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m
→‎The script: improve wording
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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 should be very easy.
    
== Usage ==
 
== Usage ==
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XDS [http://strucbio.biologie.uni-konstanz.de/~dikay/XDS_html_doc/html_doc/xds_parameters.html#NAME_TEMPLATE_OF_DATA_FRAMES= supports] bzip2-ed frames. Thus, when specifying the frame name parameter of the script, you should leave out any .bz2 extension.
 
XDS [http://strucbio.biologie.uni-konstanz.de/~dikay/XDS_html_doc/html_doc/xds_parameters.html#NAME_TEMPLATE_OF_DATA_FRAMES= supports] bzip2-ed frames. Thus, when specifying the frame name parameter of the script, you should leave out any .bz2 extension.
   −
For improved interaction with [[XDSGUI]], it is advantageous to use an ''absolute'' filename - one that starts with a slash ("/").
+
For improved interaction with [[XDSGUI]], it is advantageous to provide an ''absolute'' filename for the data files - one that starts with a slash ("/").
    
== The script ==
 
== The script ==
    
<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, RAXIS (in-house) 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.                                   
 
#                                                                                                           
 
#                                                                                                           
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# revision 0.35 . KD 6/2013 - reduce 7000 to 6000 for shadow detection; insert comment about *_RESOLUTION_RANGE lines
 
# revision 0.35 . KD 6/2013 - reduce 7000 to 6000 for shadow detection; insert comment about *_RESOLUTION_RANGE lines
 
# revision 0.36 . KD 6/2013 - insert NUMBER_OF_PROFILE_GRID* lines for Pilatus (suggested by C.Vonrhein)
 
# revision 0.36 . KD 6/2013 - insert NUMBER_OF_PROFILE_GRID* lines for Pilatus (suggested by C.Vonrhein)
# revision 0.37 . Keitaro 10/2013 - fix for MX225HS detector on SPring-8 BL32XU (Ignore case when matching marccd in header); but cannot decide reverse-phi because of missing detector S/N
+
# revision 0.37 . Keitaro 10/2013 - fix for MX225HS detector on SPring-8 BL32XU (Ignore case when matching marccd in header); see also rev-0.39
 
# revision 0.38 . KD 2/2014 - change defaults for REFINE(IDXREF) and REFINE(INTEGRATE) such that more stable results are obtained for difficult datasets
 
# revision 0.38 . KD 2/2014 - change defaults for REFINE(IDXREF) and REFINE(INTEGRATE) such that more stable results are obtained for difficult datasets
 
# revision 0.39 . Keitaro 4/2014 - automatically set ROTATION_AXIS=-1 0 0 for MX225HS at SPring-8 BL32XU.
 
# revision 0.39 . Keitaro 4/2014 - automatically set ROTATION_AXIS=-1 0 0 for MX225HS at SPring-8 BL32XU.
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# revision 0.44 . Keitaro 5/2014 automatically set ROTATION_AXIS=-1 0 0 for PILATUS3 at SPring-8 BL41XU.
 
# revision 0.44 . Keitaro 5/2014 automatically set ROTATION_AXIS=-1 0 0 for PILATUS3 at SPring-8 BL41XU.
 
# revision 0.45 . KD cope with blanks in filenames
 
# revision 0.45 . KD cope with blanks in filenames
REVISION="0.45 (28-May-2014)"
+
# 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 0.48 . 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 0.50 . KD 03/2015 workaround for Mar-1 change of parameter name "DISTANCE" to "POSITION" in REFINE(*) keywords
 +
# revision 0.51 . Keitaro 03/2015 add .gz and .xz support and remove limitation - frame numbers can start with any.
 +
# revision 0.52 . Keitaro 05/2015 fix ADSC beam center convention for SPring-8 and DET_SN acquisition for PILATUS (didn't work on Mac)
 +
# revision 0.53 . KD add ADSC beam center convention for APS Argonne but only as commented line in XDS.INP (not detector serial no)
 +
# revision 0.54 . KD add ADSC S/N 911 for APS Argonne, and fix spurious output arising from THETADISTANCE (?!)
 +
# revision 0.55 . KD add ADSC S/N 446 for APS, and check w/ 12 datasets from data.sbgrid.org. No rule found: S/N 916 @ APS 24_ID_E !
 +
# revision 0.56 . Keitaro 12/2015 show error message when user's input didn't match any files
 +
# revision 0.57 . KD 12/2015 start to take care of vertical ROTATION_AXIS at Diamond I24 - for now only introduce comment
 +
# revision 0.58 . Keitaro 01/2016 fix for dTREK image: take 'rotation axis' information from header
 +
# revision 0.59 . KD 04/04/2016 check for ADSC detector _after_ 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 0.61 . Keitaro 10/04/2016 Add Eiger hdf5 support (may be incomplete; UNTRUSTED_RECTANGLE=s not set) NEED h5dump.
 +
# revision 0.62 . Keitaro 11/04/2016 Can give foo_master.h5 instead of foo_??????.h5.
 +
# revision 0.63 . Keitaro 13/04/2016 Set UNTRUSTED_RECTANGLE=s for EIGER 9M and 16M (KD).
 +
# 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 0.66 . KD 15/09/2016 add Bruker PHOTON II with .cbf frames
 +
# revision 0.67 . KD 02/10/2016 add BM30A (ADSC SERIAL 924) reverse_phi
 +
# revision 0.68 . KD 24/10/2016 add -H option (follow symlinks) to "find" command (thanks to Jan Gebauer!)
 +
# revision 0.69 . KD 04/11/2016 add CMOS-1 MBC Detector at ALS 4.2.2
 +
# revision 0.70beta . KD 08/12/2016 ROTATION_AXIS=0 -1 0 at Diamond I24; depending on CBF header
 +
# revision 0.70 . KD 12/01/2017 remove error message if h5dump does not find /entry/sample/transformations/omega/vector
 +
# revision 0.71 . KD 27/02/2017 implement rule for S/N 916 @ APS 24_ID_E
 +
# revision 0.72 . KD 8/03/2017 fix nframes lookup in Eiger master file
 +
# revision 0.73 . KD 18/05/2017 for Andrey Nascimento: add Pilatus 2M S/N 24-0109 with ROTATION_AXIS=-1 0 0
 +
# revision 0.74 . Keitaro 02/08/2017 Add PILATUS3 6M, S/N 60-0127 at CHESS F1 with  ROTATION_AXIS=-1 0 0
 +
# revision 0.75 . KD 30/08/2017 reversed ORGX and ORGY for marCCD @ BM14 (Indian beamline @ ESRF)
 +
# revision 0.76 . KD 4/09/2017 include POSITION into REFINE(IDXREF) because latest XDS is more robust. Add comments to keywords.
 +
# revision 0.77 . KD 19/12/2017 obtain QX QY from CBF header.
 +
# revision 0.78 . KD 21/12/2017 if possible and sensible, provide LIB= line with hardcoded /usr/local/lib64/dectris-neggia.so .
 +
# revision 0.79 . KD 16/01/2018 read OVERLOAD from Pilatus miniCBF header instead of fixing at 1048576
 +
# revision 0.80 . KD 13/02/2018 remove DISTANCE keyword from REFINE() list; remove POSITION from REFINE(IDXREF)
 +
# revision 0.81 . KD 21/02/2018 when encountering CBF files from Eiger (ESRF), treat as Pilatus detector
 +
# 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 0.84 . KD 10/10/2018 implement Pilatus detector with d*TREK header
 +
# revision 0.85 . Jie Nan 09/01/2019 STARTING_ANGLE for Eiger
 +
# revision 0.86 . Keitaro 03/05/2019 Add PILATUS3 6M, S/N 60-0123 at SSRF BL18U-1 with ROTATION_AXIS=-1 0 0
 +
# revision 0.87 . KD 12/10/2019 Add PILATUS XXX, S/N XX-XXX at SSRF BL19U1 and MarCCD detector #43 at BL17B1 with ROTATION_AXIS=-1 0 0
 +
# revision 0.88 . KD 16/10/2019 fixes for SSRF, add "-maxdepth 1" to "find -H ..."
 +
# revision 0.89 . KD 21/10/2019 add ADSC S/N 905 at ALS 8.2.1, S/N 928 at Australian Synchrotron MX2 beamline; final SSRF fixes
 +
# revision 0.90 . KD 25/10/2019 add OLDMAR detector type. Tested w/ SBGrid data set 6. Anomalous signal may have wrong hand!
 +
# revision 0.91 . KD 16/01/2020 Allow negative starting angle for Eiger (found -33 at SLS !).
 +
# 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 0.94 . 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 0.96 . KD 03/10/2020 make script echo detector serial number if inverted ROTATION_AXIS is detected.
 +
# revision 0.97 . KD 19/10/2020 add UNTRUSTED_RECTANGLEs for Eiger2 (which has a few pixels less than Eiger (thanks to Andreas Förster)
 +
# revision 0.98 . Thomas Hauß (HZB) 06/11/2020 switch Python print syntax to Python3
 +
# revision 0.99 . Aaron Finke (CHESS) 07/11/2020 add ROTATION_AXIS=-1 0 0 for EIGER2 16M detector at MX beamline ID7B2 (CHESS)
 +
# 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 1.02 . 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 1.04 . 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 1.06 . KD fix URLs in output. Availability of Apple M1 processor dectris-neggia-Apple-arm64.so . LC_ALL=C .
 +
REVISION="1.06 (15-OCT-2021)"
 +
 
 
#                                                                                                             
 
#                                                                                                             
 
# 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.                                                                 
#                                                                                                           
  −
# limitations:                                                                                             
  −
# - frame numbers are assumed to start with 1 and run consecutively                                         
   
#                                                                                                             
 
#                                                                                                             
 
# 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 Mac OS X, Xcode (from http://developer.apple.com/tools/xcode) might be needed - not sure about this                             
+
# - on Mac OS X, the Xcode command line tools (from https://developer.apple.com/download/more/) are needed.                           
 
