##############################################################################
# #
# Image CIF Dictionary (imgCIF) #
# and Crystallographic Binary File Dictionary (CBF) #
# Extending the Macromolecular CIF Dictionary (mmCIF) #
# #
# Version 1.5.4 #
# of 2007-07-28 #
# ################################################################### #
# # *** WARNING *** THIS IS A DRAFT FOR DISCUSSSION *** WARNING *** # #
# # SUBJECT TO CHANGE WITHOUT NOTICE # #
# # SEND COMMENTS TO imgcif-l@iucr.org CITING THE VERSION # #
# ################################################################### #
# This draft edited by H. J. Bernstein #
# #
# by Andrew P. Hammersley, Herbert J. Bernstein and John D. Westbrook #
# #
# This dictionary was adapted from format discussed at the imgCIF Workshop, #
# held at BNL Oct 1997 and the Crystallographic Binary File Format Draft #
# Proposal by Andrew Hammersley. The first DDL 2.1 Version was created by #
# John Westbrook. This version was drafted by Herbert J. Bernstein and #
# incorporates comments by I. David Brown, John Westbrook, Brian McMahon, #
# Bob Sweet, Paul Ellis, Harry Powell, Wilfred Li, Gotzon Madariaga, #
# Frances C. Bernstein, Chris Nielsen, Nicola Ashcroft and others. #
##############################################################################
data_cif_img.dic
_dictionary.title cif_img.dic
_dictionary.version 1.5.4
_dictionary.datablock_id cif_img.dic
##############################################################################
# CONTENTS
#
# CATEGORY_GROUP_LIST
# SUB_CATEGORY
#
# category ARRAY_DATA
#
# _array_data.array_id
# _array_data.binary_id
# _array_data.data
# _array_data.header_contents
# _array_data.header_convention
#
# category ARRAY_ELEMENT_SIZE
#
# _array_element_size.array_id
# _array_element_size.index
# _array_element_size.size
#
# category ARRAY_INTENSITIES
#
# _array_intensities.array_id
# _array_intensities.binary_id
# _array_intensities.gain
# _array_intensities.gain_esd
# _array_intensities.linearity
# _array_intensities.offset
# _array_intensities.scaling
# _array_intensities.overload
# _array_intensities.undefined_value
# _array_intensities.pixel_fast_bin_size
# _array_intensities.pixel_slow_bin_size
# _array_intensities.pixel_binning_method
#
# category ARRAY_STRUCTURE
#
# _array_structure.byte_order
# _array_structure.compression_type
# _array_structure.compression_type_flag
# _array_structure.encoding_type
# _array_structure.id
#
# category ARRAY_STRUCTURE_LIST
#
# _array_structure_list.axis_set_id
# _array_structure_list.array_id
# _array_structure_list.dimension
# _array_structure_list.direction
# _array_structure_list.index
# _array_structure_list.precedence
#
# category ARRAY_STRUCTURE_LIST_AXIS
#
# _array_structure_list_axis.axis_id
# _array_structure_list_axis.axis_set_id
# _array_structure_list_axis.angle
# _array_structure_list_axis.angle_increment
# _array_structure_list_axis.displacement
# _array_structure_list_axis.fract_displacement
# _array_structure_list_axis.displacement_increment
# _array_structure_list_axis.fract_displacement_increment
# _array_structure_list_axis.angular_pitch
# _array_structure_list_axis.radial_pitch
# _array_structure_list_axis.reference_angle
# _array_structure_list_axis.reference_displacement
#
# category AXIS
#
# _axis.depends_on
# _axis.equipment
# _axis.id
# _axis.offset[1]
# _axis.offset[2]
# _axis.offset[3]
# _axis.type
# _axis.system
# _axis.vector[1]
# _axis.vector[2]
# _axis.vector[3]
#
# category DIFFRN_DATA_FRAME
#
# _diffrn_data_frame.array_id
# _diffrn_data_frame.binary_id
# _diffrn_data_frame.center_fast
# _diffrn_data_frame.center_slow
# _diffrn_data_frame.center_units
# _diffrn_data_frame.detector_element_id
# _diffrn_data_frame.id
# _diffrn_data_frame.details
#
# category DIFFRN_DETECTOR
#
# _diffrn_detector.details
# _diffrn_detector.detector
# _diffrn_detector.diffrn_id
# _diffrn_detector.dtime
# _diffrn_detector.id
# _diffrn_detector.number_of_axes
# _diffrn_detector.type
#
# category DIFFRN_DETECTOR_AXIS
#
# _diffrn_detector_axis.axis_id
# _diffrn_detector_axis.detector_id
#
# category DIFFRN_DETECTOR_ELEMENT
#
# _diffrn_detector_element.id
# _diffrn_detector_element.detector_id
# _diffrn_detector_element.reference_center_fast
# _diffrn_detector_element.reference_center_slow
# _diffrn_detector_element.reference_center_units
#
# category DIFFRN_MEASUREMENT
#
# _diffrn_measurement.diffrn_id
# _diffrn_measurement.details
# _diffrn_measurement.device
# _diffrn_measurement.device_details
# _diffrn_measurement.device_type
# _diffrn_measurement.id
# _diffrn_measurement.method
# _diffrn_measurement.number_of_axes
# _diffrn_measurement.sample_detector_distance
# _diffrn_measurement.sample_detector_voffset
# _diffrn_measurement.specimen_support
#
# category DIFFRN_MEASUREMENT_AXIS
#
# _diffrn_measurement_axis.axis_id
# _diffrn_measurement_axis.measurement_device
# _diffrn_measurement_axis.measurement_id
#
# category DIFFRN_RADIATION
#
# _diffrn_radiation.collimation
# _diffrn_radiation.diffrn_id
# _diffrn_radiation.div_x_source
# _diffrn_radiation.div_y_source
# _diffrn_radiation.div_x_y_source
# _diffrn_radiation.filter_edge'
# _diffrn_radiation.inhomogeneity
# _diffrn_radiation.monochromator
# _diffrn_radiation.polarisn_norm
# _diffrn_radiation.polarisn_ratio
# _diffrn_radiation.polarizn_source_norm
# _diffrn_radiation.polarizn_source_ratio
# _diffrn_radiation.probe
# _diffrn_radiation.type
# _diffrn_radiation.xray_symbol
# _diffrn_radiation.wavelength_id
#
# category DIFFRN_REFLN
#
# _diffrn_refln.frame_id
#
# category DIFFRN_SCAN
#
# _diffrn_scan.id
# _diffrn_scan.date_end
# _diffrn_scan.date_start
# _diffrn_scan.integration_time
# _diffrn_scan.frame_id_start
# _diffrn_scan.frame_id_end
# _diffrn_scan.frames
#
# category DIFFRN_SCAN_AXIS
#
# _diffrn_scan_axis.axis_id
# _diffrn_scan_axis.angle_start
# _diffrn_scan_axis.angle_range
# _diffrn_scan_axis.angle_increment
# _diffrn_scan_axis.angle_rstrt_incr
# _diffrn_scan_axis.displacement_start
# _diffrn_scan_axis.displacement_range
# _diffrn_scan_axis.displacement_increment
# _diffrn_scan_axis.displacement_rstrt_incr
# _diffrn_scan_axis.reference_angle
# _diffrn_scan_axis.reference_displacement
# _diffrn_scan_axis.scan_id
#
# category DIFFRN_SCAN_FRAME
#
# _diffrn_scan_frame.date
# _diffrn_scan_frame.frame_id
# _diffrn_scan_frame.frame_number
# _diffrn_scan_frame.integration_time
# _diffrn_scan_frame.scan_id
#
# category DIFFRN_SCAN_FRAME_AXIS
#
# _diffrn_scan_frame_axis.axis_id
# _diffrn_scan_frame_axis.angle
# _diffrn_scan_frame_axis.angle_increment
# _diffrn_scan_frame_axis.angle_rstrt_incr
# _diffrn_scan_frame_axis.displacement
# _diffrn_scan_frame_axis.displacement_increment
# _diffrn_scan_frame_axis.displacement_rstrt_incr
# _diffrn_scan_frame_axis.reference_angle
# _diffrn_scan_frame_axis.reference_displacement
# _diffrn_scan_frame_axis.frame_id
#
# categor MAP
#
# _map.details
# _map.diffrn_id
# _map.entry_id
# _map.id
#
# categor MAP_SEGMENT
#
# _map_segment.array_id
# _map_segment.binary_id
# _map_segment.mask_array_id
# _map_segment.mask_binary_id
# _map_segment.id
# _map_segment.map_id
# _map_segment.details
#
# ***DEPRECATED*** data items
#
# _diffrn_detector_axis.id
# _diffrn_detector_element.center[1]
# _diffrn_detector_element.center[2]
# _diffrn_measurement_axis.id
#
# ***DEPRECATED*** category DIFFRN_FRAME_DATA
#
# _diffrn_frame_data.array_id
# _diffrn_frame_data.binary_id
# _diffrn_frame_data.detector_element_id
# _diffrn_frame_data.id
# _diffrn_frame_data.details
#
#
# ITEM_TYPE_LIST
# ITEM_UNITS_LIST
# DICTIONARY_HISTORY
#
##############################################################################
#########################
## CATEGORY_GROUP_LIST ##
#########################
loop_
_category_group_list.id
_category_group_list.parent_id
_category_group_list.description
'inclusive_group' .
