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Generate XDS.INP: Difference between revisions

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Generate XDS.INP (view source)

Revision as of 23:16, 27 February 2020

1,042 bytes added ,  27 February 2020
→‎The script: add Eiger @ DLS . hopefully not messing up !
(→‎The script: add Eiger @ DLS . hopefully not messing up !)
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# revision 0.90 . KD 25/10/2019 add OLDMAR detector type. Tested w/ SBGrid data set 6. Anomalous signal may have wrong hand!
# revision 0.90 . 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 0.91 . KD 16/01/2020 Allow negative starting angle for Eiger (found -33 at SLS !).
REVISION="0.91 (16-Jan-2020)"
# revision 0.92 . KD 27/02/2020 read *_master.h5 from Diamond Light Source
REVISION="0.92 (27-Feb-2020)"


#                                                                                                             
#                                                                                                             
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       fi
       fi
# insert similar code for Petra P14 here
# insert similar code for Petra P14 here
elif [ "$DET" == "eiger" ]; then
elif [ "$DET" == "eiger" ]; then
   OVERLOAD=`h5dump -d "/entry/instrument/detector/detectorSpecific/countrate_correction_count_cutoff" $FIRSTFRAME | awk '/\(0\):/{print $2}' `
# 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
    OVERLOAD=`h5dump -d "/entry/instrument/detector/saturation_value" $FIRSTFRAME | awk '/\(0\):/{print $2}'`
    OSCILLATION_RANGE=`h5dump -d "/entry/data/omega" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $3-$2}'`
    STARTING_ANGLE=`h5dump    -d "/entry/data/omega" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2}' | sed -e "s/,//"`
    echo OSCILLATION_RANGE=$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}'`
  # 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"`
  # Eiger 16M SSRF BL17U1
    SN=`h5dump -d "/entry/instrument/detector/detector_number" $FIRSTFRAME | awk '/\(0\): /{print $2}' | sed s/\"//g`
    if [ "$SN" == "E-32-0111" ]; then
      rotation_axis="-1 0 0"
      echo SSRF BL17U1 with inverted rotation axis
    fi
  fi
   DETECTOR="EIGER MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD= $OVERLOAD"
   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}'`
   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}'`
   QY=`h5dump -d "/entry/instrument/detector/y_pixel_size" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2*1000}'`


   echo Data from a Eiger hdf5
   echo OVERLOAD=$OVERLOAD
   SENSOR_THICKNESS=`h5dump -d "/entry/instrument/detector/sensor_thickness" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2*1000}'`
   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}'`
   X_RAY_WAVELENGTH=`h5dump -d "/entry/instrument/beam/incident_wavelength" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2}'`
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   ORGY=`h5dump -d "/entry/instrument/detector/beam_center_y" $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 and OSCILLATION_RANGE:
   # find DETECTOR_DISTANCE :
   DETECTOR_DISTANCE=`h5dump -d "/entry/instrument/detector/detector_distance" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2*1000}'`
   DETECTOR_DISTANCE=`h5dump -d "/entry/instrument/detector/detector_distance" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2*1000}'`
  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 :
  STARTING_ANGLE=`h5dump -d "/entry/sample/goniometer/omega_start" $FIRSTFRAME | awk '/\(0\): [\-0-9]/{print $2}'`
 
  # 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"`
  # Eiger 16M SSRF BL17U1
  SN=`h5dump -d "/entry/instrument/detector/detector_number" $FIRSTFRAME | awk '/\(0\): /{print $2}' | sed s/\"//g`
  if [ "$SN" == "E-32-0111" ]; then
    rotation_axis="-1 0 0"
    echo SSRF BL17U1 with inverted rotation axis
  fi


   SEPMIN=4
   SEPMIN=4
   CLUSTER_RADIUS=2
   CLUSTER_RADIUS=2
 
 
elif [ "$DET" == "raxis" ]; then
elif [ "$DET" == "raxis" ]; then
   echo Data from a RAXIS detector
   echo Data from a RAXIS detector
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