Generate XDS.INP: Difference between revisions

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This script generates XDS.INP based on a list of frame names supplied on the commandline.
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.


Currently works for MarCCD, ADSC and Pilatus 6M detectors. Also supports bzip2-ed frames (when specifying the frame names, leave out the .bz2 extension, as [http://strucbio.biologie.uni-konstanz.de/~dikay/XDS_html_doc/html_doc/xds_parameters.html#NAME_TEMPLATE_OF_DATA_FRAMES= documented] for XDS!).
== Usage ==


Installation: ask your system adminstrator to cut-and-paste it into e.g. /usr/local/bin/generate_XDS.INP , and to make it "executable". Usage is then just (don't forget the quotation marks!):
Usage is just (don't forget the quotation marks!):
  generate_XDS.INP "frms/mydata_1_???.img"
  generate_XDS.INP "/home/myname/frms/mydata_1_???.img"
But you may also just cut-and-paste the script from this webpage into e.g. your home directory; the filename should be generate_XDS.INP. After creating the file, make it executable - e.g. if it's in your $HOME, use:
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.
chmod +x ~/generate_XDS.INP
 
After that, you can just run it in the same way:
For improved interaction with [[XDSGUI]], it is advantageous to provide an ''absolute'' filename for the data files - one that starts with a slash ("/").
~/generate_XDS.INP "frms/mydata_1_???.img"
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.


Instead of cut-and-paste, you could try
== The script ==
wget http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP -O - | awk '/^#/,/rm -f tmp1 tmp2/' | \
  sed -e s/\&nbsp\;/\ /g -e s/\&gt\;/\>/g -e s/\&lt\;/\</g -e s/amp\;//g -e s/\&quot\;/\"/g > generate_XDS.INP
to copy the script from this website into the file generate_XDS.INP in your current directory.


This is the script:
<pre>
<pre>
#!/bin/bash
 
# purpose: generate XDS.INP
#!/bin/bash                                                                  
#
# purpose: generate XDS.INP                                                  
# tested with some datasets from ALS, SSRL, SLS, ESRF and BESSY; only MARCCD, ADSC/SMV, PILATUS 6M detectors;  
#                                                                            
# for other detectors, values marked with XXX must be manually filled in.
# 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.                                
# revision 0.03 . Kay Diederichs 2/2010  
#                                                                                                        
# revision 0.04 . Kay Diederichs 4/2010 - include alternative ORGX, ORGY calculations for ADSC
# revision 0.03 . Kay Diederichs 2/2010                                                                  
# revision 0.05 . Kay Diederichs 5/2010 - grep for "Corrected" in addition to "marccd"; needed for BESSY  
# 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 0.06 . 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="0.20 (15-Jul-2011)"
# 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
# usage: e.g. generate_XDS.INP "frms/mydata_1_???.img"
# revision 0.23 . KD 1/2012 - add UNTRUSTED_QUADRILATERAL, remove MINIMUM_ZETA (0.05 is default now)
# make sure to have the two quotation marks !
# revision 0.24 . KD 3/2012 - remove revision 0.10 since XDS now takes much longer paths
# the ? are wildcards for the frame numbers.
# revision 0.25 . KD 3/2012 - remove revision 0.22 for PSI Pilatus 2M; see http://www.globalphasing.com/autoproc/wiki/index.cgi?TroubleShootingKnownIssues
#  
# revision 0.26 . KD 7/2012 - Mac-compatibility: replace od flags --skip-bytes= and --read-bytes= with -j and -N (thanks to Oliver Clarke for working this out!)
# limitations:
# revision 0.27 . KD 11/2012 - EXCLUDE_RESOLUTION_RANGE lines and generic Pilatus Flat_field test
# - frame numbers are assumed to start with 1 and run consecutively
# revision 0.28 . Keitaro 11/2012 - for MarCCD: read oscillation range from the position 1024+736 (fix for omega rotation)
#
# revision 0.29 . KD 1/2013 - include UNTRUSTED_RECTANGLEs for Pilatus 6M; never hurts but needed if the beamline software does not mark them with -2 or such
# known problems:
# revision 0.30 . Keitaro 3/2013 - for ADSC: write all possible beam center conventions in XDS.INP as comments
# revision 0.31 . Keitaro 3/2013 - add comment for reversed phi for SPring-8
# revision 0.32 . Keitaro 3/2013 - add RAXIS support. only tested with RAXIS IV++ and VII.
# revision 0.33 . Keitaro 5/2013 - automatically set ROTATION_AXIS=-1 0 0 for SPring-8 BL32XU/41XU/44XU beamlines based on detector serial numbers.
# revision 0.34 . Keitaro 5/2013 - recognize ADSC detectors in Photon Factory and choose correct beam center convention based on detector serial numbers.
# 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 0.37 . 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 0.39 . Keitaro 4/2014 - automatically set ROTATION_AXIS=-1 0 0 for MX225HS at SPring-8 BL32XU.
# revision 0.40 . Jan Gebauer /KD 4/2014 - simple implementation of MAR345 detector
# revision 0.41 . recognize header starting with R-AXIS instead of RAXIS
# revision 0.42 . Keitaro 5/2014 automatically set ROTATION_AXIS=-1 0 0 for Q315 at SPring-8 BL38B1.
# revision 0.43 . Keitaro 5/2014 add experimental support of dTREK format (raxis_smv)
# 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 0.46 . 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"                                                      
# make sure to have the two quotation marks !                                                              
# the ? are wildcards for the frame numbers.                                                                
#                                                                                                          
# 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, the Xcode command line tools (from https://developer.apple.com/download/more/) are needed.                           
# notes for debugging of the script:
#                                                                                                               
# - add the -v option to the first line, to see where an error occurs
# notes for debugging of the script:                                                                            
# - comment out the removal of tmp1 and tmp2 in the last line
# - 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                                                  
# ====== Start of script ======
#                                                                                                              
echo generate_XDS.INP version $REVISION . Obtain the latest version from
# ====== Start of script ======                                                                                
echo http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP
echo generate_XDS.INP version $REVISION . Obtain the latest version from                                        
if [ "$1" == "help" ] || [ "$1" == "-help" ] || [ "$1" == "-h" ]; then
echo http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP                                
   echo usage: generate_XDS.INP \"frms/mydata_1_???.img\"  \(_with_ the quotation marks!\)
if [ "$1" == "help" ] || [ "$1" == "-help" ] || [ "$1" == "-h" ]; then                                          
   echo if the frames are compressed with bzip2, leave out the .bz2 extension!
   echo usage: generate_XDS.INP \"/file/system/frms/mydata_1_???.img\"  \(_with_ the quotation marks!\)                      
   exit
   echo if the frames are compressed with bzip2, leave out the .bz2 extension!                                  
   exit                                                                                                          
fi                                                                                                             
# make sure the locale does not interfere with e.g. awk calculations:
LC_ALL="C";export LC_ALL
#                                                                                                               
# defaults:                                                                                                     
#     
# conversion radian / degrees:
DEGTOR=57.2957795
                                                                                                       
