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<HTML>
<HEAD>
<TITLE>CBFlib Manual</TITLE>
<style>
h1,
h2
{
text-align: center;
}
h1,
h2,
h3,
h4
{
color: #0808A0;
font-weight: bold;
}
pre
{
border: 1px solid grey;
font-family: "", "monospace";
padding: 0.5em;
white-space: pre;
}
code
{
font-family: "", "monospace";
white-space: normal;
}
ul.mini-ToC
{
list-style-type: none;
}
ul.see-also
{
list-style-type: none;
padding-left: 0;
}
table.hdf5-types
{
border-collapse: collapse;
margin: auto;
}
table.hdf5-types td
{
border: 1px solid black;
padding: 0.5em;
}
table.params
{
border-collapse: separate;
margin: 0;
width: 100%;
}
table.params td
{
border: none;
padding: 0 0.5em;
}
table.params th
{
font-weight: bold;
padding: 0 0 0 0.5em;
}
table.params td.type,
table.params td.name
{
font-family: "", "monospace";
}
</style>
</HEAD>
<body bgcolor="#FAFAFF" text="#000000"
BACKGROUND="../html_graphics/cbflibbackground.jpg">
<a href="http://www.iucr.org/iucr-top/welcome.html">
<img alt="[IUCr Home Page]" src="../html_graphics/iucrhome.jpg"></a>
<a href="http://www.iucr.org/iucr-top/cif/home.html">
<img alt="[CIF Home Page]" src="../html_graphics/cifhome.jpg"></a>
<A HREF="cbf_definition_rev.html"><IMG SRC="../html_graphics/CBFbutton.jpg"
ALT="[CBF/imgCIF]"></A>
<IMG SRC="../html_graphics/cbflibbutton.jpg">
<hr />
<CENTER>
| <a href="http://www.iucr.org/iucr-top/welcome.html">IUCr Home Page</a>
| <a href="http://www.iucr.org/iucr-top/cif/home.html">CIF Home Page</a>
| <A HREF="cbf_definition_rev.html">CBF/imgCIF</a>
| CBFlib
|<br />
| <A HREF = "CBFlib_NOTICES.html">NOTICE</A>
| <a href=gpl.txt>GPL</a>
| <a href=lgpl.txt>LGPL</a>
| <a href="cif_img_1.7.10.html">imgCIF dictionary</a>
|<br />
| <a href="http://arcib.dowling.edu/donation.shtml">Click Here to Make a Donation</a>
|<P>
<IMG SRC="../html_graphics/cbflibbig.jpg" ALT="">
</CENTER>
<font color="#0808A0">
<H2 ALIGN=CENTER>CBFlib</H2>
<CENTER>
<b>An API for CBF/imgCIF<br />
Crystallographic Binary Files with ASCII Support</b><br />
Version 0.9.8<BR />
3 April 2025<BR />/
<p>
</CENTER>
</font><font color="#000000">
<p>
<CENTER>
by<br />
Paul J. Ellis<br />
Stanford Synchrotron Radiation Laboratory<br />
<p>
and<br />
Herbert J. Bernstein<br />
Information Systems Consultant<br />
<script language="javascript" type="text/javascript">
<!--
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var domain = "bnl";
var domext = ".gov";
document.write ("<a href=\"mailto:" + name + domain + domext + "\">" + name + " <b>at</b> " + domain + " <b>dot</b> "+ domext+"</a>");
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</script>
<noscript>
hbernstein <b>at</b> bnl <b>dot</b> gov
</noscript>
<p>
© Copyright 2006, 2007, 2008, 2011, 2013, 2014, 2025 Herbert J. Bernstein
<P>
<hr />
<b>YOU MAY REDISTRIBUTE THE CBFLIB PACKAGE UNDER THE TERMS OF THE <a href=gpl.txt>GPL</a>.
<P>
ALTERNATIVELY YOU MAY REDISTRIBUTE THE CBFLIB API UNDER THE TERMS
OF THE <a href=lgpl.txt>LGPL<a/>.</b>
</CENTER>
<p>
<hr />
<H3 ALIGN=CENTER>
Before using this software, please read the <br />
<A HREF = "CBFlib_NOTICES.html"> <IMG SRC="../html_graphics/noticeButton.jpg" ALT="NOTICE"></A><br />
for important disclaimers and the IUCr Policy
on the Use of the Crystallographic Information File (CIF) and for other important
information.
</h3>
<P>
Work on imgCIF and CBFlib currentlysupported in part by the
the National Institutes of Health under grant R24-GM154040-01
and in the past by U. S. Department of Energy (DOE) under
grants ER63601-1021466-0009501 and ER64212-1027708-0011962,
by the U. S. National Science Foundation (NSF) under grants
DBI-0610407, DBI-0315281 and EF-0312612, the U. S. National
Institutes of Health (NIH) under grants 1R15GM078077 from
NIGMS and 1R13RR023192 from NCRR and funding from the International
Union for Crystallographyn (IUCr). The content is solely the
responsibility of the authors and does not necessarily represent the
official views of DOE, NSF, NIH, NIGMS, NCRR or IUCr.
Recent work on integration among CBF, HDF5 and NeXus supported in part
by Pandata ODI (EU 7th Framework Programme)
<p>
<hr />
</font><font color="#0808A0">
<h2 ALIGN=CENTER>Version History</H2>
</font><font color="#000000">
<p>
<TABLE>
<tr><th align="left">Version
<th align="left">Date<th align="left">By<th align="left">Description
<tr>
<td valign="top"> 0.1<td valign="top"> Apr. 1998
<td valign="top"> PJE
<td> This was the
first CBFlib release. It
supported binary CBF files using binary strings.
<tr>
<td valign="top"> <a href="ChangeLog.html#0.2">0.2</a>
<td valign="top"> Aug. 1998
<td valign="top"> HJB<td> This release
added ascii imgCIF support using MIME-encoded binary sections, added
the option of MIME headers for the binary strings was well. MIME code
adapted from mpack 1.5. Added hooks needed for DDL1-style names without
categories.
<tr>
<td valign="top"> <a href="ChangeLog.html#0.3">0.3</a>
<td valign="top"> Sep. 1998
<td valign="top"> PJE<td> This release
cleaned up the changes made for version 0.2, allowing multi-threaded use of
the code, and removing dependence on the mpack package.