#                                                                                                                 
 
#                                                                                                                 
 
# notes for debugging of the script:                                                                             
 
# notes for debugging of the script:                                                                             
# - add the -v option to the first line, to see where an error occurs                                             
+
# - add the -x option to the 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                                                     
 
#                                                                                                                 
 
#                                                                                                                 
Line 87: Line 148:  
   exit                                                                                                           
 
   exit                                                                                                           
 
fi                                                                                                               
 
fi                                                                                                               
 +
# make sure the locale does not interfere with e.g. awk calculations:
 +
LC_ALL="C";export LC_ALL
 
#                                                                                                                 
 
#                                                                                                                 
 
# defaults:                                                                                                       
 
# defaults:                                                                                                       
#                                                                                                              
+
#      
 +
# conversion radian / degrees:
 +
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"
Line 103: Line 169:  
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
 +
MNOPIAS=3
 +
# default DIRECTION_OF_DETECTOR_X-AXIS
 +
DIRECTION_OF_DETECTOR_X_AXIS="1 0 0"
 +
# default FRACTION_OF_POLARIZATION
 +
pol_frac=0.98
 +
STARTING_ANGLE=0
 +
dtrek_det=""
 +
SEPMIN=7.0
 +
CLUSTER_RADIUS=3.5
 +
REFINE_CORRECT="CELL BEAM ORIENTATION AXIS POSITION ! Default is: refine everything"
 +
 +
dname=`echo "$1" | xargs dirname`
 +
test "${dname}" == "" && dname="."
 +
bname=`echo "$1" | xargs basename`
 
# see how we are called:                                                                                         
 
# see how we are called:                                                                                         
NAME_TEMPLATE_OF_DATA_FRAMES="$1"
+
NAME_TEMPLATE_OF_DATA_FRAMES="${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'
/bin/ls -C1 $1 $1.bz2 2>/dev/null | egrep -v "_00000.cbf|_000.img" > tmp1 || exit 1
+
find -H $dname -maxdepth 1 -name "$bname" -or -name "${bname}.bz2" -or -name "${bname}.gz" -or -name "${bname}.xz" | egrep -v "_00000.cbf|_000.img" | sort > tmp1
 +
if [ ! -s tmp1 ]
 +
then
 +
echo "Error! No files matched: $1"
 +
rm -f tmp1
 +
exit 1
 +
fi
 
unset IFS
 
unset IFS
 
# we can continue - the frames are found
 
# we can continue - the frames are found
   −
# set upper limit of DATA_RANGE to number of frames (see "limitations" above)
+
if echo $NAME_TEMPLATE_OF_DATA_FRAMES | grep '_master.h5$' > /dev/null; then
DATA_RANGE=`wc -l tmp1 | awk '{print $1}'`                                  
+
NAME_TEMPLATE_OF_DATA_FRAMES=`echo "$NAME_TEMPLATE_OF_DATA_FRAMES" | sed -e 's/_master.h5$/_??????.h5/'`
 +
else
 +
# Find the first '?' position and the number of '?' to determine DATA_RANGE=.
 +
pos1=`echo "$NAME_TEMPLATE_OF_DATA_FRAMES" | awk '{print index($0, "?")}'`
 +
pos2=`echo "$NAME_TEMPLATE_OF_DATA_FRAMES" | sed -e "s/[^\?]//g" | awk '{print length+'$pos1' - 1}'`
 +
data_first=`cut -b $pos1-$pos2 tmp1 | head -n1 | bc`
 +
data_last=`cut -b $pos1-$pos2 tmp1 | tail -n1 | bc`
 +
DATA_RANGE="$data_first $data_last"
 +
echo DATA_RANGE=$DATA_RANGE
 +
 +
# 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"
 +
fi
   −
# set upper limit of SPOT_RANGE to half of DATA_RANGE, but not less than 1
+
FIRSTFRAME=`head -1 tmp1`
SPOT_RANGE=`echo "scale=0; $DATA_RANGE/2" | bc -l`                      
+
echo $FIRSTFRAME | grep "\.h5$" && is_h5=1 || is_h5=0
SPOT_RANGE=`echo "if ($SPOT_RANGE<1) 1;if ($SPOT_RANGE>1) $SPOT_RANGE" | bc -l`
  −
 
  −
echo DATA_RANGE=1 $DATA_RANGE
      
# find out detector type
 
# find out detector type
 
DET=XXX               
 
DET=XXX               
 
IFS=$'\n'     
 
IFS=$'\n'     
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.
strings $FIRSTFRAME > tmp2 
+
echo $FIRSTFRAME | grep -q '\.gz$' && zcat < $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                                                 
grep -q BEAM_CENTER_X tmp2       && DET=adsc                               
+
egrep -qi 'marccd|Corrected' tmp2 && DET=mccd                                 
head -n1 tmp2 | grep -q "^RAXIS" && DET=raxis
+
grep -q PILATUS tmp2            && DET=pilatus  
head -n1 tmp2 | grep -q "^R-AXIS" && DET=raxis
+
grep -iq Eiger tmp2             && DET=pilatus                           
grep -q "^DETECTOR_TYPE=RAXIS" tmp2 && DET=raxis_smv
+
head -n1 tmp2 | grep -q "^RAXIS" && DET=raxis
grep -q mar345 tmp2 && DET=MAR345                        
+
head -n1 tmp2 | grep -q "^R-AXIS" && DET=raxis
 +
grep -q "^SOURCE_WAVELENGTH= *1" tmp2 && DET=dtrek
 +
grep -q BEAM_CENTER_X tmp2      && DET=adsc                               
 +
grep -q mar345 tmp2 && DET=MAR345
 +
# rev. 1.02: in one case, mar555 data could be processed pretending it is mar345, so:
 +
grep -q mar555 tmp2 && DET=MAR345
 +
grep -q BRUKER tmp2 && grep -q CBF tmp2  && DET=Bruker-cbf 
 +
grep -q CMOS1 tmp2 && DET=adsc-CMOS1 
 +
grep -q MARCONTROL tmp2 && DET=OLDMAR 
 +
grep -q "WAVELENGTH=0.0" tmp2 && DET=experimental-ED                                   
 +
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 151: Line 265:  
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
 
                                    
 
                                    
 
   DETECTOR="CCDCHESS MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65500"
 
   DETECTOR="CCDCHESS MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65500"
Line 157: Line 272:     
   # Check detector serial number and recognize beamline for reversed-phi setting.
 
   # Check detector serial number and recognize beamline for reversed-phi setting.
   # Known detectors for reversed-phi in SPring-8: 31: BL32XU MX225HE, 38: BL44XU MX225HE, 42: BL44XU MX300HE, 40: BL41XU MX225HE, 106: BL32XU MX225HS
+
   # Known detectors for reversed-phi in SPring-8: 24: BL26B2 Mar225, 31: BL32XU MX225HE, 38: BL44XU MX225HE, 42: BL44XU MX300HE, 40: BL41XU MX225HE, 106: BL32XU MX225HS
 +
  # same for SSRF: BL17B1 rayonix MX300. As on 2019-10-13, this also needs doubling of ORGX and ORGY. But the beamline staff (Wenming) wants to fix the header.
 
   REVERSEPHI_SNs="
 
   REVERSEPHI_SNs="
 +
24
 
31
 
31
 
38
 
38
 
40
 
40
 
42
 
42
 +
43
 
106
 
106
 
"
 
"
Line 169: Line 287:  
   if echo "${DET_SN}${REVERSEPHI_SNs}" | sort | uniq -d | grep [0-9] > /dev/null; then
 
   if echo "${DET_SN}${REVERSEPHI_SNs}" | sort | uniq -d | grep [0-9] > /dev/null; then
 
     REVERSE_PHI="yes"
 
     REVERSE_PHI="yes"
 +
    echo inverted ROTATION_AXIS since Detector Serial Number is "${DET_SN}"
 
   fi
 
   fi
   Line 183: Line 302:  
   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
 +
  let SKIP=1724
 +
  TWOTHETA=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}')
 +
  TWOTHETA=`echo "scale=3; $TWOTHETA/1000" | bc -l`
 +
  echo 2THETA= $TWOTHETA
 +
 
 +
  let SKIP=1024+256+128+256+44
 +
  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 `
 +
  echo STARTING_ANGLE= $STARTING_ANGLE 
 +
                                                                                                     
 
   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 $2}')             
Line 190: Line 320:  
   ORGY=$(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; $ORGY/1000" | bc -l `                                                               
 +
# fixed Aug 30, 2017 after IUCr2017 @ Hyderabad
 +
  if [ "$DET_SN" == "4" ]; then
 +
    TEMP=$ORGY
 +
    ORGY=$ORGX
 +
    ORGX=$TEMP
 +
    echo reversed ORGX and ORGY for marCCD @ ESRF BM14
 +
  fi
    
   let SKIP=1024+736
 
   let SKIP=1024+736
Line 230: Line 367:  
       # 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=//`                                           
 
       QX=`grep PIXEL_SIZE tmp2 | sed s/PIXEL_SIZE=//`
 
       QX=`grep PIXEL_SIZE tmp2 | sed s/PIXEL_SIZE=//`
# FIXME - next 2 lines should be done properly, from header
  −
      NY=$NX                                             
   
       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=//`
# fix 2010-04-26 - tell user about possible ORGX, ORGY alternatives -  
+
   
 
       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, 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 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,..."
+
! ORGX= $ORGX1 ORGY= $ORGY1 ! For ESRF, PF, APS, AS MX2 ..."
 
# this 2nd alternative convention should be used at the following beamlines (pls complete the list): ALS 5.0.3, ...
 
# this 2nd alternative convention should be used at the following beamlines (pls complete the list): ALS 5.0.3, ...
 
       ORGX2=`echo "scale=1; $NX-$BEAM_CENTER_X/$QX" | bc -l `
 
       ORGX2=`echo "scale=1; $NX-$BEAM_CENTER_X/$QX" | bc -l `
Line 252: Line 388:  
! 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.
 
