(IUCr) CIF Definition save__array_data.data

DRAFT DICTIONARY CBF/imgCIF Extensions Dictionary | Draft version 1.5 for comment

#

Index

##### Image dictionary (imgCIF) version 1.5.4

# _array_data.data

Name:
`'_array_data.data'`

Definition:

           The value of _array_data.data contains the array data
                  encapsulated in a STAR string.

                  The representation used is a variant on the
                  Multipurpose Internet Mail Extensions (MIME) specified
                  in RFC 2045-2049 by N. Freed et al.  The boundary
                  delimiter used in writing an imgCIF or CBF is
                  '\n--CIF-BINARY-FORMAT-SECTION--' (including the
                  required initial '\n--').

                  The Content-Type may be any of the discrete types permitted
                  in RFC 2045; 'application/octet-stream' is recommended
                  for diffraction images in the ARRAY_DATA category.
                  Note:  When appropriate in other categories, e.g. for
                  photographs of crystals, more precise types, such as
                  'image/jpeg', 'image/tiff', 'image/png', etc. should be used.

                  If an octet stream was compressed, the compression should
                  be specified by the parameter
                    'conversions="X-CBF_PACKED"'
                  or the parameter
                    'conversions="X-CBF_CANONICAL"'
                  or the parameter
                    'conversions="X-CBF_BYTE_OFFSET"'

                  If the parameter
                    'conversions="X-CBF_PACKED"'
                  is given it may be further modified with the parameters
                    '"uncorrelated_sections"'
                  or
                    '"flat"'

                  If the '"uncorrelated_sections"' parameter is
                  given, each section will be compressed without using
                  the prior section for averaging.

                  If the '"flat"' parameter is given, each the
                  image will be treated as one long row.

                  The Content-Transfer-Encoding may be 'BASE64',
                  'Quoted-Printable', 'X-BASE8', 'X-BASE10',
                  'X-BASE16' or 'X-BASE32K', for an imgCIF or 'BINARY'
                  for a CBF.  The octal, decimal and hexadecimal transfer
                  encodings are provided for convenience in debugging and
                  are not recommended for archiving and data interchange.

                  In a CIF, one of the parameters 'charset=us-ascii',
                  'charset=utf-8' or 'charset=utf-16' may be used on the
                  Content-Transfer-Encoding to specify the character set
                  used for the external presentation of the encoded data.
                  If no charset parameter is given, the character set of
                  the enclosing CIF is assumed.  In any case, if a BOM
                  flag is detected (FE FF for big-endian UTF-16, FF FE for
                  little-endian UTF-16 or EF BB BF for UTF-8) is detected,
                  the indicated charset will be assumed until the end of the
                  encoded data or the detection of a different BOM.  The
                  charset of the Content-Transfer-Encoding is not the character
                  set of the encoded data, only the character set of the
                  presentation of the encoded data and should be respecified
                  for each distinct STAR string.

                  In an imgCIF file, the encoded binary data begins after
                  the empty line terminating the header.  In an imgCIF file,
                  the encoded binary data ends with the terminating boundary
                  delimiter '\n--CIF-BINARY-FORMAT-SECTION----'
                  in the currently effective charset or with the '\n; '
                  that terminates the STAR string.

                  In a CBF, the raw binary data begins after an empty line
                  terminating the header and after the sequence:

                  Octet   Hex   Decimal  Purpose
                    0     0C       12    (ctrl-L) Page break
                    1     1A       26    (ctrl-Z) Stop listings in MS-DOS
                    2     04       04    (Ctrl-D) Stop listings in UNIX
                    3     D5      213    Binary section begins

                  None of these octets are included in the calculation of
                  the message size or in the calculation of the
                  message digest.

                  The X-Binary-Size header specifies the size of the
                  equivalent binary data in octets.  If compression was
                  used, this size is the size after compression, including
                  any book-keeping fields.  An adjustment is made for
                  the deprecated binary formats in which eight bytes of binary
                  header are used for the compression type.  In this case,
                  the eight bytes used for the compression type are subtracted
                  from the size, so that the same size will be reported
                  if the compression type is supplied in the MIME header.
                  Use of the MIME header is the recommended way to
                  supply the compression type.  In general, no portion of
                  the  binary header is included in the calculation of the size.

                  The X-Binary-Element-Type header specifies the type of
                  binary data in the octets, using the same descriptive
                  phrases as in _array_structure.encoding_type.  The default
                  value is 'unsigned 32-bit integer'.

                  An MD5 message digest may, optionally, be used. The 'RSA Data
                  Security, Inc. MD5 Message-Digest Algorithm' should be used.
                  No portion of the header is included in the calculation of the
                  message digest.

