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Generate XDS.INP: Difference between revisions
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More efficient frame string extraction; Print help if multiple arguments; Set full path for frames; Comment out FRACTION_OF_POLARIZATION if wavelength is copper K-alpha; 2-theta offset, rotation axis, starting angle, and flipping updated for all dtrek detectors; Untrusted rectangle for Saturn944
(More efficient frame string extraction; Print help if multiple arguments; Set full path for frames; Comment out FRACTION_OF_POLARIZATION if wavelength is copper K-alpha; 2-theta offset, rotation axis, starting angle, and flipping updated for all dtrek detectors; Untrusted rectangle for Saturn944) |
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<pre> | <pre> | ||
#!/bin/bash | |||
#!/bin/bash | # purpose: generate XDS.INP | ||
# purpose: generate XDS.INP | # | ||
# | # tested with some datasets from ALS, SSRL, SLS, ESRF, BESSY, SPring-8 and PF; only MAR, ADSC/SMV, PILATUS, Eiger, RAXIS (in-house), Bruker (PHOTON II) detectors; | ||
# tested with some datasets from ALS, SSRL, SLS, ESRF, BESSY, SPring-8 and PF; only MAR, ADSC/SMV, PILATUS, Eiger, RAXIS (in-house), Bruker (PHOTON II) detectors; | # for other detectors, values marked with XXX must be manually filled in. | ||
# for other detectors, values marked with XXX must be manually filled in. | # | ||
# | # revision 0.03 . Kay Diederichs 2/2010 | ||
# revision 0.03 . Kay Diederichs 2/2010 | # revision 0.04 . Kay Diederichs 4/2010 - include alternative ORGX, ORGY calculations for ADSC | ||
# 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 0.05 . 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 0.06 . 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 0.07 . 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 0.08 . 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 0.09 . 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 0.10 . 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 0.11 . KD 7/2010 - for MarCCD: look for distance info at different byte position | # revision 0.12 . KD 7/2010 - fix for negative PHISTART | ||
# revision 0.12 . KD 7/2010 - fix for negative PHISTART | # revision 0.13 . KD 8/2010 - store correct NX NY QX QY in XDS.INP | ||
# revision 0.13 . 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 0.14 . 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 0.15 . 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 0.17 . KD 3/2011 - make it work for .bz2 frames; improve screen output | # revision 0.17 . KD 3/2011 - make it work for .bz2 frames; improve screen output | ||
# revision 0.18 . KD 4/2011 - faster by doing "strings" only once; revert "images/${1##/*/}" "correction" | # revision 0.18 . KD 4/2011 - faster by doing "strings" only once; revert "images/${1##/*/}" "correction" | ||
# revision 0.19 . KD 6/2011 - bugfix for 0.18 | # revision 0.19 . KD 6/2011 - bugfix for 0.18 | ||
# revision 0.20 . KD 7/2011 - redirect stderr of /bin/ls to /dev/null | # revision 0.20 . KD 7/2011 - redirect stderr of /bin/ls to /dev/null | ||
# revision 0.21 . KD 11/2011 - SEPMIN, CLUSTER_RADIUS hints; read NX NY from header (for Pilatus 2M) | # revision 0.21 . KD 11/2011 - SEPMIN, CLUSTER_RADIUS hints; read NX NY from header (for Pilatus 2M) | ||
# revision 0.22 . KD 12/2011 - Pilatus 2M UNTRUSTED_RECTANGLE lines, SENSOR_THICKNESS from header | # revision 0.22 . KD 12/2011 - Pilatus 2M UNTRUSTED_RECTANGLE lines, SENSOR_THICKNESS from header | ||
| Line 64: | Line 63: | ||
# revision 0.46 . Keitaro 6/2014 automatically set ROTATION_AXIS=-1 0 0 for Mar225 at SPring-8 BL26B2. | # revision 0.46 . Keitaro 6/2014 automatically set ROTATION_AXIS=-1 0 0 for Mar225 at SPring-8 BL26B2. | ||
# revision 0.47 . Keitaro 7/2014 more generic dTREK format support (Saturn and RAXIS) | # revision 0.47 . Keitaro 7/2014 more generic dTREK format support (Saturn and RAXIS) | ||
# revision 0.48 . Kip Guja 11/2014 add detector serial number for ALS 5.0.2 to beam center convention 1 | # revision 0.48 . Kip Guja 11/2014 add detector serial number for ALS 5.0.2 to beam center convention 1 | ||
# revision 0.49 . Nobuhisa 2/2015 add detector serial number for AichiSR BL2S1 to beam center convention 1 | # revision 0.49 . 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 | ||
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# revision 0.82 . KD 01/03/2018 STARTING_ANGLE for MarCCD/Pilatus/PHOTON, enabling to use dials.rs_mapper with spot2pdb. | # revision 0.82 . KD 01/03/2018 STARTING_ANGLE for MarCCD/Pilatus/PHOTON, enabling to use dials.rs_mapper with spot2pdb. | ||
# revision 0.83 . KD 25/06/2018 for ADSC detector #458 at APS BM19, revert the definition of ROTATION_AXIS=-1 0 0. See "Beamline notes" in this wiki. | # revision 0.83 . KD 25/06/2018 for ADSC detector #458 at APS BM19, revert the definition of ROTATION_AXIS=-1 0 0. See "Beamline notes" in this wiki. | ||
# revision 0.84 . KD 10/10/2018 implement Pilatus detector with d*TREK header | # revision 0.84 . KD 10/10/2018 implement Pilatus detector with d*TREK header | ||
# revision 0.85 . Jie Nan 09/01/2019 STARTING_ANGLE for Eiger | # revision 0.85 . Jie Nan 09/01/2019 STARTING_ANGLE for Eiger | ||
# revision 0.86 . Keitaro 03/05/2019 Add PILATUS3 6M, S/N 60-0123 at SSRF BL18U-1 with ROTATION_AXIS=-1 0 0 | # revision 0.86 . Keitaro 03/05/2019 Add PILATUS3 6M, S/N 60-0123 at SSRF BL18U-1 with ROTATION_AXIS=-1 0 0 | ||
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# revision 0.92 . KD 27/02/2020 read *_master.h5 from Diamond Light Source | # revision 0.92 . KD 27/02/2020 read *_master.h5 from Diamond Light Source | ||
# revision 0.93 . KD 13/03/2020 print out 2theta for MarCCD (DETECTOR_*_AXIS can be derived from this) | # revision 0.93 . KD 13/03/2020 print out 2theta for MarCCD (DETECTOR_*_AXIS can be derived from this) | ||
# revision 0.94 . KD 16/03/2020 bugfix for Bruker-cbf to make bc accept e.g. 3.1e-005 by using awk printf "%.5f" instead of awk print | # revision 0.94 . KD 16/03/2020 bugfix for Bruker-cbf to make bc accept e.g. 3.1e-005 by using awk printf "%.5f" instead of awk print | ||
# revision 0.95 . KD 29/07/2020 fix DLS Eiger HDF5 variant OSCILLATION_RANGE, STARTING_ANGLE. Attention: DLS Eiger variant needs h5dump 1.10 for OVERLOAD! | # revision 0.95 . KD 29/07/2020 fix DLS Eiger HDF5 variant OSCILLATION_RANGE, STARTING_ANGLE. Attention: DLS Eiger variant needs h5dump 1.10 for OVERLOAD! | ||
# revision 0.96 . KD 03/10/2020 make script echo detector serial number if inverted ROTATION_AXIS is detected. | # revision 0.96 . KD 03/10/2020 make script echo detector serial number if inverted ROTATION_AXIS is detected. | ||
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# revision 1.00 . Gleb Bourenkov 10/11/2020 add ROTATION_AXIS=0 -1 0 for beamline P14 (EMBL Hamburg) detectors Eiger 16M S/N E-32-0107; previously Eiger 4M S/N E-08-0107 and PILATUS 6M-F, S/N 60-0115-F | # revision 1.00 . Gleb Bourenkov 10/11/2020 add ROTATION_AXIS=0 -1 0 for beamline P14 (EMBL Hamburg) detectors Eiger 16M S/N E-32-0107; previously Eiger 4M S/N E-08-0107 and PILATUS 6M-F, S/N 60-0115-F | ||
# revision 1.01 . KD 07/12/2020 ROTATION_AXIS=0 -1 0 for Pilatus3 2M, S/N 24-0118 at ID23-2 (http://www.globalphasing.com/autoproc/wiki/index.cgi?BeamlineSettings) | # revision 1.01 . KD 07/12/2020 ROTATION_AXIS=0 -1 0 for Pilatus3 2M, S/N 24-0118 at ID23-2 (http://www.globalphasing.com/autoproc/wiki/index.cgi?BeamlineSettings) | ||
# revision 1.02 . KD 11/01/2021 recognize mar555 detector as mar345 (thanks to Thomas Hauß, HZB) | # revision 1.02 . KD 11/01/2021 recognize mar555 detector as mar345 (thanks to Thomas Hauß, HZB) | ||
# revision 1.03 . Feng Yu 18/7/2021 fix/expand information about Shanghai Synchrotron Radiation Facility (SSRF) | # revision 1.03 . Feng Yu 18/7/2021 fix/expand information about Shanghai Synchrotron Radiation Facility (SSRF) | ||
# revision 1.04 . Zhipu Luo 13/08/2021 extract ORGX,ORGY for electron diffraction from SMV header if the wavelength value starts with 0.0 | # revision 1.04 . Zhipu Luo 13/08/2021 extract ORGX,ORGY for electron diffraction from SMV header if the wavelength value starts with 0.0 | ||
# revision 1.05 . KD specialcase extraction of number of images for BNL detectors E-32-0101 and E-18-0104 | # revision 1.05 . KD specialcase extraction of number of images for BNL detectors E-32-0101 and E-18-0104 | ||
# revision 1.06 . KD fix URLs in output. Availability of Apple M1 processor dectris-neggia-Apple-arm64.so . LC_ALL=C . | # revision 1.06 . KD fix URLs in output. Availability of Apple M1 processor dectris-neggia-Apple-arm64.so . LC_ALL=C . | ||
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# revision 1.11 . KD / Helena Taberman ROTATION_AXIS=-1 0 0 for Eiger .cbf data from Petra P14 | # revision 1.11 . KD / Helena Taberman ROTATION_AXIS=-1 0 0 for Eiger .cbf data from Petra P14 | ||
