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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 (often ending with .h5). However, with the [[LIB]] feature of XDS and a suitable plugin ([https://github.com/dectris/neggia ''Neggia''] or [https://github.com/DiamondLightSource/durin ''Durin'']), processing is as straightforward as before.


# 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 16M. 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.
== General aspects ==
# 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 - note the .bin filename extension!
# The framecache of XDS uses memory to save on I/O; it saves a frame in RAM after reading it for the first time. By default, each XDS (or mcolspot/mintegrate) job stores NUMBER_OF_IMAGES_IN_CACHE=DELPHI/OSCILLATION_RANGE images in memory which corresponds to one DELPHI-sized batch of data. This requires (number of pixels)*(number of jobs)*4 Bytes per frame which amounts to 72 MB in case of the Eiger 16M when running with MAXIMUM_NUBER_OF_JOBS=1. (If DELPHI=20 and OSCILLATION_RANGE=0.05 your computer thus has to have at least 400*72MB = 29GB of memory for each job!). If memory allocation fails, the fallback is to the old behaviour of reading each frame three times (instead of once).
# 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. The amount of additional RAM this requires is modest (about (number of pixels)*(number of threads) bytes).
# Dectris provides the ''Neggia'' library ([https://github.com/dectris/neggia source],[https://www.dectris.com/support/downloads/sign-in binary]) for native reading of HDF5 files, which can be loaded into XDS at runtime using the <code>[[LIB]]=</code> [http://xds.mpimf-heidelberg.mpg.de/html_doc/xds_parameters.html#LIB= keyword]. With this library (which can also be found at https://{{SERVERNAME}}/pub/linux_bin for Linux, and at https://{{SERVERNAME}}/pub/mac_bin for MacOS), no conversion to CBF or otherwise is necessary. It is therefore just as fast and efficient to read HDF5 files as any other file format. At Diamond Light Source, a different HDF5 format was developed, and this requires the [https://github.com/DiamondLightSource/durin/releases/latest ''Durin'' plugin]. The latter can also read the HDF5 files written by the Dectris software.


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 (below) can be used if XDS.INP is not available.
A suitable [[XDS.INP]] may have been written by the data collection (beamline) software. Latest [[generate_XDS.INP]] (<code>generate_XDS.INP xxx_master.h5</code>) or the [[Eiger#Script_for_generating_XDS.INP_from_master.h5|XDS_from_H5.py script]] can be used if XDS.INP is not available.


The number of pixels of the Eiger 16M is three times higher than that of the Pilatus 6M, but since the Eiger firmware update in November 2015, the ("bit shufflle LZ4") compression of the .h5 files containing data is better than that of CBF files, which mostly compensates for the increased number of pixels. However, the size of the *master.h5 file from a Eiger 16M experiment at SLS X06SA is more than 300MB, ''no matter how many frames are collected''. It is therefore advisable to compress (by ~75%) the *master.h5 files on-site, before transferring them home using disk or internet. The fastest (parallel) program with the best compression that I found is [http://lbzip2.org lbzip2] (available from the EPEL repository for RHEL clones). It is supposedly fully compatible with bzip2.
== Compression ==


== A script for faster XDS processing of Eiger data ==
The number of pixels of the Eiger 16M is three times higher than that of the Pilatus 6M, but since the Eiger firmware update in November 2015, the ("bit shufflle LZ4") compression of the .h5 files containing data is better than that of CBF files, which mostly compensates for the increased number of pixels.
 
The size of the *master.h5 file from a Eiger 16M experiment at SLS X06SA is more than 300MB, ''no matter how many frames are collected''. It is therefore advisable to compress (by ~75%) the *master.h5 files on-site, before transferring them home using disk or internet. A very fast (parallel) program is [http://lbzip2.org lbzip2] (available from the EPEL repository for RHEL clones). It is supposedly fully compatible with bzip2.
 