DETECTOR="XXX MINIMUM_VALID_PIXEL_VALUE=XXX OVERLOAD=XXX"                                                       
REVERSE_PHI="no"
ORGX=XXX                                                                                                       
ORGY=XXX                                                                                                       
DETECTOR_DISTANCE=XXX                                                                                           
OSCILLATION_RANGE=XXX                                                                                           
X_RAY_WAVELENGTH=XXX                                                                                           
QX=XXX                                                                                                         
QY=XXX                                                                                                         
NX=XXX                                                                                                         
NY=XXX                                                                                                         
SENSOR_THICKNESS=0 
TRUSTED_REGION="0.0 1.2 ! partially use corners of detector (0 1.4143: use all pixels)"                                                                                         
# default MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT
MNOPIAS=3
# default DIRECTION_OF_DETECTOR_X-AXIS
DIRECTION_OF_DETECTOR_X_AXIS="1 0 0"
# default FRACTION_OF_POLARIZATION
pol_frac=0.98
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 "$1" | xargs basename`
# see how we are called:                                                                                       
NAME_TEMPLATE_OF_DATA_FRAMES="${dname}/${bname}"
# list frames matching the wildcards in NAME_TEMPLATE_OF_DATA_FRAMES
# don't accept the "direct beam" shot at SLS/Pilatus PX-I and PX-II
# cope with blanks in directory / file name
IFS=$'\n'
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
fi
#
unset IFS
# defaults:
# we can continue - the frames are found
#
DETECTOR="XXX MINIMUM_VALID_PIXEL_VALUE=XXX OVERLOAD=XXX"
ORGX=XXX
ORGY=XXX
DETECTOR_DISTANCE=XXX
OSCILLATION_RANGE=XXX
X_RAY_WAVELENGTH=XXX
QX=XXX
QY=XXX
NX=XXX
NY=XXX
SENSOR_THICKNESS=0
# see how we are called:
NAME_TEMPLATE_OF_DATA_FRAMES="$1"


# check that the image template name does not exceed 72 characters
if echo $NAME_TEMPLATE_OF_DATA_FRAMES | grep '_master.h5$' > /dev/null; then
# and set a link if necessary
NAME_TEMPLATE_OF_DATA_FRAMES=`echo "$NAME_TEMPLATE_OF_DATA_FRAMES" | sed -e 's/_master.h5$/_??????.h5/'`
if [ ${#1} -gt 72 ]; then
else
    TMP_PATH=$(/bin/ls -C1 $1 $1.bz2 2>/dev/null | head -1)
# Find the first '?' position and the number of '?' to determine DATA_RANGE=.
    TMP_FILENAME=$(basename ${TMP_PATH})
pos1=`echo "$NAME_TEMPLATE_OF_DATA_FRAMES" | awk '{print index($0, "?")}'`
    if [ ${#TMP_FILENAME} -gt 65 ]; then
pos2=`echo "$NAME_TEMPLATE_OF_DATA_FRAMES" | sed -e "s/[^\?]//g" | awk '{print length+'$pos1' - 1}'`
echo "---> Unable to proceed: image filename "
data_first=`cut -b $pos1-$pos2 tmp1 | head -n1 | bc`
echo "--->  \"${TMP_FILENAME}\""
data_last=`cut -b $pos1-$pos2 tmp1 | tail -n1 | bc`
        echo "---> exceeds 72 characters."
  DATA_RANGE="$data_first $data_last"
        echo "---> Please rename files or set links."
echo DATA_RANGE=$DATA_RANGE
exit
    else
# set SPOT_RANGE to first half of DATA_RANGE
echo "---> Warning: Template name exceeds 72 characters. Setting link \"images\""
data_num=`wc -l tmp1 | awk '{print $1}'`
        echo "              to image directory"
data_half=`echo "scale=0; $data_num/2" | bc -l`                       
TMP_DIRNAME=$(dirname ${TMP_PATH})
data_half=`echo "if ($data_half<=1) 1;if ($data_half>1) $data_half" | bc -l`
if [ -e "images" ]; then
spot_last=`echo "scale=0; $data_first+$data_half-1" | bc -l`
    echo "*** Error:  The file or directory \"images\" already exists. Please remove"
SPOT_RANGE="$data_first $spot_last"
    echo "              and re-run."
    exit
else
    ln -s ${TMP_DIRNAME} images
fi
NAME_TEMPLATE_OF_DATA_FRAMES="images/${1##/*/}"
# KD 30.3.11 I believe the previous line should be changed to:
#      NAME_TEMPLATE_OF_DATA_FRAMES="images/${TMP_FILENAME}"  
# but I have not had the time to properly test this
echo "             Using template filename \"${NAME_TEMPLATE_OF_DATA_FRAMES}\""
    fi
fi
fi