# revision 1.12 . KD / Helena Taberman correct rev 1.11 to be 0 -1 0 | # revision 1.12 . KD / Helena Taberman correct rev 1.11 to be 0 -1 0 | ||
# revision 1.13 . KD variables for /usr/local/lib64/dectris-neggia.so and durin-plugin.so . Remove h5dump error messages. | # revision 1.13 . KD variables for /usr/local/lib64/dectris-neggia.so and durin-plugin.so . Remove h5dump error messages. | ||
REVISION="1. | # revision 1.14 . Juno Krahn 16/03/2023 Modified initial string header extraction; added exit to awk token extractions | ||
# Print help if multiple arguments (e.g. forgot quotes) or if neither '???' or master.h5 | |||
# Set full path for frames; needed by some tools (e.g. show frame with predicted spots) | |||
# Comment out FRACTION_OF_POLARIZATION if wavelength is copper K-alpha | |||
# 2-theta offset, rotation axis, starting angle, and flipping updated for all dtrek detectors | |||
# Untrusted rectangle for Saturn944 | |||
# Environment variables to define alternate paths for dectris-neggia.so and durin-plugin.so | |||
# Append detector specific parameters from $HOME/.xds-site/${DET}_${DET_SN} | |||
# Cleaned up section for creating XDS.INP | |||
REVISION="1.14 (12-Apr-2023)" | |||
# | # | ||
# 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: | ||
# - for ADSC detectors, there are at least three ways to obtain ORGX and ORGY values from the header (see below); | # - 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) | # - the same might be a problem for MAR headers, too (not sure about this) | ||
# - on macOS, the "Command Line Tools for Xcode" (from https://developer.apple.com/download/more/) are needed. | # - on macOS, the "Command Line Tools for Xcode" (from https://developer.apple.com/download/more/) are needed. | ||
# | # | ||
# notes for debugging of the script: | # notes for debugging of the script: | ||
# - add the -x option to #!/bin/bash in first line, to see where an error occurs | # - add the -x option to #!/bin/bash in first line, to see where an error occurs | ||
# - comment out the removal of tmp1 and tmp2 in the last line | # - comment out the removal of tmp1 and tmp2 in the last line | ||
# | # | ||
# ====== Start of script ====== | # ====== Start of script ====== | ||
echo generate_XDS.INP version $REVISION . Obtain the latest version from | echo generate_XDS.INP version $REVISION . Obtain the latest version from | ||
echo http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP | 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" ] || [ "$1" == "" ] || [ "$2" != "" ] || ! [[ "$1" =~ \?\?|_master\.h5 ]]; then | ||
echo usage: generate_XDS.INP \"/file/system/frms/mydata_1_???.img\" \(_with_ the quotation marks!\) | echo usage: generate_XDS.INP \"/file/system/frms/mydata_1_???.img\" \(_with_ the quotation marks!\) | ||
echo | echo If the frames are compressed leave out the extension .bz2, .gz, or .xz! | ||
exit | echo for .h5 files: generate_XDS.INP /file/system/frms/mydata_1_master.h5 | ||
fi | exit | ||
fi | |||
# make sure the locale does not interfere with e.g. awk calculations: | # make sure the locale does not interfere with e.g. awk calculations: | ||
LC_ALL="C" | export LC_ALL="C" | ||
# | # | ||
# defaults: | # defaults: | ||
# | # | ||
# conversion radian / degrees: | # conversion radian / degrees: | ||
DEGTOR=57.2957795 | DEGTOR=57.2957795 | ||
DETECTOR="XXX MINIMUM_VALID_PIXEL_VALUE=XXX OVERLOAD=XXX" | DETECTOR="XXX MINIMUM_VALID_PIXEL_VALUE=XXX OVERLOAD=XXX" | ||
REVERSE_PHI="no" | REVERSE_PHI="no" | ||
ORGX=XXX | ORGX=XXX | ||
ORGY=XXX | ORGY=XXX | ||
DETECTOR_DISTANCE=XXX | DETECTOR_DISTANCE=XXX | ||
OSCILLATION_RANGE=XXX | OSCILLATION_RANGE=XXX | ||
X_RAY_WAVELENGTH=XXX | X_RAY_WAVELENGTH=XXX | ||
QX=XXX | QX=XXX | ||
QY=XXX | QY=XXX | ||
NX=XXX | NX=XXX | ||
NY=XXX | NY=XXX | ||
SENSOR_THICKNESS=0 | SENSOR_THICKNESS=0 | ||
TRUSTED_REGION="0.0 1.2 ! partially use corners of detector (0 1.4143: use all pixels)" | 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 | # default MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT | ||
MNOPIAS=3 | MNOPIAS=3 | ||
# default DIRECTION_OF_DETECTOR_X-AXIS | # default DIRECTION_OF_DETECTOR_X-AXIS | ||
DIRECTION_OF_DETECTOR_X_AXIS="1 0 0" | DIRECTION_OF_DETECTOR_X_AXIS="1 0 0" | ||
| Line 184: | Line 193: | ||
# default FRACTION_OF_POLARIZATION | # default FRACTION_OF_POLARIZATION | ||
pol_frac=0.98 | pol_frac=0.98 | ||
# default POLARIZATION_PLANE_NORMAL | |||
POLARIZATION_PLANE_NORMAL="0 1 0" | |||
STARTING_ANGLE=0 | STARTING_ANGLE=0 | ||
dtrek_det="" | dtrek_det="" | ||
| Line 190: | Line 201: | ||
REFINE_CORRECT="CELL BEAM ORIENTATION AXIS POSITION ! Default is: refine everything" | REFINE_CORRECT="CELL BEAM ORIENTATION AXIS POSITION ! Default is: refine everything" | ||
dname= | dname=$(dirname "$1") | ||
# Convert to full path (verify 'realpath' is available first) | |||
command -v realpath &> /dev/null && dname=$(realpath $dname) | |||
test "${dname}" == "" && dname="." | test "${dname}" == "" && dname="." | ||
bname= | bname=$(basename "$1") | ||
# see how we are called: | # see how we are called: | ||
NAME_TEMPLATE_OF_DATA_FRAMES="${dname}/${bname}" | NAME_TEMPLATE_OF_DATA_FRAMES="${dname}/${bname}" | ||
# list frames matching the wildcards in NAME_TEMPLATE_OF_DATA_FRAMES | # list frames matching the wildcards in NAME_TEMPLATE_OF_DATA_FRAMES | ||
# don't accept the "direct beam" shot at SLS/Pilatus PX-I and PX-II | # don't accept the "direct beam" shot at SLS/Pilatus PX-I and PX-II | ||
# cope with blanks in directory / file name | # cope with blanks in directory / file name | ||
IFS=$'\n' | IFS=$'\n' | ||
| Line 219: | Line 232: | ||
DATA_RANGE="$data_first $data_last" | DATA_RANGE="$data_first $data_last" | ||
echo DATA_RANGE=$DATA_RANGE | echo DATA_RANGE=$DATA_RANGE | ||
# set SPOT_RANGE to first half of DATA_RANGE | # set SPOT_RANGE to first half of DATA_RANGE | ||
data_num=`wc -l tmp1 | awk '{print $1}'` | data_num=`wc -l tmp1 | awk '{print $1}'` | ||
data_half=`echo "scale=0; $data_num/2" | bc -l` | data_half=`echo "scale=0; $data_num/2" | bc -l` | ||
data_half=`echo "if ($data_half<=1) 1;if ($data_half>1) $data_half" | bc -l` | data_half=`echo "if ($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_last=`echo "scale=0; $data_first+$data_half-1" | bc -l` | ||
| Line 232: | Line 245: | ||
# find out detector type | # find out detector type | ||
DET=XXX | DET=XXX | ||
IFS=$'\n' | IFS=$'\n' | ||
echo $FIRSTFRAME | grep -q '\.bz2$' && bzcat $FIRSTFRAME > tmp1 && FIRSTFRAME=tmp1 | echo $FIRSTFRAME | grep -q '\.bz2$' && bzcat $FIRSTFRAME > tmp1 && FIRSTFRAME=tmp1 | ||
# for mac/linux compatibility. zcat foo.gz doesn't work on mac. | # for mac/linux compatibility. zcat foo.gz doesn't work on mac. | ||
| Line 241: | Line 254: | ||
unset IFS | unset IFS | ||
if [ "$is_h5" == 0 ]; then | if [ "$is_h5" == 0 ]; then | ||
strings $FIRSTFRAME > tmp2 | # extract strings from binary file header, removing leading '#' (Pilatus) and trailing ';' (CBF) | ||
strings $FIRSTFRAME | head -400 | sed 's/^ *#\|; *$//;' >tmp2 | |||
# TODO: whenever FIRSTFRAME is used below, it should be copied to tmp2 (using IFS as above), and tmp2 should be used instead | # TODO: whenever FIRSTFRAME is used below, it should be copied to tmp2 (using IFS as above), and tmp2 should be used instead | ||
# this was done for "mccd", but still has to be done for the "raxis" detector types | # this was done for "mccd", but still has to be done for the "raxis" detector types | ||
# the reason is that FIRSTFRAME may contain a blank, which makes some commands fail | # the reason is that FIRSTFRAME may contain a blank, which makes some commands fail | ||
egrep -qi 'marccd|Corrected' tmp2 && DET=mccd | egrep -qi 'marccd|Corrected' tmp2 && DET=mccd | ||
grep -q PILATUS tmp2 && DET=pilatus | grep -q PILATUS tmp2 && DET=pilatus | ||
grep -iq Eiger tmp2 && DET=pilatus | grep -iq Eiger tmp2 && DET=pilatus | ||
head -n1 tmp2 | grep -q "^RAXIS" && DET=raxis | head -n1 tmp2 | grep -q "^RAXIS" && DET=raxis | ||