; Categories that belong to the dictionary extension.
;
'array_data_group'
'inclusive_group'
; Categories that describe array data.
;
'axis_group'
'inclusive_group'
; Categories that describe axes.
;
'diffrn_group'
'inclusive_group'
; Categories that describe details of the diffraction experiment.
;
##################
## SUB_CATEGORY ##
##################
loop_
_sub_category.id
_sub_category.description
'matrix'
; The collection of elements of a matrix.
;
'vector'
; The collection of elements of a vector.
;
##############
# ARRAY_DATA #
##############
save_ARRAY_DATA
_category.description
; Data items in the ARRAY_DATA category are the containers for
the array data items described in the category ARRAY_STRUCTURE.
It is recognized that the data in this category needs to be used in
two distinct ways. During a data collection the lack of ancillary
data and timing constraints in processing data may dictate the
need to make a 'miniCBF' nothing more than an essential minimum
of information to record the results of the data collection. In that
case it is proper to use the ARRAY_DATA category as a
container for just a single image and a compacted, beam-line
dependent list of data collection parameter values. In such
a case, only the tags '_array_data.header_convention',
'_array_data.header_contents' and '_array_data.data' need be
populated.
For full processing and archiving, most of the tags in this
dictionary will need to be populated.
;
_category.id array_data
_category.mandatory_code no
loop_
_category_key.name '_array_data.array_id'
'_array_data.binary_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 -
This example shows two binary data blocks. The first one
was compressed by the CBF_CANONICAL compression algorithm and is
presented as hexadecimal data. The first character 'H' on the
data lines means hexadecimal. It could have been 'O' for octal
or 'D' for decimal. The second character on the line shows
the number of bytes in each word (in this case '4'), which then
requires eight hexadecimal digits per word. The third character
gives the order of octets within a word, in this case '<'
for the ordering 4321 (i.e. 'big-endian'). Alternatively, the
character '>' could have been used for the ordering 1234
(i.e. 'little-endian'). The block has a 'message digest'
to check the integrity of the data.
The second block is similar, but uses CBF_PACKED compression
and BASE64 encoding. Note that the size and the digest are
different.
;
;
loop_
_array_data.array_id
_array_data.binary_id
_array_data.data
image_1 1
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="X-CBF_CANONICAL"
Content-Transfer-Encoding: X-BASE16
X-Binary-Size: 3927126
X-Binary-ID: 1
Content-MD5: u2sTJEovAHkmkDjPi+gWsg==
# Hexadecimal encoding, byte 0, byte order ...21
#
H4< 0050B810 00000000 00000000 00000000 000F423F 00000000 00000000 ...
....
--CIF-BINARY-FORMAT-SECTION----
;
image_2 2
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="X-CBF-PACKED"
Content-Transfer-Encoding: BASE64
X-Binary-Size: 3745758
X-Binary-ID: 2
Content-MD5: 1zsJjWPfol2GYl2V+QSXrw==
ELhQAAAAAAAA...
...
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 2 -
This example shows a single image in a miniCBF, provided by
E. Eikenberry. The entire CBF consists of one data block
containing one category and three tags. The CBFlib
program convert_miniCBF and a suitable template file
can be used to convert this miniCBF to a full imgCIF
file.
;
;
###CBF: VERSION 1.5
# CBF file written by CBFlib v0.7.8
data_insulin_pilatus6m
_array_data.header_convention SLS_1.0
_array_data.header_contents
;
# Detector: PILATUS 6M SN: 60-0001
# 2007/Jun/17 15:12:36.928
# Pixel_size 172e-6 m x 172e-6 m
# Silicon sensor, thickness 0.000320 m
# Exposure_time 0.995000 s
# Exposure_period 1.000000 s
# Tau = 194.0e-09 s
# Count_cutoff 1048575 counts
# Threshold_setting 5000 eV
# Wavelength 1.2398 A
# Energy_range (0, 0) eV
# Detector_distance 0.15500 m
# Detector_Voffset -0.01003 m
# Beam_xy (1231.00, 1277.00) pixels
# Flux 22487563295 ph/s
# Filter_transmission 0.0008
# Start_angle 13.0000 deg.
# Angle_increment 1.0000 deg.
# Detector_2theta 0.0000 deg.
# Polarization 0.990
# Alpha 0.0000 deg.
# Kappa 0.0000 deg.
# Phi 0.0000 deg.
# Chi 0.0000 deg.
# Oscillation_axis X, CW
# N_oscillations 1
;
_array_data.data
;
--CIF-BINARY-FORMAT-SECTION--
Content-Type: application/octet-stream;
conversions="x-CBF_BYTE_OFFSET"
Content-Transfer-Encoding: BINARY
X-Binary-Size: 6247567
X-Binary-ID: 1
X-Binary-Element-Type: "signed 32-bit integer"
X-Binary-Element-Byte-Order: LITTLE_ENDIAN
Content-MD5: 8wO6i2+899lf5iO8QPdgrw==
X-Binary-Number-of-Elements: 6224001
X-Binary-Size-Fastest-Dimension: 2463
X-Binary-Size-Second-Dimension: 2527
X-Binary-Size-Padding: 4095
...
--CIF-BINARY-FORMAT-SECTION----
;
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_data.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
If not given, it defaults to 1.
;
_item.name '_array_data.array_id'
_item.category_id array_data
_item.mandatory_code implicit
_item_type.code code
save_
save__array_data.binary_id
_item_description.description
; This item is an integer identifier which, along with
_array_data.array_id, should uniquely identify the
particular block of array data.
If _array_data.binary_id is not explicitly given,
it defaults to 1.
The value of _array_data.binary_id distinguishes
among multiple sets of data with the same array
structure.
If the MIME header of the data array specifies a
value for X-Binary-ID, the value of _array_data.binary_id
should be equal to the value given for X-Binary-ID.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_data.binary_id' array_data
implicit
'_diffrn_data_frame.binary_id' diffrn_data_frame
implicit
'_array_intensities.binary_id' array_intensities
implicit
loop_
_item_linked.child_name
_item_linked.parent_name
'_diffrn_data_frame.binary_id' '_array_data.binary_id'
'_array_intensities.binary_id' '_array_data.binary_id'
_item_default.value 1
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_data.data
_item_description.description
; 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.