Update 2016-06-05 (Toine Schreurs): a HDF5 file may be compressed with [https://www.hdfgroup.org/HDF5/docNewFeatures/FileSpace/h5repack.htm h5repack], ''e.g.'' by <code>h5repack -i <in.h5> -o <out.h5> -f GZIP=6</code> (6 is the default compression level of gzip). This should be a good way to reduce the size of master files while keeping them compatible with processing, but needs to be tested. Whether h5repack uses parallel gzip is not clear from the docs.
 
== Troubleshooting ==
* make sure that master.h5 and the corresponding data.h5 files remain together as collected, and '''don't rename the data.h5 files''' - they are referred to from master.h5.  If you change the names of the data.h5 files or copy them somewhere else, that link is broken unless you fix master.h5.
 
== Script by Andreas Förster (Dectris) for generating XDS.INP from master.h5 ==
<div class="mw-collapsible mw-collapsed">
Expand code section below (i.e. click on blue <code>[Expand]</code> at the end of this line if there is no code visible), download it and save as XDS_from_H5.py .
<div class="mw-collapsible-content">
<pre>
<pre>
#!/bin/bash
# -*- coding: utf-8 -*-
# Kay Diederichs 10/2015
# store temporary files from H5ToXds in fast local directory, instead of NFS
#
# Installation: This script should reside in $PATH, e.g. /usr/local/bin/H5ToXds
#              Dectris' H5ToXds should be /usr/local/bin/H5ToXds.bin
#
# Recommendation:
# - for the fast local directory one should use a RAMdisk (one GB size at most)
# - /dev/shm seems to be set up for that purpose on most distributions
#
tempfile="/dev/shm/H5ToXds${PWD//\//_}.$3"
#
# the next line runs Dectris' H5ToXds binary, so we specify the absolute path.
#
/usr/local/bin/H5ToXds.bin $1 $2 "$tempfile"
ln -sf "$tempfile" $3 2>/dev/null
</pre>


== XDS_from_H5.py script for generating XDS.INP given a master .h5 file ==
__author__ = "AndF"
This script could be made executable and put into /usr/local/bin. It requires the [https://www.dectris.com/albula.html#main_head_navigation ALBULA API] to be installed.
__date__ = "2017/03/08"
<pre>
__reviewer__ = ""
#!/usr/bin/python
__version__ = "0.1.1"
# coding: utf8


import sys
import sys
# Path needs to be be set only if dectris.albula is not found
# Path needs to be be set only if dectris.albula is not found
# i.e. if ALBULA was installed without "--python=</path/to/python_interpreter>"
# i.e. if ALBULA was installed without "--python=</path/to/python_interpreter>"
# Define correct path to ALBULA API:
# Uncomment below (and define correct path to ALBULA API)
sys.path.insert(0,"/usr/local/dectris/albula/3.1/python")
# sys.path.insert(0,"/usr/local/dectris/albula/3.2/python")
try:
try:
   import dectris.albula as dec
   import dectris.albula as dec
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!    Characters to the right of an exclamation mark are comments.
!    Characters to the right of an exclamation mark are comments.
!
!
!    This file was autogenerated by XDS_from_H5.py (Oct 2015).
!    This file was autogenerated by XDS_from_H5.py (Mar 2017).
!    Please check default values before processing.
!    Please check default values before processing.
!
!
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!====================== DETECTOR PARAMETERS ==================================
!====================== DETECTOR PARAMETERS ==================================
  DETECTOR=%(family)s
  DETECTOR=%(family)s
LIB= /usr/local/lib64/dectris-neggia.so
  MINIMUM_VALID_PIXEL_VALUE=0
  MINIMUM_VALID_PIXEL_VALUE=0
  OVERLOAD= %(cutoff)i ! taken from HDF5 header item
  OVERLOAD= %(cutoff)i ! taken from HDF5 header item
Line 89: Line 84:


