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Generate XDS.INP: Difference between revisions
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# revision 1.11 . KD / Helena Taberman ROTATION_AXIS=-1 0 0 for Eiger .cbf data from Petra P14 | # 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 1.12 . KD / Helena Taberman correct rev 1.11 to be 0 -1 0 | ||
REVISION="1. | # 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: | ||
| Line 600: | Line 600: | ||
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 == | ||