;
_item.name '_array_data.data'
_item.category_id array_data
_item.mandatory_code yes
_item_type.code binary
save_
save__array_data.header_contents
_item_description.description
; This item is an text field for use in minimal CBF files to carry
essential header information to be kept with image data
in _array_data.data when the tags that normally carry the
structured metadata for the image have not been populated.
Normally this data item should not appear when the full set
of tags have been populated and _diffrn_data_frame.details
appears.
;
_item.name '_array_data.header_contents'
_item.category_id array_data
_item.mandatory_code no
_item_type.code text
save_
save__array_data.header_convention
_item_description.description
; This item is an identifier for the convention followed in
constructing the contents of _array_data.header_contents
The permitted values are of the of an image creator identifier
followed by an underscore and a version string. To avoid
confusion about conventions, all creator identifiers
should be registered with the IUCr and the conventions
for all identifiers and versions should be posted on
the MEDSBIO.org web site.
;
_item.name '_array_data.header_convention'
_item.category_id array_data
_item.mandatory_code no
_item_type.code code
save_
######################
# ARRAY_ELEMENT_SIZE #
######################
save_ARRAY_ELEMENT_SIZE
_category.description
; Data items in the ARRAY_ELEMENT_SIZE category record the physical
size of array elements along each array dimension.
;
_category.id array_element_size
_category.mandatory_code no
loop_
_category_key.name '_array_element_size.array_id'
'_array_element_size.index'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - A regular 2D array with a uniform element dimension
of 1220 nanometres.
;
;
loop_
_array_element_size.array_id
_array_element_size.index
_array_element_size.size
image_1 1 1.22e-6
image_1 2 1.22e-6
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_element_size.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_element_size.array_id'
_item.category_id array_element_size
_item.mandatory_code implicit
_item_type.code code
save_
save__array_element_size.index
_item_description.description
; This item is a pointer to _array_structure_list.index in
the ARRAY_STRUCTURE_LIST category.
;
_item.name '_array_element_size.index'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code code
save_
save__array_element_size.size
_item_description.description
; The size in metres of an image element in this
dimension. This supposes that the elements are arranged
on a regular grid.
;
_item.name '_array_element_size.size'
_item.category_id array_element_size
_item.mandatory_code yes
_item_type.code float
_item_units.code 'metres'
loop_
_item_range.maximum
_item_range.minimum
. 0.0
save_
#####################
# ARRAY_INTENSITIES #
#####################
save_ARRAY_INTENSITIES
_category.description
; Data items in the ARRAY_INTENSITIES category record the
information required to recover the intensity data from
the set of data values stored in the ARRAY_DATA category.
The detector may have a complex relationship
between the raw intensity values and the number of
incident photons. In most cases, the number stored
in the final array will have a simple linear relationship
to the actual number of incident photons, given by
_array_intensities.gain. If raw, uncorrected values
are presented (e.g. for calibration experiments), the
value of _array_intensities.linearity will be 'raw'
and _array_intensities.gain will not be used.
;
_category.id array_intensities
_category.mandatory_code no
loop_
_category_key.name '_array_intensities.array_id'
'_array_intensities.binary_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1
;
;
loop_
_array_intensities.array_id
_array_intensities.linearity
_array_intensities.gain
_array_intensities.overload
_array_intensities.undefined_value
_array_intensities.pixel_fast_bin_size
_array_intensities.pixel_slow_bin_size
_array_intensities.pixel_binning_method
image_1 linear 1.2 655535 0 2 2 hardware
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_intensities.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_intensities.array_id'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code code
save_
save__array_intensities.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_array_intensities.binary_id'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code int
save_
save__array_intensities.gain
_item_description.description
; Detector 'gain'. The factor by which linearized
intensity count values should be divided to produce
true photon counts.
;
_item.name '_array_intensities.gain'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code float
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'counts_per_photon'
loop_
_item_related.related_name
_item_related.function_code '_array_intensities.gain_esd'
'associated_value'
save_
save__array_intensities.gain_esd
_item_description.description
; The estimated standard deviation in detector 'gain'.
;
_item.name '_array_intensities.gain_esd'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code float
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'counts_per_photon'
loop_
_item_related.related_name
_item_related.function_code '_array_intensities.gain'
'associated_esd'
save_
save__array_intensities.linearity
_item_description.description
; The intensity linearity scaling method used to convert
from the raw intensity to the stored element value:
'linear' is linear.
'offset' means that the value defined by
_array_intensities.offset should be added to each
element value.
'scaling' means that the value defined by
_array_intensities.scaling should be multiplied with each
element value.
'scaling_offset' is the combination of the two previous cases,
with the scale factor applied before the offset value.
'sqrt_scaled' means that the square root of raw
intensities multiplied by _array_intensities.scaling is
calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by _array_intensities.scaling and squaring the
result.
'logarithmic_scaled' means that the logarithm base 10 of
raw intensities multiplied by _array_intensities.scaling
is calculated and stored, perhaps rounded to the nearest
integer. Thus, linearization involves dividing the stored
values by _array_intensities.scaling and calculating 10
to the power of this number.
'raw' means that the data are a set of raw values straight
from the detector.
;
_item.name '_array_intensities.linearity'
_item.category_id array_intensities
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'linear' .
'offset'
; The value defined by _array_intensities.offset should
be added to each element value.
;
'scaling'
; The value defined by _array_intensities.scaling should be
multiplied with each element value.
;
'scaling_offset'
; The combination of the scaling and offset
with the scale factor applied before the offset value.
;
'sqrt_scaled'
; The square root of raw intensities multiplied by
_array_intensities.scaling is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored
values by _array_intensities.scaling and squaring the
result.
;
'logarithmic_scaled'
; The logarithm base 10 of raw intensities multiplied by
_array_intensities.scaling is calculated and stored,
perhaps rounded to the nearest integer. Thus,
linearization involves dividing the stored values by
_array_intensities.scaling and calculating 10 to the
power of this number.
;
'raw'
; The array consists of raw values to which no corrections have
been applied. While the handling of the data is similar to
that given for 'linear' data with no offset, the meaning of
the data differs in that the number of incident photons is
not necessarily linearly related to the number of counts
reported. This value is intended for use either in
calibration experiments or to allow for handling more
complex data-fitting algorithms than are allowed for by
this data item.
;
save_
save__array_intensities.offset
_item_description.description
; Offset value to add to array element values in the manner
described by the item _array_intensities.linearity.
;
_item.name '_array_intensities.offset'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.overload
_item_description.description
; The saturation intensity level for this data array.
;
_item.name '_array_intensities.overload'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
_item_units.code 'counts'
save_
save__array_intensities.pixel_fast_bin_size
_item_description.description
; The value of _array_intensities.pixel_fast_bin_size specifies
the number of pixels that compose one element in the direction
of the most rapidly varying array dimension.
Typical values are 1, 2, 4 or 8. When there is 1 pixel per
array element in both directions, the value given for
_array_intensities.pixel_binning_method normally should be
'none'.
It is specified as a float to allow for binning algorithms that
create array elements that are not integer multiples of the
detector pixel size.
;
_item.name '_array_intensities.pixel_fast_bin_size'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code float
_item_default.value 1.
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'pixels_per_element'
save_
save__array_intensities.pixel_slow_bin_size
_item_description.description
; The value of _array_intensities.pixel_slow_bin_size specifies
the number of pixels that compose one element in the direction
of the second most rapidly varying array dimension.
Typical values are 1, 2, 4 or 8. When there is 1 pixel per
array element in both directions, the value given for
_array_intensities.pixel_binning_method normally should be
'none'.