head -n1 tmp2 | grep -q "^R-AXIS" && DET=raxis | head -n1 tmp2 | grep -q "^R-AXIS" && DET=raxis | ||
grep -q "^SOURCE_WAVELENGTH= *1" tmp2 && DET=dtrek | grep -q "^SOURCE_WAVELENGTH= *1" tmp2 && DET=dtrek | ||
grep -q BEAM_CENTER_X tmp2 && DET=adsc | grep -q BEAM_CENTER_X tmp2 && DET=adsc | ||
grep -q mar345 tmp2 && DET=MAR345 | grep -q mar345 tmp2 && DET=MAR345 | ||
# rev. 1.02: in one case, mar555 data could be processed pretending it is mar345, so: | # rev. 1.02: in one case, mar555 data could be processed pretending it is mar345, so: | ||
grep -q mar555 tmp2 && DET=MAR345 | grep -q mar555 tmp2 && DET=MAR345 | ||
grep -q BRUKER tmp2 && grep -q CBF tmp2 && DET=Bruker-cbf | grep -q BRUKER tmp2 && grep -q CBF tmp2 && DET=Bruker-cbf | ||
grep -q CMOS1 tmp2 && DET=adsc-CMOS1 | grep -q CMOS1 tmp2 && DET=adsc-CMOS1 | ||
grep -q MARCONTROL tmp2 && DET=OLDMAR | grep -q MARCONTROL tmp2 && DET=OLDMAR | ||
grep -q "WAVELENGTH=0.0" tmp2 && DET=experimental-ED | grep -q "WAVELENGTH=0.0" tmp2 && DET=experimental-ED | ||
else | else | ||
h5dump -d "/entry/instrument/detector/description" $FIRSTFRAME | grep -i Eiger > /dev/null && DET=eiger | h5dump -d "/entry/instrument/detector/description" $FIRSTFRAME | grep -i Eiger > /dev/null && DET=eiger | ||
fi | fi | ||
# identify other detector types in the same way | # identify other detector types in the same way | ||
# parse ASCII header of first frame | # parse ASCII header of first frame | ||
if [ "$DET" == "XXX" ]; then | if [ "$DET" == "XXX" ]; then | ||
echo " | echo "Detector type unknown -- fill in XXX values manually!" | ||
DETECTOR="XXX MINIMUM_VALID_PIXEL_VALUE=XXX OVERLOAD=XXX" | DETECTOR="XXX MINIMUM_VALID_PIXEL_VALUE=XXX OVERLOAD=XXX" | ||
# find parameters of first frame | # find parameters of first frame | ||
elif [ "$DET" == "mccd" ]; then | elif [ "$DET" == "mccd" ]; then | ||
echo Data from a MarCCD detector | echo Data from a MarCCD detector | ||
# http://www.sb.fsu.edu/~xray/Manuals/marCCD165header.html has header information | # http://www.sb.fsu.edu/~xray/Manuals/marCCD165header.html has header information | ||
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 | ||
# Check detector serial number and recognize beamline for reversed-phi setting. | # Check detector serial number and recognize beamline for reversed-phi setting. | ||
| Line 303: | Line 317: | ||
cp $FIRSTFRAME tmp2 | cp $FIRSTFRAME tmp2 | ||
unset IFS | unset IFS | ||
let SKIP=1024+80 | let SKIP=1024+80 | ||
NX=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}') | NX=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}') | ||
let SKIP=$SKIP+4 | let SKIP=$SKIP+4 | ||
NY=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}') | NY=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}') | ||
let SKIP=1720 | let SKIP=1720 | ||
DETECTOR_DISTANCE=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}') | DETECTOR_DISTANCE=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}') | ||
DETECTOR_DISTANCE=`echo "scale=3; $DETECTOR_DISTANCE/1000" | bc -l` | DETECTOR_DISTANCE=`echo "scale=3; $DETECTOR_DISTANCE/1000" | bc -l` | ||
# Mar 12, 2020 KD | # Mar 12, 2020 KD | ||
| Line 319: | Line 333: | ||
let SKIP=1024+256+128+256+44 | let SKIP=1024+256+128+256+44 | ||
STARTING_ANGLE=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}') | STARTING_ANGLE=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}') | ||
STARTING_ANGLE=`echo "scale=2; $STARTING_ANGLE/1000" | bc -l ` | STARTING_ANGLE=`echo "scale=2; $STARTING_ANGLE/1000" | bc -l ` | ||
let SKIP=1024+256+128+256+4 | |||
let SKIP=1024+256+128+256+4 | ORGX=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}') | ||
ORGX=$(od -t dI -j $SKIP -N 4 tmp2 | 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 -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}') | ||
ORGY=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}') | ORGY=`echo "scale=2; $ORGY/1000" | bc -l ` | ||
ORGY=`echo "scale=2; $ORGY/1000" | bc -l ` | # fixed Aug 30, 2017 after IUCr2017 @ Hyderabad | ||
# fixed Aug 30, 2017 after IUCr2017 @ Hyderabad | |||
if [ "$DET_SN" == "4" ]; then | if [ "$DET_SN" == "4" ]; then | ||
TEMP=$ORGY | TEMP=$ORGY | ||
| Line 338: | Line 351: | ||
let SKIP=1024+736 | let SKIP=1024+736 | ||
OSCILLATION_RANGE=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}') | OSCILLATION_RANGE=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}') | ||
OSCILLATION_RANGE=`echo "scale=3; $OSCILLATION_RANGE/1000" | bc -l` | OSCILLATION_RANGE=`echo "scale=3; $OSCILLATION_RANGE/1000" | bc -l` | ||
let SKIP=1024+256+128+256+128+4 | let SKIP=1024+256+128+256+128+4 | ||
QX=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}') | QX=$(od -t dI -j $SKIP -N 4 tmp2 | 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 -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}') | QY=$(od -t dI -j $SKIP -N 4 tmp2 | 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 -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}') | X_RAY_WAVELENGTH=$(od -t dI -j $SKIP -N 4 tmp2 | 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` | ||
# at most BLs, ORGX and ORGY are in pixels, but sometimes in mm ... guess: | # at most BLs, ORGX and ORGY are in pixels, but sometimes in mm ... guess: | ||
NXBYFOUR=`echo "scale=0; $NX/4" | bc -l ` | NXBYFOUR=`echo "scale=0; $NX/4" | bc -l ` | ||
ORGXINT=`echo "scale=0; $ORGX/1" | bc -l ` | ORGXINT=`echo "scale=0; $ORGX/1" | bc -l ` | ||
if [ $ORGXINT -lt $NXBYFOUR ]; then | if [ $ORGXINT -lt $NXBYFOUR ]; then | ||
ORGX=`echo "scale=1; $ORGX/$QX" | bc -l` | ORGX=`echo "scale=1; $ORGX/$QX" | bc -l` | ||
ORGY=`echo "scale=1; $ORGY/$QY" | bc -l` | ORGY=`echo "scale=1; $ORGY/$QY" | bc -l` | ||
echo MARCCD detector: header ORGX, ORGY seem to be in mm ... converting to pixels | echo MARCCD detector: header ORGX, ORGY seem to be in mm ... converting to pixels | ||
else | else | ||
echo MARCCD detector: header ORGX, ORGY seem to be in pixel units | echo MARCCD detector: header ORGX, ORGY seem to be in pixel units | ||
fi | fi | ||
elif [ "$DET" == "adsc" ]; then | elif [ "$DET" == "adsc" ]; then | ||
| Line 367: | Line 380: | ||
DETECTOR="ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000" | DETECTOR="ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000" | ||
echo Data from ADSC detector. Obtaining ORGX, ORGY depends on beamline setup: | echo Data from ADSC detector. Obtaining ORGX, ORGY depends on beamline setup: | ||
SENSOR_THICKNESS=0.01 | SENSOR_THICKNESS=0.01 | ||
# find X_RAY_WAVELENGTH: | # find X_RAY_WAVELENGTH: | ||
| Line 376: | Line 387: | ||
# find NX, QX, ORGX and ORGY: | # find NX, QX, ORGX and ORGY: | ||
NX=`grep SIZE1 tmp2 | tail -1 | sed s/SIZE1=//` | NX=`grep SIZE1 tmp2 | tail -1 | sed s/SIZE1=//` | ||
NY=`grep SIZE2 tmp2 | tail -1 | sed s/SIZE2=//` | NY=`grep SIZE2 tmp2 | tail -1 | sed s/SIZE2=//` | ||
QX=`grep PIXEL_SIZE tmp2 | sed s/PIXEL_SIZE=//` | QX=`grep PIXEL_SIZE tmp2 | sed s/PIXEL_SIZE=//` | ||
QY=$QX | QY=$QX | ||
BEAM_CENTER_X=`grep BEAM_CENTER_X tmp2 | sed s/BEAM_CENTER_X=//` | 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=//` | BEAM_CENTER_Y=`grep BEAM_CENTER_Y tmp2 | sed s/BEAM_CENTER_Y=//` | ||
COMMENT_ORGXY=" | COMMENT_ORGXY=" | ||
! Following are possible beam center interpretations for ADSC detectors" | ! Following are possible beam center interpretations for ADSC detectors" | ||
# at ESRF, PF, ALS 5.0.2, AS MX2 and ... (pls fill in!) the following should be used: | # at ESRF, PF, ALS 5.0.2, AS MX2 and ... (pls fill in!) the following should be used: | ||
ORGX1=`echo "scale=1; $BEAM_CENTER_Y/$QX" | bc -l` | ORGX1=`echo "scale=1; $BEAM_CENTER_Y/$QX" | bc -l` | ||
ORGY1=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l` | ORGY1=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l` | ||
echo - at ESRF, PF, ALS 8.2.1, APS Argonne BLs use: ORGX=$ORGX1 ORGY=$ORGY1 | echo - at ESRF, PF, ALS 8.2.1, APS Argonne BLs use: ORGX=$ORGX1 ORGY=$ORGY1 | ||
COMMENT_ORGXY="${COMMENT_ORGXY} | COMMENT_ORGXY="${COMMENT_ORGXY} | ||
! ORGX= $ORGX1 ORGY= $ORGY1 ! For ESRF, PF, APS, AS MX2 ..." | ! ORGX= $ORGX1 ORGY= $ORGY1 ! For ESRF, PF, APS, AS MX2 ..." | ||
| Line 393: | Line 404: | ||
ORGX2=`echo "scale=1; $NX-$BEAM_CENTER_X/$QX" | bc -l ` | ORGX2=`echo "scale=1; $NX-$BEAM_CENTER_X/$QX" | bc -l ` | ||
ORGY2=`echo "scale=1; $BEAM_CENTER_Y/$QX" | bc -l ` | ORGY2=`echo "scale=1; $BEAM_CENTER_Y/$QX" | bc -l ` | ||
echo - at e.g. ALS 5.0.3 use: ORGX=$ORGX2 ORGY=$ORGY2 | echo - at e.g. ALS 5.0.3 use: ORGX=$ORGX2 ORGY=$ORGY2 | ||