<tr>
<td valign="top"> <a href="ChangeLog.html#0.4">0.4</a>
<td valign="top"> Nov. 1998
<td valign="top"> HJB
<td> This release
merged much of the message digest code into the general file reading and
writing to reduce the number of passes. More consistency checking between
the MIME header and the binary header was introduced. The size in the
MIME header was adjusted to agree with the version 0.2 documentation.
<tr>
<td valign="top"> <a href="ChangeLog.html#0.5">0.5</a>
<td valign="top"> Dec. 1998
<td valign="top"> PJE<td> This release
greatly increased the speed of processing by allowing for deferred digest
evaluation.
<tr>
<td valign="top"> <a href="ChangeLog.html#0.6">0.6</a>
<td valign="top"> Jan. 1999
<td valign="top"> HJB
<td> This release
removed the redundant information (binary id, size, compression id)
from a binary header when there is a MIME header, removed the unused
repeat argument, and made the memory allocation for buffering and
tables with many rows sensitive to the current memory allocation already used.
<tr>
<td valign="top"> <a href="ChangeLog.html#0.6.1">0.6.1</a>
<td valign="top"> Feb. 2001
<td valign="top"> HP (per HJB)
<td> This release
fixed a memory leak due to misallocation by size of cbf_handle instead of cbf_handle_struct
<tr>
<td valign="top"> <a href="ChangeLog.html#0.7">0.7</a>
<td valign="top"> Mar. 2001
<td valign="top"> PJE
<td> This release
added high-level instructions based on the imgCIF dictionary
version 1.1.
<tr>
<td valign="top"> <a href="ChangeLog.html#0.7.1">0.7.1</a>
<td valign="top"> Mar. 2001
<td valign="top"> PJE
<td> The high-level functions were revised to permit future expansion to
files with multiple images.
<tr>
<td valign="top"> <a href="ChangeLog.html#0.7.2">0.7.2</a>
<td valign="top"> Apr. 2001
<td valign="top"> HJB
<td> This release
adjusted cbf_cimple.c to conform to cif_img.dic version 1.1.3
<tr>
<td valign="top"> <a href="ChangeLog.html#0.7.2.1">0.7.2.1</a>
<td valign="top"> May 2001
<td valign="top"> PJE
<td> This release
corrected an if nesting error in the prior mod to cbf_cimple.c.
<tr>
<td valign="top"> <a href="ChangeLog.html#0.7.3">0.7.3</a>
<td valign="top"> Oct. 2002
<td valign="top"> PJE
<td> This release
modified cbf_simple.c to reorder image data on read so that the
indices are always increasing in memory (this behavior was
undefined previously).
<tr>
<td valign="top"> <a href="ChangeLog.html#0.7.4">0.7.4</a>
<td valign="top"> Jan 2004
<td valign="top"> HJB
<td> This release fixes a parse error for
quoted strings, adds code to get and set character string types, and removes compiler warnings
<tr>
<td valign="top"> <a href="ChangeLog.html#0.7.5">0.7.5</a>
<td valign="top"> Apr 2006
<td valign="top"> HJB
<td> This release cleans up some
compiler warnings, corrects a parse error on quoted strings with
a leading blank as adds the new routines for support of
aliases, dictionaries and real arrays, higher level routines
to get and set pixel sizes, do cell computations, and to set beam centers,
improves support for conversion of images, picking up more data from
headers.
<tr>
<td valign="top"> <a href="ChangeLog.html#0.7.6">0.7.6</a>
<td valign="top"> Jul 2006
<td valign="top"> HJB
<td> This release reorganizes the kit
into two pieces: CBFlib_0.7.6_Data_Files and CBFlib_0.7.6. An optional local copy
of getopt is added. The 1.4 draft dictionary has been added. cif2cbf
updated to support vcif2 validation. convert_image and cif2cbf updated
to report text of error messages. convert_image updated to support
tag and category aliases, default to adxv images. convert_image and
img updated to support row-major images. Support added for binning.
API Support added for validation, wide files and line folding.
Logic changed for beam center reporting. Added new routines:
cbf_validate,
cbf_get_bin_sizes,
cbf_set_bin_sizes,
cbf_find_last_typed_child,
cbf_compose_itemname,
cbf_set_cbf_logfile,
cbf_make_widefile,
cbf_read_anyfile,
cbf_read_widefile,
cbf_write_local_file,
cbf_write_widefile,
cbf_column_number,
cbf_blockitem_number,
cbf_log,
cbf_check_category_tags,
cbf_set_beam_center
<tr>
<td valign="top"> <a href="ChangeLog.html#0.7.7">0.7.7</a>
<td valign="top"> February 2007
<td valign="top"> HJB
<td> This release reflects changes
for base 32K support developed by G. Darakev, and changes
for support of reals, 3d arrays, byte_offset compression and
J. P. Abrahams packed compression
made in consultation with (in alphabetic order) E. Eikenberry,
A. Hammerley, W. Kabsch, M. Kobas, J. Wright and others at PSI
and ESRF in January 2007, as well accumulated changes fixing
problems in release 0.7.6.
<tr>
<td valign="top"> <a href="ChangeLog.html#0.7.7.1">0.7.7.1</a>
<td valign="top"> February 2007
<td valign="top"> HJB
<td> This release is a patch
to 0.7.7 to change the treatment of the byteorder parameter from
strcpy semantics to return of a pointer to a string constant.
Our thanks to E. Eikenberry for pointing out the problem.
<tr>
<td valign="top"> <a href="ChangeLog.html#0.7.7.2">0.7.7.2</a>
<td valign="top"> February 2007
<td valign="top"> HJB
<td> This release is a patch
to 0.7.7.1 to add testing for JPA packed compression and to respect
signs declared in the MIME header.
<tr>
<td valign="top"> <a href="ChangeLog.html#0.7.7.3">0.7.7.3</a>
<td valign="top"> April 2007
<td valign="top"> HJB
<td> This release is a patch
to 0.7.7.3 to add f90 support for reading of CBF byte-offset and
packed compression, to fix problems with gcc 4.4.1 and to correct
errors in multidimensional packed compression.
<tr>
<td valign="top"> <a href="ChangeLog.html#0.7.7.4">0.7.7.4</a>
<td valign="top"> May 2007
<td valign="top"> HJB
<td> Corrects in handling SLS
detector mincbfs and reorder dimensions versus arrays for some
f90 compilers as per H. Powell.