It is specified as a float to allow for binning algorithms that
create array elements that are not integer multiples of the
detector pixel size.
;
_item.name '_array_intensities.pixel_slow_bin_size'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code float
_item_default.value 1.
loop_
_item_range.maximum
_item_range.minimum
. 0.0
_item_units.code 'pixels_per_element'
save_
save__array_intensities.pixel_binning_method
_item_description.description
; The value of _array_intensities.pixel_binning_method specifies
the method used to derive array elements from multiple pixels.
;
_item.name '_array_intensities.pixel_binning_method'
_item.category_id array_intensities
_item.mandatory_code implicit
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'hardware'
; The element intensities were derived from the raw data of one
or more pixels by used of hardware in the detector, e.g. by use
of shift registers in a CCD to combine pixels into super-pixels.
;
'software'
; The element intensities were derived from the raw data of more
than one pixel by use of software.
;
'combined'
; The element intensities were derived from the raw data of more
than one pixel by use of both hardware and software, as when
hardware binning is used in one direction and software in the
other.
;
'none'
; In the both directions, the data has not been binned. The
number of pixels is equal to the number of elements.
When the value of _array_intensities.pixel_binning_method is
'none' the values of _array_intensities.pixel_fast_bin_size
and _array_intensities.pixel_slow_bin_size both must be 1.
;
'unspecified'
; The method used to derive element intensities is not specified.
;
_item_default.value 'unspecified'
save_
save__array_intensities.scaling
_item_description.description
; Multiplicative scaling value to be applied to array data
in the manner described by item
_array_intensities.linearity.
;
_item.name '_array_intensities.scaling'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
save__array_intensities.undefined_value
_item_description.description
; A value to be substituted for undefined values in
the data array.
;
_item.name '_array_intensities.undefined_value'
_item.category_id array_intensities
_item.mandatory_code no
_item_type.code float
save_
###################
# ARRAY_STRUCTURE #
###################
save_ARRAY_STRUCTURE
_category.description
; Data items in the ARRAY_STRUCTURE category record the organization and
encoding of array data that may be stored in the ARRAY_DATA category.
;
_category.id array_structure
_category.mandatory_code no
_category_key.name '_array_structure.id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 -
;
;
loop_
_array_structure.id
_array_structure.encoding_type
_array_structure.compression_type
_array_structure.byte_order
image_1 "unsigned 16-bit integer" none little_endian
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure.byte_order
_item_description.description
; The order of bytes for integer values which require more
than 1 byte.
(IBM-PC's and compatibles and DEC VAXs use low-byte-first
ordered integers, whereas Hewlett Packard 700
series, Sun-4 and Silicon Graphics use high-byte-first
ordered integers. DEC Alphas can produce/use either
depending on a compiler switch.)
;
_item.name '_array_structure.byte_order'
_item.category_id array_structure
_item.mandatory_code yes
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail
'big_endian'
; The first byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
;
'little_endian'
; The last byte in the byte stream of the bytes which make up an
integer value is the most significant byte of an integer.
;
save_
save__array_structure.compression_type
_item_description.description
; Type of data-compression method used to compress the array
data.
;
_item.name '_array_structure.compression_type'
_item.category_id array_structure
_item.mandatory_code no
_item_type.code ucode
_item_default.value 'none'
loop_
_item_enumeration.value
_item_enumeration.detail
'byte_offset'
; Using the 'byte_offset' compression scheme as per A. Hammersley
and the CBFlib manual, section 3.3.3
;
'canonical'
; Using the 'canonical' compression scheme (International Tables
for Crystallography Volume G, Section 5.6.3.1) and CBFlib
manual section 3.3.1
;
'none'
; Data are stored in normal format as defined by
_array_structure.encoding_type and
_array_structure.byte_order.
;
'packed'
; Using the 'packed' compression scheme, a CCP4-style packing
as per J. P. Abrahams pack_c.c and CBFlib manual, section 3.3.2.
;
'packed_v2'
; Using the 'packed' compression scheme, version 2, as per
J. P. Abrahams pack_c.c and CBFlib manual, section 3.3.2.
;
save_
save__array_structure.compression_type_flag
_item_description.description
; Flags modifying the type of data-compression method used to
compress the arraydata.
;
_item.name '_array_structure.compression_type_flag'
_item.category_id array_structure
_item.mandatory_code no
_item_type.code ucode
loop_
_item_enumeration.value
_item_enumeration.detail
'uncorrelated_sections'
; When applying packed or packed_v2 compression on an array with
uncorrelated sections, do not average in points from the prior
section.
;
'flat'
; When applying packed or packed_v2 compression on an array with
treat the entire image as a single line set the maximum number
of bits for an offset to 65 bits.
The flag is included for compatibility with software prior to
CBFlib_0.7.7, and should not be used for new data sets.
;
save_
save__array_structure.encoding_type
_item_description.description
; Data encoding of a single element of array data.
The type 'unsigned 1-bit integer' is used for
packed Booleans arrays for masks. Each element
of the array corresponds to a single bit
packed in unsigned 8-bit data.
In several cases, the IEEE format is referenced.
See IEEE Standard 754-1985 (IEEE, 1985).
Ref: IEEE (1985). IEEE Standard for Binary Floating-Point
Arithmetic. ANSI/IEEE Std 754-1985. New York: Institute of
Electrical and Electronics Engineers.
;
_item.name '_array_structure.encoding_type'
_item.category_id array_structure
_item.mandatory_code yes
_item_type.code uline
loop_
_item_enumeration.value
'unsigned 1-bit integer'
'unsigned 8-bit integer'
'signed 8-bit integer'
'unsigned 16-bit integer'
'signed 16-bit integer'
'unsigned 32-bit integer'
'signed 32-bit integer'
'signed 32-bit real IEEE'
'signed 64-bit real IEEE'
'signed 32-bit complex IEEE'
save_
save__array_structure.id
_item_description.description
; The value of _array_structure.id must uniquely identify
each item of array data.
This item has been made implicit and given a default value of 1
as a convenience in writing miniCBF files. Normally an
explicit name with useful content should be used.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure.id' array_structure implicit
'_array_data.array_id' array_data implicit
'_array_structure_list.array_id' array_structure_list implicit
'_array_intensities.array_id' array_intensities implicit
'_diffrn_data_frame.array_id' diffrn_data_frame implicit
_item_default.value 1
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_data.array_id' '_array_structure.id'
'_array_structure_list.array_id' '_array_structure.id'
'_array_intensities.array_id' '_array_structure.id'
'_diffrn_data_frame.array_id' '_array_structure.id'
save_
########################
# ARRAY_STRUCTURE_LIST #
########################
save_ARRAY_STRUCTURE_LIST
_category.description
; Data items in the ARRAY_STRUCTURE_LIST category record the size
and organization of each array dimension.
The relationship to physical axes may be given.
;
_category.id array_structure_list
_category.mandatory_code no
loop_
_category_key.name '_array_structure_list.array_id'
'_array_structure_list.index'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - An image array of 1300 x 1200 elements. The raster
order of the image is left to right (increasing) in the
first dimension and bottom to top (decreasing) in
the second dimension.
;
;
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_set_id
image_1 1 1300 1 increasing ELEMENT_X
image_1 2 1200 2 decreasing ELEMENY_Y
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__array_structure_list.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_array_structure_list.array_id'
_item.category_id array_structure_list
_item.mandatory_code implicit
_item_type.code code
save_
save__array_structure_list.axis_set_id
_item_description.description
; This is a descriptor for the physical axis or set of axes
corresponding to an array index.
This data item is related to the axes of the detector
itself given in DIFFRN_DETECTOR_AXIS, but usually differs
in that the axes in this category are the axes of the
coordinate system of reported data points, while the axes in
DIFFRN_DETECTOR_AXIS are the physical axes
of the detector describing the 'poise' of the detector as an
overall physical object.