       ORGX3=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l `
 
       ORGX3=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l `
 
       ORGY3=`echo "scale=1; $NX-$BEAM_CENTER_Y/$QX" | bc -l `
 
       ORGY3=`echo "scale=1; $NX-$BEAM_CENTER_Y/$QX" | bc -l `
       echo - at e.g. ALS 8.2.2 use: ORGX=$ORGX3 ORGY=$ORGY3 - this is written to XDS.INP                            
+
       echo - at e.g. ALS 8.2.2 use: ORGX=$ORGX3 ORGY=$ORGY3 - this is written to XDS.INP if beamline is not detected
 
       COMMENT_ORGXY="${COMMENT_ORGXY}
 
       COMMENT_ORGXY="${COMMENT_ORGXY}
! ORGX= $ORGX3 ORGY= $ORGY3 ! For ALS 8.2.2, SPring-8,.."
+
! ORGX= $ORGX3 ORGY= $ORGY3 ! For 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.
+
# this 4th alternative convention should be used at the following beamlines (pls complete the list): SPring-8, ...
 +
      ORGX4=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l `
 +
      ORGY4=`echo "scale=1; $BEAM_CENTER_Y/$QX" | bc -l `
 +
      echo - at e.g. SPring-8 use: ORGX=$ORGX4 ORGY=$ORGY4
 +
      COMMENT_ORGXY="${COMMENT_ORGXY}
 +
! ORGX= $ORGX4 ORGY= $ORGY4 ! For SPring-8,.."
    
       # Decision of beam center convention based on detector serial numbers.
 
       # Decision of beam center convention based on detector serial numbers.
 
       DET_SN=`grep DETECTOR_SN tmp2 | sed -e "s/DETECTOR_SN=//"`
 
       DET_SN=`grep DETECTOR_SN tmp2 | sed -e "s/DETECTOR_SN=//"`
       # For convention 1; Known PF detectors = 449: NW12A Q210, 472: NE3A Q270, 474: BL17A Q270, 912: BL5A Q315
+
      echo Detector serial number is $DET_SN
 +
       # For convention 1; Known PF detectors = 449: NW12A Q210, 472: NE3A Q270, 474: BL17A Q270, 912: BL5A Q315, 923: ALS BL5.0.2 Q315, 933: AichiSR BL2S1 Q315, 916: APS 24 IDE, 928: AS MX2
 
       ORG1_SNs="
 
       ORG1_SNs="
 
449
 
449
Line 267: Line 410:  
474
 
474
 
912
 
912
 +
923
 +
933
 +
911
 +
446
 +
916
 +
905
 +
928
 +
"
 +
      ORG4_SNs="
 +
915
 
"
 
"
 
       if echo "${DET_SN}${ORG1_SNs}" | sort | uniq -d | grep [0-9] > /dev/null; then
 
       if echo "${DET_SN}${ORG1_SNs}" | sort | uniq -d | grep [0-9] > /dev/null; then
 
       ORGX=$ORGX1
 
       ORGX=$ORGX1
 
       ORGY=$ORGY1
 
       ORGY=$ORGY1
 +
      echo the following was chosen based on detector serial number:
 +
      elif echo "${DET_SN}${ORG4_SNs}" | sort | uniq -d | grep [0-9] > /dev/null; then
 +
      ORGX=$ORGX4
 +
      ORGY=$ORGY4
 +
      echo the following was chosen based on detector serial number:
 
       else
 
       else
 
       ORGX=$ORGX3
 
       ORGX=$ORGX3
 
       ORGY=$ORGY3
 
       ORGY=$ORGY3
 +
      echo the following default was chosen because the detector serial number was not special-cased:
 
       fi
 
       fi
    
       # Check detector serial number and recognize beamline for reversed-phi setting.
 
       # Check detector serial number and recognize beamline for reversed-phi setting.
       # Known detectors for reversed-phi in SPring-8: 915: BL38B1 Q315
+
       # Known detectors for reversed-phi in SPring-8: 915: BL38B1 Q315; APS 19-ID: 458; BM30A: 924
 +
      # 928 is at Australian Beamline MX2
 +
      # revision 0.83 of this script removes 458 from the list!
 
       REVERSEPHI_SNs="
 
       REVERSEPHI_SNs="
 
915
 
915
 +
924
 +
928
 
"
 
"
 
       if echo "${DET_SN}${REVERSEPHI_SNs}" | sort | uniq -d | grep [0-9] > /dev/null; then
 
       if echo "${DET_SN}${REVERSEPHI_SNs}" | sort | uniq -d | grep [0-9] > /dev/null; then
 
         REVERSE_PHI="yes"
 
         REVERSE_PHI="yes"
 +
        echo inverted ROTATION_AXIS since detector serial number is ${DET_SN}
 
       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 [ "$DET" == "adsc-CMOS1" ]; then
 +
  DETECTOR="ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000"
 +
  echo Data from CMOS1 MBC detector.
 +
  SENSOR_THICKNESS=0.01                                                       
 +
  sed s/\;// tmp2 > tmp1                                                     
 +
  mv tmp1 tmp2                                                               
 +
  X_RAY_WAVELENGTH=`grep WAVELENGTH tmp2 | head -1 | sed s/WAVELENGTH=//`
 +
  NX=`grep SIZE1 tmp2 | tail -1 | sed s/SIZE1=//`
 +
  QX=`grep PIXEL_SIZE tmp2 | sed s/PIXEL_SIZE=//`
 +
  NY=`grep SIZE2 tmp2 | tail -1 | sed s/SIZE2=//`                                           
 +
  QY=$QX                                             
 +
  ORGX=`grep BEAM_CENTER_X tmp2 | sed s/BEAM_CENTER_X=//`
 +
  ORGY=`grep BEAM_CENTER_Y tmp2 | sed s/BEAM_CENTER_Y=//`
 +
  REVERSE_PHI="yes"
 +
  DETECTOR_DISTANCE=`grep ^DISTANCE tmp2 | sed s/DISTANCE=/-/`                                                                   
 +
  OSCILLATION_RANGE=`grep OMEGA_DELTA tmp2 | sed s/OMEGA_DELTA=//` 
 +
  DIRECTION_OF_DETECTOR_X_AXIS="-1 0 0"
 +
                                                               
 +
elif [ "$DET" == "experimental-ED" ]; then
 +
  DETECTOR="ADSC MINIMUM_VALID_PIXEL_VALUE= 1 OVERLOAD= 65000  ! OVERLOAD is really unknown "
 +
  echo --- Electron diffraction data in SMV format!
 +
  SENSOR_THICKNESS=0.01                                                       
 +
  sed s/\;// tmp2 > tmp1                                                     
 +
  mv tmp1 tmp2                                                               
 +
  X_RAY_WAVELENGTH=`grep WAVELENGTH tmp2 | head -1 | sed s/WAVELENGTH=//`
 +
  NX=`grep SIZE1 tmp2 | tail -1 | sed s/SIZE1=//`
 +
  QX=`grep PIXEL_SIZE tmp2 | sed s/PIXEL_SIZE=//`
 +
  NY=`grep SIZE2 tmp2 | tail -1 | sed s/SIZE2=//`                                           
 +
  QY=$QX 
 +
  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=//`
 +
  QXY=`echo "scale=1; $QX*($BEAM_CENTER_X+$BEAM_CENTER_Y)" | bc -l`
 +
      if [ "$QXY" "<" "$BEAM_CENTER_X" ] ; then
 +
      ORGX=`echo "scale=2; $BEAM_CENTER_Y/$QX" | bc -l`
 +
      ORGY=`echo "scale=2; $BEAM_CENTER_X/$QX" | bc -l`
 +
      else
 +
      ORGX=`echo "scale=2; $BEAM_CENTER_X/1" | bc -l`
 +
      ORGY=`echo "scale=2; $BEAM_CENTER_Y/1" | bc -l`
 +
      fi
 +
  DETECTOR_DISTANCE=`grep ^DISTANCE tmp2 | sed s/DISTANCE=//`                                                                   
 +
  OSCILLATION_RANGE=`grep OSC_RANGE tmp2 | sed s/OSC_RANGE=//`
 +
  STARTING_ANGLE=`grep OSC_START tmp2 | sed s/OSC_START=//`
 +
  echo --- For TIMEPIX detector, please fix ROTATION_AXIS yourself!
 +
  DIRECTION_OF_DETECTOR_X_AXIS="1 0 0"
 +
  REFINE_CORRECT="ORIENTATION CELL AXIS BEAM ! for ED, no POSITION when CELL is refined"
    
elif [ "$DET" == "pilatus" ]; then
 
elif [ "$DET" == "pilatus" ]; then
  DETECTOR="PILATUS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD= 1048576  !PILATUS"
  −
  QX=0.172 QY=0.172                                                       
   
   echo Data from a Pilatus detector                                         
 
   echo Data from a Pilatus detector                                         
 
   sed s/#// tmp2 > tmp1                                                     
 
   sed s/#// tmp2 > tmp1                                                     
 
   mv tmp1 tmp2                                                               
 
   mv tmp1 tmp2                                                               
 +
  OVERLOAD=1048574
 +
  SEPMIN=4
 +
  CLUSTER_RADIUS=2
 +
  grep -q Count_cutoff tmp2 && OVERLOAD=`awk '/Count_cutoff/{print $2}' tmp2`
 +
  DETECTOR="PILATUS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD= $OVERLOAD  !PILATUS"
 +
  QX=0.172 QY=0.172                                                       
 +
# 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 && QY=`awk '/Pixel_size/{print 1000*$5}' tmp2`                                                   
    
       # find SENSOR_THICKNESS:
 
       # find SENSOR_THICKNESS:
Line 309: Line 526:  
       ORGY=`grep Beam_xy tmp2 | sed -e s/\(// -e s/\)// -e s/\,// | awk '{print $3}'`
 