<tr>
<td valign="top"> <a href="ChangeLog.html#0.7.7.5">0.7.7.5</a>
<td valign="top"> May 2007
<td valign="top"> HJB
<td> Fix to cbf_get_image for bug
reported by F. Remacle, fixes for windows builds as per J. Wright
and F. Remacle.
<tr>
<td valign="top"> <a href="ChangeLog.html#0.7.7.6">0.7.7.6</a>
<td valign="top"> Jun 2007
<td valign="top"> HJB
<td> Fix to CBF byte-offset compression
writes, fix to Makefiles and m4 for f90 test programs to allow adjustable
record length.
<tr>
<td valign="top"> <a href="ChangeLog.html#0.7.8">0.7.8</a>
<td valign="top"> Jul 2007
<td valign="top"> HJB<td> Release for full support of
SLS data files with updated convert_minicbf, and support for gfortran
from gcc 4.2.
<tr>
<td valign="top"> <a href="ChangeLog.html#0.7.8.1">0.7.8.1</a><td
valign="top"> Jul 2007<td
valign="top"> HJB<td> Update to 0.7.8 release to fix
memory leaks reported by N. Sauter and to update validation checks
for recent changes.
<tr>
<td valign="top"> <a href="ChangeLog.html#0.7.8.2">0.7.8.2</a><td
valign="top"> Dec 2007<td
valign="top"> CN, HJB<td> Update to 0.7.8.1 to add
ADSC jiffie by Chris Nielsen, and to add ..._fs and ..._sf macros.
<tr>
<td valign="top"> <a href="ChangeLog.html#0.7.9">0.7.9</a><td
valign="top"> Dec 2007<td
valign="top"> CN, HJB<td>Identical to 0.7.8.2 except for
a cleanup of deprecated examples, e.g. diffrn_frame_data
<tr>
<td valign="top"> <a href="ChangeLog.html#0.7.9.1">0.7.9.1</a><td
valign="top"> Jan 2008<td
valign="top"> CN, HJB<td> Update to 0.7.8.2 to add
inverse ADSC jiffie by Chris Nielsen, to clean up problems in
handling maps for RasMol.
<tr>
<td valign="top"> <a href="ChangeLog.html#0.8.0">0.8.0</a><td
valign="top"> Jul 2008<td
valign="top"> GT, HJB<td> Cleanup of 0.7.9.1 to start
0.8 series.
<tr>
<td valign="top"> <a href="ChangeLog.html#0.8.1">0.8.1</a>
<td valign="top"> Jul 2009
<td valign="top"> EZ, CN, PC, GW, JH, HJB
<td>
Release with EZ's 2008 DDLm support using JH's PyCifRW, also
cbff f95 wrapper code, PC's java bindings.
<tr>
<td valign="top"> <a href="ChangeLog.html#0.9.1">0.9.1</a><td
valign="top"> Aug 2010<td
valign="top"> PC, EE, JLM, NS, EZ, HJB<td>
Release with EE's Dectris template software,
also with vcif3, new arvai_test, sequence_match.
<tr>
<td valign="top"> <a href="ChangeLog.html#0.9.2">0.9.2</a></td>
<td valign="top"> Feb 2011</td>
<td valign="top"> PC, EE, JLM, NS, EZ, HJB<td>
New default release with updated pycbf, tiff support, removal of
default use of PyCifRW to avoid Fedora license issue.</td>
</tr>
<tr>
<td valign="top"> <a href="ChangeLog.html#0.9.3">0.9.3</a></td>
<td valign="top"> Oct 2013</td>
<td valign="top"> JS, HJB</td>
<td> Added low-level 'cbf_H5*' functions for interacting with HDF5, higher level functions for converting CBF or miniCBF files to NeXus format, two utility programs to convert CBF or miniCBF files to NeXus format and some unit tests for the low-level 'cbf_H5*' functions. Add initial FEL detector support.</td>
</tr>
<tr>
<td valign="top"> <a href="ChangeLog.html#0.9.4">0.9.4</a></td>
<td valign="top"> March 2014</td>
<td valign="top"> JS, HJB</td>
<td> Refactored implementation of the NXMX application defintion
functional mapping with improvements to cmake support and a preliminary
effort at handling Stokes polarization mapping. This release had serious
issues in the functional mapping axis mapping and should not be used for
production involving NeXus files.
</td>
</tr>
<tr>
<td valign="top"> <a href="ChangeLog.html#0.9.5">0.9.5</a></td>
<td valign="top"> April 2014</td>
<td valign="top"> HJB</td>
<td> This is a production release for single detector module
single crystal MX NeXus support.
</td>
</tr>
<tr>
<td valign="top"> <a href="ChangeLog.html#0.9.6">0.9.6</a></td>
<td valign="top"> May 2020</td>
<td valign="top"> HJB</td>
<td> This is the full release supporting the integration of CBF
and NeXus, including support for the NeXus NXpdb embedding of CIF files in
NeXus files. *** IMPORTANT: Because of the requirements of dynamic loading
to support the compressions used by the Dectris NeXus/HDF5 format, all
applications require setting of library and plugin paths. See the
initialization file cbflib.ini, which should be sourced before running any
applications ***..