# list frames matching the wildcards in NAME_TEMPLATE_OF_DATA_FRAMES
FIRSTFRAME=`head -1 tmp1`
# don't accept the "direct beam" shot at SLS/Pilatus PX-I and PX-II
echo $FIRSTFRAME | grep "\.h5$" && is_h5=1 || is_h5=0
/bin/ls -C1 $1 $1.bz2 2>/dev/null | egrep -v "_00000.cbf|_000.img" > tmp1 || exit 1


# we can continue - the frames are found
# find out detector type
DET=XXX             
IFS=$'\n'   
echo $FIRSTFRAME | grep -q '\.bz2$' && bzcat $FIRSTFRAME > tmp1 && FIRSTFRAME=tmp1
# for mac/linux compatibility. zcat foo.gz doesn't work on mac.
echo $FIRSTFRAME | grep -q '\.gz$' && zcat < $FIRSTFRAME > tmp1 && FIRSTFRAME=tmp1
echo $FIRSTFRAME | grep -q '\.xz$' && xzcat $FIRSTFRAME > tmp1 && FIRSTFRAME=tmp1


# set upper limit of DATA_RANGE to number of frames (see "limitations" above)
unset IFS
DATA_RANGE=`wc -l tmp1 | awk '{print $1}'`
if [ "$is_h5" == 0 ]; then
strings $FIRSTFRAME > tmp2 
# 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
# the reason is that FIRSTFRAME may contain a blank, which makes some commands fail                                               
egrep -qi 'marccd|Corrected' tmp2 && DET=mccd                               
grep -q PILATUS tmp2            && DET=pilatus
grep -iq Eiger tmp2              && DET=pilatus                           
head -n1 tmp2 | grep -q "^RAXIS" && DET=raxis
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


# set upper limit of SPOT_RANGE to half of DATA_RANGE, but not less than 1
# identify other detector types in the same way  
SPOT_RANGE=`echo "scale=0; $DATA_RANGE/2" | bc -l`
SPOT_RANGE=`echo "if ($SPOT_RANGE<1) 1;if ($SPOT_RANGE>1) $SPOT_RANGE" | bc -l`
 
echo DATA_RANGE=1 $DATA_RANGE
 
# find out detector type
DET=XXX
FIRSTFRAME=`head -1 tmp1`
echo $FIRSTFRAME | grep -q bz2 && bzcat $FIRSTFRAME > tmp1 && FIRSTFRAME=tmp1
strings $FIRSTFRAME > tmp2
egrep -q 'marccd|Corrected' tmp2 && DET=mccd
grep -q PILATUS tmp2            && DET=pilatus
grep -q BEAM_CENTER_X tmp2      && DET=adsc
# identify other detector types in the same way (MAR IP would be straightforward)


# parse ASCII header of first frame
# parse ASCII header of first frame
Line 143: Line 260:
if [ "$DET" == "XXX" ]; then
if [ "$DET" == "XXX" ]; then
   echo "this is not a MAR, ADSC/SMV or PILATUS detector - fill in XXX values manually!"
   echo "this is not a MAR, ADSC/SMV or PILATUS detector - 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
                                 
   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              


   # offsets are documented; values can be find in mccd_xdsparams.pl script
  # Check detector serial number and recognize beamline for reversed-phi setting.
   let SKIP=1024+80
  # 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
   NX=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
  # same for SSRF: BL17B1 rayonix MX300. As on 2019-10-13, this also needs doubling of ORGX and ORGY. But the beamline staff (Wenming) wants to fix the header.
   let SKIP=$SKIP+4
  REVERSEPHI_SNs="
   NY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
24
31
38
40
42
43
106
"
  # get detector serial number and check if it is included in the list
  DET_SN=`grep "Detector Serial Number =" tmp2 | sed "s/Detector Serial Number = //"`
  if echo "${DET_SN}${REVERSEPHI_SNs}" | sort | uniq -d | grep [0-9] > /dev/null; then
    REVERSE_PHI="yes"
    echo inverted ROTATION_AXIS since Detector Serial Number is "${DET_SN}"
  fi
 