       ORGY=`grep Beam_xy tmp2 | sed -e s/\(// -e s/\)// -e s/\,// | awk '{print $3}'`
   −
       # find DETECTOR_DISTANCE and OSCILLATION_RANGE:
+
       # find DETECTOR_DISTANCE, OSCILLATION_RANGE, and STARTING_ANGLE:
       DETECTOR_DISTANCE=`awk '/distance/{print $2}' tmp2`
+
       DETECTOR_DISTANCE=`awk '/Detector_distance/{print $2}' tmp2`
 
       DETECTOR_DISTANCE=`echo "$DETECTOR_DISTANCE*1000" | bc -l`
 
       DETECTOR_DISTANCE=`echo "$DETECTOR_DISTANCE*1000" | bc -l`
   −
       OSCILLATION_RANGE=`awk '/Angle/{print $2}' tmp2`
+
       OSCILLATION_RANGE=`awk '/Angle_increment/{print $2}' tmp2`
 +
 
 +
      STARTING_ANGLE=`awk '/Start_angle/{print $2}' tmp2`
 +
      echo STARTING_ANGLE= $STARTING_ANGLE 
    
       # 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
 
       # Known detectors for reversed-phi in SPring-8: BL41XU PILATUS3 6M 60-0125
 
       # Known detectors for reversed-phi in SPring-8: BL41XU PILATUS3 6M 60-0125
       DET_SN=`grep "Detector:" tmp2 | sed "s/^.*Detector: \?//"`
+
      # Known detectors for reversed-phi in APS: 19ID PILATUS3 6M 60-0132
 +
      # Known detectors for reversed-phi at MX2 beamline (Brazilian Synchrotron National Laboratory - LNLS)
 +
      # Known detectors for reversed-phi at CHESS F1 PILATUS3 6M, S/N 60-0127
 +
      # Known detectors for reversed-phi at SSRF BL18U1 (S/N 60-0123) and BL19U1 (S/N XX-XXX) (!; 2019-10-19: staff will fix this)
 +
       DET_SN=`grep "Detector:" tmp2 | sed "s/^.*Detector: *//"`
 
       REVERSEPHI_SNs="
 
       REVERSEPHI_SNs="
 
PILATUS3 6M, S/N 60-0125
 
PILATUS3 6M, S/N 60-0125
 +
PILATUS3 6M, S/N 60-0132
 +
PILATUS 2M, S/N 24-0109
 +
PILATUS3 6M, S/N 60-0127
 +
PILATUS3 6M, S/N 60-0123
 
"
 
"
 
       if echo "${DET_SN}${REVERSEPHI_SNs}" | sort | uniq -d | grep [0-9] > /dev/null; then
 
       if echo "${DET_SN}${REVERSEPHI_SNs}" | sort | uniq -d | grep [0-9] > /dev/null; then
 
         REVERSE_PHI="yes"
 
         REVERSE_PHI="yes"
 +
        echo inverted ROTATION_AXIS since detector serial number is ${DET_SN}
 +
      fi
 +
      if [ "$DET_SN" == "PILATUS XXX, S/N XX-XXX" ] ; then
 +
        REVERSE_PHI="yes"
 +
        echo inverted rotation axis at SSRF BL19U1
 +
      fi
 +
     
 +
# Diamond I24:
 +
      if [ "$DET_SN" == "PILATUS3 6M, S/N 60-0119" ] ; then
 +
        if grep -q "Oscillation_axis X.CW +SLOW" tmp2 ; then
 +
          rotation_axis="0 -1 0"
 +
          echo ROTATION_AXIS="0 -1 0" at Diamond I24
 +
        fi
 +
      fi
 +
# PETRA P14: raw data from Eiger are stored as CBF files so this is treated as Pilatus
 +
      if [ "$DET_SN" == "Dectris Eiger 16M, E-32-0107" -o "$DET_SN" == "Dectris Eiger 4M, E-08-0107" -o "$DET_SN" == "PILATUS 6M-F, S/N 60-0115-F" ] ; then
 +
        rotation_axis="0 -1 0"
 +
        echo ROTATION_AXIS="0 -1 0" at PETRA P14
 +
      fi
 +
# ESRF ID23-2:
 +
      if [ "$DET_SN" == "PILATUS3 2M, S/N 24-0118, ESRF ID23" ] ; then
 +
        rotation_axis="0 -1 0"
 +
        echo ROTATION_AXIS="0 -1 0" at ESRF ID23-2
 +
      fi
 +
 +
elif [ "$DET" == "eiger" ]; then
 +
nframes=`h5dump -d "/entry/instrument/detector/detectorSpecific/nimages" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2}'`
 +
DATA_RANGE="1 $nframes"
 +
SPOT_RANGE="1 `echo "scale=0; if (${nframes}<2) 1; if (${nframes}>1) ${nframes}/2"|bc -l`"
 +
 +
# find out if HDF5 from Diamond (DLS=1) or Dectris (DLS=0)
 +
  DLS=0
 +
  OVERLOAD=`h5dump -d "/entry/instrument/detector/detectorSpecific/countrate_correction_count_cutoff" $FIRSTFRAME 2>/dev/null` || DLS=1
 +
  if [ "$DLS" == 1 ]; then
 +
    echo Eiger HDF5 from Diamond
 +
# unfortunately h5dump 1.10 is required to get this right for the DLS .h5 files. This version is available at DLS but maybe not elsewhere
 +
    OVERLOAD=`h5dump -d "/entry/instrument/detector/saturation_value" $FIRSTFRAME | awk '/\(0\):/{print $2}'`
 +
  # v0.95: fix the next 2 lines by taking care of negative values with the \- , and stop after first "(0)"
 +
    OSCILLATION_RANGE=`h5dump -d "/entry/data/omega" $FIRSTFRAME | awk '/\(0\): [\-0-9]/{print $3-$2;exit}'`
 +
    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
 +
  # 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
 +
  else
 +
    echo Eiger HDF5 from Dectris
 +
    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}'`
 +
  # STARTING_ANGLE:  the \- was introduced in version 0.91 to allow negative values :
 +
    STARTING_ANGLE=`h5dump -d "/entry/sample/goniometer/omega_start" $FIRSTFRAME | awk '/\(0\): [\-0-9]/{print $2}'`
 +
  # /entry/sample/goniometer/omega_start is missing in some eiger2 detectors (e.g. Eiger2 9M with fw version release-2020.2.1 and SIMPLON API 1.8) (Feng YU 2021-07-18)
 +
    if [ "$STARTING_ANGLE" == "" ]; then
 +
  echo "/entry/sample/goniometer/omega_start not found, try /entry/sample/goniometer/omega"
 +
  STARTING_ANGLE=`h5dump -d /entry/sample/goniometer/omega $FIRSTFRAME | grep "(0):" | head -n 1 | awk '{print $2}' | sed -e "s/,//g"`
 +
    fi
 +
    echo "STARTING_ANGLE=$STARTING_ANGLE"
 +
  # If rotation vector 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
 +
    SN=`h5dump -d "/entry/instrument/detector/detector_number" $FIRSTFRAME | awk '/\(0\): /{print $2}' | sed s/\"//g`
 +
    if [ "$SN" == "E-32-0123" ]; then
 +
      rotation_axis="-1 0 0"
 +
      echo CHESS ID7B2 with inverted rotation axis
 +
    fi
 +
  # SSRF BL17U1 and SSRF BL10U2 (Feng YU 2021-07-18)
 +
  # 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.
 +
# 2021-02-01 00:00:00 CST time stamp is 1612108800
 +
    if [ "$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/\.\(.*\)/CST/g; s/\"//g"`
 +
      if [ `uname -s` == "Darwin" ]; then
 +
        collection_timestamp=`date -j -f "%Y-%m-%dT%H:%M:%S%Z" $collection_time +%s`
 +
      elif [ `uname -s` == "Linux" ]; then
 +
        collection_timestamp=`date -d $collection_time +%s`
 +
      else
 +
        collection_timestamp=0
 +
      fi
 +
      if [ $collection_timestamp -eq 0 ]; then
 +
        is_rotation_axis_set=1
 +
        rotation_axis=`h5dump -d "/SSRF/RotationAxis" $FIRSTFRAME 2>/dev/null || is_rotation_axis_set=0`
 +
        if [ "$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 $rotation_axis"
 +
        else
 +
          rotation_axis="-1 0 0    ! Cannot determine rotation axis. SSRF BL17U1: -1 0 0; SSRF BL02U1: 0 -1 0"
 +
        fi
 +
      elif [ $collection_timestamp -ge 0 ] && [ $collection_timestamp -le 1612108800 ]; then
 +
        # SSRF BL17U1
 +
        rotation_axis="-1 0 0"
 +
        echo "SSRF BL17U1 (Eiger X 16M) with inverted rotation axis"
 +
      else
 +
        # SSRF BL10U2
 +
        is_rotation_axis_set=1
 +
        rotation_axis=`h5dump -d "/SSRF/RotationAxis" $FIRSTFRAME 2>/dev/null || is_rotation_axis_set=0`
 +
        if [ "$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 $rotation_axis"
 +
        else
 +
          rotation_axis="0 -1 0"
 +
          echo "SSRF BL10U2 (Eiger X 16M) with vertical rotation axis"
 +
        fi
 +
      fi
 +
    fi
 +
  # SSRF BL02U1 (Feng YU 2021-07-18)
 +
  # EIGER2 S 9M SSRF BL02U1 has S/N E-18-0121
 +
    if [ "$SN" == "E-18-0121" ]; then
 +
      is_rotation_axis_set=1
 +
      rotation_axis=`h5dump -d "/SSRF/RotationAxis" $FIRSTFRAME 2>/dev/null || is_rotation_axis_set=0`
 +
      if [ "$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 $rotation_axis"
 +
      else
 +
        rotation_axis="1 0 0"
 +
        echo "SSRF BL02U1 (Eiger2 S 9M) with horizontal rotation axis"
 
       fi
 
       fi
 +
    fi
 +
# revision 1.05 specialcase nframes for Eiger detectors at BNL
 +
    if [ "$SN" == "E-18-0121" -o "$SN" == "E-32-0101" ]; then
 +
      echo specialcase nframes for Eiger detectors at BNL:
 +
      nframes=`h5dump -A -g "/entry/data" $FIRSTFRAME | grep "DATASPACE  SIMPLE" | sed -e "s/,.*//" | awk '{a+=$5}END{print a}'`
 +
      DATA_RANGE="1 $nframes"
 +
      SPOT_RANGE="1 `echo "scale=0; if (${nframes}<2) 1; if (${nframes}>1) ${nframes}/2"|bc -l`"
 +
    fi
 +
  fi
 +
  echo DATA_RANGE=$DATA_RANGE
 +
  DETECTOR="EIGER MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD= $OVERLOAD"
 +
  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 $2*1000}'`
 +
 +
  echo OVERLOAD=$OVERLOAD
 +
  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 :
 +
  DETECTOR_DISTANCE=`h5dump -d "/entry/instrument/detector/detector_distance" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2*1000}'` 
 +
 +
  SEPMIN=4
 +
  CLUSTER_RADIUS=2
    
elif [ "$DET" == "raxis" ]; then
 
elif [ "$DET" == "raxis" ]; then
Line 331: Line 701:  
   #let SKIP=768
 
   #let SKIP=768
 
   #NX=$(od -t x -j $SKIP -N 4 $FIRSTFRAME |awk 'NR==1{print toupper($2)}'|perl -nle '@array= $_ =~/.{2}/g; print "ibase=16;obase=A;".join("",reverse @array)'|bc)
 