The changes from 0.9.5 to 0.9.6 are:
<br />improve error reporting in examples/cbf2nexus.c
<br />improve examples/cbf_standardize_numbers.c
<br />add bslz4 compression option to hdf5 in cif2cbf
<br />minor cleanup in examples/convert_minicbf.c
<br />minor cleanup in examples/nexus2cbf.c
<br />minor cleanup in examples/sequence_match.c
<br />minor cleanup in include/cbf_context.h
<br />add value clipping to cbf_copy
<br />minor cleanuo in cbf_hdf5.h
</td>
</tr>
<tr>
<td valign="top"> <a href="ChangeLog.html#0.9.7">0.9.7</a></td>
<td valign="top"> June 2021</td>
<td valign="top"> HJB</td>
<td> This is a production release with misc minor updates. The changes
from 0.9.6 to 0.9.7 are:
<br />update the manual
<br />cleanup minor bugs is examples/adscimg2cbf.c, adscimg2cbf_sub.c, cbf2adscimg_sub.c
<br />fix examples/cbf_standardize_numbers.c
<br />fix examples/testcbf.c
<br />fix examples/testcbf.java
<br />fix examples/testhdf5.c
<br />fix include/cbf_hdf5.h
<br />fix include/img.h
<br />fix Java.txt
<br />fix handling of hex to be int in fcblib_defines, fcb_next_binary, fcb_packed, fcb_read_bits,
fcb_read_xds_i2
<br />fix pycbf/cbf_autoscrolled_window.py, cbf_axis_text.py, various wrappers, bytestrings in tests,
xmas/readmarheader.py, xmasheaders.py
<br />fix cbf.c
<br />fix cbf_context.c, cbf_copy.c, cbf_hdf5.c, cbf_hdf5_filter.c, cbf_simple.c, cbf_stx.c
<br />fix fcb_atol_wcnt.f90, fcb_nblen_array.f90, fcb_read_line.f90, fcb_skip_whitespace.f90
<br />fix img.c
</td>
</tr>
<tr>
<td valign="top"> <a href="ChangeLog.html#0.9.8">0.9.8</a></td>
<td valign="top"> April 2025</td>
<td valign="top"> DP, JH, ND, HJB</td>
<td> This is a final CBFlib release prior to moving all future
development under the auspices of the DIALS project. In the past the main
repository for CBFlib was at
<a http://github.com/yayahjb/cbflib target="_blank">http://github.com/yayahjb/cbflib</a>.
In the future tha main repository for CBFlib will be at
<a http://github.com/dials/cbflib target="_blank">http://github.com/dials/cbflib</a>.
For the convenience of users of legacy versions of CBFlib, there will be
legacy fork of the repository frozen at the 0.9.8 revision level
<a http://github.com/nsls-ii-mx/cbflib target="_blank">http://github.com/nsls-ii-mx/cbflib</a>
The changes from 0.9.7 to 0.9.8 are:
<br />in cif2cbf add -I-1, -I-2, -I-4, and -I-8 options for unsigned integers,
--{sum|summing} sumrange option to sum images,
and --xdsb2z|rotate-xds-beam-to-z beamcentx,beamcenty,beamcentz
assume the beam is along [beamx, beamy, beamz] relative to the
image and rotate the image so that the beam is along [0,0,-1]
<br />split support for languages other than C/C++ to use the 2022 swig-fortran kit
for fortran and a recent swig kit for python
<br />update tiff2cbf for multiple compression options
<br />update cbf_copy options and fix typos
<br />drop all support for python2 in favor of python3
<br />fix buffer overruns in examples/dectris_cbf_template_test/cbf_template_t.c
<br />fix errors in examples/testcbf.java
<br />add zstd compression option for hdf5 files
<br />update fcblib_defines
<br />update pycbf wrappers
<br />fix buffer overflow in cbf_binary.c
<br />fix parens in cbf_codes.c
<br />fix bug in cbf_nibble_offset.c
<br />fix tab definition in fcb_skip_whitespace.f90
<br />preliminary changes for move from make to cmake by J. Hattne
<br />add third dimension in examples/img2cif.c, examples/makecbf.c, examples/nexus2cbf.c
<br />fix bugs in examples/tiff2cbf.c examples/tif_sprint.c
<br />make handling of version number changes in tests data general
<br />fix typoi in test_cbf_airy_disk call
<br />fix bug in pycbf_test1.py
<br />fix regex dependency handling in cbf_hdf5.c
</td>
</tr>
</TABLE>
<hr />
</font><font color="#0808A0">
<h2 ALIGN=CENTER>Known Problems</H2>
<h2 ALIGN=CENTER>Foreword</H2>
</font><font color="#000000">
<p>
In order to work with CBFlib, you need:
the source code from github by downloadng a release or the lastest code
from
<a href="http://github.com/dials/cbflib" target="_blank">http://github.com/dials/cbflib</a>
</ul>
<P>
<P>
<b>Be careful about space. A full build and test can use 2GB or more.
</b>
<P>
<p>
To run the test programs, you will also need
Paul Ellis's sample MAR345 image,
example.mar2300,
Chris Nielsen's sample ADSC Quantum 315 image,
mb_LP_1_001.img, and Eric Eikenberry's SLS sample Pilatus 6m image,
insulin_pilatus6m, as sample data. In addition there are
is a PDB mmCIF file, 9ins.cif, and 3 special test files
testflatin.cbf, testflatpackedin.cbf and testrealin.cbf.
All these files will be
dowloaded and extracted by the Makefile from CBFlib_0.9.8_Data_Files_Input. Do
not download copies into the top level directory.
<P>
In addition, the kit will need tiff and hdf5 libraries.
<p>
Future versions of CBFlib will use the cmake build system. Version 0.9.8 is
the last Makefile build,
<p>
<B>The Makefiles use GNU make constructs, such as ifeq
and ifneq. If you need to use a different version of
make, you will need to edit out the conditionals</b>
<p>
The operation of the Makefiles is sensitive to the
following environment variables:
<p>
<ul>
<li><b>CBFLIB_USE_PYCIFRW</b> If you define this environment variable,
you may rebuild the Makefiles to include James Hester's PyCifRW. The
process under bash is:<p>
<pre>
export CBFLIB_USE_PYCIFRW=yes
cd CBFlib_0.9.5
touch m4/Makefile.m4
make Makefiles
</pre>
</li>
<li><b>CBF_DONT_USE_LONG_LONG</b> If you define this environment variable,
use of the <tt>long long</tt> data type in CBFlib is replaced by
use of a struct. The Makefiles do not need to be rebuilt. Makefile_MINGW
does not use the <tt>long long</tt> data type even without defining
this variable.
</li>
<li><b>NOFORTRAN</b> If you define this environment variable,
use of the fortran compiler is suppressed.
</li>
</ul>
<p>
If necessary, adjust the definition of CC and C++ and
other defintions in
Makefile to point to your compilers.
Set the definition of CFLAGS to an appropriate value
for your C and C++ compilers,
the definition of F90C to point to your
Fortan-90/95 compiler, and the definitions of
F90FLAGS and F90LDFLAGS to approriate values
for your Fortan-90/95 compilers, and then
<p>
<b>make all</b><br />
<b>make tests</b>
<P>
If you do not have a fortran compiler, you will need
edit the Makefile or to define the variable NOFORTRAN, either in the Makefile
or in the environment
<P>
<p>
We have included examples of
CBF/imgCIF files produced by CBFlib in the test data
<A HREF="http://downloads.sf.net/cbflib/CBFlib_0.9.5_Data_Files_Output.tar.gz">CBFlib_0.9.5_Data_Files_Output.tar.gz</a>,
the current best draft of
the
<A HREF="cif_img_1.7.10.html">CBF Extensions Dictionary</A>,
and of Andy Hammersley's CBF definition, updated to become a
<A HREF="cbf_definition_rev.html">
DRAFT CBF/ImgCIF DEFINITION</A>.
