Generate XDS.INP: Difference between revisions

# 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!

#                                                                                                             

  grep -q "^SOURCE_WAVELENGTH= *1" tmp2 && DET=dtrek

  grep -q BEAM_CENTER_X tmp2      && DET=adsc                                 

  grep -q BRUKER tmp2 && grep -q CBF tmp2  && DET=Bruker-cbf   

  grep -q CMOS1 tmp2 && DET=adsc-CMOS1   

         fi

       fi

elif [ "$DET" == "eiger" ]; then

   if [ "$DLS" == 1 ]; then

     echo Eiger HDF5 from Diamond

     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)"

   # 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"`

     SN=`h5dump -d "/entry/instrument/detector/detector_number" $FIRSTFRAME | awk '/\(0\): /{print $2}' | sed s/\"//g`

       rotation_axis="-1 0 0"

     fi  

   fi

   #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)

elif [ "$DET" == "dtrek" ]; then

  DETECTOR="MAR345  MINIMUM_VALID_PIXEL_VALUE=0  OVERLOAD=130000"

  NX=`awk '/FORMAT/{print $2}' tmp2`

  QX=`awk '/PIXEL/{print $3/1000.}' tmp2`

  QY=`awk '/PIXEL/{print $5/1000.}' tmp2`

!                                                  and does not seem to have any downsides.  

eof

     if ! grep -q Flat_field tmp2 ; then

     cat >> XDS.INP << eof

eof

     fi

# Pilatus 6M

# FIXME: here we could test if a Flat_field correction was applied like we do for 2M

UNTRUSTED_RECTANGLE=  0 2464  2315 2333

eof

# Eiger 9M

     cat >> XDS.INP << eof

UNTRUSTED_RECTANGLE= 0 3110 2717 2757

eof

# Eiger 16M

     cat >> XDS.INP << eof

  UNTRUSTED_RECTANGLE= 2069 2082      0 4371  

  UNTRUSTED_RECTANGLE= 3109 3122      0 4371

eof

   fi

See also [[Generate_XDS.INP#Dependencies]] below, and the [[Installation]] article.

== Obtaining generate_XDS.INP from this webpage ==

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.

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.

* 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.

* 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.

== See also ==