COMMENT_ORGXY="${COMMENT_ORGXY} | COMMENT_ORGXY="${COMMENT_ORGXY} | ||
! ORGX= $ORGX2 ORGY= $ORGY2 ! For ALS 5.0.3,.." | ! ORGX= $ORGX2 ORGY= $ORGY2 ! For ALS 5.0.3,.." | ||
# 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, ... | ||
# this alternative is written into the generated XDS.INP ! You have to correct this manually in XDS.INP, or adjust this script. | # this alternative is written into the generated XDS.INP ! You have to correct this manually in XDS.INP, or adjust this script. | ||
ORGX3=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l ` | ORGX3=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l ` | ||
| Line 406: | Line 417: | ||
ORGX4=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l ` | ORGX4=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l ` | ||
ORGY4=`echo "scale=1; $BEAM_CENTER_Y/$QX" | bc -l ` | ORGY4=`echo "scale=1; $BEAM_CENTER_Y/$QX" | bc -l ` | ||
echo - at e.g. SPring-8 use: ORGX=$ORGX4 ORGY=$ORGY4 | echo - at e.g. SPring-8 use: ORGX=$ORGX4 ORGY=$ORGY4 | ||
COMMENT_ORGXY="${COMMENT_ORGXY} | COMMENT_ORGXY="${COMMENT_ORGXY} | ||
! ORGX= $ORGX4 ORGY= $ORGY4 ! For SPring-8,.." | ! ORGX= $ORGX4 ORGY= $ORGY4 ! For SPring-8,.." | ||
| Line 458: | Line 469: | ||
fi | fi | ||
# find DETECTOR_DISTANCE and OSCILLATION_RANGE: | # find DETECTOR_DISTANCE and OSCILLATION_RANGE: | ||
DETECTOR_DISTANCE=`grep ^DISTANCE tmp2 | sed s/DISTANCE=//` | DETECTOR_DISTANCE=`grep ^DISTANCE tmp2 | sed s/DISTANCE=//` | ||
OSCILLATION_RANGE=`grep OSC_RANGE tmp2 | sed s/OSC_RANGE=//` | OSCILLATION_RANGE=`grep OSC_RANGE tmp2 | sed s/OSC_RANGE=//` | ||
elif [ "$DET" == "adsc-CMOS1" ]; then | elif [ "$DET" == "adsc-CMOS1" ]; then | ||
DETECTOR="ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000" | DETECTOR="ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000" | ||
echo Data from CMOS1 MBC detector. | echo Data from CMOS1 MBC detector. | ||
SENSOR_THICKNESS=0.01 | SENSOR_THICKNESS=0.01 | ||
X_RAY_WAVELENGTH=`grep WAVELENGTH tmp2 | head -1 | sed s/WAVELENGTH=//` | X_RAY_WAVELENGTH=`grep WAVELENGTH tmp2 | head -1 | sed s/WAVELENGTH=//` | ||
NX=`grep SIZE1 tmp2 | tail -1 | sed s/SIZE1=//` | NX=`grep SIZE1 tmp2 | tail -1 | sed s/SIZE1=//` | ||
QX=`grep PIXEL_SIZE tmp2 | sed s/PIXEL_SIZE=//` | QX=`grep PIXEL_SIZE tmp2 | sed s/PIXEL_SIZE=//` | ||
NY=`grep SIZE2 tmp2 | tail -1 | sed s/SIZE2=//` | NY=`grep SIZE2 tmp2 | tail -1 | sed s/SIZE2=//` | ||
QY=$QX | QY=$QX | ||
ORGX=`grep BEAM_CENTER_X tmp2 | sed s/BEAM_CENTER_X=//` | ORGX=`grep BEAM_CENTER_X tmp2 | sed s/BEAM_CENTER_X=//` | ||
ORGY=`grep BEAM_CENTER_Y tmp2 | sed s/BEAM_CENTER_Y=//` | ORGY=`grep BEAM_CENTER_Y tmp2 | sed s/BEAM_CENTER_Y=//` | ||
REVERSE_PHI="yes" | REVERSE_PHI="yes" | ||
DETECTOR_DISTANCE=`grep ^DISTANCE tmp2 | sed s/DISTANCE=/-/` | DETECTOR_DISTANCE=`grep ^DISTANCE tmp2 | sed s/DISTANCE=/-/` | ||
OSCILLATION_RANGE=`grep OMEGA_DELTA tmp2 | sed s/OMEGA_DELTA=//` | OSCILLATION_RANGE=`grep OMEGA_DELTA tmp2 | sed s/OMEGA_DELTA=//` | ||
DETECTOR_X_AXIS="-1 0 0" | DETECTOR_X_AXIS="-1 0 0" | ||
elif [ "$DET" == "experimental-ED" ]; then | elif [ "$DET" == "experimental-ED" ]; then | ||
DETECTOR="ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000 ! OVERLOAD is really unknown " | DETECTOR="ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000 ! OVERLOAD is really unknown " | ||
echo --- Electron diffraction data in SMV format! | echo --- Electron diffraction data in SMV format! | ||
SENSOR_THICKNESS=0.01 | SENSOR_THICKNESS=0.01 | ||
X_RAY_WAVELENGTH=`grep WAVELENGTH tmp2 | head -1 | sed s/WAVELENGTH=//` | X_RAY_WAVELENGTH=`grep WAVELENGTH tmp2 | head -1 | sed s/WAVELENGTH=//` | ||
NX=`grep SIZE1 tmp2 | tail -1 | sed s/SIZE1=//` | NX=`grep SIZE1 tmp2 | tail -1 | sed s/SIZE1=//` | ||
QX=`grep PIXEL_SIZE tmp2 | sed s/PIXEL_SIZE=//` | QX=`grep PIXEL_SIZE tmp2 | sed s/PIXEL_SIZE=//` | ||
NY=`grep SIZE2 tmp2 | tail -1 | sed s/SIZE2=//` | NY=`grep SIZE2 tmp2 | tail -1 | sed s/SIZE2=//` | ||
QY=$QX | QY=$QX | ||
BEAM_CENTER_X=`grep BEAM_CENTER_X tmp2 | sed s/BEAM_CENTER_X=//` | 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=//` | BEAM_CENTER_Y=`grep BEAM_CENTER_Y tmp2 | sed s/BEAM_CENTER_Y=//` | ||
QXY=`echo "scale=1; $QX*($BEAM_CENTER_X+$BEAM_CENTER_Y)" | bc -l` | QXY=`echo "scale=1; $QX*($BEAM_CENTER_X+$BEAM_CENTER_Y)" | bc -l` | ||
if [ "$QXY" "<" "$BEAM_CENTER_X" ] ; then | if [ "$QXY" "<" "$BEAM_CENTER_X" ] ; then | ||
| Line 501: | Line 508: | ||
ORGY=`echo "scale=2; $BEAM_CENTER_Y/1" | bc -l` | ORGY=`echo "scale=2; $BEAM_CENTER_Y/1" | bc -l` | ||
fi | fi | ||
DETECTOR_DISTANCE=`grep ^DISTANCE tmp2 | sed s/DISTANCE=//` | DETECTOR_DISTANCE=`grep ^DISTANCE tmp2 | sed s/DISTANCE=//` | ||
OSCILLATION_RANGE=`grep OSC_RANGE tmp2 | sed s/OSC_RANGE=//` | OSCILLATION_RANGE=`grep OSC_RANGE tmp2 | sed s/OSC_RANGE=//` | ||
STARTING_ANGLE=`grep OSC_START tmp2 | sed s/OSC_START=//` | STARTING_ANGLE=`grep OSC_START tmp2 | sed s/OSC_START=//` | ||
echo --- For TIMEPIX detector, please fix ROTATION_AXIS yourself! | echo --- For TIMEPIX detector, please fix ROTATION_AXIS yourself! | ||
DIRECTION_OF_DETECTOR_X_AXIS="1 0 0" | DIRECTION_OF_DETECTOR_X_AXIS="1 0 0" | ||
REFINE_CORRECT="ORIENTATION CELL AXIS BEAM ! for ED, no POSITION when CELL is refined" | REFINE_CORRECT="ORIENTATION CELL AXIS BEAM ! for ED, no POSITION when CELL is refined" | ||
elif [ "$DET" == "pilatus" ]; then | elif [ "$DET" == "pilatus" ]; then | ||
echo Data from a Pilatus detector | echo Data from a Pilatus detector | ||
OVERLOAD=1048574 | OVERLOAD=1048574 | ||
SEPMIN=4 | SEPMIN=4 | ||
CLUSTER_RADIUS=2 | CLUSTER_RADIUS=2 | ||
grep -q Count_cutoff tmp2 && OVERLOAD=`awk '/Count_cutoff/{print $2}' tmp2` | grep -q Count_cutoff tmp2 && OVERLOAD=`awk '/Count_cutoff/{print $2;exit}' tmp2` | ||
DETECTOR="PILATUS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD= $OVERLOAD !PILATUS" | DETECTOR="PILATUS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD= $OVERLOAD !PILATUS" | ||
QX=0.172 QY=0.172 | QX=0.172 QY=0.172 | ||
# the default above guards against missing Pixel_size line in CBF header | # the default above guards against missing Pixel_size line in CBF header | ||
grep -q Pixel_size tmp2 && QX=`awk '/Pixel_size/{print 1000*$2}' tmp2` | grep -q Pixel_size tmp2 && QX=`awk '/Pixel_size/{print 1000*$2;exit}' tmp2` | ||
grep -q Pixel_size tmp2 && QY=`awk '/Pixel_size/{print 1000*$5}' tmp2` | grep -q Pixel_size tmp2 && QY=`awk '/Pixel_size/{print 1000*$5;exit}' tmp2` | ||
# find SENSOR_THICKNESS: | # find SENSOR_THICKNESS: | ||
SENSOR_THICKNESS=`grep thickness tmp2 | sed -e s/'Si.* sensor, thickness'// | awk '{print $1*1000}'` | SENSOR_THICKNESS=`grep thickness tmp2 | sed -e s/'Si.* sensor, thickness'// | awk '{print $1*1000}'` | ||
# find X_RAY_WAVELENGTH: | # find X_RAY_WAVELENGTH: | ||
X_RAY_WAVELENGTH=`grep Wavelength tmp2 | sed -e s/Wavelength// -e s/A// | awk '{print $1}'` | X_RAY_WAVELENGTH=`grep Wavelength tmp2 | sed -e s/Wavelength// -e s/A// | awk '{print $1}'` | ||
# find NX and NY; 2463/2527 is 6M, 1475/1679 is 2M | # find NX and NY; 2463/2527 is 6M, 1475/1679 is 2M | ||
NX=`grep X-Binary-Size-Fastest-Dimension tmp2 | awk '{print $2}'` | NX=`grep X-Binary-Size-Fastest-Dimension tmp2 | awk '{print $2}'` | ||
NY=`grep X-Binary-Size-Second-Dimension tmp2 | awk '{print $2}'` | NY=`grep X-Binary-Size-Second-Dimension tmp2 | awk '{print $2}'` | ||
# find ORGX and ORGY: | # find ORGX and ORGY: | ||
| Line 536: | Line 541: | ||
# find DETECTOR_DISTANCE, OSCILLATION_RANGE, and STARTING_ANGLE: | # find DETECTOR_DISTANCE, OSCILLATION_RANGE, and STARTING_ANGLE: | ||
DETECTOR_DISTANCE=`awk '/Detector_distance/{print $2}' tmp2` | DETECTOR_DISTANCE=`awk '/Detector_distance/{print $2;exit}' tmp2` | ||
DETECTOR_DISTANCE=`echo "$DETECTOR_DISTANCE*1000" | bc -l` | DETECTOR_DISTANCE=`echo "$DETECTOR_DISTANCE*1000" | bc -l` | ||
OSCILLATION_RANGE=`awk '/Angle_increment/{print $2}' tmp2` | OSCILLATION_RANGE=`awk '/Angle_increment/{print $2;exit}' tmp2` | ||
STARTING_ANGLE=`awk '/Start_angle/{print $2}' tmp2` | STARTING_ANGLE=`awk '/Start_angle/{print $2;exit}' tmp2` | ||
# get detector serial number and check if it is included in the list | # get detector serial number and check if it is included in the list | ||
| Line 566: | Line 570: | ||
echo inverted rotation axis at SSRF BL19U1 | echo inverted rotation axis at SSRF BL19U1 | ||
fi | fi | ||
# Diamond I24: | # Diamond I24: | ||
if [ "$DET_SN" == "PILATUS3 6M, S/N 60-0119" ] ; then | if [ "$DET_SN" == "PILATUS3 6M, S/N 60-0119" ] ; then | ||