<p>
CBFlib 0.9.5 includes a program, tiff2cbf, to convert from tiff files
to CBF files, that requires an augmented version of tiff-3.9.4 called
tiff-3.9.4-rev-6Feb11, that installs into the CBFlib_0.9.2.11 directory.
If a system copy is desired, download and install
<a href="http://downloads.sf.net/cbflib/tiff-3.9.4-rev-6Feb11.tar.gz">
http://downloads.sf.net/cbflib/tiff-3.9.4-rev-6Feb11.tar.gz</a>
<hr />
</font><font color="#0808A0">
<H2 ALIGN=CENTER>Contents</H2>
</font><font color="#000000">
<p>
<UL>
<LI><A HREF="#1. Introduction">1. Introduction</A>
<LI><A HREF="#2.">2. Function descriptions</A>
<UL>
<LI><A HREF="#2.1">2.1 General description</A>
<UL>
<LI><A HREF="#2.1.1">2.1.1 CBF handles</A>
<LI><A HREF="#2.1.2">2.1.2 CBF goniometer handles</A>
<LI><A HREF="#2.1.3">2.1.3 CBF detector handles</A>
<LI><A HREF="#2.1.4">2.1.4 CBF positioner handles</A>
<LI><A HREF="#2.1.5">2.1.5 Return values</A>
</UL>
<LI><A HREF="#2.2">2.2 Reading and writing files containing binary sections</A>
<UL>
<LI><A HREF="#2.2.1">2.2.1 Reading binary sections</A>
<LI><A HREF="#2.2.2">2.2.2 Writing binary sections</A>
<LI><A HREF="#2.2.3">2.2.3 Summary of reading and writing files containing binary sections</A>
<LI><A HREF="#2.2.4">2.2.4 Ordering of array indices</A>
</UL>
<LI><A HREF="#2.3">2.3 Low-level function prototypes</A>
<UL>
<LI><A HREF="#2.3.1">2.3.1 cbf_make_handle</A>
<LI><A HREF="#2.3.2">2.3.2 cbf_free_handle</A>
<LI><A HREF="#2.3.3">2.3.3 cbf_read_file, cbf_read_widefile</A>
<LI><a href="#2.3.4">2.3.4 cbf_write_file, cbf_write_widefile</a>
<LI><A HREF="#2.3.5">2.3.5 cbf_new_datablock, cbf_new_saveframe</A>
<LI><A HREF="#2.3.6">2.3.6 cbf_force_new_datablock, cbf_force_new_saveframe</A>
<LI><A HREF="#2.3.7">2.3.7 cbf_new_category</A>
<LI><A HREF="#2.3.8">2.3.8 cbf_force_new_category</A>
<LI><A HREF="#2.3.9">2.3.9 cbf_new_column</A>
<LI><A HREF="#2.3.10">2.3.10 cbf_new_row</A>
<LI><A HREF="#2.3.11">2.3.11 cbf_insert_row</A>
<LI><A HREF="#2.3.12">2.3.12 cbf_delete_row</A>
<LI><A HREF="#2.3.13">2.3.13 cbf_set_datablockname, cbf_set_saveframename</A>
<LI><A HREF="#2.3.14">2.3.14 cbf_reset_datablocks</A>
<LI><A HREF="#2.3.15">2.3.15 cbf_reset_datablock, cbf_reset_saveframe</A>
<LI><A HREF="#2.3.16">2.3.16 cbf_reset_category</A>
<LI><A HREF="#2.3.17">2.3.17 cbf_remove_datablock, cbf_remove_saveframe</A>
<LI><A HREF="#2.3.18">2.3.18 cbf_remove_category</A>
<LI><A HREF="#2.3.19">2.3.19 cbf_remove_column</A>
<LI><A HREF="#2.3.20">2.3.20 cbf_remove_row</A>
<LI><A HREF="#2.3.21">2.3.21 cbf_rewind_datablock</A>
<LI><A HREF="#2.3.22">2.3.22 cbf_rewind_category, cbf_rewind_saveframe, cbf_rewind_blockitem</A>
<LI><A HREF="#2.3.23">2.3.23 cbf_rewind_column</A>
<LI><A HREF="#2.3.24">2.3.24 cbf_rewind_row</A>
<LI><A HREF="#2.3.25">2.3.25 cbf_next_datablock</A>
<LI><A HREF="#2.3.26">2.3.26 cbf_next_category, cbf_next_saveframe, cbf_next_blockitem</A>
<LI><A HREF="#2.3.27">2.3.27 cbf_next_column</A>
<LI><A HREF="#2.3.28">2.3.28 cbf_next_row</A>
<LI><A HREF="#2.3.29">2.3.29 cbf_find_datablock</A>
<LI><A HREF="#2.3.30">2.3.30 cbf_find_category, cbf_find_saveframe, cbf_find_blockitem</A>
<LI><A HREF="#2.3.31">2.3.31 cbf_find_column</A>
<LI><A HREF="#2.3.32">2.3.32 cbf_find_row</A>
<LI><A HREF="#2.3.33">2.3.33 cbf_find_nextrow</A>
<LI><A HREF="#2.3.34">2.3.34 cbf_count_datablocks</A>
<LI><A HREF="#2.3.35">2.3.35 cbf_count_categories, cbf_count_saveframes, cbf_count_blockitems</A>
<LI><A HREF="#2.3.36">2.3.36 cbf_count_columns</A>
<LI><A HREF="#2.3.37">2.3.37 cbf_count_rows</A>
<LI><A HREF="#2.3.38">2.3.38 cbf_select_datablock</A>
<LI><A HREF="#2.3.39">2.3.39 cbf_select_category, cbf_select_saveframe, cbf_select_blockitem</A>
<LI><A HREF="#2.3.40">2.3.40 cbf_select_column</A>
<LI><A HREF="#2.3.41">2.3.41 cbf_select_row</A>
<LI><A HREF="#2.3.42">2.3.42 cbf_datablock_name</A>
