graeme-winter
78 lines
2.3 KiB
Markdown
78 lines
2.3 KiB
Markdown
Durin
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=====
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XDS plugin for reading HDF5 files following the NeXuS format or those written by Dectris Eiger detectors.
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See:
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* https://www.nexusformat.org
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* https://www.dectris.com/features/features-eiger-x/hdf5-and-nexus
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* https://strucbio.biologie.uni-konstanz.de/xdswiki
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## Usage
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In your XDS.INP add:
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```
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LIB=[path to durin-plugin.so]
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NAME_TEMPLATE_OF_DATA_FRAMES=[data_path]/data_images_??????.h5
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```
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XDS will instruct the plugin to load `[data_path]/data_images_master.h5` and this must be the
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Eiger master file or the NeXus file for the data collection.
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It is generally assumed that the files `[data_path]/data_images_data_xxxxxx.h5` contain the actual
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datasets and the master file contains HDF5 external links to these, but that is not required, so long as
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the master file contains an `NXdata` or `NXdetector` group with either a dataset named `data` or a
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series of datasets named `data_000001`, `data_000002`, etc.
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## Requirements
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* HDF5 Library (https://www.hdfgroup.org/downloads)
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## Building
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First ensure that the HDF5 libraries are compiled with:
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```
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export CFLAGS=-fPIC
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./configure --enable-threadsafe=yes --enable-unsupported
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```
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former is neeed to ensure that XDS in parallel mode will work, latter
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to ensure that the chunk read (which for opaque reasons is defined to
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be _high level_) works. Then make sure that wherever this was
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installed, the h5cc is in PATH before:
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```
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cd durin
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make
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```
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Plugin file is `build/durin-plugin.so` - this should be added to the
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XDS.INP file i.e. as:
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```
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DETECTOR=PILATUS MINIMUM_VALID_PIXEL_VALUE=0 OVERLOAD=4096
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LIB=/opt/durin/build/durin-plugin.so
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SENSOR_THICKNESS= 0.450
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!SENSOR_MATERIAL / THICKNESS Si 0.450
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!SILICON= 3.953379
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DIRECTION_OF_DETECTOR_X-AXIS= 1.00000 0.00000 0.00000
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DIRECTION_OF_DETECTOR_Y-AXIS= 0.00000 1.00000 0.00000
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NX=2070 NY=2164 QX=0.0750 QY=0.0750
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DETECTOR_DISTANCE= 194.633000
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ORGX= 1041.30 ORGY= 1160.90
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ROTATION_AXIS= 0.00000 -1.00000 -0.00000
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STARTING_ANGLE= -30.000
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OSCILLATION_RANGE= 0.100
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X-RAY_WAVELENGTH= 0.97891
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INCIDENT_BEAM_DIRECTION= -0.000 -0.000 1.022
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FRACTION_OF_POLARIZATION= 0.999
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POLARIZATION_PLANE_NORMAL= 0.000 1.000 0.000
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NAME_TEMPLATE_OF_DATA_FRAMES= ../image_9264_??????.h5
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TRUSTED_REGION= 0.0 1.41
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DATA_RANGE= 1 600
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JOB=XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT
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```
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N.B. the master file is needed, not the .nxs one which follows the
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standard.
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