{print length+'$pos1' - 1'}` | |||
data_first=`cat tmp1 | cut -b $pos1-$pos2 | head -n1|bc` | |||
data_last=`cat tmp1 | cut -b $pos1-$pos2 | tail -n1|bc` | |||
DATA_RANGE="$data_first $data_last" | |||
# set | # set SPOT_RANGE to first half of DATA_RANGE | ||
data_num=`wc -l tmp1 | awk '{print $1}'` | |||
data_half=`echo "scale=0; $data_num/2" | bc -l` | |||
data_half=`echo "if ($data_half<=1) 1;if ($data_half>1) $data_half" | bc -l` | |||
spot_last=`echo "scale=0; $data_first+$data_half-1" | bc -l` | |||
SPOT_RANGE="$data_first $spot_last" | |||
echo DATA_RANGE= | echo DATA_RANGE=$DATA_RANGE | ||
# find out detector type | # find out detector type | ||
| Line 131: | Line 136: | ||
IFS=$'\n' | IFS=$'\n' | ||
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 | ||
# for mac/linux compatibility. zcat foo.gz doesn't work on mac. | |||
echo $FIRSTFRAME | grep -q '\.gz$' && zcat < $FIRSTFRAME > tmp1 && FIRSTFRAME=tmp1 | |||
echo $FIRSTFRAME | grep -q '\.xz$' && xzcat $FIRSTFRAME > tmp1 && FIRSTFRAME=tmp1 | |||
strings $FIRSTFRAME > tmp2 | strings $FIRSTFRAME > tmp2 | ||
unset IFS | unset IFS | ||
| Line 458: | Line 467: | ||
NAME_TEMPLATE_OF_DATA_FRAMES=$NAME_TEMPLATE_OF_DATA_FRAMES | NAME_TEMPLATE_OF_DATA_FRAMES=$NAME_TEMPLATE_OF_DATA_FRAMES | ||
! REFERENCE_DATA_SET=xxx/XDS_ASCII.HKL ! e.g. to ensure consistent indexing | ! REFERENCE_DATA_SET=xxx/XDS_ASCII.HKL ! e.g. to ensure consistent indexing | ||
DATA_RANGE= | DATA_RANGE=$DATA_RANGE | ||
SPOT_RANGE= | SPOT_RANGE=$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) | ||