Durin

XDS plugin for reading HDF5 files following the NeXuS format or those written by Dectris Eiger detectors.

See:

• https://www.nexusformat.org
• https://www.dectris.com/features/features-eiger-x/hdf5-and-nexus
• https://strucbio.biologie.uni-konstanz.de/xdswiki

Usage

In your XDS.INP add:

LIB=[path to durin-plugin.so]
NAME_TEMPLATE_OF_DATA_FRAMES=[data_path]/data_images_??????.h5

XDS will instruct the plugin to load [data_path]/data_images_master.h5 and this must be the Eiger master file or the NeXus file for the data collection.

It is generally assumed that the files [data_path]/data_images_data_xxxxxx.h5 contain the actual datasets and the master file contains HDF5 external links to these, but that is not required, so long as the master file contains an NXdata or NXdetector group with either a dataset named data or a series of datasets named data_000001, data_000002, etc.

Requirements

• HDF5 Library (https://www.hdfgroup.org/downloads)

Building

First ensure that the HDF5 libraries are compiled with:

export CFLAGS=-fPIC
./configure --enable-threadsafe=yes --enable-unsupported

former is neeed to ensure that XDS in parallel mode will work, latter to ensure that the chunk read (which for opaque reasons is defined to be high level) works. Then make sure that wherever this was installed, the h5cc is in PATH before:

cd durin
make

Plugin file is build/durin-plugin.so - this should be added to the XDS.INP file i.e. as:

DETECTOR=PILATUS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=4096
LIB=/opt/durin/build/durin-plugin.so
SENSOR_THICKNESS= 0.450
!SENSOR_MATERIAL / THICKNESS Si 0.450
!SILICON= 3.953379
DIRECTION_OF_DETECTOR_X-AXIS= 1.00000 0.00000 0.00000
DIRECTION_OF_DETECTOR_Y-AXIS= 0.00000 1.00000 0.00000
NX=2070 NY=2164 QX=0.0750 QY=0.0750
DETECTOR_DISTANCE= 194.633000
ORGX= 1041.30 ORGY= 1160.90
ROTATION_AXIS= 0.00000 -1.00000 -0.00000
STARTING_ANGLE= -30.000
OSCILLATION_RANGE= 0.100
X-RAY_WAVELENGTH= 0.97891
INCIDENT_BEAM_DIRECTION= -0.000 -0.000 1.022
FRACTION_OF_POLARIZATION= 0.999
POLARIZATION_PLANE_NORMAL= 0.000 1.000 0.000
NAME_TEMPLATE_OF_DATA_FRAMES= ../image_9264_??????.h5
TRUSTED_REGION= 0.0 1.41
DATA_RANGE= 1 600
JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT

N.B. the master file is needed, not the .nxs one which follows the standard.