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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). However, with the [https://github.com/dectris/neggia | 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). However, with the [https://github.com/dectris/neggia ''Neggia'' plugin for XDS], processing is as straightforward as before. | ||
== General aspects == | == General aspects == | ||
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* Make sure no nonsense has been extracted from master.h5. | * Make sure no nonsense has been extracted from master.h5. | ||
* Make sure INCIDENT_BEAM_DIRECTION= corresponds to the experimental geometry. | * Make sure INCIDENT_BEAM_DIRECTION= corresponds to the experimental geometry. | ||
* Point LIB= to where Neggia is saved. | * Point LIB= to where Neggia is saved (if in current directory, use <code>LIB=./dectris-neggia.so</code> i.e. specify directory!). | ||
** Comment out LIB= if Neggia isn't used (not recommended). | ** Comment out LIB= if Neggia isn't used (not recommended). | ||
* Set MAXIMUM_NUMBER_OF_JOBS= and MAXIMUM_NUMBER_OF_PROCESSORS= to similar values whose product is slightly smaller than the total number of threads on your system. | * Set MAXIMUM_NUMBER_OF_JOBS= and MAXIMUM_NUMBER_OF_PROCESSORS= to similar values whose product is slightly smaller than the total number of threads on your system. | ||
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= Less efficient way of processing Eiger data, using conversion to CBF= | = Less efficient way of processing Eiger data, using conversion to CBF= | ||
Since the release of | Since the release of Neggia, a plugin for XDS that parallelizes the reading of images from HDF5 data, conversion to H5ToXds should no longer required in most usage scenarios. The sections below nevertheless describe this possibility, since preliminary experience with some less common network file systems (apparently GPFS, but not NFS) seems to indicate low performance of Neggia. | ||
Conversion program options: Dectris provides [https://www.dectris.com/news.html?page=2 H5ToXds] (Linux only!). That program converts (as the name indicates) the HDF5 files to CBF files; however, it does not write the geometry and other information into the CBF header (therefore, [[generate_XDS.INP]] or MOSFLM does not work with these files). Alternatives are GlobalPhasing's hdf2mini-cbf program (needs autoPROC license) or, from http://www.mrc-lmb.cam.ac.uk/harry/imosflm/ver721/downloads, the eiger2cbf-osx or eiger2cbf-linux program written by T. Nakane. The latter programs do write a useful CBF header. | Conversion program options: Dectris provides [https://www.dectris.com/news.html?page=2 H5ToXds] (Linux only!). That program converts (as the name indicates) the HDF5 files to CBF files; however, it does not write the geometry and other information into the CBF header (therefore, [[generate_XDS.INP]] or MOSFLM does not work with these files). Alternatives are GlobalPhasing's hdf2mini-cbf program (needs autoPROC license) or, from http://www.mrc-lmb.cam.ac.uk/harry/imosflm/ver721/downloads, the eiger2cbf-osx or eiger2cbf-linux program written by T. Nakane. The latter programs do write a useful CBF header. | ||