   # offsets are documented; values can be found in mccd_xdsparams.pl script
  IFS=$'\n'
  cp $FIRSTFRAME tmp2
  unset IFS
   let SKIP=1024+80                                                      
   NX=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}')
   let SKIP=$SKIP+4                                                                        
   NY=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}')


   let SKIP=1720
   let SKIP=1720
   DETECTOR_DISTANCE=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | 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`                                    
   
 
   let SKIP=1024+256+128+256+4
# Mar 12, 2020 KD
   ORGX=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
   let SKIP=1724
   ORGX=`echo "scale=2; $ORGX/1000" | bc -l `
   TWOTHETA=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}')
   let SKIP=$SKIP+4
   TWOTHETA=`echo "scale=3; $TWOTHETA/1000" | bc -l`
  ORGY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
   echo 2THETA= $TWOTHETA
  ORGY=`echo "scale=2; $ORGY/1000" | bc -l `


   let SKIP=1024+256+128+256+44
   let SKIP=1024+256+128+256+44
   PHISTART=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
   STARTING_ANGLE=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}')  
   let SKIP=1024+256+128+256+76
  STARTING_ANGLE=`echo "scale=2; $STARTING_ANGLE/1000" | bc -l `
   PHIEND=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
  echo STARTING_ANGLE= $STARTING_ANGLE 
   OSCILLATION_RANGE=`echo "scale=3; ($PHIEND-($PHISTART))/1000" | bc -l`
                                                                                                     
 
   let SKIP=1024+256+128+256+4                                                                           
   let SKIP=1024+256+128+256+128+4
   ORGX=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}')           
   QX=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
  ORGX=`echo "scale=2; $ORGX/1000" | bc -l `                                                             
   QX=`echo "scale=10; $QX/1000000" |bc -l `
  let SKIP=$SKIP+4                                                                                       
   let SKIP=$SKIP+4
  ORGY=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}')           
   QY=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | head -1 | awk '{print $2}')
  ORGY=`echo "scale=2; $ORGY/1000" | bc -l `                                                             
   QY=`echo "scale=10; $QY/1000000" |bc -l `
# fixed Aug 30, 2017 after IUCr2017 @ Hyderabad
  if [ "$DET_SN" == "4" ]; then
    TEMP=$ORGY
    ORGY=$ORGX
    ORGX=$TEMP
    echo reversed ORGX and ORGY for marCCD @ ESRF BM14
  fi
 
  let SKIP=1024+736
  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`  
                                                                                               
   let SKIP=1024+256+128+256+128+4                                                              
   QX=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}')    
   QX=`echo "scale=10; $QX/1000000" |bc -l `                                                    
   let SKIP=$SKIP+4                                                                              
   QY=$(od -t dI -j $SKIP -N 4 tmp2 | head -1 | awk '{print $2}')    
   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=$(od -t dI --skip-bytes=$SKIP --read-bytes=4 $FIRSTFRAME | 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 202: Line 358:
   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                                                      
   sed s/\;// tmp2 > tmp1
   sed s/\;// tmp2 > tmp1                                                      
   mv tmp1 tmp2
   mv tmp1 tmp2                                                                


       # find X_RAY_WAVELENGTH:
       # find X_RAY_WAVELENGTH:
Line 211: 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
       QY=$QX                                              
      NY=$NX     
       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 - 
# at ESRF and ... (pls fill in!) the following should be used:
      COMMENT_ORGXY="
       ORGX=`echo "scale=1; $BEAM_CENTER_Y/$QX" | bc -l `
! Following are possible beam center interpretations for ADSC detectors"
       ORGY=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l `
# at ESRF, PF, ALS 5.0.2, AS MX2 and ... (pls fill in!) the following should be used:        
       echo - at ESRF BLs use: ORGX=$ORGX ORGY=$ORGY
       ORGX1=`echo "scale=1; $BEAM_CENTER_Y/$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                   
      COMMENT_ORGXY="${COMMENT_ORGXY}
! 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, ...
       ORGX=`echo "scale=1; $NX-$BEAM_CENTER_X/$QX" | bc -l `
       ORGX2=`echo "scale=1; $NX-$BEAM_CENTER_X/$QX" | bc -l `
       ORGY=`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=$ORGX ORGY=$ORGY
       echo - at e.g. ALS 5.0.3 use: ORGX=$ORGX2 ORGY=$ORGY2                                                         
      COMMENT_ORGXY="${COMMENT_ORGXY}
! 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, ...  
       ORGX=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l `
# this alternative is written into the generated XDS.INP ! You have to correct this manually in XDS.INP, or adjust this script.
       ORGY=`echo "scale=1; $NX-$BEAM_CENTER_Y/$QX" | bc -l `
       ORGX3=`echo "scale=1; $BEAM_CENTER_X/$QX" | bc -l `
       echo - at e.g. ALS 8.2.2 use: ORGX=$ORGX ORGY=$ORGY - this is written to XDS.INP
       ORGY3=`echo "scale=1; $NX-$BEAM_CENTER_Y/$QX" | bc -l `
# the latter alternative is written into the generated XDS.INP ! You have to correct this manually in XDS.INP, or adjust this script.
       echo - at e.g. ALS 8.2.2 use: ORGX=$ORGX3 ORGY=$ORGY3 - this is written to XDS.INP if beamline is not detected
       # find DETECTOR_DISTANCE and OSCILLATION_RANGE:
      COMMENT_ORGXY="${COMMENT_ORGXY}
       DETECTOR_DISTANCE=`grep DISTANCE tmp2 | sed s/DISTANCE=//`
! ORGX= $ORGX3 ORGY= $ORGY3 ! For ALS 8.2.2,.."
       OSCILLATION_RANGE=`grep OSC_RANGE tmp2 | sed s/OSC_RANGE=//`
# 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.
      DET_SN=`grep DETECTOR_SN tmp2 | sed -e "s/DETECTOR_SN=//"`
      echo Detector serial number is $DET_SN
      # For convention 1; Known PF detectors = 449: NW12A Q210, 472: NE3A Q270, 474: BL17A Q270, 912: BL5A Q315, 923: ALS BL5.0.2 Q315, 933: AichiSR BL2S1 Q315, 916: APS 24 IDE, 928: AS MX2
      ORG1_SNs="
449
472
474
912
923
933
911
446
916
905
928
"
      ORG4_SNs="
915
"
      if echo "${DET_SN}${ORG1_SNs}" | sort | uniq -d | grep [0-9] > /dev/null; then
      ORGX=$ORGX1
      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=$ORGY4
      echo the following was chosen based on detector serial number:
      else
      ORGX=$ORGX3
      ORGY=$ORGY3
      echo the following default was chosen because the detector serial number was not special-cased:
      fi
 