<LI><A HREF="#2.3.43">2.3.43 cbf_category_name</A>
<LI><A HREF="#2.3.44">2.3.44 cbf_column_name, cbf_set_column_name</A>
<LI><A HREF="#2.3.45">2.3.45 cbf_row_number</A>
<LI><A HREF="#2.3.46">2.3.46 cbf_get_value, cbf_require_value</A>
<LI><A HREF="#2.3.47">2.3.47 cbf_set_value</A>
<LI><A HREF="#2.3.48">2.3.48 cbf_get_typeofvalue</A>
<LI><A HREF="#2.3.49">2.3.49 cbf_set_typeofvalue</A>
<LI><A HREF="#2.3.50">2.3.50 cbf_get_integervalue, cbf_require_integervalue</A>
<LI><A HREF="#2.3.51">2.3.51 cbf_set_integervalue</A>
<LI><A HREF="#2.3.52">2.3.52 cbf_get_doublevalue, cbf_require_doublevalue</A>
<LI><A HREF="#2.3.53">2.3.53 cbf_set_doublevalue</A>
<LI><A HREF="#2.3.54">2.3.54 cbf_get_integerarrayparameters,</a><br />
<A HREF="#2.3.54">cbf_get_integerarrayparameters_wdims, cbf_get_integerarrayparameters_wdims_fs, cbf_get_integerarrayparameters_wdims_sf</a><br />
<A HREF="#2.3.54">cbf_get_realarrayparameters,</a><br />
<A HREF="#2.3.54">cbf_get_realarrayparameters_wdims, cbf_get_realarrayparameters_wdims_fs, cbf_get_realarrayparameters_wdims_sf</A>
<LI><A HREF="#2.3.55">2.3.55 cbf_get_integerarray, cbf_get_realarray</A>
<LI><A HREF="#2.3.56">2.3.56 cbf_set_integerarray,</a><br />
<A HREF="#2.3.56">cbf_set_integerarray_wdims, cbf_set_integerarray_wdims_fs, cbf_set_integerarray_wdims_sf,</a><br />
<A HREF="#2.3.56">cbf_set_realarray,</a><br />
<A HREF="#2.3.56">cbf_set_realarray_wdims, cbf_set_realarray_wdims_fs, cbf_set_realarray_wdims_sf</A>
<LI><A HREF="#2.3.57">2.3.57 cbf_failnez</A>
<LI><A HREF="#2.3.58">2.3.58 cbf_onfailnez</A>
<LI><A HREF="#2.3.59">2.3.59 cbf_require_datablock</A>
<LI><A HREF="#2.3.60">2.3.60 cbf_require_category</A>
<LI><A HREF="#2.3.61">2.3.61 cbf_require_column</A>
<LI><A HREF="#2.3.62">2.3.62 cbf_require_column_value</A>
<LI><A HREF="#2.3.63">2.3.63 cbf_require_column_integervalue</A>
<LI><A HREF="#2.3.64">2.3.64 cbf_require_column_doublevalue</A>
<LI><A HREF="#2.3.65">2.3.65 cbf_get_local_integer_byte_order,
cbf_get_local_real_byte_order, cbf_get_local_real_format</A>
<LI><A HREF="#2.3.66">2.3.66 cbf_get_dictionary, cbf_set_dictionary, cbf_require_dictionary</A>
<LI><A HREF="#2.3.67">2.3.67 cbf_convert_dictionary</A>
<LI><A HREF="#2.3.68">2.3.68 cbf_find_tag, cbf_find_local_tag</A>
<LI><A HREF="#2.3.69">2.3.69 cbf_find_category_root, cbf_set_category_root, cbf_require_category_root</A>
<LI><A HREF="#2.3.70">2.3.70 cbf_find_tag_root, cbf_set_tag_root, cbf_require_tag_root</A>
<LI><A HREF="#2.3.71">2.3.71 cbf_find_tag_category, cbf_set_tag_category</A>
</UL>
<LI><A HREF="#2.4">2.4 High-level function prototypes (new for version 0.7)</a>
<UL>
<LI><A HREF="#2.4.1">2.4.1 cbf_read_template</a>
<LI><A HREF="#2.4.2">2.4.2 cbf_get_diffrn_id, cbf_require_diffrn_id</a>
<LI><A HREF="#2.4.3">2.4.3 cbf_set_diffrn_id</a>
<LI><A HREF="#2.4.4">2.4.4 cbf_get_crystal_id</a>
<LI><A HREF="#2.4.5">2.4.5 cbf_set_crystal_id</a>
<LI><A HREF="#2.4.6">2.4.6 cbf_get_wavelength</a>
<LI><A HREF="#2.4.7">2.4.7 cbf_set_wavelength</a>
<LI><A HREF="#2.4.8">2.4.8 cbf_get_polarization</a>
<LI><A HREF="#2.4.9">2.4.9 cbf_set_polarization</a>
<LI><A HREF="#2.4.10">2.4.10 cbf_get_divergence</a>
<LI><A HREF="#2.4.11">2.4.11 cbf_set_divergence</a>
<LI><A HREF="#2.4.12">2.4.12 cbf_count_elements</a>
<LI><A HREF="#2.4.13">2.4.13 cbf_get_element_number, cbf_get_element_id</a>
<LI><A HREF="#2.4.14">2.4.14 cbf_get_gain</a>
<LI><A HREF="#2.4.15">2.4.15 cbf_set_gain</a>
<LI><A HREF="#2.4.16">2.4.16 cbf_get_overload</a>
<LI><A HREF="#2.4.17">2.4.17 cbf_set_overload</a>
<LI><A HREF="#2.4.18">2.4.18 cbf_get_integration_time</a>
<LI><A HREF="#2.4.19">2.4.19 cbf_set_integration_time</a>
<LI><A HREF="#2.4.20">2.4.20 cbf_get_time</a>
<LI><A HREF="#2.4.21">2.4.21 cbf_set_time</a>
<LI><A HREF="#2.4.22">2.4.22 cbf_get_date</a>
<LI><A HREF="#2.4.23">2.4.23 cbf_set_date</a>
<LI><A HREF="#2.4.24">2.4.24 cbf_set_current_time</a>