   #NX=$(od -t x -j $SKIP -N 4 $FIRSTFRAME |awk 'NR==1{print toupper($2)}'|perl -nle '@array= $_ =~/.{2}/g; print "ibase=16;obase=A;".join("",reverse @array)'|bc)
  NX=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(768);print "%.4d"%struct.unpack(">i",f.read(4))')
+
NX=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(768);print "%.4d"%struct.unpack(">i",f.read(4))')
  NY=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(772);print "%.4d"%struct.unpack(">i",f.read(4))')
+
NY=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(772);print "%.4d"%struct.unpack(">i",f.read(4))')
 
+
  NX=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(768);print("%.4d"%struct.unpack(">i",f.read(4)))')
   DETECTOR_DISTANCE=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(344);print "-%.4f"%struct.unpack(">f",f.read(4))')
+
   NY=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(772);print("%.4d"%struct.unpack(">i",f.read(4)))')
   −
  ORGX=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(540);print "%.4f"%struct.unpack(">f",f.read(4))')
+
!  DETECTOR_DISTANCE=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(344);print "-%.4f"%struct.unpack(">f",f.read(4))')
   ORGY=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(544);print "%.4f"%struct.unpack(">f",f.read(4))')
+
   DETECTOR_DISTANCE=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(344);print("-%.4f"%struct.unpack(">f",f.read(4)))')
   −
  OSCILLATION_RANGE=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(524);phis,phie=struct.unpack(">ff",f.read(8));print "%.4f"%(phie-phis)')
+
!  ORGX=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(540);print "%.4f"%struct.unpack(">f",f.read(4))')
 +
!  ORGY=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(544);print "%.4f"%struct.unpack(">f",f.read(4))')
 +
  ORGX=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(540);print("%.4f"%struct.unpack(">f",f.read(4)))')
 +
  ORGY=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(544);print("%.4f"%struct.unpack(">f",f.read(4)))')
   −
  QX=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(776);print "%.6f"%struct.unpack(">f",f.read(4))')
+
!  OSCILLATION_RANGE=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(524);phis,phie=struct.unpack(">ff",f.read(8));print "%.4f"%(phie-phis)')
   QY=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(780);print "%.6f"%struct.unpack(">f",f.read(4))')
+
   OSCILLATION_RANGE=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(524);phis,phie=struct.unpack(">ff",f.read(8));print("%.4f"%(phie-phis))')
   −
   X_RAY_WAVELENGTH=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(292);print "%.6f"%struct.unpack(">f",f.read(4))')
+
!  QX=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(776);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))')
 +
  QX=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(776);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)))')
   −
elif [ "$DET" == "raxis_smv" ]; then
+
!  X_RAY_WAVELENGTH=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(292);print "%.6f"%struct.unpack(">f",f.read(4))')
   echo "Data from a RAXIS detector with SMV header (dTREK image)"
+
   X_RAY_WAVELENGTH=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(292);print("%.6f"%struct.unpack(">f",f.read(4)))')
   −
   DETECTOR="RAXIS MINIMUM_VALID_PIXEL_VALUE=0"
+
elif [ "$DET" == "dtrek" ]; then
 +
   echo "Data from a RAXIS or Saturn or Pilatus detector with dTREK format"
    
   sed s/\;// tmp2 > tmp1
 
   sed s/\;// tmp2 > tmp1
 
   mv tmp1 tmp2
 
   mv tmp1 tmp2
    +
  dname=`grep "DETECTOR_NAMES=" tmp2 | sed -e "s/.*=//"`
 +
  flip=1
 +
  if [ "$dname" == "CCD_" ]; then
 +
    DETECTOR="SATURN MINIMUM_VALID_PIXEL_VALUE=1"
 +
    dtrek_det="saturn"
 +
 +
    # Find rotation axis. Warning: currently not support flipping (det(tmpmat)<0)
 +
    # I'm not sure this method is really valid - but at least mosflm seems to read this to determine rotation axis.
 +
    tmpmat=(`grep ${dname}SPATIAL_DISTORTION_VECTORS= tmp2 | tail -1 | sed -e "s/.*=//"`)
 +
    rotx=`echo "scale=6; -1.0*${tmpmat[0]}" | 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]}*${tmpmat[2]}))/1"|bc` -lt 0 ]; then
 +
    echo ""
 +
    echo "WARNING!! not-supported SPATIAL_DISTORTION_VECTORS header detected."
 +
    echo "Please report this to XDSwiki author."
 +
    echo ""
 +
  fi
 +
  elif [ "$dname" == "PILT_" ]; then
 +
    DETECTOR="PILATUS MINIMUM_VALID_PIXEL_VALUE=0"
 +
    dtrek_det="pilatus"
 +
    SEPMIN=3
 +
    CLUSTER_RADIUS=1.5
 +
    rotation_axis="0 1 0"  # TODO: read from header
 +
    flip=-1
 +
    SENSOR_THICKNESS=0.45  # TODO: read from header
 +
# 2theta
 +
    TWOTHETA=`awk '/PILT_GONIO_VALUES=/{print $2}' tmp2`
 +
    echo TWOTHETA=$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 $R3"
 +
  elif [ "$dname" == "RX_" ]; then
 +
    DETECTOR="RAXIS MINIMUM_VALID_PIXEL_VALUE=0"
 +
    dtrek_det="raxis"
 +
  else
 +
    DETECTOR="XXX MINIMUM_VALID_PIXEL_VALUE=XXX"
 +
    dtrek_det="unknown"
 +
  fi
 
   # 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 363: Line 779:     
   # find NX,NY,QX,QY
 
   # find NX,NY,QX,QY
  # NOTE that "RX_" may be different. probably we should check DETECTOR_NAMES= in header (RX_ is expected currently).
+
   # NX,NY should be read from *_DETECTOR_DIMENSIONS?
   # NX,NY should be read from RX_DETECTOR_DIMENSIONS?
   
   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=//`
   DET_SIZE=(`grep RX_DETECTOR_SIZE tmp2 | tail -1 | sed s/RX_DETECTOR_SIZE=//`)
+
   DET_SIZE=(`grep ${dname}DETECTOR_SIZE tmp2 | tail -1 | sed s/.*_DETECTOR_SIZE=//`)
   QX=`echo "scale=1; ${DET_SIZE[0]} / $NX" | bc -l`
+
   QX=`echo "scale=6; ${DET_SIZE[0]} / $NX" | bc -l`
   QY=`echo "scale=1; ${DET_SIZE[1]} / $NY" | bc -l`
+
   QY=`echo "scale=6; ${DET_SIZE[1]} / $NY" | bc -l`
    
   # find ORGX, ORGY
 
   # find ORGX, ORGY
   SPATIAL_DISTORTION_INFO=(`grep RX_SPATIAL_DISTORTION_INFO tmp2 | tail -1 | sed s/RX_SPATIAL_DISTORTION_INFO=//`)
+
   SPATIAL_DISTORTION_INFO=(`grep ${dname}SPATIAL_DISTORTION_INFO tmp2 | tail -1 | sed s/.*_SPATIAL_DISTORTION_INFO=//`)
 
   ORGX=${SPATIAL_DISTORTION_INFO[0]}
 
   ORGX=${SPATIAL_DISTORTION_INFO[0]}
 
   ORGY=${SPATIAL_DISTORTION_INFO[1]}
 
   ORGY=${SPATIAL_DISTORTION_INFO[1]}
    
   # find DETECTOR_DISTANCE  
 
   # find DETECTOR_DISTANCE  
   GONIO_NAMES=(`grep RX_GONIO_NAMES tmp2 | tail -1 | sed s/RX_GONIO_NAMES=//`)
+
   GONIO_NAMES=(`grep ${dname}GONIO_NAMES= tmp2 | tail -1 | sed s/.*_GONIO_NAMES=//`)
   GONIO_VALUES=(`grep RX_GONIO_VALUES tmp2 | tail -1 | sed s/RX_GONIO_VALUES=//`)
+
   GONIO_VALUES=(`grep ${dname}GONIO_VALUES= tmp2 | tail -1 | sed s/.*_GONIO_VALUES=//`)
  GONIO_UNITS=(`grep RX_GONIO_UNITS tmp2 | tail -1 | sed s/RX_GONIO_UNITS=//`)
+
GONIO_UNITS=(`grep ${dname}GONIO_UNITS= tmp2 | tail -1 | sed s/.*_GONIO_UNITS=//`)
 
   for i in `seq 1 ${#GONIO_NAMES[*]}`
 
   for i in `seq 1 ${#GONIO_NAMES[*]}`
 
   do
 
   do
 
   idx=$((i-1))
 
   idx=$((i-1))
 
   if [ "${GONIO_NAMES[$idx]}" == "Distance" ]; then
 
   if [ "${GONIO_NAMES[$idx]}" == "Distance" ]; then
 +
    DETECTOR_DISTANCE="${GONIO_VALUES[$idx]}"
 +
    # TODO: Check unit!! - ${GONIO_UNITS[$idx]}
 +
  fi
 +
  if [ $flip -gt 0 ]; then
 