if grep -q "Oscillation_axis X.CW +SLOW" tmp2 ; then | if grep -q "Oscillation_axis X.CW +SLOW" tmp2 ; then | ||
ROTATION_AXIS="0 -1 0" | |||
echo ROTATION_AXIS="0 -1 0" at Diamond I24 | echo ROTATION_AXIS="0 -1 0" at Diamond I24 | ||
fi | fi | ||
| Line 577: | Line 581: | ||
if [ "$DET_SN" == "Dectris Eiger 4M, E-08-0107" -o "$DET_SN" == "PILATUS 6M-F, S/N 60-0115-F" \ | if [ "$DET_SN" == "Dectris Eiger 4M, E-08-0107" -o "$DET_SN" == "PILATUS 6M-F, S/N 60-0115-F" \ | ||
-o "$DET_SN" == "Dectris EIGER2 CdTe 16M, E-32-0129" ] ; then | -o "$DET_SN" == "Dectris EIGER2 CdTe 16M, E-32-0129" ] ; then | ||
ROTATION_AXIS="0 -1 0" | |||
echo ROTATION_AXIS="0 -1 0" at PETRA P14 | echo ROTATION_AXIS="0 -1 0" at PETRA P14 | ||
fi | fi | ||
| Line 586: | Line 590: | ||
echo using the default ROTATION_AXIS=1 0 0 at PETRA P13 | echo using the default ROTATION_AXIS=1 0 0 at PETRA P13 | ||
else | else | ||
ROTATION_AXIS="0 -1 0" | |||
echo ROTATION_AXIS="0 -1 0" at PETRA P14 | echo ROTATION_AXIS="0 -1 0" at PETRA P14 | ||
fi | fi | ||
| Line 592: | Line 596: | ||
# ESRF ID23-2: | # ESRF ID23-2: | ||
if [ "$DET_SN" == "PILATUS3 2M, S/N 24-0118, ESRF ID23" ] ; then | if [ "$DET_SN" == "PILATUS3 2M, S/N 24-0118, ESRF ID23" ] ; then | ||
ROTATION_AXIS="0 -1 0" | |||
echo ROTATION_AXIS="0 -1 0" at ESRF ID23-2 | echo ROTATION_AXIS="0 -1 0" at ESRF ID23-2 | ||
fi | fi | ||
| Line 600: | Line 604: | ||
DATA_RANGE="1 $nframes" | DATA_RANGE="1 $nframes" | ||
SPOT_RANGE="1 `echo "scale=0; if (${nframes}<2) 1; if (${nframes}>1) ${nframes}/2"|bc -l`" | SPOT_RANGE="1 `echo "scale=0; if (${nframes}<2) 1; if (${nframes}>1) ${nframes}/2"|bc -l`" | ||
DET_SN=`h5dump -d "/entry/instrument/detector/detector_number" $FIRSTFRAME | awk '/\(0\): /{print $2}' | sed s/\"//g` | |||
echo detector serial number is $ | echo detector serial number is $DET_SN | ||
# find out if HDF5 from Diamond (DLS=1) or Dectris (DLS=0) | # find out if HDF5 from Diamond (DLS=1) or Dectris (DLS=0) | ||
DLS=0 | DLS=0 | ||
OVERLOAD=`h5dump -d "/entry/instrument/detector/detectorSpecific/countrate_correction_count_cutoff" $FIRSTFRAME 2>/dev/null` || DLS=1 | OVERLOAD=`h5dump -d "/entry/instrument/detector/detectorSpecific/countrate_correction_count_cutoff" $FIRSTFRAME 2>/dev/null` || DLS=1 | ||
if [ "$DLS" == 1 ]; then | if [ "$DLS" == 1 ]; then | ||
echo Eiger HDF5 from Diamond | echo Eiger HDF5 from Diamond | ||
| Line 614: | Line 618: | ||
STARTING_ANGLE=`h5dump -d "/entry/data/omega" $FIRSTFRAME | awk '/\(0\): [\-0-9]/{print $2;exit}' | sed -e "s/,//"` | STARTING_ANGLE=`h5dump -d "/entry/data/omega" $FIRSTFRAME | awk '/\(0\): [\-0-9]/{print $2;exit}' | sed -e "s/,//"` | ||
echo OSCILLATION_RANGE=$OSCILLATION_RANGE STARTING_ANGLE=$STARTING_ANGLE | echo OSCILLATION_RANGE=$OSCILLATION_RANGE STARTING_ANGLE=$STARTING_ANGLE | ||
# | # ROTATION_AXIS=`h5dump -a "/entry/sample/transformations/omega/vector" $FIRSTFRAME 2>/dev/null | grep "(0):" | sed -e "s/^.*://; s/,//g"` | ||
# the above gives -1 0 0 for DLS data instead of the correct 1 0 0, so commented out for now | # the above gives -1 0 0 for DLS data instead of the correct 1 0 0, so commented out for now | ||
# comment while implementing rev 1.10: this is because the DLS headers are NeXus, so DIRECTION_OF_DETECTOR_X/Y_AXIS must be adjusted. | # comment while implementing rev 1.10: this is because the DLS headers are NeXus, so DIRECTION_OF_DETECTOR_X/Y_AXIS must be adjusted. | ||
else | else | ||
echo Eiger HDF5 from Dectris | echo Eiger HDF5 from Dectris | ||
OVERLOAD=`h5dump -d "/entry/instrument/detector/detectorSpecific/countrate_correction_count_cutoff" $FIRSTFRAME | awk '/\(0\):/{print $2}'` | OVERLOAD=`h5dump -d "/entry/instrument/detector/detectorSpecific/countrate_correction_count_cutoff" $FIRSTFRAME | awk '/\(0\):/{print $2}'` | ||
OSCILLATION_RANGE=`h5dump -d "/entry/sample/goniometer/omega_range_average" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2}'` | OSCILLATION_RANGE=`h5dump -d "/entry/sample/goniometer/omega_range_average" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2}'` | ||
# STARTING_ANGLE: the \- was introduced in version 0.91 to allow negative values : | # STARTING_ANGLE: the \- was introduced in version 0.91 to allow negative values : | ||
| Line 628: | Line 632: | ||
STARTING_ANGLE=`h5dump -d /entry/sample/goniometer/omega $FIRSTFRAME | grep "(0):" | head -n 1 | awk '{print $2}' | sed -e "s/,//g"` | STARTING_ANGLE=`h5dump -d /entry/sample/goniometer/omega $FIRSTFRAME | grep "(0):" | head -n 1 | awk '{print $2}' | sed -e "s/,//g"` | ||
fi | fi | ||
# If rotation axis set (NeXus) | # If rotation axis set (NeXus) | ||
ROTATION_AXIS=`h5dump -a "/entry/sample/transformations/omega/vector" $FIRSTFRAME 2>/dev/null | grep "(0):" | sed -e "s/^.*://; s/,//g"` | |||
# EIGER2 16M CHESS ID7B2 has S/N E-32-0123 (A. Finke 2020-11-07) v0.99 | # EIGER2 16M CHESS ID7B2 has S/N E-32-0123 (A. Finke 2020-11-07) v0.99 | ||
if [ "$ | if [ "$DET_SN" == "E-32-0123" ]; then | ||
ROTATION_AXIS="-1 0 0" | |||
echo CHESS ID7B2 with inverted rotation axis | echo CHESS ID7B2 with inverted rotation axis | ||
fi | fi | ||
| Line 639: | Line 642: | ||
# Eiger X 16M (S/N E-32-0111) was installed at SSRF BL17U1 from Oct 2017 to Feb 2021. After Feb 2021, it was moved back to SSRF BL10U2. | # Eiger X 16M (S/N E-32-0111) was installed at SSRF BL17U1 from Oct 2017 to Feb 2021. After Feb 2021, it was moved back to SSRF BL10U2. | ||
# 2021-03-01 00:00:00 time stamp is 1614528000 | # 2021-03-01 00:00:00 time stamp is 1614528000 | ||
if [ "$ | if [ "$DET_SN" == "E-32-0111" ]; then | ||
collection_time=`h5dump -d "/entry/instrument/detector/detectorSpecific/data_collection_date" $FIRSTFRAME | grep "(0):" | awk '{print $2}' | sed -e "s/\.\(.*\)//g; s/\"//g"` | collection_time=`h5dump -d "/entry/instrument/detector/detectorSpecific/data_collection_date" $FIRSTFRAME | grep "(0):" | awk '{print $2}' | sed -e "s/\.\(.*\)//g; s/\"//g"` | ||
if [ `uname -s` == "Darwin" ]; then | if [ `uname -s` == "Darwin" ]; then | ||
| Line 649: | Line 652: | ||
fi | fi | ||
if [ $collection_timestamp -eq 0 ]; then | if [ $collection_timestamp -eq 0 ]; then | ||
is_ROTATION_AXIS_set=1 | |||
ROTATION_AXIS=`h5dump -d "/SSRF/RotationAxis" $FIRSTFRAME 2>/dev/null || is_ROTATION_AXIS_set=0` | |||
if [ "$ | if [ "$is_ROTATION_AXIS_set" == "1" ]; then | ||
ROTATION_AXIS=`h5dump -d "/SSRF/RotationAxis" $FIRSTFRAME | grep "(0):" | sed -e "s/^.*://; s/,//g"` | |||
echo "The rotation axis of SSRF BL10U2 (Eiger X 16M) is $ | echo "The rotation axis of SSRF BL10U2 (Eiger X 16M) is $ROTATION_AXIS" | ||
else | else | ||
ROTATION_AXIS="-1 0 0 ! Cannot determine rotation axis. SSRF BL17U1: -1 0 0; SSRF BL02U1: 0 -1 0" | |||
fi | fi | ||
elif [ $collection_timestamp -ge 0 ] && [ $collection_timestamp -le 1614528000 ]; then | elif [ $collection_timestamp -ge 0 ] && [ $collection_timestamp -le 1614528000 ]; then | ||
# SSRF BL17U1 | # SSRF BL17U1 | ||
ROTATION_AXIS="-1 0 0" | |||
echo "SSRF BL17U1 (Eiger X 16M) with inverted rotation axis" | echo "SSRF BL17U1 (Eiger X 16M) with inverted rotation axis" | ||
else | else | ||
# SSRF BL10U2 | # SSRF BL10U2 | ||
is_ROTATION_AXIS_set=1 | |||
ROTATION_AXIS=`h5dump -d "/SSRF/RotationAxis" $FIRSTFRAME 2>/dev/null || is_ROTATION_AXIS_set=0` | |||
if [ "$ | if [ "$is_ROTATION_AXIS_set" == "1" ]; then | ||
ROTATION_AXIS=`h5dump -d "/SSRF/RotationAxis" $FIRSTFRAME | grep "(0):" | sed -e "s/^.*://; s/,//g"` | |||
echo "The rotation axis of SSRF BL10U2 (Eiger X 16M) is $ | echo "The rotation axis of SSRF BL10U2 (Eiger X 16M) is $ROTATION_AXIS" | ||
else | else | ||
ROTATION_AXIS="0 -1 0" | |||
echo "SSRF BL10U2 (Eiger X 16M) with vertical rotation axis" | echo "SSRF BL10U2 (Eiger X 16M) with vertical rotation axis" | ||
fi | fi | ||
| Line 676: | Line 679: | ||
# SSRF BL02U1 (Feng YU 2021-07-18) | # SSRF BL02U1 (Feng YU 2021-07-18) | ||
# EIGER2 S 9M SSRF BL02U1 has S/N E-18-0121 | # EIGER2 S 9M SSRF BL02U1 has S/N E-18-0121 | ||
if [ "$ | if [ "$DET_SN" == "E-18-0121" ]; then | ||
is_ROTATION_AXIS_set=1 | |||
ROTATION_AXIS=`h5dump -d "/SSRF/RotationAxis" $FIRSTFRAME 2>/dev/null || is_ROTATION_AXIS_set=0` | |||
if [ "$ | if [ "$is_ROTATION_AXIS_set" == "1" ]; then | ||
ROTATION_AXIS=`h5dump -d "/SSRF/RotationAxis" $FIRSTFRAME | grep "(0):" | sed -e "s/^.*://; s/,//g"` | |||
echo "The rotation axis of SSRF BL02U1 (Eiger2 S 9M) is $ | echo "The rotation axis of SSRF BL02U1 (Eiger2 S 9M) is $ROTATION_AXIS" | ||
else | else | ||
ROTATION_AXIS="1 0 0" | |||