      # Check detector serial number and recognize beamline for reversed-phi setting.
      # 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="
915
924
928
"
      if echo "${DET_SN}${REVERSEPHI_SNs}" | sort | uniq -d | grep [0-9] > /dev/null; then
        REVERSE_PHI="yes"
        echo inverted ROTATION_AXIS since detector serial number is ${DET_SN}
      fi
 
       # find DETECTOR_DISTANCE and OSCILLATION_RANGE:                                                                              
      DETECTOR_DISTANCE=`grep ^DISTANCE tmp2 | sed s/DISTANCE=//`                                                                   
       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 6M"
  echo Data from a Pilatus detector                                       
   SENSOR_THICKNESS=0.32
  sed s/#// tmp2 > tmp1                                                   
  NX=2463 NY=2527 QX=0.172 QY=0.172
  mv tmp1 tmp2                                                             
   echo Data from a Pilatus detector
  OVERLOAD=1048574
   sed s/#// tmp2 > tmp1
  SEPMIN=4
  mv tmp1 tmp2
  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:
      SENSOR_THICKNESS=`grep thickness tmp2 | sed -e s/'Silicon sensor, thickness'// | awk '{print $1*1000}'`
      # find X_RAY_WAVELENGTH:                                                                             
      X_RAY_WAVELENGTH=`grep Wavelength tmp2 | sed -e s/Wavelength// -e s/A// | awk '{print $1}'`           


       # find X_RAY_WAVELENGTH:
       # find NX and NY; 2463/2527 is 6M, 1475/1679 is 2M
       X_RAY_WAVELENGTH=`grep Wavelength tmp2 | sed -e s/Wavelength// -e s/A// | awk '{print $1}'`
       NX=`grep X-Binary-Size-Fastest-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 250: 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
      # Known detectors for reversed-phi in SPring-8: BL41XU PILATUS3 6M 60-0125
      # 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="
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
        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 $rotation_axis"
      else
        rotation_axis="1 0 0"
        echo "SSRF BL02U1 (Eiger2 S 9M) with horizontal rotation axis"
      fi
    fi
# revision 1.05 specialcase nframes for Eiger detectors at BNL
    if [ "$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
  echo Data from a RAXIS detector
  DETECTOR="RAXIS MINIMUM_VALID_PIXEL_VALUE=0  OVERLOAD=2000000"
  #let SKIP=768
  #NX=$(od -t x -j $SKIP -N 4 $FIRSTFRAME |awk 'NR==1{print toupper($2)}'|perl -nle '@array= $_ =~/.{2}/g; print "ibase=16;obase=A;".join("",reverse @array)'|bc)
!  NX=$(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("'$FIRSTFRAME'","rb");f.seek(772);print "%.4d"%struct.unpack(">i",f.read(4))')
  NX=$(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("'$FIRSTFRAME'","rb");f.seek(772);print("%.4d"%struct.unpack(">i",f.read(4)))')
!  DETECTOR_DISTANCE=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(344);print "-%.4f"%struct.unpack(">f",f.read(4))')
  DETECTOR_DISTANCE=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(344);print("-%.4f"%struct.unpack(">f",f.read(4)))')
!  ORGX=$(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("'$FIRSTFRAME'","rb");f.seek(544);print("%.4f"%struct.unpack(">f",f.read(4)))')
!  OSCILLATION_RANGE=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(524);phis,phie=struct.unpack(">ff",f.read(8));print "%.4f"%(phie-phis)')
  OSCILLATION_RANGE=$(python -c 'import struct; f=open("'$FIRSTFRAME'","rb");f.seek(524);phis,phie=struct.unpack(">ff",f.read(8));print("%.4f"%(phie-phis))')
!  QX=$(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("'$FIRSTFRAME'","rb");f.seek(780);print("%.6f"%struct.unpack(">f",f.read(4)))')
!  X_RAY_WAVELENGTH=$(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("'$FIRSTFRAME'","rb");f.seek(292);print("%.6f"%struct.unpack(">f",f.read(4)))')
elif [ "$DET" == "dtrek" ]; then
  echo "Data from a RAXIS or Saturn or Pilatus detector with dTREK format"
  sed s/\;// tmp2 > tmp1
  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
  SATURATED_VALUE=`grep SATURATED_VALUE tmp2 | head -1 | sed s/SATURATED_VALUE=//`
  DETECTOR="${DETECTOR}  OVERLOAD=${SATURATED_VALUE}"
  # find X_RAY_WAVELENGTH:
  X_RAY_WAVELENGTH=(`grep SOURCE_WAVELENGTH tmp2 | head -1 | sed s/SOURCE_WAVELENGTH=//`)
  X_RAY_WAVELENGTH=${X_RAY_WAVELENGTH[1]}
  # find NX,NY,QX,QY
  # NX,NY should be read from *_DETECTOR_DIMENSIONS?
  NX=`grep SIZE1 tmp2 | tail -1 | sed s/SIZE1=//`
  NY=`grep SIZE2 tmp2 | tail -1 | sed s/SIZE2=//`
  DET_SIZE=(`grep ${dname}DETECTOR_SIZE tmp2 | tail -1 | sed s/.*_DETECTOR_SIZE=//`)
  QX=`echo "scale=6; ${DET_SIZE[0]} / $NX" | bc -l`
  QY=`echo "scale=6; ${DET_SIZE[1]} / $NY" | bc -l`
  # find ORGX, ORGY
  SPATIAL_DISTORTION_INFO=(`grep ${dname}SPATIAL_DISTORTION_INFO tmp2 | tail -1 | sed s/.*_SPATIAL_DISTORTION_INFO=//`)
  ORGX=${SPATIAL_DISTORTION_INFO[0]}
  ORGY=${SPATIAL_DISTORTION_INFO[1]}
  # find DETECTOR_DISTANCE
  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_UNITS=(`grep ${dname}GONIO_UNITS= tmp2 | tail -1 | sed s/.*_GONIO_UNITS=//`)
  for i in `seq 1 ${#GONIO_NAMES[*]}`
  do
  idx=$((i-1))
  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]}"
    # TODO: Check unit!! - ${GONIO_UNITS[$idx]}
    echo "using distance <0"
  fi
  done
  # find OSCILLATION_RANGE
  ROTATION=(`grep "^ROTATION=" tmp2 | tail -1 | sed s/ROTATION=//`)
  OSCILLATION_RANGE=${ROTATION[2]}
elif [ "$DET" == "MAR345" ]; then
 
