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Generate XDS.INP: Difference between revisions
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# revision 1.09 . KD, Feng Yu 7/11/2021 fix detector number BNL E-18-0121 to be E-18-0104 | # revision 1.09 . KD, Feng Yu 7/11/2021 fix detector number BNL E-18-0121 to be E-18-0104 | ||
# revision 1.10 . KD NeXus header for Eiger | # revision 1.10 . KD NeXus header for Eiger | ||
REVISION="1. | # revision 1.11 . KD / Helena Taberman ROTATION_AXIS=-1 0 0 for Eiger .cbf data from Petra P14 | ||
# revision 1.12 . KD / Helena Taberman correct rev 1.11 to be 0 -1 0 | |||
# revision 1.13 . KD variables for /usr/local/lib64/dectris-neggia.so and durin-plugin.so . Remove h5dump error messages. | |||
REVISION="1.13 (04-Jun-2022)" | |||
# | # | ||
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# | # | ||
# known problems: | # known problems: | ||
# - for ADSC detectors, there are at least three ways to obtain ORGX and ORGY values from the header (see below); | # - for ADSC detectors, there are at least three ways to obtain ORGX and ORGY values from the header (see below); | ||
# - the same might be a problem for MAR headers, too (not sure about this) | # - the same might be a problem for MAR headers, too (not sure about this) | ||
# - on | # - on macOS, the "Command Line Tools for Xcode" (from https://developer.apple.com/download/more/) are needed. | ||
# | # | ||
# notes for debugging of the script: | # notes for debugging of the script: | ||
# - add the -x option to | # - add the -x option to #!/bin/bash in first line, to see where an error occurs | ||
# - comment out the removal of tmp1 and tmp2 in the last line | # - comment out the removal of tmp1 and tmp2 in the last line | ||
# | # | ||
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DETECTOR_DISTANCE=`grep ^DISTANCE tmp2 | sed s/DISTANCE=/-/` | DETECTOR_DISTANCE=`grep ^DISTANCE tmp2 | sed s/DISTANCE=/-/` | ||
OSCILLATION_RANGE=`grep OMEGA_DELTA tmp2 | sed s/OMEGA_DELTA=//` | OSCILLATION_RANGE=`grep OMEGA_DELTA tmp2 | sed s/OMEGA_DELTA=//` | ||
DETECTOR_X_AXIS="-1 0 0" | |||
elif [ "$DET" == "experimental-ED" ]; then | elif [ "$DET" == "experimental-ED" ]; then | ||
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fi | fi | ||
# PETRA P14: raw data from Eiger are stored as CBF files so this is treated as Pilatus | # PETRA P14: raw data from Eiger are stored as CBF files so this is treated as Pilatus | ||
if [ "$DET_SN" == "Dectris Eiger 4M, E-08-0107" -o "$DET_SN" == "PILATUS 6M-F, S/N 60-0115-F" ] ; then | if [ "$DET_SN" == "Dectris Eiger 4M, E-08-0107" -o "$DET_SN" == "PILATUS 6M-F, S/N 60-0115-F" \ | ||
-o "$DET_SN" == "Dectris EIGER2 CdTe 16M, E-32-0129" ] ; then | |||
rotation_axis="0 -1 0" | rotation_axis="0 -1 0" | ||
echo ROTATION_AXIS="0 -1 0" at PETRA P14 | echo ROTATION_AXIS="0 -1 0" at PETRA P14 | ||
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DATA_RANGE="1 $nframes" | DATA_RANGE="1 $nframes" | ||
SPOT_RANGE="1 `echo "scale=0; if (${nframes}<2) 1; if (${nframes}>1) ${nframes}/2"|bc -l`" | SPOT_RANGE="1 `echo "scale=0; if (${nframes}<2) 1; if (${nframes}>1) ${nframes}/2"|bc -l`" | ||
SN=`h5dump -d "/entry/instrument/detector/detector_number" $FIRSTFRAME | awk '/\(0\): /{print $2}' | sed s/\"//g` | |||
echo detector serial number is $SN | |||
# find out if HDF5 from Diamond (DLS=1) or Dectris (DLS=0) | # find out if HDF5 from Diamond (DLS=1) or Dectris (DLS=0) | ||
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OSCILLATION_RANGE=`h5dump -d "/entry/sample/goniometer/omega_range_average" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2}'` | OSCILLATION_RANGE=`h5dump -d "/entry/sample/goniometer/omega_range_average" $FIRSTFRAME | awk '/\(0\): [0-9]/{print $2}'` | ||
# STARTING_ANGLE: the \- was introduced in version 0.91 to allow negative values : | # STARTING_ANGLE: the \- was introduced in version 0.91 to allow negative values : | ||
STARTING_ANGLE=`h5dump -d "/entry/sample/goniometer/omega_start" $FIRSTFRAME | awk '/\(0\): [\-0-9]/{print $2}'` | STARTING_ANGLE=`h5dump -d "/entry/sample/goniometer/omega_start" $FIRSTFRAME 2>/dev/null | awk '/\(0\): [\-0-9]/{print $2}'` | ||
# /entry/sample/goniometer/omega_start is missing in some eiger2 detectors (e.g. Eiger2 9M with fw version release-2020.2.1 and SIMPLON API 1.8) (Feng YU 2021-07-18) | # /entry/sample/goniometer/omega_start is missing in some eiger2 detectors (e.g. Eiger2 9M with fw version release-2020.2.1 and SIMPLON API 1.8) (Feng YU 2021-07-18) | ||
if [ "$STARTING_ANGLE" == "" ]; then | if [ "$STARTING_ANGLE" == "" ]; then | ||
echo "/entry/sample/goniometer/omega_start not found, | echo "/entry/sample/goniometer/omega_start not found, trying /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"` | STARTING_ANGLE=`h5dump -d /entry/sample/goniometer/omega $FIRSTFRAME | grep "(0):" | head -n 1 | awk '{print $2}' | sed -e "s/,//g"` | ||
fi | fi | ||