                  If the Transfer Encoding is 'X-BASE8', 'X-BASE10' or
                  'X-BASE16', the data are presented as octal, decimal or
                  hexadecimal data organized into lines or words.  Each word
                  is created by composing octets of data in fixed groups of
                  2, 3, 4, 6 or 8 octets, either in the order ...4321 ('big-
                  endian') or 1234... ('little-endian').  If there are fewer
                  than the specified number of octets to fill the last word,
                  then the missing octets are presented as '==' for each
                  missing octet.  Exactly two equal signs are used for each
                  missing octet even for octal and decimal encoding.
                  The format of lines is:

                  rnd xxxxxx xxxxxx xxxxxx

                  where r is 'H', 'O' or 'D' for hexadecimal, octal or
                  decimal, n is the number of octets per word and d is '<'
                  or '>' for the '...4321' and '1234...' octet orderings,
                  respectively.  The '==' padding for the last word should
                  be on the appropriate side to correspond to the missing
                  octets, e.g.

                  H4< FFFFFFFF FFFFFFFF 07FFFFFF ====0000

                  or

                  H3> FF0700 00====

                  For these hexadecimal, octal and decimal formats only,
                  comments beginning with '#' are permitted to improve
                  readability.

                  BASE64 encoding follows MIME conventions.  Octets are
                  in groups of three: c1, c2, c3.  The resulting 24 bits
                  are broken into four six-bit quantities, starting with
                  the high-order six bits (c1 >> 2) of the first octet, then
                  the low-order two bits of the first octet followed by the
                  high-order four bits of the second octet [(c1 & 3)<<4 | (c2>>4)],
                  then the bottom four bits of the second octet followed by the
                  high-order two bits of the last octet [(c2 & 15)<<2 | (c3>>6)],
                  then the bottom six bits of the last octet (c3 & 63).  Each
                  of these four quantities is translated into an ASCII character
                  using the mapping:

                            1         2         3         4         5         6
                  0123456789012345678901234567890123456789012345678901234567890123
                  |         |         |         |         |         |         |
                  ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/

                  With short groups of octets padded on the right with one '='
                  if c3 is missing, and with '==' if both c2 and c3 are missing.

                  X-BASE32K encoding is similar to BASE64 encoding, except that
                  sets of 15 octets are encoded as sets of 8 16-bit unicode
                  characters, by breaking the 120 bits into 8 15-bit quantities.
                  256 is added to each 15 bit quantity to bring it into a
                  printable uncode range.  When encoding, zero padding is used
                  to fill out the last 15 bit quantity.  If 8 or more bits of
                  padding are used, a single equals sign (hexadecimal 003D) is
                  appended.  Embedded whitespace and newlines are introduced
                  to produce lines of no more than 80 characters each.  On
                  decoding, all printable ascii characters and ascii whitespace
                  characters are ignored except for any trailing equals signs.
                  The number of trailing equals signs indicated the number of
                  trailing octets to be trimmed from the end of the decoded data.
                  (see Georgi Darakev, Vassil Litchev, Kostadin Z. Mitev, Herbert
                  J. Bernstein, 'Efficient Support of Binary Data in the XML
                  Implementation of the NeXus File Format',absract W0165,
                  ACA Summer Meeting, Honolulu, HI, July 2006).

                  QUOTED-PRINTABLE encoding also follows MIME conventions, copying
                  octets without translation if their ASCII values are 32...38,
                  42, 48...57, 59, 60, 62, 64...126 and the octet is not a ';'
                  in column 1.  All other characters are translated to =nn, where
                  nn is the hexadecimal encoding of the octet.  All lines are
                  'wrapped' with a terminating '=' (i.e. the MIME conventions
                  for an implicit line terminator are never used).

                  The "X-Binary-Element-Byte-Order" can specify either
                  '"BIG_ENDIAN"' or '"LITTLE_ENDIAN"' byte order of the imaage
                  data.  Only LITTLE_ENDIAN is recommended.  Processors
                  may treat BIG_ENDIAN as a warning of data that can
                  only be processed by special software.

                  The "X-Binary-Number-of-Elements" specifies the number of
                  elements (not the number of octets) in the decompressed, decoded
                  image.

                  The optional "X-Binary-Size-Fastest-Dimension" specifies the
                  number of elements (not the number of octets) in one row of the
                  fastest changing dimension of the binary data array. This
                  information must be in the MIME header for proper operation of
                  some of the decompression algorithms.

                  The optional "X-Binary-Size-Second-Dimension" specifies the
                  number of elements (not the number of octets) in one column of
                  the second-fastest changing dimension of the binary data array.
                  This information must be in the MIME header for proper operation
                  of some of the decompression algorithms.

                  The optional "X-Binary-Size-Third-Dimension" specifies the
                  number of sections for the third-fastest changing dimension of
                  the binary data array.

                  The optional "X-Binary-Size-Padding" specifies the size in
                  octets of an optional padding after the binary array data and
                  before the closing flags for a binary section.

Type: binary

Mandatory item: yes

Category: array_data

#### HTML version of draft dictionary created by modified version of makedicthtml by B. McMahon from modified version of imgCIF dcitionary 1.3.2 which is subject to the following copyright:

Copyright © 2005 International Union of Crystallography