If there is only one axis in the set, the identifier of
that axis should be used as the identifier of the set.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure_list.axis_set_id'
array_structure_list yes
'_array_structure_list_axis.axis_set_id'
array_structure_list_axis implicit
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_structure_list_axis.axis_set_id'
'_array_structure_list.axis_set_id'
save_
save__array_structure_list.dimension
_item_description.description
; The number of elements stored in the array structure in
this dimension.
;
_item.name '_array_structure_list.dimension'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.direction
_item_description.description
; Identifies the direction in which this array index changes.
;
_item.name '_array_structure_list.direction'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
'increasing'
; Indicates the index changes from 1 to the maximum dimension.
;
'decreasing'
; Indicates the index changes from the maximum dimension to 1.
;
save_
save__array_structure_list.index
_item_description.description
; Identifies the one-based index of the row or column in the
array structure.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_array_structure_list.index' array_structure_list yes
'_array_structure_list.precedence' array_structure_list yes
'_array_element_size.index' array_element_size yes
_item_type.code int
loop_
_item_linked.child_name
_item_linked.parent_name
'_array_element_size.index' '_array_structure_list.index'
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
save__array_structure_list.precedence
_item_description.description
; Identifies the rank order in which this array index changes
with respect to other array indices. The precedence of 1
indicates the index which changes fastest.
;
_item.name '_array_structure_list.precedence'
_item.category_id array_structure_list
_item.mandatory_code yes
_item_type.code int
loop_
_item_range.maximum
_item_range.minimum
1 1
. 1
save_
#############################
# ARRAY_STRUCTURE_LIST_AXIS #
#############################
save_ARRAY_STRUCTURE_LIST_AXIS
_category.description
; Data items in the ARRAY_STRUCTURE_LIST_AXIS category describe
the physical settings of sets of axes for the centres of pixels that
correspond to data points described in the
ARRAY_STRUCTURE_LIST category.
In the simplest cases, the physical increments of a single axis correspond
to the increments of a single array index. More complex organizations,
e.g. spiral scans, may require coupled motions along multiple axes.
Note that a spiral scan uses two coupled axes: one for the angular
direction and one for the radial direction. This differs from a
cylindrical scan for which the two axes are not coupled into one
set.
;
_category.id array_structure_list_axis
_category.mandatory_code no
loop_
_category_key.name
'_array_structure_list_axis.axis_set_id'
'_array_structure_list_axis.axis_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
save_
save__array_structure_list_axis.axis_id
_item_description.description
; The value of this data item is the identifier of one of
the axes in the set of axes for which settings are being
specified.
Multiple axes may be specified for the same value of
_array_structure_list_axis.axis_set_id.
This item is a pointer to _axis.id in the
AXIS category.
;
_item.name '_array_structure_list_axis.axis_id'
_item.category_id array_structure_list_axis
_item.mandatory_code yes
_item_type.code code
save_
save__array_structure_list_axis.axis_set_id
_item_description.description
; The value of this data item is the identifier of the
set of axes for which axis settings are being specified.
Multiple axes may be specified for the same value of
_array_structure_list_axis.axis_set_id.
This item is a pointer to
_array_structure_list.axis_set_id
in the ARRAY_STRUCTURE_LIST category.
If this item is not specified, it defaults to the corresponding
axis identifier.
;
_item.name '_array_structure_list_axis.axis_set_id'
_item.category_id array_structure_list_axis
_item.mandatory_code implicit
_item_type.code code
save_
save__array_structure_list_axis.angle
_item_description.description
; The setting of the specified axis in degrees for the first
data point of the array index with the corresponding value
of _array_structure_list.axis_set_id. If the index is
specified as 'increasing', this will be the centre of the
pixel with index value 1. If the index is specified as
'decreasing', this will be the centre of the pixel with
maximum index value.
;
_item.name '_array_structure_list_axis.angle'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.angle_increment
_item_description.description
; The pixel-centre-to-pixel-centre increment in the angular
setting of the specified axis in degrees. This is not
meaningful in the case of 'constant velocity' spiral scans
and should not be specified for this case.
See _array_structure_list_axis.angular_pitch.
;
_item.name '_array_structure_list_axis.angle_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.displacement
_item_description.description
; The setting of the specified axis in millimetres for the first
data point of the array index with the corresponding value
of _array_structure_list.axis_set_id. If the index is
specified as 'increasing', this will be the centre of the
pixel with index value 1. If the index is specified as
'decreasing', this will be the centre of the pixel with
maximum index value.
;
_item.name '_array_structure_list_axis.displacement'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.fract_displacement
_item_description.description
; The setting of the specified axis as a decimal fraction of
the axis unit vector for the first data point of the array
index with the corresponding value of
_array_structure_list.axis_set_id.
If the index is specified as 'increasing', this will be the
centre of the pixel with index value 1. If the index is
specified as 'decreasing', this will be the centre of the
pixel with maximum index value.
;
_item.name '_array_structure_list_axis.fract_displacement'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
save_
save__array_structure_list_axis.displacement_increment
_item_description.description
; The pixel-centre-to-pixel-centre increment for the displacement
setting of the specified axis in millimetres.
;
_item.name
'_array_structure_list_axis.displacement_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.fract_displacement_increment
_item_description.description
; The pixel-centre-to-pixel-centre increment for the displacement
setting of the specified axis as a decimal fraction of the
axis unit vector.
;
_item.name
'_array_structure_list_axis.fract_displacement_increment'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.angular_pitch
_item_description.description
; The pixel-centre-to-pixel-centre distance for a one-step
change in the setting of the specified axis in millimetres.
This is meaningful only for 'constant velocity' spiral scans
or for uncoupled angular scans at a constant radius
(cylindrical scans) and should not be specified for cases
in which the angle between pixels (rather than the distance
between pixels) is uniform.
See _array_structure_list_axis.angle_increment.
;
_item.name '_array_structure_list_axis.angular_pitch'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.radial_pitch
_item_description.description
; The radial distance from one 'cylinder' of pixels to the
next in millimetres. If the scan is a 'constant velocity'
scan with differing angular displacements between pixels,
the value of this item may differ significantly from the
value of _array_structure_list_axis.displacement_increment.
;
_item.name '_array_structure_list_axis.radial_pitch'
_item.category_id array_structure_list_axis
_item.mandatory_code no
_item_default.value 0.0
_item_type.code float
_item_units.code 'millimetres'
save_
save__array_structure_list_axis.reference_angle
_item_description.description
; The value of _array_structure_list_axis.reference_angle
specifies the setting of the angle of this axis used for
determining a reference beam center and a reference detector
distance. It is normally expected to be identical to the
value of _array_structure_list.angle.
;
_item.name '_array_structure_list_axis.reference_angle'
_item.category_id array_structure_list_axis
_item.mandatory_code implicit
_item_type.code float
_item_units.code 'degrees'
save_
save__array_structure_list_axis.reference_displacement
_item_description.description
; The value of _array_structure_list_axis.reference_displacement
specifies the setting of the displacement of this axis used
for determining a reference beam center and a reference detector
distance. It is normally expected to be identical to the value
of _array_structure_list.displacement.
;
_item.name '_array_structure_list_axis.reference_displacement'
_item.category_id array_structure_list_axis
_item.mandatory_code implicit
_item_type.code float
_item_units.code 'millimetres'
save_
########
# AXIS #
########
save_AXIS
_category.description
; Data items in the AXIS category record the information required
to describe the various goniometer, detector, source and other
axes needed to specify a data collection or the axes defining the
coordinate system of an image.
The location of each axis is specified by two vectors: the axis
itself, given by a unit vector in the direction of the axis, and
an offset to the base of the unit vector.
