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

Get Durin

Latest release at https://github.com/DiamondLightSource/durin/releases/tag/2019v1

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

Building HDF5 library

The HDF5 library used when building durin must have been compiled with specific switches enabled to allow the durin plugin to be built and used.

Download the HDF5 source code (https://www.hdfgroup.org/downloads/hdf5/source-code) and extract to any directory (referred to as /hdf5_dir), and run the following commands.

cd /hdf5_dir
mkdir build
cd build
export CFLAGS=-fPIC
../configure --enable-threadsafe --enable-deprecated-symbols --enable-hl --enable-unsupported
make
make check
make install

The hdf5 tools and libraries should now be located in /hdf5_dir/build/hdf5

For reference, the plugin requires the thread-safe switch and the optimised chunk read function. The chunk read function may be defined in the high level library instead of the regular library, depending on the exact HDF5 version downloaded (hence the --enable-deprecated-symbols and --enable-hl). The unsupported flag enables building with both threadsafe and high-level enabled.

Building durin plugin

The plugin makefile will use the "h5cc" compiler wrapper, provided by the HDF5 library, which must be on your PATH. Download or clone the plugin source code (https://github.com/DiamondLightSource/durin) into any directory (referred to as /durin_dir) and run the following commands.

cd /durin_dir
PATH=/hdf5_dir/build/hdf5/bin:$PATH
make

The plugin is located at /durin_dir/build/durin-plugin.so and should be added to the XDS.INP file as LIB=/durin_dir/build/durin-plugin.so

Example XDS.INP

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
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.