     DETECTOR_DISTANCE="-${GONIO_VALUES[$idx]}"
 
     DETECTOR_DISTANCE="-${GONIO_VALUES[$idx]}"
 
     # TODO: Check unit!! - ${GONIO_UNITS[$idx]}
 
     # TODO: Check unit!! - ${GONIO_UNITS[$idx]}
 +
    echo "using distance <0"
 
   fi
 
   fi
 
   done
 
   done
Line 392: Line 812:  
   ROTATION=(`grep "^ROTATION=" tmp2 | tail -1 | sed s/ROTATION=//`)
 
   ROTATION=(`grep "^ROTATION=" tmp2 | tail -1 | sed s/ROTATION=//`)
 
   OSCILLATION_RANGE=${ROTATION[2]}
 
   OSCILLATION_RANGE=${ROTATION[2]}
  −
  # NOTE: how can we know correct ROTATION_AXIS=?
      
elif [ "$DET" == "MAR345" ]; then
 
elif [ "$DET" == "MAR345" ]; then
Line 400: Line 818:  
  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 $2}' tmp2`
  NY=$NX
+
# next line is rev 1.02 (previously NY= $NX):
 +
  NY=`awk -v NX=$NX '/FORMAT/{print $4/NX}' tmp2`
 
  QX=`awk '/PIXEL/{print $3/1000.}' tmp2`
 
  QX=`awk '/PIXEL/{print $3/1000.}' tmp2`
 
  QY=`awk '/PIXEL/{print $5/1000.}' tmp2`
 
  QY=`awk '/PIXEL/{print $5/1000.}' tmp2`
Line 415: Line 834:  
  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
 +
 
 +
echo  "Data from old type MAR image plate detector"
 +
DETECTOR="MAR  MINIMUM_VALID_PIXEL_VALUE=0  OVERLOAD=130000"
 +
NX=`awk 'NR==2 {print $2}' tmp2`
 +
NY=$NX
 +
QX=`awk 'NR==2 {print $15}' tmp2`
 +
QY=$QX
 +
ORGX=`awk 'NR==2 {print $19}' tmp2`
 +
ORGY=`awk 'NR==2 {print $20}' tmp2`
 +
DETECTOR_DISTANCE=`awk 'NR==2 {print $22}' tmp2`             
 +
X_RAY_WAVELENGTH=`awk 'NR==2 {print $21}' tmp2`
 +
OSCILLATION_RANGE=`awk 'NR==2 {print $24-$23}' tmp2`   
 +
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!
 +
        
 +
elif [ "$DET" == "Bruker-cbf" ]; then
 +
 
 +
echo  "Data from a Bruker-cbf detector"
 +
# 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`
 +
# 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`
 +
DELTAOMEGA=`awk '/OMEGA \? \? \?/{printf "%.5f",$6}' tmp2`
 +
PHI=`awk '/PHI \? \? \?/{printf "%.5f",$5}' tmp2`
 +
DELTAPHI=`awk '/PHI \? \? \?/{printf "%.5f",$6}' tmp2`
 +
KAPPA=`awk '/CHI \? \? \?/{printf "%.5f",$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}
 +
    STARTING_ANGLE=${PHI}
 +
# here we could check if DELTAPHI is <0, and if so, negate it and rotation_axis
 +
else
 +
    echo OMEGA scan
 +
    rotation_axis="0 -1 0"
 +
    OSCILLATION_RANGE=${DELTAOMEGA}
 +
    STARTING_ANGLE=${OMEGA}
 +
# here we could check if DELTAOMEGA is <0, and if so, negate it and rotation_axis
 +
fi
 +
echo STARTING_ANGLE= $STARTING_ANGLE        ! only read by IDXREF               
 +
 
 +
# 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
 
else
 
   echo should never come here
 
   echo should never come here
Line 422: Line 921:     
echo ORGX= $ORGX ORGY= $ORGY - check these values with adxv !
 
echo ORGX= $ORGX ORGY= $ORGY - check these values with adxv !
echo DETECTOR_DISTANCE= $DETECTOR_DISTANCE                  
+
echo DETECTOR_DISTANCE= $DETECTOR_DISTANCE ! only read by XYCORR, IDXREF                   
echo OSCILLATION_RANGE= $OSCILLATION_RANGE                  
+
echo OSCILLATION_RANGE= $OSCILLATION_RANGE ! only read by IDXREF
echo X-RAY_WAVELENGTH= $X_RAY_WAVELENGTH                    
+
echo X-RAY_WAVELENGTH= $X_RAY_WAVELENGTH   ! only read by IDXREF                 
    
# now we know everything that is required to generate XDS.INP
 
# now we know everything that is required to generate XDS.INP
Line 431: Line 930:  
! written by generate_XDS.INP version $REVISION
 
! written by generate_XDS.INP version $REVISION
 
JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT
 
JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT
ORGX= $ORGX ORGY= $ORGY  ! check these values with adxv !\
+
ORGX= $ORGX ORGY= $ORGY  ! values from frame header; only read by XYCORR, IDXREF   
 
$COMMENT_ORGXY
 
$COMMENT_ORGXY
DETECTOR_DISTANCE= $DETECTOR_DISTANCE                  
+
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               
 
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=1 $DATA_RANGE                                                     
+
DATA_RANGE=$DATA_RANGE                                                     
SPOT_RANGE=1 $SPOT_RANGE                                                     
+
SPOT_RANGE=$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)   
   Line 465: Line 965:  
VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS=6000. 30000. ! often 7000 or 8000 is ok
 
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)
 
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=$MNOPIAS ! default of 6 is sometimes too high
! close spots: reduce SEPMIN and CLUSTER_RADIUS from their defaults of 6 and 3, e.g. to 4 and 2
+
! close spots/long cell axis: reduce SEPMIN and CLUSTER_RADIUS from their defaults of 7 and 3.5
! nowadays headers are usually correct so refine DISTANCE in INTEGRATE but not IDXREF
+
SEPMIN=$SEPMIN  CLUSTER_RADIUS=$CLUSTER_RADIUS ! 4 and 2 for Pixel Array Detectors
REFINE(IDXREF)=CELL BEAM ORIENTATION AXIS ! DISTANCE
+
! since XDS 01-MAR-2015, POSITION supersedes DISTANCE.
REFINE(INTEGRATE)= DISTANCE BEAM ORIENTATION ! AXIS CELL
+
! nowadays headers are usually correct so refine POSITION in INTEGRATE but not IDXREF if low to medium resolution
! REFINE(CORRECT)=CELL BEAM ORIENTATION AXIS DISTANCE ! Default is: refine everything
+
! however, if the spots from COLSPOT extend to 2A then POSITION could, and if 1.5A POSITION should be refined
 
+
REFINE(IDXREF)=CELL BEAM ORIENTATION AXIS ! add POSITION if high resolution, or DETECTOR_DISTANCE inaccurate
 +
REFINE(INTEGRATE)= POSITION BEAM ORIENTATION ! AXIS CELL . If 1.5A or higher it is ok to refine CELL (unless electron diffraction)
 +
REFINE(CORRECT)= $REFINE_CORRECT
 
! parameters specifically for this detector and beamline:
 
! parameters specifically for this detector and beamline:
 
DETECTOR= $DETECTOR
 
DETECTOR= $DETECTOR
 
SENSOR_THICKNESS= $SENSOR_THICKNESS
 
SENSOR_THICKNESS= $SENSOR_THICKNESS
 
! attention CCD detectors: for very high resolution (better than 1A) make sure to specify SILICON
 
! attention CCD detectors: for very high resolution (better than 1A) make sure to specify SILICON
! as about 32* what CORRECT.LP suggests (absorption of phosphor is much higher than that of silicon)
+
! as about 32* what CORRECT.LP suggests (absorption of phosphor is much higher than that of 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
    
eof
 
eof
if [ "$DET" == "raxis" -o "$DET" == "raxis_smv" ]; then
+
 
 +
if [ "$DET" == "eiger" ] && [ "$is_h5" == 1 ]; then
 +
  if [ "$DLS" == 0 ] ; then
 +
    if [ -e /usr/local/lib64/dectris-neggia.so ]; then
 +
      echo LIB=/usr/local/lib64/dectris-neggia.so >> XDS.INP
 +
      echo LIB= line was written to XDS.INP . For Apple ARM64 processors, you must modify the name.
 +
    else
 +
      echo !LIB=/usr/local/lib64/dectris-neggia.so >> XDS.INP
 +
      echo /usr/local/lib64/dectris-neggia.so was not found - specify location manually!
 +
    fi
 +
  else
 +
    if [ -e /usr/local/lib64/durin-plugin.so ]; then
 +
      echo LIB=/usr/local/lib64/durin-plugin.so >> XDS.INP
 +
      echo LIB= line was written to XDS.INP
 +
    else
 +
      echo !LIB=/usr/local/lib64/durin-plugin.so >> XDS.INP
 +
      echo /usr/local/lib64/durin-plugin.so was not found - specify location manually!
 +
    fi
 +
  fi
 +
fi
 +
 