The vectors defining an axis are referenced to an appropriate
coordinate system. The axis vector, itself, is a dimensionless
unit vector. Where meaningful, the offset vector is given in
millimetres. In coordinate systems not measured in metres,
the offset is not specified and is taken as zero.
The available coordinate systems are:
The imgCIF standard laboratory coordinate system
The direct lattice (fractional atomic coordinates)
The orthogonal Cartesian coordinate system (real space)
The reciprocal lattice
An abstract orthogonal Cartesian coordinate frame
For consistency in this discussion, we call the three coordinate
system axes X, Y and Z. This is appropriate for the imgCIF
standard laboratory coordinate system, and last two Cartesian
coordinate systems, but for the direct lattice, X corresponds
to a, Y to b and Z to c, while for the reciprocal lattice,
X corresponds to a*, Y to b* and Z to c*.
For purposes of visualization, all the coordinate systems are
taken as right-handed, i.e., using the convention that the extended
thumb of a right hand could point along the first (X) axis, the
straightened pointer finger could point along the second (Y) axis
and the middle finger folded inward could point along the third (Z)
axis.
THE IMGCIF STANDARD LABORATORY COORDINATE SYSTEM
The imgCIF standard laboratory coordinate system is a right-handed
orthogonal coordinate similar to the MOSFLM coordinate system,
but imgCIF puts Z along the X-ray beam, rather than putting X along the
X-ray beam as in MOSFLM.
The vectors for the imgCIF standard laboratory coordinate system
form a right-handed Cartesian coordinate system with its origin
in the sample or specimen. The origin of the axis system should,
if possible, be defined in terms of mechanically stable axes to be
be both in the sample and in the beam. If the sample goniometer or other
sample positioner has two axes the intersection of which defines a
unique point at which the sample should be mounted to be bathed
by the beam, that will be the origin of the axis system. If no such
point is defined, then the midpoint of the line of intersection
between the sample and the center of the beam will define the origin.
For this definition the sample positioning system will be set at
its initial reference position for the experiment.
| Y (to complete right-handed system)
|
|
|
|
|
|________________X
/ principal goniometer axis
/
/
/
/
/Z (to source)
Axis 1 (X): The X-axis is aligned to the mechanical axis pointing from
the sample or specimen along the principal axis of the goniometer or
sample positioning system if the sample positioning system has an axis
that intersects the origin and which form an angle of more than 22.5
degrees with the beam axis.
Axis 2 (Y): The Y-axis completes an orthogonal right-handed system
defined by the X-axis and the Z-axis (see below).
Axis 3 (Z): The Z-axis is derived from the source axis which goes from
the sample to the source. The Z-axis is the component of the source axis
in the direction of the source orthogonal to the X-axis in the plane
defined by the X-axis and the source axis.
If the conditions for the X-axis can be met, the coordinate system
will be based on the goniometer or other sample positioning system
and the beam and not on the orientation of the detector, gravity etc.
The vectors necessary to specify all other axes are given by sets of
three components in the order (X, Y, Z).
If the axis involved is a rotation axis, it is right-handed, i.e. as
one views the object to be rotated from the origin (the tail) of the
unit vector, the rotation is clockwise. If a translation axis is
specified, the direction of the unit vector specifies the sense of
positive translation.
Note: This choice of coordinate system is similar to but significantly
different from the choice in MOSFLM (Leslie & Powell, 2004). In MOSFLM,
X is along the X-ray beam (the CBF/imgCIF Z axis) and Z is along the
rotation axis.
In some experimental techniques, there is no goniometer or the principal
axis of the goniometer is at a small acute angle with respect to
the source axis. In such cases, other reference axes are needed
to define a useful coordinate system. The order of priority in
defining directions in such cases is to use the detector, then
gravity, then north.
If the X-axis cannot be defined as above, then the
direction (not the origin) of the X-axis should be parallel to the axis
of the primary detector element corresponding to the most rapidly
varying dimension of that detector element's data array, with its
positive sense corresponding to increasing values of the index for
that dimension. If the detector is such that such a direction cannot
be defined (as with a point detector) or that direction forms an
angle of less than 22.5 degrees with respect to the source axis, then
the X-axis should be chosen so that if the Y-axis is chosen
in the direction of gravity, and the Z-axis is chosen to be along
the source axis, a right-handed orthogonal coordinate system is chosen.
In the case of a vertical source axis, as a last resort, the
X-axis should be chosen to point North.
All rotations are given in degrees and all translations are given in mm.
Axes may be dependent on one another. The X-axis is the only goniometer
axis the direction of which is strictly connected to the hardware. All
other axes are specified by the positions they would assume when the
axes upon which they depend are at their zero points.
When specifying detector axes, the axis is given to the beam centre.
The location of the beam centre on the detector should be given in the
DIFFRN_DETECTOR category in distortion-corrected millimetres from
the (0,0) corner of the detector.
It should be noted that many different origins arise in the definition
of an experiment. In particular, as noted above, it is necessary to
specify the location of the beam centre on the detector in terms
of the origin of the detector, which is, of course, not coincident
with the centre of the sample.
The unit cell, reciprocal cell and crystallographic orthogonal
Cartesian coordinate system are defined by the CELL and the matrices
in the ATOM_SITES category.
THE DIRECT LATTICE (FRACTIONAL COORDINATES)
The direct lattice coordinate system is a system of fractional
coordinates aligned to the crystal, rather than to the laboratory.
This is a natural coordinate system for maps and atomic coordinates.
It is the simplest coordinate system in which to apply symmetry.
The axes are determined by the cell edges, and are not necessarily
othogonal. This coordinate system is not uniquely defined and
depends on the cell parameters in the CELL category and the
settings chosen to index the crystal.
Molecules in a crystal studied by X-ray diffracraction are organized
into a repeating regular array of unit cells. Each unit cell is defined
by three vectors, a, b and c. To quote from Drenth,
"The choice of the unit cell is not unique and therefore, guidelines
have been established for selecting the standard basis vectors and
the origin. They are based on symmetry and metric considerations:
"(1) The axial system should be right handed.
(2) The basis vectors should coincide as much as possible with
directions of highest symmetry."
(3) The cell taken should be the smallest one that satisfies
condition (2)
(4) Of all the lattice vectors, none is shorter than a.
(5) Of those not directed along a, none is shorter than b.
(6) Of those not lying in the ab plane, none is shorter than c.
(7) The three angles between the basis vectors a, b and c are
either all acute (<90\%) or all obtuse (≥90\%)."
These rules do not produce a unique result that is stable under
the assumption of experimental errors, and the the resulting cell
may not be primitive.
In this coordinate system, the vector (.5, .5, .5) is in the middle
of the given unit cell.
Grid coordinates are an important variation on fractional coordinates
used when working with maps. In imgCIF, the conversion from
fractional to grid coordinates is implicit in the array indexing
specified by _array_structure_list.dimension. Note that this
implicit grid-coordinate scheme is 1-based, not zero-based, i.e.
the origin of the cell for axes along the cell edges with no
specified _array_structure_list_axis.displacement will have
grid coordinates of (1,1,1), i.e. array indices of (1,1,1).
THE ORTHOGONAL CARTESIAN COORDINATE SYSTEM (REAL SPACE)
The orthogonal Cartesian coordinate system is a transformation of
the direct lattice to the actual physical coordinates of atoms in
space. It is similar to the laboratory coordinate system, but
is anchored to and moves with the crystal, rather than being
schored to the laboratory. The transformation from fractional
to orthogonal cartesian coordinates is given by the
_atom_sites.Cartn_transf_matrix[i][j] and
_atom_sites.Cartn_transf_vector[i]
tags. A common choice for the matrix of the transformation is
given in the 1992 PDB format document
| a b cos(\g) c cos(\b) |
| 0 b sin(\g) c (cos(\a) - cos(\b)cos(\g))/sin(\g) |
| 0 0 V/(a b sin(\g)) |
This is a convenient coordinate system in which to do fitting
of models to maps and in which to understand the chemistry of
a molecule.