echo "SSRF BL02U1 (Eiger2 S 9M) with horizontal rotation axis" | echo "SSRF BL02U1 (Eiger2 S 9M) with horizontal rotation axis" | ||
fi | fi | ||
fi | fi | ||
# revision 1.05 specialcase nframes for Eiger detectors at BNL | # revision 1.05 specialcase nframes for Eiger detectors at BNL | ||
if [ "$ | if [ "$DET_SN" == "E-18-0104" -o "$DET_SN" == "E-32-0101" ]; then | ||
nframes=`h5dump -A -g "/entry/data" $FIRSTFRAME | grep "DATASPACE SIMPLE" | sed -e "s/,.*//" | awk '{a+=$5}END{print a}'` | nframes=`h5dump -A -g "/entry/data" $FIRSTFRAME | grep "DATASPACE SIMPLE" | sed -e "s/,.*//" | awk '{a+=$5}END{print a}'` | ||
DATA_RANGE="1 $nframes" | DATA_RANGE="1 $nframes" | ||
SPOT_RANGE="1 `echo "scale=0; if (${nframes}<2) 1; if (${nframes}>1) ${nframes}/2"|bc -l`" | SPOT_RANGE="1 `echo "scale=0; if (${nframes}<2) 1; if (${nframes}>1) ${nframes}/2"|bc -l`" | ||
echo Special case nframes for Eiger detectors at BNL: nframes=$nframes | |||
fi | fi | ||
fi | fi | ||
# rev 1.10: check for NeXus header. If found, its geometry will overwrite any | # rev 1.10: check for NeXus header. If found, its geometry will overwrite any ROTATION_AXIS set until here. | ||
NeXus=0 | NeXus=0 | ||
h5dump -d "/entry/definition" $FIRSTFRAME 2>/dev/null | grep -q NXmx && NeXus=1 | h5dump -d "/entry/definition" $FIRSTFRAME 2>/dev/null | grep -q NXmx && NeXus=1 | ||
| Line 702: | Line 705: | ||
DIRECTION_OF_DETECTOR_X_AXIS=$(h5dump -d "/entry/instrument/detector/module/fast_pixel_direction" $FIRSTFRAME 2>/dev/null | grep "(0):" | tail -1 | sed -e "s/^.*://; s/,//g") | DIRECTION_OF_DETECTOR_X_AXIS=$(h5dump -d "/entry/instrument/detector/module/fast_pixel_direction" $FIRSTFRAME 2>/dev/null | grep "(0):" | tail -1 | sed -e "s/^.*://; s/,//g") | ||
DIRECTION_OF_DETECTOR_Y_AXIS=$(h5dump -d "/entry/instrument/detector/module/slow_pixel_direction" $FIRSTFRAME 2>/dev/null | grep "(0):" | tail -1 | sed -e "s/^.*://; s/,//g") | DIRECTION_OF_DETECTOR_Y_AXIS=$(h5dump -d "/entry/instrument/detector/module/slow_pixel_direction" $FIRSTFRAME 2>/dev/null | grep "(0):" | tail -1 | sed -e "s/^.*://; s/,//g") | ||
ROTATION_AXIS=$(h5dump -a "/entry/sample/transformations/omega/vector" $FIRSTFRAME 2>/dev/null | grep "(0):" | sed -e "s/^.*://; s/,//g") | |||
else | else | ||
echo no NeXus header found. | echo no NeXus header found. | ||
| Line 723: | Line 726: | ||
# find DETECTOR_DISTANCE : | # find DETECTOR_DISTANCE : | ||
DETECTOR_DISTANCE=`h5dump -d "/entry/instrument/detector/detector_distance" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2*1000}'` | DETECTOR_DISTANCE=`h5dump -d "/entry/instrument/detector/detector_distance" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2*1000}'` | ||
SEPMIN=4 | SEPMIN=4 | ||
| Line 743: | Line 746: | ||
QY=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(780);print("%.6f"%struct.unpack(">f",f.read(4)))') | QY=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(780);print("%.6f"%struct.unpack(">f",f.read(4)))') | ||
X_RAY_WAVELENGTH=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(292);print("%.6f"%struct.unpack(">f",f.read(4)))') | X_RAY_WAVELENGTH=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(292);print("%.6f"%struct.unpack(">f",f.read(4)))') | ||
DIRECTION_OF_DETECTOR_Y_AXIS="0 -1 0" | |||
POLARIZATION_PLANE_NORMAL="1 0 0" | |||
ROTATION_AXIS="0 1 0" | |||
elif [ "$DET" == "dtrek" ]; then | elif [ "$DET" == "dtrek" ]; then | ||
dname=`grep "DETECTOR_NAMES=" tmp2 | sed -e "s/.*=//"` | dname=`grep "DETECTOR_NAMES=" tmp2 | sed -e "s/.*=//"` | ||
if [ "$dname" == "CCD_" ]; then | if [ "$dname" == "CCD_" ]; then | ||
DETECTOR="SATURN MINIMUM_VALID_PIXEL_VALUE=1" | DETECTOR="SATURN MINIMUM_VALID_PIXEL_VALUE=1" | ||
dtrek_det="saturn" | dtrek_det="saturn" | ||
elif [ "$dname" == "PILT_" ]; then | elif [ "$dname" == "PILT_" ]; then | ||
DETECTOR="PILATUS MINIMUM_VALID_PIXEL_VALUE=0" | DETECTOR="PILATUS MINIMUM_VALID_PIXEL_VALUE=0" | ||
| Line 773: | Line 761: | ||
SEPMIN=3 | SEPMIN=3 | ||
CLUSTER_RADIUS=1.5 | CLUSTER_RADIUS=1.5 | ||
SENSOR_THICKNESS=$(awk 'match($0,/SENSOR_THICKNESS= *(\S*)/,a){printf"%.3f",1000*a[1];exit}ENDFILE{print "0.45"}' tmp2) | |||
SENSOR_THICKNESS= | |||
elif [ "$dname" == "RX_" ]; then | elif [ "$dname" == "RX_" ]; then | ||
DETECTOR="RAXIS MINIMUM_VALID_PIXEL_VALUE=0" | DETECTOR="RAXIS MINIMUM_VALID_PIXEL_VALUE=0" | ||
dtrek_det="raxis" | dtrek_det="raxis" | ||
POLARIZATION_PLANE_NORMAL="1 0 0" | |||
ROTATION_AXIS="0 1 0" | |||
else | else | ||
DETECTOR="XXX MINIMUM_VALID_PIXEL_VALUE=XXX" | DETECTOR="XXX MINIMUM_VALID_PIXEL_VALUE=XXX" | ||
dtrek_det="unknown" | dtrek_det="unknown" | ||
echo "WARNING: Unsupported dTREK detector, check parameters" | |||
fi | fi | ||
DET_SN=`awk '/_DETECTOR_IDENTIFICATION=/{print;exit}' tmp2 | sed 's/.*DETECTOR_IDENTIFICATION=//'` | |||
echo "Data from a $dtrek_det detector with dTREK format, ID=$DET_SN" | |||
# Find rotation axis and flipping | |||
# I'm not sure this method is really valid - but at least mosflm seems to read this to determine rotation axis. | |||
tmpmat=(`grep ${dname}SPATIAL_DISTORTION_VECTORS= tmp2 | tail -1 | sed -e "s/.*=//"`) | |||
flip=`echo "(${tmpmat[0]}*${tmpmat[3]}-(${tmpmat[1]}*${tmpmat[2]}))/1"|bc` | |||
if [ "$flip" -ne 1 -a "$flip" -ne -1 ]; then | |||
echo "" | |||
echo "WARNING!! not-supported SPATIAL_DISTORTION_VECTORS header." | |||
echo "Please report this to XDSwiki author." | |||
echo "" | |||
elif [ "$flip" -eq -1 ]; then | |||
echo "Detector is flipped (from SPATIAL_DISTORTION_VECTORS header)" | |||
fi | |||
rotx=`echo "scale=6; -1.0*$flip*${tmpmat[0]}" | bc -l` | |||
roty=`echo "scale=6; -1.0*$flip*${tmpmat[1]}" | bc -l` | |||
ROTATION_AXIS="$rotx $roty 0" | |||
# 2theta | |||
TWOTHETA=`awk '/'${dname}'GONIO_VALUES=/{print $2;exit}' tmp2` | |||
R1=`echo "scale=7; $flip*-c($TWOTHETA/$DEGTOR)" | bc -l` | |||
R3=`echo "scale=7; $flip* s($TWOTHETA/$DEGTOR)" | bc -l` | |||
DIRECTION_OF_DETECTOR_X_AXIS="$R1 0 $R3" | |||
echo "Detector 2-theta = $TWOTHETA " | |||
echo DIRECTION_OF_DETECTOR_X_AXIS="$R1 0 $R3" | |||
# find OVERLOAD | # find OVERLOAD | ||
SATURATED_VALUE=`grep SATURATED_VALUE tmp2 | head -1 | sed s/SATURATED_VALUE=//` | SATURATED_VALUE=`grep SATURATED_VALUE tmp2 | head -1 | sed s/SATURATED_VALUE=//` | ||
| Line 810: | Line 817: | ||
ORGY=${SPATIAL_DISTORTION_INFO[1]} | ORGY=${SPATIAL_DISTORTION_INFO[1]} | ||
# find DETECTOR_DISTANCE | # find DETECTOR_DISTANCE | ||
GONIO_NAMES=(`grep ${dname}GONIO_NAMES= tmp2 | tail -1 | sed s/.*_GONIO_NAMES=//`) | GONIO_NAMES=(`grep ${dname}GONIO_NAMES= tmp2 | tail -1 | sed s/.*_GONIO_NAMES=//`) | ||
GONIO_VALUES=(`grep ${dname}GONIO_VALUES= tmp2 | tail -1 | sed s/.*_GONIO_VALUES=//`) | GONIO_VALUES=(`grep ${dname}GONIO_VALUES= tmp2 | tail -1 | sed s/.*_GONIO_VALUES=//`) | ||
| Line 818: | Line 825: | ||
idx=$((i-1)) | idx=$((i-1)) | ||
if [ "${GONIO_NAMES[$idx]}" == "Distance" ]; then | if [ "${GONIO_NAMES[$idx]}" == "Distance" ]; then | ||
if [ $flip -gt 0 ]; then | |||
DETECTOR_DISTANCE="-${GONIO_VALUES[$idx]}" | |||
echo "Detector not flipped; using negative distance" | |||
else | |||
DETECTOR_DISTANCE="${GONIO_VALUES[$idx]}" | |||
echo "Detector flipped; using positive distance" | |||
fi | |||
break | |||
fi | fi | ||
done | done | ||
# find | # find OSCILLATION start and range | ||
ROTATION=(`grep "^ROTATION=" tmp2 | tail -1 | sed s/ROTATION=//`) | ROTATION=(`grep "^ROTATION=" tmp2 | tail -1 | sed s/ROTATION=//`) | ||
STARTING_ANGLE=${ROTATION[0]} | |||
OSCILLATION_RANGE=${ROTATION[2]} | OSCILLATION_RANGE=${ROTATION[2]} | ||
elif [ "$DET" == "MAR345" ]; then | elif [ "$DET" == "MAR345" ]; then | ||
echo "Data from a Mar345 image plate detector" | echo "Data from a Mar345 image plate detector" | ||
DETECTOR="MAR345 MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=130000" | DETECTOR="MAR345 MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=130000" | ||
NX=`awk '/FORMAT/{print $2}' tmp2` | NX=`awk '/FORMAT/{print $2;exit}' tmp2` | ||
# next line is rev 1.02 (previously NY= $NX): | # next line is rev 1.02 (previously NY= $NX): | ||
NY=`awk -v NX=$NX '/FORMAT/{print $4/NX}' tmp2` | NY=`awk -v NX=$NX '/FORMAT/{print $4/NX;exit}' tmp2` | ||
QX=`awk '/PIXEL/{print $3/1000.}' tmp2` | QX=`awk '/PIXEL/{print $3/1000.;exit}' tmp2` | ||
QY=`awk '/PIXEL/{print $5/1000.}' tmp2` | QY=`awk '/PIXEL/{print $5/1000.;exit}' tmp2` | ||
if grep -q 'CENTER' tmp2; then | if grep -q 'CENTER' tmp2; then | ||
echo Beam center found. | echo Beam center found. | ||
| Line 850: | Line 859: | ||