echo  "Data from a Mar345 image plate detector"
DETECTOR="MAR345  MINIMUM_VALID_PIXEL_VALUE=0  OVERLOAD=130000"
NX=`awk '/FORMAT/{print $2}' tmp2`
# 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`
QY=`awk '/PIXEL/{print $5/1000.}' tmp2`
if grep -q 'CENTER' tmp2; then
  echo Beam center found.
  ORGX=`grep 'CENTER' tmp2 | awk '{print $3}'`
  ORGY=`grep 'CENTER' tmp2 | awk '{print $5}'`
else
  echo No beam center was found. Setting beam center to the middle of the detector.
  ORGX=`echo $NX / 2 | bc`
  ORGY=`echo $NY / 2 | bc`
fi
DETECTOR_DISTANCE=`grep 'DISTANCE' tmp2 | awk '{print $2}'`             
X_RAY_WAVELENGTH=`grep 'WAVELENGTH' tmp2 | awk '{print $2}'`
OSCILLATION_RANGE=`grep 'PHI' tmp2 | awk '{print $5-$3}'`   
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
   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 !
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


cat > XDS.INP << eof
cat > XDS.INP << eof
! 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   
DETECTOR_DISTANCE= $DETECTOR_DISTANCE
$COMMENT_ORGXY
OSCILLATION_RANGE= $OSCILLATION_RANGE
DETECTOR_DISTANCE= $DETECTOR_DISTANCE !read by XYCORR, IDXREF. Negative if detector normal points to crystal.             
X-RAY_WAVELENGTH= $X_RAY_WAVELENGTH
OSCILLATION_RANGE= $OSCILLATION_RANGE  
STARTING_ANGLE= $STARTING_ANGLE               
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)  


SPACE_GROUP_NUMBER=0                  ! 0 if unknown
SPACE_GROUP_NUMBER=0                  ! 0 if unknown
UNIT_CELL_CONSTANTS= 70 80 90 90 90 90 ! put correct values if known
UNIT_CELL_CONSTANTS= 70 80 90 90 90 90 ! put correct values if known
INCLUDE_RESOLUTION_RANGE=50 0  ! after CORRECT, insert high resol limit; re-run CORRECT
INCLUDE_RESOLUTION_RANGE=50 0  ! after CORRECT, insert high resol limit; re-run CORRECT
! IDXREF now obeys INCLUDE_RESOLUTION_RANGE and EXCLUDE_RESOLUTION_RANGE to exclude ice-rings


FRIEDEL'S_LAW=FALSE    ! This acts only on the CORRECT step
FRIEDEL'S_LAW=FALSE    ! This acts only on the CORRECT step
Line 296: Line 959:
! UNTRUSTED_RECTANGLE= 1800 1950 2100 2150 ! x-min x-max y-min y-max ! repeat
! UNTRUSTED_RECTANGLE= 1800 1950 2100 2150 ! x-min x-max y-min y-max ! repeat
! UNTRUSTED_ELLIPSE= 2034 2070 1850 2240 ! x-min x-max y-min y-max ! if needed
! UNTRUSTED_ELLIPSE= 2034 2070 1850 2240 ! x-min x-max y-min y-max ! if needed
! UNTRUSTED_QUADRILATERAL= x1 y1 x2 y2 x3 y3 x4 y4 ! see documentation
!
!
! parameters with changes wrt default values:
! parameters with changes wrt default values:
TRUSTED_REGION=0.00 1.2  ! partially use corners of detectors; 1.41421=full use
TRUSTED_REGION=$TRUSTED_REGION
VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS=7000. 30000. ! often 8000 is ok
VALUE_RANGE_FOR_TRUSTED_DETECTOR_PIXELS=6000. 30000. ! often 7000 or 8000 is ok
MINIMUM_ZETA=0.05        ! integrate close to the Lorentz zone; 0.15 is default
STRONG_PIXEL=4           ! COLSPOT: only use strong reflections (default is 3)
STRONG_PIXEL=6           ! COLSPOT: only use strong reflections (default is 3)
MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=$MNOPIAS ! default of 6 is sometimes too high
MINIMUM_NUMBER_OF_PIXELS_IN_A_SPOT=3 ! default of 6 is sometimes too high
! close spots/long cell axis: reduce SEPMIN and CLUSTER_RADIUS from their defaults of 7 and 3.5
REFINE(INTEGRATE)=CELL BEAM ORIENTATION ! AXIS DISTANCE
SEPMIN=$SEPMIN  CLUSTER_RADIUS=$CLUSTER_RADIUS ! 4 and 2 for Pixel Array Detectors
 