!====================== JOB CONTROL PARAMETERS ===============================
!====================== JOB CONTROL PARAMETERS ===============================
  JOB= XYCORR INIT COLSPOT IDXREF DEFPIX ! XPLAN INTEGRATE CORRECT
!JOB= XYCORR INIT COLSPOT IDXREF DEFPIX ! XPLAN INTEGRATE CORRECT
  JOB= XYCORR INIT COLSPOT IDXREF DEFPIX INTEGRATE CORRECT
!JOB= INTEGRATE CORRECT


!Set maximum number of jobs and processors so that their products comes close
!to the number of CPUs of the machine.
  MAXIMUM_NUMBER_OF_JOBS=8  !Speeds up COLSPOT & INTEGRATE on multicore machine
  MAXIMUM_NUMBER_OF_JOBS=8  !Speeds up COLSPOT & INTEGRATE on multicore machine
  MAXIMUM_NUMBER_OF_PROCESSORS=4!<32;ignored by single cpu version of xds
  MAXIMUM_NUMBER_OF_PROCESSORS=4!<99;ignored by single cpu version of xds
!SECONDS=0  !Maximum number of seconds to wait until data image must appear
!SECONDS=0  !Maximum number of seconds to wait until data image must appear
!TEST=1    !Test flag. 1,2 additional diagnostics and images
!TEST=1    !Test flag. 1,2 additional diagnostics and images
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!ORGX and ORGY are often close to the image center, i.e. ORGX=NX/2, ORGY=NY/2
!ORGX and ORGY are often close to the image center, i.e. ORGX=NX/2, ORGY=NY/2
  ORGX= %(orgx).1f  ORGY= %(orgy).1f    !Detector origin (pixels).  ORGX=NX/2; ORGY=NY/2
  ORGX= %(orgx).1f  ORGY= %(orgy).1f    !Detector origin (pixels).  ORGX=NX/2; ORGY=NY/2
  DETECTOR_DISTANCE= %(dist)i   ! [mm]
  DETECTOR_DISTANCE= %(dist).2f   ! [mm]


  ROTATION_AXIS= 1.0 0.0 0.0
  ROTATION_AXIS= 1.0 0.0 0.0
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!REIDX=  0  0 -1  0  0 -1  0  0 -1  0  0  0
!REIDX=  0  0 -1  0  0 -1  0  0 -1  0  0  0


FRIEDEL'S_LAW=FALSE ! Default is TRUE.
!FRIEDEL'S_LAW=FALSE ! Default is TRUE.


!REFERENCE_DATA_SET= CK.HKL  ! Name of a reference data set (optional)
!REFERENCE_DATA_SET= CK.HKL  ! Name of a reference data set (optional)
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!REFLECTING_RANGE_E.S.D.=  0.113 !half-width (mosaicity) of REFLECTING_RANGE
!REFLECTING_RANGE_E.S.D.=  0.113 !half-width (mosaicity) of REFLECTING_RANGE


  NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA=21!used by: INTEGRATE
!The next two values could be increased up to 21 for best profiles.
  NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA=21     !used by: INTEGRATE
  NUMBER_OF_PROFILE_GRID_POINTS_ALONG_ALPHA/BETA=13!used by: INTEGRATE
  NUMBER_OF_PROFILE_GRID_POINTS_ALONG_GAMMA=13     !used by: INTEGRATE