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rotation_axis=`h5dump -a "/entry/sample/transformations/omega/vector" $FIRSTFRAME 2>/dev/null | grep "(0):" | sed -e "s/^.*://; s/,//g"` | rotation_axis=`h5dump -a "/entry/sample/transformations/omega/vector" $FIRSTFRAME 2>/dev/null | grep "(0):" | sed -e "s/^.*://; s/,//g"` | ||
# EIGER2 16M CHESS ID7B2 has S/N E-32-0123 (A. Finke 2020-11-07) v0.99 | # EIGER2 16M CHESS ID7B2 has S/N E-32-0123 (A. Finke 2020-11-07) v0.99 | ||
if [ "$SN" == "E-32-0123" ]; then | if [ "$SN" == "E-32-0123" ]; then | ||
rotation_axis="-1 0 0" | rotation_axis="-1 0 0" | ||
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# rev 1.10: check for NeXus header. If found, its geometry will overwrite any rotation_axis set until here. | # rev 1.10: check for NeXus header. If found, its geometry will overwrite any rotation_axis set until here. | ||
NeXus=0 | NeXus=0 | ||
h5dump -d "/entry/definition" $FIRSTFRAME | grep -q NXmx && NeXus=1 | h5dump -d "/entry/definition" $FIRSTFRAME 2>/dev/null | grep -q NXmx && NeXus=1 | ||
if [ "$NeXus" == "1" ]; then | if [ "$NeXus" == "1" ]; then | ||
echo NeXus header found. This defines DIRECTION_OF_DETECTOR_X/Y-AXIS and ROTATION_AXIS. | echo NeXus header found. This defines DIRECTION_OF_DETECTOR_X/Y-AXIS and ROTATION_AXIS. | ||
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if [ "$DET" == "eiger" ] && [ "$is_h5" == 1 ]; then | if [ "$DET" == "eiger" ] && [ "$is_h5" == 1 ]; then | ||
if [ "$DLS" == 0 ] ; then | if [ "$DLS" == 0 ] ; then | ||
neggia_path=/usr/local/lib64/dectris-neggia.so | |||
echo LIB= | if [ -e $neggia_path ]; then | ||
echo LIB= | echo LIB=$neggia_path >> XDS.INP | ||
echo "LIB= <dectris-neggia> was written to XDS.INP . Check the path! For Apple M1 processors, modify the name." | |||
else | else | ||
echo !LIB=/usr/local/lib64/dectris-neggia.so >> XDS.INP | echo !LIB=/usr/local/lib64/dectris-neggia.so >> XDS.INP | ||
echo | echo "dectris-neggia.so not found. Specify LIB=<path-to-dectris-neggia> in XDS.INP & fix your generate_XDS.INP !" | ||
fi | fi | ||
else | else | ||
durin_path=/usr/local/lib64/durin-plugin.so | |||
echo LIB= | if [ -e $durin_path ]; then | ||
echo LIB= | echo LIB=$durin_path >> XDS.INP | ||
echo "LIB= <durin-plugin> was written to XDS.INP . Check the path! For Apple M1 processors, modify the name." | |||
else | else | ||
echo !LIB=/usr/local/lib64/durin-plugin.so >> XDS.INP | echo !LIB=/usr/local/lib64/durin-plugin.so >> XDS.INP | ||
echo | echo "durin-plugin.so not found. Specify LIB=<path-to-durin-plugin> in XDS.INP & fix your generate_XDS.INP !" | ||
fi | fi | ||
fi | fi | ||
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Ask your system adminstrator to cut-and-paste the script into e.g. /usr/local/bin/generate_XDS.INP, and to make it "executable". | Ask your system adminstrator to cut-and-paste the script into e.g. /usr/local/bin/generate_XDS.INP, and to make it "executable". | ||
If you work with Eiger data, you may want to make a one-line change to the script after downloading, in order to point to the correct path on your system of the Dectris' Neggia library, or the Durin plugin, respectively. Just open the script with an editor and adjust neggia_path or durin_path ! This relieves users from having to change the LIB= line for every data set. You should also insert that path into the Menu / Settings / "generic library" in [[XDSGUI]] . | |||
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: | 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: | ||
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</pre> | </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 “Ô in XDS.INP. And the more you click “save” button, the more “Ô appear. This looks like e.g. <br>SPACE_GROUP_NUMBER=0 à ! 0 if unknown <br>UNIT_CELL_CONSTANTS= 70 80 90 90 90 90 à <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.'' | 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 “Ô in XDS.INP. And the more you click “save” button, the more “Ô appear. This looks like e.g. <br>SPACE_GROUP_NUMBER=0 à ! 0 if unknown <br>UNIT_CELL_CONSTANTS= 70 80 90 90 90 90 à <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.'' | ||
Attention beamline staff: it would be great if you could make a one-line change to the script after downloading, in order to point to the correct path to Dectris' Neggia library, or the Durin plugin, respectively. Just open the script with an editor and adjust neggia_path or durin_path ! This relieves users from having to change the LIB= line for every data set. | |||
== Calling generate_XDS.INP from a Python script == | == Calling generate_XDS.INP from a Python script == | ||
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* 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. | * 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 always be determined 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 . | * 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 always be determined 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 == | == See also == | ||