! since XDS 01-MAR-2015, POSITION supersedes DISTANCE.
! nowadays headers are usually correct so refine POSITION in INTEGRATE but not IDXREF if low to medium resolution
! 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= $QY ! to make CORRECT happy if frames are unavailable
eof
if [ "$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
DIRECTION_OF_DETECTOR_X-AXIS=1 0 0
DIRECTION_OF_DETECTOR_X-AXIS=1 0 0
DIRECTION_OF_DETECTOR_Y-AXIS=0 -1 0
INCIDENT_BEAM_DIRECTION=0 0 1  ! only read by IDXREF
ROTATION_AXIS=0 1 0            ! only read by IDXREF
!FRACTION_OF_POLARIZATION=0.98  ! uncomment if synchrotron; only used by CORRECT
POLARIZATION_PLANE_NORMAL=1 0 0  ! only used by CORRECT
eof
else
if [ "$rotation_axis" != "" ]; then
  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
  echo 'ROTATION_AXIS=-1 0 0  ! if this is wrong, please contact author.' >> XDS.INP
fi
if [ "$dtrek_det" == "saturn" ]; then
cat >> XDS.INP << eof
DIRECTION_OF_DETECTOR_X-AXIS=-1 0 0
DIRECTION_OF_DETECTOR_Y-AXIS= 0 1 0
eof
else
cat >> XDS.INP << eof
DIRECTION_OF_DETECTOR_X-AXIS=$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
ROTATION_AXIS=1 0 0    ! at e.g. SERCAT ID-22, APS 19-ID, Australian Synchrotron this needs to be -1 0 0
FRACTION_OF_POLARIZATION=0.98  ! better value is provided by beamline staff!
POLARIZATION_PLANE_NORMAL=0 1 0
eof
eof
fi
cat >> XDS.INP << eof
INCIDENT_BEAM_DIRECTION=0 0 1          ! only read by IDXREF
FRACTION_OF_POLARIZATION=${pol_frac}  ! better value is provided by beamline staff!
POLARIZATION_PLANE_NORMAL=0 1 0        ! only used by CORRECT
eof
fi
cat >> XDS.INP << eof
!used by DEFPIX and CORRECT to exclude ice-reflections / ice rings - uncomment if necessary
!fine-grained list is in Thorn et al http://journals.iucr.org/d/issues/2017/09/00/hi5647/index.html
!EXCLUDE_RESOLUTION_RANGE= 3.93 3.87 !ice-ring at 3.897 Angstrom
!EXCLUDE_RESOLUTION_RANGE= 3.70 3.64 !ice-ring at 3.669 Angstrom
!EXCLUDE_RESOLUTION_RANGE= 3.47 3.41 !ice-ring at 3.441 Angstrom
!EXCLUDE_RESOLUTION_RANGE= 2.70 2.64 !ice-ring at 2.671 Angstrom
!EXCLUDE_RESOLUTION_RANGE= 2.28 2.22 !ice-ring at 2.249 Angstrom
!EXCLUDE_RESOLUTION_RANGE= 2.102 2.042 !ice-ring at 2.072 Angstrom - strong
!EXCLUDE_RESOLUTION_RANGE= 1.978 1.918 !ice-ring at 1.948 Angstrom - weak
!EXCLUDE_RESOLUTION_RANGE= 1.948 1.888 !ice-ring at 1.918 Angstrom - strong
!EXCLUDE_RESOLUTION_RANGE= 1.913 1.853 !ice-ring at 1.883 Angstrom - weak
!EXCLUDE_RESOLUTION_RANGE= 1.751 1.691 !ice-ring at 1.721 Angstrom - weak
! additional ice-ring resolution ranges: 1.524 1.519, 1.473 1.470, 1.444 1.440, 1.372 1.368, 1.367 1.363,
! 1.299 1.296, 1.275 1.274, 1.261 1.259, 1.224 1.222, 1.171 1.168, 1.124 1.122 (compiled by GlobalPhasing)
eof
if [ "$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 "$DET" == "eiger" ]; then
cat >> XDS.INP << eof
NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA=13 ! Default is 9 - Increasing may improve data
NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA=13      ! accuracy, particularly if finely-sliced on phi,
!                                                  and does not seem to have any downsides.
eof
  if [ "$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
    cat >> XDS.INP << eof
! the following specifications are for a detector _without_ proper
! flat_field correction; they cut away one additional pixel adjacent
! to each UNTRUSTED_RECTANGLE
!EXCLUSION OF VERTICAL DEAD AREAS OF THE PILATUS 2M DETECTOR
UNTRUSTED_RECTANGLE= 486  496    0 1680
UNTRUSTED_RECTANGLE= 980  990    0 1680
!EXCLUSION OF HORIZONTAL DEAD AREAS OF THE PILATUS 2M DETECTOR
UNTRUSTED_RECTANGLE=  0 1476  194  214
UNTRUSTED_RECTANGLE=  0 1476  406  426
UNTRUSTED_RECTANGLE=  0 1476  618  638
UNTRUSTED_RECTANGLE=  0 1476  830  850
UNTRUSTED_RECTANGLE=  0 1476  1042 1062
UNTRUSTED_RECTANGLE=  0 1476  1254 1274
UNTRUSTED_RECTANGLE=  0 1476  1466 1486
eof
    else
    cat >> XDS.INP << eof
!EXCLUSION OF VERTICAL DEAD AREAS OF THE PILATUS 2M DETECTOR
UNTRUSTED_RECTANGLE= 487  495    0 1680
UNTRUSTED_RECTANGLE= 981  989    0 1680
!EXCLUSION OF HORIZONTAL DEAD AREAS OF THE PILATUS 2M DETECTOR
UNTRUSTED_RECTANGLE=  0 1476  195  213
UNTRUSTED_RECTANGLE=  0 1476  407  425
UNTRUSTED_RECTANGLE=  0 1476  619  637
UNTRUSTED_RECTANGLE=  0 1476  831  849
UNTRUSTED_RECTANGLE=  0 1476  1043 1061
UNTRUSTED_RECTANGLE=  0 1476  1255 1273
UNTRUSTED_RECTANGLE=  0 1476  1467 1485
eof
    fi
  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 [ "$NX" == "2463" ]; then
# Pilatus 6M
# FIXME: here we could test if a Flat_field correction was applied like we do for 2M
    cat >> XDS.INP << eof
UNTRUSTED_RECTANGLE= 487  495    0 2528
UNTRUSTED_RECTANGLE= 981  989    0 2528
UNTRUSTED_RECTANGLE=1475 1483    0 2528
UNTRUSTED_RECTANGLE=1969 1977    0 2528
UNTRUSTED_RECTANGLE=  0 2464  195  213
UNTRUSTED_RECTANGLE=  0 2464  407  425
UNTRUSTED_RECTANGLE=  0 2464  619  637
UNTRUSTED_RECTANGLE=  0 2464  831  849
UNTRUSTED_RECTANGLE=  0 2464  1043 1061
UNTRUSTED_RECTANGLE=  0 2464  1255 1273
UNTRUSTED_RECTANGLE=  0 2464  1467 1485
UNTRUSTED_RECTANGLE=  0 2464  1679 1697
UNTRUSTED_RECTANGLE=  0 2464  1891 1909
UNTRUSTED_RECTANGLE=  0 2464  2103 2121
UNTRUSTED_RECTANGLE=  0 2464  2315 2333
eof
  elif [ "$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
  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
 
