International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

International Tables for Crystallography (2006). Vol. G, ch. 2.3, p. 37

Section 2.3.1. Introduction

H. J. Bernsteina* and A. P. Hammersleyb

aDepartment of Mathematics and Computer Science, Kramer Science Center, Dowling College, Idle Hour Blvd, Oakdale, NY 11769, USA, and bESRF/EMBL Grenoble, 6 rue Jules Horowitz, France
Correspondence e-mail:  yaya@bernstein-plus-sons.com

2.3.1. Introduction

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The Crystallographic Binary File (CBF) format is a complementary format to the Crystallographic Information File (CIF) (Hall et al., 1991[link]) supporting efficient storage of large quantities of experimental data in a self-describing binary format. The image-supporting Crystallographic Information File (imgCIF) is an extension to CIF to assist in ASCII debugging and archiving of CBF files and to allow for convenient and standardized inclusion of images, such as maps, diagrams and molecular drawings, into CIFs for publication. The binary CBF format is useful for handling large images within laboratories and for interchange among collaborating groups. For smaller blocks of binary data, either format should be suitable. The ASCII imgCIF format is appropriate for interchange of smaller images and for long-term archiving.

CBF is designed to support efficient storage of raw experimental data (images) from area detectors with no loss of information, unlike some existing formats intended for this purpose. The format enables very efficient reading and writing of raw data, and encourages economical use of disk space. It may be coded easily and is portable across platforms. It is also flexible and extensible so that new data structures can be added without affecting the present definitions.

These goals are achieved by a simple file format, combining a CIF-like file header with compressed binary information. The file header consists of ASCII text giving information about the binary data as CIF tag–value pairs and tables. Each binary image is presented as a text-field value, either as raw octets of binary data in a CBF data set, or as an ASCII-based encoding of the same binary information in a true ASCII imgCIF data set. The ASCII-based encoded format uses e-mail MIME (Multipurpose Internet Mail Extensions) conventions to encode the binary data (Freed & Borenstein, 1996a[link],b[link],c[link]; Freed et al., 1996[link]; Moore, 1996[link]). The present version of the format tries to deal only with simple Cartesian data. These are essentially the `raw' diffraction data that typically are stored in commercial formats or individual formats internal to particular institutes. Other forms of binary image data could be accommodated. It is hoped that CBF will replace individual laboratory or institute formats for `home-built' detector systems, will be used as an inter-program data-exchange format, and will be offered as an output choice by commercial detector manufacturers specializing in X-ray and other detector systems. In this chapter we discuss the basic framework within which binary data and images are stored. The categories and data items that are used to describe beam and equipment axes, rastering methodologies, and image compression techniques are described in Chapter 3.7[link] . The CBF/imgCIF dictionary is given in Chapter 4.6[link] . An application programming interface (API) for the manipulation of image data is described in Chapter 5.6[link] .

References

Freed, N. & Borenstein, N. (1996a). Multipurpose Internet Mail Extensions (MIME) part five: Conformance criteria and examples. RFC 2049. Network Working Group. http://www.ietf.org/rfc/rfc2049.txt .
Freed, N. & Borenstein, N. (1996b). Multipurpose Internet Mail Extensions (MIME) part one: Format of Internet message bodies. RFC 2045. Network Working Group. http://www.ietf.org/rfc/rfc2045.txt .
Freed, N. & Borenstein, N. (1996c). Multipurpose Internet Mail Extensions (MIME) part two: Media types. RFC 2046. Network Working Group. http://www.ietf.org/rfc/rfc2046.txt .
Freed, N., Klensin, J. & Postel, J. (1996). Multipurpose Internet Mail Extensions (MIME) part four: Registration procedures. RFC 2048. Network Working Group. http://www.ietf.org/rfc/rfc2048.txt .
Hall, S. R., Allen, F. H. & Brown, I. D. (1991). The Crystallographic Information File (CIF): a new standard archive file for crystallography. Acta Cryst. A47, 655–685.
Moore, K. (1996). MIME (Multipurpose Internet Mail Extensions) part three: Message header extensions for non-ASCII text. RFC 2047. Network Working Group. http://www.ietf.org/rfc/rfc2047.txt .








































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