THE RECIPROCAL LATTICE
The reciprocal lattice coordinate system is used for diffraction
intensitities. It is based on the reciprocal cell, the dual of the cell,
in which reciprocal cell edges are derived from direct cell faces:
a* = bc sin(\a)/V b* = ac sin(\b)/V c* = ab sin(\g)/V
cos(\a*) = (cos(\b) cos(\g) - cos(\a))/(sin(\b) sin(\g))
cos(\b*) = (cos(\a) cos(\g) - cos(\b))/(sin(\a) sin(\g))
cos(\g*) = (cos(\a) cos(\b) - cos(\g))/(sin(\a) sin(\b))
V = abc SQRT(1 - cos(\a)^2^
- cos(\b)^2^
- cos(\g)^2^
+ 2 cos(\a) cos(\b) cos(\g) )
In this form the dimensions of the reciprocal lattice are in reciprocal
\%Angstroms (\%A^-1^). A dimensionless form can be obtained by
multiplying by the wavelength. Reflections are commonly indexed against
this coordinate system as (h, k, l) triples.
References:
Drenth, J., "Introduction to basic crystallography." chapter
2.1 in Rossmann, M. G. and Arnold, E. "Crystallography of
biological macromolecules", Volume F of the IUCr's "International
tables for crystallography", Kluwer, Dordrecht 2001, pp 44 -- 63
Leslie, A. G. W. and Powell, H. (2004). MOSFLM v6.11.
MRC Laboratory of Molecular Biology, Hills Road, Cambridge, England.
http://www.CCP4.ac.uk/dist/X-windows/Mosflm/.
Stout, G. H. and Jensen, L. H., "X-ray structure determination",
2nd ed., Wiley, New York, 1989, 453 pp.
__, "PROTEIN DATA BANK ATOMIC COORDINATE AND BIBLIOGRAPHIC ENTRY
FORMAT DESCRIPTION," Brookhaven National Laboratory, February 1992.
;
_category.id axis
_category.mandatory_code no
loop_
_category_key.name '_axis.id'
'_axis.equipment'
loop_
_category_group.id 'inclusive_group'
'axis_group'
'diffrn_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 -
This example shows the axis specification of the axes of a kappa-
geometry goniometer [see Stout, G. H. & Jensen, L. H. (1989). X-ray
structure determination. A practical
guide, 2nd ed. p. 134. New York: Wiley Interscience].
There are three axes specified, and no offsets. The outermost axis,
omega, is pointed along the X axis. The next innermost axis, kappa,
is at a 50 degree angle to the X axis, pointed away from the source.
The innermost axis, phi, aligns with the X axis when omega and
phi are at their zero points. If T-omega, T-kappa and T-phi
are the transformation matrices derived from the axis settings,
the complete transformation would be:
X' = (T-omega) (T-kappa) (T-phi) X
;
;
loop_
_axis.id
_axis.type
_axis.equipment
_axis.depends_on
_axis.vector[1] _axis.vector[2] _axis.vector[3]
omega rotation goniometer . 1 0 0
kappa rotation goniometer omega -.64279 0 -.76604
phi rotation goniometer kappa 1 0 0
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 2 -
This example shows the axis specification of the axes of a
detector, source and gravity. The order has been changed as a
reminder that the ordering of presentation of tokens is not
significant. The centre of rotation of the detector has been taken
to be 68 millimetres in the direction away from the source.
;
;
loop_
_axis.id
_axis.type
_axis.equipment
_axis.depends_on
_axis.vector[1] _axis.vector[2] _axis.vector[3]
_axis.offset[1] _axis.offset[2] _axis.offset[3]
source . source . 0 0 1 . . .
gravity . gravity . 0 -1 0 . . .
tranz translation detector rotz 0 0 1 0 0 -68
twotheta rotation detector . 1 0 0 . . .
roty rotation detector twotheta 0 1 0 0 0 -68
rotz rotation detector roty 0 0 1 0 0 -68
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 3 -
This example show the axis specification of the axes for a map,
using fractional coordinates. Each cell edge has been divided
into a grid of 50 divisions in the ARRAY_STRUCTURE_LIST_AXIS
category. The map is using only the first octant of the grid
in the ARRAY_STRUCTURE_LIST category.
The fastest changing axis is the gris along A, then along B,
and the slowest is along C.
The map sampling is being done in the middle of each grid
division
;
;
loop_
_axis.id
_axis.system
_axis.vector[1] _axis.vector[2] _axis.vector[3]
CELL_A_AXIS fractional 1 0 0
CELL_B_AXIS fractional 0 1 0
CELL_C_AXIS fractional 0 0 1
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_id
MAP 1 25 1 increasing CELL_A_AXIS
MAP 1 25 2 increasing CELL_B_AXIS
MAP 1 25 3 increasing CELL_C_AXIS
loop_
_array_structure_list_axis.axis_id
_array_structure_list_axis.fract_displacement
_array_structure_list_axis.fract_displacement_increment
CELL_A_AXIS 0.01 0.02
CELL_B_AXIS 0.01 0.02
CELL_C_AXIS 0.01 0.02
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 4 -
This example show the axis specification of the axes for a map,
this time as orthogonal \%Angstroms, using the same coordinate system
as for the atomic coordinates. The map is sampling every 1.5
\%Angstroms (1.5e-7 millimeters) in a map segment 37.5 \%Angstroms on
a side.
;
;
loop_
_axis.id
_axis.system
_axis.vector[1] _axis.vector[2] _axis.vector[3]
X orthogonal 1 0 0
Y orthogonal 0 1 0
Z orthogonal 0 0 1
loop_
_array_structure_list.array_id
_array_structure_list.index
_array_structure_list.dimension
_array_structure_list.precedence
_array_structure_list.direction
_array_structure_list.axis_id
MAP 1 25 1 increasing X
MAP 2 25 2 increasing Y
MAP 3 25 3 increasing Z
loop_
_array_structure_list_axis.axis_id
_array_structure_list_axis.displacement
_array_structure_list_axis.displacement_increment
X 7.5e-8 1.5e-7
Y 7.5e-8 1.5e-7
Z 7.5e-8 1.5e-7
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__axis.depends_on
_item_description.description
; The value of _axis.depends_on specifies the next outermost
axis upon which this axis depends.
This item is a pointer to _axis.id in the same category.
;
_item.name '_axis.depends_on'
_item.category_id axis
_item.mandatory_code no
save_
save__axis.equipment
_item_description.description
; The value of _axis.equipment specifies the type of
equipment using the axis: 'goniometer', 'detector',
'gravity', 'source' or 'general'.
;
_item.name '_axis.equipment'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value general
loop_
_item_enumeration.value
_item_enumeration.detail goniometer
'equipment used to orient or position samples'
detector
'equipment used to detect reflections'
general
'equipment used for general purposes'
gravity
'axis specifying the downward direction'
source
'axis specifying the direction sample to source'
save_
save__axis.offset[1]
_item_description.description
; The [1] element of the three-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres.
;
_item.name '_axis.offset[1]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.offset[2]
_item_description.description
; The [2] element of the three-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres.
;
_item.name '_axis.offset[2]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.offset[3]
_item_description.description
; The [3] element of the three-element vector used to specify
the offset to the base of a rotation or translation axis.
The vector is specified in millimetres.