<LI><a HREF="#2.4.25">2.4.25 cbf_get_image_size, cbf_get_image_size_fs, cbf_get_image_size_fs,</a><br />
<A HREF="#2.4.25">cbf_get_3d_image_size, cbf_get_3d_image_size_fs, cbf_get_3d_image_size_sf</a>
<LI><A HREF="#2.4.26">2.4.26 cbf_get_image, cbf_get_image_fs, cbf_get_image_sf,</a><br />
<A HREF="#2.4.26">cbf_get_real_image, cbf_get_real_image_fs, cbf_get_real_image_sf,</a><br />
<A HREF="#2.4.26">cbf_get_3d_image, cbf_get_3d_image_fs, cbf_get_3d_image_sf,</a><br />
<A HREF="#2.4.26">cbf_get_real_3d_image, cbf_get_real_3d_image_fs, cbf_get_real_3d_image_sf</a>
<LI><A HREF="#2.4.27">2.4.27 cbf_set_image, cbf_set_image_fs, cbf_set_image_sf,</a><br />
<A HREF="#2.4.27">cbf_set_real_image, cbf_set_real_image_fs, cbf_set_real_image_sf,</a><br />
<A HREF="#2.4.27">cbf_set_3d_image, cbf_set_3d_image, cbf_set_3d_image,</a><br >
<A HREF="#2.4.27">cbf_set_real_3d_image, cbf_set_real_3d_image_fs, cbf_set_real_3d_image_sf</a>
<LI><A HREF="#2.4.28">2.4.28 cbf_get_axis_ancestor,
cbf_get_axis_depends_on,
cbf_get_axis_equipment,
cbf_get_axis_equipment_component,
cbf_get_axis_offset,
cbf_get_axis_rotation,
cbf_get_axis_rotation_axis,
cbf_get_axis_setting,
cbf_get_axis_type,
cbf_get_axis_vector</a>
<LI><A HREF="#2.4.29">2.4.29 cbf_set_axis_setting</a>
<LI><A HREF="#2.4.30">2.4.30 cbf_construct_goniometer</a>
<LI><A HREF="#2.4.31">2.4.31 cbf_free_goniometer</a>
<LI><A HREF="#2.4.32">2.4.32 cbf_get_rotation_axis</a>
<LI><A HREF="#2.4.33">2.4.33 cbf_get_rotation_range</a>
<LI><A HREF="#2.4.34">2.4.34 cbf_rotate_vector</a>
<LI><A HREF="#2.4.35">2.4.35 cbf_get_reciprocal</a>
<LI><A HREF="#2.4.36">2.4.36 cbf_construct_detector, cbf_construct_reference_detector, cbf_require_reference_detector</a>
<LI><A HREF="#2.4.37">2.4.37 cbf_free_detector</a>
<LI><A HREF="#2.4.38">2.4.38 cbf_construct_positioner, cbf_construct_reference_positioner</a>
<LI><A HREF="#2.4.39">2.4.39 cbf_free_positioner</a>
<LI><A HREF="#2.4.40">2.4.40 cbf_get_beam_center, cbf_get_beam_center_fs, cbf_get_beam_center_sf,</a><br />
<A HREF="#2.4.40">cbf_set_beam_center, cbf_set_beam_center_fs, cbf_set_beam_center_sf,</a><br />
<A HREF="#2.4.40">cbf_set_reference_beam_center, cbf_set_reference_beam_center_fs, cbf_set_reference_beam_center_sf</a>
<LI><A HREF="#2.4.41">2.4.41 cbf_get_detector_distance</a>
<LI><A HREF="#2.4.42">2.4.42 cbf_get_detector_normal</a>
<LI><A HREF="#2.4.43">2.4.43 cbf_get_detector_axis_slow, cbf_get_detector_axis_fast, cbf_get_detector_axes, cbf_get_detector_axes_fs, cbf_get_detector_axes_sf,
cbf_get_detector_surface_axes
<LI><A HREF="#2.4.44">2.4.44 cbf_get_pixel_coordinates, cbf_get_pixel_coordinates_fs, cbf_get_pixel_coordinates_sf</a>
<LI><A HREF="#2.4.45">2.4.45 cbf_get_pixel_normal, cbf_get_pixel_normal_fs, cbf_get_pixel_normal_sf</a>
<LI><A HREF="#2.4.46">2.4.46 cbf_get_pixel_area, cbf_get_pixel_area_fs, cbf_get_pixel_area_sf</a>
<LI><A HREF="#2.4.47">2.4.47 cbf_get_pixel_size, cbf_get_pixel_size_fs, cbf_get_pixel_size_sf</a>
<LI><A HREF="#2.4.48">2.4.48 cbf_set_pixel_size, cbf_set_pixel_size_fs, cbf_set_pixel_size_sf</a>
<LI><A HREF="#2.4.49">2.4.49 cbf_get_inferred_pixel_size, cbf_get_inferred_pixel_size_fs, cbf_get_inferred_pixel_size_sf</a>
<LI><A HREF="#2.4.50">2.4.50 cbf_get_unit_cell</a>
<LI><A HREF="#2.4.51">2.4.51 cbf_set_unit_cell</a>
<LI><A HREF="#2.4.52">2.4.52 cbf_get_reciprocal_cell</a>
<LI><A HREF="#2.4.53">2.4.53 cbf_set_reciprocal_cell</a>
<LI><A HREF="#2.4.54">2.4.54 cbf_compute_cell_volume</a>
<LI><A HREF="#2.4.55">2.4.55 cbf_compute_reciprocal_cell</a>
<LI><A HREF="#2.4.56">2.4.56 cbf_get_orientation_matrix, cbf_set_orientation_matrix</a>
<LI><A HREF="#2.4.57">2.4.57 cbf_get_bin_sizes, cbf_set_bin_sizes</a>
<LI><A HREF="#2.4.58">2.4.58 cbf_get_axis_poise, cbf_get_goniometer_poise, cbf_get_axis_reference_poise</a>
<LI><A HREF="#2.4.59">2.4.59 cbf_airy_disk, cbf_airy_disk_volume</a>