</pre>
 
== System-wide or personal installation ==
 
Ask your system adminstrator to cut-and-paste the script into e.g. /usr/local/bin/generate_XDS.INP, and to make it "executable".
 
But you may also cut-and-paste the script from this webpage into a file in e.g. your home directory; the filename should be generate_XDS.INP. After creating the file, make it executable - e.g. if it's in your $HOME, use:
chmod +x ~/generate_XDS.INP
After that, you can just run it in a similar way as if it were installed in your $PATH:
~/generate_XDS.INP "frms/mydata_1_???.img"
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.
 
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]].
 
== 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
<pre>
wget http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP -O - | \
  sed -e s/\&nbsp\;/\ /g -e s/\&gt\;/\>/g -e s/\&lt\;/\</g -e s/amp\;//g -e s/\&quot\;/\"/g -e s/\&\#\1\6\0\;/\ /g | \
  sed '/# end of generate_XDS.INP/,$d' | awk '/^#/,/rm -f tmp1 tmp2/' > generate_XDS.INP
chmod +x generate_XDS.INP
</pre>
to copy the script from this website into an executable file generate_XDS.INP in your current directory. On a Mac (which does not seem to have wget), one could try
<pre>
curl -L -o - http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP | \
  sed -e s/\&nbsp\;/\ /g -e s/\&gt\;/\>/g -e s/\&lt\;/\</g -e s/amp\;//g -e s/\&quot\;/\"/g -e s/\&\#\1\6\0\;/\ /g | \
  sed '/# end of generate_XDS.INP/,$d' | awk '/^#/,/rm -f tmp1 tmp2/' > generate_XDS.INP
chmod +x generate_XDS.INP
</pre>
If you do use cut-and-paste from the webpage, be aware of the following problem report: On the Mac, after loading frames, by clicking “generate XDS.INP”, the program gives some strange symbol “” in XDS.INP. And the more you click “save” button, the more “” appear. This looks like e.g. <br>SPACE_GROUP_NUMBER=0  ! 0 if unknown <br>UNIT_CELL_CONSTANTS= 70 80 90 90 90 90  <br> ''The problem is due to the “Rich text” format in TextEdit when saving "generate_XDS.INP". It is solved by re-downloading the script, and changing format to Plain - everything should work then.''
 
== Calling generate_XDS.INP from a Python script ==
 
It is recommended to use the [http://docs.python.org/2/library/subprocess.html subprocess.Popen()] module instead of [http://docs.python.org/2/library/os.html os.system()]:
<pre>
subprocess.Popen(["generate_XDS.INP",imagepath],stdout=outputfile)
</pre>
where imagepath is a string containing the path to an image and outputfile is either a chosen variable for an output file or subprocess.PIPE if you're not interested in the output of the script.
 
The module os.system() internally uses /bin/sh to execute the command and overrides #!/bin/bash at the beginning of the script. While this is not a problem on most operating systems, /bin/sh points to dash instead of bash on Ubuntu, which leads to a program crash with the error message
<pre>
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 ==
* 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 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. 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
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