ORGY=`echo $NY / 2 | bc` | ORGY=`echo $NY / 2 | bc` | ||
fi | fi | ||
DETECTOR_DISTANCE=`grep 'DISTANCE' tmp2 | awk '{print $2}'` | DETECTOR_DISTANCE=`grep 'DISTANCE' tmp2 | awk '{print $2}'` | ||
X_RAY_WAVELENGTH=`grep 'WAVELENGTH' tmp2 | awk '{print $2}'` | X_RAY_WAVELENGTH=`grep 'WAVELENGTH' tmp2 | awk '{print $2}'` | ||
OSCILLATION_RANGE=`grep 'PHI' tmp2 | awk '{print $5-$3}'` | OSCILLATION_RANGE=`grep 'PHI' tmp2 | awk '{print $5-$3}'` | ||
TRUSTED_REGION="0 0.99" | TRUSTED_REGION="0 0.99" | ||
elif [ "$DET" == "OLDMAR" ]; then | elif [ "$DET" == "OLDMAR" ]; then | ||
echo "Data from old type MAR image plate detector" | echo "Data from old type MAR image plate detector" | ||
DETECTOR="MAR MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=130000" | DETECTOR="MAR MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=130000" | ||
NX=`awk 'NR==2 {print $2}' tmp2` | NX=`awk 'NR==2 {print $2;exit}' tmp2` | ||
NY=$NX | NY=$NX | ||
QX=`awk 'NR==2 {print $15}' tmp2` | QX=`awk 'NR==2 {print $15;exit}' tmp2` | ||
QY=$QX | QY=$QX | ||
ORGX=`awk 'NR==2 {print $19}' tmp2` | ORGX=`awk 'NR==2 {print $19;exit}' tmp2` | ||
ORGY=`awk 'NR==2 {print $20}' tmp2` | ORGY=`awk 'NR==2 {print $20;exit}' tmp2` | ||
DETECTOR_DISTANCE=`awk 'NR==2 {print $22}' tmp2` | DETECTOR_DISTANCE=`awk 'NR==2 {print $22;exit}' tmp2` | ||
X_RAY_WAVELENGTH=`awk 'NR==2 {print $21}' tmp2` | X_RAY_WAVELENGTH=`awk 'NR==2 {print $21;exit}' tmp2` | ||
OSCILLATION_RANGE=`awk 'NR==2 {print $24-$23}' tmp2` | OSCILLATION_RANGE=`awk 'NR==2 {print $24-$23;exit}' tmp2` | ||
TRUSTED_REGION="0 0.99" | TRUSTED_REGION="0 0.99" | ||
ROTATION_AXIS="0 1 0" | |||
echo unsure if sign of anomalous signal is correct - please verify or try both hands! | echo unsure if sign of anomalous signal is correct - please verify or try both hands! | ||
elif [ "$DET" == "Bruker-cbf" ]; then | elif [ "$DET" == "Bruker-cbf" ]; then | ||
echo "Data from a Bruker-cbf detector" | echo "Data from a Bruker-cbf detector" | ||
# MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT: | # MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT: | ||
MNOPIAS=6 | MNOPIAS=6 | ||
# use complete detector including corners: | # use complete detector including corners: | ||
TRUSTED_REGION="0 1.42" | TRUSTED_REGION="0 1.42" | ||
# polarization | # polarization | ||
pol_frac=`awk '/polarizn_source_ratio/{print $2}' tmp2` | pol_frac=`awk '/polarizn_source_ratio/{print $2;exit}' tmp2` | ||
pol_frac=`echo "${pol_frac}+0.5" | bc -l` | pol_frac=`echo "${pol_frac}+0.5" | bc -l` | ||
OVERLOAD=`awk '/_array_intensities.overload/{print $2}' tmp2` | OVERLOAD=`awk '/_array_intensities.overload/{print $2;exit}' tmp2` | ||
DETECTOR="BRUKER MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=${OVERLOAD}" | DETECTOR="BRUKER MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=${OVERLOAD}" | ||
NX=`awk '/X-Binary-Size-Fastest-Dimension/{print $2}' tmp2` | NX=`awk '/X-Binary-Size-Fastest-Dimension/{print $2;exit}' tmp2` | ||
NY=`awk '/X-Binary-Size-Second-Dimension/{print $2}' tmp2` | NY=`awk '/X-Binary-Size-Second-Dimension/{print $2;exit}' tmp2` | ||
QX=`awk '/ELEMENT_X ELEMENT_X/{print $4}' tmp2` | QX=`awk '/ELEMENT_X ELEMENT_X/{print $4;exit}' tmp2` | ||
QY=`awk '/ELEMENT_Y ELEMENT_Y/{print $4}' tmp2` | QY=`awk '/ELEMENT_Y ELEMENT_Y/{print $4;exit}' tmp2` | ||
# ORGX/Y-offsets relative to center of detector: | # ORGX/Y-offsets relative to center of detector: | ||
| Line 897: | Line 906: | ||
ORGY=`echo "scale=2; ${NY}/2-($ORGY/$QY)" | bc -l` | ORGY=`echo "scale=2; ${NY}/2-($ORGY/$QY)" | bc -l` | ||
DETECTOR_DISTANCE=`grep "0 0 ? ? ?" tmp2 | awk '/DX /{print $2}'` | DETECTOR_DISTANCE=`grep "0 0 ? ? ?" tmp2 | awk '/DX /{print $2}'` | ||
X_RAY_WAVELENGTH=`awk '/diffrn_radiation_wavelength.wavelength/{print $2}' tmp2` | X_RAY_WAVELENGTH=`awk '/diffrn_radiation_wavelength.wavelength/{print $2;exit}' tmp2` | ||
# fix 16.3.20: instead of print, use printf "%.5f", because bc does not accept e.g. 3.1e-005 | # fix 16.3.20: instead of print, use printf "%.5f", because bc does not accept e.g. 3.1e-005 | ||
OMEGA=`awk '/OMEGA \? \? \?/{printf "%.5f",$5}' tmp2` | OMEGA=`awk '/OMEGA \? \? \?/{printf "%.5f",$5;exit}' tmp2` | ||
DELTAOMEGA=`awk '/OMEGA \? \? \?/{printf "%.5f",$6}' tmp2` | DELTAOMEGA=`awk '/OMEGA \? \? \?/{printf "%.5f",$6;exit}' tmp2` | ||
PHI=`awk '/PHI \? \? \?/{printf "%.5f",$5}' tmp2` | PHI=`awk '/PHI \? \? \?/{printf "%.5f",$5;exit}' tmp2` | ||
DELTAPHI=`awk '/PHI \? \? \?/{printf "%.5f",$6}' tmp2` | DELTAPHI=`awk '/PHI \? \? \?/{printf "%.5f",$6;exit}' tmp2` | ||
KAPPA=`awk '/CHI \? \? \?/{printf "%.5f",$5}' tmp2` | KAPPA=`awk '/CHI \? \? \?/{printf "%.5f",$5;exit}' tmp2` | ||
# echo OMEGA DELTAOMEGA PHI DELTAPHI KAPPA= $OMEGA $DELTAOMEGA $PHI $DELTAPHI $KAPPA | # echo OMEGA DELTAOMEGA PHI DELTAPHI KAPPA= $OMEGA $DELTAOMEGA $PHI $DELTAPHI $KAPPA | ||
| Line 914: | Line 923: | ||
R1=`echo "scale=7; s($KAPPA/$DEGTOR)*c($OMEGA/$DEGTOR)" | bc -l` | R1=`echo "scale=7; s($KAPPA/$DEGTOR)*c($OMEGA/$DEGTOR)" | bc -l` | ||
R2=`echo "scale=7; c($KAPPA/$DEGTOR) " | bc -l` | R2=`echo "scale=7; c($KAPPA/$DEGTOR) " | bc -l` | ||
ROTATION_AXIS="$R1 $R2 $R3" | |||
OSCILLATION_RANGE=${DELTAPHI} | OSCILLATION_RANGE=${DELTAPHI} | ||
STARTING_ANGLE=${PHI} | STARTING_ANGLE=${PHI} | ||
# here we could check if DELTAPHI is <0, and if so, negate it and | # here we could check if DELTAPHI is <0, and if so, negate it and ROTATION_AXIS | ||
else | else | ||
echo OMEGA scan | echo OMEGA scan | ||
ROTATION_AXIS="0 -1 0" | |||
OSCILLATION_RANGE=${DELTAOMEGA} | OSCILLATION_RANGE=${DELTAOMEGA} | ||
STARTING_ANGLE=${OMEGA} | STARTING_ANGLE=${OMEGA} | ||
# here we could check if DELTAOMEGA is <0, and if so, negate it and | # here we could check if DELTAOMEGA is <0, and if so, negate it and ROTATION_AXIS | ||
fi | fi | ||
# 2theta | # 2theta | ||
TWOTHETA=`awk '/TWOTHETA \? \? \?/{print $5}' tmp2` | TWOTHETA=`awk '/TWOTHETA \? \? \?/{print $5;exit}' tmp2` | ||
echo TWOTHETA=$TWOTHETA | echo TWOTHETA=$TWOTHETA | ||
R1=`echo "scale=7; c($TWOTHETA/$DEGTOR)" | bc -l` | R1=`echo "scale=7; c($TWOTHETA/$DEGTOR)" | bc -l` | ||
| Line 936: | Line 944: | ||
else | else | ||
echo should never come here | echo should never come here | ||
exit 1 | exit 1 | ||
fi | fi | ||
echo ORGX= $ORGX ORGY= $ORGY - check these values with adxv ! | echo ORGX= $ORGX ORGY= $ORGY - check these values with adxv or xdsgui ! | ||
echo DETECTOR_DISTANCE= $DETECTOR_DISTANCE ! only read by XYCORR, IDXREF | echo DETECTOR_DISTANCE= $DETECTOR_DISTANCE ! only read by XYCORR, IDXREF | ||
echo OSCILLATION_RANGE= $OSCILLATION_RANGE ! only read by IDXREF | echo STARTING_ANGLE= $STARTING_ANGLE ! only read by IDXREF | ||
echo X-RAY_WAVELENGTH= $X_RAY_WAVELENGTH ! only read by IDXREF | echo OSCILLATION_RANGE= $OSCILLATION_RANGE ! only read by IDXREF | ||
echo X-RAY_WAVELENGTH= $X_RAY_WAVELENGTH ! only read by IDXREF | |||
if (( $(echo "$X_RAY_WAVELENGTH > 1.54 && $X_RAY_WAVELENGTH < 1.55" |bc -l) )); then | |||
echo "Copper K-alpha source, FRACTION_OF_POLARIZATION commented out" | |||
not_synchrotron='!' | |||
fi | |||
if [ "$DET" == "eiger" ] && [ "$is_h5" == 1 ]; then | |||
if [ "$DLS" == 0 ] ; then | |||
neggia_path=${NEGGIA_PATH-/usr/local/lib64/dectris-neggia.so} | |||
if [ -e $neggia_path ]; then | |||
LIB="LIB=$neggia_path" | |||
echo "LIB= <dectris-neggia> was written to XDS.INP . Check the path! For Apple M1 processors, modify the name or set \$NEGGIA_PATH." | |||
else | |||
LIB="!LIB=/usr/local/lib64/dectris-neggia.so" | |||
echo "dectris-neggia.so not found. Specify LIB=<path-to-dectris-neggia> in XDS.INP -- set \$NEGGIA_PATH to specify the path!" | |||
fi | |||
else | |||
durin_path=${DURIN_PATH-/usr/local/lib64/durin-plugin.so} | |||
if [ -e $durin_path ]; then | |||
LIB="LIB=$durin_path" | |||
echo "LIB= <durin-plugin> was written to XDS.INP . Check the path! For Apple M1 processors, modify the name or set \$NEGGIA_PATH." | |||
else | |||
LIB="!LIB=/usr/local/lib64/durin-plugin.so" | |||
echo "durin-plugin.so not found. Specify LIB=<path-to-durin-plugin> in XDS.INP -- set \$NEGGIA_PATH to specify the path!" | |||
fi | |||
fi | |||
fi | |||
if [ "$ROTATION_AXIS" != "" ]; then | |||
ROTATION_AXIS="$ROTATION_AXIS ! only read by IDXREF" | |||
elif [ "$REVERSE_PHI" == "no" ]; then | |||
ROTATION_AXIS='1 0 0 ! Australian Synchrotron, SERCAT ID-22 (?), APS 19-ID (?), ESRF BM30A, SPring-8, SSRF need -1 0 0. Diamond ID24 needs 0 -1 0' | |||
else | |||
ROTATION_AXIS='-1 0 0 ! Default; if this is wrong, please contact author.' | |||