</UL>
<LI><A HREF="#2.5">2.5 F90 function interfaces</A>
<UL>
<LI><A HREF="#2.5.1">2.5.1 FCB_ATOL_WCNT</a>
<LI><A HREF="#2.5.2">2.5.2 FCB_CI_STRNCMPARR</a>
<LI><A HREF="#2.5.3">2.5.3 FCB_EXIT_BINARY</a>
<LI><A HREF="#2.5.4">2.5.4 FCB_NBLEN_ARRAY</a>
<LI><A HREF="#2.5.5">2.5.5 FCB_NEXT_BINARY</a>
<LI><A HREF="#2.5.6">2.5.6 FCB_OPEN_CIFIN</a>
<LI><A HREF="#2.5.7">2.5.7 FCB_PACKED: FCB_DECOMPRESS_PACKED_I2, FCB_DECOMPRESS_PACKED_I4, FCB_DECOMPRESS_PACKED_3D_I2, FCB_DECOMPRESS_PACKED_3D_I4</a>
<LI><A HREF="#2.5.8">2.5.8 FCB_READ_BITS</a>
<LI><A HREF="#2.5.9">2.5.9 FCB_READ_BYTE</a>
<LI><A HREF="#2.5.10">2.5.10 FCB_READ_IMAGE_I2, FCB_READ_IMAGE_I4, FCB_READ_IMAGE_3D_I2, FCB_READ_IMAGE_3D_I4</a>
<LI><A HREF="#2.5.11">2.5.11 FCB_READ_LINE</a>
<LI><A HREF="#2.5.12">2.5.12 FCB_READ_XDS_I2</a>
<LI><A HREF="#2.5.13">2.5.13 FCB_SKIP_WHITESPACE</a>
</UL>
<li>
<a href="#2.6">2.6 HDF5 abstraction layer and convenience functions</a>
<ul>
<li>
<a href="#2.6.1">2.6.1 cbf_H5Acreate</a>
</li>
<li>
<a href="#2.6.2">2.6.2 cbf_H5Afind</a>
</li>
<li>
<a href="#2.6.3">2.6.3 cbf_H5Aread</a>
</li>
<li>
<a href="#2.6.4">2.6.4 cbf_H5Aread_string</a>
</li>
<li>
<a href="#2.6.5">2.6.5 cbf_H5Awrite</a>
</li>
<li>
<a href="#2.6.6">2.6.6 cbf_H5Arequire_cmp2</a>
</li>
<li>
<a href="#2.6.7">2.6.7 cbf_H5Arequire_cmp2_ULP</a>
</li>
<li>
<a href="#2.6.8">2.6.8 cbf_H5Arequire_string</a>
</li>
<li>
<a href="#2.6.9">2.6.9 cbf_H5Afree</a>
</li>
<li>
<a href="#2.6.10">2.6.10 cbf_H5Dcreate</a>
</li>
<li>
<a href="#2.6.11">2.6.11 cbf_H5Dfind2</a>
</li>
<li>
<a href="#2.6.12">2.6.12 cbf_H5Drequire</a>
</li>
<li>
<a href="#2.6.13">2.6.13 cbf_H5Dinsert</a>
</li>
<li>
<a href="#2.6.14">2.6.14 cbf_H5Dset_extent</a>
</li>
<li>
<a href="#2.6.15">2.6.15 cbf_H5Dwrite2</a>
</li>
<li>
<a href="#2.6.16">2.6.16 cbf_H5Dread2</a>
</li>
<li>
<a href="#2.6.17">2.6.17 cbf_H5Drequire_scalar_F64LE2</a>
</li>
<li>
<a href="#2.6.18">2.6.18 cbf_H5Drequire_scalar_F64LE2_ULP</a>
</li>
<li>
<a href="#2.6.19">2.6.19 cbf_H5Drequire_flstring</a>
</li>
<li>
<a href="#2.6.20">2.6.20 cbf_H5Dfree</a>
</li>
<li>
<a href="#2.6.21">2.6.21 cbf_H5Fopen</a>
</li>
<li>
<a href="#2.6.22">2.6.22 cbf_H5Fclose</a>
</li>
<li>
<a href="#2.6.23">2.6.23 cbf_H5Gcreate</a>
</li>
<li>
<a href="#2.6.24">2.6.24 cbf_H5Gfind</a>
</li>
<li>
<a href="#2.6.25">2.6.25 cbf_H5Grequire</a>
</li>
<li>
<a href="#2.6.26">2.6.26 cbf_H5Gfree</a>
</li>
<li>
<a href="#2.6.27">2.6.27 cbf_H5Ivalid</a>
</li>
<li>
<a href="#2.6.28">2.6.28 cbf_H5Ocmp</a>
</li>
<li>
<a href="#2.6.29">2.6.29 cbf_H5Ofree</a>
</li>
<li>
<a href="#2.6.30">2.6.30 cbf_H5Screate</a>
</li>
<li>
<a href="#2.6.31">2.6.31 cbf_H5Sfree</a>
</li>
<li>
<a href="#2.6.32">2.6.32 cbf_H5Tcreate_string</a>
</li>
<li>
<a href="#2.6.33">2.6.33 cbf_H5Tfree</a>
</li>
</ul>
</li>
<li>
<a href="#2.7">2.7 High-level NeXus-related functions</a>
<ul>
<li>
<a href="#2.7.1">2.7.1 cbf_h5handle_get_file</a>
</li>
<li>
<a href="#2.7.2">2.7.2 cbf_h5handle_set_file</a>
</li>
<li>
<a href="#2.7.3">2.7.3 cbf_h5handle_get_entry</a>
</li>
<li>
<a href="#2.7.4">2.7.4 cbf_h5handle_set_entry</a>
</li>
<li>
<a href="#2.7.5">2.7.5 cbf_h5handle_require_entry</a>
</li>
<li>
<a href="#2.7.6">2.7.6 cbf_h5handle_require_entry_definition</a>
</li>
<li>
<a href="#2.7.7">2.7.7 cbf_h5handle_get_sample</a>
</li>
<li>
<a href="#2.7.8">2.7.8 cbf_h5handle_set_sample</a>
</li>
<li>
<a href="#2.7.9">2.7.9 cbf_h5handle_require_sample</a>
</li>
<li>
<a href="#2.7.10">2.7.10 cbf_h5handle_get_beam</a>
</li>
<li>
<a href="#2.7.11">2.7.11 cbf_h5handle_set_beam</a>
</li>
<li>
<a href="#2.7.12">2.7.12 cbf_h5handle_require_beam</a>
</li>
<li>
<a href="#2.7.13">2.7.13 cbf_h5handle_get_instrument</a>
</li>
<li>
<a href="#2.7.14">2.7.14 cbf_h5handle_set_instrument</a>
</li>
<li>
<a href="#2.7.15">2.7.15 cbf_h5handle_find_instrument</a>
</li>