!DELPHI= 6.0!controls the number of reference profiles and scaling factors
!DELPHI= 6.0!controls the number of reference profiles and scaling factors
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         'orgx': float(parameters["/entry/instrument/detector/beam_center_x"]),
         'orgx': float(parameters["/entry/instrument/detector/beam_center_x"]),
         'orgy': float(parameters["/entry/instrument/detector/beam_center_y"]),
         'orgy': float(parameters["/entry/instrument/detector/beam_center_y"]),
         'dist': int(float(parameters["/entry/instrument/detector/detector_distance"]) * 1000.0),
         'dist': float(parameters["/entry/instrument/detector/detector_distance"]) * 1000.0,
         'osc_range': float(parameters["/entry/sample/goniometer/omega_range_average"]),
         'osc_range': float(parameters["/entry/sample/goniometer/omega_range_average"]),
         'wavelength': float(parameters["/entry/instrument/beam/incident_wavelength"]),
         'wavelength': float(parameters["/entry/instrument/beam/incident_wavelength"]),
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             gap[1] + 1 + offset + n_excluded_edge_pixels,
             gap[1] + 1 + offset + n_excluded_edge_pixels,
             0,
             0,
             detector_families[fam]['sizes'][det][1] + 1))
             detector_families[fam]['sizes'][det][1] + offset))
     param_lines.append('\n')
     param_lines.append('\n')
     param_lines.append('!EXCLUSION OF HORIZONTAL DEAD AREAS OF THE '
     param_lines.append('!EXCLUSION OF HORIZONTAL DEAD AREAS OF THE '
Line 423: Line 423:
         param_lines.append(' UNTRUSTED_RECTANGLE= %4d %4d  %4d %4d \n' % (
         param_lines.append(' UNTRUSTED_RECTANGLE= %4d %4d  %4d %4d \n' % (
             0,
             0,
             detector_families[fam]['sizes'][det][0] + 1,
             detector_families[fam]['sizes'][det][0] + offset,
             gap[0] - 1 + offset - n_excluded_edge_pixels,
             gap[0] - 1 + offset - n_excluded_edge_pixels,
             gap[1] + 1 + offset + n_excluded_edge_pixels))
             gap[1] + 1 + offset + n_excluded_edge_pixels))
Line 431: Line 431:
     return ('\nThis script extracts from a given HDF5 master file all metadata\n'
     return ('\nThis script extracts from a given HDF5 master file all metadata\n'
             'required to write XDS.INP.  The user is prompted for missing metadata.\n'
             'required to write XDS.INP.  The user is prompted for missing metadata.\n'
            'If there are errors in the metadata, XDS.INP will be incorrect.\n'
             '\n'
             '\n'
            'WARNING - This script is a proof-of-principle, pre-alpha.\n'
             'Please report shortcomings and errors to docandreas@gmail.com\n')
            'Do not rely on it for anything serious.  Things will go wrong.\n'
            'In particular, this does not work for data collected in ROI mode.\n'
            '\n'
             'Please report shortcomings and errors to andreas.foerster@dectris.com\n')


def help():
def help():
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             'python XDS_from_H5.py <name>_master.h5\n')
             'python XDS_from_H5.py <name>_master.h5\n')


