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Eiger: Difference between revisions
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Processing of [https://www.dectris.com/EIGER_X_Features.html Eiger] data is different from processing of conventional data, because the frames are wrapped into [http://www.hdfgroup.org HDF5] files (ending with .h5). | Processing of [https://www.dectris.com/EIGER_X_Features.html Eiger] data is different from processing of conventional data, because the frames are wrapped into [http://www.hdfgroup.org HDF5] files (ending with .h5). | ||
# It is advisable to use the most recent 64bit version of XDS (since version Oct 15, 2015 the 32bit versions are no longer distributed anyway). | # It is advisable to use the most recent 64bit version of XDS (since version Oct 15, 2015 the 32bit versions are no longer distributed anyway). The idea of the new framecache in XDS is that RAM is used to save on I/O. To this end, XDS tries to store NUMBER_OF_IMAGES_IN_CACHE=DELPHI/OSCILLATION_RANGE images in memory. Each frame is stored as (number of pixels)*(4 bytes) which means 72 MB in case of the Eiger. As an example: if DELPHI=20 and OSCILLATION_RANGE=0.05 your computer has to have 400*72MB = 29GB of memory (plus some more for the program and the operating system). If it has not, the fallback is to the old behaviour of reading each frame three times. | ||
# Dectris provides [https://www.dectris.com/tl_files/root/download/H5ToXds_x86_64.zip H5ToXds] which is needed by XDS. H5ToXds should be copied to e.g. /usr/local/bin/H5ToXds.bin . | # Dectris provides [https://www.dectris.com/tl_files/root/download/H5ToXds_x86_64.zip H5ToXds] which is needed by XDS. H5ToXds should be copied to e.g. /usr/local/bin/H5ToXds.bin . | ||
# For faster processing, the shell script below should be copied to /usr/local/bin/H5ToXds and made executable (<code>chmod a+rx /usr/local/bin/H5ToXds*</code>) | # For faster processing, the shell script below should be copied to /usr/local/bin/H5ToXds and made executable (<code>chmod a+rx /usr/local/bin/H5ToXds*</code>). This script ''also'' uses RAM to speed up processing; it uses it for fast storage of the temporary file that Dectris' H5ToXds writes, and that each parallel thread ("processor") of XDS reads. | ||
A suitable XDS.INP should normally be written by the beamline software; [[generate_XDS.INP]] does not (yet) write it. The XDS_from_H5.py script can be used if XDS.INP is not available. | A suitable XDS.INP should normally be written by the beamline software; [[generate_XDS.INP]] does not (yet) write it. The XDS_from_H5.py script can be used if XDS.INP is not available. | ||