 +
if [ "$DET" == "raxis" -o "$dtrek_det" == "raxis" ]; then
 
  cat >> XDS.INP << eof
 
  cat >> XDS.INP << eof
 
DIRECTION_OF_DETECTOR_X-AXIS=1 0 0
 
DIRECTION_OF_DETECTOR_X-AXIS=1 0 0
 
DIRECTION_OF_DETECTOR_Y-AXIS=0 -1 0
 
DIRECTION_OF_DETECTOR_Y-AXIS=0 -1 0
INCIDENT_BEAM_DIRECTION=0 0 1
+
INCIDENT_BEAM_DIRECTION=0 0 1   ! only read by IDXREF
ROTATION_AXIS=0 1 0
+
ROTATION_AXIS=0 1 0             ! only read by IDXREF
!FRACTION_OF_POLARIZATION=0.98  ! uncomment if synchrotron
+
!FRACTION_OF_POLARIZATION=0.98  ! uncomment if synchrotron; only used by CORRECT
POLARIZATION_PLANE_NORMAL=1 0 0
+
POLARIZATION_PLANE_NORMAL=1 0 0 ! only used by CORRECT
 
eof
 
eof
 
else
 
else
  if [ "$REVERSE_PHI" == "no" ]; then
+
  if [ "$rotation_axis" != "" ]; then
   echo 'ROTATION_AXIS=1 0 0  ! at e.g. Australian Synchrotron, SERCAT ID-22 (?), APS 19-ID (?), ESRF BM30A, SPring-8 this needs to be -1 0 0' >> XDS.INP
+
  echo "ROTATION_AXIS= $rotation_axis  ! only read by IDXREF" >> XDS.INP
 +
elif [ "$REVERSE_PHI" == "no" ]; then
 +
   echo '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' >> XDS.INP
 
  else
 
  else
 
   echo 'ROTATION_AXIS=-1 0 0  ! if this is wrong, please contact author.' >> XDS.INP
 
   echo 'ROTATION_AXIS=-1 0 0  ! if this is wrong, please contact author.' >> XDS.INP
 
  fi
 
  fi
 +
if [ "$dtrek_det" == "saturn" ]; then
 +
cat >> XDS.INP << eof
 +
DIRECTION_OF_DETECTOR_X-AXIS=-1 0 0
 +
DIRECTION_OF_DETECTOR_Y-AXIS= 0 1 0
 +
eof
 +
else
 
  cat >> XDS.INP << eof
 
  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
 
DIRECTION_OF_DETECTOR_Y-AXIS=0 1 0
INCIDENT_BEAM_DIRECTION=0 0 1
+
eof
FRACTION_OF_POLARIZATION=0.98   ! better value is provided by beamline staff!
+
fi
POLARIZATION_PLANE_NORMAL=0 1 0
+
cat >> XDS.INP << eof
 +
INCIDENT_BEAM_DIRECTION=0 0 1         ! only read by IDXREF
 +
FRACTION_OF_POLARIZATION=${pol_frac}   ! better value is provided by beamline staff!
 +
POLARIZATION_PLANE_NORMAL=0 1 0       ! only used by CORRECT
 
eof
 
eof
 
fi
 
fi
 
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
 +
!fine-grained list is in Thorn et al http://journals.iucr.org/d/issues/2017/09/00/hi5647/index.html
 
!EXCLUDE_RESOLUTION_RANGE= 3.93 3.87 !ice-ring at 3.897 Angstrom
 
!EXCLUDE_RESOLUTION_RANGE= 3.93 3.87 !ice-ring at 3.897 Angstrom
 
!EXCLUDE_RESOLUTION_RANGE= 3.70 3.64 !ice-ring at 3.669 Angstrom
 
!EXCLUDE_RESOLUTION_RANGE= 3.70 3.64 !ice-ring at 3.669 Angstrom
Line 515: Line 1,051:  
!EXCLUDE_RESOLUTION_RANGE= 1.913 1.853 !ice-ring at 1.883 Angstrom - weak
 
!EXCLUDE_RESOLUTION_RANGE= 1.913 1.853 !ice-ring at 1.883 Angstrom - weak
 
!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
 +
! additional ice-ring resolution ranges: 1.524 1.519, 1.473 1.470, 1.444 1.440, 1.372 1.368, 1.367 1.363,
 +
! 1.299 1.296, 1.275 1.274, 1.261 1.259, 1.224 1.222, 1.171 1.168, 1.124 1.122 (compiled by GlobalPhasing)
 +
 
eof
 
eof
if [ "$DET" == "pilatus" ]; then
+
if [ "$DET" == "Bruker-cbf" ]; then
 +
  echo "DELPHI=15 ! refine less often than the default of 5" >> XDS.INP
 +
elif [ "$DET" == "adsc-CMOS1" ]; then
 +
  echo UNTRUSTED_RECTANGLE= 0 1468  2451 2631  >> XDS.INP
 +
elif [ "$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  
Line 522: Line 1,065:  
!                                                  and does not seem to have any downsides.  
 
!                                                  and does not seem to have any downsides.  
 
eof
 
eof
   if [ $NX == "1475" ]; then
+
   if [ "$NX" == "1028"  -a "$NY" == "1062" ]; then
 +
# Eiger2 1M ; v0.97 numbers from Andreas Förster
 +
    cat >> XDS.INP << eof
 +
UNTRUSTED_RECTANGLE=    0 1029    512  551
 +
eof
 +
  elif [ "$NX" == "1475" ]; then
 
     if ! grep -q Flat_field tmp2 ; then
 
     if ! grep -q Flat_field tmp2 ; then
 
     cat >> XDS.INP << eof
 
     cat >> XDS.INP << eof
Line 555: Line 1,103:  
eof
 
eof
 
     fi
 
     fi
   elif [ $NX == "2463" ]; then
+
   elif [ "$NX" == "2068"  -a "$NY" == "2162" ]; then
 +
# Eiger2 4M ; v0.97 numbers from Andreas Förster
 +
    cat >> XDS.INP << eof
 +
!EXCLUSION OF VERTICAL DEAD AREAS OF THE EIGER2 4M DETECTOR
 +
UNTRUSTED_RECTANGLE= 1028 1041      0 2163
 +
!EXCLUSION OF HORIZONTAL DEAD AREAS OF THE EIGER 4M DETECTOR
 +
UNTRUSTED_RECTANGLE=    0 2069    512  551
 +
UNTRUSTED_RECTANGLE=    0 2069  1062 1101
 +
UNTRUSTED_RECTANGLE=    0 2069  1612 1651
 +
eof
 +
  elif [ "$NX" == "2463" ]; then
 
# Pilatus 6M
 
# Pilatus 6M
 
# FIXME: here we could test if a Flat_field correction was applied like we do for 2M
 
# FIXME: here we could test if a Flat_field correction was applied like we do for 2M
Line 574: Line 1,132:  
UNTRUSTED_RECTANGLE=  0 2464  2103 2121
 
UNTRUSTED_RECTANGLE=  0 2464  2103 2121
 
UNTRUSTED_RECTANGLE=  0 2464  2315 2333
 
UNTRUSTED_RECTANGLE=  0 2464  2315 2333
 +
eof
 +
  elif [ "$NX" == "3110"  -a "$NY" == "3269" ]; then
 +
# Eiger 9M
 +
    cat >> XDS.INP << eof
 +
!EXCLUSION OF VERTICAL DEAD AREAS OF THE EIGER 9M DETECTOR
 +
UNTRUSTED_RECTANGLE= 1029 1042 0 3269
 +
UNTRUSTED_RECTANGLE= 2069 2082 0 3269
 +
!EXCLUSION OF HORIZONTAL DEAD AREAS OF THE EIGER 9M DETECTOR
 +
UNTRUSTED_RECTANGLE= 0 3110  513  553
 +
UNTRUSTED_RECTANGLE= 0 3110 1064 1104
 +
UNTRUSTED_RECTANGLE= 0 3110 1615 1655
 +
UNTRUSTED_RECTANGLE= 0 3110 2166 2206
 +
UNTRUSTED_RECTANGLE= 0 3110 2717 2757
 +
eof
 +
  elif [ "$NX" == "3108"  -a "$NY" == "3262" ]; then
 +
# Eiger2 9M ; v0.97 numbers from Andreas Förster
 +
    cat >> XDS.INP << eof
 +
!EXCLUSION OF VERTICAL DEAD AREAS OF THE EIGER2 9M DETECTOR
 +
UNTRUSTED_RECTANGLE= 1028 1041      0 3262
 +
UNTRUSTED_RECTANGLE= 2068 2081      0 3263
 +
!EXCLUSION OF HORIZONTAL DEAD AREAS OF THE EIGER2 9M DETECTOR
 +
UNTRUSTED_RECTANGLE=    0 3109    512  551
 +
UNTRUSTED_RECTANGLE=    0 3109  1062 1101
 +
UNTRUSTED_RECTANGLE=    0 3109  1612 1651
 +
UNTRUSTED_RECTANGLE=    0 3109  2162 2201
 +
UNTRUSTED_RECTANGLE=    0 3109  2712 2751
 +
eof
 +
  elif [ "$NX" == "4150" -a "$NY" == "4371" ]; then
 +
# Eiger 16M
 +
    cat >> XDS.INP << eof
 +
!EXCLUSION OF HORIZONTAL DEAD AREAS OF THE EIGER 16M DETECTOR + ONE PIXEL ON EACH SIDE
 +
UNTRUSTED_RECTANGLE=    0 4150    513  553
 +
UNTRUSTED_RECTANGLE=    0 4150  1064 1104
 +
UNTRUSTED_RECTANGLE=    0 4150  1615 1655
 +
UNTRUSTED_RECTANGLE=    0 4150  2166 2206
 +
UNTRUSTED_RECTANGLE=    0 4150  2717 2757
 +
UNTRUSTED_RECTANGLE=    0 4150  3268 3308
 +
UNTRUSTED_RECTANGLE=    0 4150  3819 3859
 +
!EXCLUSION OF VERTICAL DEAD AREAS OF THE EIGER 16M DETECTOR + ONE PIXEL ON EACH SIDE
 +
UNTRUSTED_RECTANGLE= 1029 1042      0 4371
 +
UNTRUSTED_RECTANGLE= 2069 2082      0 4371
 +
UNTRUSTED_RECTANGLE= 3109 3122      0 4371
 +
eof
 +
  elif [ "$NX" == "4148" -a "$NY" == "4362" ]; then
 +
# Eiger2 16M ; v0.97 numbers from Andreas Förster
 +
    cat >> XDS.INP << eof
 +
!EXCLUSION OF HORIZONTAL DEAD AREAS OF THE EIGER2 16M DETECTOR
 +
UNTRUSTED_RECTANGLE= 1028 1041      0 4363
 +
UNTRUSTED_RECTANGLE= 2068 2081      0 4363
 +
UNTRUSTED_RECTANGLE= 3108 3121      0 4363
 +
!EXCLUSION OF VERTICAL DEAD AREAS OF THE EIGER2 16M DETECTOR
 +
UNTRUSTED_RECTANGLE=    0 4149    512  551
 +
UNTRUSTED_RECTANGLE=    0 4149  1062 1101
 +
UNTRUSTED_RECTANGLE=    0 4149  1612 1651
 +
UNTRUSTED_RECTANGLE=    0 4149  2162 2201
 +
UNTRUSTED_RECTANGLE=    0 4149  2712 2751
 +
UNTRUSTED_RECTANGLE=    0 4149  3262 3301
 +
UNTRUSTED_RECTANGLE=    0 4149  3812 3851
 