permitted_versions = ["1.5.1", "1.5.0", "1.2.0", "1.2.1", "1.3", "1.3.0", "1.4.0"]
def version_check(version):
def version_check(version):
     if (str(version) in permitted_versions):
     if float(re.search('^\d+\.\d+', version).group(0)) > 1.2:
         return 1
         return 1
     else:
     else:
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         return raw_input("Please enter the maximum trusted pixel value.\n")
         return raw_input("Please enter the maximum trusted pixel value.\n")
     elif (parameter == resolution_cutoff):
     elif (parameter == resolution_cutoff):
         return raw_input("Please enter a resolution limit for processing.\n")
         print "Please enter a resolution limit for processing."
        return raw_input("Enter '0' to let XDS decide.\n") or 0
     else:
     else:
         print "Unknown software version.  Please check."
         print "Unknown software version.  Please check."
Line 594: Line 591:
                 else:
                 else:
                     print "\nThe HDF5 file was created with version %s of the detector firmware" % (para_version)
                     print "\nThe HDF5 file was created with version %s of the detector firmware" % (para_version)
                     print "This script supports versions 1.2 and up."
                     print "This script supports versions 1.5 and up."
                     print "\nFile XDS.INP was not created."
                     print "\nFile XDS.INP was not created."
                     print "Please extract metadata with hdfview or h5dump.\n"
                     print "Please extract metadata with hdfview or h5dump.\n"
Line 612: Line 609:
         exit(-1)
         exit(-1)
</pre>
</pre>
</div>
</div>
Then,
* Make script executable and put into /usr/local/bin.
* Install [https://www.dectris.com/albula.html#main_head_navigation ALBULA API]
* Install numpy (yum -y install numpy) as root if you get the error message
** ImportError: No module named numpy.core.multiarray
Once XDS.INP has been generated,
* Make sure no nonsense has been extracted from master.h5.
* Make sure INCIDENT_BEAM_DIRECTION= corresponds to the experimental geometry.
* 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).
* 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.
= Less efficient way of processing Eiger data, using conversion to CBF =
Since the release of Neggia, a plugin for XDS that parallelizes the reading of images from HDF5 data, conversion by H5ToXds should no longer be 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 (does ''not'' need 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.
H5ToXds and eiger2cbf-osx / eiger2cbf-linux do not work with files produced at Diamond Light Source.
== A script for faster XDS processing of CBF-converted Eiger data (this is only shown out of historic interest) ==
For faster processing, the [[Eiger#A_script_for_faster_XDS_processing_of_CBF-converted Eiger data|shell script]] below should be copied to /usr/local/bin/H5ToXds and made executable (<code>chmod a+rx /usr/local/bin/H5ToXds*</code>). The binary H5ToXds then should be named e.g. /usr/local/bin/H5ToXds.bin - note the .bin filename extension! The script ''also'' uses RAM to speed up processing; it uses it for fast storage of the temporary CBF file that H5ToXds/eiger2cbf/hdf2mini-cbf writes, and that each parallel thread ("processor") of XDS reads. The amount of additional RAM this requires is modest (about (number of pixels)*(number of threads) bytes).
<pre>
#!/bin/bash
# Kay Diederichs 10/2015
# 3/2017 include RAMdisk creation for MacOS; only lightly tested!
# 3/2016 adapt for eiger2cbf and hdf2mini-cbf
# for the latter see https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;58a4ee1.1603 and
# https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;a048b4e8.1603
#
# Idea: put temporary files into fast local directory, instead of NFS
#
# Installation: Rename Dectris' H5ToXds to H5ToXds.bin
#              This script should be called H5ToXds and reside in $PATH
#              Modify this script according to which binary you use - see comments below.
#
# Recommendation:
# - for the fast local directory one should use a RAMdisk (one GB size at most)
# - /dev/shm seems to be already set up for that purpose on most Linux distributions
# - on MacOS you can easily set this up as described at http://stackoverflow.com/questions/2033362/does-os-x-have-an-equivalent-to-dev-shm
# example on MacOS for 1GB RAMdisk (needs to be repeated after booting):
# diskutil eraseVolume HFS+ RAMdisk $(hdiutil attach -nomount ram://$((2 * 1024 * 1000)))
#
# on MacOS the next line should then be:
# tempfile="/Volumes/RAMdisk/H5ToXds${PWD//\//_}.$3"
# and on Linux:
tempfile="/dev/shm/H5ToXds${PWD//\//_}.$3"
#
# choose between H5ToXds.bin,  eiger2cbf and hdf2mini-cbf; un/comment accordingly
/usr/local/bin/H5ToXds.bin $1 $2 "$tempfile" || rm "$tempfile"
#/usr/local/bin/eiger2cbf-linux $1 $2 "$tempfile" >& /dev/null  || rm "$tempfile"
#/usr/local/bin/eiger2cbf-osx $1 $2 "$tempfile" >& /dev/null  || rm "$tempfile"
#/usr/local/bin/hdf2mini-cbf $1 $2 "$tempfile"  || rm "$tempfile"
ln -sf "$tempfile" $3 2>/dev/null
</pre>
= See also =
[[Performance]]
[https://github.com/keitaroyam/yamtbx/blob/master/doc/eiger-en.md Keitaro Yamashita's Eiger page, with some emphasis on SPring-8]
Kay
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