fi | |||
# Append 2-theta comment if defined | |||
if (( $(echo "${TWOTHETA}0 != 0"|bc -l) )); then | |||
COMMENT_ORGXY="$COMMENT_ORGXY | |||
! TWOTHETA=$TWOTHETA -- if fails, check DIRECTION_OF_DETECTOR_X-AXIS" | |||
fi | |||
# now we know almost everything that is required to generate XDS.INP | |||
cat > XDS.INP << eof | cat > XDS.INP << eof | ||
!============================================================================= | |||
! written by generate_XDS.INP version $REVISION | ! written by generate_XDS.INP version $REVISION | ||
! For more details on XDS parameters, please check the online documentation at | |||
! http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html | |||
! | |||
! Full documentation, including complete detector templates, at xds.mr.mpg.de . | |||
! More documentation in strucbio.biologie.uni-konstanz.de/xdswiki/index.php . | |||
! After running xds, inspect at least the agreement of predicted and observed | |||
! spots in FRAME.cbf! | |||
!============================================================================= | |||
JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT | JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT | ||
ORGX= $ORGX ORGY= $ORGY ! values from frame header; only read by XYCORR, IDXREF | ORGX= $ORGX ORGY= $ORGY ! values from frame header; only read by XYCORR, IDXREF | ||
$COMMENT_ORGXY | $COMMENT_ORGXY | ||
DETECTOR_DISTANCE= $DETECTOR_DISTANCE !read by XYCORR, IDXREF. Negative if detector normal points to crystal. | DETECTOR_DISTANCE= $DETECTOR_DISTANCE !read by XYCORR, IDXREF. Negative if detector normal points to crystal. | ||
OSCILLATION_RANGE= $OSCILLATION_RANGE | OSCILLATION_RANGE= $OSCILLATION_RANGE | ||
STARTING_ANGLE= $STARTING_ANGLE | STARTING_ANGLE= $STARTING_ANGLE | ||
X-RAY_WAVELENGTH= $X_RAY_WAVELENGTH | X-RAY_WAVELENGTH= $X_RAY_WAVELENGTH | ||
NAME_TEMPLATE_OF_DATA_FRAMES=$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=$DATA_RANGE | ||
SPOT_RANGE=$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) | ||
SPACE_GROUP_NUMBER=0 ! 0 if unknown | SPACE_GROUP_NUMBER=0 ! 0 if unknown | ||
| Line 1,000: | Line 1,056: | ||
! Better: read the article http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/SILICON . | ! Better: read the article http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/SILICON . | ||
NX= $NX NY= $NY QX= $QX QY= $QY ! to make CORRECT happy if frames are unavailable | NX= $NX NY= $NY QX= $QX QY= $QY ! to make CORRECT happy if frames are unavailable | ||
$LIB | |||
ROTATION_AXIS=$ROTATION_AXIS | |||
ROTATION_AXIS= | |||
DIRECTION_OF_DETECTOR_X-AXIS=$DIRECTION_OF_DETECTOR_X_AXIS | DIRECTION_OF_DETECTOR_X-AXIS=$DIRECTION_OF_DETECTOR_X_AXIS | ||
DIRECTION_OF_DETECTOR_Y-AXIS=$DIRECTION_OF_DETECTOR_Y_AXIS | DIRECTION_OF_DETECTOR_Y-AXIS=$DIRECTION_OF_DETECTOR_Y_AXIS | ||
INCIDENT_BEAM_DIRECTION=0 0 1 ! only read by IDXREF | |||
${not_synchrotron}FRACTION_OF_POLARIZATION=${pol_frac} ! comment out if not synchrotron; only use by CORRECT | |||
! better value is provided by beamline staff! | |||
POLARIZATION_PLANE_NORMAL=$POLARIZATION_PLANE_NORMAL ! only used by CORRECT | |||
eof | eof | ||
# --------- Append known detector untrusted regions ----------- | |||
cat >> XDS.INP << eof | cat >> XDS.INP << eof | ||
!used by DEFPIX and CORRECT to exclude ice-reflections / ice rings - uncomment if necessary | !used by DEFPIX and CORRECT to exclude ice-reflections / ice rings - uncomment if necessary | ||
| Line 1,080: | Line 1,088: | ||
elif [ "$DET" == "adsc-CMOS1" ]; then | elif [ "$DET" == "adsc-CMOS1" ]; then | ||
echo UNTRUSTED_RECTANGLE= 0 1468 2451 2631 >> XDS.INP | echo UNTRUSTED_RECTANGLE= 0 1468 2451 2631 >> XDS.INP | ||
elif [ "$dtrek_det" == "pilatus" -a "$NX" == 487 -a "$NY" = "407" ]; then | |||
echo UNTRUSTED_RECTANGLE= 1 487 196 212 >> XDS.INP # Dectris Pilatus 200K | |||
elif [ "$DET" == "pilatus" -o "$DET" == "eiger" ]; then | elif [ "$DET" == "pilatus" -o "$DET" == "eiger" ]; then | ||
cat >> XDS.INP << eof | cat >> XDS.INP << eof | ||
NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA=13 ! Default is 9 - Increasing may improve data | NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA=13 ! Default is 9 - Increasing may improve data | ||
NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA=13 ! accuracy, particularly if finely-sliced on phi, | NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA=13 ! accuracy, particularly if finely-sliced on phi, | ||
! and does not seem to have any downsides. | ! and does not seem to have any downsides. | ||
eof | eof | ||
if [ "$NX" == "1028" -a "$NY" == "1062" ]; then | if [ "$NX" == "1028" -a "$NY" == "1062" ]; then | ||
| Line 1,095: | Line 1,105: | ||
cat >> XDS.INP << eof | cat >> XDS.INP << eof | ||
! the following specifications are for a detector _without_ proper | ! the following specifications are for a detector _without_ proper | ||
! flat_field correction; they cut away one additional pixel adjacent | ! flat_field correction; they cut away one additional pixel adjacent | ||
! to each UNTRUSTED_RECTANGLE | ! to each UNTRUSTED_RECTANGLE | ||
!EXCLUSION OF VERTICAL DEAD AREAS OF THE PILATUS 2M DETECTOR | !EXCLUSION OF VERTICAL DEAD AREAS OF THE PILATUS 2M DETECTOR | ||
| Line 1,193: | Line 1,203: | ||
!EXCLUSION OF VERTICAL DEAD AREAS OF THE EIGER 16M DETECTOR + ONE PIXEL ON EACH SIDE | !EXCLUSION OF VERTICAL DEAD AREAS OF THE EIGER 16M DETECTOR + ONE PIXEL ON EACH SIDE | ||
UNTRUSTED_RECTANGLE= 1029 1042 0 4371 | UNTRUSTED_RECTANGLE= 1029 1042 0 4371 | ||
UNTRUSTED_RECTANGLE= 2069 2082 0 4371 | UNTRUSTED_RECTANGLE= 2069 2082 0 4371 | ||
UNTRUSTED_RECTANGLE= 3109 3122 0 4371 | UNTRUSTED_RECTANGLE= 3109 3122 0 4371 | ||
eof | eof | ||
| Line 1,203: | Line 1,213: | ||
UNTRUSTED_RECTANGLE= 2068 2081 0 4363 | UNTRUSTED_RECTANGLE= 2068 2081 0 4363 | ||
UNTRUSTED_RECTANGLE= 3108 3121 0 4363 | UNTRUSTED_RECTANGLE= 3108 3121 0 4363 | ||
!EXCLUSION OF VERTICAL DEAD AREAS OF THE EIGER2 16M DETECTOR | !EXCLUSION OF VERTICAL DEAD AREAS OF THE EIGER2 16M DETECTOR | ||
UNTRUSTED_RECTANGLE= 0 4149 512 551 | UNTRUSTED_RECTANGLE= 0 4149 512 551 | ||
UNTRUSTED_RECTANGLE= 0 4149 1062 1101 | UNTRUSTED_RECTANGLE= 0 4149 1062 1101 | ||
| Line 1,213: | Line 1,223: | ||
eof | eof | ||
fi | fi | ||
fi | |||
# Mechanism to append detector-specific parameters without editing this file: | |||
# TODO: some detectors don't set DET_SN so this is not always unique | |||
test "$DET_SN" != "" && DET="${DET}_$DET_SN" | |||
DET=$(echo $DET | sed 's/ /_/g;s/\W//g;') | |||
file="$HOME/.xds-site/$DET" | |||
if [ -f $file ]; then | |||
echo Appending site parameters from: $file | |||
echo "! Parameters from $file" >> XDS.INP | |||
echo "Site parameters:" | |||
cat $file | |||
echo | |||
# Only FRACTION_POLARIZATION and ROTATION_AXIS are commented out automatically because they | |||
# are the most likely to not match defaults | |||
# Also likely adjustments are UNTRUSTED regions and maybe SILICON, but those don't replace existing parameters | |||
# Create a pattern like "XX\|YY" to search overriden parameters. | |||
pattern=$(grep "POLARIZATION\|ROTATION_AXIS\|TRUSTED_REGION" $file | \ | |||
awk 'match($0,/^ *(\w+) *=/,a){x=x"\\|"a[1];}END{print substr(x,3);}') | |||
if [ "$pattern" != "" ]; then | |||
sed 's/\(^ *\('$pattern'\) *=\)/!!\1/;' XDS.INP >tmp1 | |||
mv tmp1 XDS.INP | |||
echo "Overridden parameters:" | |||
grep "^!!*$pattern" XDS.INP | |||
echo | |||
fi | |||
cat $file >> XDS.INP | |||
else | |||
echo "Detector specific parameters can be placed in: $file" | |||
echo "! Detector specific parameters can be placed in:" >> XDS.INP | |||
echo "! $file" >> XDS.INP | |||
echo "! FRACTION_OF_POLARIZATION, ROTATION_AXIS and TRUDTED_REGION will auto-comment the replaced parameters" >> XDS.INP | |||
fi | fi | ||
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 Full documentation, including complete detector templates, at xds.mr.mpg.de . | echo Full documentation, including complete detector templates, at xds.mr.mpg.de . | ||
echo More documentation in strucbio.biologie.uni-konstanz.de/xdswiki/index.php . | echo More documentation in strucbio.biologie.uni-konstanz.de/xdswiki/index.php . | ||
echo After running xds, inspect at least the agreement of predicted and observed | echo After running xds, inspect at least the agreement of predicted and observed | ||
echo spots in FRAME.cbf! | echo spots in FRAME.cbf! | ||
rm -f tmp1 tmp2 | rm -f tmp1 tmp2 | ||
</pre> | </pre> | ||