eof
 
eof
 
   fi
 
   fi
 
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, is at
+
echo Full documentation, including complete detector templates, at xds.mr.mpg.de .
echo http://www.mpimf-heidelberg.mpg.de/~kabsch/xds . More documentation in XDSwiki
+
echo More documentation in strucbio.biologie.uni-konstanz.de/xdswiki/index.php .
echo After running xds, inspect, using XDS-Viewer, at least the beamstop mask in
+
echo After running xds, inspect at least the agreement of predicted and observed  
echo BKGPIX.cbf, and the agreement of predicted and observed spots in FRAME.cbf!
+
echo spots in FRAME.cbf!
 
rm -f tmp1 tmp2
 
rm -f tmp1 tmp2
# end of generate_XDS.INP
+
 
 
</pre>
 
</pre>
   Line 596: Line 1,212:  
By using your own file, you can easily update to the latest revision, or even change the script, without having to bother the system administrator.
 
By using your own file, you can easily update to the latest revision, or even change the script, without having to bother the system administrator.
   −
On Mac OS X, installation of the "Command Line Tools" (from http://developer.apple.com/downloads; requires Apple ID) is required (I think). These are also part of the (larger, but also free) [http://developer.apple.com/tools/xcode Xcode] package.
+
See also [[Generate_XDS.INP#Dependencies]] below, and the [[Installation]] article.
 +
 
 +
== Copying generate_XDS.INP from XDSwiki webserver ==
 +
On Linux:
 +
wget https://strucbio.biologie.uni-konstanz.de/pub/linux_bin/generate_XDS.INP
 +
chmod a+x generate_XDS.INP
 +
On Mac:
 +
curl -o generate_XDS.INP https://strucbio.biologie.uni-konstanz.de/pub/linux_bin/generate_XDS.INP
 +
chmod a+x generate_XDS.INP
 +
See also [[Installation]].
   −
== Generating generate_XDS.INP from this webpage ==
+
== Obtaining generate_XDS.INP from this webpage ==
    
Instead of cutting-and-pasting the lines of the script, you (or the system administrator) could just cut-and-paste the following four lines
 
Instead of cutting-and-pasting the lines of the script, you (or the system administrator) could just cut-and-paste the following four lines
Line 628: Line 1,253:  
  sh: 1: Syntax error: Bad fd number
 
  sh: 1: Syntax error: Bad fd number
 
</pre>
 
</pre>
 +
 +
== Dependencies ==
 +
The script makes use of many GNU commands, like <code>ls, grep, egrep, awk, cut, cat, echo, wc, bc, head, sed, tail, cp, od, python</code>. Some of them (like <code>od</code> and <code>python</code>) are only used in case of specific detectors (MarCCD and RAXIS, respectively).
 +
The script will only work if all the required commands are available. They reside in either the <code>coreutils</code> RPM, or specific RPMs (<code>gawk, sed, bc, grep, python</code> ...). Please note that to get the <code>strings</code> command on some Linux distributions (e.g. FC23) you need to install the <code>binutils</code> RPM package.
 +
For Eiger data processing, the <code>h5dump</code> program must be installed. This is part of <code>hdf5-tools</code> (Ubuntu) or <code>hdf5</code> (RHEL). The .h5 files collected at Diamond Light Source require a very new version of h5dump (namely h5dump 1.10) to extract the OVERLOAD parameter from the .h5 file; this version is available by default in Ubuntu 20.04 and RHEL/CentOS 8.
 +
 +
On Mac OS X, installation of the "Command Line Tools" (from http://developer.apple.com/downloads; requires Apple ID) is required (open a terminal and type <code>xcode-select --install</code>). These are also part of the (larger, but also free) [http://developer.apple.com/tools/xcode Xcode] package. This package comes with a license that has to be accepted by the user when running a Command Line Tool (e.g. <code>strings</code>) for the first time.
 +
 +
One way to check for missing programs is
 +
#!/bin/bash
 +
for i in  ls grep egrep awk cut cat echo wc bc head sed tail cp od python strings h5dump ; do
 +
    if [ ! -x /bin/$i ] && [ ! -x /usr/bin/$i ]; then
 +
      echo $i not found
 +
    fi
 +
done
 +
 +
A command that should go a long way in providing all these tools for RedHat-derived distros is (as root)
 +
yum -y install coreutils binutils gawk sed bc grep python hdf5
 +
and for Ubuntu this would be (untested!)
 +
sudo apt-get install coreutils binutils gawk sed bc grep python hdf5-tools
 +
 +
See also [[Installation]].
    
== Limitations ==
 
== Limitations ==
   −
* The script tries to interpret the header of the frames, so is currently limited to Dectris (Pilatus), ADSC (Quantum), Rigaku (several types) and MAR (CCD and image plate) detectors. Other detectors need some values to be manually filled into XDS.INP - the relevant places are marked with XXX. These are detector properties (type, pixel size and number, min and max counts in a pixel), and experimental parameters like oscillation range, wavelength, distance, and direct beam position (or rather: point of detector that is closest to the crystal). For fine-tuning of detector parameters, see the [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_prepare.html detector-specific templates].
+
* The script tries to interpret the header of the frames, so is currently limited to Dectris (Pilatus, Eiger), ADSC (Quantum), Rigaku (several types), MAR (CCD and image plate) detectors, and one Bruker detector. Other detectors need some values to be manually filled into XDS.INP - the relevant places are marked with XXX. These are detector properties (type, pixel size and number, min and max counts in a pixel), and experimental parameters like ROTATION_AXIS, OSCILLATION_RANGE, X-RAY_WAVELENGTH, DETECTOR_DISTANCE, and XORG, YORG. For fine-tuning of detector parameters, see the [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_prepare.html detector-specific templates].
* The authors have made a "best effort" to provide a XDS.INP that results in the correct sign of the anomalous signal. In the case of one detector type (internally called Rigaku SMV) this requires reversal of one detector axis, and a negative DETECTOR_DISTANCE, as is found in some of the [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_prepare.html detector-specific templates]. '''For an unusual or unknown detector setup, the correct sign of the anomalous signal needs to be established and verified e.g. with a good dataset from a test crystal that has a anomalous signal.''' The authors do not take any responsibility for problems arising from incorrect sign of the anomalous signal, nor - obviously! - for any other mischief arising in or from data processing.
+
* The authors have made a "best effort" to provide a XDS.INP that results in the correct sign of the anomalous signal. In the case of one detector type (internally called Rigaku SMV) this requires reversal of one detector axis, and a negative DETECTOR_DISTANCE, as is found in some of the [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_prepare.html detector-specific templates]. '''For an unusual or unknown detector setup, the correct sign of the anomalous signal needs to be established and verified e.g. with a good dataset from a test crystal that has an anomalous signal.''' The authors do not take any responsibility for problems arising from incorrect sign of the anomalous signal, nor - obviously! - for any other mischief arising in or from data processing.
* At some beamlines, the ROTATION_AXIS should be -1 0 0 ("backwards") instead of the usual 1 0 0 ("horizontal"), or even 0 1 0 ("vertical") like at one of the PETRA Hamburg BLs. We have no exhaustive list of these beamlines, and the frame headers do not have this information, so the default chosen by [[generate_XDS.INP]] may be wrong and need manual correction.
+
* At some beamlines, the ROTATION_AXIS should be -1 0 0 ("backwards") instead of the usual 1 0 0 ("horizontal"), or even 0 1 0 ("vertical") like at one of the PETRA Hamburg BLs. The frame headers do not have this information, so the default chosen by [[generate_XDS.INP]] may be wrong and need manual correction. Pls also see the article [[Beamline notes]].
 +
* Sometimes, the x- and y- values of the primary beam position recorded in the header should be used for ORGY and ORGX (i.e reversed) instead of as ORGX and ORGY. For ADSC, this has been implemented in the script for a number of beamlines.
 +
* there are apparently several flavours of HDF5 files produced at Diamond Light Source. They differ e.g. in the naming of the header items. This means that items like NX, NY, DETECTOR_DISTANCE and number of images cannot be found by the [[generate_XDS.INP]] script. Example: The data at /dls/i04-1/data/2021/mx28114-9/processing/Lenye_Diamini/ThiL/ThiL found during the CCP4 2021 online Cape Town workshop. A workaround is to use e.g. xia2 pipeline=3dii to process these files, and - if needed - extract those items from its output files, e.g. from DEFAULT/NATIVE/SWEEP1/index/XDS.INP .
 +
 
 +
== See also ==
 +
 
 +
* GlobalPhasing's list of beamlines and their settings is at http://www.globalphasing.com/autoproc/wiki/index.cgi?BeamlineSettings .
 +
* [[Beamline notes]] to collect information about specific settings
 +
* [[spot2pdb]] for visualizing reciprocal space
2,461

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