;
_item.name '_axis.offset[3]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
_item_units.code millimetres
save_
save__axis.id
_item_description.description
; The value of _axis.id must uniquely identify
each axis relevant to the experiment. Note that multiple
pieces of equipment may share the same axis (e.g. a twotheta
arm), so the category key for AXIS also includes the
equipment.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_axis.id' axis yes
'_array_structure_list_axis.axis_id'
array_structure_list_axis
yes
'_diffrn_detector_axis.axis_id' diffrn_detector_axis yes
'_diffrn_measurement_axis.axis_id' diffrn_measurement_axis yes
'_diffrn_scan_axis.axis_id' diffrn_scan_axis yes
'_diffrn_scan_frame_axis.axis_id' diffrn_scan_frame_axis yes
_item_type.code code
loop_
_item_linked.child_name
_item_linked.parent_name
'_axis.depends_on' '_axis.id'
'_array_structure_list_axis.axis_id' '_axis.id'
'_diffrn_detector_axis.axis_id' '_axis.id'
'_diffrn_measurement_axis.axis_id' '_axis.id'
'_diffrn_scan_axis.axis_id' '_axis.id'
'_diffrn_scan_frame_axis.axis_id' '_axis.id'
save_
save__axis.system
_item_description.description
; The value of _axis.system specifies the coordinate
system used to define the axis: 'laboratory', 'direct',
'orthogonal', 'reciprocal' or 'abstract'.
;
_item.name '_axis.system'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value laboratory
loop_
_item_enumeration.value
_item_enumeration.detail
laboratory
; the axis is referenced to the imgCIF standard laboratory Cartesian
coordinate system
;
direct
; the axis is referenced to the direct lattice
;
orthogonal
; the axis is referenced to the cell Cartesian orthogonal coordinates
;
reciprocal
; the axis is referenced to the reciprocal lattice
;
abstract
; the axis is referenced to abstract Cartesian cooridinate system
;
save_
save__axis.type
_item_description.description
; The value of _axis.type specifies the type of
axis: 'rotation' or 'translation' (or 'general' when
the type is not relevant, as for gravity).
;
_item.name '_axis.type'
_item.category_id axis
_item.mandatory_code no
_item_type.code ucode
_item_default.value general
loop_
_item_enumeration.value
_item_enumeration.detail rotation
'right-handed axis of rotation'
translation
'translation in the direction of the axis'
general
'axis for which the type is not relevant'
save_
save__axis.vector[1]
_item_description.description
; The [1] element of the three-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector and
is dimensionless.
;
_item.name '_axis.vector[1]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.vector[2]
_item_description.description
; The [2] element of the three-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector and
is dimensionless.
;
_item.name '_axis.vector[2]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
save__axis.vector[3]
_item_description.description
; The [3] element of the three-element vector used to specify
the direction of a rotation or translation axis.
The vector should be normalized to be a unit vector and
is dimensionless.
;
_item.name '_axis.vector[3]'
_item.category_id axis
_item.mandatory_code no
_item_default.value 0.0
_item_sub_category.id vector
_item_type.code float
save_
#####################
# DIFFRN_DATA_FRAME #
#####################
save_DIFFRN_DATA_FRAME
_category.description
; Data items in the DIFFRN_DATA_FRAME category record
the details about each frame of data.
The items in this category were previously in a
DIFFRN_FRAME_DATA category, which is now deprecated.
The items from the old category are provided
as aliases but should not be used for new work.
;
_category.id diffrn_data_frame
_category.mandatory_code no
loop_
_category_key.name '_diffrn_data_frame.id'
'_diffrn_data_frame.detector_element_id'
loop_
_category_group.id 'inclusive_group'
'array_data_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
; Example 1 - A frame containing data from 4 frame elements.
Each frame element has a common array configuration
'array_1' described in ARRAY_STRUCTURE and related
categories. The data for each detector element are
stored in four groups of binary data in the
ARRAY_DATA category, linked by the array_id and
binary_id.
;
;
loop_
_diffrn_data_frame.id
_diffrn_data_frame.detector_element_id
_diffrn_data_frame.array_id
_diffrn_data_frame.binary_id
frame_1 d1_ccd_1 array_1 1
frame_1 d1_ccd_2 array_1 2
frame_1 d1_ccd_3 array_1 3
frame_1 d1_ccd_4 array_1 4
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__diffrn_data_frame.array_id
_item_description.description
; This item is a pointer to _array_structure.id in the
ARRAY_STRUCTURE category.
;
_item.name '_diffrn_data_frame.array_id'
_item.category_id diffrn_data_frame
_item.mandatory_code implicit
_item_aliases.alias_name '_diffrn_frame_data.array_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
save__diffrn_data_frame.binary_id
_item_description.description
; This item is a pointer to _array_data.binary_id in the
ARRAY_DATA category.
;
_item.name '_diffrn_data_frame.binary_id'
_item.category_id diffrn_data_frame
_item.mandatory_code implicit
_item_aliases.alias_name '_diffrn_frame_data.binary_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code int
save_
save__diffrn_data_frame.center_fast
_item_description.description
; The value of _diffrn_data_frame.center_fast is
the fast index axis beam center position relative to the detector
element face in the units specified in the data item
'_diffrn_data_frame.center_units' along the fast
axis of the detector from the center of the first pixel to
the point at which the Z-axis (which should be colinear with the
beam) intersects the face of the detector, if in fact is does.
At the time of the measurement the current setting of detector
positioner given frame are used.
It is important to note that for measurements in millimetres,
the sense of the axis is used, rather than the sign of the
pixel-to-pixel increments.
;
_item.name '_diffrn_data_frame.center_fast'
_item.category_id diffrn_data_frame
_item.mandatory_code no
_item_type.code float
save_
save__diffrn_data_frame.center_slow
_item_description.description
; The value of _diffrn_data_frame.center_slow is
the slow index axis beam center position relative to the detector
element face in the units specified in the data item
'_diffrn_data_frame.center_units' along the slow
axis of the detector from the center of the first pixel to
the point at which the Z-axis (which should be colinear with the
beam) intersects the face of the detector, if in fact is does.
At the time of the measurement the current setting of detector
positioner given frame are used.
It is important to note that the sense of the axis is used,
rather than the sign of the pixel-to-pixel increments.
;
_item.name '_diffrn_data_frame.center_slow'
_item.category_id diffrn_data_frame
_item.mandatory_code no
_item_type.code float
save_
save__diffrn_data_frame.center_units
_item_description.description
; The value of _diffrn_data_frame.center_units
specifies the units in which the values of
'_diffrn_data_frame.center_fast' and
'_diffrn_data_frame.center_slow'
are presented. The default is 'mm' for millimetres. The
alternatives are 'pixels' and 'bins'. In all cases the
center distances are measured from the center of the
first pixel, i.e. in a 2x2 binning, the measuring origin
is offset from the centers of the bins by one half pixel
towards the first pixel.
If 'bins' is specified, the data in
'_array_intensities.pixel_fast_bin_size',
'_array_intensities.pixel_slow_bin_size', and
'_array_intensities.pixel_binning_method'
is used to define the binning scheme.
;
_item.name '_diffrn_data_frame.center_units'
_item.category_id diffrn_data_frame
_item.mandatory_code no
_item_type.code code
loop_
_item_enumeration.value
_item_enumeration.detail
mm 'millimetres'
pixels 'detector pixels'
bins 'detector bins'
save_
save__diffrn_data_frame.detector_element_id
_item_description.description
; This item is a pointer to _diffrn_detector_element.id
in the DIFFRN_DETECTOR_ELEMENT category.
;
_item.name '_diffrn_data_frame.detector_element_id'
_item.category_id diffrn_data_frame
_item.mandatory_code yes
_item_aliases.alias_name '_diffrn_frame_data.detector_element_id'
_item_aliases.dictionary cif_img.dic
_item_aliases.version 1.0
_item_type.code code
save_
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